Citrus Sinensis ID: 033755

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110--
Protein Sequence
MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI
Secondary Structure (PSIPRED)
cccccccccEEEEEEEEEEEEEcccccccccEEEEEEcccccHHHHHHHccccEEEEEEccccccccEEEEEEEEEEcccccccEEEEEEcccccccccccEEEEEEEcccc
Secondary Structure Prediction (SSPRO)
cccccccccEEEEEEEEEEEEccccccccccEEEEEEEccccHcccEEEEccEEEEEEEEcccccccEEEEEEEEEEcccccccEEEEEEcccccHHHcccEEEEEEccccc
Coil and Loop (DISEMBL)
mvkgrqgerVRLYVRGTILgykrsksnqypntsliqiegvntkedvsWYCGKRMAYIYKAKVkkngshyrciwgkvarphgnsgvvrakfksnlppksmgdrvrvfmypsni
Flexible Loop (DISEMBL)
mvkgrqgervrlyvrgtilgykrsksnqypntsliqiegvntkEDVSWYCGKRMAYIYKAKVKKNGSHYRCIWGkvarphgnsgvvrakfksnlppksmgdrvrvfmypsni
Low Complexity Region (SEG)
MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI
Disordered region (IsUnstruct)
*********VRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRCIWGKVARPHGNSGVV**************************
Disordered Region (DISOPRED)
*************VRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI
Disordered Region (DISEMBL)
********RVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI
Disordered Region (DISPRO)
*******ERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSN*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI
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	112	2.2.26 [Sep-21-2011]
Q9LMK0	112	60S ribosomal protein L35	yes	no	1.0	1.0	0.919	7e-56
Q9C912	112	60S ribosomal protein L35	yes	no	1.0	1.0	0.919	9e-56
Q9FZH0	111	60S ribosomal protein L35	no	no	0.991	1.0	0.891	6e-54
P51422	111	60S ribosomal protein L35	no	no	0.991	1.0	0.882	9e-54
P05744	107	60S ribosomal protein L33	yes	no	0.946	0.990	0.575	1e-29
P41056	107	60S ribosomal protein L33	yes	no	0.946	0.990	0.566	5e-29
Q9USX4	108	60S ribosomal protein L33	yes	no	0.910	0.944	0.529	3e-27
P49180	124	60S ribosomal protein L35	yes	no	0.910	0.822	0.518	7e-27
Q9USG6	108	60S ribosomal protein L33	no	no	0.910	0.944	0.519	2e-26
Q55BN7	105	60S ribosomal protein L35	yes	no	0.910	0.971	0.514	3e-26

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

 Score =  215 bits (547), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 103/112 (91%), Positives = 106/112 (94%)

Query: 1   MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA 60
           MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSL+Q+EGVNT E+VSWY GKRMAYIYKA
Sbjct: 1   MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLVQVEGVNTTEEVSWYKGKRMAYIYKA 60

Query: 61  KVKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
           K KKNGSHYRCIWGKV RPHGNSGVVRAKF SNLPPKSMG RVRVFMYPSNI
Sbjct: 61  KTKKNGSHYRCIWGKVTRPHGNSGVVRAKFTSNLPPKSMGSRVRVFMYPSNI 112

Arabidopsis thaliana (taxid: 3702)

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

 Score =  214 bits (546), Expect = 9e-56,   Method: Compositional matrix adjust.
 Identities = 103/112 (91%), Positives = 107/112 (95%)

Query: 1   MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA 60
           MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSL+QIEGVNT+E+V+WY GKRMAYIYKA
Sbjct: 1   MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLVQIEGVNTQEEVNWYKGKRMAYIYKA 60

Query: 61  KVKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
           K KKNGSHYRCIWGKV RPHGNSGVVRAKF SNLPPKSMG RVRVFMYPSNI
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 =  208 bits (530), Expect = 6e-54,   Method: Compositional matrix adjust.
 Identities = 99/111 (89%), Positives = 106/111 (95%)

Query: 2   VKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAK 61
           +KGRQGERVRLYVRGT+LGYKRSKSNQYPNTSLIQIEGVNT+E+V+WY GKR+AYIYKAK
Sbjct: 1   MKGRQGERVRLYVRGTVLGYKRSKSNQYPNTSLIQIEGVNTQEEVNWYKGKRLAYIYKAK 60

Query: 62  VKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
            KKNGSHYRCIWGKV RPHGNSGVVR+KF SNLPPKSMG RVRVFMYPSNI
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 =  208 bits (529), Expect = 9e-54,   Method: Compositional matrix adjust.
 Identities = 98/111 (88%), Positives = 106/111 (95%)

Query: 2   VKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAK 61
           +KGRQGERVRLYVRGT+LGYKRSKSNQYPNTSL+QIEGVNT+E+V+WY GKR+AYIYKAK
Sbjct: 1   MKGRQGERVRLYVRGTVLGYKRSKSNQYPNTSLVQIEGVNTQEEVNWYKGKRLAYIYKAK 60

Query: 62  VKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
            KKNGSHYRCIWGKV RPHGNSGVVR+KF SNLPPKSMG RVRVFMYPSNI
Sbjct: 61  TKKNGSHYRCIWGKVTRPHGNSGVVRSKFTSNLPPKSMGARVRVFMYPSNI 111

Arabidopsis thaliana (taxid: 3702)

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

 Score =  128 bits (321), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 61/106 (57%), Positives = 76/106 (71%)

Query: 7   GERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNG 66
            E  RLYV+G  L Y+RSK    PN SLI+IEGV T +D  +Y GKR+AY+Y+A  +  G
Sbjct: 2   AESHRLYVKGKHLSYQRSKRVNNPNVSLIKIEGVATPQDAQFYLGKRIAYVYRASKEVRG 61

Query: 67  SHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
           S  R +WGKV R HGNSGVVRA F++NLP K+ G  VR+F+YPSNI
Sbjct: 62  SKIRVMWGKVTRTHGNSGVVRATFRNNLPAKTFGASVRIFLYPSNI 107

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

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

 Score =  126 bits (316), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 60/106 (56%), Positives = 76/106 (71%)

Query: 7   GERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNG 66
            E  RLYV+G  L Y+RSK    PN SLI+IEGV T ++  +Y GKR+AY+Y+A  +  G
Sbjct: 2   AESHRLYVKGKHLSYQRSKRVNNPNVSLIKIEGVATPQEAQFYLGKRIAYVYRASKEVRG 61

Query: 67  SHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
           S  R +WGKV R HGNSGVVRA F++NLP K+ G  VR+F+YPSNI
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 =  120 bits (301), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 54/102 (52%), Positives = 74/102 (72%)

Query: 11  RLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYR 70
           RLYV+   L ++RSK   +P TSL++IEG ++KE+  +Y GKR+ ++YK+     GS  R
Sbjct: 7   RLYVKAKHLSFQRSKHVIHPGTSLVKIEGCDSKEEAQFYLGKRICFVYKSNKPVRGSKIR 66

Query: 71  CIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
            IWG V+RPHGNSGVVRA+F  NLPPK+ G  +RV +YPSN+
Sbjct: 67  VIWGTVSRPHGNSGVVRARFTHNLPPKTFGASLRVMLYPSNV 108

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

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

 Score =  119 bits (297), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 56/108 (51%), Positives = 73/108 (67%), Gaps = 6/108 (5%)

Query: 11  RLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA--KVKKNG-- 66
           RLYV+    G+KR    Q  +TSL+++EGV  KED  +Y GKR+ Y+YKA  K  K G  
Sbjct: 17  RLYVKAIFTGFKRGLRTQSEHTSLLKLEGVFNKEDAGFYAGKRVVYLYKAHNKTLKTGHT 76

Query: 67  --SHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
             +  R IWGK+ RPHGN+G VRAKF  N+PP ++G R+RV +YPSNI
Sbjct: 77  VATRTRAIWGKITRPHGNAGAVRAKFHHNIPPSALGKRIRVLLYPSNI 124

Caenorhabditis elegans (taxid: 6239)

>sp|Q9USG6|RL33B_SCHPO 60S ribosomal protein L33-B OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpl33b PE=1 SV=1

 Score =  117 bits (293), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 53/102 (51%), Positives = 72/102 (70%)

Query: 11  RLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYR 70
           RLYV+   L ++RSK   +P TS+++IEG ++KE+  +Y GKR+ Y+YK+     GS  R
Sbjct: 7   RLYVKAKHLSFQRSKHVIHPGTSIVKIEGCDSKEEAQFYLGKRVCYVYKSSKAVRGSKIR 66

Query: 71  CIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
            IWG +ARPHGNSG VRA+F  NLP K+ G  +RV +YPSNI
Sbjct: 67  VIWGTIARPHGNSGAVRARFVHNLPAKTFGSSLRVMLYPSNI 108

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

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

 Score =  117 bits (292), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 53/103 (51%), Positives = 79/103 (76%), Gaps = 1/103 (0%)

Query: 11  RLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYK-AKVKKNGSHY 69
           ++Y +G +LGY+RS++ QYPN SLI+IEGV ++ED ++Y GK++  + K +K  KN + +
Sbjct: 3   KIYSKGVVLGYRRSQATQYPNISLIKIEGVVSREDSTFYLGKKVCLVSKVSKSAKNPTGH 62

Query: 70  RCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
           +  WGK+ + HG+SGVV+A+F  NLPPK+MG  VRV +YPSNI
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)

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	112
449465053	446	PREDICTED: probable sugar phosphate/phos	1.0	0.251	0.928	3e-57
313586489	112	60S ribosomal protein L35aA [Hevea brasi	1.0	1.0	0.964	7e-57
225440584	112	PREDICTED: 60S ribosomal protein L35a-1-	1.0	1.0	0.946	4e-56
209967441	112	60S ribosomal protein L35a [Vernicia for	1.0	1.0	0.955	9e-56
224112609	112	predicted protein [Populus trichocarpa]	1.0	1.0	0.937	1e-55
224101037	112	predicted protein [Populus trichocarpa]	1.0	1.0	0.946	1e-55
13430186	112	ribosomal protein L33 [Castanea sativa]	1.0	1.0	0.946	1e-55
357492529	657	Maturase [Medicago truncatula] gi|355517	1.0	0.170	0.866	2e-55
449531591	112	PREDICTED: 60S ribosomal protein L35a-1-	1.0	1.0	0.928	2e-55
224098507	112	predicted protein [Populus trichocarpa]	1.0	1.0	0.928	4e-55

