Citrus Sinensis ID: 043613

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90
Protein Sequence
MAFTQHGRNALRQITKESSDRVLHHPLLFSCQGVKYRRLEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQRR
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHHHccccccccEEEEEccEEEEEEEEEEccccccccccccEEEEcccccccccccccHHccccHHHHHHHHHHHc
Secondary Structure Prediction (SSPRO)
ccHHHHcHHHHHHHHHHcccccEHcHHHHHHcccEEEEEEEEEEccHHHccccccEEEEcccHHHHccccHHccHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MAFTQHGRNALRQITKessdrvlhhpllfscqgvkyrRLEVILTTKVdklgkvgetvkvapgyfhnhlmPKLLAVLNIEKFAHLIREQRR
Flexible Loop (DISEMBL)
maftqhgrnALRQitkessdrvlhhpllfscqgvkyrRLEVILTtkvdklgkvgETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQRR
Low Complexity Region (SEG)
MAFTQHGRNALRQITKESSDRVLHHPLLFSCQGVKYRRLEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQRR
Disordered region (IsUnstruct)
********************RVLHHPLLFSCQGVKYRRLEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLI*****
Disordered Region (DISOPRED)
********NA***ITK*****VLHHPLLFSCQGVKYRRLEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLI*****
Disordered Region (DISEMBL)
*********ALRQITKESSDRVLHHPLLFSCQGVKYRRLEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQRR
Disordered Region (DISPRO)
*AFTQHGRNALRQITKESSDRVLHHPLLFSCQGVKYRRLEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQR*
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAFTQHGRNALRQITKESSDRVLHHPLLFSCQGVKYRRLEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQRR
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	90	2.2.26 [Sep-21-2011]
A1AM21	151	50S ribosomal protein L9	yes	no	0.577	0.344	0.480	3e-06
B0JQ94	152	50S ribosomal protein L9	yes	no	0.444	0.263	0.55	3e-06
B1WTN1	152	50S ribosomal protein L9	yes	no	0.588	0.348	0.444	8e-06
B5EHW6	147	50S ribosomal protein L9	yes	no	0.577	0.353	0.461	8e-06
B7KAD1	152	50S ribosomal protein L9	yes	no	0.588	0.348	0.444	8e-06
B3E6H6	147	50S ribosomal protein L9	yes	no	0.577	0.353	0.423	1e-05
C6E506	147	50S ribosomal protein L9	yes	no	0.577	0.353	0.442	2e-05
Q01QR6	148	50S ribosomal protein L9	yes	no	0.577	0.351	0.423	2e-05
Q74FE1	148	50S ribosomal protein L9	yes	no	0.577	0.351	0.423	5e-05
Q8YZA0	152	50S ribosomal protein L9	yes	no	0.422	0.25	0.5	5e-05

>sp|A1AM21|RL9_PELPD 50S ribosomal protein L9 OS=Pelobacter propionicus (strain DSM 2379) GN=rplI PE=3 SV=1

 Score = 50.4 bits (119), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 25/52 (48%), Positives = 34/52 (65%)

Query: 39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQRR 90
          ++VIL   +D LG +G+ VKVAPGY  N+L+PK LAV   EK A  +   +R
Sbjct: 1  MKVILKENIDTLGHIGDIVKVAPGYARNYLLPKGLAVEATEKNAKALEHVKR 52

Binds to the 23S rRNA.
Pelobacter propionicus (strain DSM 2379) (taxid: 338966)

>sp|B0JQ94|RL9_MICAN 50S ribosomal protein L9 OS=Microcystis aeruginosa (strain NIES-843) GN=rplI PE=3 SV=1

 Score = 50.4 bits (119), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 22/40 (55%), Positives = 32/40 (80%)

Query: 37 RRLEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVL 76
          +R++VIL  KV KLG+ G+ V+VAPGY  N+L+P+ +AVL
Sbjct: 3  KRMQVILNQKVSKLGENGDVVEVAPGYARNYLIPQGVAVL 42

Binds to the 23S rRNA.

Microcystis aeruginosa (strain NIES-843) (taxid: 449447)

>sp|B1WTN1|RL9_CYAA5 50S ribosomal protein L9 OS=Cyanothece sp. (strain ATCC 51142) GN=rplI PE=3 SV=1

 Score = 49.3 bits (116), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 24/54 (44%), Positives = 36/54 (66%), Gaps = 1/54 (1%)

Query: 37 RRLEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQRR 90
          +R++V+L   ++KLGK G+ V+VAPGY  N+L+P+ LA L        + EQRR
Sbjct: 3  KRVQVVLNESINKLGKDGDLVEVAPGYARNYLLPQKLATLATPGILKQV-EQRR 55

Binds to the 23S rRNA.

Cyanothece sp. (strain ATCC 51142) (taxid: 43989)

>sp|B5EHW6|RL9_GEOBB 50S ribosomal protein L9 OS=Geobacter bemidjiensis (strain Bem / ATCC BAA-1014 / DSM 16622) GN=rplI PE=3 SV=1

 Score = 49.3 bits (116), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 24/52 (46%), Positives = 32/52 (61%)

Query: 39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQRR 90
          ++VIL   VD LG +G+ VKVAPGY  N L+PK  A+   EK A  +   +R
Sbjct: 1  MKVILKENVDNLGHIGDIVKVAPGYARNFLLPKGFAIEATEKNAKALEHAKR 52

Binds to the 23S rRNA.

Geobacter bemidjiensis (strain Bem / ATCC BAA-1014 / DSM 16622) (taxid: 404380)

>sp|B7KAD1|RL9_CYAP7 50S ribosomal protein L9 OS=Cyanothece sp. (strain PCC 7424) GN=rplI PE=3 SV=1

 Score = 48.9 bits (115), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 24/54 (44%), Positives = 37/54 (68%), Gaps = 1/54 (1%)

Query: 37 RRLEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQRR 90
          +R++V+LT  V+KLGK G+ V+VAPGY  N+L+P+ +A +        + EQRR
Sbjct: 3  KRVQVVLTKNVNKLGKSGDLVEVAPGYARNYLLPQGIANIATPGILRQV-EQRR 55

Binds to the 23S rRNA.

Cyanothece sp. (strain PCC 7424) (taxid: 65393)

>sp|B3E6H6|RL9_GEOLS 50S ribosomal protein L9 OS=Geobacter lovleyi (strain ATCC BAA-1151 / DSM 17278 / SZ) GN=rplI PE=3 SV=1

 Score = 48.1 bits (113), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/52 (42%), Positives = 35/52 (67%)

Query: 39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQRR 90
          +++IL   ++ LG++G+ VKVAPGY  N+L+PK LA+   EK A  +   +R
Sbjct: 1  MKLILKENIEHLGQIGDIVKVAPGYARNYLLPKGLAIEATEKNAKALEHAKR 52

Binds to the 23S rRNA.

Geobacter lovleyi (strain ATCC BAA-1151 / DSM 17278 / SZ) (taxid: 398767)

>sp|C6E506|RL9_GEOSM 50S ribosomal protein L9 OS=Geobacter sp. (strain M21) GN=rplI PE=3 SV=1

 Score = 47.8 bits (112), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/52 (44%), Positives = 32/52 (61%)

Query: 39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQRR 90
          +++IL   VD LG +G+ VKVAPGY  N L+PK  A+   EK A  +   +R
Sbjct: 1  MKLILKENVDNLGHIGDIVKVAPGYARNFLLPKGFAIEATEKNAKALEHAKR 52

Binds to the 23S rRNA.

Geobacter sp. (strain M21) (taxid: 443144)

>sp|Q01QR6|RL9_SOLUE 50S ribosomal protein L9 OS=Solibacter usitatus (strain Ellin6076) GN=rplI PE=3 SV=1

 Score = 47.4 bits (111), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/52 (42%), Positives = 33/52 (63%)

Query: 39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQRR 90
          +EVIL   ++ LG  G+ VKVAPGY  N L+PK +AV   E    ++ ++R+
Sbjct: 1  MEVILREDIENLGTRGQLVKVAPGYARNFLLPKRMAVAATEANRKIVEQERQ 52

Binds to the 23S rRNA.

