Citrus Sinensis ID: 042762

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90------
Protein Sequence
TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI
Secondary Structure (PSIPRED)
cEEEEEcccccccccEEEEEEcccccHHHHHHHccccEEEEEcccccccccEEEEEEEEEEcEEccccEEEEEEcccccccccccEEEEEEEcccc
Secondary Structure Prediction (SSPRO)
cEcEEccccccccccEEEEEEEccccHcccEEEEccEEEEEEEEcccccccEEEEEEEEEEcccccccEEEEEEcccccHHHcccEEEEEEccccc
Coil and Loop (DISEMBL)
tilgykrsksnqypntsliqiegvntKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKvarshgnsgvvraefksnlppksmgdkvrvfmypsni
Flexible Loop (DISEMBL)
tilgykrsksnqypntsliqiegvnTKEKVVWYCCKHLAYIykaktkkswTHYRCIWGKVarshgnsgvvraefksnlppksmgdkvrvFMYPSNI
Low Complexity Region (SEG)
TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI
Disordered region (IsUnstruct)
****************SLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVARSHGNSGVV**************************
Disordered Region (DISOPRED)
TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI
Disordered Region (DISEMBL)
TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI
Disordered Region (DISPRO)
TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSN*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI
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	96	2.2.26 [Sep-21-2011]
Q9C912	112	60S ribosomal protein L35	yes	no	1.0	0.857	0.822	2e-41
Q9LMK0	112	60S ribosomal protein L35	yes	no	1.0	0.857	0.812	3e-41
Q9FZH0	111	60S ribosomal protein L35	no	no	1.0	0.864	0.822	3e-41
P51422	111	60S ribosomal protein L35	yes	no	1.0	0.864	0.812	5e-41
P41056	107	60S ribosomal protein L33	yes	no	0.979	0.878	0.531	4e-24
P05744	107	60S ribosomal protein L33	yes	no	0.979	0.878	0.531	6e-24
Q55BN7	105	60S ribosomal protein L35	yes	no	1.0	0.914	0.505	1e-22
Q9USX4	108	60S ribosomal protein L33	yes	no	0.979	0.870	0.478	3e-21
P02434	110	60S ribosomal protein L35	N/A	no	1.0	0.872	0.485	6e-21
Q90YT3	110	60S ribosomal protein L35	N/A	no	0.958	0.836	0.505	1e-20

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

 Score =  167 bits (423), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 79/96 (82%), Positives = 87/96 (90%)

Query: 1   TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKV 60
           TILGYKRSKSNQYPNTSL+QIEGVNT+E+V WY  K +AYIYKAKTKK+ +HYRCIWGKV
Sbjct: 17  TILGYKRSKSNQYPNTSLVQIEGVNTQEEVNWYKGKRMAYIYKAKTKKNGSHYRCIWGKV 76

Query: 61  ARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
            R HGNSGVVRA+F SNLPPKSMG +VRVFMYPSNI
Sbjct: 77  TRPHGNSGVVRAKFTSNLPPKSMGSRVRVFMYPSNI 112

Arabidopsis thaliana (taxid: 3702)

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

 Score =  166 bits (421), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 78/96 (81%), Positives = 86/96 (89%)

Query: 1   TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKV 60
           TILGYKRSKSNQYPNTSL+Q+EGVNT E+V WY  K +AYIYKAKTKK+ +HYRCIWGKV
Sbjct: 17  TILGYKRSKSNQYPNTSLVQVEGVNTTEEVSWYKGKRMAYIYKAKTKKNGSHYRCIWGKV 76

Query: 61  ARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
            R HGNSGVVRA+F SNLPPKSMG +VRVFMYPSNI
Sbjct: 77  TRPHGNSGVVRAKFTSNLPPKSMGSRVRVFMYPSNI 112

Arabidopsis thaliana (taxid: 3702)

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

 Score =  166 bits (421), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 79/96 (82%), Positives = 87/96 (90%)

Query: 1   TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKV 60
           T+LGYKRSKSNQYPNTSLIQIEGVNT+E+V WY  K LAYIYKAKTKK+ +HYRCIWGKV
Sbjct: 16  TVLGYKRSKSNQYPNTSLIQIEGVNTQEEVNWYKGKRLAYIYKAKTKKNGSHYRCIWGKV 75

Query: 61  ARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
            R HGNSGVVR++F SNLPPKSMG +VRVFMYPSNI
Sbjct: 76  TRPHGNSGVVRSKFTSNLPPKSMGARVRVFMYPSNI 111

Arabidopsis thaliana (taxid: 3702)

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

 Score =  166 bits (419), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 78/96 (81%), Positives = 87/96 (90%)

Query: 1   TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKV 60
           T+LGYKRSKSNQYPNTSL+QIEGVNT+E+V WY  K LAYIYKAKTKK+ +HYRCIWGKV
Sbjct: 16  TVLGYKRSKSNQYPNTSLVQIEGVNTQEEVNWYKGKRLAYIYKAKTKKNGSHYRCIWGKV 75

Query: 61  ARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
            R HGNSGVVR++F SNLPPKSMG +VRVFMYPSNI
Sbjct: 76  TRPHGNSGVVRSKFTSNLPPKSMGARVRVFMYPSNI 111

Arabidopsis thaliana (taxid: 3702)

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

 Score =  109 bits (273), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 50/94 (53%), Positives = 67/94 (71%)

Query: 3   LGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVAR 62
           L Y+RSK    PN SLI+IEGV T ++  +Y  K +AY+Y+A  +   +  R +WGKV R
Sbjct: 14  LSYQRSKRVNNPNVSLIKIEGVATPQEAQFYLGKRIAYVYRASKEVRGSKIRVMWGKVTR 73

Query: 63  SHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
           +HGNSGVVRA F++NLP K+ G  VR+F+YPSNI
Sbjct: 74  THGNSGVVRATFRNNLPAKTFGASVRIFLYPSNI 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 =  109 bits (272), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 50/94 (53%), Positives = 66/94 (70%)

Query: 3   LGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVAR 62
           L Y+RSK    PN SLI+IEGV T +   +Y  K +AY+Y+A  +   +  R +WGKV R
Sbjct: 14  LSYQRSKRVNNPNVSLIKIEGVATPQDAQFYLGKRIAYVYRASKEVRGSKIRVMWGKVTR 73

Query: 63  SHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
           +HGNSGVVRA F++NLP K+ G  VR+F+YPSNI
Sbjct: 74  THGNSGVVRATFRNNLPAKTFGASVRIFLYPSNI 107

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

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

 Score =  105 bits (261), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 49/97 (50%), Positives = 71/97 (73%), Gaps = 1/97 (1%)

Query: 1   TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYK-AKTKKSWTHYRCIWGK 59
            +LGY+RS++ QYPN SLI+IEGV ++E   +Y  K +  + K +K+ K+ T ++  WGK
Sbjct: 9   VVLGYRRSQATQYPNISLIKIEGVVSREDSTFYLGKKVCLVSKVSKSAKNPTGHKISWGK 68

Query: 60  VARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
           + ++HG+SGVV+A F  NLPPK+MG  VRV +YPSNI
Sbjct: 69  ICKTHGSSGVVQARFARNLPPKAMGAPVRVMLYPSNI 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|Q9USX4|RL33A_SCHPO 60S ribosomal protein L33-A OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpl33a PE=3 SV=2

 Score =  100 bits (248), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 45/94 (47%), Positives = 64/94 (68%)

Query: 3   LGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVAR 62
           L ++RSK   +P TSL++IEG ++KE+  +Y  K + ++YK+      +  R IWG V+R
Sbjct: 15  LSFQRSKHVIHPGTSLVKIEGCDSKEEAQFYLGKRICFVYKSNKPVRGSKIRVIWGTVSR 74

Query: 63  SHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
            HGNSGVVRA F  NLPPK+ G  +RV +YPSN+
Sbjct: 75  PHGNSGVVRARFTHNLPPKTFGASLRVMLYPSNV 108

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

>sp|P02434|RL35A_XENLA 60S ribosomal protein L35a OS=Xenopus laevis GN=rpl35a PE=3 SV=2

 Score = 99.4 bits (246), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 49/101 (48%), Positives = 67/101 (66%), Gaps = 5/101 (4%)

Query: 1   TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSW-----THYRC 55
           T  GYKR   NQ  +T+L++IEGV  +++  +Y  K  AY+YKAK             R 
Sbjct: 10  TFAGYKRGLRNQREHTALLKIEGVYARDETEFYFGKRCAYVYKAKNNTVTPGGKPNRTRV 69

Query: 56  IWGKVARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
           IWGKV R+HGNSG+VRA+F+SNLP K++G ++RV +YPS I
Sbjct: 70  IWGKVTRAHGNSGMVRAKFRSNLPAKAIGHRIRVMLYPSRI 110

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.

Xenopus laevis (taxid: 8355)

>sp|Q90YT3|RL35A_ICTPU 60S ribosomal protein L35a OS=Ictalurus punctatus GN=rpl35a PE=3 SV=1

 Score = 98.6 bits (244), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 50/99 (50%), Positives = 70/99 (70%), Gaps = 7/99 (7%)

Query: 4   GYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWT------HYRCIW 57
           GYKR   NQ  +T+L+++EGV ++ +V +Y  K  AY+YKAK K + T        R IW
Sbjct: 13  GYKRGLRNQREHTALLKVEGVYSRNEVDFYLGKRCAYVYKAK-KTTVTPGGKPNKTRVIW 71

Query: 58  GKVARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
           GKV R+HGNSG+VRA+F SNLPPK++G ++RV +YPS +
Sbjct: 72  GKVTRAHGNSGMVRAKFTSNLPPKAIGHRIRVMLYPSRV 110

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.

Ictalurus punctatus (taxid: 7998)

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	96
313586489	112	60S ribosomal protein L35aA [Hevea brasi	1.0	0.857	0.854	6e-42
449465053	446	PREDICTED: probable sugar phosphate/phos	1.0	0.215	0.833	8e-42
225440584	112	PREDICTED: 60S ribosomal protein L35a-1-	1.0	0.857	0.843	2e-41
449480800	112	PREDICTED: 60S ribosomal protein L35a-1-	1.0	0.857	0.822	3e-41
449531591	112	PREDICTED: 60S ribosomal protein L35a-1-	1.0	0.857	0.833	4e-41
13430186	112	ribosomal protein L33 [Castanea sativa]	1.0	0.857	0.843	5e-41
224101037	112	predicted protein [Populus trichocarpa]	1.0	0.857	0.843	5e-41
255573911	112	60S ribosomal protein L35a, putative [Ri	1.0	0.857	0.822	6e-41
192910904	112	ribosomal protein L35A [Elaeis guineensi	1.0	0.857	0.854	9e-41
255579118	112	60S ribosomal protein L35a, putative [Ri	1.0	0.857	0.843	1e-40

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

 Score =  174 bits (441), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 82/96 (85%), Positives = 88/96 (91%)

Query: 1   TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKV 60
           TILGYKRSKSNQYPNTSLIQIEGVNTKE+V WY  K +AYIYKAK KK+ +HYRCIWGKV
Sbjct: 17  TILGYKRSKSNQYPNTSLIQIEGVNTKEEVAWYAGKRMAYIYKAKVKKNGSHYRCIWGKV 76

Query: 61  ARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
            R HGNSGVVRA+FKSNLPPKSMGD+VRVFMYPSNI
Sbjct: 77  TRPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112

Source: Hevea brasiliensis

Species: Hevea brasiliensis

Genus: Hevea

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  174 bits (440), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 80/96 (83%), Positives = 89/96 (92%)

Query: 1   TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKV 60
           TILGYKRSKSNQYPNTSL+QIEGVN+K++V WY  K LAYIYKAK KK+ +HYRCIWGKV
Sbjct: 17  TILGYKRSKSNQYPNTSLLQIEGVNSKDEVSWYQGKRLAYIYKAKVKKNGSHYRCIWGKV 76