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

 Score =  225 bits (573), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 104/112 (92%), Positives = 110/112 (98%)

Query: 1   MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA 60
           MVKGRQGERVRLY RGTILGYKRSKSNQYPNTSL+QIEGVN+K++VSWY GKR+AYIYKA
Sbjct: 1   MVKGRQGERVRLYTRGTILGYKRSKSNQYPNTSLLQIEGVNSKDEVSWYQGKRLAYIYKA 60

Query: 61  KVKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
           KVKKNGSHYRCIWGKVARPHGNSG+VRAKFKSNLPPKSMGDRVRVFMYPSNI
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 =  224 bits (570), Expect = 7e-57,   Method: Compositional matrix adjust.
 Identities = 108/112 (96%), Positives = 110/112 (98%)

Query: 1   MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA 60
           MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKE+V+WY GKRMAYIYKA
Sbjct: 1   MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEEVAWYAGKRMAYIYKA 60

Query: 61  KVKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
           KVKKNGSHYRCIWGKV RPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI
Sbjct: 61  KVKKNGSHYRCIWGKVTRPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112

Source: Hevea brasiliensis

Species: Hevea brasiliensis

Genus: Hevea

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225440584|ref|XP_002277272.1| PREDICTED: 60S ribosomal protein L35a-1-like isoform 1 [Vitis vinifera] gi|225449234|ref|XP_002280039.1| PREDICTED: 60S ribosomal protein L35a-1 [Vitis vinifera] gi|359481695|ref|XP_003632660.1| PREDICTED: 60S ribosomal protein L35a-1-like isoform 2 [Vitis vinifera] gi|147823354|emb|CAN64195.1| hypothetical protein VITISV_014336 [Vitis vinifera] gi|296086107|emb|CBI31548.3| unnamed protein product [Vitis vinifera] gi|297740261|emb|CBI30443.3| unnamed protein product [Vitis vinifera]

 Score =  221 bits (564), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 106/112 (94%), Positives = 110/112 (98%)

Query: 1   MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA 60
           MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKE+V+WYCGKRMAYIYKA
Sbjct: 1   MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEEVAWYCGKRMAYIYKA 60

Query: 61  KVKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
           KVKK+GSH+RCIWGKV RPHGNSGVVRAKFKSNLPPKSMG RVRVFMYPSNI
Sbjct: 61  KVKKDGSHFRCIWGKVTRPHGNSGVVRAKFKSNLPPKSMGARVRVFMYPSNI 112

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  220 bits (560), Expect = 9e-56,   Method: Compositional matrix adjust.
 Identities = 107/112 (95%), Positives = 108/112 (96%)

Query: 1   MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA 60
           MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKE+V WY GKRMAYIYKA
Sbjct: 1   MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEEVGWYAGKRMAYIYKA 60

Query: 61  KVKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
           KVKKNGSHYRCIWGKV RPHGNSGVVRAKFKSNLPPKSMG RVRVFMYPSNI
Sbjct: 61  KVKKNGSHYRCIWGKVTRPHGNSGVVRAKFKSNLPPKSMGARVRVFMYPSNI 112

Source: Vernicia fordii

Species: Vernicia fordii

Genus: Vernicia

Family: Euphorbiaceae

Order: Malpighiales

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 =  220 bits (560), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 105/112 (93%), Positives = 109/112 (97%)

Query: 1   MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA 60
           MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSL+Q+EGVNTKE+V+WY GKRMAYIYKA
Sbjct: 1   MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLVQVEGVNTKEEVAWYAGKRMAYIYKA 60

Query: 61  KVKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
           KVKKNGSHYRCIWGKV RPHGNSGVVRAKFKSNLPPKSMG RVRVFMYPSNI
Sbjct: 61  KVKKNGSHYRCIWGKVTRPHGNSGVVRAKFKSNLPPKSMGARVRVFMYPSNI 112

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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 =  219 bits (559), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 106/112 (94%), Positives = 108/112 (96%)

Query: 1   MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA 60
           MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKE+V+WY GKRMAYIYKA
Sbjct: 1   MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEEVAWYAGKRMAYIYKA 60

Query: 61  KVKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
           KVKK GSHYRCIWGKV RPHGNSGVVRAKFKSNLPPKSMG RVRVFMYPSNI
Sbjct: 61  KVKKQGSHYRCIWGKVTRPHGNSGVVRAKFKSNLPPKSMGTRVRVFMYPSNI 112

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  219 bits (559), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 106/112 (94%), Positives = 109/112 (97%)

Query: 1   MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA 60
           MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKE+V WY GKRMAY+YKA
Sbjct: 1   MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEEVGWYAGKRMAYVYKA 60

Query: 61  KVKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
           KVKK+GSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMG RVRVFMYPSNI
Sbjct: 61  KVKKDGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGARVRVFMYPSNI 112

Source: Castanea sativa

Species: Castanea sativa

Genus: Castanea

Family: Fagaceae

Order: Fagales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357492529|ref|XP_003616553.1| Maturase [Medicago truncatula] gi|355517888|gb|AES99511.1| Maturase [Medicago truncatula]

 Score =  219 bits (558), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 97/112 (86%), Positives = 106/112 (94%)

Query: 1   MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA 60
           MVKGRQGER+RLYVRGT+LGYKRSK NQYPNTSL+QIEGVNTKE+V+WY GK++AYIYKA
Sbjct: 26  MVKGRQGERIRLYVRGTVLGYKRSKVNQYPNTSLVQIEGVNTKEEVAWYAGKKLAYIYKA 85

Query: 61  KVKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
           KVKK+GSHYRCIWGKV RPHGNSG+VRAKFKSNLPPKSMG RVRVFMYP  I
Sbjct: 86  KVKKDGSHYRCIWGKVTRPHGNSGIVRAKFKSNLPPKSMGARVRVFMYPIGI 137

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  219 bits (557), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 104/112 (92%), Positives = 110/112 (98%)

Query: 1   MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA 60
           MVKGRQGERVRLY RGTILGYKRSKSNQYPNTSL+QIEGVN+K++VSWY GKR+AYIYKA
Sbjct: 1   MVKGRQGERVRLYTRGTILGYKRSKSNQYPNTSLLQIEGVNSKDEVSWYQGKRLAYIYKA 60

Query: 61  KVKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
           KVKKNGSHYRCIWGKVARPHGNSG+VRAKFKSNLPPKSMGDRVRVFMYPSNI
Sbjct: 61  KVKKNGSHYRCIWGKVARPHGNSGIVRAKFKSNLPPKSMGDRVRVFMYPSNI 112

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224098507|ref|XP_002311198.1| predicted protein [Populus trichocarpa] gi|118483364|gb|ABK93583.1| unknown [Populus trichocarpa] gi|118484807|gb|ABK94271.1| unknown [Populus trichocarpa] gi|222851018|gb|EEE88565.1| predicted protein [Populus trichocarpa]

 Score =  218 bits (555), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 104/112 (92%), Positives = 109/112 (97%)

Query: 1   MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA 60
           MVKGRQGERVRLYVRGT+LGYKRSKSNQYPNTSLIQIEGVNTKE+V+WY GKRMAYIYKA
Sbjct: 1   MVKGRQGERVRLYVRGTVLGYKRSKSNQYPNTSLIQIEGVNTKEEVAWYAGKRMAYIYKA 60

Query: 61  KVKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
           KVK++GSHYRCIWGKV RPHGNSGVVRAKFKSNLPPKSMG RVRVFMYPSNI
Sbjct: 61  KVKRDGSHYRCIWGKVTRPHGNSGVVRAKFKSNLPPKSMGARVRVFMYPSNI 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	112
TAIR|locus:2007422	112	AT1G07070 [Arabidopsis thalian	1.0	1.0	0.919	8.9e-54
TAIR|locus:2019627	112	AT1G74270 [Arabidopsis thalian	1.0	1.0	0.919	8.9e-54
TAIR|locus:2033548	111	AT1G41880 [Arabidopsis thalian	0.991	1.0	0.891	4.4e-52
TAIR|locus:2078991	111	AT3G55750 [Arabidopsis thalian	0.991	1.0	0.882	5.6e-52
GENEDB_PFALCIPARUM|PF11_0438	140	PF11_0438 "Ribosomal protein,	0.937	0.75	0.6	2.9e-32
UNIPROTKB|Q8IHT9	140	PF11_0438 "60S ribosomal prote	0.937	0.75	0.6	2.9e-32
ASPGD|ASPL0000041158	109	AN2980 [Emericella nidulans (t	0.910	0.935	0.598	7.1e-29
SGD|S000006064	107	RPL33A "Ribosomal 60S subunit	0.937	0.981	0.580	1.2e-28
SGD|S000005760	107	RPL33B "Ribosomal 60S subunit	0.937	0.981	0.571	3.1e-28
POMBASE|SPBC1921.01c	108	rpl35b "60S ribosomal protein	0.910	0.944	0.529	1.5e-26

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

 Score = 556 (200.8 bits), Expect = 8.9e-54, P = 8.9e-54
 Identities = 103/112 (91%), Positives = 106/112 (94%)

Query:     1 MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA 60
             MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSL+Q+EGVNT E+VSWY GKRMAYIYKA
Sbjct:     1 MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLVQVEGVNTTEEVSWYKGKRMAYIYKA 60

Query:    61 KVKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
             K KKNGSHYRCIWGKV RPHGNSGVVRAKF SNLPPKSMG RVRVFMYPSNI
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:2019627 AT1G74270 [Arabidopsis thaliana (taxid:3702)]

 Score = 556 (200.8 bits), Expect = 8.9e-54, P = 8.9e-54
 Identities = 103/112 (91%), Positives = 107/112 (95%)

Query:     1 MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA 60
             MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSL+QIEGVNT+E+V+WY GKRMAYIYKA
Sbjct:     1 MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLVQIEGVNTQEEVNWYKGKRMAYIYKA 60

Query:    61 KVKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
             K KKNGSHYRCIWGKV RPHGNSGVVRAKF SNLPPKSMG RVRVFMYPSNI
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:2033548 AT1G41880 [Arabidopsis thaliana (taxid:3702)]

 Score = 540 (195.1 bits), Expect = 4.4e-52, P = 4.4e-52
 Identities = 99/111 (89%), Positives = 106/111 (95%)