Solibacter usitatus (strain Ellin6076) (taxid: 234267)

>sp|Q74FE1|RL9_GEOSL 50S ribosomal protein L9 OS=Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA) GN=rplI PE=3 SV=1

 Score = 46.6 bits (109), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 22/52 (42%), Positives = 33/52 (63%)

Query: 39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQRR 90
          ++VIL   V+ LG +G+ VKVAPGY  N+L+P+  A+   EK A  +   +R
Sbjct: 1  MKVILKENVENLGHIGDIVKVAPGYARNYLIPRNFAIEATEKNAKALEHAKR 52

Binds to the 23S rRNA.

Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA) (taxid: 243231)

>sp|Q8YZA0|RL9_NOSS1 50S ribosomal protein L9 OS=Nostoc sp. (strain PCC 7120 / UTEX 2576) GN=rplI PE=3 SV=1

 Score = 46.6 bits (109), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 19/38 (50%), Positives = 29/38 (76%)

Query: 37 RRLEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLA 74
          +R++++LT  V KLG+ G+ V VAPGY  N+L+P+ LA
Sbjct: 3  KRVQLVLTKDVSKLGRSGDLVDVAPGYARNYLIPQSLA 40

Binds to the 23S rRNA.

Nostoc sp. (strain PCC 7120 / UTEX 2576) (taxid: 103690)

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	90
225455342	217	PREDICTED: 50S ribosomal protein L9 [Vit	0.988	0.410	0.712	3e-30
224115542	219	predicted protein [Populus trichocarpa]	0.988	0.406	0.684	4e-29
224146953	219	predicted protein [Populus trichocarpa]	0.988	0.406	0.684	4e-29
224118314	219	predicted protein [Populus trichocarpa]	0.988	0.406	0.684	5e-29
297792663	221	ribosomal protein L9 family protein [Ara	1.0	0.407	0.631	1e-28
15237342	221	Ribosomal protein L9/RNase H1 [Arabidops	1.0	0.407	0.621	2e-28
449456985	218	PREDICTED: 50S ribosomal protein L9-like	0.988	0.408	0.670	1e-27
255561860	225	structural constituent of ribosome, puta	1.0	0.4	0.622	7e-27
388493818	222	unknown [Lotus japonicus]	1.0	0.405	0.595	8e-25
356558761	222	PREDICTED: 50S ribosomal protein L9-like	1.0	0.405	0.595	2e-24

>gi|225455342|ref|XP_002276719.1| PREDICTED: 50S ribosomal protein L9 [Vitis vinifera] gi|302143920|emb|CBI23025.3| unnamed protein product [Vitis vinifera]

 Score =  135 bits (340), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 67/94 (71%), Positives = 78/94 (82%), Gaps = 5/94 (5%)

Query: 1  MAFTQHGRNALRQITKE----SSDRVLHHPLLFSCQGVKYRRLEVILTTKVDKLGKVGET 56
          MA+ Q+GRN LR I K+     SDRV++ PLL+ CQGV+YR+LEVILTT +DKLGK GET
Sbjct: 1  MAYMQYGRNILRHIVKDVGSQCSDRVVN-PLLYVCQGVRYRKLEVILTTNIDKLGKAGET 59

Query: 57 VKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQRR 90
          VKVAPGYF NHLMPKLLAV NIEKFA+LI EQR+
Sbjct: 60 VKVAPGYFRNHLMPKLLAVPNIEKFAYLISEQRK 93

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224115542|ref|XP_002332160.1| predicted protein [Populus trichocarpa] gi|222875210|gb|EEF12341.1| predicted protein [Populus trichocarpa]

 Score =  131 bits (330), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 65/95 (68%), Positives = 78/95 (82%), Gaps = 6/95 (6%)

Query: 1  MAFTQHGRNALRQITKE-----SSDRVLHHPLLFSCQGVKYRRLEVILTTKVDKLGKVGE 55
          MA  QH RNALR+I  +     SSD  +H PLL++CQGV+Y++LEVILTT ++KLGK G+
Sbjct: 1  MACIQHSRNALRRIVAKETNLKSSDGAIH-PLLYACQGVRYKKLEVILTTSIEKLGKAGQ 59

Query: 56 TVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQRR 90
          TVKVAPG+F NHLMPKLLAV NIEKFAHLIREQR+
Sbjct: 60 TVKVAPGHFRNHLMPKLLAVPNIEKFAHLIREQRK 94

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224146953|ref|XP_002336372.1| predicted protein [Populus trichocarpa] gi|222834835|gb|EEE73284.1| predicted protein [Populus trichocarpa]

 Score =  131 bits (330), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 65/95 (68%), Positives = 79/95 (83%), Gaps = 6/95 (6%)

Query: 1  MAFTQHGRNALRQI-----TKESSDRVLHHPLLFSCQGVKYRRLEVILTTKVDKLGKVGE 55
          MA  QH RNALR+I     + +SSD  +H PLL++CQGV+Y++LEVILTT ++KLGK G+
Sbjct: 1  MACIQHSRNALRRIIAKETSLKSSDGAIH-PLLYACQGVRYKKLEVILTTSIEKLGKAGQ 59

Query: 56 TVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQRR 90
          TVKVAPG+F NHLMPKLLAV NIEKFAHLIREQR+
Sbjct: 60 TVKVAPGHFRNHLMPKLLAVPNIEKFAHLIREQRK 94

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224118314|ref|XP_002317788.1| predicted protein [Populus trichocarpa] gi|222858461|gb|EEE96008.1| predicted protein [Populus trichocarpa]

 Score =  131 bits (330), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 65/95 (68%), Positives = 79/95 (83%), Gaps = 6/95 (6%)

Query: 1  MAFTQHGRNALRQI-----TKESSDRVLHHPLLFSCQGVKYRRLEVILTTKVDKLGKVGE 55
          MA  QH RNALR+I     + +SSD  +H PLL++CQGV+Y++LEVILTT ++KLGK G+
Sbjct: 1  MACIQHSRNALRRIIAKETSLKSSDGAIH-PLLYACQGVRYKKLEVILTTSIEKLGKAGQ 59

Query: 56 TVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQRR 90
          TVKVAPG+F NHLMPKLLAV NIEKFAHLIREQR+
Sbjct: 60 TVKVAPGHFRNHLMPKLLAVPNIEKFAHLIREQRK 94

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297792663|ref|XP_002864216.1| ribosomal protein L9 family protein [Arabidopsis lyrata subsp. lyrata] gi|297310051|gb|EFH40475.1| ribosomal protein L9 family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  130 bits (326), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 60/95 (63%), Positives = 74/95 (77%), Gaps = 5/95 (5%)

Query: 1  MAFTQHGRNALRQITKES-----SDRVLHHPLLFSCQGVKYRRLEVILTTKVDKLGKVGE 55
          MA+    RN +R +         S+  +HHPLLF+CQGV+YR+LEVILTT ++KLGK GE
Sbjct: 1  MAYVGQSRNVIRHVVTRGTAYHKSENAIHHPLLFACQGVRYRKLEVILTTGIEKLGKAGE 60

Query: 56 TVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQRR 90
          TVKVAPGYF NHLMPKLLAV NI+K+A+LIREQR+
Sbjct: 61 TVKVAPGYFRNHLMPKLLAVPNIDKYAYLIREQRK 95

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15237342|ref|NP_200119.1| Ribosomal protein L9/RNase H1 [Arabidopsis thaliana] gi|8809596|dbj|BAA97147.1| unnamed protein product [Arabidopsis thaliana] gi|27754507|gb|AAO22701.1| unknown protein [Arabidopsis thaliana] gi|28393965|gb|AAO42390.1| unknown protein [Arabidopsis thaliana] gi|332008917|gb|AED96300.1| Ribosomal protein L9/RNase H1 [Arabidopsis thaliana]

 Score =  129 bits (324), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 59/95 (62%), Positives = 74/95 (77%), Gaps = 5/95 (5%)

Query: 1  MAFTQHGRNALRQITKESS-----DRVLHHPLLFSCQGVKYRRLEVILTTKVDKLGKVGE 55
          MA+    RN +R +    +     +  +HHPLLF+CQGV+YR+LEVILTT ++KLGK GE
Sbjct: 1  MAYVGQSRNVIRHVVSRGTAYHKYENAIHHPLLFACQGVRYRKLEVILTTGIEKLGKAGE 60