Query: 61  ARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
           AR HGNSG+VRA+FKSNLPPKSMGD+VRVFMYPSNI
Sbjct: 77  ARPHGNSGIVRAKFKSNLPPKSMGDRVRVFMYPSNI 112

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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 =  172 bits (437), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 81/96 (84%), Positives = 87/96 (90%)

Query: 1   TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKV 60
           TILGYKRSKSNQYPNTSLIQIEGVNTKE+V WYC K +AYIYKAK KK  +H+RCIWGKV
Sbjct: 17  TILGYKRSKSNQYPNTSLIQIEGVNTKEEVAWYCGKRMAYIYKAKVKKDGSHFRCIWGKV 76

Query: 61  ARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
            R HGNSGVVRA+FKSNLPPKSMG +VRVFMYPSNI
Sbjct: 77  TRPHGNSGVVRAKFKSNLPPKSMGARVRVFMYPSNI 112

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449480800|ref|XP_004155999.1| PREDICTED: 60S ribosomal protein L35a-1-like [Cucumis sativus]

 Score =  172 bits (435), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 79/96 (82%), Positives = 88/96 (91%)

Query: 1   TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKV 60
           T+LGYKRSKSNQYP TSLIQIEGVNT+E+V WY  K LAYIYKAK K++ THYRCIWGKV
Sbjct: 17  TVLGYKRSKSNQYPRTSLIQIEGVNTREEVAWYAGKRLAYIYKAKVKQNGTHYRCIWGKV 76

Query: 61  ARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
           +R HGNSG+VRA+FKSNLPPKSMGDK+RVFMYPSNI
Sbjct: 77  SRPHGNSGIVRAKFKSNLPPKSMGDKIRVFMYPSNI 112

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  171 bits (434), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 80/96 (83%), Positives = 89/96 (92%)

Query: 1   TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKV 60
           TILGYKRSKSNQYPNTSL+QIEGVN+K++V WY  K LAYIYKAK KK+ +HYRCIWGKV
Sbjct: 17  TILGYKRSKSNQYPNTSLLQIEGVNSKDEVSWYQGKRLAYIYKAKVKKNGSHYRCIWGKV 76

Query: 61  ARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
           AR HGNSG+VRA+FKSNLPPKSMGD+VRVFMYPSNI
Sbjct: 77  ARPHGNSGIVRAKFKSNLPPKSMGDRVRVFMYPSNI 112

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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 = 81/96 (84%), Positives = 87/96 (90%)

Query: 1   TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKV 60
           TILGYKRSKSNQYPNTSLIQIEGVNTKE+V WY  K +AY+YKAK KK  +HYRCIWGKV
Sbjct: 17  TILGYKRSKSNQYPNTSLIQIEGVNTKEEVGWYAGKRMAYVYKAKVKKDGSHYRCIWGKV 76

Query: 61  ARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
           AR HGNSGVVRA+FKSNLPPKSMG +VRVFMYPSNI
Sbjct: 77  ARPHGNSGVVRAKFKSNLPPKSMGARVRVFMYPSNI 112

Source: Castanea sativa

Species: Castanea sativa

Genus: Castanea

Family: Fagaceae

Order: Fagales

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 =  171 bits (433), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 81/96 (84%), Positives = 86/96 (89%)

Query: 1   TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKV 60
           TILGYKRSKSNQYPNTSLIQIEGVNTKE+V WY  K +AYIYKAK KK  +HYRCIWGKV
Sbjct: 17  TILGYKRSKSNQYPNTSLIQIEGVNTKEEVAWYAGKRMAYIYKAKVKKQGSHYRCIWGKV 76

Query: 61  ARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
            R HGNSGVVRA+FKSNLPPKSMG +VRVFMYPSNI
Sbjct: 77  TRPHGNSGVVRAKFKSNLPPKSMGTRVRVFMYPSNI 112

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255573911|ref|XP_002527874.1| 60S ribosomal protein L35a, putative [Ricinus communis] gi|223532725|gb|EEF34505.1| 60S ribosomal protein L35a, putative [Ricinus communis]

 Score =  171 bits (433), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 79/96 (82%), Positives = 88/96 (91%)

Query: 1   TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKV 60
           TILGYKRSKSNQYP+TSLIQ+EGVNTKE+V WY  K +AY+YKAK KK+ +HYRCIWGKV
Sbjct: 17  TILGYKRSKSNQYPSTSLIQVEGVNTKEEVAWYTGKRMAYVYKAKVKKNGSHYRCIWGKV 76

Query: 61  ARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
            R HGNSGVVRA+FKSNLPP+SMGDKVRVFMYPSNI
Sbjct: 77  TRPHGNSGVVRAKFKSNLPPRSMGDKVRVFMYPSNI 112

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|192910904|gb|ACF06560.1| ribosomal protein L35A [Elaeis guineensis]

 Score =  170 bits (431), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 82/96 (85%), Positives = 85/96 (88%)

Query: 1   TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKV 60
           TILGYKRSKSNQY NTSLIQIEGVNTKE+V WYC K +AYIYKAKTK   T YRCIWGKV
Sbjct: 17  TILGYKRSKSNQYENTSLIQIEGVNTKEEVAWYCGKRMAYIYKAKTKSDGTRYRCIWGKV 76

Query: 61  ARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
            R HGNSGVVRA+FKSNLPPKSMG KVRVFMYPSNI
Sbjct: 77  TRPHGNSGVVRAKFKSNLPPKSMGGKVRVFMYPSNI 112

Source: Elaeis guineensis

Species: Elaeis guineensis

Genus: Elaeis

Family: Arecaceae

Order: Arecales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255579118|ref|XP_002530407.1| 60S ribosomal protein L35a, putative [Ricinus communis] gi|223530056|gb|EEF31977.1| 60S ribosomal protein L35a, putative [Ricinus communis]

 Score =  170 bits (431), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 81/96 (84%), Positives = 88/96 (91%)

Query: 1   TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKV 60
           TILGYKRSKSNQYP+TSLIQIEGVNTKE+V WY  K +AYIYKAK KK+ +HYRCIWGKV
Sbjct: 17  TILGYKRSKSNQYPSTSLIQIEGVNTKEEVGWYAGKKMAYIYKAKVKKNGSHYRCIWGKV 76

Query: 61  ARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
            R HGNSGVVRA+FKSNLPP+SMGDKVRVFMYPSNI
Sbjct: 77  IRPHGNSGVVRAKFKSNLPPRSMGDKVRVFMYPSNI 112

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	96
TAIR|locus:2019627	112	AT1G74270 [Arabidopsis thalian	1.0	0.857	0.822	4.2e-40
TAIR|locus:2007422	112	AT1G07070 [Arabidopsis thalian	1.0	0.857	0.812	6.8e-40
TAIR|locus:2033548	111	AT1G41880 [Arabidopsis thalian	1.0	0.864	0.822	8.7e-40
TAIR|locus:2078991	111	AT3G55750 [Arabidopsis thalian	1.0	0.864	0.812	1.1e-39
GENEDB_PFALCIPARUM|PF11_0438	140	PF11_0438 "Ribosomal protein,	0.989	0.678	0.557	1.5e-26
UNIPROTKB|Q8IHT9	140	PF11_0438 "60S ribosomal prote	0.989	0.678	0.557	1.5e-26
SGD|S000005760	107	RPL33B "Ribosomal 60S subunit	0.979	0.878	0.531	4.8e-23
ASPGD|ASPL0000041158	109	AN2980 [Emericella nidulans (t	0.979	0.862	0.553	6.1e-23
SGD|S000006064	107	RPL33A "Ribosomal 60S subunit	0.979	0.878	0.531	7.8e-23
DICTYBASE|DDB_G0270424	105	rpl35a "S60 ribosomal protein	0.989	0.904	0.510	2.6e-22

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

 Score = 427 (155.4 bits), Expect = 4.2e-40, P = 4.2e-40
 Identities = 79/96 (82%), Positives = 87/96 (90%)

Query:     1 TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKV 60
             TILGYKRSKSNQYPNTSL+QIEGVNT+E+V WY  K +AYIYKAKTKK+ +HYRCIWGKV
Sbjct:    17 TILGYKRSKSNQYPNTSLVQIEGVNTQEEVNWYKGKRMAYIYKAKTKKNGSHYRCIWGKV 76

Query:    61 ARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
              R HGNSGVVRA+F SNLPPKSMG +VRVFMYPSNI
Sbjct:    77 TRPHGNSGVVRAKFTSNLPPKSMGSRVRVFMYPSNI 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 = 425 (154.7 bits), Expect = 6.8e-40, P = 6.8e-40
 Identities = 78/96 (81%), Positives = 86/96 (89%)

Query:     1 TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKV 60
             TILGYKRSKSNQYPNTSL+Q+EGVNT E+V WY  K +AYIYKAKTKK+ +HYRCIWGKV
Sbjct:    17 TILGYKRSKSNQYPNTSLVQVEGVNTTEEVSWYKGKRMAYIYKAKTKKNGSHYRCIWGKV 76

Query:    61 ARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
              R HGNSGVVRA+F SNLPPKSMG +VRVFMYPSNI
Sbjct:    77 TRPHGNSGVVRAKFTSNLPPKSMGSRVRVFMYPSNI 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 = 424 (154.3 bits), Expect = 8.7e-40, P = 8.7e-40
 Identities = 79/96 (82%), Positives = 87/96 (90%)

Query:     1 TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKV 60
             T+LGYKRSKSNQYPNTSLIQIEGVNT+E+V WY  K LAYIYKAKTKK+ +HYRCIWGKV
Sbjct:    16 TVLGYKRSKSNQYPNTSLIQIEGVNTQEEVNWYKGKRLAYIYKAKTKKNGSHYRCIWGKV 75

Query:    61 ARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
              R HGNSGVVR++F SNLPPKSMG +VRVFMYPSNI
Sbjct:    76 TRPHGNSGVVRSKFTSNLPPKSMGARVRVFMYPSNI 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 = 423 (154.0 bits), Expect = 1.1e-39, P = 1.1e-39
 Identities = 78/96 (81%), Positives = 87/96 (90%)

Query:     1 TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKV 60
             T+LGYKRSKSNQYPNTSL+QIEGVNT+E+V WY  K LAYIYKAKTKK+ +HYRCIWGKV
Sbjct:    16 TVLGYKRSKSNQYPNTSLVQIEGVNTQEEVNWYKGKRLAYIYKAKTKKNGSHYRCIWGKV 75

Query:    61 ARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
              R HGNSGVVR++F SNLPPKSMG +VRVFMYPSNI
Sbjct:    76 TRPHGNSGVVRSKFTSNLPPKSMGARVRVFMYPSNI 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 = 299 (110.3 bits), Expect = 1.5e-26, P = 1.5e-26
 Identities = 53/95 (55%), Positives = 71/95 (74%)

Query:     2 ILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVA 61
             ILGYKRS+ NQ PN +LI I+ VNTK+   +Y  K +AY+Y+          +CIWGKV 
Sbjct:    46 ILGYKRSQRNQDPNFTLISIKNVNTKKHAQFYVGKRVAYVYRTTKHHDGVKIKCIWGKVC 105

Query:    62 RSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
             R+HGNSGV+RA+FK+++PPK+ GD+VR+ MYPSNI
Sbjct:   106 RTHGNSGVIRAKFKTHIPPKAFGDRVRILMYPSNI 140

GO:0015934 "large ribosomal subunit" evidence=ISS

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

 Score = 299 (110.3 bits), Expect = 1.5e-26, P = 1.5e-26
 Identities = 53/95 (55%), Positives = 71/95 (74%)

Query:     2 ILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVA 61
             ILGYKRS+ NQ PN +LI I+ VNTK+   +Y  K +AY+Y+          +CIWGKV 
Sbjct:    46 ILGYKRSQRNQDPNFTLISIKNVNTKKHAQFYVGKRVAYVYRTTKHHDGVKIKCIWGKVC 105

