Citrus Sinensis ID: 031865

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-
Protein Sequence
MASMISFNLKFCPLCPSSSSVRASRGSSLRLALSNKLNNSLRLNSSYSISASPLLFRHNNLPTTVTQNRPQTVTVFAAKGYKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCLPYLKVNRQAK
Secondary Structure (PSIPRED)
ccccEEEcccccccccccccccccccccHHHHHHHHcccccccccccccccccccccccccccccccccccEEEEcccccccccccccccccEEEEccccEEEcccccccccccccHHHHHcccccccccHHcHHHHHHcccccccccccc
Secondary Structure Prediction (SSPRO)
ccEEEEEEcccccccccccccEEEEccEEEcccccccccccEcccccccccccEEccccccccccccccccEEEEEEccccEEccHHHHHHHEEEcccccEEEccccHHHHcccccHHHHHHHcccEEEccccHHHHHHHcHHHHHHHccc
Coil and Loop (DISEMBL)
masmisfnlkfcplcpssssvrasrgsSLRLALSNKLNnslrlnssysisaspllfrhnnlpttvtqnrpqTVTVFAAKGykmkthkaSAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKmhevsrsdydnvigclpylkvnrqak
Flexible Loop (DISEMBL)
MASMISFNLKFCPLCPSSSSVRASRGSSLRLALSNKLNNSLRLNSSYSISASPLLFRhnnlpttvtqnrpqTVTVFAAkgykmkthkasakrfrvtgkgkilrrragkqhllakkntkrklrlskmhevsrsdydnvigclpylkvnrqak
Low Complexity Region (SEG)
MASMISFNLKFCPLCPssssvrasrgsslrlalsnklnnslrlnssysisasPLLFRHNNLPTTVTQNRPQTVTVFAAKGYKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCLPYLKVNRQAK
Disordered region (IsUnstruct)
*****SFNLKFCPLC*********************************I*ASPLLFRHNNLPTTVTQNRPQTVTVFAAKGYKMKTH*****RFRVTGKGKIL******************************DYDNVIGCLPYLKV*****
Disordered Region (DISOPRED)
********LKFCPLCP**********************************************************************KASAKRFRVTGKGKILRRRAGKQHL****************EVSRSDYDNVIGCLPYLKV*****
Disordered Region (DISEMBL)
MASMISFNLKFCPLCP************LRLALSNKLNNSLRLNSSYSISASPLLFRHNNLPTTVTQNRPQTVTVFAAKGYKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCLPYLKVNRQAK
Disordered Region (DISPRO)
*ASMISFNLKFCPLCPSSSSVRASRGSSLRLALSNKLNNSLRLNSSYSISASPLLFRHNNLPTTVTQNRPQTVTVFAAKGYKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCLPYLKVNRQ**
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MASMISFNLKFCPLCPSSSSVRASRGSSLRLALSNKLNNSLRLNSSYSISASPLLFRHNNLPTTVTQNRPQTVTVFAAKGYKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCLPYLKVNRQAK
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	151	2.2.26 [Sep-21-2011]
P23326	159	50S ribosomal protein L35	N/A	no	0.966	0.918	0.572	3e-33
Q8YRL9	65	50S ribosomal protein L35	yes	no	0.417	0.969	0.571	3e-11
Q3M7I2	65	50S ribosomal protein L35	yes	no	0.417	0.969	0.571	3e-11
B2J0D1	65	50S ribosomal protein L35	yes	no	0.417	0.969	0.555	6e-10
A5GQ04	66	50S ribosomal protein L35	yes	no	0.410	0.939	0.548	6e-10
B5YLD0	66	50S ribosomal protein L35	yes	no	0.410	0.939	0.483	1e-09
A9BDA5	65	50S ribosomal protein L35	yes	no	0.410	0.953	0.548	1e-09
B7K4V5	67	50S ribosomal protein L35	yes	no	0.417	0.940	0.584	2e-09
Q5N5F4	66	50S ribosomal protein L35	yes	no	0.410	0.939	0.516	2e-09
Q31NR1	66	50S ribosomal protein L35	yes	no	0.410	0.939	0.516	2e-09

>sp|P23326|RK35_SPIOL 50S ribosomal protein L35, chloroplastic OS=Spinacia oleracea GN=RPL35 PE=1 SV=1

 Score =  140 bits (353), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 87/152 (57%), Positives = 108/152 (71%), Gaps = 6/152 (3%)

Query: 3   SMISFNLKFCPLCPSSSSVRASRGSSLRLALSNKLNNSLRLNSSYSIS---ASPLLFRHN 59
           + +SF      L P S+   A++G SL    + +L ++L L+SS SIS     P++ ++ 
Sbjct: 8   ATLSFKTPSLSLSPPSTRCSAAQGISL-THFNKQLKSTLNLSSSSSISSSKVQPIVLKNK 66

Query: 60  NLPTTVTQNRPQT--VTVFAAKGYKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNT 117
            + T  +     +   TVFAAKGYKMKTHKASAKRFRVTGKGKI+RRRAGKQHLLAKKNT
Sbjct: 67  RISTVDSSVSTSSPSFTVFAAKGYKMKTHKASAKRFRVTGKGKIVRRRAGKQHLLAKKNT 126

Query: 118 KRKLRLSKMHEVSRSDYDNVIGCLPYLKVNRQ 149
           KRK RLSK+ +V RSDYDNVIG LPYLKVNR+
Sbjct: 127 KRKNRLSKLIQVDRSDYDNVIGALPYLKVNRK 158

Spinacia oleracea (taxid: 3562)

>sp|Q8YRL9|RL35_NOSS1 50S ribosomal protein L35 OS=Nostoc sp. (strain PCC 7120 / UTEX 2576) GN=rpmI PE=3 SV=1

 Score = 67.4 bits (163), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 36/63 (57%), Positives = 44/63 (69%)

Query: 82  KMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCL 141
           K+KT KA+AKRFR TG GKI+RR+A K HLL  K T +K + SKM  V+  D +NV   L
Sbjct: 3   KLKTRKAAAKRFRATGTGKIVRRKAFKNHLLEHKTTNKKRQFSKMAIVNERDEENVRLML 62

Query: 142 PYL 144
           PYL
Sbjct: 63  PYL 65

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

>sp|Q3M7I2|RL35_ANAVT 50S ribosomal protein L35 OS=Anabaena variabilis (strain ATCC 29413 / PCC 7937) GN=rpmI PE=3 SV=1

 Score = 67.4 bits (163), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 36/63 (57%), Positives = 44/63 (69%)

Query: 82  KMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCL 141
           K+KT KA+AKRFR TG GKI+RR+A K HLL  K T +K + SKM  V+  D +NV   L
Sbjct: 3   KLKTRKAAAKRFRATGTGKIVRRKAFKNHLLEHKTTNKKRQFSKMAIVNERDEENVRLML 62

Query: 142 PYL 144
           PYL
Sbjct: 63  PYL 65

Anabaena variabilis (strain ATCC 29413 / PCC 7937) (taxid: 240292)

>sp|B2J0D1|RL35_NOSP7 50S ribosomal protein L35 OS=Nostoc punctiforme (strain ATCC 29133 / PCC 73102) GN=rpmI PE=3 SV=1

 Score = 63.2 bits (152), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 35/63 (55%), Positives = 43/63 (68%)

Query: 82  KMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCL 141
           K+KT KA+AKRFR TG GKI+RR+AGK HLL  K++ +K  +SK   V   D  NV   L
Sbjct: 3   KLKTRKAAAKRFRATGTGKIVRRKAGKSHLLEHKSSDKKRSMSKTTLVHERDELNVRLML 62

Query: 142 PYL 144
           PYL
Sbjct: 63  PYL 65

Nostoc punctiforme (strain ATCC 29133 / PCC 73102) (taxid: 63737)

>sp|A5GQ04|RL35_SYNR3 50S ribosomal protein L35 OS=Synechococcus sp. (strain RCC307) GN=rpmI PE=3 SV=1

 Score = 63.2 bits (152), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 34/62 (54%), Positives = 40/62 (64%)

Query: 82  KMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCL 141
           K+KT +A+AKRFRVTG GK +RRRA   HLL  K+ KRK  L  M  V   D+D V   L
Sbjct: 3   KLKTRRAAAKRFRVTGSGKFMRRRAFHNHLLDHKSPKRKRYLGTMAVVDERDHDRVSHML 62

Query: 142 PY 143
           PY
Sbjct: 63  PY 64

Synechococcus sp. (strain RCC307) (taxid: 316278)

>sp|B5YLD0|RL35_THEYD 50S ribosomal protein L35 OS=Thermodesulfovibrio yellowstonii (strain ATCC 51303 / DSM 11347 / YP87) GN=rpmI PE=3 SV=1

 Score = 62.4 bits (150), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/62 (48%), Positives = 42/62 (67%)

Query: 82  KMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCL 141
           K+KTH+ +AKRF+VTG GKI+RRRA K HLL  K +KR   L ++ +V  + Y  +   +
Sbjct: 3   KLKTHRGAAKRFKVTGTGKIMRRRANKSHLLTGKPSKRTRHLRQIAQVDETQYKAIRMLI 62