Query: 56 TVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQRR 90
          TVKVAPGYF NHLMPKLLAV NI+K+A+LIREQR+
Sbjct: 61 TVKVAPGYFRNHLMPKLLAVPNIDKYAYLIREQRK 95

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449456985|ref|XP_004146229.1| PREDICTED: 50S ribosomal protein L9-like [Cucumis sativus] gi|449517603|ref|XP_004165835.1| PREDICTED: 50S ribosomal protein L9-like [Cucumis sativus]

 Score =  127 bits (318), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 63/94 (67%), Positives = 78/94 (82%), Gaps = 5/94 (5%)

Query: 1  MAFTQHGRNALRQITKES----SDRVLHHPLLFSCQGVKYRRLEVILTTKVDKLGKVGET 56
          MA  Q+ RNALR I K++    SD+++  PLLFS QGV++R+LEVILTT ++KLGK GET
Sbjct: 1  MACIQYCRNALRNIIKDTKLHPSDQMMQ-PLLFSGQGVRHRKLEVILTTSIEKLGKAGET 59

Query: 57 VKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQRR 90
          VKVAPGYF NHLMPK+LAV NIEK+A+LI+EQRR
Sbjct: 60 VKVAPGYFRNHLMPKILAVPNIEKYAYLIKEQRR 93

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255561860|ref|XP_002521939.1| structural constituent of ribosome, putative [Ricinus communis] gi|223538864|gb|EEF40463.1| structural constituent of ribosome, putative [Ricinus communis]

 Score =  124 bits (311), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 61/98 (62%), Positives = 73/98 (74%), Gaps = 8/98 (8%)

Query: 1  MAFTQHGRNALRQI--------TKESSDRVLHHPLLFSCQGVKYRRLEVILTTKVDKLGK 52
          MA+ Q GRNALR I        +  S      HPL F+ QGV++R+L+VILTT ++KLGK
Sbjct: 1  MAYVQQGRNALRHIIIKEANLRSTSSQSHAAIHPLHFASQGVRFRKLDVILTTNIEKLGK 60

Query: 53 VGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQRR 90
           GETVKVAPGYF NHLMPKLLAV NI+KFA+LIREQR+
Sbjct: 61 AGETVKVAPGYFRNHLMPKLLAVPNIDKFAYLIREQRK 98

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388493818|gb|AFK34975.1| unknown [Lotus japonicus]

 Score =  117 bits (293), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 56/94 (59%), Positives = 75/94 (79%), Gaps = 4/94 (4%)

Query: 1  MAFTQHGRNALRQITK---ESSDRVLHHPLLFSCQGVKY-RRLEVILTTKVDKLGKVGET 56
          M + Q+GR  +RQI +    SS+  + +PLL++ QG++Y R+L+VILTT +DKLGK G+T
Sbjct: 1  MGYLQYGRLGVRQIIRFRDSSSNSAVVNPLLYASQGLRYNRKLQVILTTDIDKLGKAGDT 60

Query: 57 VKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQRR 90
          VKVAPGYF NHLMPKLLAV NI+KFA+L+ EQR+
Sbjct: 61 VKVAPGYFRNHLMPKLLAVPNIDKFAYLLTEQRK 94

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356558761|ref|XP_003547671.1| PREDICTED: 50S ribosomal protein L9-like [Glycine max]

 Score =  115 bits (289), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 56/94 (59%), Positives = 73/94 (77%), Gaps = 4/94 (4%)

Query: 1  MAFTQHGRNALRQITK---ESSDRVLHHPLLFSCQGVKYRR-LEVILTTKVDKLGKVGET 56
          M + Q GR+ +RQI +    S D V+ +PLL++ QG++Y+R L+VILTT +D LGK G+T
Sbjct: 1  MGYLQFGRHGVRQIIRFRDASYDNVVVNPLLYASQGLRYKRKLQVILTTDIDNLGKAGDT 60

Query: 57 VKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQRR 90
          VKVAPGYF NHLMPKLLA  NI+KFAHL+ EQR+
Sbjct: 61 VKVAPGYFRNHLMPKLLAFPNIDKFAHLLNEQRK 94

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	90
TAIR|locus:2168377	221	AT5G53070 [Arabidopsis thalian	1.0	0.407	0.621	3.9e-28
TIGR_CMR|GSU_0668	148	GSU_0668 "ribosomal protein L9	0.577	0.351	0.423	1.6e-06
UNIPROTKB|P66315	152	rplI "50S ribosomal protein L9	0.566	0.335	0.425	2.4e-05
TIGR_CMR|CHY_0039	151	CHY_0039 "ribosomal protein L9	0.566	0.337	0.450	3.9e-05
TIGR_CMR|CPS_0418	150	CPS_0418 "ribosomal protein L9	0.477	0.286	0.446	0.00027
UNIPROTKB|Q9KUY9	149	rplI "50S ribosomal protein L9	0.422	0.255	0.447	0.00097
TIGR_CMR|VC_0369	149	VC_0369 "ribosomal protein L9"	0.422	0.255	0.447	0.00097

TAIR|locus:2168377 AT5G53070 [Arabidopsis thaliana (taxid:3702)]

 Score = 314 (115.6 bits), Expect = 3.9e-28, P = 3.9e-28
 Identities = 59/95 (62%), Positives = 74/95 (77%)

Query:     1 MAFTQHGRNALRQITKESS-----DRVLHHPLLFSCQGVKYRRLEVILTTKVDKLGKVGE 55
             MA+    RN +R +    +     +  +HHPLLF+CQGV+YR+LEVILTT ++KLGK GE
Sbjct:     1 MAYVGQSRNVIRHVVSRGTAYHKYENAIHHPLLFACQGVRYRKLEVILTTGIEKLGKAGE 60

Query:    56 TVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQRR 90
             TVKVAPGYF NHLMPKLLAV NI+K+A+LIREQR+
Sbjct:    61 TVKVAPGYFRNHLMPKLLAVPNIDKYAYLIREQRK 95

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

GO:0005622 "intracellular" evidence=IEA

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=ISM

GO:0042254 "ribosome biogenesis" evidence=ISS

TIGR_CMR|GSU_0668 GSU_0668 "ribosomal protein L9" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 110 (43.8 bits), Expect = 1.6e-06, P = 1.6e-06
 Identities = 22/52 (42%), Positives = 33/52 (63%)

Query:    39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQRR 90
             ++VIL   V+ LG +G+ VKVAPGY  N+L+P+  A+   EK A  +   +R
Sbjct:     1 MKVILKENVENLGHIGDIVKVAPGYARNYLIPRNFAIEATEKNAKALEHAKR 52

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

GO:0006412 "translation" evidence=ISS

GO:0042254 "ribosome biogenesis" evidence=ISS

UNIPROTKB|P66315 rplI "50S ribosomal protein L9" [Mycobacterium tuberculosis (taxid:1773)]

 Score = 99 (39.9 bits), Expect = 2.4e-05, P = 2.4e-05
 Identities = 23/54 (42%), Positives = 34/54 (62%)

Query:    39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVL---NIEKFAHLIREQR 89
             +++ILT  VD LG +G+TV+V  GY  N L+P+ LA++     +K A  IR  R
Sbjct:     1 MKLILTADVDHLGSIGDTVEVKDGYGRNFLLPRGLAIVASRGAQKQADEIRRAR 54

GO:0005618 "cell wall" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

TIGR_CMR|CHY_0039 CHY_0039 "ribosomal protein L9" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 97 (39.2 bits), Expect = 3.9e-05, P = 3.9e-05
 Identities = 23/51 (45%), Positives = 34/51 (66%)

Query:    39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQR 89
             ++VIL T+V KLGK G+ V+VA GY  N+L+ K LAV   E     +++Q+
Sbjct:     1 MKVILLTEVKKLGKKGDVVEVAEGYGRNYLIAKGLAVEATEGKLKELQQQK 51

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

GO:0006412 "translation" evidence=ISS

TIGR_CMR|CPS_0418 CPS_0418 "ribosomal protein L9" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 89 (36.4 bits), Expect = 0.00027, P = 0.00027
 Identities = 21/47 (44%), Positives = 29/47 (61%)