Query:    62 RSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
             R+HGNSGV+RA+FK+++PPK+ GD+VR+ MYPSNI
Sbjct:   106 RTHGNSGVIRAKFKTHIPPKAFGDRVRILMYPSNI 140

GO:0015934 "large ribosomal subunit" evidence=ISS

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

 Score = 266 (98.7 bits), Expect = 4.8e-23, P = 4.8e-23
 Identities = 50/94 (53%), Positives = 67/94 (71%)

Query:     3 LGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVAR 62
             L Y+RSK    PN SLI+IEGV T ++  +Y  K +AY+Y+A  +   +  R +WGKV R
Sbjct:    14 LSYQRSKRVNNPNVSLIKIEGVATPQEAQFYLGKRIAYVYRASKEVRGSKIRVMWGKVTR 73

Query:    63 SHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
             +HGNSGVVRA F++NLP K+ G  VR+F+YPSNI
Sbjct:    74 THGNSGVVRATFRNNLPAKTFGASVRIFLYPSNI 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

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

 Score = 265 (98.3 bits), Expect = 6.1e-23, P = 6.1e-23
 Identities = 52/94 (55%), Positives = 67/94 (71%)

Query:     3 LGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVAR 62
             L Y+RSK    PNTSLI+I+GV+  E   +Y  K +A++Y+AK +   ++ R IWGKV R
Sbjct:    16 LSYQRSKRAVNPNTSLIKIDGVDNTEAANFYLGKKVAFVYRAKREVRGSNIRVIWGKVTR 75

Query:    63 SHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
              HGNSGVVRA+F+ NLP KS G  VRV +YPSNI
Sbjct:    76 PHGNSGVVRAQFRHNLPAKSFGATVRVMLYPSNI 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 = 264 (98.0 bits), Expect = 7.8e-23, P = 7.8e-23
 Identities = 50/94 (53%), Positives = 66/94 (70%)

Query:     3 LGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVAR 62
             L Y+RSK    PN SLI+IEGV T +   +Y  K +AY+Y+A  +   +  R +WGKV R
Sbjct:    14 LSYQRSKRVNNPNVSLIKIEGVATPQDAQFYLGKRIAYVYRASKEVRGSKIRVMWGKVTR 73

Query:    63 SHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
             +HGNSGVVRA F++NLP K+ G  VR+F+YPSNI
Sbjct:    74 THGNSGVVRATFRNNLPAKTFGASVRIFLYPSNI 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

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

 Score = 259 (96.2 bits), Expect = 2.6e-22, P = 2.6e-22
 Identities = 49/96 (51%), Positives = 71/96 (73%)

Query:     2 ILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYK-AKTKKSWTHYRCIWGKV 60
             +LGY+RS++ QYPN SLI+IEGV ++E   +Y  K +  + K +K+ K+ T ++  WGK+
Sbjct:    10 VLGYRRSQATQYPNISLIKIEGVVSREDSTFYLGKKVCLVSKVSKSAKNPTGHKISWGKI 69

Query:    61 ARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
              ++HG+SGVV+A F  NLPPK+MG  VRV +YPSNI
Sbjct:    70 CKTHGSSGVVQARFARNLPPKAMGAPVRVMLYPSNI 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

---

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	0.8229	1.0	0.8571	yes	no
Q9FZH0	R35A2_ARATH	No assigned EC number	0.8229	1.0	0.8648	no	no
P41056	RL33B_YEAST	No assigned EC number	0.5319	0.9791	0.8785	yes	no
Q9LMK0	R35A1_ARATH	No assigned EC number	0.8125	1.0	0.8571	yes	no
O74099	RL35A_PYRHO	No assigned EC number	0.3111	0.8541	0.9425	yes	no
Q9USX4	RL33A_SCHPO	No assigned EC number	0.4787	0.9791	0.8703	yes	no
Q5R8K6	RL35A_PONAB	No assigned EC number	0.4897	0.9687	0.8454	yes	no
P18077	RL35A_HUMAN	No assigned EC number	0.4897	0.9687	0.8454	yes	no
P04646	RL35A_RAT	No assigned EC number	0.4897	0.9687	0.8454	yes	no
Q55BN7	RL35A_DICDI	No assigned EC number	0.5051	1.0	0.9142	yes	no
Q90YT3	RL35A_ICTPU	No assigned EC number	0.5050	0.9583	0.8363	N/A	no
Q8TZV6	RL35A_PYRFU	No assigned EC number	0.3222	0.8541	0.9425	yes	no
O55142	RL35A_MOUSE	No assigned EC number	0.4897	0.9687	0.8454	yes	no
P05744	RL33A_YEAST	No assigned EC number	0.5319	0.9791	0.8785	yes	no
Q9V1P2	RL35A_PYRAB	No assigned EC number	0.3333	0.8541	0.9425	yes	no
Q56JY1	RL35A_BOVIN	No assigned EC number	0.4795	0.9687	0.8454	yes	no
P51422	R35A4_ARATH	No assigned EC number	0.8125	1.0	0.8648	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	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	96
pfam01247	95	pfam01247, Ribosomal_L35Ae, Ribosomal protein L35A	5e-47
PTZ00041	120	PTZ00041, PTZ00041, 60S ribosomal protein L35a; Pr	7e-47
COG2451	100	COG2451, COG2451, Ribosomal protein L35AE/L33A [Tr	1e-29
PRK04337	87	PRK04337, PRK04337, 50S ribosomal protein L35Ae; V	5e-15

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

 Score =  144 bits (366), Expect = 5e-47
 Identities = 56/90 (62%), Positives = 70/90 (77%)

Query: 1  TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKV 60
            LGY+R K NQ+PNTSL++IEGVNTKE   +Y  K +AY+YKAK KK+ +  R IWGKV
Sbjct: 6  VFLGYRRGKRNQHPNTSLLKIEGVNTKEDAQFYLGKRVAYVYKAKKKKNGSKIRVIWGKV 65

Query: 61 ARSHGNSGVVRAEFKSNLPPKSMGDKVRVF 90
           R HGNSGVVRA+F+ NLPP++MG +VRV 
Sbjct: 66 TRPHGNSGVVRAKFRRNLPPQAMGARVRVM 95

Length = 95

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

 Score =  145 bits (368), Expect = 7e-47
 Identities = 61/96 (63%), Positives = 75/96 (78%)

Query: 1   TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKV 60
             LGYKRSK NQYPN +L++IEGVNT+E   +Y  K +AY+YKAK  K+ T +R IWGK+
Sbjct: 25  VFLGYKRSKVNQYPNVALLKIEGVNTREDARFYLGKRVAYVYKAKKLKNGTKFRAIWGKI 84

Query: 61  ARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
            R HGNSGVVRA F  NLPPK++G +VRVF+YPSNI
Sbjct: 85  TRPHGNSGVVRARFNKNLPPKAIGSRVRVFLYPSNI 120

Length = 120

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

 Score =  101 bits (253), Expect = 1e-29
 Identities = 46/96 (47%), Positives = 63/96 (65%), Gaps = 7/96 (7%)

Query: 1   TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKV 60
            +L Y+RSK  Q+PN SLI+IEGV++ E+  +Y  K + Y Y++         R I GKV
Sbjct: 12  VVLSYRRSKRTQHPNVSLIKIEGVDSPEEAQFYLGKRVCYKYRSSG-------RVIKGKV 64

Query: 61  ARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
            R+HGNSG VRA F+ NLP +++G  V V +YPSNI
Sbjct: 65  VRTHGNSGAVRARFERNLPGQALGTSVEVKLYPSNI 100

Length = 100

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

 Score = 63.9 bits (156), Expect = 5e-15
 Identities = 31/88 (35%), Positives = 47/88 (53%), Gaps = 8/88 (9%)

Query: 2  ILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVA 61
          IL Y+R K+ QY    +I+  GV+ +E+      + +  I+K  T   +       GK+ 
Sbjct: 7  ILSYRRGKNTQYNRQVIIKPLGVDDREEAAKLIGRKV--IWKDPTGNKYV------GKIV 58

Query: 62 RSHGNSGVVRAEFKSNLPPKSMGDKVRV 89
          R HGN G VRA FK  LP +++GD V +
Sbjct: 59 RVHGNRGEVRARFKPGLPGQALGDYVEI 86

Length = 87

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	96
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	95.94
PF01782	84	RimM: RimM N-terminal domain; InterPro: IPR002676	94.43
TIGR02273	165	16S_RimM 16S rRNA processing protein RimM. This fa	92.79
PRK14592	165	rimM 16S rRNA-processing protein RimM; Provisional	92.21
PRK13829	162	rimM 16S rRNA-processing protein RimM; Provisional	92.02
PRK14591	169	rimM 16S rRNA-processing protein RimM; Provisional	91.94
PRK13828	161	rimM 16S rRNA-processing protein RimM; Provisional	91.15
PF01782	84	RimM: RimM N-terminal domain; InterPro: IPR002676	90.7
PRK00122	172	rimM 16S rRNA-processing protein RimM; Provisional	90.69
PRK14594	166	rimM 16S rRNA-processing protein RimM; Provisional	90.48
PRK14590	171	rimM 16S rRNA-processing protein RimM; Provisional	90.31
PRK00122	172	rimM 16S rRNA-processing protein RimM; Provisional	89.73
PRK14594	166	rimM 16S rRNA-processing protein RimM; Provisional	89.45
TIGR02273	165	16S_RimM 16S rRNA processing protein RimM. This fa	86.96
PRK14593	184	rimM 16S rRNA-processing protein RimM; Provisional	85.24
PRK14592	165	rimM 16S rRNA-processing protein RimM; Provisional	84.99
PRK14591	169	rimM 16S rRNA-processing protein RimM; Provisional	84.15
PRK14593	184	rimM 16S rRNA-processing protein RimM; Provisional	83.08
PF04950	297	DUF663: Protein of unknown function (DUF663); Inte	82.38
cd04479	101	RPA3 RPA3: A subfamily of OB folds similar to huma	82.19
PRK14590	171	rimM 16S rRNA-processing protein RimM; Provisional	80.38

>PTZ00041 60S ribosomal protein L35a; Provisional

Probab=100.00  E-value=2.5e-60  Score=336.65  Aligned_cols=96  Identities=64%  Similarity=1.113  Sum_probs=94.7

Q ss_pred             CeeeccccCCCCCCCeeEEEecCcCChhhhhhhccceEEEEEecccCCCCceeEEEEEEEEceeCCCceEEEEeCCCCCc
Q 042762            1 TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVARSHGNSGVVRAEFKSNLPP   80 (96)
Q Consensus         1 ~~~gykRg~~~Q~~~~aLlKiegV~~~~~a~fylGKrvayvyk~k~~~~g~k~R~iwGkV~r~HGnsGvVrAkF~~nLP~   80 (96)
                      +|+|||||++||+|||||||||||+++|||+|||||||||||+++++++|+|+|+|||||+|+|||||+|||+|++||||
T Consensus        25 v~lgYkRg~~nQ~~~~aLlKieGV~~~~~a~fYlGKrvayvyka~~~~~~~k~RviwGKVtR~HGnsGvVrAkF~~nLPp  104 (120)
T PTZ00041         25 VFLGYKRSKVNQYPNVALLKIEGVNTREDARFYLGKRVAYVYKAKKLKNGTKFRAIWGKITRPHGNSGVVRARFNKNLPP  104 (120)
T ss_pred             EEEEeccccccCCCceEEEEecCcCChhhhHhhccceEEEEEcCccccCCcceeEEEEEEEcccCCCcEEEEEeCCCCCh
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCeEEEEEeecCC
Q 042762           81 KSMGDKVRVFMYPSNI   96 (96)
Q Consensus        81 ~aiG~~vrVmLyps~i   96 (96)
                      ||||++||||||||+|
T Consensus       105 ~A~G~~VrVmlyPs~i  120 (120)
T PTZ00041        105 KAIGSRVRVFLYPSNI  120 (120)
T ss_pred             HHcCCeEEEEEccCCC
Confidence            9999999999999997