Query:     2 VKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAK 61
             +KGRQGERVRLYVRGT+LGYKRSKSNQYPNTSLIQIEGVNT+E+V+WY GKR+AYIYKAK
Sbjct:     1 MKGRQGERVRLYVRGTVLGYKRSKSNQYPNTSLIQIEGVNTQEEVNWYKGKRLAYIYKAK 60

Query:    62 VKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
              KKNGSHYRCIWGKV RPHGNSGVVR+KF SNLPPKSMG RVRVFMYPSNI
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 = 539 (194.8 bits), Expect = 5.6e-52, P = 5.6e-52
 Identities = 98/111 (88%), Positives = 106/111 (95%)

Query:     2 VKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAK 61
             +KGRQGERVRLYVRGT+LGYKRSKSNQYPNTSL+QIEGVNT+E+V+WY GKR+AYIYKAK
Sbjct:     1 MKGRQGERVRLYVRGTVLGYKRSKSNQYPNTSLVQIEGVNTQEEVNWYKGKRLAYIYKAK 60

Query:    62 VKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
              KKNGSHYRCIWGKV RPHGNSGVVR+KF SNLPPKSMG RVRVFMYPSNI
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 = 353 (129.3 bits), Expect = 2.9e-32, P = 2.9e-32
 Identities = 63/105 (60%), Positives = 81/105 (77%)

Query:     8 ERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGS 67
             + VRLY +G ILGYKRS+ NQ PN +LI I+ VNTK+   +Y GKR+AY+Y+     +G 
Sbjct:    36 QAVRLYEKGVILGYKRSQRNQDPNFTLISIKNVNTKKHAQFYVGKRVAYVYRTTKHHDGV 95

Query:    68 HYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
               +CIWGKV R HGNSGV+RAKFK+++PPK+ GDRVR+ MYPSNI
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 = 353 (129.3 bits), Expect = 2.9e-32, P = 2.9e-32
 Identities = 63/105 (60%), Positives = 81/105 (77%)

Query:     8 ERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGS 67
             + VRLY +G ILGYKRS+ NQ PN +LI I+ VNTK+   +Y GKR+AY+Y+     +G 
Sbjct:    36 QAVRLYEKGVILGYKRSQRNQDPNFTLISIKNVNTKKHAQFYVGKRVAYVYRTTKHHDGV 95

Query:    68 HYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
               +CIWGKV R HGNSGV+RAKFK+++PPK+ GDRVR+ MYPSNI
Sbjct:    96 KIKCIWGKVCRTHGNSGVIRAKFKTHIPPKAFGDRVRILMYPSNI 140

GO:0015934 "large ribosomal subunit" evidence=ISS

ASPGD|ASPL0000041158 AN2980 [Emericella nidulans (taxid:162425)]

 Score = 321 (118.1 bits), Expect = 7.1e-29, P = 7.1e-29
 Identities = 61/102 (59%), Positives = 78/102 (76%)

Query:    11 RLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYR 70
             RLYV+G  L Y+RSK    PNTSLI+I+GV+  E  ++Y GK++A++Y+AK +  GS+ R
Sbjct:     8 RLYVKGRHLSYQRSKRAVNPNTSLIKIDGVDNTEAANFYLGKKVAFVYRAKREVRGSNIR 67

Query:    71 CIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
              IWGKV RPHGNSGVVRA+F+ NLP KS G  VRV +YPSNI
Sbjct:    68 VIWGKVTRPHGNSGVVRAQFRHNLPAKSFGATVRVMLYPSNI 109

GO:0005730 "nucleolus" evidence=IEA

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

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

GO:0002181 "cytoplasmic translation" evidence=IEA

SGD|S000006064 RPL33A "Ribosomal 60S subunit protein L33A" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 319 (117.4 bits), Expect = 1.2e-28, P = 1.2e-28
 Identities = 61/105 (58%), Positives = 76/105 (72%)

Query:     8 ERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGS 67
             E  RLYV+G  L Y+RSK    PN SLI+IEGV T +D  +Y GKR+AY+Y+A  +  GS
Sbjct:     3 ESHRLYVKGKHLSYQRSKRVNNPNVSLIKIEGVATPQDAQFYLGKRIAYVYRASKEVRGS 62

Query:    68 HYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
               R +WGKV R HGNSGVVRA F++NLP K+ G  VR+F+YPSNI
Sbjct:    63 KIRVMWGKVTRTHGNSGVVRATFRNNLPAKTFGASVRIFLYPSNI 107

GO:0005737 "cytoplasm" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0002181 "cytoplasmic translation" evidence=IDA

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

GO:0005622 "intracellular" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

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

SGD|S000005760 RPL33B "Ribosomal 60S subunit protein L33B" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 315 (115.9 bits), Expect = 3.1e-28, P = 3.1e-28
 Identities = 60/105 (57%), Positives = 76/105 (72%)

Query:     8 ERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGS 67
             E  RLYV+G  L Y+RSK    PN SLI+IEGV T ++  +Y GKR+AY+Y+A  +  GS
Sbjct:     3 ESHRLYVKGKHLSYQRSKRVNNPNVSLIKIEGVATPQEAQFYLGKRIAYVYRASKEVRGS 62

Query:    68 HYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
               R +WGKV R HGNSGVVRA F++NLP K+ G  VR+F+YPSNI
Sbjct:    63 KIRVMWGKVTRTHGNSGVVRATFRNNLPAKTFGASVRIFLYPSNI 107

GO:0005840 "ribosome" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

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

GO:0002181 "cytoplasmic translation" evidence=IDA

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0006412 "translation" evidence=IEA

POMBASE|SPBC1921.01c rpl35b "60S ribosomal protein L35a (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 299 (110.3 bits), Expect = 1.5e-26, P = 1.5e-26
 Identities = 54/102 (52%), Positives = 74/102 (72%)

Query:    11 RLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYR 70
             RLYV+   L ++RSK   +P TSL++IEG ++KE+  +Y GKR+ ++YK+     GS  R
Sbjct:     7 RLYVKAKHLSFQRSKHVIHPGTSLVKIEGCDSKEEAQFYLGKRICFVYKSNKPVRGSKIR 66

Query:    71 CIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
              IWG V+RPHGNSGVVRA+F  NLPPK+ G  +RV +YPSN+
Sbjct:    67 VIWGTVSRPHGNSGVVRARFTHNLPPKTFGASLRVMLYPSNV 108

GO:0002181 "cytoplasmic translation" evidence=NAS

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

GO:0005730 "nucleolus" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0006412 "translation" evidence=ISO

GO:0008270 "zinc ion binding" evidence=ISS

GO:0019843 "rRNA binding" evidence=ISS

GO:0022625 "cytosolic large ribosomal subunit" 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	0.9196	1.0	1.0	yes	no
P61272	RL35A_MACFA	No assigned EC number	0.5233	0.9107	0.9272	N/A	no
Q9FZH0	R35A2_ARATH	No assigned EC number	0.8918	0.9910	1.0	no	no
P41056	RL33B_YEAST	No assigned EC number	0.5660	0.9464	0.9906	yes	no
Q9LMK0	R35A1_ARATH	No assigned EC number	0.9196	1.0	1.0	yes	no
P0DJ22	RL35A_TETTS	No assigned EC number	0.5049	0.8928	0.8849	N/A	no
Q9USX4	RL33A_SCHPO	No assigned EC number	0.5294	0.9107	0.9444	yes	no
Q5R8K6	RL35A_PONAB	No assigned EC number	0.5233	0.9107	0.9272	yes	no
P49180	RL35A_CAEEL	No assigned EC number	0.5185	0.9107	0.8225	yes	no
P18077	RL35A_HUMAN	No assigned EC number	0.5233	0.9107	0.9272	yes	no
P04646	RL35A_RAT	No assigned EC number	0.5233	0.9107	0.9272	yes	no
Q55BN7	RL35A_DICDI	No assigned EC number	0.5145	0.9107	0.9714	yes	no
Q90YT3	RL35A_ICTPU	No assigned EC number	0.5233	0.9107	0.9272	N/A	no
O55142	RL35A_MOUSE	No assigned EC number	0.5233	0.9107	0.9272	yes	no
P02434	RL35A_XENLA	No assigned EC number	0.5327	0.9107	0.9272	N/A	no
P05744	RL33A_YEAST	No assigned EC number	0.5754	0.9464	0.9906	yes	no
Q56JY1	RL35A_BOVIN	No assigned EC number	0.5140	0.9107	0.9272	yes	no
P51422	R35A4_ARATH	No assigned EC number	0.8828	0.9910	1.0	no	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	estExt_fgenesh4_kg.C_LG_VIII0028	SubName- Full=Putative uncharacterized protein; (113 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	estExt_Genewise1_v1.C_LG_V1341	SubName- Full=Putative uncharacterized protein; (133 aa)			•	•		•			0.561
	estExt_Genewise1_v1.C_LG_II0811	SubName- Full=Putative uncharacterized protein; (133 aa)			•	•		•			0.559
	fgenesh4_pm.C_LG_III000548	RecName- Full=Ribosomal protein S27; (86 aa)			•	•		•			0.559
	estExt_fgenesh4_pg.C_LG_I0594	RecName- Full=Ribosomal protein S27; (86 aa)			•	•		•			0.559
	estExt_Genewise1_v1.C_LG_X4452	SubName- Full=Putative uncharacterized protein; (134 aa)			•	•		•			0.541
	eugene3.00081552	SubName- Full=Putative uncharacterized protein; (135 aa)			•	•		•			0.540
	eugene3.00011799	RecName- Full=60S ribosomal protein L6; (232 aa)				•	•	•			0.492
	estExt_fgenesh4_pg.C_LG_IX0938	RecName- Full=60S ribosomal protein L6; (232 aa)				•	•	•			0.487
	estExt_fgenesh4_pg.C_410046	SubName- Full=Putative uncharacterized protein; (128 aa)			•	•					0.486
	estExt_Genewise1_v1.C_LG_XIX2192	SubName- Full=Putative uncharacterized protein; (128 aa)			•	•					0.481

---

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	112
PTZ00041	120	PTZ00041, PTZ00041, 60S ribosomal protein L35a; Pr	5e-56
pfam01247	95	pfam01247, Ribosomal_L35Ae, Ribosomal protein L35A	2e-54
COG2451	100	COG2451, COG2451, Ribosomal protein L35AE/L33A [Tr	4e-34
PRK04337	87	PRK04337, PRK04337, 50S ribosomal protein L35Ae; V	2e-17