Query:    39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVL----NIEKF 81
             +EVIL  K+ KLG +G+ V V  GY  N+L+P+  AV     N+E F
Sbjct:     1 MEVILLDKIAKLGGLGDKVSVKSGYARNYLLPQGKAVFASEANVEHF 47

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

GO:0006412 "translation" evidence=ISS

GO:0015934 "large ribosomal subunit" evidence=ISS

UNIPROTKB|Q9KUY9 rplI "50S ribosomal protein L9" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)]

 Score = 84 (34.6 bits), Expect = 0.00097, P = 0.00097
 Identities = 17/38 (44%), Positives = 25/38 (65%)

Query:    39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVL 76
             ++VIL  K+  LG +G+TV V  GY  N L+P+  AV+
Sbjct:     1 MQVILLDKIGNLGSLGDTVNVKSGYARNFLIPQGKAVM 38

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

GO:0006412 "translation" evidence=ISS

TIGR_CMR|VC_0369 VC_0369 "ribosomal protein L9" [Vibrio cholerae O1 biovar El Tor (taxid:686)]

 Score = 84 (34.6 bits), Expect = 0.00097, P = 0.00097
 Identities = 17/38 (44%), Positives = 25/38 (65%)

Query:    39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVL 76
             ++VIL  K+  LG +G+TV V  GY  N L+P+  AV+
Sbjct:     1 MQVILLDKIGNLGSLGDTVNVKSGYARNFLIPQGKAVM 38


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.326   0.139   0.405    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0       90        90   0.00091  102 3  11 22  0.41    29
                                                     29  0.39    31


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  7
  No. of states in DFA:  507 (54 KB)
  Total size of DFA:  96 KB (2069 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  9.78u 0.17s 9.95t   Elapsed:  00:00:01
  Total cpu time:  9.78u 0.17s 9.95t   Elapsed:  00:00:01
  Start:  Mon May 20 23:09:09 2013   End:  Mon May 20 23:09:10 2013

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

GO:0006412 "translation" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00037239001 SubName- Full=Chromosome chr16 scaffold_86, whole genome shotgun sequence; (217 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	90
pfam01281	48	pfam01281, Ribosomal_L9_N, Ribosomal protein L9, N	7e-14
PRK00137	147	PRK00137, rplI, 50S ribosomal protein L9; Reviewed	5e-11
COG0359	148	COG0359, RplI, Ribosomal protein L9 [Translation,	3e-09
TIGR00158	148	TIGR00158, L9, ribosomal protein L9	3e-08
CHL00160	153	CHL00160, rpl9, ribosomal protein L9; Provisional	2e-06

>gnl|CDD|201708 pfam01281, Ribosomal_L9_N, Ribosomal protein L9, N-terminal domain

 Score = 59.4 bits (145), Expect = 7e-14
 Identities = 21/48 (43%), Positives = 30/48 (62%), Gaps = 4/48 (8%)

Query: 39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVL----NIEKFA 82
          ++VIL   V+ LGK G+ V+V PGY  N L+PK LAV     N+++  
Sbjct: 1  MKVILLEDVEGLGKKGDIVEVKPGYARNFLLPKGLAVYATPENLKELE 48

Length = 48

>gnl|CDD|234659 PRK00137, rplI, 50S ribosomal protein L9; Reviewed

 Score = 54.7 bits (133), Expect = 5e-11
 Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 4/55 (7%)

Query: 40 EVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVL----NIEKFAHLIREQRR 90
          +VIL   V  LGK G+ V+V  GY  N L+P+  AV     N+++      E   
Sbjct: 2  KVILLEDVKNLGKKGDVVEVKDGYARNFLIPQGKAVRATKGNLKQLEARRAELEA 56

Length = 147

>gnl|CDD|223436 COG0359, RplI, Ribosomal protein L9 [Translation, ribosomal structure and biogenesis]

 Score = 50.3 bits (121), Expect = 3e-09
 Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 4/55 (7%)

Query: 40 EVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVL----NIEKFAHLIREQRR 90
          +VIL   V  LGK G+ V+V  GY  N L+PK LAV     N++       +  +
Sbjct: 2  KVILLEDVKGLGKKGDIVEVKDGYARNFLIPKGLAVPATKGNLKLLEARRAKLEK 56

Length = 148

>gnl|CDD|129262 TIGR00158, L9, ribosomal protein L9

 Score = 47.4 bits (113), Expect = 3e-08
 Identities = 26/56 (46%), Positives = 31/56 (55%), Gaps = 9/56 (16%)

Query: 39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVL----NIEKFAHLIREQRR 90
          ++VIL   V  LGK G+ V+V  GY  N L+PK LAV     NIE F     E RR
Sbjct: 1  MKVILLEDVANLGKRGDVVEVKDGYARNFLIPKGLAVPATKKNIEFF-----EARR 51

Ribosomal protein L9 appears to be universal in, but restricted to, eubacteria and chloroplast [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 148

>gnl|CDD|214378 CHL00160, rpl9, ribosomal protein L9; Provisional

 Score = 42.5 bits (100), Expect = 2e-06
 Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 6/59 (10%)

Query: 37 RRLEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLA------VLNIEKFAHLIREQR 89
          ++++VIL   + KLGK G  +KV  GY  N+L+P  +A       L  +K    I + +
Sbjct: 4  KKIQVILKENIQKLGKSGTVIKVKSGYARNYLIPNKMAKVATQGSLKQQKMYQKILDLK 62

Length = 153

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	90
PF01281	48	Ribosomal_L9_N: Ribosomal protein L9, N-terminal d	99.91
CHL00160	153	rpl9 ribosomal protein L9; Provisional	99.9
TIGR00158	148	L9 ribosomal protein L9. Ribosomal protein L9 appe	99.89
PRK00137	147	rplI 50S ribosomal protein L9; Reviewed	99.89
COG0359	148	RplI Ribosomal protein L9 [Translation, ribosomal	99.84
KOG4607	222	consensus Mitochondrial ribosomal protein L9 [Tran	99.72
PRK14538	838	putative bifunctional signaling protein/50S riboso	99.68

>PF01281 Ribosomal_L9_N: Ribosomal protein L9, N-terminal domain; InterPro: IPR020070 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.91  E-value=1.4e-25  Score=137.04  Aligned_cols=48  Identities=40%  Similarity=0.607  Sum_probs=44.8

Q ss_pred             eEEEEeccccccCCCCcEEEecCcceecccccccccccchHHHHHHHH
Q 043613           39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIR   86 (90)
Q Consensus        39 m~VILl~dV~gLGk~GdvV~Vk~GYARN~LiP~glA~~At~~~~~~l~   86 (90)
                      |+|||++||||+|++||+|+|++|||||||+|+++|+|||++++++++
T Consensus         1 m~ViL~~dv~~lG~~Gdiv~V~~Gy~RN~L~p~~~A~~at~~~~~~~e   48 (48)
T PF01281_consen    1 MKVILLKDVPGLGKKGDIVEVKPGYARNFLIPQGLAVYATPENLKQLE   48 (48)
T ss_dssp             -EEEESSCCTTSBSTTEEEE-SHHHHHHTTTTTTSEEECSHHHHHHHH
T ss_pred             CEEEEcccccccCCCCCEEEEccceeeehccCCCceeeCCHHHHHhcC
Confidence            799999999999999999999999999999999999999999999874

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 [, ]. Ribosomal protein L9 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L9 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins grouped on the basis of sequence similarities [, ]. The crystal structure of Bacillus stearothermophilus L9 shows the 149-residue protein comprises two globular domains connected by a rigid linker []. Each domain contains an rRNA binding site, and the protein functions as a structural protein in the large subunit of the ribosome. The C-terminal domain consists of two loops, an alpha-helix and a three-stranded mixed parallel, anti-parallel beta-sheet packed against the central alpha-helix. The long central alpha-helix is exposed to solvent in the middle and participates in the hydrophobic cores of the two domains at both ends. ; PDB: 3D5B_I 3PYV_H 3F1H_I 3PYR_H 3MRZ_H 1VSP_G 3MS1_H 1VSA_G 3PYT_H 2WH4_I ....