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

Probab=100.00  E-value=3.6e-57  Score=315.93  Aligned_cols=96  Identities=63%  Similarity=1.020  Sum_probs=94.4

Q ss_pred             CeeeccccCCCCCCCeeEEEecCcCChhhhhhhccceEEEEEecccCCCCceeEEEEEEEEceeCCCceEEEEeCCCCCc
Q 042762            1 TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVARSHGNSGVVRAEFKSNLPP   80 (96)
Q Consensus         1 ~~~gykRg~~~Q~~~~aLlKiegV~~~~~a~fylGKrvayvyk~k~~~~g~k~R~iwGkV~r~HGnsGvVrAkF~~nLP~   80 (96)
                      +|+||+||+++|+|||+|||||||+++|||+||+||||+||||+++..+++|+|+|||||||+|||||+|||+|.+||||
T Consensus        16 ~~~~~kr~~r~~~~~t~llkIEGv~skeEa~fYlGkR~~yvYKa~~~~~~~k~RvIWGkVTr~HGNsG~VrAkF~~Nlp~   95 (111)
T KOG0887|consen   16 TFLGYKRGKRNQHPNTSLLKIEGVYSKEEASFYLGKRCVYVYKAKPEVRGSKTRVIWGKVTRPHGNSGVVRAKFTSNLPP   95 (111)
T ss_pred             EEeeeeecccccCCCcEEEEEecccchhhhheeecCcEEEEEecCCCCCCceEEEEEEEEecccCCcceEEEEeccCCCh
Confidence            48999999999999999999999999999999999999999999998899999999999999999999999999999999


Q ss_pred             cCCCCeEEEEEeecCC
Q 042762           81 KSMGDKVRVFMYPSNI   96 (96)
Q Consensus        81 ~aiG~~vrVmLyps~i   96 (96)
                      +|||++||||||||+|
T Consensus        96 Ka~G~rvrVmLYps~i  111 (111)
T KOG0887|consen   96 KAMGHRVRVMLYPSNI  111 (111)
T ss_pred             hHcCcEEEEEEecccC
Confidence            9999999999999998

>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=7.8e-55  Score=298.21  Aligned_cols=90  Identities=62%  Similarity=1.024  Sum_probs=84.0

Q ss_pred             CeeeccccCCCCCCCeeEEEecCcCChhhhhhhccceEEEEEecccCCCCceeEEEEEEEEceeCCCceEEEEeCCCCCc
Q 042762            1 TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVARSHGNSGVVRAEFKSNLPP   80 (96)
Q Consensus         1 ~~~gykRg~~~Q~~~~aLlKiegV~~~~~a~fylGKrvayvyk~k~~~~g~k~R~iwGkV~r~HGnsGvVrAkF~~nLP~   80 (96)
                      +|+|||||++||+|||||||||||+|+|||+|||||||+|||++++++++++.|+|||||+|+|||||+|||+|++||||
T Consensus         6 v~~gykRg~~~Q~~~~aLlKiegV~~~~~a~fylGKrv~yvyk~~~~~~~~k~r~iwGkV~r~HGnsGvVrAkF~~nLP~   85 (95)
T PF01247_consen    6 VFLGYKRGKRNQHPNTALLKIEGVNTKEDAQFYLGKRVAYVYKAKNKKNGSKGRVIWGKVTRPHGNSGVVRAKFKKNLPP   85 (95)
T ss_dssp             EEEEEEEETSTTCEEEEEEEESS-STCHHHHTTTT-EEEEEECE-SSSTTECSEEEEEEEEEESTTTTEEEEEESS--ST
T ss_pred             EEEeecccccccCCCeeEEeecCccCHHHHHhhcCcEEEEEEecccccCCCcEeEEEEEEEeEEcCCCEEEEEeCCCCCh
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCeEEEE
Q 042762           81 KSMGDKVRVF   90 (96)
Q Consensus        81 ~aiG~~vrVm   90 (96)
                      ||||++||||
T Consensus        86 ~a~G~~VrVm   95 (95)
T PF01247_consen   86 QAIGSRVRVM   95 (95)
T ss_dssp             TGCSSEEEEE
T ss_pred             HHcCCEEEeC
Confidence            9999999999

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=2.9e-50  Score=272.24  Aligned_cols=82  Identities=34%  Similarity=0.567  Sum_probs=79.0

Q ss_pred             CeeeccccCCCCCCCeeEEEecCcCChhhhhhhccceEEEEEecccCCCCceeEEEEEEEEceeCCCceEEEEeCCCCCc
Q 042762            1 TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVARSHGNSGVVRAEFKSNLPP   80 (96)
Q Consensus         1 ~~~gykRg~~~Q~~~~aLlKiegV~~~~~a~fylGKrvayvyk~k~~~~g~k~R~iwGkV~r~HGnsGvVrAkF~~nLP~   80 (96)
                      +|+|||||++||+|||||||||||+++|||+|||||||+|||++     |   |+|||||+|+|||||+|||+|++||||
T Consensus         6 v~~gykRg~~nQ~~~~aLlkiegv~~~~~a~fylGKrv~yvyk~-----g---rviwGKItR~HGnsGvVrAkF~~nLP~   77 (87)
T PRK04337          6 VILSYRRGKNTQYNRQVIIKPLGVDDREEAAKLIGRKVIWKDPT-----G---NKYVGKIVRVHGNRGEVRARFKPGLPG   77 (87)
T ss_pred             EEEEeccccCccCCceEEEEEcCcCCHHHHHhhcCceEEEEeCC-----C---CEEEEEEEeeeCCCceEEEEECCCCCh
Confidence            58999999999999999999999999999999999999999986     3   699999999999999999999999999


Q ss_pred             cCCCCeEEEE
Q 042762           81 KSMGDKVRVF   90 (96)
Q Consensus        81 ~aiG~~vrVm   90 (96)
                      ||||++|+|.
T Consensus        78 ~a~G~~vrv~   87 (87)
T PRK04337         78 QALGDYVEII   87 (87)
T ss_pred             HHcCCEEEeC
Confidence            9999999983

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

Probab=100.00  E-value=6.8e-47  Score=260.21  Aligned_cols=89  Identities=53%  Similarity=0.870  Sum_probs=85.5

Q ss_pred             CeeeccccCCCCCCCeeEEEecCcCChhhhhhhccceEEEEEecccCCCCceeEEEEEEEEceeCCCceEEEEeCCCCCc
Q 042762            1 TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVARSHGNSGVVRAEFKSNLPP   80 (96)
Q Consensus         1 ~~~gykRg~~~Q~~~~aLlKiegV~~~~~a~fylGKrvayvyk~k~~~~g~k~R~iwGkV~r~HGnsGvVrAkF~~nLP~   80 (96)
                      ++||||||+++|+|+++|||||||+|+|||+|||||+|+|+|+.    +|   |+|||+|+|+|||||+|||+|.+||||
T Consensus        12 v~lsyrR~k~~q~P~~~liKi~gv~s~~eA~~y~gk~v~yk~~~----~G---~Vi~G~V~R~HGnsGaVrarF~~~LP~   84 (100)
T COG2451          12 VVLSYRRSKRTQHPNVSLIKIEGVDSPEEAQFYLGKRVCYKYRS----SG---RVIKGKVVRTHGNSGAVRARFERNLPG   84 (100)
T ss_pred             EEEEEEecccccCCceEEEEEecCCCHHHHHhhhccEEEEEeCC----CC---cEEEEEEEEecCCcceEEEEecCCCCc
Confidence            58999999999999999999999999999999999999998876    25   899999999999999999999999999


Q ss_pred             cCCCCeEEEEEeecCC
Q 042762           81 KSMGDKVRVFMYPSNI   96 (96)
Q Consensus        81 ~aiG~~vrVmLyps~i   96 (96)
                      ||+|+.|+||||||+|
T Consensus        85 qa~G~~v~v~ly~~~~  100 (100)
T COG2451          85 QALGTSVEVKLYPSNI  100 (100)
T ss_pred             hhcCcEEEEEEccCCC
Confidence            9999999999999986

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

Probab=95.94  E-value=0.015  Score=36.46  Aligned_cols=33  Identities=33%  Similarity=0.529  Sum_probs=27.1

Q ss_pred             EEEEEEEceeCCCceEEEEeCCCCCccCCCCeEEEEEe
Q 042762           55 CIWGKVARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMY   92 (96)
Q Consensus        55 ~iwGkV~r~HGnsGvVrAkF~~nLP~~aiG~~vrVmLy   92 (96)
                      +++++|+ +||||    |++.++||+.-+|.++.|.+-
T Consensus        17 ~~~~~vk-~~Gns----a~v~p~lPkeyiGK~v~iiil   49 (53)
T PF09853_consen   17 TFIGVVK-PFGNS----ARVYPSLPKEYIGKKVIIIIL   49 (53)
T ss_pred             EEEEEEE-ecCcc----eeEcCCCChHHcCcEEEEEEe
Confidence            5566665 99999    567899999999999988754

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

Probab=94.43  E-value=0.044  Score=34.98  Aligned_cols=28  Identities=14%  Similarity=0.190  Sum_probs=22.2

Q ss_pred             CCCCeeEEEecCcCChhhhhhhccceEE
Q 042762           12 QYPNTSLIQIEGVNTKEKVVWYCCKHLA   39 (96)
Q Consensus        12 Q~~~~aLlKiegV~~~~~a~fylGKrva   39 (96)
                      .+.+..|++++|++|+++|+.+.|..+.
T Consensus        52 ~~~~~~i~~~~gi~~r~~Ae~l~g~~l~   79 (84)
T PF01782_consen   52 PHGKSLIVKFEGIDDREAAEALRGCELY   79 (84)
T ss_dssp             EETTEEEEEETT--SHHHHHTTTT-EEE
T ss_pred             EeCCEEEEEEcCCCCHHHHHhhCCCEEE
Confidence            3478999999999999999999999874

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=92.79  E-value=0.1  Score=37.56  Aligned_cols=28  Identities=18%  Similarity=0.213  Sum_probs=24.6

Q ss_pred             CCCeeEEEecCcCChhhhhhhccceEEE
Q 042762           13 YPNTSLIQIEGVNTKEKVVWYCCKHLAY   40 (96)
Q Consensus        13 ~~~~aLlKiegV~~~~~a~fylGKrvay   40 (96)
                      +.+..|||++|++|+++|+.+.|..+..
T Consensus        55 ~~~~~lv~f~gi~~~~~Ae~L~g~~l~i   82 (165)
T TIGR02273        55 QNNKLIVKFEGIDDREAAEALKGLELFV   82 (165)
T ss_pred             ECCEEEEEECCCCCHHHHHHhcCCEEEE
Confidence            4567899999999999999999998744

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.