Query: 142 PY 143
           PY
Sbjct: 63  PY 64

Thermodesulfovibrio yellowstonii (strain ATCC 51303 / DSM 11347 / YP87) (taxid: 289376)

>sp|A9BDA5|RL35_PROM4 50S ribosomal protein L35 OS=Prochlorococcus marinus (strain MIT 9211) GN=rpmI PE=3 SV=1

 Score = 62.0 bits (149), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 34/62 (54%), Positives = 41/62 (66%)

Query: 82  KMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCL 141
           K+KT KA+AKRF+VTG GK +RRRA + HLL  K+TK K  L+    V   D DNV   L
Sbjct: 3   KLKTRKAAAKRFKVTGTGKFMRRRAFRNHLLDHKSTKLKRHLATKAVVDERDADNVSLML 62

Query: 142 PY 143
           PY
Sbjct: 63  PY 64

Prochlorococcus marinus (strain MIT 9211) (taxid: 93059)

>sp|B7K4V5|RL35_CYAP8 50S ribosomal protein L35 OS=Cyanothece sp. (strain PCC 8801) GN=rpmI PE=3 SV=1

 Score = 61.6 bits (148), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 38/65 (58%), Positives = 45/65 (69%), Gaps = 2/65 (3%)

Query: 82  KMKTHKASAKRFRVTGKG-KILRRRAGKQHLLAKKNTKRKL-RLSKMHEVSRSDYDNVIG 139
           K+KT KA+AKRFRVTG G KI RR+A K HLL  K+++RK  RLS +  VS  D  NV  
Sbjct: 3   KLKTRKAAAKRFRVTGSGKKIFRRKAFKNHLLQHKSSERKFRRLSGLSLVSEQDEANVRL 62

Query: 140 CLPYL 144
            LPYL
Sbjct: 63  MLPYL 67

Cyanothece sp. (strain PCC 8801) (taxid: 41431)

>sp|Q5N5F4|RL35_SYNP6 50S ribosomal protein L35 OS=Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1) GN=rpmI PE=3 SV=1

 Score = 61.6 bits (148), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 32/62 (51%), Positives = 42/62 (67%)

Query: 82  KMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCL 141
           K+KT KA+AKRFR++G GK +RR+A K HLL  KN  R+ RLS+   V  +D + V   L
Sbjct: 3   KLKTRKAAAKRFRISGNGKAIRRKAFKNHLLQHKNATRRRRLSQPEVVHETDQERVKLML 62

Query: 142 PY 143
           PY
Sbjct: 63  PY 64

Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1) (taxid: 269084)

>sp|Q31NR1|RL35_SYNE7 50S ribosomal protein L35 OS=Synechococcus elongatus (strain PCC 7942) GN=rpmI PE=3 SV=1

 Score = 61.6 bits (148), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 32/62 (51%), Positives = 42/62 (67%)

Query: 82  KMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCL 141
           K+KT KA+AKRFR++G GK +RR+A K HLL  KN  R+ RLS+   V  +D + V   L
Sbjct: 3   KLKTRKAAAKRFRISGNGKAIRRKAFKNHLLQHKNATRRRRLSQPEVVHETDQERVKLML 62

Query: 142 PY 143
           PY
Sbjct: 63  PY 64

Synechococcus elongatus (strain PCC 7942) (taxid: 1140)

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	151
118483883	150	unknown [Populus trichocarpa]	0.973	0.98	0.703	3e-44
224142343	150	predicted protein [Populus trichocarpa]	0.973	0.98	0.697	3e-43
449457865	151	PREDICTED: 50S ribosomal protein L35, ch	0.947	0.947	0.651	9e-40
351725085	147	uncharacterized protein LOC100305559 [Gl	0.953	0.979	0.625	9e-36
388499438	148	unknown [Lotus japonicus] gi|388516355|g	0.860	0.878	0.659	2e-35
297821677	140	ribosomal protein L35 [Arabidopsis lyrat	0.907	0.978	0.583	4e-35
225470652	153	PREDICTED: 50S ribosomal protein L35, ch	0.735	0.725	0.719	1e-34
225470127	153	PREDICTED: 50S ribosomal protein L35, ch	0.735	0.725	0.710	6e-34
351721053	138	uncharacterized protein LOC100306481 [Gl	0.735	0.804	0.710	1e-32
255574972	134	50S ribosomal protein L35, chloroplast p	0.841	0.947	0.6	2e-32

>gi|118483883|gb|ABK93832.1| unknown [Populus trichocarpa]

 Score =  182 bits (463), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 107/152 (70%), Positives = 119/152 (78%), Gaps = 5/152 (3%)

Query: 1   MASM--ISFNLKFCPLCPSSSSVRASRGSSLRLALSNKLNNSLRLNSSYSISASPLLFRH 58
           MAS+  +SFNLK CPL   S S R S GS+ +LA  NK+N+SLRL+S  +IS S  L   
Sbjct: 1   MASLTVLSFNLKSCPL--HSFSTRVSYGSA-QLAPLNKVNSSLRLSSCRNISGSRSLSPL 57

Query: 59  NNLPTTVTQNRPQTVTVFAAKGYKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTK 118
                T    R Q++TVFAAKGYKMKTHKASAKRFRVTGKGKI+RRRAGKQHLLAKKNTK
Sbjct: 58  KPCSITSLTQRFQSLTVFAAKGYKMKTHKASAKRFRVTGKGKIVRRRAGKQHLLAKKNTK 117

Query: 119 RKLRLSKMHEVSRSDYDNVIGCLPYLKVNRQA 150
           RKLRLSKMH VSRSDYDNVIG LPYLKVNR+A
Sbjct: 118 RKLRLSKMHPVSRSDYDNVIGALPYLKVNRKA 149

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224142343|ref|XP_002324518.1| predicted protein [Populus trichocarpa] gi|222865952|gb|EEF03083.1| predicted protein [Populus trichocarpa]

 Score =  179 bits (455), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 106/152 (69%), Positives = 118/152 (77%), Gaps = 5/152 (3%)

Query: 1   MASM--ISFNLKFCPLCPSSSSVRASRGSSLRLALSNKLNNSLRLNSSYSISASPLLFRH 58
           MAS+  +SFNLK CPL   S S R S GS+ +LA   K+N+SLRL+S  +IS S  L   
Sbjct: 1   MASLTVLSFNLKSCPL--HSFSTRVSYGSA-QLAPLIKVNSSLRLSSCRNISGSRSLSPL 57

Query: 59  NNLPTTVTQNRPQTVTVFAAKGYKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTK 118
                T    R Q++TVFAAKGYKMKTHKASAKRFRVTGKGKI+RRRAGKQHLLAKKNTK
Sbjct: 58  KPCSITSLTQRFQSLTVFAAKGYKMKTHKASAKRFRVTGKGKIVRRRAGKQHLLAKKNTK 117

Query: 119 RKLRLSKMHEVSRSDYDNVIGCLPYLKVNRQA 150
           RKLRLSKMH VSRSDYDNVIG LPYLKVNR+A
Sbjct: 118 RKLRLSKMHPVSRSDYDNVIGALPYLKVNRKA 149

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449457865|ref|XP_004146668.1| PREDICTED: 50S ribosomal protein L35, chloroplastic-like [Cucumis sativus] gi|449503151|ref|XP_004161859.1| PREDICTED: 50S ribosomal protein L35, chloroplastic-like [Cucumis sativus]

 Score =  167 bits (424), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 101/155 (65%), Positives = 118/155 (76%), Gaps = 12/155 (7%)

Query: 2   ASM-ISFNLKFCPLCPSSSSVRASRGSSLRLALSNKLNNSLRLNSSYSISASPLLFRHNN 60
           ASM +SF L+F PLC S  S R S  +S+ +A  NK+N SL+L+SS++IS     F  N+
Sbjct: 4   ASMAVSFGLRFSPLC-SRPSFRVSH-TSVGIASVNKVN-SLKLSSSHNISG----FGFNS 56

Query: 61  L--PTTV--TQNRPQTVTVFAAKGYKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKN 116
           L  P+ +  T       TVFAAKGYKMKTHKASAKRFRVTG+GKI+RRRAGKQHLL KKN
Sbjct: 57  LQKPSHISPTSQIRTPFTVFAAKGYKMKTHKASAKRFRVTGRGKIVRRRAGKQHLLCKKN 116

Query: 117 TKRKLRLSKMHEVSRSDYDNVIGCLPYLKVNRQAK 151
            KR+LRLSKMH VSRSDYDNVIG LPYLKVNRQA+
Sbjct: 117 AKRRLRLSKMHPVSRSDYDNVIGALPYLKVNRQAQ 151

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351725085|ref|NP_001237080.1| uncharacterized protein LOC100305559 [Glycine max] gi|255625911|gb|ACU13300.1| unknown [Glycine max]

 Score =  154 bits (390), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 95/152 (62%), Positives = 109/152 (71%), Gaps = 8/152 (5%)

