Citrus Sinensis ID: 040088

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-
Protein Sequence
MATVGGQLIWEIVKKNNCFLVKEFGRGSASAHAVITCSVYKFGGRKIECSTFVFGRFCGNRGKKIKLKTVTIQPGKDQVVVLATTKTKKQNKPIALLHKSVMKHEIHRMAKVIANRVGDNYYQPDLKNAVE
Secondary Structure (PSIPRED)
ccccccccEEEEEEcccEEEEEEcccccccccccEEccEEEEcccccEEccEEEccccccccccccccEEEEEEcccccEEEEEEccccccccccEEEEEEEcccHHHHHHHHHHHHccccccHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccccccEEEEEEEccccEEEEEccccccccccccccccEEEccccccccEEEEccccccccEEEEcEEEEEEEcccccEEEEEEccccccccccccEEEEccccHHHHHHHHHHHHHHccccHHHHHHcc
Coil and Loop (DISEMBL)
MATVGGQLIWEIVKKNNCFlvkefgrgsasaHAVITCSvykfggrkiecstfvfgrfcgnrgkkiklktvtiqpgkdQVVVLATTktkkqnkpiaLLHKSVMKHEIHRMAKVIANrvgdnyyqpdlknave
Flexible Loop (DISEMBL)
MATVGGQLIWEIVKKNNCFLVKEfgrgsasahAVITCSVYKFGGRKIECSTFVFgrfcgnrgkkiklktvtiqpgkdqVVVLATtktkkqnkpiallHKSVMKHEIHRMAKVIAnrvgdnyyqpdlknave
Low Complexity Region (SEG)
MATVGGQLIWEIVKKNNCFLVKEFGRGSASAHAVITCSVYKFGGRKIECSTFVFGRFCGNRGKKIKLKTVTIQPGKDQVVVLATTKTKKQNKPIALLHKSVMKHEIHRMAKVIANRVGDNYYQPDLKNAVE
Disordered region (IsUnstruct)
***VGGQLIWEIVKKNNCFLVKEFGRGSASAHAVITCSVYKFGGRKIECSTFVFGRFCGNRGKKIKLKTVTIQPGKDQVVVLATTKTKKQNKPIALLHKSVMKHEIHRMAKVIANRVGDNYY*********
Disordered Region (DISOPRED)
****GGQLIWEIVKKNNCFLVK************ITCSVYKFGGRKIECSTFVFGRFCGNRGKKIKLKTVTIQPGKDQVVV******************************VIANRVGDNYYQ*DL*****
Disordered Region (DISEMBL)
MATVGGQLIWEIVKKNNCFLVKEFGRGSASAHAVITCSVYKFGGRKIECSTFVFGRFCGNRGKKIKLKTVTIQPGKDQVVVLATTKTKKQNKPIALLHKSVMKHEIHRMAKVIANRVGDNYYQPDLKNAVE
Disordered Region (DISPRO)
****GGQLIWEIVKKNNCFLVKEFGRGSASAHAVITCSVYKFGGRKIECSTFVFGRFCGNRGKKIKLKTVTIQPGKDQVVVLATTKTKKQNKPIALLHKSVMKHEIHRMAKVIANRVGDNYYQPDLKNAV*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MATVGGQLIWEIVKKNNCFLVKEFGRGSASAHAVITCSVYKFGGRKIECSTFVFGRFCGNRGKKIKLKTVTIQPGKDQVVVLATTKTKKQNKPIALLHKSVMKHEIHRMAKVIANRVGDNYYQPDLKNAVE
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	131	2.2.26 [Sep-21-2011]
Q9M0E2	143	60S ribosomal protein L28	yes	no	0.839	0.769	0.522	4e-29
O82204	143	60S ribosomal protein L28	no	no	0.847	0.776	0.518	6e-28
O14069	134	Probable 60S ribosomal pr	yes	no	0.816	0.798	0.320	0.0001

>sp|Q9M0E2|RL282_ARATH 60S ribosomal protein L28-2 OS=Arabidopsis thaliana GN=RPL28C PE=2 SV=1

 Score =  126 bits (316), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 71/136 (52%), Positives = 89/136 (65%), Gaps = 26/136 (19%)

Query: 1   MATVGGQLIWEIVKKNNCFLVKEFGRGSA------SAHAVITCSVYKFGGRKIECSTFVF 54
           MATV GQLIWEIVK+NNCFLVK+FGRG+A       ++ ++  + YK  G          
Sbjct: 1   MATVPGQLIWEIVKRNNCFLVKQFGRGNAKVQFSKESNNLVNINSYKHSG---------- 50

Query: 55  GRFCGNRGKKIKLKTVTIQP-GKDQVVVLATTKTKKQNKPIALLHKSVMKHEIHRMAKVI 113
                N+      KTVTIQ  GKDQ VVL TTKTK+QNKP   ++KS++K E  RM+KV+
Sbjct: 51  ---LANK------KTVTIQAAGKDQGVVLGTTKTKRQNKPKLSVNKSILKKEFSRMSKVV 101

Query: 114 ANRVGDNYYQPDLKNA 129
           AN+V DNYY+PDLK A
Sbjct: 102 ANQVVDNYYRPDLKKA 117

Arabidopsis thaliana (taxid: 3702)

>sp|O82204|RL281_ARATH 60S ribosomal protein L28-1 OS=Arabidopsis thaliana GN=RPL28A PE=1 SV=1

 Score =  122 bits (306), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 71/137 (51%), Positives = 83/137 (60%), Gaps = 26/137 (18%)