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

 Score =  169 bits (429), Expect = 5e-56
 Identities = 72/105 (68%), Positives = 88/105 (83%)

Query: 8   ERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGS 67
           + VRLYV+   LGYKRSK NQYPN +L++IEGVNT+ED  +Y GKR+AY+YKAK  KNG+
Sbjct: 16  KPVRLYVKAVFLGYKRSKVNQYPNVALLKIEGVNTREDARFYLGKRVAYVYKAKKLKNGT 75

Query: 68  HYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
            +R IWGK+ RPHGNSGVVRA+F  NLPPK++G RVRVF+YPSNI
Sbjct: 76  KFRAIWGKITRPHGNSGVVRARFNKNLPPKAIGSRVRVFLYPSNI 120

Length = 120

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

 Score =  164 bits (417), Expect = 2e-54
 Identities = 68/95 (71%), Positives = 79/95 (83%)

Query: 12  LYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRC 71
           LYV+   LGY+R K NQ+PNTSL++IEGVNTKED  +Y GKR+AY+YKAK KKNGS  R 
Sbjct: 1   LYVKAVFLGYRRGKRNQHPNTSLLKIEGVNTKEDAQFYLGKRVAYVYKAKKKKNGSKIRV 60

Query: 72  IWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVF 106
           IWGKV RPHGNSGVVRAKF+ NLPP++MG RVRV 
Sbjct: 61  IWGKVTRPHGNSGVVRAKFRRNLPPQAMGARVRVM 95

Length = 95

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

 Score =  113 bits (284), Expect = 4e-34
 Identities = 53/105 (50%), Positives = 71/105 (67%), Gaps = 7/105 (6%)

Query: 8   ERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGS 67
           E  RL ++G +L Y+RSK  Q+PN SLI+IEGV++ E+  +Y GKR+ Y Y+       S
Sbjct: 3   EGHRLRIKGVVLSYRRSKRTQHPNVSLIKIEGVDSPEEAQFYLGKRVCYKYR-------S 55

Query: 68  HYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
             R I GKV R HGNSG VRA+F+ NLP +++G  V V +YPSNI
Sbjct: 56  SGRVIKGKVVRTHGNSGAVRARFERNLPGQALGTSVEVKLYPSNI 100

Length = 100

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

 Score = 70.4 bits (173), Expect = 2e-17
 Identities = 32/92 (34%), Positives = 53/92 (57%), Gaps = 8/92 (8%)

Query: 14  VRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRCIW 73
           ++G IL Y+R K+ QY    +I+  GV+ +E+ +   G+++ +         G+ Y    
Sbjct: 3   MKGVILSYRRGKNTQYNRQVIIKPLGVDDREEAAKLIGRKVIW-----KDPTGNKYV--- 54

Query: 74  GKVARPHGNSGVVRAKFKSNLPPKSMGDRVRV 105
           GK+ R HGN G VRA+FK  LP +++GD V +
Sbjct: 55  GKIVRVHGNRGEVRARFKPGLPGQALGDYVEI 86

Length = 87

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	112
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
PRK04337	87	50S ribosomal protein L35Ae; Validated	100.0
COG2451	100	Ribosomal protein L35AE/L33A [Translation, ribosom	100.0
PF09853	53	DUF2080: Putative transposon-encoded protein (DUF2	95.61
PF01782	84	RimM: RimM N-terminal domain; InterPro: IPR002676	93.68
TIGR02273	165	16S_RimM 16S rRNA processing protein RimM. This fa	90.86
PRK14591	169	rimM 16S rRNA-processing protein RimM; Provisional	90.4
PRK14592	165	rimM 16S rRNA-processing protein RimM; Provisional	89.59
PRK13829	162	rimM 16S rRNA-processing protein RimM; Provisional	89.47
PRK13828	161	rimM 16S rRNA-processing protein RimM; Provisional	88.4
PF01782	84	RimM: RimM N-terminal domain; InterPro: IPR002676	87.93
PRK14594	166	rimM 16S rRNA-processing protein RimM; Provisional	87.17
PRK00122	172	rimM 16S rRNA-processing protein RimM; Provisional	87.16
PRK00122	172	rimM 16S rRNA-processing protein RimM; Provisional	87.13
PRK14590	171	rimM 16S rRNA-processing protein RimM; Provisional	87.01
PRK14594	166	rimM 16S rRNA-processing protein RimM; Provisional	86.96
TIGR02273	165	16S_RimM 16S rRNA processing protein RimM. This fa	84.1
PRK14593	184	rimM 16S rRNA-processing protein RimM; Provisional	81.2
PRK14592	165	rimM 16S rRNA-processing protein RimM; Provisional	80.45

>PTZ00041 60S ribosomal protein L35a; Provisional

Probab=100.00  E-value=9.2e-64  Score=363.91  Aligned_cols=110  Identities=66%  Similarity=1.193  Sum_probs=106.3

Q ss_pred             CCCCCceeeeEEEEEEEeeecccCCCCCCeeEEEecCcCCcchhceeecceEEEEEecccccCCceeEEEEEEEEceeCC
Q 033755            3 KGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRCIWGKVARPHGN   82 (112)
Q Consensus         3 ~~~~~~~~RLy~kgv~~gykRg~~~Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~k~~~~g~k~rviwGKV~r~HGn   82 (112)
                      +++..++.|||+||+|+|||||++||+|||||||||||+++|||+|||||||||||+++++++|+++|+|||||+|+|||
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            44556689999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CceEEEEecCCCCccCCCCeEEEEEeecCC
Q 033755           83 SGVVRAKFKSNLPPKSMGDRVRVFMYPSNI  112 (112)
Q Consensus        83 sGvVrAkF~~nLPp~aiG~~vrVmLyps~i  112 (112)
                      ||+|||+|++||||||||++||||||||+|
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=6.4e-60  Score=338.71  Aligned_cols=110  Identities=71%  Similarity=1.153  Sum_probs=107.2

Q ss_pred             CCCCCceeeeEEEEEEEeeecccCCCCCCeeEEEecCcCCcchhceeecceEEEEEecccccCCceeEEEEEEEEceeCC
Q 033755            3 KGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRCIWGKVARPHGN   82 (112)
Q Consensus         3 ~~~~~~~~RLy~kgv~~gykRg~~~Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~k~~~~g~k~rviwGKV~r~HGn   82 (112)
                      +..|.+.+|||+||+|+||+||+++|+|||+|||||||+++|||+||+||||+||||+++..+++++|+|||||||+|||
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            45678889999999999999999999999999999999999999999999999999999988999999999999999999


Q ss_pred             CceEEEEecCCCCccCCCCeEEEEEeecCC
Q 033755           83 SGVVRAKFKSNLPPKSMGDRVRVFMYPSNI  112 (112)
Q Consensus        83 sGvVrAkF~~nLPp~aiG~~vrVmLyps~i  112 (112)
                      ||+|||+|.+||||+|||++||||||||+|
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=1.2e-56  Score=315.59  Aligned_cols=95  Identities=73%  Similarity=1.200  Sum_probs=88.5

Q ss_pred             eEEEEEEEeeecccCCCCCCeeEEEecCcCCcchhceeecceEEEEEecccccCCceeEEEEEEEEceeCCCceEEEEec
Q 033755           12 LYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRCIWGKVARPHGNSGVVRAKFK   91 (112)
Q Consensus        12 Ly~kgv~~gykRg~~~Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~k~~~~g~k~rviwGKV~r~HGnsGvVrAkF~   91 (112)
                      ||+||+|+|||||++||+|||||||||||+|+|||+|||||||+|||++++++++++.|+|||||+|+|||||+|||+|+
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            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCccCCCCeEEEE
Q 033755           92 SNLPPKSMGDRVRVF  106 (112)
Q Consensus        92 ~nLPp~aiG~~vrVm  106 (112)
                      +||||||||++||||
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.

>PRK04337 50S ribosomal protein L35Ae; Validated

Probab=100.00  E-value=1e-50  Score=281.88  Aligned_cols=85  Identities=36%  Similarity=0.689  Sum_probs=82.2

Q ss_pred             EEEEEEeeecccCCCCCCeeEEEecCcCCcchhceeecceEEEEEecccccCCceeEEEEEEEEceeCCCceEEEEecCC
Q 033755           14 VRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRCIWGKVARPHGNSGVVRAKFKSN   93 (112)
Q Consensus        14 ~kgv~~gykRg~~~Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~k~~~~g~k~rviwGKV~r~HGnsGvVrAkF~~n   93 (112)
                      +||+|+|||||++||+|||||||||||+++|||+|||||||+|||++     |   |+|||||+|+|||||+|||+|++|
T Consensus         3 ~kgv~~gykRg~~nQ~~~~aLlkiegv~~~~~a~fylGKrv~yvyk~-----g---rviwGKItR~HGnsGvVrAkF~~n   74 (87)
T PRK04337          3 MKGVILSYRRGKNTQYNRQVIIKPLGVDDREEAAKLIGRKVIWKDPT-----G---NKYVGKIVRVHGNRGEVRARFKPG   74 (87)
T ss_pred             ceEEEEEeccccCccCCceEEEEEcCcCCHHHHHhhcCceEEEEeCC-----C---CEEEEEEEeeeCCCceEEEEECCC
Confidence            69999999999999999999999999999999999999999999986     3   799999999999999999999999


Q ss_pred             CCccCCCCeEEEE
Q 033755           94 LPPKSMGDRVRVF  106 (112)
Q Consensus        94 LPp~aiG~~vrVm  106 (112)
                      |||||||++|||.
T Consensus        75 LP~~a~G~~vrv~   87 (87)
T PRK04337         75 LPGQALGDYVEII   87 (87)
T ss_pred             CChHHcCCEEEeC
Confidence            9999999999983

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

Probab=100.00  E-value=1.3e-48  Score=275.94  Aligned_cols=100  Identities=53%  Similarity=0.922  Sum_probs=94.9