Query: 1   MASMISFNLKFCPLCPSSSSVRASRGSSLRLALSNKLNNSLRLNSSYSISASPLLFRHNN 60
           MAS +SF +   P   SS   R S GS     L+N   N L+L+SS +IS SP+L  H  
Sbjct: 1   MAS-VSFAVGLLPCSSSSCYTRVSYGSVRFPVLNNA--NPLKLSSSANIS-SPIL--HQK 54

Query: 61  LPTTVT--QNRPQTVTVFAAKGYKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTK 118
           L T  +    RP+ +T+ +AKGYKMKTHKASAKRFRVTG+GKI+ RRAGKQHLL KKNTK
Sbjct: 55  LCTVPSPLALRPRPLTIVSAKGYKMKTHKASAKRFRVTGRGKIVCRRAGKQHLLVKKNTK 114

Query: 119 RKLRLSKMHEVSRSDYDNVIGCLPYLKVNRQA 150
           RK RLSKMH VSRSDYDNVIG LPYLKVNR A
Sbjct: 115 RKSRLSKMHAVSRSDYDNVIGALPYLKVNRNA 146

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388499438|gb|AFK37785.1| unknown [Lotus japonicus] gi|388516355|gb|AFK46239.1| unknown [Lotus japonicus]

 Score =  153 bits (387), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 89/135 (65%), Positives = 103/135 (76%), Gaps = 5/135 (3%)

Query: 16  PSSSSVRASRGSSLRLALSNKLNNSLRLNSSYSISASPLLFRHNNLPTTVTQNRPQTVTV 75
           P SSS      +S+RL  S+K  NS++L+SS  IS    +F+      TVT    +++T+
Sbjct: 18  PCSSSPTRLSYASVRLPPSHK-TNSVKLSSSACISTP--IFQQKLC--TVTPPSSRSLTI 72

Query: 76  FAAKGYKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYD 135
            AAKGYKMKTHKASAKRFRVTGKGKI+RRRAGKQHLL KKNTKRKLRLSKMH V+RSDYD
Sbjct: 73  VAAKGYKMKTHKASAKRFRVTGKGKIVRRRAGKQHLLQKKNTKRKLRLSKMHPVNRSDYD 132

Query: 136 NVIGCLPYLKVNRQA 150
           NVIG LPYLKVNR A
Sbjct: 133 NVIGALPYLKVNRNA 147

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297821677|ref|XP_002878721.1| ribosomal protein L35 [Arabidopsis lyrata subsp. lyrata] gi|297324560|gb|EFH54980.1| ribosomal protein L35 [Arabidopsis lyrata subsp. lyrata]

 Score =  152 bits (385), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 87/149 (58%), Positives = 106/149 (71%), Gaps = 12/149 (8%)

Query: 4   MISFNLKFCPLCPSSSSVRASRGSSLRLALSNKLNNSLRLNSSYSISASPLLFRHNNLPT 63
           M S N+ FC         R  R SS +++L + +  +  L SS+SIS    +F    + T
Sbjct: 1   MASVNVSFC---------RPLRSSSPKVSLRSSVQFATSLASSHSISGLRAVF-PQKIST 50

Query: 64  TVTQN--RPQTVTVFAAKGYKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKL 121
             + N  + Q+ TVFA KGYK+KTHKASAKRFRVTG+GKI+RRR+GKQHLLAKKN KRKL
Sbjct: 51  VASPNSQKFQSFTVFAHKGYKLKTHKASAKRFRVTGRGKIVRRRSGKQHLLAKKNNKRKL 110

Query: 122 RLSKMHEVSRSDYDNVIGCLPYLKVNRQA 150
           RLSKM EV+RSDYDNVIG LPYLKVNR+A
Sbjct: 111 RLSKMTEVNRSDYDNVIGALPYLKVNRKA 139

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225470652|ref|XP_002267813.1| PREDICTED: 50S ribosomal protein L35, chloroplastic [Vitis vinifera] gi|147785813|emb|CAN77631.1| hypothetical protein VITISV_001803 [Vitis vinifera] gi|147799145|emb|CAN63703.1| hypothetical protein VITISV_039205 [Vitis vinifera]

 Score =  150 bits (380), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 82/114 (71%), Positives = 99/114 (86%), Gaps = 3/114 (2%)

Query: 40  SLRLNSSYSISA-SPLL-FRHNNLPTTVTQNRPQTVTVFAAKGYKMKTHKASAKRFRVTG 97
           SL+L+SS +IS  +P+L  RH+ L  + + ++P ++TV +AKGYKMKTHKASAKRFRVTG
Sbjct: 41  SLKLSSSRNISGFAPILPLRHSTL-NSPSPSQPSSLTVVSAKGYKMKTHKASAKRFRVTG 99

Query: 98  KGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCLPYLKVNRQAK 151
           +GKI+RRRAGKQHLLAKKN KR+LRLSKMH VSRSDYDNVIG LPYLKVNR+AK
Sbjct: 100 RGKIVRRRAGKQHLLAKKNAKRRLRLSKMHPVSRSDYDNVIGALPYLKVNREAK 153

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225470127|ref|XP_002264584.1| PREDICTED: 50S ribosomal protein L35, chloroplastic [Vitis vinifera]

 Score =  148 bits (374), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 81/114 (71%), Positives = 98/114 (85%), Gaps = 3/114 (2%)

Query: 40  SLRLNSSYSISA-SPLL-FRHNNLPTTVTQNRPQTVTVFAAKGYKMKTHKASAKRFRVTG 97
           SL+L+SS +IS  +P+L  RH+ L  + + ++P ++TV +AKGYKMKTHKASAKRFRVTG
Sbjct: 41  SLKLSSSRNISGFAPILPLRHSTL-NSPSPSQPSSLTVVSAKGYKMKTHKASAKRFRVTG 99

Query: 98  KGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCLPYLKVNRQAK 151
           +GKI+RRRAGKQHLLAKKN KR+LRLSKMH VSRSDYDNVIG LPYLKVNR+ K
Sbjct: 100 RGKIVRRRAGKQHLLAKKNAKRRLRLSKMHPVSRSDYDNVIGALPYLKVNREVK 153

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351721053|ref|NP_001235661.1| uncharacterized protein LOC100306481 [Glycine max] gi|255628681|gb|ACU14685.1| unknown [Glycine max]

 Score =  144 bits (363), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 81/114 (71%), Positives = 93/114 (81%), Gaps = 3/114 (2%)

Query: 39  NSLRLNSSYSISASPLLFRH--NNLPTTVTQNRPQTVTVFAAKGYKMKTHKASAKRFRVT 96
           NSL+L+SS SIS +P+L +   + L       RP+ +T+ +AKGYKMKTHKASAKRFRVT
Sbjct: 25  NSLKLSSSASIS-TPILQQKLCSLLSPLPLSPRPRPLTIVSAKGYKMKTHKASAKRFRVT 83

Query: 97  GKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCLPYLKVNRQA 150
           G+GKI+RRRAGKQHLL KKNTKRK RLSKMH VSRSDYDNVIG LPYLKVNR A
Sbjct: 84  GQGKIVRRRAGKQHLLVKKNTKRKSRLSKMHAVSRSDYDNVIGALPYLKVNRNA 137

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255574972|ref|XP_002528392.1| 50S ribosomal protein L35, chloroplast precursor, putative [Ricinus communis] gi|223532180|gb|EEF33985.1| 50S ribosomal protein L35, chloroplast precursor, putative [Ricinus communis]

 Score =  144 bits (362), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 84/140 (60%), Positives = 100/140 (71%), Gaps = 13/140 (9%)

Query: 3   SMISFNLKFCPLCPSSSSVRASRGSSLRLALSNKLNNSLRLNSSYSISASPLLFRHNNLP 62
           +M+SF+LK CPL  S  + R S GS+ +L+  N LNNSLRL SS++IS S  +F   +  
Sbjct: 5   TMLSFSLKLCPL-QSPPTARLSYGSA-QLSPFNNLNNSLRLGSSHNISGSHSIFYQKSSS 62

Query: 63  TTVTQNRPQTVTVFAAKGYKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLR 122
                 + Q++TVFAAKGYKMKTHKASAKRFRVTGKGKI+RRRAGKQHLLAKKNTKRKLR
Sbjct: 63  IATLTQKFQSLTVFAAKGYKMKTHKASAKRFRVTGKGKIMRRRAGKQHLLAKKNTKRKLR 122