>CHL00160 rpl9 ribosomal protein L9; Provisional

Probab=99.90  E-value=1.6e-24  Score=156.77  Aligned_cols=53  Identities=30%  Similarity=0.529  Sum_probs=50.1

Q ss_pred             eeeEEEEeccccccCCCCcEEEecCcceecccccccccccchHHHHHHHHHhh
Q 043613           37 RRLEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQR   89 (90)
Q Consensus        37 ~km~VILl~dV~gLGk~GdvV~Vk~GYARN~LiP~glA~~At~~~~~~l~~~~   89 (90)
                      ++|+|||++||++||+.||+|+|+||||||||||+|+|++||+.++++++..+
T Consensus         4 kkmkVIL~~dV~~LGk~Gdiv~Vk~GYaRNyLiP~glA~~AT~~n~~~~e~~~   56 (153)
T CHL00160          4 KKIQVILKENIQKLGKSGTVIKVKSGYARNYLIPNKMAKVATQGSLKQQKMYQ   56 (153)
T ss_pred             ceEEEEEcccccccCCCCCEEEEcCchHhhhhcccCchhhCCHHHHHHHHHHH
Confidence            57999999999999999999999999999999999999999999999877654

>TIGR00158 L9 ribosomal protein L9

Probab=99.89  E-value=4e-24  Score=153.43  Aligned_cols=51  Identities=41%  Similarity=0.607  Sum_probs=48.7

Q ss_pred             eEEEEeccccccCCCCcEEEecCcceecccccccccccchHHHHHHHHHhh
Q 043613           39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQR   89 (90)
Q Consensus        39 m~VILl~dV~gLGk~GdvV~Vk~GYARN~LiP~glA~~At~~~~~~l~~~~   89 (90)
                      |+|||++||++||++||+|+|+||||||||||+|+|++||++++++++.++
T Consensus         1 MkVIL~~dV~~lGk~GdiV~Vk~GYaRNyLiP~g~A~~aT~~nl~~~e~~~   51 (148)
T TIGR00158         1 MKVILLEDVANLGKRGDVVEVKDGYARNFLIPKGLAVPATKKNIEFFEARR   51 (148)
T ss_pred             CeEEEcccccccCCCCCEEEEcccchhhhhcccCchhhCCHHHHHHHHHHH
Confidence            899999999999999999999999999999999999999999999987654

Ribosomal protein L9 appears to be universal in, but restricted to, eubacteria and chloroplast.

>PRK00137 rplI 50S ribosomal protein L9; Reviewed

Probab=99.89  E-value=5e-24  Score=152.19  Aligned_cols=51  Identities=35%  Similarity=0.523  Sum_probs=48.7

Q ss_pred             eEEEEeccccccCCCCcEEEecCcceecccccccccccchHHHHHHHHHhh
Q 043613           39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQR   89 (90)
Q Consensus        39 m~VILl~dV~gLGk~GdvV~Vk~GYARN~LiP~glA~~At~~~~~~l~~~~   89 (90)
                      |+|||++||+|||++||+|+|+||||||||||+|+|+|||++++++++..+
T Consensus         1 mkVIL~~dv~~lGk~Gdiv~Vk~GYaRNyLiP~~lA~~aT~~~~~~~~~~~   51 (147)
T PRK00137          1 MKVILLEDVKNLGKKGDVVEVKDGYARNFLIPQGKAVRATKGNLKQLEARR   51 (147)
T ss_pred             CeEEEcccccccCCCCCEEEEcCcchhhhhccCCceeeCCHHHHHHHHHHH
Confidence            899999999999999999999999999999999999999999999987654

>COG0359 RplI Ribosomal protein L9 [Translation, ribosomal structure and biogenesis]

Probab=99.84  E-value=9.4e-22  Score=142.96  Aligned_cols=51  Identities=41%  Similarity=0.593  Sum_probs=48.9

Q ss_pred             eEEEEeccccccCCCCcEEEecCcceecccccccccccchHHHHHHHHHhh
Q 043613           39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQR   89 (90)
Q Consensus        39 m~VILl~dV~gLGk~GdvV~Vk~GYARN~LiP~glA~~At~~~~~~l~~~~   89 (90)
                      |+|||++||++||+.||+|+|++|||||||||+|+|+.||+.+++.+..++
T Consensus         1 MkVILl~dV~~lGk~Gdiv~VkdGYarNfLiPkglAv~At~~n~~~~e~~r   51 (148)
T COG0359           1 MKVILLEDVKGLGKKGDIVEVKDGYARNFLIPKGLAVPATKGNLKLLEARR   51 (148)
T ss_pred             CeEEEecchhhcCCCCCEEEecchhhhhhhccccchhhCCHHHHHHHHHHH
Confidence            899999999999999999999999999999999999999999999887754

>KOG4607 consensus Mitochondrial ribosomal protein L9 [Translation, ribosomal structure and biogenesis]

Probab=99.72  E-value=2.5e-18  Score=132.28  Aligned_cols=59  Identities=46%  Similarity=0.548  Sum_probs=55.6

Q ss_pred             hheeeecceeeeeeEEEEeccccccCCCCcEEEecCcceecccccccccccchHHHHHH
Q 043613           26 PLLFSCQGVKYRRLEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHL   84 (90)
Q Consensus        26 p~~~~~q~~r~~km~VILl~dV~gLGk~GdvV~Vk~GYARN~LiP~glA~~At~~~~~~   84 (90)
                      +++.-+|++.+..++|||++||+|||+.||+|+|++||+||+|+|+|+|+|+++.+.++
T Consensus        36 ~lv~~~~~k~k~~levIL~~~Ve~lG~qGdvVsVk~g~~RN~Llp~glAvy~tp~~~~~   94 (222)
T KOG4607|consen   36 ELVEFTQKKPKPNLEVILKTDVEKLGKQGDVVSVKRGYFRNFLLPKGLAVYNTPLNLKK   94 (222)
T ss_pred             hHhHhhhccCCcceeeeeehhhhhhcccCcEEEeecchhhhhcccccccccCChhhHHH
Confidence            78888999999999999999999999999999999999999999999999999999444

>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional

Probab=99.68  E-value=5.4e-18  Score=147.26  Aligned_cols=51  Identities=31%  Similarity=0.440  Sum_probs=48.5

Q ss_pred             eeEEEEeccccccCCCCcEEEecCcceecccccccccccchHHHHHHHHHhh
Q 043613           38 RLEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQR   89 (90)
Q Consensus        38 km~VILl~dV~gLGk~GdvV~Vk~GYARN~LiP~glA~~At~~~~~~l~~~~   89 (90)
                      .|+|||++||++||++||+|+|+|||| |||||+|+|++||++++++++.++
T Consensus       688 ~MkVIL~~dv~~lGk~Gdvv~Vk~GYa-NfLiP~~~A~~aT~~nlk~~e~~~  738 (838)
T PRK14538        688 NMEIILLTDIKNKGKKHEIIKVNNGYG-NFLIQNKKALLADKENLAKIKKKK  738 (838)
T ss_pred             hhhHHHHHHHHhcCCCCCEEEECCCch-hhhccCCchhhcCHHHHHHHHHHH
Confidence            599999999999999999999999999 999999999999999999977664

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	90
1vsa_G	148	Crystal Structure Of A 70s Ribosome-Trna Complex Re		3e-05
2hgj_K	148	Crystal Structure Of The 70s Thermus Thermophilus R		3e-05
2v47_I	148	Structure Of The Ribosome Recycling Factor Bound To		3e-05
3uxq_I	148	The Structure Of Thermorubin In Complex With The 70		3e-05
3tve_K	146	Crystal Structure Analysis Of Ribosomal Decoding. T		4e-05
3pyo_H	145	Crystal Structure Of A Complex Containing Domain 3		4e-05
3fin_I	146	T. Thermophilus 70s Ribosome In Complex With Mrna,		4e-05

>pdb|1VSA|G Chain G, Crystal Structure Of A 70s Ribosome-Trna Complex Reveals Functional Interactions And Rearrangements. This File, 1vsa, Contains The 50s Ribosome Subunit. 30s Ribosome Subunit Is In The File 2ow8 Length = 148

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 28/41 (68%)
Query: 39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIE 79
          ++VIL   ++ LG VG+ V V PGY  N+L+P+ LAVL  E
Sbjct: 1  MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATE 41