Q ss_pred             CCceeeeEEEEEEEeeecccCCCCCCeeEEEecCcCCcchhceeecceEEEEEecccccCCceeEEEEEEEEceeCCCce
Q 033755            6 QGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRCIWGKVARPHGNSGV   85 (112)
Q Consensus         6 ~~~~~RLy~kgv~~gykRg~~~Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~k~~~~g~k~rviwGKV~r~HGnsGv   85 (112)
                      |.+..|+++||+++|||||+++|||+++|||||||+|+|||+|||||+|+|+|+..    |   |+|||+|+|+|||||+
T Consensus         1 ~~~~~r~~ikgv~lsyrR~k~~q~P~~~liKi~gv~s~~eA~~y~gk~v~yk~~~~----G---~Vi~G~V~R~HGnsGa   73 (100)
T COG2451           1 MAEGHRLRIKGVVLSYRRSKRTQHPNVSLIKIEGVDSPEEAQFYLGKRVCYKYRSS----G---RVIKGKVVRTHGNSGA   73 (100)
T ss_pred             CCccceEEEeeEEEEEEecccccCCceEEEEEecCCCHHHHHhhhccEEEEEeCCC----C---cEEEEEEEEecCCcce
Confidence            34558999999999999999999999999999999999999999999999988762    5   8999999999999999


Q ss_pred             EEEEecCCCCccCCCCeEEEEEeecCC
Q 033755           86 VRAKFKSNLPPKSMGDRVRVFMYPSNI  112 (112)
Q Consensus        86 VrAkF~~nLPp~aiG~~vrVmLyps~i  112 (112)
                      |||+|.+||||||+|+.|+||||||+|
T Consensus        74 VrarF~~~LP~qa~G~~v~v~ly~~~~  100 (100)
T COG2451          74 VRARFERNLPGQALGTSVEVKLYPSNI  100 (100)
T ss_pred             EEEEecCCCCchhcCcEEEEEEccCCC
Confidence            999999999999999999999999986

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

Probab=95.61  E-value=0.023  Score=36.64  Aligned_cols=34  Identities=32%  Similarity=0.597  Sum_probs=27.4

Q ss_pred             EEEEEEEceeCCCceEEEEecCCCCccCCCCeEEEEEee
Q 033755           71 CIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYP  109 (112)
Q Consensus        71 viwGKV~r~HGnsGvVrAkF~~nLPp~aiG~~vrVmLyp  109 (112)
                      +++++|+ +||||    |++..+||+.-+|.++.|.+..
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            4566665 99999    5678999999999999887643

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

Probab=93.68  E-value=0.14  Score=33.56  Aligned_cols=36  Identities=11%  Similarity=0.208  Sum_probs=26.2

Q ss_pred             EEEEeeecccCCCCCCeeEEEecCcCCcchhceeecceEEE
Q 033755           16 GTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAY   56 (112)
Q Consensus        16 gv~~gykRg~~~Q~~~~aLlKIegV~~~~~a~fylGKrvay   56 (112)
                      -.+.+++     .+.+..|++++|++|+++|+.+.|..+..
T Consensus        45 ~~v~~~~-----~~~~~~i~~~~gi~~r~~Ae~l~g~~l~v   80 (84)
T PF01782_consen   45 LKVESVR-----PHGKSLIVKFEGIDDREAAEALRGCELYV   80 (84)
T ss_dssp             EEEEEEE-----EETTEEEEEETT--SHHHHHTTTT-EEEE
T ss_pred             EEEEEEE-----EeCCEEEEEEcCCCCHHHHHhhCCCEEEE
Confidence            4555555     33789999999999999999999987753

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=90.86  E-value=0.17  Score=37.49  Aligned_cols=28  Identities=18%  Similarity=0.326  Sum_probs=24.7

Q ss_pred             CCCeeEEEecCcCCcchhceeecceEEE
Q 033755           29 YPNTSLIQIEGVNTKEDVSWYCGKRMAY   56 (112)
Q Consensus        29 ~~~~aLlKIegV~~~~~a~fylGKrvay   56 (112)
                      +.+..||+++|++|+++|+.+.|..+..
T Consensus        55 ~~~~~lv~f~gi~~~~~Ae~L~g~~l~i   82 (165)
T TIGR02273        55 QNNKLIVKFEGIDDREAAEALKGLELFV   82 (165)
T ss_pred             ECCEEEEEECCCCCHHHHHHhcCCEEEE
Confidence            4567899999999999999999998764

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.

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

Probab=90.40  E-value=0.27  Score=36.89  Aligned_cols=29  Identities=10%  Similarity=0.276  Sum_probs=25.4

Q ss_pred             CCCCeeEEEecCcCCcchhceeecceEEE
Q 033755           28 QYPNTSLIQIEGVNTKEDVSWYCGKRMAY   56 (112)
Q Consensus        28 Q~~~~aLlKIegV~~~~~a~fylGKrvay   56 (112)
                      ++.+..|++++|++|+++|+.+.|..+..
T Consensus        59 ~~~~~~lv~f~gi~dr~~Ae~l~g~~l~v   87 (169)
T PRK14591         59 KRADKVYIKLANINNADTAKKYVNALIGV   87 (169)
T ss_pred             EECCEEEEEEcCCCCHHHHHHhcCCEEEE
Confidence            45677899999999999999999998753

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

Probab=89.59  E-value=0.28  Score=36.63  Aligned_cols=32  Identities=16%  Similarity=0.295  Sum_probs=26.4

Q ss_pred             CCCCeeEEEecCcCCcchhceeecceEEEEEec
Q 033755           28 QYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA   60 (112)
Q Consensus        28 Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~   60 (112)
                      ++.+..|++++|++|+++|+.+.|..+.. .++
T Consensus        51 ~~~~~~lv~f~gi~~~~~Ae~l~g~~l~v-~~~   82 (165)
T PRK14592         51 IGANLVIAKISGINSRTEAELLRNKKLYV-ERS   82 (165)
T ss_pred             ecCCEEEEEEcCCCCHHHHHHhcCCEEEE-EHH
Confidence            44567899999999999999999998764 443

>PRK13829 rimM 16S rRNA-processing protein RimM; Provisional

Probab=89.47  E-value=0.26  Score=36.84  Aligned_cols=32  Identities=19%  Similarity=0.286  Sum_probs=26.5

Q ss_pred             CCCCeeEEEecCcCCcchhceeecceEEEEEec
Q 033755           28 QYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA   60 (112)
Q Consensus        28 Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~   60 (112)
                      ++.+..|++++|++|+++|+.+.|..+. |.++
T Consensus        48 ~~~~~~l~~f~gi~~r~~Ae~l~g~~l~-v~~~   79 (162)
T PRK13829         48 RVGPELVLHLAGVTSREGAEALVGLRVY-ADDA   79 (162)
T ss_pred             EECCEEEEEECCCCCHHHHHHhcCCEEE-EEHH
Confidence            4466789999999999999999999876 3443

>PRK13828 rimM 16S rRNA-processing protein RimM; Provisional

Probab=88.40  E-value=0.35  Score=36.05  Aligned_cols=32  Identities=16%  Similarity=0.199  Sum_probs=26.5

Q ss_pred             CCCCeeEEEecCcCCcchhceeecceEEEEEec
Q 033755           28 QYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA   60 (112)
Q Consensus        28 Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~   60 (112)
                      ++.+..|++++|++|+++|+.+.|..+.. .+.
T Consensus        39 ~~~~~~lv~f~gi~dr~~Ae~L~g~~l~i-~~~   70 (161)
T PRK13828         39 PAKDGLVARLKGVATREAAEALRGLELYV-PRD   70 (161)
T ss_pred             EECCEEEEEECCCCCHHHHHHhcCCEEEE-EHH
Confidence            44566899999999999999999998764 443

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

Probab=87.93  E-value=0.66  Score=30.30  Aligned_cols=28  Identities=25%  Similarity=0.622  Sum_probs=22.8

Q ss_pred             EEEEEceeCCCceEEEEecCCCCccCCC
Q 033755           73 WGKVARPHGNSGVVRAKFKSNLPPKSMG  100 (112)
Q Consensus        73 wGKV~r~HGnsGvVrAkF~~nLPp~aiG  100 (112)
                      -|+|.+|||-.|-|++..-.+.|.....
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            4999999999999999998887765443

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.

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

Probab=87.17  E-value=0.38  Score=36.06  Aligned_cols=32  Identities=19%  Similarity=0.193  Sum_probs=26.2

Q ss_pred             CCCCeeEEEecCcCCcchhceeecceEEEEEec
Q 033755           28 QYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA   60 (112)
Q Consensus        28 Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~   60 (112)
                      .+.+..|++++|++|+++|+.+.|..+. |.++
T Consensus        56 ~~~~~~lvkf~gi~dr~~Ae~L~g~~l~-v~~~   87 (166)
T PRK14594         56 LKNNSLLLKFEEFNAPEPIKPLIGFELW-VDDE   87 (166)
T ss_pred             EECCEEEEEEcCCCCHHHHHHhcCCEEE-EEHH
Confidence            3456689999999999999999998775 4554

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

Probab=87.16  E-value=0.43  Score=35.63  Aligned_cols=29  Identities=14%  Similarity=0.182  Sum_probs=24.9

Q ss_pred             CCCCeeEEEecCcCCcchhceeecceEEE
Q 033755           28 QYPNTSLIQIEGVNTKEDVSWYCGKRMAY   56 (112)
Q Consensus        28 Q~~~~aLlKIegV~~~~~a~fylGKrvay   56 (112)
                      .+.+..|+|++|++|+++|+.|.|..+..
T Consensus        59 ~~~~~~lvkf~gi~~~~~Ae~l~g~~l~i   87 (172)
T PRK00122         59 FHKGFLIVKFEGVDDRNAAEALKGCELFV   87 (172)
T ss_pred             EECCEEEEEECCCCCHHHHHHhCCCEEEE
Confidence            34566899999999999999999998764

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

Probab=87.13  E-value=0.74  Score=34.36  Aligned_cols=30  Identities=27%  Similarity=0.480  Sum_probs=26.3

Q ss_pred             EEEEEEEEceeCCCceEEEEecCCCCccCC
Q 033755           70 RCIWGKVARPHGNSGVVRAKFKSNLPPKSM   99 (112)
Q Consensus        70 rviwGKV~r~HGnsGvVrAkF~~nLPp~ai   99 (112)
                      .+..|+|++|||-.|-|+++.-.+.|...+
T Consensus         7 ~v~iG~i~~~hGlkGevkv~~~td~p~~~~   36 (172)
T PRK00122          7 LLVVGKIVSAHGIKGEVKVKSFTDFPERIF   36 (172)
T ss_pred             eEEEEEEECCCcccEEEEEEEecCCHHHHc
Confidence            478999999999999999999988886544