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

Probab=92.21  E-value=0.15  Score=36.90  Aligned_cols=32  Identities=19%  Similarity=0.269  Sum_probs=26.4

Q ss_pred             CCCCeeEEEecCcCChhhhhhhccceEEEEEec
Q 042762           12 QYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKA   44 (96)
Q Consensus        12 Q~~~~aLlKiegV~~~~~a~fylGKrvayvyk~   44 (96)
                      +..+..|++++|++|+++|+.+.|..+. +.++
T Consensus        51 ~~~~~~lv~f~gi~~~~~Ae~l~g~~l~-v~~~   82 (165)
T PRK14592         51 IGANLVIAKISGINSRTEAELLRNKKLY-VERS   82 (165)
T ss_pred             ecCCEEEEEEcCCCCHHHHHHhcCCEEE-EEHH
Confidence            3456789999999999999999999884 4444

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

Probab=92.02  E-value=0.12  Score=37.56  Aligned_cols=32  Identities=16%  Similarity=0.226  Sum_probs=26.6

Q ss_pred             CCCCeeEEEecCcCChhhhhhhccceEEEEEec
Q 042762           12 QYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKA   44 (96)
Q Consensus        12 Q~~~~aLlKiegV~~~~~a~fylGKrvayvyk~   44 (96)
                      .+.+..|++++|++|+++|+.+.|..+ |+.++
T Consensus        48 ~~~~~~l~~f~gi~~r~~Ae~l~g~~l-~v~~~   79 (162)
T PRK13829         48 RVGPELVLHLAGVTSREGAEALVGLRV-YADDA   79 (162)
T ss_pred             EECCEEEEEECCCCCHHHHHHhcCCEE-EEEHH
Confidence            446678999999999999999999988 44543

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

Probab=91.94  E-value=0.13  Score=37.53  Aligned_cols=32  Identities=13%  Similarity=0.208  Sum_probs=26.4

Q ss_pred             CCCCeeEEEecCcCChhhhhhhccceEEEEEec
Q 042762           12 QYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKA   44 (96)
Q Consensus        12 Q~~~~aLlKiegV~~~~~a~fylGKrvayvyk~   44 (96)
                      ++.+..|++++|++|+++|+.|.|..+ ||.+.
T Consensus        59 ~~~~~~lv~f~gi~dr~~Ae~l~g~~l-~v~~~   90 (169)
T PRK14591         59 KRADKVYIKLANINNADTAKKYVNALI-GVPKR   90 (169)
T ss_pred             EECCEEEEEEcCCCCHHHHHHhcCCEE-EEEHH
Confidence            345678999999999999999999988 44443

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

Probab=91.15  E-value=0.21  Score=36.16  Aligned_cols=32  Identities=16%  Similarity=0.143  Sum_probs=26.4

Q ss_pred             CCCCeeEEEecCcCChhhhhhhccceEEEEEec
Q 042762           12 QYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKA   44 (96)
Q Consensus        12 Q~~~~aLlKiegV~~~~~a~fylGKrvayvyk~   44 (96)
                      ++.+..|++++|++|+++|+.|.|..+. +.+.
T Consensus        39 ~~~~~~lv~f~gi~dr~~Ae~L~g~~l~-i~~~   70 (161)
T PRK13828         39 PAKDGLVARLKGVATREAAEALRGLELY-VPRD   70 (161)
T ss_pred             EECCEEEEEECCCCCHHHHHHhcCCEEE-EEHH
Confidence            3456689999999999999999999884 4454

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

Probab=90.70  E-value=0.34  Score=30.80  Aligned_cols=28  Identities=21%  Similarity=0.509  Sum_probs=23.0

Q ss_pred             EEEEEceeCCCceEEEEeCCCCCccCCC
Q 042762           57 WGKVARSHGNSGVVRAEFKSNLPPKSMG   84 (96)
Q Consensus        57 wGkV~r~HGnsGvVrAkF~~nLP~~aiG   84 (96)
                      -|+|.+|||-.|.|++..-.+.|.....
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            4999999999999999999887765444

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=90.69  E-value=0.24  Score=35.95  Aligned_cols=31  Identities=13%  Similarity=0.148  Sum_probs=25.7

Q ss_pred             CCCeeEEEecCcCChhhhhhhccceEEEEEec
Q 042762           13 YPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKA   44 (96)
Q Consensus        13 ~~~~aLlKiegV~~~~~a~fylGKrvayvyk~   44 (96)
                      +.+..|+|++|++|+++|+.|.|..+. +.++
T Consensus        60 ~~~~~lvkf~gi~~~~~Ae~l~g~~l~-i~~~   90 (172)
T PRK00122         60 HKGFLIVKFEGVDDRNAAEALKGCELF-VPRS   90 (172)
T ss_pred             ECCEEEEEECCCCCHHHHHHhCCCEEE-EEHH
Confidence            456689999999999999999999874 4444

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

Probab=90.48  E-value=0.22  Score=36.24  Aligned_cols=31  Identities=19%  Similarity=0.201  Sum_probs=26.2

Q ss_pred             CCCeeEEEecCcCChhhhhhhccceEEEEEec
Q 042762           13 YPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKA   44 (96)
Q Consensus        13 ~~~~aLlKiegV~~~~~a~fylGKrvayvyk~   44 (96)
                      +.+..|+|++|++|+++|+.|.|..+ |+.++
T Consensus        57 ~~~~~lvkf~gi~dr~~Ae~L~g~~l-~v~~~   87 (166)
T PRK14594         57 KNNSLLLKFEEFNAPEPIKPLIGFEL-WVDDE   87 (166)
T ss_pred             ECCEEEEEEcCCCCHHHHHHhcCCEE-EEEHH
Confidence            45668999999999999999999987 55554

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

Probab=90.31  E-value=0.27  Score=36.09  Aligned_cols=32  Identities=22%  Similarity=0.316  Sum_probs=26.5

Q ss_pred             CCCCeeEEEecCcCChhhhhhhccceEEEEEec
Q 042762           12 QYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKA   44 (96)
Q Consensus        12 Q~~~~aLlKiegV~~~~~a~fylGKrvayvyk~   44 (96)
                      ++.+..|++++|++|+++|+.+.|..+ |+.++
T Consensus        55 ~~~~~~lv~f~gi~~~e~Ae~L~g~~l-~i~~~   86 (171)
T PRK14590         55 PHGGKFLVRFEGYDTPEEAVKWRGGSL-FLPQE   86 (171)
T ss_pred             EECCEEEEEECCCCCHHHHHHhcCCEE-EEEHH
Confidence            345668999999999999999999988 44554

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

Probab=89.73  E-value=0.39  Score=34.79  Aligned_cols=30  Identities=23%  Similarity=0.466  Sum_probs=26.3

Q ss_pred             EEEEEEEEceeCCCceEEEEeCCCCCccCC
Q 042762           54 RCIWGKVARSHGNSGVVRAEFKSNLPPKSM   83 (96)
Q Consensus        54 R~iwGkV~r~HGnsGvVrAkF~~nLP~~ai   83 (96)
                      .+..|+|++|||-.|-|+++.....|...+
T Consensus         7 ~v~iG~i~~~hGlkGevkv~~~td~p~~~~   36 (172)
T PRK00122          7 LLVVGKIVSAHGIKGEVKVKSFTDFPERIF   36 (172)
T ss_pred             eEEEEEEECCCcccEEEEEEEecCCHHHHc
Confidence            578999999999999999999998886544

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

Probab=89.45  E-value=0.38  Score=35.03  Aligned_cols=27  Identities=22%  Similarity=0.138  Sum_probs=23.6

Q ss_pred             EEEEEEEceeCCCceEEEEeCCCCCcc
Q 042762           55 CIWGKVARSHGNSGVVRAEFKSNLPPK   81 (96)
Q Consensus        55 ~iwGkV~r~HGnsGvVrAkF~~nLP~~   81 (96)
                      ++.|+|++|||=.|.|+.+.-..-|+.
T Consensus         2 ~~iG~I~~~hGlkGevkV~~~td~~~~   28 (166)
T PRK14594          2 FVKGIILSSYGINGYAKVKSISNNFCD   28 (166)
T ss_pred             EEEEEEECceeeeEEEEEEEccCCHHH
Confidence            578999999999999999988775555

>TIGR02273 16S_RimM 16S rRNA processing protein RimM

Probab=86.96  E-value=1  Score=32.38  Aligned_cols=29  Identities=24%  Similarity=0.462  Sum_probs=25.1

Q ss_pred             EEEEEEEceeCCCceEEEEeCCCCCccCC
Q 042762           55 CIWGKVARSHGNSGVVRAEFKSNLPPKSM   83 (96)
Q Consensus        55 ~iwGkV~r~HGnsGvVrAkF~~nLP~~ai   83 (96)
                      +..|+|++|||=.|-|+++.....|...+
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=85.24  E-value=0.97  Score=33.34  Aligned_cols=28  Identities=21%  Similarity=0.451  Sum_probs=24.9

Q ss_pred             EEEEEEEceeCCCceEEEEeCCCCCccC
Q 042762           55 CIWGKVARSHGNSGVVRAEFKSNLPPKS   82 (96)
Q Consensus        55 ~iwGkV~r~HGnsGvVrAkF~~nLP~~a   82 (96)
                      +..|+|+++||-.|-|+......-|...
T Consensus         5 i~iG~I~~~hGikGevkv~~~td~pe~~   32 (184)
T PRK14593          5 LLVGRIGKSVGLNGGLKLHLESDFPECL   32 (184)
T ss_pred             EEEEEEECCEeeeEEEEEEECCCCHHHh
Confidence            6789999999999999999998877754

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

Probab=84.99  E-value=1.1  Score=32.48  Aligned_cols=29  Identities=21%  Similarity=0.283  Sum_probs=25.3

Q ss_pred             EEEEEEEceeCCCceEEEEeCCCCCccCC
Q 042762           55 CIWGKVARSHGNSGVVRAEFKSNLPPKSM   83 (96)
Q Consensus        55 ~iwGkV~r~HGnsGvVrAkF~~nLP~~ai   83 (96)
                      +..|+|++|||=.|-|+++.-..-|....
T Consensus         3 v~iG~I~~~hGlkGevkv~~~td~p~~~~   31 (165)
T PRK14592          3 ICLGVITSPHGIKGHVKIKTFTEDPENIS   31 (165)
T ss_pred             EEEEEEECCCccCEEEEEEECCCCHHHhc
Confidence            56899999999999999999988777543

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

Probab=84.15  E-value=1.4  Score=32.09  Aligned_cols=29  Identities=10%  Similarity=-0.114  Sum_probs=25.5

Q ss_pred             EEEEEEEEceeCCCceEEEEeCCCCCccC
Q 042762           54 RCIWGKVARSHGNSGVVRAEFKSNLPPKS   82 (96)
Q Consensus        54 R~iwGkV~r~HGnsGvVrAkF~~nLP~~a   82 (96)
                      -+..|+|++|||=.|-|+++.....|...
T Consensus         5 ~v~vG~I~~~hGlkGevkv~~~td~p~~~   33 (169)
T PRK14591          5 FVEIAKIGATYKLNGELNLYPLANSIETL   33 (169)
T ss_pred             EEEEEEEeCCccccEEEEEEECCCCHHHh
Confidence            47889999999999999999988877744

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

Probab=83.08  E-value=0.87  Score=33.58  Aligned_cols=26  Identities=27%  Similarity=0.311  Sum_probs=22.8

Q ss_pred             EEEecCcCChhhhhhhccceEEEEEec
Q 042762           18 LIQIEGVNTKEKVVWYCCKHLAYIYKA   44 (96)
Q Consensus        18 LlKiegV~~~~~a~fylGKrvayvyk~   44 (96)
                      +++++|++|+++|+.+.|..+ |+.++
T Consensus        66 ~v~f~gi~dr~~Ae~l~g~~l-~i~~~   91 (184)
T PRK14593         66 LLFLETIHTPEKAKELTNLGL-FMSEA   91 (184)
T ss_pred             EEEEcCCCCHHHHHHhcCCEE-EEEHH
Confidence            799999999999999999987 45554

>PF04950 DUF663: Protein of unknown function (DUF663); InterPro: IPR007034 This domain is found at the C terminus of the ribosome biogenesis protein BMS1 and TSR1 families, which may act as a molecular switch during maturation of the 40S ribosomal subunit in the nucleolus

Probab=82.38  E-value=1.7  Score=34.76  Aligned_cols=62  Identities=27%  Similarity=0.470  Sum_probs=36.1

Q ss_pred             CeeEEEecCcCChhhhhhhccceEEEEEecccCCCCceeEEEEEEEEceeCCCceEEEEeCCCCCccCCCCeEEEEEe
Q 042762           15 NTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMY   92 (96)
Q Consensus        15 ~~aLlKiegV~~~~~a~fylGKrvayvyk~k~~~~g~k~R~iwGkV~r~HGnsGvVrAkF~~nLP~~aiG~~vrVmLy   92 (96)
                      ++|.||-= -++.+|..++.|-.+    +++   .|  .|   |.|..+-|..|.++|-|...|=.   .+.|..-||
T Consensus       233 ~~a~vr~M-F~~~~dv~~F~~~~l----~T~---~G--~r---G~Ik~~lgt~G~fka~F~~~i~~---~D~V~~~ly  294 (297)
T PF04950_consen  233 RTAVVRGM-FFNPEDVAWFKGAEL----RTK---SG--IR---GHIKESLGTHGYFKATFEDKIKQ---SDIVFMRLY  294 (297)
T ss_dssp             SSCEECSS-SSTCCHHHHS-S--B----EET---TS---B---EEEEE-BTTTTBBEEEESS---S---S-EEEEE--
T ss_pred             ceEEhhhh-cCCHHHHHhhcCCEE----Eee---cc--CC---CEECeeECCCCcEEEEECCcCCC---CCEEEEecC
Confidence            45555543 466777777777766    332   23  34   99999999999999999988754   455655555

; PDB: 1WB1_D 1WB3_B 1WB2_A.