>pdb|2HGJ|K Chain K, Crystal Structure Of The 70s Thermus Thermophilus Ribosome Showing How The 16s 3'-End Mimicks Mrna E And P Codons. This Entry 2hgj Contains 50s Ribosomal Subunit. The 30s Ribosomal Subunit Can Be Found In Pdb Entry 2hgi. Length = 148

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 28/41 (68%)
Query: 39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIE 79
          ++VIL   ++ LG VG+ V V PGY  N+L+P+ LAVL  E
Sbjct: 1  MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATE 41

>pdb|2V47|I Chain I, Structure Of The Ribosome Recycling Factor Bound To The Thermus Thermophilus 70s Ribosome With Mrna, Asl-Phe And Trna-Fmet (Part 2 Of 4). This File Contains The 50s Subunit For Molecule 1. Length = 148

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 28/41 (68%)
Query: 39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIE 79
          ++VIL   ++ LG VG+ V V PGY  N+L+P+ LAVL  E
Sbjct: 1  MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATE 41

>pdb|3UXQ|I Chain I, The Structure Of Thermorubin In Complex With The 70s Ribosome From Thermus Thermophilus. This File Contains The 50s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes. Length = 148

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 28/41 (68%)
Query: 39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIE 79
          ++VIL   ++ LG VG+ V V PGY  N+L+P+ LAVL  E
Sbjct: 1  MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATE 41

>pdb|3TVE|K Chain K, Crystal Structure Analysis Of Ribosomal Decoding. This Entry Contains The 50s Ribosomal Subunit Of The First 70s Molecule In The Asymmetric Unit For The Cognate Trna-Leu Complex Length = 146

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 28/41 (68%)
Query: 39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIE 79
          ++VIL   ++ LG VG+ V V PGY  N+L+P+ LAVL  E
Sbjct: 1  MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATE 41

>pdb|3PYO|H Chain H, Crystal Structure Of A Complex Containing Domain 3 From The Psiv Igr Ires Rna Bound To The 70s Ribosome. This File Contains The 50s Subunit Of The First 70s Ribosome. Length = 145

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 28/41 (68%)
Query: 39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIE 79
          ++VIL   ++ LG VG+ V V PGY  N+L+P+ LAVL  E
Sbjct: 1  MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATE 41

>pdb|3FIN|I Chain I, T. Thermophilus 70s Ribosome In Complex With Mrna, Trnas And Ef- Tu.Gdp.Kirromycin Ternary Complex, Fitted To A 6.4 A Cryo-Em Map. This File Contains The 50s Subunit Length = 146

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 28/41 (68%)
Query: 39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIE 79
          ++VIL   ++ LG VG+ V V PGY  N+L+P+ LAVL  E
Sbjct: 1  MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATE 41

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	90
3bbo_J	197	Ribosomal protein L9; large ribosomal subunit, spi	6e-12
3r8s_H	149	50S ribosomal protein L9; protein biosynthesis, RN	2e-11
1div_A	149	Ribosomal protein L9; rRNA-binding; 2.60A {Geobaci	2e-11
3v2d_I	148	50S ribosomal protein L9; ribosome associated inhi	3e-11
2hba_A	52	BL17, 50S ribosomal protein L9; NTL9, K12M, RNA bi	5e-11
1nkw_F	146	50S ribosomal protein L9; ribosome, large subunit,	2e-09

>3bbo_J Ribosomal protein L9; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1 Length = 197

 Score = 57.4 bits (139), Expect = 6e-12
 Identities = 20/91 (21%), Positives = 31/91 (34%), Gaps = 7/91 (7%)

Query: 4   TQHGRNALRQITKESSDRVLHHPLLFSCQGVKYRRLEVILTTKVDKLGKVGETVKVAPGY 63
           +        +  K S  R          Q    +  +VIL   V  LGK G+ + V  G+
Sbjct: 18  SHSFNGGANETLKVSERRF---NFEVVSQKKAKKLRKVILKEDVTDLGKQGQLLDVKAGF 74

Query: 64  FHNHLMPKLLAVL----NIEKFAHLIREQRR 90
           F N L+P   A L     +++          
Sbjct: 75  FRNFLLPTGKAQLMTPLLLKELKMEDERIEA 105

>3r8s_H 50S ribosomal protein L9; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_F 1p86_F 1vs8_H 1vs6_H 2aw4_H 2awb_H 2gya_F 2gyc_F 1vt2_H 2i2v_H 2j28_H 2i2t_H* 2qao_H* 2qba_H* 2qbc_H* 2qbe_H 2qbg_H 2qbi_H* 2qbk_H* 2qov_H ... Length = 149

 Score = 55.3 bits (134), Expect = 2e-11
 Identities = 22/55 (40%), Positives = 27/55 (49%), Gaps = 4/55 (7%)

Query: 40 EVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVL----NIEKFAHLIREQRR 90
          +VIL  KV  LG +G+ V V  GY  N L+P+  AV     NIE F     E   
Sbjct: 2  QVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEA 56

>1div_A Ribosomal protein L9; rRNA-binding; 2.60A {Geobacillus stearothermophilus} SCOP: d.99.1.1 d.100.1.1 PDB: 1giy_K 1yl3_K 2b66_I 2b9n_I 2b9p_I 487d_K Length = 149

 Score = 55.3 bits (134), Expect = 2e-11
 Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 4/55 (7%)

Query: 40 EVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVL----NIEKFAHLIREQRR 90
          +VI    V   GK GE   VA GY +N L  + LA+     N++      ++++R
Sbjct: 2  KVIFLKDVKGKGKKGEIKNVADGYANNFLFKQGLAIEATPANLKALEAQKQKEQR 56

>3v2d_I 50S ribosomal protein L9; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 2j03_I 2jl6_I 2jl8_I 2v47_I 2v49_I 2wdi_I 2wdj_I 2wdl_I 2wdn_I 2wh2_I 2x9s_I 2x9u_I 2xg0_I 2xg2_I 3hux_I 3huz_I 3i8f_K 3i8i_K 3i9c_K 3i9e_K ... Length = 148

 Score = 54.9 bits (133), Expect = 3e-11
 Identities = 23/55 (41%), Positives = 33/55 (60%), Gaps = 4/55 (7%)

Query: 40 EVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVL----NIEKFAHLIREQRR 90
          +VIL   ++ LG VG+ V V PGY  N+L+P+ LAVL    N++     IR Q +
Sbjct: 2  KVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATESNLKALEARIRAQAK 56

>2hba_A BL17, 50S ribosomal protein L9; NTL9, K12M, RNA binding protein; 1.25A {Geobacillus stearothermophilus} SCOP: d.100.1.1 PDB: 1cqu_A 2hbb_A 2hvf_A Length = 52

 Score = 51.9 bits (125), Expect = 5e-11
 Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 4/46 (8%)

Query: 40 EVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVL----NIEKF 81
          +VI    V  +GK GE   VA GY +N L  + LA+     N++  
Sbjct: 2  KVIFLKDVKGMGKKGEIKNVADGYANNFLFKQGLAIEATPANLKAL 47

>1nkw_F 50S ribosomal protein L9; ribosome, large subunit, X- RAY structure, peptidyl-transferase, peptide bond formation; 3.10A {Deinococcus radiodurans} SCOP: i.1.1.2 PDB: 1nwx_F* 1nwy_F* 1sm1_F* 1xbp_F* 1pnu_F 1pny_F 1vor_I 1vou_I 1vow_I 1voy_I 1vp0_I Length = 146

 Score = 49.9 bits (120), Expect = 2e-09
 Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 5/55 (9%)

Query: 40 EVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVL----NIEKFAHLIREQRR 90
          +VIL     +LGK GE V V  GY  N L+P+ LAV     N++     +R   +
Sbjct: 2  QVILLEPS-RLGKTGEVVSVKDGYARNWLIPQGLAVSATRTNMKTLEAQLRSIEK 55

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	90
2hba_A	52	BL17, 50S ribosomal protein L9; NTL9, K12M, RNA bi	99.94
3bbo_J	197	Ribosomal protein L9; large ribosomal subunit, spi	99.91
1div_A	149	Ribosomal protein L9; rRNA-binding; 2.60A {Geobaci	99.89
3v2d_I	148	50S ribosomal protein L9; ribosome associated inhi	99.89
3r8s_H	149	50S ribosomal protein L9; protein biosynthesis, RN	99.88
1nkw_F	146	50S ribosomal protein L9; ribosome, large subunit,	99.88