>PRK14590 rimM 16S rRNA-processing protein RimM; Provisional

Probab=87.01  E-value=0.45  Score=35.95  Aligned_cols=32  Identities=19%  Similarity=0.257  Sum_probs=26.7

Q ss_pred             CCCCeeEEEecCcCCcchhceeecceEEEEEec
Q 033755           28 QYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA   60 (112)
Q Consensus        28 Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~   60 (112)
                      ++.+..|++++|++|+++|+.+.|..+.. .++
T Consensus        55 ~~~~~~lv~f~gi~~~e~Ae~L~g~~l~i-~~~   86 (171)
T PRK14590         55 PHGGKFLVRFEGYDTPEEAVKWRGGSLFL-PQE   86 (171)
T ss_pred             EECCEEEEEECCCCCHHHHHHhcCCEEEE-EHH
Confidence            44566899999999999999999998864 453

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

Probab=86.96  E-value=0.67  Score=34.74  Aligned_cols=28  Identities=21%  Similarity=0.102  Sum_probs=24.0

Q ss_pred             EEEEEEEceeCCCceEEEEecCCCCccC
Q 033755           71 CIWGKVARPHGNSGVVRAKFKSNLPPKS   98 (112)
Q Consensus        71 viwGKV~r~HGnsGvVrAkF~~nLPp~a   98 (112)
                      +++|+|++|||=.|-|+++.-..-|+..
T Consensus         2 ~~iG~I~~~hGlkGevkV~~~td~~~~~   29 (166)
T PRK14594          2 FVKGIILSSYGINGYAKVKSISNNFCDF   29 (166)
T ss_pred             EEEEEEECceeeeEEEEEEEccCCHHHh
Confidence            5789999999999999999887766553

>TIGR02273 16S_RimM 16S rRNA processing protein RimM

Probab=84.10  E-value=1.7  Score=32.17  Aligned_cols=29  Identities=31%  Similarity=0.567  Sum_probs=25.0

Q ss_pred             EEEEEEEceeCCCceEEEEecCCCCccCC
Q 033755           71 CIWGKVARPHGNSGVVRAKFKSNLPPKSM   99 (112)
Q Consensus        71 viwGKV~r~HGnsGvVrAkF~~nLPp~ai   99 (112)
                      +..|+|.+|||=.|-|+++.-...|...+
T Consensus         2 v~iG~I~~~hGlkGevkv~~~td~p~~~~   30 (165)
T TIGR02273         2 LVVGKIGGPHGIKGEVKVKSFTDFPESLF   30 (165)
T ss_pred             EEEEEEECCcccCEEEEEEEcCCCHHHHc
Confidence            46799999999999999999888886554

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=81.20  E-value=1.7  Score=32.98  Aligned_cols=29  Identities=17%  Similarity=0.401  Sum_probs=25.2

Q ss_pred             EEEEEEEceeCCCceEEEEecCCCCccCC
Q 033755           71 CIWGKVARPHGNSGVVRAKFKSNLPPKSM   99 (112)
Q Consensus        71 viwGKV~r~HGnsGvVrAkF~~nLPp~ai   99 (112)
                      +..|+|.++||-.|-|++..-..-|....
T Consensus         5 i~iG~I~~~hGikGevkv~~~td~pe~~~   33 (184)
T PRK14593          5 LLVGRIGKSVGLNGGLKLHLESDFPECLK   33 (184)
T ss_pred             EEEEEEECCEeeeEEEEEEECCCCHHHhc
Confidence            57899999999999999999988777543

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

Probab=80.45  E-value=2.1  Score=31.94  Aligned_cols=29  Identities=28%  Similarity=0.389  Sum_probs=25.2

Q ss_pred             EEEEEEEceeCCCceEEEEecCCCCccCC
Q 033755           71 CIWGKVARPHGNSGVVRAKFKSNLPPKSM   99 (112)
Q Consensus        71 viwGKV~r~HGnsGvVrAkF~~nLPp~ai   99 (112)
                      +..|+|++|||=.|-|+++.-.+-|....
T Consensus         3 v~iG~I~~~hGlkGevkv~~~td~p~~~~   31 (165)
T PRK14592          3 ICLGVITSPHGIKGHVKIKTFTEDPENIS   31 (165)
T ss_pred             EEEEEEECCCccCEEEEEEECCCCHHHhc
Confidence            56899999999999999999988777543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	112
3izr_j	111	Localization Of The Large Subunit Ribosomal Protein		4e-50
3izs_j	107	Localization Of The Large Subunit Ribosomal Protein		1e-30
4a18_H	113	T.Thermophila 60s Ribosomal Subunit In Complex With		3e-27
3zf7_l	149	High-resolution Cryo-electron Microscopy Structure		5e-24
1sqr_A	95	Solution Structure Of The 50s Ribosomal Protein L35		7e-11
3j21_c	87	Promiscuous Behavior Of Proteins In Archaeal Riboso		1e-10

>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 =  192 bits (488), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 91/111 (81%), Positives = 100/111 (90%)
Query: 2   VKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAK 61
           +KGRQG+RVRLYVRGTILGYKRSKSNQY NTSL+QIEGVNTKE+V WY GKR+AY+YKAK
Sbjct: 1   MKGRQGQRVRLYVRGTILGYKRSKSNQYENTSLLQIEGVNTKEEVGWYAGKRIAYVYKAK 60
Query: 62  VKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
            K N S  RCIWGKV RPHGNSGVVRAKF+SNLPP SMG +VRVFMYPS+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 =  128 bits (321), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 61/106 (57%), Positives = 76/106 (71%)
Query: 7   GERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNG 66
            E  RLYV+G  L Y+RSK    PN SLI+IEGV T +D  +Y GKR+AY+Y+A  +  G
Sbjct: 2   AESHRLYVKGKHLSYQRSKRVNNPNVSLIKIEGVATPQDAQFYLGKRIAYVYRASKEVRG 61
Query: 67  SHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
           S  R +WGKV R HGNSGVVRA F++NLP K+ G  VR+F+YPSNI
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 =  116 bits (290), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 51/101 (50%), Positives = 76/101 (75%), Gaps = 1/101 (0%)
Query: 10  VRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHY 69
            RL+V+    G++RSK  Q  N +L++++ VNTKEDV++Y GKR+ YIYK + KKNGS+Y
Sbjct: 12  TRLWVKAAFTGFRRSKHTQNSNQALLKLQNVNTKEDVAFYQGKRVVYIYKGQ-KKNGSNY 70
Query: 70  RCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPS 110
           R IWG++ + HGN+GV  A+F  NLPP+++G  +RV +YP+
Sbjct: 71  RTIWGRIGKAHGNNGVAVARFAHNLPPQAIGSVLRVMLYPN 111

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

Iteration: 1
 Score =  105 bits (263), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 52/113 (46%), Positives = 71/113 (62%), Gaps = 11/113 (9%)
Query: 11  RLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYK----------A 60
           RLY++GT+ GY R    Q  NT+L++IE VNT ED  WY GKR+ Y+Y           +
Sbjct: 37  RLYMKGTLAGYTRGLHGQNKNTALVRIENVNTTEDAKWYVGKRVCYVYHGYKIKRCVRWS 96
Query: 61  KVKKNGSHYRCIWGKVARPHGNSGVVRAKFK-SNLPPKSMGDRVRVFMYPSNI 112
           K     S+ R IWG++ RPHG SG VR KF  S++P  ++G R+RV++YPS 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 = 62.4 bits (150), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 30/96 (31%), Positives = 54/96 (56%), Gaps = 8/96 (8%)
Query: 12  LYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRC 71
           + ++G +L Y+RSK NQ+ N  +I+   VN++E+ S   G+ + +             + 
Sbjct: 1   MRIKGVVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGRLVLW--------KSPSGKI 52
Query: 72  IWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFM 107
           + GK+ R HG  G VRA+F+  LP +++GD V + +
Sbjct: 53  LKGKIVRVHGTKGAVRARFEKGLPGQALGDYVEIVL 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 = 61.2 bits (147), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 30/95 (31%), Positives = 53/95 (55%), Gaps = 8/95 (8%)
Query: 12  LYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRC 71
           + ++G +L Y+RSK NQ+ N  +I+   VN++E+ S   G+ + +             + 
Sbjct: 1   MRIKGVVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGRLVLW--------KSPSGKI 52
Query: 72  IWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVF 106
           + GK+ R HG  G VRA+F+  LP +++GD V + 
Sbjct: 53  LKGKIVRVHGTKGAVRARFEKGLPGQALGDYVEIV 87

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	112
3iz5_J	166	60S ribosomal protein L12 (L11P); eukaryotic ribos	2e-54
3izc_j	107	60S ribosomal protein RPL33 (L35AE); eukaryotic ri	5e-53
4a18_H	113	RPL35A; ribosome, eukaryotic initiation factor 6,	1e-48
1sqr_A	95	50S ribosomal protein L35AE; PFR48, structure, aut	7e-44

>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 =  149 bits (378), Expect = 1e-48
 Identities = 51/106 (48%), Positives = 76/106 (71%), Gaps = 1/106 (0%)

Query: 5   RQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKK 64
                 RL+V+    G++RSK  Q  N +L++++ VNTKEDV++Y GKR+ YIYK + KK
Sbjct: 7   SPVAPTRLWVKAAFTGFRRSKHTQNSNQALLKLQNVNTKEDVAFYQGKRVVYIYKGQ-KK 65

Query: 65  NGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPS 110
           NGS+YR IWG++ + HGN+GV  A+F  NLPP+++G  +RV +YP+
Sbjct: 66  NGSNYRTIWGRIGKAHGNNGVAVARFAHNLPPQAIGSVLRVMLYPN 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 =  137 bits (346), Expect = 7e-44
 Identities = 30/101 (29%), Positives = 56/101 (55%), Gaps = 8/101 (7%)

Query: 12  LYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRC 71
           + ++G +L Y+RSK NQ+ N  +I+   VN++E+ S   G+ + +   +         + 
Sbjct: 1   MRIKGVVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGRLVLWKSPSG--------KI 52

Query: 72  IWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
           + GK+ R HG  G VRA+F+  LP +++GD V + +   + 
Sbjct: 53  LKGKIVRVHGTKGAVRARFEKGLPGQALGDYVEIVLEHHHH 93