>cd04479 RPA3 RPA3: A subfamily of OB folds similar to human RPA3 (also called RPA14)

Probab=82.19  E-value=7.2  Score=26.14  Aligned_cols=35  Identities=31%  Similarity=0.453  Sum_probs=23.9

Q ss_pred             EEEEEEEceeCC-------Cc-eEEEEeCCCCCccCCCCeEEEE
Q 042762           55 CIWGKVARSHGN-------SG-VVRAEFKSNLPPKSMGDKVRVF   90 (96)
Q Consensus        55 ~iwGkV~r~HGn-------sG-vVrAkF~~nLP~~aiG~~vrVm   90 (96)
                      .++|||++.||+       .| .|.+.....+ ...+++-|.|.
T Consensus        19 ~ivGkV~~~~~~~~~~~~~Dg~~v~v~l~~~~-~~~~~~~vEVi   61 (101)
T cd04479          19 RIVGKVEKVDGDSLTLISSDGVNVTVELNRPL-DLPISGYVEVI   61 (101)
T ss_pred             EEEEEEEEecCCeEEEEcCCCCEEEEEeCCCC-CcccCCEEEEE
Confidence            467999999998       44 6777777654 34556666654

RPA3 is the smallest subunit of Replication protein A (RPA). RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA3 is believed to have a structural role in assembly of the RPA heterotrimer.

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

Probab=80.38  E-value=1.7  Score=31.84  Aligned_cols=27  Identities=15%  Similarity=0.294  Sum_probs=23.5

Q ss_pred             EEEEEEceeCCCceEEEEeCCCCCccC
Q 042762           56 IWGKVARSHGNSGVVRAEFKSNLPPKS   82 (96)
Q Consensus        56 iwGkV~r~HGnsGvVrAkF~~nLP~~a   82 (96)
                      ..|+|++|||-.|.|+......-|...
T Consensus         2 ~vG~I~~~hGlkGevkv~~~td~pe~~   28 (171)
T PRK14590          2 SLGQLGKPFGIKGWLRVNVRGETLHTL   28 (171)
T ss_pred             eEEEEeCCEeeCeEEEEEEccCCHHHh
Confidence            479999999999999999888877643

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	96
3izr_j	111	Localization Of The Large Subunit Ribosomal Protein		6e-39
3izs_j	107	Localization Of The Large Subunit Ribosomal Protein		4e-25
4a18_H	113	T.Thermophila 60s Ribosomal Subunit In Complex With		2e-21
3zf7_l	149	High-resolution Cryo-electron Microscopy Structure		5e-17
1sqr_A	95	Solution Structure Of The 50s Ribosomal Protein L35		2e-08
3j21_c	87	Promiscuous Behavior Of Proteins In Archaeal Riboso		5e-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 =  155 bits (391), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 74/96 (77%), Positives = 83/96 (86%)
Query: 1   TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKV 60
           TILGYKRSKSNQY NTSL+QIEGVNTKE+V WY  K +AY+YKAKTK + +  RCIWGKV
Sbjct: 16  TILGYKRSKSNQYENTSLLQIEGVNTKEEVGWYAGKRIAYVYKAKTKSNDSTIRCIWGKV 75
Query: 61  ARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
            R HGNSGVVRA+F+SNLPP SMG KVRVFMYPS+I
Sbjct: 76  TRPHGNSGVVRAKFRSNLPPTSMGKKVRVFMYPSSI 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 =  109 bits (272), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 50/94 (53%), Positives = 66/94 (70%)
Query: 3   LGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVAR 62
           L Y+RSK    PN SLI+IEGV T +   +Y  K +AY+Y+A  +   +  R +WGKV R
Sbjct: 14  LSYQRSKRVNNPNVSLIKIEGVATPQDAQFYLGKRIAYVYRASKEVRGSKIRVMWGKVTR 73
Query: 63  SHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
           +HGNSGVVRA F++NLP K+ G  VR+F+YPSNI
Sbjct: 74  THGNSGVVRATFRNNLPAKTFGASVRIFLYPSNI 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 = 97.1 bits (240), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 42/91 (46%), Positives = 66/91 (72%), Gaps = 1/91 (1%)
Query: 4   GYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVARS 63
           G++RSK  Q  N +L++++ VNTKE V +Y  K + YIYK + KK+ ++YR IWG++ ++
Sbjct: 22  GFRRSKHTQNSNQALLKLQNVNTKEDVAFYQGKRVVYIYKGQ-KKNGSNYRTIWGRIGKA 80
Query: 64  HGNSGVVRAEFKSNLPPKSMGDKVRVFMYPS 94
           HGN+GV  A F  NLPP+++G  +RV +YP+
Sbjct: 81  HGNNGVAVARFAHNLPPQAIGSVLRVMLYPN 111

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

Iteration: 1
 Score = 82.8 bits (203), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 44/109 (40%), Positives = 63/109 (57%), Gaps = 15/109 (13%)
Query: 1   TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIY------------KAKTKK 48
           T+ GY R    Q  NT+L++IE VNT E   WY  K + Y+Y            KA  ++
Sbjct: 43  TLAGYTRGLHGQNKNTALVRIENVNTTEDAKWYVGKRVCYVYHGYKIKRCVRWSKAPARR 102
Query: 49  SWTHYRCIWGKVARSHGNSGVVRAEFK-SNLPPKSMGDKVRVFMYPSNI 96
           S T  R IWG++ R HG SG VR +F  S++P  ++G ++RV++YPS I
Sbjct: 103 SNT--RAIWGRITRPHGTSGTVRVKFNGSSVPASAIGRRIRVYLYPSRI 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 = 53.9 bits (128), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 29/91 (31%), Positives = 50/91 (54%), Gaps = 8/91 (8%)
Query: 1  TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKV 60
           +L Y+RSK NQ+ N  +I+   VN++E+      +    ++K+ + K       + GK+
Sbjct: 6  VVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGR--LVLWKSPSGK------ILKGKI 57
Query: 61 ARSHGNSGVVRAEFKSNLPPKSMGDKVRVFM 91
           R HG  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 = 52.8 bits (125), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 29/90 (32%), Positives = 49/90 (54%), Gaps = 8/90 (8%)
Query: 1  TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKV 60
           +L Y+RSK NQ+ N  +I+   VN++E+      +    ++K+ + K       + GK+
Sbjct: 6  VVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGR--LVLWKSPSGK------ILKGKI 57
Query: 61 ARSHGNSGVVRAEFKSNLPPKSMGDKVRVF 90
           R HG  G VRA F+  LP +++GD V + 
Sbjct: 58 VRVHGTKGAVRARFEKGLPGQALGDYVEIV 87

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	96
3iz5_J	166	60S ribosomal protein L12 (L11P); eukaryotic ribos	5e-45
3izc_j	107	60S ribosomal protein RPL33 (L35AE); eukaryotic ri	1e-44
4a18_H	113	RPL35A; ribosome, eukaryotic initiation factor 6,	2e-40
1sqr_A	95	50S ribosomal protein L35AE; PFR48, structure, aut	9e-38

>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 =  128 bits (322), Expect = 2e-40
 Identities = 41/94 (43%), Positives = 64/94 (68%), Gaps = 1/94 (1%)

Query: 1   TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKV 60
              G++RSK  Q  N +L++++ VNTKE V +Y  K + YIYK + K   ++YR IWG++
Sbjct: 19  AFTGFRRSKHTQNSNQALLKLQNVNTKEDVAFYQGKRVVYIYKGQKKN-GSNYRTIWGRI 77

Query: 61  ARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPS 94
            ++HGN+GV  A F  NLPP+++G  +RV +YP+
Sbjct: 78  GKAHGNNGVAVARFAHNLPPQAIGSVLRVMLYPN 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 =  121 bits (304), Expect = 9e-38
 Identities = 27/96 (28%), Positives = 49/96 (51%), Gaps = 8/96 (8%)

Query: 1  TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKV 60
           +L Y+RSK NQ+ N  +I+   VN++E+      + + +   +         + + GK+
Sbjct: 6  VVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGRLVLWKSPSG--------KILKGKI 57

Query: 61 ARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
           R HG  G VRA F+  LP +++GD V + +   + 
Sbjct: 58 VRVHGTKGAVRARFEKGLPGQALGDYVEIVLEHHHH 93

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	96
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	92.64
3h9n_A	177	Ribosome maturation factor RIMM; structural genomi	90.46
2dyi_A	162	Probable 16S rRNA-processing protein RIMM; ribosom	90.05
2qgg_A	182	16S rRNA-processing protein RIMM; X-RAY, NESG, ASR	89.56
2f1l_A	187	16S rRNA processing protein; structural genomics,	89.35
3h9n_A	177	Ribosome maturation factor RIMM; structural genomi	82.94
3kdf_A	121	Replication protein A 14 kDa subunit; wheat GERM c	82.04
2qgg_A	182	16S rRNA-processing protein RIMM; X-RAY, NESG, ASR	81.29
4gop_A	114	Putative uncharacterized protein; OB fold, ssDNA b	80.9
2dyi_A	162	Probable 16S rRNA-processing protein RIMM; ribosom	80.38

>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=5.4e-60  Score=331.14  Aligned_cols=94  Identities=44%  Similarity=0.892  Sum_probs=92.2

Q ss_pred             CeeeccccCCCCCCCeeEEEecCcCChhhhhhhccceEEEEEecccCCCCceeEEEEEEEEceeCCCceEEEEeCCCCCc
Q 042762            1 TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVARSHGNSGVVRAEFKSNLPP   80 (96)
Q Consensus         1 ~~~gykRg~~~Q~~~~aLlKiegV~~~~~a~fylGKrvayvyk~k~~~~g~k~R~iwGkV~r~HGnsGvVrAkF~~nLP~   80 (96)
                      +|+|||||++||+|||||||||||+++|||+||||||||||||++++ .|+|+|+|||||+|+|||||+|||+|++||||
T Consensus        19 v~lgYkRg~~nQ~~~taLlKIeGV~~~~~a~fylGKrvayvykak~~-~g~k~RviwGKVtR~HGnsGvVrAkF~~nLP~   97 (113)
T 4a18_H           19 AFTGFRRSKHTQNSNQALLKLQNVNTKEDVAFYQGKRVVYIYKGQKK-NGSNYRTIWGRIGKAHGNNGVAVARFAHNLPP   97 (113)
T ss_dssp             EEEEEEEETTEEEEEEEEEEETTCCSHHHHHTTTTCEEEEEEEEEEE-TTEEEEEEEEEEEEEETTTTEEEEEESSCCCG
T ss_pred             EEEecccccCCCCCCeEEEEEcCcCCHHHHHhhcCCeEEEEEecCCC-CCCeEEEEEEEEEeeeCCCCeEEEEeCCCCCh
Confidence            58999999999999999999999999999999999999999999987 89999999999999999999999999999999