>2hba_A BL17, 50S ribosomal protein L9; NTL9, K12M, RNA binding protein; 1.25A {Geobacillus stearothermophilus} SCOP: d.100.1.1 PDB: 1cqu_A 2hbb_A 2hvf_A

Probab=99.94  E-value=7.9e-28  Score=148.36  Aligned_cols=52  Identities=31%  Similarity=0.446  Sum_probs=50.3

Q ss_pred             eEEEEeccccccCCCCcEEEecCcceecccccccccccchHHHHHHHHHhhC
Q 043613           39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQRR   90 (90)
Q Consensus        39 m~VILl~dV~gLGk~GdvV~Vk~GYARN~LiP~glA~~At~~~~~~l~~~~~   90 (90)
                      |+|||++||++||++||+|+|++|||||||||+|+|++||++++++++.+++
T Consensus         1 MkVIL~~dV~~lG~~Gdvv~V~~GYaRN~LiP~g~A~~AT~~n~~~~~~~~~   52 (52)
T 2hba_A            1 MKVIFLKDVKGMGKKGEIKNVADGYANNFLFKQGLAIEATPANLKALEAQKQ   52 (52)
T ss_dssp             CEEEESSCBTTTBCTTCEEECCHHHHHHTTTTTTSEEECCHHHHHHHHHHHC
T ss_pred             CEEEEcccccccCcCCCEEEEcCCceehhhccCCceeeCCHHHHHHHHHhhC
Confidence            8999999999999999999999999999999999999999999999998864

>3bbo_J Ribosomal protein L9; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1

Probab=99.91  E-value=2.5e-26  Score=171.15  Aligned_cols=63  Identities=27%  Similarity=0.372  Sum_probs=49.3

Q ss_pred             heeeecceeeeeeEEEEeccccccCCCCcEEEecCcceecccccccccccchHHHHHHHHHhh
Q 043613           27 LLFSCQGVKYRRLEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQR   89 (90)
Q Consensus        27 ~~~~~q~~r~~km~VILl~dV~gLGk~GdvV~Vk~GYARN~LiP~glA~~At~~~~~~l~~~~   89 (90)
                      +++.+++.+.++|+|||++||+|||++||+|+|++|||||||||+|+|++||++++++++.++
T Consensus        38 lvv~~~k~~~k~MkVILledV~~LGk~GdvV~Vk~GYARNfLiP~glAv~AT~~nlk~~e~~~  100 (197)
T 3bbo_J           38 FEVVSQKKAKKLRKVILKEDVTDLGKQGQLLDVKAGFFRNFLLPTGKAQLMTPLLLKELKMED  100 (197)
T ss_dssp             ------------CCCCCCSCSSSSCSSCCCSCCCSSSCCCCCTTTTCCCCCCHHHHHHHHTTT
T ss_pred             EEEEeccccCCceEEEEcccccccCCCCCEEEEcCcceeehcccCCceecCCHHHHHHHHHhH
Confidence            777999999999999999999999999999999999999999999999999999999987764

>1div_A Ribosomal protein L9; rRNA-binding; 2.60A {Geobacillus stearothermophilus} SCOP: d.99.1.1 d.100.1.1 PDB: 1giy_K 1yl3_K 2b66_I 2b9n_I 2b9p_I 487d_K

Probab=99.89  E-value=1.5e-24  Score=155.02  Aligned_cols=51  Identities=31%  Similarity=0.413  Sum_probs=49.0

Q ss_pred             eEEEEeccccccCCCCcEEEecCcceecccccccccccchHHHHHHHHHhh
Q 043613           39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQR   89 (90)
Q Consensus        39 m~VILl~dV~gLGk~GdvV~Vk~GYARN~LiP~glA~~At~~~~~~l~~~~   89 (90)
                      |+|||++||+|||++||+|+|+||||||||||+|+|++||++++++++.++
T Consensus         1 MkVILl~dV~~LG~~GdvV~Vk~GYaRNfLiP~glA~~AT~~n~~~~e~~~   51 (149)
T 1div_A            1 MKVIFLKDVKGKGKKGEIKNVADGYANNFLFKQGLAIEATPANLKALEAQK   51 (149)
T ss_dssp             CEEEECSBSSSBGGGTEEEECCTTHHHHTTTTTTSEEECCHHHHHHHHHHH
T ss_pred             CEEEEcccccccCCCCCEEEEcCCceeeeeccCCceecCCHHHHHHHHHHH
Confidence            899999999999999999999999999999999999999999999987765

>3v2d_I 50S ribosomal protein L9; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 2j03_I 2jl6_I 2jl8_I 2v47_I 2v49_I 2wdi_I 2wdj_I 2wdl_I 2wdn_I 2wh2_I 2x9s_I 2x9u_I 2xg0_I 2xg2_I 3hux_I 3huz_I 3i8f_K 3i8i_K 3i9c_K 3i9e_K ...

Probab=99.89  E-value=1.5e-24  Score=154.89  Aligned_cols=51  Identities=39%  Similarity=0.634  Sum_probs=49.1

Q ss_pred             eEEEEeccccccCCCCcEEEecCcceecccccccccccchHHHHHHHHHhh
Q 043613           39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQR   89 (90)
Q Consensus        39 m~VILl~dV~gLGk~GdvV~Vk~GYARN~LiP~glA~~At~~~~~~l~~~~   89 (90)
                      |+|||++||+|||+.||+|+|+||||||||||+|+|++||+.++++++.++
T Consensus         1 MkVILl~dV~~LG~~GdvV~Vk~GYaRNfLiP~g~A~~AT~~n~k~~e~~~   51 (148)
T 3v2d_I            1 MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATESNLKALEARI   51 (148)
T ss_dssp             CEEEESSCBTTTBSTTCEEECCHHHHHHTTGGGTSEEECCHHHHHHHHHHH
T ss_pred             CeEEEccccccCCCCccEEEEcCCceehhhcccCchhhcCHHHHHHHHHHH
Confidence            899999999999999999999999999999999999999999999988764

>3r8s_H 50S ribosomal protein L9; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_F 1p86_F 1vs8_H 1vs6_H 2aw4_H 2awb_H 2gya_F 2gyc_F 1vt2_H 2i2v_H 2j28_H 2i2t_H* 2qao_H* 2qba_H* 2qbc_H* 2qbe_H 2qbg_H 2qbi_H* 2qbk_H* 2qov_H ...

Probab=99.88  E-value=1.5e-24  Score=154.92  Aligned_cols=51  Identities=37%  Similarity=0.580  Sum_probs=48.8

Q ss_pred             eEEEEeccccccCCCCcEEEecCcceecccccccccccchHHHHHHHHHhh
Q 043613           39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQR   89 (90)
Q Consensus        39 m~VILl~dV~gLGk~GdvV~Vk~GYARN~LiP~glA~~At~~~~~~l~~~~   89 (90)
                      |+|||++||++||+.||+|+|+||||||||||+|+|++||+.++++++.++
T Consensus         1 MkVIL~~dV~~LG~~GdvV~Vk~GYaRNfLiP~glA~~AT~~n~k~~e~~~   51 (149)
T 3r8s_H            1 MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARR   51 (149)
T ss_dssp             CCCEESSCCTTTCCSSCBCCCCHHHHTTTTSSSSSEECCCSHHHHHHHHHH
T ss_pred             CeEEEecccccCCCCCCEEEEcCcceehhhccCCceeeCCHHHHHHHHHHH
Confidence            899999999999999999999999999999999999999999999887765

>1nkw_F 50S ribosomal protein L9; ribosome, large subunit, X- RAY structure, peptidyl-transferase, peptide bond formation; 3.10A {Deinococcus radiodurans} SCOP: i.1.1.2 PDB: 1nwx_F* 1nwy_F* 1sm1_F* 1xbp_F* 1pnu_F 1pny_F 1vor_I 1vou_I 1vow_I 1voy_I 1vp0_I

Probab=99.88  E-value=1.4e-23  Score=149.51  Aligned_cols=50  Identities=38%  Similarity=0.536  Sum_probs=48.0