Query: 123 LSKMHEVSRSDYDNVIGCLP 142
           LSKM           +G LP
Sbjct: 123 LSKM-----------VGSLP 131

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	151
TAIR|locus:2061441	145	PRPL35 "plastid ribosomal prot	0.509	0.531	0.883	1.1e-33
TIGR_CMR|CBU_1324	64	CBU_1324 "ribosomal protein L3	0.344	0.812	0.538	2e-10
UNIPROTKB|P0A7Q1	65	rpmI "50S ribosomal subunit pr	0.410	0.953	0.483	6.6e-10
TIGR_CMR|BA_4818	66	BA_4818 "ribosomal protein L35	0.423	0.969	0.453	5.9e-09
TIGR_CMR|CHY_1577	64	CHY_1577 "ribosomal protein L3	0.410	0.968	0.483	7.6e-09
TIGR_CMR|GSU_1517	65	GSU_1517 "ribosomal protein L3	0.417	0.969	0.412	1.6e-08
TIGR_CMR|DET_0751	67	DET_0751 "ribosomal protein L3	0.410	0.925	0.403	6.8e-08
TIGR_CMR|SO_2301	64	SO_2301 "ribosomal protein L35	0.403	0.953	0.419	2.1e-06
GENEDB_PFALCIPARUM|PFI0375w	191	PFI0375w "ribosomal protein L3	0.291	0.230	0.454	3.5e-06
UNIPROTKB|Q8I373	191	PFI0375w "50S ribosomal protei	0.291	0.230	0.454	3.5e-06

TAIR|locus:2061441 PRPL35 "plastid ribosomal protein L35" [Arabidopsis thaliana (taxid:3702)]

 Score = 347 (127.2 bits), Expect = 1.1e-33, Sum P(2) = 1.1e-33
 Identities = 68/77 (88%), Positives = 73/77 (94%)

Query:    74 TVFAAKGYKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSD 133
             TVFA KGYKMKTHKASAKRFRVTG+GKI+RRR+GKQHLLAKKN KRKLRLSKM EV+RSD
Sbjct:    68 TVFAHKGYKMKTHKASAKRFRVTGRGKIVRRRSGKQHLLAKKNNKRKLRLSKMTEVNRSD 127

Query:   134 YDNVIGCLPYLKVNRQA 150
             YDNVIG LPYLKVNR+A
Sbjct:   128 YDNVIGALPYLKVNRKA 144

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;IDA

GO:0006098 "pentose-phosphate shunt" evidence=RCA

TIGR_CMR|CBU_1324 CBU_1324 "ribosomal protein L35" [Coxiella burnetii RSA 493 (taxid:227377)]

 Score = 147 (56.8 bits), Expect = 2.0e-10, P = 2.0e-10
 Identities = 28/52 (53%), Positives = 38/52 (73%)

Query:    82 KMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSD 133
             K+KT++ + KRF+VTG GKI R  +   H+L KK+ KRK RL K+HEV+ SD
Sbjct:     3 KLKTNRGAVKRFKVTGSGKIKRAASNHNHILTKKSQKRKRRLRKIHEVAPSD 54

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

UNIPROTKB|P0A7Q1 rpmI "50S ribosomal subunit protein L35" [Escherichia coli K-12 (taxid:83333)]

 Score = 142 (55.0 bits), Expect = 6.6e-10, P = 6.6e-10
 Identities = 30/62 (48%), Positives = 38/62 (61%)

Query:    82 KMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCL 141
             K+KT + +AKRF+ TGKG    + A  +H+L KK TKRK  L     VS+ D   VI CL
Sbjct:     3 KIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIACL 62

Query:   142 PY 143
             PY
Sbjct:    63 PY 64

GO:0006412 "translation" evidence=IEA

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

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

TIGR_CMR|BA_4818 BA_4818 "ribosomal protein L35" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 133 (51.9 bits), Expect = 5.9e-09, P = 5.9e-09
 Identities = 29/64 (45%), Positives = 37/64 (57%)

Query:    82 KMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCL 141
             K KTH+ +AKRF+ TG GK+ R  A   HL A K+TK K +L K   VS  D+  +   L
Sbjct:     3 KQKTHRGAAKRFKKTGSGKLKRSHAYTSHLFANKSTKAKRKLRKAGVVSAGDFKRIRQML 62

Query:   142 PYLK 145
               LK
Sbjct:    63 DNLK 66

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

GO:0006412 "translation" evidence=ISS

TIGR_CMR|CHY_1577 CHY_1577 "ribosomal protein L35" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 132 (51.5 bits), Expect = 7.6e-09, P = 7.6e-09
 Identities = 30/62 (48%), Positives = 37/62 (59%)

Query:    82 KMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCL 141
             K+KT KA+AKRF+ TG GK+    A   HLL  K +KRK RL K   VS+ D   +   L
Sbjct:     3 KIKTKKAAAKRFKKTGSGKVKHFHAFHSHLLGHKTSKRKRRLRKSAIVSKGDMKIIKKIL 62

Query:   142 PY 143
             PY
Sbjct:    63 PY 64

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

GO:0006412 "translation" evidence=ISS

TIGR_CMR|GSU_1517 GSU_1517 "ribosomal protein L35" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 129 (50.5 bits), Expect = 1.6e-08, P = 1.6e-08
 Identities = 26/63 (41%), Positives = 38/63 (60%)

Query:    82 KMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCL 141
             K+KT++ +AKRF+ TG GKI R  A   H+L  K  KRK +L     V+  D+ N+   +
Sbjct:     3 KIKTNRGAAKRFKKTGTGKIKRSHAFTSHILTSKTRKRKRQLRSSAVVAAVDHKNIAKLI 62

Query:   142 PYL 144
             PY+
Sbjct:    63 PYM 65

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

GO:0006412 "translation" evidence=ISS

GO:0042254 "ribosome biogenesis" evidence=ISS

TIGR_CMR|DET_0751 DET_0751 "ribosomal protein L35" [Dehalococcoides ethenogenes 195 (taxid:243164)]

 Score = 123 (48.4 bits), Expect = 6.8e-08, P = 6.8e-08
 Identities = 25/62 (40%), Positives = 37/62 (59%)

Query:    82 KMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCL 141
             KMKT K +AKRF VTG GKI+R +  K HL   K+ + + +  +M +V+  D   +   +
Sbjct:     3 KMKTRKTAAKRFHVTGTGKIMRSKGMKSHLRRNKSARVRRQFDEMSQVAGVDRARIQKLI 62

Query:   142 PY 143
             PY
Sbjct:    63 PY 64

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

GO:0006412 "translation" evidence=ISS

GO:0015934 "large ribosomal subunit" evidence=ISS

TIGR_CMR|SO_2301 SO_2301 "ribosomal protein L35" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 109 (43.4 bits), Expect = 2.1e-06, P = 2.1e-06
 Identities = 26/62 (41%), Positives = 36/62 (58%)

Query:    82 KMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCL 141
             KMKT +  AKRF+ T  G   R++A  +H+L KK+TKRK  L     V++ D   +   L
Sbjct:     3 KMKTDRGVAKRFKKTANG-FKRKQAHLRHILTKKSTKRKRHLRNKCLVAKVDVPAIARQL 61

Query:   142 PY 143
             PY
Sbjct:    62 PY 63

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

GO:0006412 "translation" evidence=ISS

GENEDB_PFALCIPARUM|PFI0375w PFI0375w "ribosomal protein L35, putative" [Plasmodium falciparum (taxid:5833)]

 Score = 108 (43.1 bits), Expect = 3.5e-06, P = 3.5e-06
 Identities = 20/44 (45%), Positives = 30/44 (68%)

Query:    82 KMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSK 125
             K KT+K+ AKRF++T  GK++R++ G+ H L KK +  K  L K
Sbjct:   129 KPKTNKSIAKRFKLTKNGKLIRKKPGRNHFLRKKTSSNKASLRK 172

GO:0020011 "apicoplast" evidence=ISS

UNIPROTKB|Q8I373 PFI0375w "50S ribosomal protein L35" [Plasmodium falciparum 3D7 (taxid:36329)]

 Score = 108 (43.1 bits), Expect = 3.5e-06, P = 3.5e-06
 Identities = 20/44 (45%), Positives = 30/44 (68%)

Query:    82 KMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSK 125
             K KT+K+ AKRF++T  GK++R++ G+ H L KK +  K  L K
Sbjct:   129 KPKTNKSIAKRFKLTKNGKLIRKKPGRNHFLRKKTSSNKASLRK 172

GO:0020011 "apicoplast" 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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P23326	RK35_SPIOL	No assigned EC number	0.5723	0.9668	0.9182	N/A	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_Genewise1_v1.C_LG_XVIII3093	RecName- Full=50S ribosomal protein L35; (151 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	estExt_Genewise1_v1.C_LG_VI2599	hypothetical protein; IF-3 binds to the 30S ribosomal subunit and shifts the equilibrum between [...] (208 aa)	•			•			•		0.926
	estExt_fgenesh4_pg.C_LG_XVIII0906	hypothetical protein; IF-3 binds to the 30S ribosomal subunit and shifts the equilibrum between [...] (278 aa)	•			•			•		0.913
	estExt_fgenesh4_pg.C_LG_II2313	hypothetical protein; Binds directly to 23S ribosomal RNA and is necessary for the in vitro ass [...] (126 aa)	•			•	•		•		0.900
	gw1.IV.3343.1	annotation not avaliable (109 aa)	•			•	•		•		0.888
	rpl20	ribosomal protein L20 ; Binds directly to 23S ribosomal RNA and is necessary for the in vitro a [...] (111 aa)	•			•	•		•		0.871
	gw1.I.3103.1	hypothetical protein (176 aa)				•	•		•		0.818
	gw1.163.69.1	SubName- Full=Putative uncharacterized protein; (192 aa)				•	•		•		0.812
	gw1.VIII.2106.1	threonine-tRNA ligase (EC-6.1.1.3) (669 aa)	•						•		0.737
	gw1.X.6174.1	annotation not avaliable (674 aa)	•						•		0.726
	grail3.18076000101	Predicted protein (60 aa)				•	•		•		0.726