Q ss_pred             cCCCCeEEEEEeecC
Q 042762           81 KSMGDKVRVFMYPSN   95 (96)
Q Consensus        81 ~aiG~~vrVmLyps~   95 (96)
                      ||||++||||||||+
T Consensus        98 kA~G~~VrVmLyPs~  112 (113)
T 4a18_H           98 QAIGSVLRVMLYPNR  112 (113)
T ss_dssp             GGGGSEEEEECCCCC
T ss_pred             HHcCCeEEEEEecCC
Confidence            999999999999997

>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=3.5e-53  Score=289.32  Aligned_cols=84  Identities=32%  Similarity=0.538  Sum_probs=80.4

Q ss_pred             CeeeccccCCCCCCCeeEEEecCcCChhhhhhhccceEEEEEecccCCCCceeEEEEEEEEceeCCCceEEEEeCCCCCc
Q 042762            1 TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVARSHGNSGVVRAEFKSNLPP   80 (96)
Q Consensus         1 ~~~gykRg~~~Q~~~~aLlKiegV~~~~~a~fylGKrvayvyk~k~~~~g~k~R~iwGkV~r~HGnsGvVrAkF~~nLP~   80 (96)
                      +|+|||||++||+|||||||||||+++|||+||||||||||||++        |+|||||||||||||+|||+|++||||
T Consensus         6 v~lgYkRg~~nQ~~~~aLlkIegV~~k~~a~fYlGKrvayvyka~--------rviwGKVtR~HGnsGvVrAkF~~nLP~   77 (95)
T 1sqr_A            6 VVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGRLVLWKSPSG--------KILKGKIVRVHGTKGAVRARFEKGLPG   77 (95)
T ss_dssp             EEEEEECCSSSSSCCEEEEEESCCCCHHHHHHHTTCEEEECCSTT--------CCEEEEEEEESSSSSCEEEECSSCCSS
T ss_pred             EEEeeccccCcCCCceEEEEEcCCCCHHHHHhhcCCeEEEEECCC--------CEEEEEEEeeeCCCCEEEEEeCCCCCh
Confidence            589999999999999999999999999999999999999999885        799999999999999999999999999


Q ss_pred             cCCCCeEEEEEe
Q 042762           81 KSMGDKVRVFMY   92 (96)
Q Consensus        81 ~aiG~~vrVmLy   92 (96)
                      ||||++|||||-
T Consensus        78 kA~G~~VrVml~   89 (95)
T 1sqr_A           78 QALGDYVEIVLE   89 (95)
T ss_dssp             SCTTCEEECC--
T ss_pred             HHcCCEEEEEEe
Confidence            999999999984

>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=1.1e-50  Score=273.26  Aligned_cols=81  Identities=33%  Similarity=0.546  Sum_probs=77.7

Q ss_pred             CeeeccccCCCCCCCeeEEEecCcCChhhhhhhccceEEEEEecccCCCCceeEEEEEEEEceeCCCceEEEEeCCCCCc
Q 042762            1 TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVARSHGNSGVVRAEFKSNLPP   80 (96)
Q Consensus         1 ~~~gykRg~~~Q~~~~aLlKiegV~~~~~a~fylGKrvayvyk~k~~~~g~k~R~iwGkV~r~HGnsGvVrAkF~~nLP~   80 (96)
                      +|+|||||++||+|||||||||||+++|||+|||||||||||++     |   ++|||||+|+|||||+|||+|++||||
T Consensus         6 ~~~gykRg~~nQ~~~taLlkieGV~~~~~a~fylGKrvayv~~~-----g---~~iwGKVtr~HGnsGvVrAkF~~nLP~   77 (87)
T 3j21_c            6 VVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGRLVLWKSPS-----G---KILKGKIVRVHGTKGAVRARFEKGLPG   77 (87)
T ss_dssp             EEEEESCCSSCCCTTCEEEEESSCCSHHHHGGGTTCEEEECCSS-----S---CCEEEEEEEECCSSSCEEEEESSCCCS
T ss_pred             EEEecccccCcCCCCeEEEEEcCcCCHHHHHhhcCceEEEEeCC-----C---CEEEEEEEeeeCCCCeEEEEeCCCCCh
Confidence            58999999999999999999999999999999999999999975     3   389999999999999999999999999


Q ss_pred             cCCCCeEEE
Q 042762           81 KSMGDKVRV   89 (96)
Q Consensus        81 ~aiG~~vrV   89 (96)
                      ||||++|||
T Consensus        78 ~a~G~~Vri   86 (87)
T 3j21_c           78 QALGDYVEI   86 (87)
T ss_dssp             SCSCCEECC
T ss_pred             HHcCCeEEe
Confidence            999999987

>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=92.64  E-value=0.028  Score=45.11  Aligned_cols=68  Identities=21%  Similarity=0.232  Sum_probs=51.2

Q ss_pred             CCCCeeEEEecCcCChhhhhhhccceEEEEEecccCCCCceeEEEEEEEEceeCCCceEEEEeCCCCCccCCCCeEEEEE
Q 042762           12 QYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVARSHGNSGVVRAEFKSNLPPKSMGDKVRVFM   91 (96)
Q Consensus        12 Q~~~~aLlKiegV~~~~~a~fylGKrvayvyk~k~~~~g~k~R~iwGkV~r~HGnsGvVrAkF~~nLP~~aiG~~vrVmL   91 (96)
                      ++.++++++=- ..+..|.++|+|.+|--  +     .|    -|+|.|..+.|.||.++|.|.-.|.++   +.|..-|
T Consensus       413 ~~~~~~i~~~l-f~~~~~~~~f~g~~v~~--~-----~g----~~~G~I~~~fg~~G~~~~~f~~~~~~~---d~v~~~~  477 (482)
T 1wb1_A          413 IDKGRTVIDGL-AQSKVAAEKLIGEEISI--E-----GK----DIVGKIKGTFGTKGLLTAEFSGNVENR---DKVILNR  477 (482)
T ss_dssp             CCSSCCEETTS-CSSHHHHHHSCSCCCEE--T-----TT----CCCBCCCCCBTTTTBBCCCBSSCCCSS---CEEEEEC
T ss_pred             EcCCEEEEEcC-ccchhhhHHhcCcEEEE--c-----CC----ceEEEEeccCCCCceEEEEecCCCCCC---Ceeeeeh
Confidence            46677776622 45667899999999965  2     23    256999999999999999999998865   5666666


Q ss_pred             eec
Q 042762           92 YPS   94 (96)
Q Consensus        92 yps   94 (96)
                      |..
T Consensus       478 ~~~  480 (482)
T 1wb1_A          478 LRR  480 (482)
T ss_dssp             CCS
T ss_pred             hhc
Confidence            643

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

Probab=90.46  E-value=0.19  Score=35.79  Aligned_cols=59  Identities=12%  Similarity=0.152  Sum_probs=39.8

Q ss_pred             CCeeEEEecCcCChhhhhhhccceEEEEEecccCC-----------CCceeE----EEEEEEEcee--CCCceEEEE
Q 042762           14 PNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKK-----------SWTHYR----CIWGKVARSH--GNSGVVRAE   73 (96)
Q Consensus        14 ~~~aLlKiegV~~~~~a~fylGKrvayvyk~k~~~-----------~g~k~R----~iwGkV~r~H--GnsGvVrAk   73 (96)
                      .+..|+|++||+|+++|+.+.|..+ ||-++.-..           -|-...    ...|+|+...  |.+-+...+
T Consensus        56 ~~~~lvkf~gi~dr~~Ae~L~G~~l-~v~~~~lp~l~edE~Y~~dLiGl~V~~~~g~~lG~V~~v~~~gandvl~V~  131 (177)
T 3h9n_A           56 NHEIIVKLKGVDDREAAQILANVEI-GVDLSVFPELEEGDYYWHDLIGCTVVNLEGYTMGTVTEMMETGSNDVLVVK  131 (177)
T ss_dssp             SSCEEEEESSCCSHHHHHTTTTCEE-EEECCCCCCCSSSCGGGGGTTTCEEEETTCCEEEEEEEEEESSSCEEEEEE
T ss_pred             CCEEEEEEcCCCCHHHHHHhcCCEE-EEEHHHCCCCCCCCCCHHHhcCCEEEeCCCCEEEEEEEEeeCCCcEEEEEE
Confidence            4678999999999999999999998 666653210           122111    2478888765  445555555

>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=90.05  E-value=0.2  Score=35.33  Aligned_cols=31  Identities=13%  Similarity=0.168  Sum_probs=26.2

Q ss_pred             CCeeEEEecCcCChhhhhhhccceEEEEEecc
Q 042762           14 PNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAK   45 (96)
Q Consensus        14 ~~~aLlKiegV~~~~~a~fylGKrvayvyk~k   45 (96)
                      .+..|+|++||+|+++|+.+.|..+ ||-++.
T Consensus        50 ~~~~ivkf~gi~~r~~Ae~L~G~~l-~v~~~~   80 (162)
T 2dyi_A           50 GEELVVHLAGVTDRTLAEALVGLRV-YAEVAD   80 (162)
T ss_dssp             TTEEEEEETTCCSHHHHHTTTTCEE-EEEGGG
T ss_pred             CCEEEEEEcCCCCHHHHHHhCCCEE-EEEHHH
Confidence            5679999999999999999999987 555543

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

Probab=89.56  E-value=0.22  Score=35.60  Aligned_cols=31  Identities=13%  Similarity=0.270  Sum_probs=26.1

Q ss_pred             CCCeeEEEecCcCChhhhhhhccceEEEEEec
Q 042762           13 YPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKA   44 (96)
Q Consensus        13 ~~~~aLlKiegV~~~~~a~fylGKrvayvyk~   44 (96)
                      +.+..|+|++||+|+++|+.+.|..+ ||-++
T Consensus        64 ~~~~~ivkf~gi~dr~~Ae~L~G~~l-~v~~~   94 (182)
T 2qgg_A           64 HGKGLVVSLKGVSDRTGAESLVASNI-WIAKS   94 (182)
T ss_dssp             ETTEEEEEETTCCSHHHHHTTTTCEE-EEETT
T ss_pred             cCCEEEEEECCCCCHHHHHHhCCCEE-EEEHH
Confidence            35678999999999999999999977 55554

>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=89.35  E-value=0.23  Score=35.88  Aligned_cols=32  Identities=9%  Similarity=0.212  Sum_probs=26.5

Q ss_pred             CCCeeEEEecCcCChhhhhhhccceEEEEEecc
Q 042762           13 YPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAK   45 (96)
Q Consensus        13 ~~~~aLlKiegV~~~~~a~fylGKrvayvyk~k   45 (96)
                      +.+..|+|++||+|+++|+.+.|..+ ||-++.
T Consensus        73 ~~~~~ivkf~gi~dr~~Ae~L~G~~l-~v~r~~  104 (187)
T 2f1l_A           73 HGKVLAAKLKGLDDREEARTFTGYEI-CIPRSE  104 (187)
T ss_dssp             ETTEEEEEETTCCSHHHHHTTTTCEE-EEEGGG
T ss_pred             ECCEEEEEEeCCCCHHHHHHhCCCEE-EEEHHH
Confidence            35679999999999999999999977 555543

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

Probab=82.94  E-value=1.5  Score=31.17  Aligned_cols=28  Identities=18%  Similarity=0.179  Sum_probs=24.0