Q ss_pred             eEEEEeccccccCCCCcEEEecCcceecccccccccccchHHHHHHHHHhh
Q 043613           39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQR   89 (90)
Q Consensus        39 m~VILl~dV~gLGk~GdvV~Vk~GYARN~LiP~glA~~At~~~~~~l~~~~   89 (90)
                      |+|||++| +|||++||+|+|+||||||||||+|+|++||++++++++.++
T Consensus         1 MkVIL~~d-~~LG~~GdvV~Vk~GYaRNfLiP~glA~~AT~~n~~~~e~~~   50 (146)
T 1nkw_F            1 MQVILLEP-SRLGKTGEVVSVKDGYARNWLIPQGLAVSATRTNMKTLEAQL   50 (146)
T ss_pred             CeEEEeec-CCCCCCCCEEEEcCcceehhcccCCceecCCHHHHHHHHHHH
Confidence            89999999 999999999999999999999999999999999999988765

---

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	90
d2j01i2	55	d.100.1.1 (I:1-55) Ribosomal protein L9 N-domain {	4e-13
d2hbaa1	52	d.100.1.1 (A:1-52) Ribosomal protein L9 N-domain {	1e-12
d2gycf2	58	d.100.1.1 (F:1-58) Ribosomal protein L9 N-domain {	9e-12

>d2j01i2 d.100.1.1 (I:1-55) Ribosomal protein L9 N-domain {Thermus thermophilus [TaxId: 274]} Length = 55

class: Alpha and beta proteins (a+b)
fold: MbtH/L9 domain-like
superfamily: L9 N-domain-like
family: Ribosomal protein L9 N-domain
domain: Ribosomal protein L9 N-domain
species: Thermus thermophilus [TaxId: 274]

 Score = 56.1 bits (136), Expect = 4e-13
 Identities = 23/53 (43%), Positives = 32/53 (60%), Gaps = 4/53 (7%)

Query: 40 EVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVL----NIEKFAHLIREQ 88
          +VIL   ++ LG VG+ V V PGY  N+L+P+ LAVL    N++     IR Q
Sbjct: 2  KVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATESNLKALEARIRAQ 54

>d2hbaa1 d.100.1.1 (A:1-52) Ribosomal protein L9 N-domain {Bacillus stearothermophilus [TaxId: 1422]} Length = 52

class: Alpha and beta proteins (a+b)
fold: MbtH/L9 domain-like
superfamily: L9 N-domain-like
family: Ribosomal protein L9 N-domain
domain: Ribosomal protein L9 N-domain
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 54.6 bits (132), Expect = 1e-12
 Identities = 16/51 (31%), Positives = 24/51 (47%)

Query: 40 EVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQRR 90
          +VI    V  +GK GE   VA GY +N L  + LA+         +  Q++
Sbjct: 2  KVIFLKDVKGMGKKGEIKNVADGYANNFLFKQGLAIEATPANLKALEAQKQ 52

>d2gycf2 d.100.1.1 (F:1-58) Ribosomal protein L9 N-domain {Escherichia coli [TaxId: 562]} Length = 58

class: Alpha and beta proteins (a+b)
fold: MbtH/L9 domain-like
superfamily: L9 N-domain-like
family: Ribosomal protein L9 N-domain
domain: Ribosomal protein L9 N-domain
species: Escherichia coli [TaxId: 562]

 Score = 52.7 bits (127), Expect = 9e-12
 Identities = 19/52 (36%), Positives = 27/52 (51%)

Query: 39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQRR 90
          ++VIL  KV  LG +G+ V V  GY  N L+P+  AV   +K       +R 
Sbjct: 1  MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRA 52

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	90
d2hbaa1	52	Ribosomal protein L9 N-domain {Bacillus stearother	99.94
d2j01i2	55	Ribosomal protein L9 N-domain {Thermus thermophilu	99.93
d2gycf2	58	Ribosomal protein L9 N-domain {Escherichia coli [T	99.93

>d2hbaa1 d.100.1.1 (A:1-52) Ribosomal protein L9 N-domain {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a+b)
fold: MbtH/L9 domain-like
superfamily: L9 N-domain-like
family: Ribosomal protein L9 N-domain
domain: Ribosomal protein L9 N-domain
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=99.94  E-value=4.3e-28  Score=148.08  Aligned_cols=52  Identities=31%  Similarity=0.446  Sum_probs=50.6

Q ss_pred             eEEEEeccccccCCCCcEEEecCcceecccccccccccchHHHHHHHHHhhC
Q 043613           39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQRR   90 (90)
Q Consensus        39 m~VILl~dV~gLGk~GdvV~Vk~GYARN~LiP~glA~~At~~~~~~l~~~~~   90 (90)
                      |+|||++||++||++||+|+|++|||||||||+|+|++||++++++++.+++
T Consensus         1 MkVIL~~dv~~lG~~GdiV~Vk~GyarN~LiP~g~A~~at~~n~~~~~~~k~   52 (52)
T d2hbaa1           1 MKVIFLKDVKGMGKKGEIKNVADGYANNFLFKQGLAIEATPANLKALEAQKQ   52 (52)
T ss_dssp             CEEEESSCBTTTBCTTCEEECCHHHHHHTTTTTTSEEECCHHHHHHHHHHHC
T ss_pred             CEEEEcccccccCCCCCEEEEcccchhHhhccCCchhhCCHHHHHHHHHhhC
Confidence            8999999999999999999999999999999999999999999999998875

>d2j01i2 d.100.1.1 (I:1-55) Ribosomal protein L9 N-domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: MbtH/L9 domain-like
superfamily: L9 N-domain-like
family: Ribosomal protein L9 N-domain
domain: Ribosomal protein L9 N-domain
species: Thermus thermophilus [TaxId: 274]

Probab=99.93  E-value=7.7e-28  Score=148.44  Aligned_cols=51  Identities=39%  Similarity=0.634  Sum_probs=48.5

Q ss_pred             eEEEEeccccccCCCCcEEEecCcceecccccccccccchHHHHHHHHHhh
Q 043613           39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQR   89 (90)
Q Consensus        39 m~VILl~dV~gLGk~GdvV~Vk~GYARN~LiP~glA~~At~~~~~~l~~~~   89 (90)
                      |+|||++||++||++||||+|++|||||||||+|+|++||++++++++.++
T Consensus         1 MkVILl~dV~~lG~~Gdiv~Vk~GyaRN~LiP~~~A~~at~~nl~~~~~~~   51 (55)
T d2j01i2           1 MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATESNLKALEARI   51 (55)
T ss_dssp             CEEEECSCCSSSCSTTCEEECCHHHHHHTTTTTTSEEECCHHHHHHHHHHH
T ss_pred             CEEEEccccccCCCCCCEEEEChhhHHHHhcccCchhhcCHHHHHHHHHHH
Confidence            899999999999999999999999999999999999999999999887543

>d2gycf2 d.100.1.1 (F:1-58) Ribosomal protein L9 N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: MbtH/L9 domain-like
superfamily: L9 N-domain-like
family: Ribosomal protein L9 N-domain
domain: Ribosomal protein L9 N-domain
species: Escherichia coli [TaxId: 562]

Probab=99.93  E-value=1.6e-27  Score=147.82  Aligned_cols=51  Identities=37%  Similarity=0.580  Sum_probs=49.0

Q ss_pred             eEEEEeccccccCCCCcEEEecCcceecccccccccccchHHHHHHHHHhh
Q 043613           39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQR   89 (90)
Q Consensus        39 m~VILl~dV~gLGk~GdvV~Vk~GYARN~LiP~glA~~At~~~~~~l~~~~   89 (90)
                      |+|||++||++||++||||+|+||||||||||+|+|++||+++++.++.++
T Consensus         1 MkVIL~~dv~~lG~~Gdvv~Vk~GyaRNyLiP~glA~~at~~n~~~~~~~~   51 (58)
T d2gycf2           1 MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARR   51 (58)
T ss_dssp             CEEEECSSSSSCCCSCEEEECCTTTTTTTTTTTTSEEECCCHHHHHHHHHH
T ss_pred             CeEEEccccccCCCCCCEEEEccchhHHHhccCCceecCCHHHHHHHHHHH
Confidence            899999999999999999999999999999999999999999999887765