---

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	151
PRK00172	65	PRK00172, rpmI, 50S ribosomal protein L35; Reviewe	3e-21
TIGR00001	63	TIGR00001, rpmI_bact, ribosomal protein L35	2e-19
COG0291	65	COG0291, RpmI, Ribosomal protein L35 [Translation,	6e-17
pfam01632	61	pfam01632, Ribosomal_L35p, Ribosomal protein L35	9e-16
CHL00103	65	CHL00103, rpl35, ribosomal protein L35	6e-14

>gnl|CDD|234676 PRK00172, rpmI, 50S ribosomal protein L35; Reviewed

 Score = 80.6 bits (200), Expect = 3e-21
 Identities = 33/63 (52%), Positives = 43/63 (68%)

Query: 82  KMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCL 141
           KMKT   +AKRF+VTG GK+ R+ AGK+H+L KK+TKRK +L     VS++D   V   L
Sbjct: 3   KMKTKSGAAKRFKVTGSGKVKRKHAGKRHILTKKSTKRKRQLRGTTVVSKADAKRVKRML 62

Query: 142 PYL 144
           PY 
Sbjct: 63  PYA 65

Length = 65

>gnl|CDD|129113 TIGR00001, rpmI_bact, ribosomal protein L35

 Score = 76.6 bits (189), Expect = 2e-19
 Identities = 37/63 (58%), Positives = 45/63 (71%)

Query: 81  YKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGC 140
            KMKTHKA+AKRF++TG GKI R++AGK+HLL KK++KRK  L K   VS  D   V   
Sbjct: 1   PKMKTHKAAAKRFKITGSGKIKRKKAGKRHLLTKKSSKRKRNLRKKAIVSAGDLKRVKLL 60

Query: 141 LPY 143
           LPY
Sbjct: 61  LPY 63

This ribosomal protein is found in bacteria and organelles only. It is not closely related to any eukaryotic or archaeal ribosomal protein [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 63

>gnl|CDD|223368 COG0291, RpmI, Ribosomal protein L35 [Translation, ribosomal structure and biogenesis]

 Score = 70.0 bits (172), Expect = 6e-17
 Identities = 34/63 (53%), Positives = 43/63 (68%)

Query: 82  KMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCL 141
           KMKT K +AKRF++TG GKI R+ AGK+H+L KK+TKRK  L K   VS++D   V   L
Sbjct: 3   KMKTKKGAAKRFKITGTGKIKRKHAGKRHILTKKSTKRKRHLRKTAVVSKADLKRVKRLL 62

Query: 142 PYL 144
            Y 
Sbjct: 63  LYA 65

Length = 65

>gnl|CDD|145004 pfam01632, Ribosomal_L35p, Ribosomal protein L35

 Score = 66.9 bits (164), Expect = 9e-16
 Identities = 37/61 (60%), Positives = 43/61 (70%)

Query: 81  YKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGC 140
            KMKT KA+AKRF+ T  GKI RR+AGK+HLL KK+TKRK RL K   VS+SD   V   
Sbjct: 1   PKMKTVKAAAKRFKRTASGKIKRRKAGKRHLLTKKSTKRKRRLRKKVLVSKSDAKRVDKL 60

Query: 141 L 141
           L
Sbjct: 61  L 61

Length = 61

>gnl|CDD|214367 CHL00103, rpl35, ribosomal protein L35

 Score = 62.4 bits (152), Expect = 6e-14
 Identities = 33/64 (51%), Positives = 46/64 (71%)

Query: 81  YKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGC 140
            K+KT KA+AKR++ TG GK LRR+A K HLL KK++K+K +LS+   VS+ D  ++   
Sbjct: 2   PKLKTRKAAAKRYKKTGNGKFLRRKAFKSHLLQKKSSKQKRKLSQTVCVSKGDSKSIKLM 61

Query: 141 LPYL 144
           LPYL
Sbjct: 62  LPYL 65

Length = 65

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	151
CHL00103	65	rpl35 ribosomal protein L35	99.93
PRK00172	65	rpmI 50S ribosomal protein L35; Reviewed	99.93
TIGR00001	63	rpmI_bact ribosomal protein L35. This ribosomal pr	99.93
COG0291	65	RpmI Ribosomal protein L35 [Translation, ribosomal	99.92
PF01632	61	Ribosomal_L35p: Ribosomal protein L35; InterPro: I	99.88
KOG4316	172	consensus Uncharacterized conserved protein [Funct	95.75

>CHL00103 rpl35 ribosomal protein L35

Probab=99.93  E-value=5.8e-27  Score=162.88  Aligned_cols=65  Identities=51%  Similarity=0.673  Sum_probs=63.6

Q ss_pred             ccCcccCcccccceEEccCcceEeeccCcccccCCCChHHHhhcCCCeeeccccHHHHHHhCCCc
Q 031865           80 GYKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCLPYL  144 (151)
Q Consensus        80 ~~KmKThKgAaKRFKvTgSGKIkR~rAgkrHlltkKS~KrKRrLrk~~~V~~~d~k~IKrlLPY~  144 (151)
                      ++|||||+||+|||++||+|||+|.+||++|++++|+++++|+|+++.+|+++|.++|++||||+
T Consensus         1 MpKmKT~k~a~KRFKvT~sGKvkr~~a~k~H~l~kKs~krkR~L~~~~~v~~~d~~~ik~~lp~~   65 (65)
T CHL00103          1 MPKLKTRKAAAKRYKKTGNGKFLRRKAFKSHLLQKKSSKQKRKLSQTVCVSKGDSKSIKLMLPYL   65 (65)
T ss_pred             CCccccchhhhheeEecCCCCEEeccCCccccccCCCHHHHHhcCCCeeECHHHHHHHHHhcCCC
Confidence            58999999999999999999999999999999999999999999999999999999999999995

>PRK00172 rpmI 50S ribosomal protein L35; Reviewed

Probab=99.93  E-value=2.3e-26  Score=159.21  Aligned_cols=65  Identities=51%  Similarity=0.707  Sum_probs=63.6

Q ss_pred             ccCcccCcccccceEEccCcceEeeccCcccccCCCChHHHhhcCCCeeeccccHHHHHHhCCCc
Q 031865           80 GYKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCLPYL  144 (151)
Q Consensus        80 ~~KmKThKgAaKRFKvTgSGKIkR~rAgkrHlltkKS~KrKRrLrk~~~V~~~d~k~IKrlLPY~  144 (151)
                      |+|||||+||+|||++||+|||+|++||++|++++|+.+++|+|+++.+|+++|.++|++||||+
T Consensus         1 MpKmKT~k~akKRFk~T~~GKi~r~~a~k~H~~~~Ks~k~kR~lr~~~~v~~~~~k~ik~~lpy~   65 (65)
T PRK00172          1 MPKMKTKSGAAKRFKVTGSGKVKRKHAGKRHILTKKSTKRKRQLRGTTVVSKADAKRVKRMLPYA   65 (65)
T ss_pred             CCCcccchhhhheeEEcCCCCEEeccCCCccccccCCHHHHHhcCCCeeECHHHHHHHHHhcCCC
Confidence            57999999999999999999999999999999999999999999999999999999999999995

>TIGR00001 rpmI_bact ribosomal protein L35

Probab=99.93  E-value=2.4e-26  Score=158.48  Aligned_cols=63  Identities=59%  Similarity=0.799  Sum_probs=62.3

Q ss_pred             cCcccCcccccceEEccCcceEeeccCcccccCCCChHHHhhcCCCeeeccccHHHHHHhCCC
Q 031865           81 YKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCLPY  143 (151)
Q Consensus        81 ~KmKThKgAaKRFKvTgSGKIkR~rAgkrHlltkKS~KrKRrLrk~~~V~~~d~k~IKrlLPY  143 (151)
                      +|||||+||+|||++||+|||+|++||++|++++|+.+++|+|+++.+|+++|+++|++||||
T Consensus         1 pKmKT~~~akKRFK~T~tGKvkr~~a~k~H~l~~Ks~k~kR~L~~~~~v~~~~~~~ik~~lpy   63 (63)
T TIGR00001         1 PKMKTHKAAAKRFKITGSGKIKRKKAGKRHLLTKKSSKRKRNLRKKAIVSAGDLKRVKLLLPY   63 (63)
T ss_pred             CCcccchhhhhheEEcCCCCEEecccCcccccccCCHHHHHhcCCCeeECHHHHHHHHHhcCC
Confidence            599999999999999999999999999999999999999999999999999999999999998

This ribosomal protein is found in bacteria and organelles only. It is not closely related to any eukaryotic or archaeal ribosomal protein.