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	112
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
1wb1_A	482	Translation elongation factor SELB; selenocysteine	90.69
3h9n_A	177	Ribosome maturation factor RIMM; structural genomi	86.57
2f1l_A	187	16S rRNA processing protein; structural genomics,	86.57
2dyi_A	162	Probable 16S rRNA-processing protein RIMM; ribosom	86.48
2qgg_A	182	16S rRNA-processing protein RIMM; X-RAY, NESG, ASR	85.81

>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=1.1e-63  Score=359.49  Aligned_cols=104  Identities=48%  Similarity=0.963  Sum_probs=101.6

Q ss_pred             ceeeeEEEEEEEeeecccCCCCCCeeEEEecCcCCcchhceeecceEEEEEecccccCCceeEEEEEEEEceeCCCceEE
Q 033755            8 ERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRCIWGKVARPHGNSGVVR   87 (112)
Q Consensus         8 ~~~RLy~kgv~~gykRg~~~Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~k~~~~g~k~rviwGKV~r~HGnsGvVr   87 (112)
                      +++|||+||+|+|||||++||+|||||||||||+++|||+||||||||||||++++ .|+|+|+|||||+|+|||||+||
T Consensus        10 ~~~rly~Kgv~lgYkRg~~nQ~~~taLlKIeGV~~~~~a~fylGKrvayvykak~~-~g~k~RviwGKVtR~HGnsGvVr   88 (113)
T 4a18_H           10 APTRLWVKAAFTGFRRSKHTQNSNQALLKLQNVNTKEDVAFYQGKRVVYIYKGQKK-NGSNYRTIWGRIGKAHGNNGVAV   88 (113)
T ss_dssp             CSCCCCEEEEEEEEEEETTEEEEEEEEEEETTCCSHHHHHTTTTCEEEEEEEEEEE-TTEEEEEEEEEEEEEETTTTEEE
T ss_pred             ccceeEEEEEEEecccccCCCCCCeEEEEEcCcCCHHHHHhhcCCeEEEEEecCCC-CCCeEEEEEEEEEeeeCCCCeEE
Confidence            67899999999999999999999999999999999999999999999999999987 89999999999999999999999


Q ss_pred             EEecCCCCccCCCCeEEEEEeecCC
Q 033755           88 AKFKSNLPPKSMGDRVRVFMYPSNI  112 (112)
Q Consensus        88 AkF~~nLPp~aiG~~vrVmLyps~i  112 (112)
                      |+|++||||||||++||||||||+.
T Consensus        89 AkF~~nLP~kA~G~~VrVmLyPs~~  113 (113)
T 4a18_H           89 ARFAHNLPPQAIGSVLRVMLYPNRA  113 (113)
T ss_dssp             EEESSCCCGGGGGSEEEEECCCCCC
T ss_pred             EEeCCCCChHHcCCeEEEEEecCCC
Confidence            9999999999999999999999973

>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=5.4e-54  Score=301.30  Aligned_cols=88  Identities=34%  Similarity=0.609  Sum_probs=84.6

Q ss_pred             EEEEEEEeeecccCCCCCCeeEEEecCcCCcchhceeecceEEEEEecccccCCceeEEEEEEEEceeCCCceEEEEecC
Q 033755           13 YVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRCIWGKVARPHGNSGVVRAKFKS   92 (112)
Q Consensus        13 y~kgv~~gykRg~~~Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~k~~~~g~k~rviwGKV~r~HGnsGvVrAkF~~   92 (112)
                      |+||+|+|||||++||+|||||||||||+++|||+|||||||||||+++        |+|||||+|||||||+|||+|++
T Consensus         2 ~~Kgv~lgYkRg~~nQ~~~~aLlkIegV~~k~~a~fYlGKrvayvyka~--------rviwGKVtR~HGnsGvVrAkF~~   73 (95)
T 1sqr_A            2 RIKGVVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGRLVLWKSPSG--------KILKGKIVRVHGTKGAVRARFEK   73 (95)
T ss_dssp             CCEEEEEEEECCSSSSSCCEEEEEESCCCCHHHHHHHTTCEEEECCSTT--------CCEEEEEEEESSSSSCEEEECSS
T ss_pred             eeeEEEEeeccccCcCCCceEEEEEcCCCCHHHHHhhcCCeEEEEECCC--------CEEEEEEEeeeCCCCEEEEEeCC
Confidence            7899999999999999999999999999999999999999999999885        89999999999999999999999


Q ss_pred             CCCccCCCCeEEEEEe
Q 033755           93 NLPPKSMGDRVRVFMY  108 (112)
Q Consensus        93 nLPp~aiG~~vrVmLy  108 (112)
                      ||||||||++|||||-
T Consensus        74 nLP~kA~G~~VrVml~   89 (95)
T 1sqr_A           74 GLPGQALGDYVEIVLE   89 (95)
T ss_dssp             CCSSSCTTCEEECC--
T ss_pred             CCChHHcCCEEEEEEe
Confidence            9999999999999984

>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=9.4e-51  Score=281.09  Aligned_cols=84  Identities=37%  Similarity=0.675  Sum_probs=81.0

Q ss_pred             EEEEEEeeecccCCCCCCeeEEEecCcCCcchhceeecceEEEEEecccccCCceeEEEEEEEEceeCCCceEEEEecCC
Q 033755           14 VRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRCIWGKVARPHGNSGVVRAKFKSN   93 (112)
Q Consensus        14 ~kgv~~gykRg~~~Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~k~~~~g~k~rviwGKV~r~HGnsGvVrAkF~~n   93 (112)
                      +||+|+|||||++||+|||||||||||+++|||+|||||||||||++     |   ++|||||+|+|||||+|||+|++|
T Consensus         3 ~Kg~~~gykRg~~nQ~~~taLlkieGV~~~~~a~fylGKrvayv~~~-----g---~~iwGKVtr~HGnsGvVrAkF~~n   74 (87)
T 3j21_c            3 IKGVVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGRLVLWKSPS-----G---KILKGKIVRVHGTKGAVRARFEKG   74 (87)
T ss_dssp             EEEEEEEESCCSSCCCTTCEEEEESSCCSHHHHGGGTTCEEEECCSS-----S---CCEEEEEEEECCSSSCEEEEESSC
T ss_pred             eeEEEEecccccCcCCCCeEEEEEcCcCCHHHHHhhcCceEEEEeCC-----C---CEEEEEEEeeeCCCCeEEEEeCCC
Confidence            79999999999999999999999999999999999999999999974     3   489999999999999999999999


Q ss_pred             CCccCCCCeEEE
Q 033755           94 LPPKSMGDRVRV  105 (112)
Q Consensus        94 LPp~aiG~~vrV  105 (112)
                      |||||||++|||
T Consensus        75 LP~~a~G~~Vri   86 (87)
T 3j21_c           75 LPGQALGDYVEI   86 (87)
T ss_dssp             CCSSCSCCEECC
T ss_pred             CChHHcCCeEEe
Confidence            999999999997

>1wb1_A Translation elongation factor SELB; selenocysteine, protein synthesis, selenium, ribosome; HET: GDP DXC; 3.0A {Methanococcus maripaludis} SCOP: b.43.3.1 b.43.3.1 b.44.1.1 c.37.1.8 PDB: 1wb2_A* 1wb3_A*

Probab=90.69  E-value=0.039  Score=45.58  Aligned_cols=67  Identities=19%  Similarity=0.260  Sum_probs=50.9

Q ss_pred             CCCCeeEEEecCcCCcchhceeecceEEEEEecccccCCceeEEEEEEEEceeCCCceEEEEecCCCCccCCCCeEEEEE
Q 033755           28 QYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFM  107 (112)
Q Consensus        28 Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~k~~~~g~k~rviwGKV~r~HGnsGvVrAkF~~nLPp~aiG~~vrVmL  107 (112)
                      ++.++++++=- ..+..|.++|+|.+|.-.       .|    -|+|.|-.+.|.||.++|.|.-.|.++   +.|.+-|
T Consensus       413 ~~~~~~i~~~l-f~~~~~~~~f~g~~v~~~-------~g----~~~G~I~~~fg~~G~~~~~f~~~~~~~---d~v~~~~  477 (482)
T 1wb1_A          413 IDKGRTVIDGL-AQSKVAAEKLIGEEISIE-------GK----DIVGKIKGTFGTKGLLTAEFSGNVENR---DKVILNR  477 (482)
T ss_dssp             CCSSCCEETTS-CSSHHHHHHSCSCCCEET-------TT----CCCBCCCCCBTTTTBBCCCBSSCCCSS---CEEEEEC
T ss_pred             EcCCEEEEEcC-ccchhhhHHhcCcEEEEc-------CC----ceEEEEeccCCCCceEEEEecCCCCCC---Ceeeeeh
Confidence            46777777622 455668999999998762       23    256999999999999999999998875   5666666


Q ss_pred             ee
Q 033755          108 YP  109 (112)
Q Consensus       108 yp  109 (112)
                      |.
T Consensus       478 ~~  479 (482)
T 1wb1_A          478 LR  479 (482)
T ss_dssp             CC
T ss_pred             hh
Confidence            64

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

Probab=86.57  E-value=0.35  Score=35.45  Aligned_cols=68  Identities=13%  Similarity=0.204  Sum_probs=43.5

Q ss_pred             EEEeeecccCCCCCCeeEEEecCcCCcchhceeecceEEEEEecccc-----------cCCceeE----EEEEEEEcee-
Q 033755           17 TILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVK-----------KNGSHYR----CIWGKVARPH-   80 (112)
Q Consensus        17 v~~gykRg~~~Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~k~~-----------~~g~k~r----viwGKV~r~H-   80 (112)
                      .+.++|.     +.+..|+|++||+|+++|+.+.|..+ ||-++.--           .-|-.+.    ...|+|+... 
T Consensus        48 ~v~~~r~-----~~~~~lvkf~gi~dr~~Ae~L~G~~l-~v~~~~lp~l~edE~Y~~dLiGl~V~~~~g~~lG~V~~v~~  121 (177)
T 3h9n_A           48 ELENWRY-----HNHEIIVKLKGVDDREAAQILANVEI-GVDLSVFPELEEGDYYWHDLIGCTVVNLEGYTMGTVTEMME  121 (177)
T ss_dssp             CEEEEEE-----SSSCEEEEESSCCSHHHHHTTTTCEE-EEECCCCCCCSSSCGGGGGTTTCEEEETTCCEEEEEEEEEE
T ss_pred             EEEEEEE-----eCCEEEEEEcCCCCHHHHHHhcCCEE-EEEHHHCCCCCCCCCCHHHhcCCEEEeCCCCEEEEEEEEee
Confidence            3455554     34668999999999999999999988 45654311           0121111    2468888764 