Q ss_pred             EEEEEEEEceeCCCceEEEEeCCCCCcc
Q 042762           54 RCIWGKVARSHGNSGVVRAEFKSNLPPK   81 (96)
Q Consensus        54 R~iwGkV~r~HGnsGvVrAkF~~nLP~~   81 (96)
                      ++..|+|.++||-.|.|+..-...-|-.
T Consensus         2 ~v~vG~I~~~hGikGevkv~~~Td~pe~   29 (177)
T 3h9n_A            2 IEVVGKLGSTYGIRGWLRIYSSTEQAES   29 (177)
T ss_dssp             EEEEEEEEEECSSSSCEEEEECSSSSGG
T ss_pred             EEEEEEEeCCCccCEEEEEEECCCCHHH
Confidence            4678999999999999999877777654

>3kdf_A Replication protein A 14 kDa subunit; wheat GERM cell free, protein complex, center for eukaryotic structural genomics, PSI; HET: MSE; 1.98A {Homo sapiens} SCOP: b.40.4.3 PDB: 1quq_B 1l1o_A

Probab=82.04  E-value=7.8  Score=26.15  Aligned_cols=45  Identities=18%  Similarity=0.243  Sum_probs=31.2

Q ss_pred             hhhhhhccceEEEEEecccCCCCceeEEEEEEEEceeCC----------CceEEEEeCCCCCccCCCCeEEE
Q 042762           28 EKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVARSHGN----------SGVVRAEFKSNLPPKSMGDKVRV   89 (96)
Q Consensus        28 ~~a~fylGKrvayvyk~k~~~~g~k~R~iwGkV~r~HGn----------sGvVrAkF~~nLP~~aiG~~vrV   89 (96)
                      +.=..|+||.|                .++|||.+.|.+          .|.|..++...|+... +.-|.|
T Consensus        15 s~L~~fvgk~V----------------rivGkV~~~~~~g~~~~l~s~Dg~~Vtv~l~~p~~~~l-~~~vEV   69 (121)
T 3kdf_A           15 GMLAQFIDKPV----------------CFVGRLEKIHPTGKMFILSDGEGKNGTIELMEPLDEEI-SGIVEV   69 (121)
T ss_dssp             GGGGGGTTCEE----------------EEEEEEEEECTTSSEEEEECTTSCEEEEECSSCCSSCC-CSEEEE
T ss_pred             HHHHhhCCCeE----------------EEEEEEEEEcCCCCEEEEEeCCCCEEEEEeCCCCCccc-CcEEEE
Confidence            33456888877                567999999843          3789999988665433 556655

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

Probab=81.29  E-value=1.8  Score=30.77  Aligned_cols=27  Identities=15%  Similarity=0.127  Sum_probs=23.7

Q ss_pred             EEEEEEEEceeCCCceEEEEeCCCCCc
Q 042762           54 RCIWGKVARSHGNSGVVRAEFKSNLPP   80 (96)
Q Consensus        54 R~iwGkV~r~HGnsGvVrAkF~~nLP~   80 (96)
                      .+..|+|.++||-.|-|+.+-.+.-|.
T Consensus        11 ~v~vG~I~~~hGikGevkv~~~td~pe   37 (182)
T 2qgg_A           11 RIQIGQLRSAYGLNGWLWVYSNTEPMS   37 (182)
T ss_dssp             EEEEEEEEEEETTTTEEEEEECSSSGG
T ss_pred             EEEEEEEeCCcccCEEEEEEECCCCHH
Confidence            478899999999999999988877664

>4gop_A Putative uncharacterized protein; OB fold, ssDNA binding, DNA binding protein-DNA complex; HET: DNA; 3.10A {Ustilago maydis}

Probab=80.90  E-value=6  Score=26.37  Aligned_cols=45  Identities=24%  Similarity=0.268  Sum_probs=32.3

Q ss_pred             hhhhhccceEEEEEecccCCCCceeEEEEEEEEceeCCC--------ceEEEEeCCCCCccCCCCeEEEE
Q 042762           29 KVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVARSHGNS--------GVVRAEFKSNLPPKSMGDKVRVF   90 (96)
Q Consensus        29 ~a~fylGKrvayvyk~k~~~~g~k~R~iwGkV~r~HGns--------GvVrAkF~~nLP~~aiG~~vrVm   90 (96)
                      .-..|+|+.|                .|.|||+..||+.        |.|..++.++++.+ ++.-|.|.
T Consensus        12 ~L~~~~g~~V----------------rivGkV~~~~g~~~~l~s~d~~~Vtv~l~~~~~~~-~~~~vEVi   64 (114)
T 4gop_A           12 MLGQYVGQTV----------------RIVGKVHKVTGNTLLMQTSDLGNVEIAMTPDSDVS-SSTFVEVT   64 (114)
T ss_dssp             TGGGGTTSEE----------------EEEEEEEEEETTEEEEECTTSCEEEEECCSSCCGG-GCSEEEEE
T ss_pred             HHHhhCCCeE----------------EEEEEEeeeCCCEEEEEeCCCCEEEEEeCCCCCcc-cCcEEEEE
Confidence            3456777776                4668999998863        77888888877754 67777664

>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=80.38  E-value=1.5  Score=30.78  Aligned_cols=21  Identities=14%  Similarity=0.066  Sum_probs=18.6

Q ss_pred             EEEEEEEceeCCCceEEEEeCC
Q 042762           55 CIWGKVARSHGNSGVVRAEFKS   76 (96)
Q Consensus        55 ~iwGkV~r~HGnsGvVrAkF~~   76 (96)
                      +..|+|.++||-.|.|+. |--
T Consensus         4 v~vG~I~~~hGikGevkv-~td   24 (162)
T 2dyi_A            4 VEIGRFGAPYALKGGLRF-RGE   24 (162)
T ss_dssp             EEEEEEEEECSSSSCEEE-EEC
T ss_pred             EEEEEEeCCCccCeEEEE-EEc
Confidence            668999999999999999 654

---

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	96
d1sqra_	87	b.43.3.3 (A:) Ribosomal protein L35ae {Pyrococcus	2e-36

>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 =  116 bits (292), Expect = 2e-36
 Identities = 27/89 (30%), Positives = 47/89 (52%), Gaps = 8/89 (8%)

Query: 1  TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKV 60
           +L Y+RSK NQ+ N  +I+   VN++E+      + + +   +         + + GK+
Sbjct: 6  VVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGRLVLWKSPSG--------KILKGKI 57

Query: 61 ARSHGNSGVVRAEFKSNLPPKSMGDKVRV 89
           R HG  G VRA F+  LP +++GD V +
Sbjct: 58 VRVHGTKGAVRARFEKGLPGQALGDYVEI 86

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	96
d1sqra_	87	Ribosomal protein L35ae {Pyrococcus furiosus [TaxI	100.0
d2f1la2	89	16S rRNA processing protein RimM, N-terminal domai	95.84
d1wb1a2	79	Elongation factor SelB, domains 2 and 4 {Methanoco	94.44
d2f1la2	89	16S rRNA processing protein RimM, N-terminal domai	85.66

>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=1.4e-50  Score=271.23  Aligned_cols=82  Identities=33%  Similarity=0.551  Sum_probs=78.0

Q ss_pred             CeeeccccCCCCCCCeeEEEecCcCChhhhhhhccceEEEEEecccCCCCceeEEEEEEEEceeCCCceEEEEeCCCCCc
Q 042762            1 TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVARSHGNSGVVRAEFKSNLPP   80 (96)
Q Consensus         1 ~~~gykRg~~~Q~~~~aLlKiegV~~~~~a~fylGKrvayvyk~k~~~~g~k~R~iwGkV~r~HGnsGvVrAkF~~nLP~   80 (96)
                      +|+|||||++||+|||||||||||+++|||+||+||||+|+|++.        |+|||||+|+|||||+|||+|++||||
T Consensus         6 v~~gykRg~~nq~~~~~Llkiegv~~k~~a~fylGKrv~y~~~~~--------r~iwGKVtr~HGnsGvVrAkF~~nLP~   77 (87)
T d1sqra_           6 VVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGRLVLWKSPSG--------KILKGKIVRVHGTKGAVRARFEKGLPG   77 (87)
T ss_dssp             EEEEEECCSSSSSCCEEEEEESCCCCHHHHHHHTTCEEEECCSTT--------CCEEEEEEEESSSSSCEEEECSSCCSS
T ss_pred             EEEEeccccccCCCCEEEEEEcCcCCHHHHHhhcCcEEEEECCCC--------cEEEeeEeeecCCCceEEEEecCCCCh
Confidence            589999999999999999999999999999999999999965442        799999999999999999999999999


Q ss_pred             cCCCCeEEEE
Q 042762           81 KSMGDKVRVF   90 (96)
Q Consensus        81 ~aiG~~vrVm   90 (96)
                      ||||++||||
T Consensus        78 qa~G~~VrVm   87 (87)
T d1sqra_          78 QALGDYVEIV   87 (87)
T ss_dssp             SCTTCEEECC
T ss_pred             HHcCCEEEeC
Confidence            9999999998

>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=95.84  E-value=0.0019  Score=39.22  Aligned_cols=29  Identities=7%  Similarity=0.163  Sum_probs=25.5

Q ss_pred             CCCCCeeEEEecCcCChhhhhhhccceEE
Q 042762           11 NQYPNTSLIQIEGVNTKEKVVWYCCKHLA   39 (96)
Q Consensus        11 ~Q~~~~aLlKiegV~~~~~a~fylGKrva   39 (96)
                      .++.+..++|++||+|+|+|+.+.|+.+.
T Consensus        53 ~~~~~~~~vk~~~i~~r~~Ae~l~g~~i~   81 (89)
T d2f1la2          53 RLHGKVLAAKLKGLDDREEARTFTGYEIC   81 (89)
T ss_dssp             EEETTEEEEEETTCCSHHHHHTTTTCEEE
T ss_pred             EecccEEEEEEcCCCCHHHHHHhCCCEEE
Confidence            35567889999999999999999999873

>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=94.44  E-value=0.0026  Score=40.13  Aligned_cols=50  Identities=26%  Similarity=0.430  Sum_probs=40.6

Q ss_pred             EEecCc-CChhhhhhhccceEEEEEecccCCCCceeEEEEEEEEceeCCCceEEEEeCCCCC
Q 042762           19 IQIEGV-NTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVARSHGNSGVVRAEFKSNLP   79 (96)
Q Consensus        19 lKiegV-~~~~~a~fylGKrvayvyk~k~~~~g~k~R~iwGkV~r~HGnsGvVrAkF~~nLP   79 (96)
                      .=|||. .++..|+.+||-+|--  ..+         -|||||.-+||..|.+.|-|.-|.-
T Consensus        15 ~~IegLA~sK~~aEkLIGe~v~i--~~k---------~i~Gkik~TfGTkG~l~adF~geV~   65 (79)
T d1wb1a2          15 TVIDGLAQSKVAAEKLIGEEISI--EGK---------DIVGKIKGTFGTKGLLTAEFSGNVE   65 (79)
T ss_dssp             CEETTSCSSHHHHHHSCSCCCEE--TTT---------CCCBCCCCCBTTTTBBCCCBSSCCC
T ss_pred             EEeeecccchhHHHhhcCcEEEe--cCC---------ceEEEEeccccCceEEEEEeccccC
Confidence            346775 5788899999999855  332         4799999999999999999998764

>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=85.66  E-value=0.5  Score=27.78  Aligned_cols=26  Identities=19%  Similarity=0.194  Sum_probs=21.9

Q ss_pred             EEEEEEEceeCCCceEEEEeCCCCCc
Q 042762           55 CIWGKVARSHGNSGVVRAEFKSNLPP   80 (96)
Q Consensus        55 ~iwGkV~r~HGnsGvVrAkF~~nLP~   80 (96)
                      +..|+|.+|||=.|.|+..-...-|-
T Consensus         3 i~iGki~~~hGlkG~vki~~~t~~~~   28 (89)
T d2f1la2           3 VVIGKIVSVYGIRGEVKVYSFTDPLD   28 (89)
T ss_dssp             EEEEEEEEEETTTTEEEEEECSSSGG
T ss_pred             EEEEEEeCCEeeeEEEEEEECCCCHH
Confidence            67899999999999999887666443