>COG0291 RpmI Ribosomal protein L35 [Translation, ribosomal structure and biogenesis]

Probab=99.92  E-value=5.7e-26  Score=158.60  Aligned_cols=65  Identities=52%  Similarity=0.698  Sum_probs=63.5

Q ss_pred             ccCcccCcccccceEEccCcceEeeccCcccccCCCChHHHhhcCCCeeeccccHHHHHHhCCCc
Q 031865           80 GYKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCLPYL  144 (151)
Q Consensus        80 ~~KmKThKgAaKRFKvTgSGKIkR~rAgkrHlltkKS~KrKRrLrk~~~V~~~d~k~IKrlLPY~  144 (151)
                      ++|||||+||+|||++||+|+|+|++||++|++++|+.+++|+||+..+|+++|.++|++||||.
T Consensus         1 MPKmKT~k~aaKRFK~T~~Gkikr~~A~k~H~l~kKs~k~kR~Lr~~~~v~~~d~k~v~~~l~~~   65 (65)
T COG0291           1 MPKMKTKKGAAKRFKITGTGKIKRKHAGKRHILTKKSTKRKRHLRKTAVVSKADLKRVKRLLLYA   65 (65)
T ss_pred             CCccchhhhhHhheeecCCCcEEecccccccccccCCHHHHHhccCCceeCHHHHHHHHHhccCC
Confidence            57999999999999999999999999999999999999999999999999999999999999984

>PF01632 Ribosomal_L35p: Ribosomal protein L35; InterPro: IPR021137 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.88  E-value=7.2e-24  Score=144.64  Aligned_cols=61  Identities=57%  Similarity=0.796  Sum_probs=55.4

Q ss_pred             cCcccCcccccceEEccCcceEeeccCcccccCCCChHHHhhcCCCeeeccccHHHHHHhC
Q 031865           81 YKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCL  141 (151)
Q Consensus        81 ~KmKThKgAaKRFKvTgSGKIkR~rAgkrHlltkKS~KrKRrLrk~~~V~~~d~k~IKrlL  141 (151)
                      +|||||+|++|||++||+|+|+|++||++|++++||.+++|+|+++.+|+++|.++|++||
T Consensus         1 pKmKT~k~a~KRFk~t~sGkikr~~agk~H~~~~Ks~krkr~Lr~~~~v~~~~~k~ikklL   61 (61)
T PF01632_consen    1 PKMKTHKSAAKRFKVTGSGKIKRKRAGKRHLLTKKSSKRKRRLRKTTLVHKADVKRIKKLL   61 (61)
T ss_dssp             ---S-HHHHHTTEEEESSSEEEEE-SSSSSSSSSSSCHCTTTTSCEEESSSHHHHHHTTTT
T ss_pred             CCccchhhhHhheeEcCCCeEEeccCCcccccccCCHHHHHHcCCCEEECHHHHHHHHHhC
Confidence            6999999999999999999999999999999999999999999999999999999999987

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 [, ]. L35 is a basic protein of 60 to 70 amino-acid residues from the large subunit []. Like many basic polypeptides, L35 completely inhibits ornithine decarboxylase when present unbound in the cell, but the inhibitory function is abolished upon its incorporation into ribosomes []. It belongs to a family of ribosomal proteins, including L35 from bacteria, plant chloroplast, red algae chloroplasts and cyanelles. In plants it is a nuclear encoded gene product, which suggests a chloroplast-to-nucleus relocation during the evolution of higher plants [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2QBE_3 2QBG_3 3SGF_7 2QOV_3 3J0Y_6 3I22_3 3E1D_W 1VS6_3 2VHN_3 1VS8_3 ....

>KOG4316 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.75  E-value=0.002  Score=52.45  Aligned_cols=74  Identities=26%  Similarity=0.294  Sum_probs=68.8

Q ss_pred             CceEEEeeccccCcccCcccccceEEccCcceEeeccCcccccCCCChHHHhhcCCCeeeccccHHHHHHhC-CC
Q 031865           70 PQTVTVFAAKGYKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCL-PY  143 (151)
Q Consensus        70 ~~s~~~~~~~~~KmKThKgAaKRFKvTgSGKIkR~rAgkrHlltkKS~KrKRrLrk~~~V~~~d~k~IKrlL-PY  143 (151)
                      ..+++-|+.++.|-||-+++-+||+.-..|-..|.++|+.-.+-+|+.-.+++|..-..-+++|-+.+-+|+ ||
T Consensus        67 ~r~~t~Fs~~kGkrktvkaVldRFkRL~~G~WIr~h~Gr~Kkl~kK~~a~~krl~~~vfcnktQs~lLDKm~Tsy  141 (172)
T KOG4316|consen   67 VRSLTYFSARKGKRKTVKAVLDRFKRLHCGLWIRAHPGRHKKLYKKDEAWQKRLLYYVFCNKTQSELLDKMMTSY  141 (172)
T ss_pred             hhhhhhhhhhhcccccHHHHHHHHHhcccCeeeeecCchhhhhhhcCHHHHHHHHHhheechHHHHHHHHHhhHH
Confidence            348889999999999999999999999999999999999999999999999999999999999999998877 44

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	151
3bbo_5	159	Homology Model For The Spinach Chloroplast 50s Subu		1e-33
2aw4_3	64	Crystal Structure Of The Bacterial Ribosome From Es		7e-08
1vs6_3	65	Crystal Structure Of The Bacterial Ribosome From Es		8e-08

>pdb|3BBO|5 Chain 5, Homology Model For The Spinach Chloroplast 50s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome Length = 159

Iteration: 1
 Score =  138 bits (348), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 68/76 (89%), Positives = 72/76 (94%)
Query: 74  TVFAAKGYKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSD 133
           TVFAAKGYKMKTHKASAKRFRVTGKGKI+RRRAGKQHLLAKKNTKRK RLSK+ +V RSD
Sbjct: 83  TVFAAKGYKMKTHKASAKRFRVTGKGKIVRRRAGKQHLLAKKNTKRKNRLSKLIQVDRSD 142
Query: 134 YDNVIGCLPYLKVNRQ 149
           YDNVIG LPYLKVNR+
Sbjct: 143 YDNVIGALPYLKVNRK 158

>pdb|2AW4|3 Chain 3, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli At 3.5 A Resolution. This File Contains The 50s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400. Length = 64

Iteration: 1
 Score = 52.8 bits (125), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 30/62 (48%), Positives = 38/62 (61%)
Query: 82  KMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCL 141
           K+KT + +AKRF+ TGKG    + A  +H+L KK TKRK  L     VS+ D   VI CL
Sbjct: 2   KIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIACL 61
Query: 142 PY 143
           PY
Sbjct: 62  PY 63

>pdb|1VS6|3 Chain 3, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli In Complex With The Antibiotic Kasugamyin At 3.5a Resolution. This File Contains The 50s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400. Length = 65

Iteration: 1
 Score = 52.8 bits (125), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 30/62 (48%), Positives = 38/62 (61%)
Query: 82  KMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCL 141
           K+KT + +AKRF+ TGKG    + A  +H+L KK TKRK  L     VS+ D   VI CL
Sbjct: 3   KIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIACL 62
Query: 142 PY 143
           PY
Sbjct: 63  PY 64

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	151
3bbo_5	159	Ribosomal protein L35; large ribosomal subunit, sp	3e-30
3r8s_3	64	50S ribosomal protein L35; protein biosynthesis, R	1e-21
3v2d_8	65	50S ribosomal protein L35; ribosome associated inh	4e-21
2zjr_3	66	50S ribosomal protein L35; ribosome, large ribosom	2e-12

>3bbo_5 Ribosomal protein L35; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 159

 Score =  106 bits (265), Expect = 3e-30
 Identities = 87/154 (56%), Positives = 105/154 (68%), Gaps = 6/154 (3%)

Query: 1   MASMISFNLKFCPLCPSSSSVRASRGSSLRLALSNKLNNSLRLNSSYSISASPLLFRHNN 60
             + +SF      L P S+   A++G SL    + +L ++L L+SS SIS+S +      
Sbjct: 6   ATATLSFKTPSLSLSPPSTRCSAAQGISLT-HFNKQLKSTLNLSSSSSISSSKVQPIVLK 64

Query: 61  LPTTVTQNR-----PQTVTVFAAKGYKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKK 115
                T +        + TVFAAKGYKMKTHKASAKRFRVTGKGKI+RRRAGKQHLLAKK
Sbjct: 65  NKRISTVDSSVSTSSPSFTVFAAKGYKMKTHKASAKRFRVTGKGKIVRRRAGKQHLLAKK 124

Query: 116 NTKRKLRLSKMHEVSRSDYDNVIGCLPYLKVNRQ 149
           NTKRK RLSK+ +V RSDYDNVIG LPYLKVNR+
Sbjct: 125 NTKRKNRLSKLIQVDRSDYDNVIGALPYLKVNRK 158

>3r8s_3 50S ribosomal protein L35; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 2awb_3 2aw4_3 2i2v_3 2j28_3 2i2t_3* 2qao_3* 2qba_3* 2qbc_3* 2qbe_3 2qbg_3 2qbi_3* 2qbk_3* 2qov_3 2qox_3 2qoz_3* 2qp1_3* 2rdo_3 2vhm_3 2vhn_3 2wwq_7* ... Length = 64