Q ss_pred             -CCCceEEEEe
Q 033755           81 -GNSGVVRAKF   90 (112)
Q Consensus        81 -GnsGvVrAkF   90 (112)
                       |.+-+...+-
T Consensus       122 ~gandvl~V~~  132 (177)
T 3h9n_A          122 TGSNDVLVVKA  132 (177)
T ss_dssp             SSSCEEEEEEC
T ss_pred             CCCcEEEEEEe
Confidence             5555556653

>2f1l_A 16S rRNA processing protein; structural genomics, joint CENT structural genomics, JCSG, protein structure initiative, PS unknown function; HET: UNL; 2.46A {Pseudomonas aeruginosa} SCOP: b.41.1.4 b.43.3.4

Probab=86.57  E-value=0.86  Score=33.86  Aligned_cols=38  Identities=11%  Similarity=0.279  Sum_probs=29.7

Q ss_pred             EEEeeecccCCCCCCeeEEEecCcCCcchhceeecceEEEEEec
Q 033755           17 TILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA   60 (112)
Q Consensus        17 v~~gykRg~~~Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~   60 (112)
                      .+.++|.     +.+..|+|++||+|+++|+.+.|..+. |-++
T Consensus        66 ~v~~~r~-----~~~~~ivkf~gi~dr~~Ae~L~G~~l~-v~r~  103 (187)
T 2f1l_A           66 ELVRGRL-----HGKVLAAKLKGLDDREEARTFTGYEIC-IPRS  103 (187)
T ss_dssp             EEEEEEE-----ETTEEEEEETTCCSHHHHHTTTTCEEE-EEGG
T ss_pred             EEEEEEE-----ECCEEEEEEeCCCCHHHHHHhCCCEEE-EEHH
Confidence            4556653     346799999999999999999999775 4554

>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=86.48  E-value=0.26  Score=35.71  Aligned_cols=38  Identities=18%  Similarity=0.186  Sum_probs=30.2

Q ss_pred             EEEeeecccCCCCCCeeEEEecCcCCcchhceeecceEEEEEec
Q 033755           17 TILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA   60 (112)
Q Consensus        17 v~~gykRg~~~Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~   60 (112)
                      .+.++|.     +.+..|+|++||+|+++|+.+.|..+. |-++
T Consensus        42 ~v~~~r~-----~~~~~ivkf~gi~~r~~Ae~L~G~~l~-v~~~   79 (162)
T 2dyi_A           42 AIEDLYR-----VGEELVVHLAGVTDRTLAEALVGLRVY-AEVA   79 (162)
T ss_dssp             EEEEEEE-----ETTEEEEEETTCCSHHHHHTTTTCEEE-EEGG
T ss_pred             EEEEEEE-----ECCEEEEEEcCCCCHHHHHHhCCCEEE-EEHH
Confidence            5667764     256799999999999999999999774 4554

>2qgg_A 16S rRNA-processing protein RIMM; X-RAY, NESG, ASR73, structural genomics, PSI-2, protein structure initiative; 2.40A {Acinetobacter calcoaceticus}

Probab=85.81  E-value=0.3  Score=36.00  Aligned_cols=38  Identities=13%  Similarity=0.228  Sum_probs=29.3

Q ss_pred             EEEeeecccCCCCCCeeEEEecCcCCcchhceeecceEEEEEec
Q 033755           17 TILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA   60 (112)
Q Consensus        17 v~~gykRg~~~Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~   60 (112)
                      .+.++|.     +.+..|+|++||+|+++|+.+.|..+. |-++
T Consensus        57 ~v~~~r~-----~~~~~ivkf~gi~dr~~Ae~L~G~~l~-v~~~   94 (182)
T 2qgg_A           57 DVKRWKP-----HGKGLVVSLKGVSDRTGAESLVASNIW-IAKS   94 (182)
T ss_dssp             CEEEEEE-----ETTEEEEEETTCCSHHHHHTTTTCEEE-EETT
T ss_pred             EEEEEEE-----cCCEEEEEECCCCCHHHHHHhCCCEEE-EEHH
Confidence            3555553     356799999999999999999999764 4554

---

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	112
d1sqra_	87	b.43.3.3 (A:) Ribosomal protein L35ae {Pyrococcus	8e-42

>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 =  130 bits (329), Expect = 8e-42
 Identities = 30/94 (31%), Positives = 54/94 (57%), Gaps = 8/94 (8%)

Query: 12  LYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRC 71
           + ++G +L Y+RSK NQ+ N  +I+   VN++E+ S   G+ + +   +         + 
Sbjct: 1   MRIKGVVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGRLVLWKSPSG--------KI 52

Query: 72  IWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRV 105
           + GK+ R HG  G VRA+F+  LP +++GD V +
Sbjct: 53  LKGKIVRVHGTKGAVRARFEKGLPGQALGDYVEI 86

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	112
d1sqra_	87	Ribosomal protein L35ae {Pyrococcus furiosus [TaxI	100.0
d2f1la2	89	16S rRNA processing protein RimM, N-terminal domai	94.96
d1wb1a2	79	Elongation factor SelB, domains 2 and 4 {Methanoco	93.69
d2f1la2	89	16S rRNA processing protein RimM, N-terminal domai	82.08

>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=7.1e-53  Score=290.04  Aligned_cols=87  Identities=36%  Similarity=0.656  Sum_probs=83.4

Q ss_pred             eEEEEEEEeeecccCCCCCCeeEEEecCcCCcchhceeecceEEEEEecccccCCceeEEEEEEEEceeCCCceEEEEec
Q 033755           12 LYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRCIWGKVARPHGNSGVVRAKFK   91 (112)
Q Consensus        12 Ly~kgv~~gykRg~~~Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~k~~~~g~k~rviwGKV~r~HGnsGvVrAkF~   91 (112)
                      ||+||+|+|||||++||+|||||||||||+++|||+|||||||+|+|++     +   |+|||||+|+|||||+|||+|+
T Consensus         1 lyvKgv~~gykRg~~nq~~~~~Llkiegv~~k~~a~fylGKrv~y~~~~-----~---r~iwGKVtr~HGnsGvVrAkF~   72 (87)
T d1sqra_           1 MRIKGVVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGRLVLWKSPS-----G---KILKGKIVRVHGTKGAVRARFE   72 (87)
T ss_dssp             CCCEEEEEEEECCSSSSSCCEEEEEESCCCCHHHHHHHTTCEEEECCST-----T---CCEEEEEEEESSSSSCEEEECS
T ss_pred             CeEEEEEEEeccccccCCCCEEEEEEcCcCCHHHHHhhcCcEEEEECCC-----C---cEEEeeEeeecCCCceEEEEec
Confidence            7999999999999999999999999999999999999999999996643     2   7999999999999999999999


Q ss_pred             CCCCccCCCCeEEEE
Q 033755           92 SNLPPKSMGDRVRVF  106 (112)
Q Consensus        92 ~nLPp~aiG~~vrVm  106 (112)
                      +||||||||++||||
T Consensus        73 ~nLP~qa~G~~VrVm   87 (87)
T d1sqra_          73 KGLPGQALGDYVEIV   87 (87)
T ss_dssp             SCCSSSCTTCEEECC
T ss_pred             CCCChHHcCCEEEeC
Confidence            999999999999998

>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=94.96  E-value=0.0038  Score=38.85  Aligned_cols=30  Identities=10%  Similarity=0.291  Sum_probs=26.1

Q ss_pred             CCCCCCeeEEEecCcCCcchhceeecceEE
Q 033755           26 SNQYPNTSLIQIEGVNTKEDVSWYCGKRMA   55 (112)
Q Consensus        26 ~~Q~~~~aLlKIegV~~~~~a~fylGKrva   55 (112)
                      .+++.+..+++++||+|+|+|+.+.|+.+.
T Consensus        52 ~~~~~~~~~vk~~~i~~r~~Ae~l~g~~i~   81 (89)
T d2f1la2          52 GRLHGKVLAAKLKGLDDREEARTFTGYEIC   81 (89)
T ss_dssp             EEEETTEEEEEETTCCSHHHHHTTTTCEEE
T ss_pred             EEecccEEEEEEcCCCCHHHHHHhCCCEEE
Confidence            345667899999999999999999999875

>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=93.69  E-value=0.0036  Score=40.58  Aligned_cols=50  Identities=24%  Similarity=0.471  Sum_probs=40.5

Q ss_pred             EEecCc-CCcchhceeecceEEEEEecccccCCceeEEEEEEEEceeCCCceEEEEecCCCC
Q 033755           35 IQIEGV-NTKEDVSWYCGKRMAYIYKAKVKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLP   95 (112)
Q Consensus        35 lKIegV-~~~~~a~fylGKrvayvyk~k~~~~g~k~rviwGKV~r~HGnsGvVrAkF~~nLP   95 (112)
                      .=|||. .++..|+.++|-+|-.  .+         .-|||||.-+||..|.+.|-|.-|.-
T Consensus        15 ~~IegLA~sK~~aEkLIGe~v~i--~~---------k~i~Gkik~TfGTkG~l~adF~geV~   65 (79)
T d1wb1a2          15 TVIDGLAQSKVAAEKLIGEEISI--EG---------KDIVGKIKGTFGTKGLLTAEFSGNVE   65 (79)
T ss_dssp             CEETTSCSSHHHHHHSCSCCCEE--TT---------TCCCBCCCCCBTTTTBBCCCBSSCCC
T ss_pred             EEeeecccchhHHHhhcCcEEEe--cC---------CceEEEEeccccCceEEEEEeccccC
Confidence            446775 5788899999998865  33         24699999999999999999998764

>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=82.08  E-value=0.78  Score=27.65  Aligned_cols=25  Identities=20%  Similarity=0.208  Sum_probs=21.3

Q ss_pred             EEEEEEEceeCCCceEEEEecCCCC
Q 033755           71 CIWGKVARPHGNSGVVRAKFKSNLP   95 (112)
Q Consensus        71 viwGKV~r~HGnsGvVrAkF~~nLP   95 (112)
                      +..|+|.+|||=.|-|+..--..-|
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            6789999999999999988766644