 Score = 81.5 bits (202), Expect = 1e-21
 Identities = 30/62 (48%), Positives = 38/62 (61%)

Query: 82  KMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCL 141
           K+KT + +AKRF+ TGKG    + A  +H+L KK TKRK  L     VS+ D   VI CL
Sbjct: 2   KIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIACL 61

Query: 142 PY 143
           PY
Sbjct: 62  PY 63

>3v2d_8 50S ribosomal protein L35; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 1vsp_a 2hgj_7 2hgq_7 2hgu_7 1vsa_a 2j03_8 2jl6_8 2jl8_8 2v47_8 2v49_8 2wdi_8 2wdj_8 2wdl_8 2wdn_8 2wh2_8 2wh4_8 2wrj_8 2wrl_8 2wro_8 2wrr_8 ... Length = 65

 Score = 80.0 bits (198), Expect = 4e-21
 Identities = 20/62 (32%), Positives = 37/62 (59%)

Query: 82  KMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCL 141
           KMKTHK + KR ++T  GK++  + GK+HL  +K+ K   +  +   +++ + + +   L
Sbjct: 3   KMKTHKGAKKRVKITASGKVVAMKTGKRHLNWQKSGKEIRQKGRKFVLAKPEAERIKLLL 62

Query: 142 PY 143
           PY
Sbjct: 63  PY 64

>2zjr_3 50S ribosomal protein L35; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: d.301.1.1 PDB: 2zjp_3* 1sm1_3 2zjq_3 3cf5_3* 3dll_3* 3pio_3* 3pip_3* 1nwy_3* 1nwx_3* 1xbp_3* 1nkw_3 1yl3_8 2b66_8 2b9n_8 2b9p_8 1pnu_3 1pny_3 1vor_5 1vou_5 1vow_5 ... Length = 66

 Score = 58.0 bits (140), Expect = 2e-12
 Identities = 19/64 (29%), Positives = 36/64 (56%)

Query: 82  KMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCL 141
           KMKTHK + +R ++TG GK++  ++GK+H    K+        K   ++++++  +   L
Sbjct: 3   KMKTHKMAKRRIKITGTGKVMAFKSGKRHQNTGKSGDEIRGKGKGFVLAKAEWARMKLML 62

Query: 142 PYLK 145
           P  K
Sbjct: 63  PRGK 66

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	151
3bbo_5	159	Ribosomal protein L35; large ribosomal subunit, sp	100.0
2zjr_3	66	50S ribosomal protein L35; ribosome, large ribosom	99.94
3v2d_8	65	50S ribosomal protein L35; ribosome associated inh	99.94
3r8s_3	64	50S ribosomal protein L35; protein biosynthesis, R	99.94

>3bbo_5 Ribosomal protein L35; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}

Probab=100.00  E-value=4.7e-45  Score=288.85  Aligned_cols=142  Identities=60%  Similarity=0.793  Sum_probs=61.9

Q ss_pred             ceeeeeeeccCCCCCCcc-ccccccceeeeccccc-cccccccccceec----Cccc--ccccccCCCcccCCCCceEEE
Q 031865            4 MISFNLKFCPLCPSSSSV-RASRGSSLRLALSNKL-NNSLRLNSSYSIS----ASPL--LFRHNNLPTTVTQNRPQTVTV   75 (151)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~-~~~~~~~~s~~~~----~~~~--~~~~~~~~~~~~~~~~~s~~~   75 (151)
                      |+||++.+|||  +|+++ |++|+ +++|+++++. +.+|+|+||++|+    +||+  +++.+++.+|+.+ ++.++++
T Consensus         9 ~~~~~~~~~~~--~s~~~~~~~~~-~~~~~~~~~~~~~~~~~~ss~~is~~~~~p~~~~~~~~~~~~~~~~~-~~~~~~v   84 (159)
T 3bbo_5            9 TLSFKTPSLSL--SPPSTRCSAAQ-GISLTHFNKQLKSTLNLSSSSSISSSKVQPIVLKNKRISTVDSSVST-SSPSFTV   84 (159)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHhhcccccc--CCCCcceeecc-cccCchhHHHHhhhhhhhhccccccCCCccccccccccccccCcccc-cccceee
Confidence            89999999998  66666 99999 9999998876 4599999999998    4999  9999999999998 8999999


Q ss_pred             eeccccCcccCcccccceEEccCcceEeeccCcccccCCCChHHHhhcCCCeeeccccHHHHHHhCCCcchhcc
Q 031865           76 FAAKGYKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCLPYLKVNRQ  149 (151)
Q Consensus        76 ~~~~~~KmKThKgAaKRFKvTgSGKIkR~rAgkrHlltkKS~KrKRrLrk~~~V~~~d~k~IKrlLPY~k~~r~  149 (151)
                      ++.+|+|||||+||+||||+||+|||+|++||++|++++|+.+|+|+||++.+|+++|+++|++||||++|||+
T Consensus        85 v~~~MPKMKThsgAaKRFKvTgSGKiKR~kAgkrHiLtkKS~KrKR~LRk~~~V~~aD~k~IKrlLPy~kv~r~  158 (159)
T 3bbo_5           85 FAAKGYKMKTHKASAKRFRVTGKGKIVRRRAGKQHLLAKKNTKRKNRLSKLIQVDRSDYDNVIGALPYLKVNRK  158 (159)
T ss_dssp             ------CCCCCHHHHTTCCBCSSSCBEEECSSCTTCCSSCCSSCTTSCSEEECCSTHHHHTTTTTTTC------
T ss_pred             hhcCCcccccchhhhheeEEcCCccEEeccCCCCCCcCcCCHHHHHhcCCCeeECHHHHHHHHHhcCcchhccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999997

>2zjr_3 50S ribosomal protein L35; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: d.301.1.1 PDB: 2zjp_3* 1sm1_3 2zjq_3 3cf5_3* 3dll_3* 3pio_3* 3pip_3* 1nwy_3* 1nwx_3* 1xbp_3* 1nkw_3 1yl3_8 2b66_8 2b9n_8 2b9p_8 1pnu_3 1pny_3 1vor_5 1vou_5 1vow_5 ...

Probab=99.94  E-value=3.2e-28  Score=168.74  Aligned_cols=66  Identities=29%  Similarity=0.395  Sum_probs=64.4

Q ss_pred             ccCcccCcccccceEEccCcceEeeccCcccccCCCChHHHhhcCCCeeeccccHHHHHHhCCCcc
Q 031865           80 GYKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCLPYLK  145 (151)
Q Consensus        80 ~~KmKThKgAaKRFKvTgSGKIkR~rAgkrHlltkKS~KrKRrLrk~~~V~~~d~k~IKrlLPY~k  145 (151)
                      |+|||||+||+|||++||+|||+|++||++|++++||.+++|+|+++.+|+++|+++|++||||++
T Consensus         1 MPKmKT~~gaaKRFk~TgsGKikr~~a~k~H~l~kKs~krkR~Lr~~~~v~~~d~k~ik~lLp~~~   66 (66)
T 2zjr_3            1 MPKMKTHKMAKRRIKITGTGKVMAFKSGKRHQNTGKSGDEIRGKGKGFVLAKAEWARMKLMLPRGK   66 (66)
T ss_pred             CCCcccchhhhheeEEcCCCcEEeccCCCccCcccCCHHHHHhcCCCeeECHHHHHHHHHhcCCCC
Confidence            589999999999999999999999999999999999999999999999999999999999999974

>3v2d_8 50S ribosomal protein L35; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 1vsp_a 2hgj_7 2hgq_7 2hgu_7 1vsa_a 2j03_8 2jl6_8 2jl8_8 2v47_8 2v49_8 2wdi_8 2wdj_8 2wdl_8 2wdn_8 2wh2_8 2wh4_8 2wrj_8 2wrl_8 2wro_8 2wrr_8 ...

Probab=99.94  E-value=4.3e-28  Score=167.54  Aligned_cols=65  Identities=31%  Similarity=0.454  Sum_probs=63.2

Q ss_pred             ccCcccCcccccceEEccCcceEeeccCcccccCCCChHHHhhcCCCeeeccccHHHHHHhCCCc
Q 031865           80 GYKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCLPYL  144 (151)
Q Consensus        80 ~~KmKThKgAaKRFKvTgSGKIkR~rAgkrHlltkKS~KrKRrLrk~~~V~~~d~k~IKrlLPY~  144 (151)
                      |+|||||+||+|||++||+|||+|++||++|++++||.+++|+|+++.+|+++|+++|++||||+
T Consensus         1 MPKmKT~~ga~KRFk~TgsGKikr~~a~k~H~l~kKs~krkR~Lr~~~~v~~~d~k~vk~lLpy~   65 (65)
T 3v2d_8            1 MPKMKTHKGAKKRVKITASGKVVAMKTGKRHLNWQKSGKEIRQKGRKFVLAKPEAERIKLLLPYE   65 (65)
T ss_dssp             -CCCCCCHHHHTTEEECTTSCEEEECSSCSSCCTTSCHHHHHHTTSEEECCHHHHHHHHHTCTTC
T ss_pred             CCCcccchhhhheeEEcCCCCEEeccCCCCCCccCCCHHHHHhcCCCEEECHHHHHHHHHhcCCC
Confidence            58999999999999999999999999999999999999999999999999999999999999995

>3r8s_3 50S ribosomal protein L35; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 2awb_3 2aw4_3 2i2v_3 2j28_3 2i2t_3* 2qao_3* 2qba_3* 2qbc_3* 2qbe_3 2qbg_3 2qbi_3* 2qbk_3* 2qov_3 2qox_3 2qoz_3* 2qp1_3* 2rdo_3 2vhm_3 2vhn_3 2wwq_7* ...

Probab=99.94  E-value=1e-27  Score=165.13  Aligned_cols=64  Identities=47%  Similarity=0.679  Sum_probs=62.9

Q ss_pred             cCcccCcccccceEEccCcceEeeccCcccccCCCChHHHhhcCCCeeeccccHHHHHHhCCCc
Q 031865           81 YKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCLPYL  144 (151)
Q Consensus        81 ~KmKThKgAaKRFKvTgSGKIkR~rAgkrHlltkKS~KrKRrLrk~~~V~~~d~k~IKrlLPY~  144 (151)
                      +|||||+||+|||++||+|||+|++||++|++++||.+++|+|+++.+|+++|+++|++||||+
T Consensus         1 PKmKT~~~a~KRFk~TgsGKikr~~a~k~H~l~kKs~krkR~Lr~~~~v~~~d~k~vk~lLpy~   64 (64)
T 3r8s_3            1 PKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIACLPYA   64 (64)
T ss_dssp             CCCCCCTTTTTTCEECSSSCEEEECSSCSSSCTTSCHHHHHHTSSEEECCTTTHHHHHHHCTTC
T ss_pred             CCCccchhhhheeEEcCCCCEEeccCCCCCCccCCCHHHHHhcCCCEEECHHHHHHHHHHcCCC
Confidence            5999999999999999999999999999999999999999999999999999999999999995

---

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	151
d2j0181	64	d.301.1.1 (8:2-65) Ribosomal protein L35p {Thermus	6e-20
d2qam31	64	d.301.1.1 (3:1-64) Ribosomal protein L35p {Escheri	6e-20

>d2j0181 d.301.1.1 (8:2-65) Ribosomal protein L35p {Thermus thermophilus [TaxId: 274]} Length = 64

class: Alpha and beta proteins (a+b)
fold: L35p-like
superfamily: L35p-like
family: Ribosomal protein L35p
domain: Ribosomal protein L35p
species: Thermus thermophilus [TaxId: 274]

 Score = 75.8 bits (187), Expect = 6e-20
 Identities = 20/62 (32%), Positives = 37/62 (59%)

Query: 82  KMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCL 141
           KMKTHK + KR ++T  GK++  + GK+HL  +K+ K   +  +   +++ + + +   L
Sbjct: 2   KMKTHKGAKKRVKITASGKVVAMKTGKRHLNWQKSGKEIRQKGRKFVLAKPEAERIKLLL 61

Query: 142 PY 143
           PY
Sbjct: 62  PY 63

>d2qam31 d.301.1.1 (3:1-64) Ribosomal protein L35p {Escherichia coli [TaxId: 562]} Length = 64

class: Alpha and beta proteins (a+b)
fold: L35p-like
superfamily: L35p-like
family: Ribosomal protein L35p
domain: Ribosomal protein L35p
species: Escherichia coli [TaxId: 562]

 Score = 75.8 bits (187), Expect = 6e-20
 Identities = 30/62 (48%), Positives = 38/62 (61%)

Query: 82  KMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCL 141
           K+KT + +AKRF+ TGKG    + A  +H+L KK TKRK  L     VS+ D   VI CL
Sbjct: 2   KIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIACL 61

Query: 142 PY 143
           PY
Sbjct: 62  PY 63

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	151
d2qam31	64	Ribosomal protein L35p {Escherichia coli [TaxId: 5	99.93
d2j0181	64	Ribosomal protein L35p {Thermus thermophilus [TaxI	99.93
d2zjr31	63	Ribosomal protein L35p {Deinococcus radiodurans [T	99.92

>d2qam31 d.301.1.1 (3:1-64) Ribosomal protein L35p {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: L35p-like
superfamily: L35p-like
family: Ribosomal protein L35p
domain: Ribosomal protein L35p
species: Escherichia coli [TaxId: 562]

Probab=99.93  E-value=1.2e-27  Score=162.73  Aligned_cols=64  Identities=47%  Similarity=0.679  Sum_probs=63.0

Q ss_pred             cCcccCcccccceEEccCcceEeeccCcccccCCCChHHHhhcCCCeeeccccHHHHHHhCCCc
Q 031865           81 YKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCLPYL  144 (151)
Q Consensus        81 ~KmKThKgAaKRFKvTgSGKIkR~rAgkrHlltkKS~KrKRrLrk~~~V~~~d~k~IKrlLPY~  144 (151)
                      +|||||+||+|||++||+|||+|++||++|++++||.+++|+|+++.+|+++|.++|++||||.
T Consensus         1 PKmKT~k~akKRfkvT~sGKi~r~~agk~H~l~~Ks~krkR~lr~~~~v~~~d~k~ik~lLPYa   64 (64)
T d2qam31           1 PKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIACLPYA   64 (64)
T ss_dssp             CCCCCCTTTTTTCCCCSSSCCCBCCSSSSSCCTTSCHHHHHTTSSCBCCCSSSHHHHHHHCTTC
T ss_pred             CCCccchhhhhheeECCCCCEeeccCCCCcccccCCHHHHHhcCCCeeECHHHHHHHHHhCCCC
Confidence            6999999999999999999999999999999999999999999999999999999999999995

>d2j0181 d.301.1.1 (8:2-65) Ribosomal protein L35p {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: L35p-like
superfamily: L35p-like
family: Ribosomal protein L35p
domain: Ribosomal protein L35p
species: Thermus thermophilus [TaxId: 274]

Probab=99.93  E-value=2.4e-27  Score=161.37  Aligned_cols=63  Identities=32%  Similarity=0.502  Sum_probs=62.4

Q ss_pred             cCcccCcccccceEEccCcceEeeccCcccccCCCChHHHhhcCCCeeeccccHHHHHHhCCC
Q 031865           81 YKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCLPY  143 (151)
Q Consensus        81 ~KmKThKgAaKRFKvTgSGKIkR~rAgkrHlltkKS~KrKRrLrk~~~V~~~d~k~IKrlLPY  143 (151)
                      +|||||+||+|||++||+|||+|++||++|++++||.+++|+|+++.+|+++|.+.|++||||
T Consensus         1 PKmKT~k~a~KRFk~T~sGKikr~~ag~~H~l~~Ks~k~kR~lr~~~~v~~~~~k~ik~lLPY   63 (64)
T d2j0181           1 PKMKTHKGAKKRVKITASGKVVAMKTGKRHLNWQKSGKEIRQKGRKFVLAKPEAERIKLLLPY   63 (64)
T ss_dssp             CCCCCCHHHHHHCEECSSSCEEECCTTTTTCSSCSCCSTTTSCSCEECCSSHHHHHHTTTTTC
T ss_pred             CCCccchhhhhheeEcCCCCEEecccCCccccccCCHHHHHhcCCCeeECHHHHHHHHHhCCC
Confidence            699999999999999999999999999999999999999999999999999999999999999

>d2zjr31 d.301.1.1 (3:2-64) Ribosomal protein L35p {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a+b)
fold: L35p-like
superfamily: L35p-like
family: Ribosomal protein L35p
domain: Ribosomal protein L35p
species: Deinococcus radiodurans [TaxId: 1299]

Probab=99.92  E-value=4e-26  Score=155.22  Aligned_cols=62  Identities=29%  Similarity=0.455  Sum_probs=61.3

Q ss_pred             cCcccCcccccceEEccCcceEeeccCcccccCCCChHHHhhcCCCeeeccccHHHHHHhCC
Q 031865           81 YKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCLP  142 (151)
Q Consensus        81 ~KmKThKgAaKRFKvTgSGKIkR~rAgkrHlltkKS~KrKRrLrk~~~V~~~d~k~IKrlLP  142 (151)
                      +|||||+||+|||++||+|||+|++||++|++++||.+++|+|+++.+|+++|++.|++|||
T Consensus         1 PKmKT~k~a~KRFk~T~sGKv~r~~agk~H~l~kKs~krkR~lr~~~~v~~~~~k~ik~~LP   62 (63)
T d2zjr31           1 PKMKTHKMAKRRIKITGTGKVMAFKSGKRHQNTGKSGDEIRGKGKGFVLAKAEWARMKLMLP   62 (63)
T ss_pred             CCcccchhhhhheeECCCCCEeeccCCcccccccCCHHHHHhcCCCceeCHHHHHHHHHHCC
Confidence            69999999999999999999999999999999999999999999999999999999999999