Query: 1   MATVGGQLIWEIVKKNNCFLVKEFGRG------SASAHAVITCSVYKFGGRKIECSTFVF 54
           MATV GQLIWEIVK NNCFLVK+FGRG      S   + +     YK  G          
Sbjct: 1   MATVPGQLIWEIVKNNNCFLVKQFGRGNSKVQFSKETNNLTNVHSYKHSG---------- 50

Query: 55  GRFCGNRGKKIKLKTVTIQPG-KDQVVVLATTKTKKQNKPIALLHKSVMKHEIHRMAKVI 113
                N+      KTVTIQ   KDQ VVLATTKTKKQNKP   ++KS++K E  RM+K +
Sbjct: 51  ---LANK------KTVTIQAADKDQAVVLATTKTKKQNKPKLSVNKSILKKEFPRMSKAV 101

Query: 114 ANRVGDNYYQPDLKNAV 130
           AN+V DNYY+PDLK A 
Sbjct: 102 ANQVVDNYYRPDLKKAA 118

Arabidopsis thaliana (taxid: 3702)

>sp|O14069|RL28E_SCHPO Probable 60S ribosomal protein L28e OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpl28e PE=1 SV=1

 Score = 45.1 bits (105), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 41/128 (32%), Positives = 54/128 (42%), Gaps = 21/128 (16%)

Query: 3   TVGGQLIWEIVKKNNCFLVK--EFGRGSASAHAVITCSVYKFGGRKIECSTFVFGRFCGN 60
           +V   LIW++++ NN FLVK  EFG               +F    +  S     RF G 
Sbjct: 2   SVSNDLIWQVIRDNNRFLVKRPEFG-------------GIQFNREPVNVSGKNAQRFSG- 47

Query: 61  RGKKIKLKTVTIQPGKDQVVVLAT-TKTKKQNKPIALLHKSVMKHEIHRMA-KVIANRVG 118
                  K V +Q    + VVL T T  K   KP  L  K V+ +   R   K IA R+G
Sbjct: 48  ---LCNDKAVGVQANSPRGVVLITKTNPKNAQKPAKLFRKDVIANASSRKTYKSIAGRIG 104

Query: 119 DNYYQPDL 126
              Y+ DL
Sbjct: 105 RTGYRDDL 112

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

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	131
255549668	144	60S ribosomal protein L28, putative [Ric	0.847	0.770	0.573	7e-33
351728103	150	uncharacterized protein LOC100500189 [Gl	0.839	0.733	0.558	6e-32
356550472	150	PREDICTED: 60S ribosomal protein L28-2 [	0.877	0.766	0.580	7e-32
351722416	150	uncharacterized protein LOC100499921 [Gl	0.839	0.733	0.544	3e-31
224054432	146	predicted protein [Populus trichocarpa]	0.885	0.794	0.592	4e-31
255546219	144	60S ribosomal protein L28, putative [Ric	0.847	0.770	0.554	2e-30
225442353	149	PREDICTED: 60S ribosomal protein L28-2 [	0.847	0.744	0.558	4e-30
224073524	147	predicted protein [Populus trichocarpa]	0.847	0.755	0.562	6e-30
449458189	148	PREDICTED: 60S ribosomal protein L28-2-l	0.847	0.75	0.532	9e-30
89258491	150	putative ribosomal protein L28 [Gossypiu	0.847	0.74	0.540	9e-30

>gi|255549668|ref|XP_002515885.1| 60S ribosomal protein L28, putative [Ricinus communis] gi|223544790|gb|EEF46305.1| 60S ribosomal protein L28, putative [Ricinus communis]

 Score =  145 bits (365), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 78/136 (57%), Positives = 89/136 (65%), Gaps = 25/136 (18%)

Query: 1   MATVGGQLIWEIVKKNNCFLVKEFGRGSAS------AHAVITCSVYKFGGRKIECSTFVF 54
           MATV GQLIWE VKKNNCFLVK+FGRGSAS       + +   + YK  G          
Sbjct: 1   MATVPGQLIWEAVKKNNCFLVKQFGRGSASVQFSKEPNNLYNLNSYKHSG---------- 50

Query: 55  GRFCGNRGKKIKLKTVTIQPGKDQVVVLATTKTKKQNKPIALLHKSVMKHEIHRMAKVIA 114
                N+      KTV+IQ GKDQ V+LATTKTKKQN+P ALLHKSVMK E  RMAK + 
Sbjct: 51  ---LSNK------KTVSIQAGKDQSVILATTKTKKQNRPSALLHKSVMKKEFRRMAKAVQ 101

Query: 115 NRVGDNYYQPDLKNAV 130
           N+VGDNYY+PDLK A 
Sbjct: 102 NQVGDNYYRPDLKKAA 117

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351728103|ref|NP_001238207.1| uncharacterized protein LOC100500189 [Glycine max] gi|255629617|gb|ACU15156.1| unknown [Glycine max]

 Score =  142 bits (357), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 76/136 (55%), Positives = 89/136 (65%), Gaps = 26/136 (19%)

Query: 1   MATVGGQLIWEIVKKNNCFLVKEFGRGSAS------AHAVITCSVYKFGGRKIECSTFVF 54
           MATV GQLIWE+VKKNN FLVKEFGRG+ S       + +   + +K+ G          
Sbjct: 1   MATVPGQLIWEVVKKNNSFLVKEFGRGTQSVQFSREPNNLYNLNTFKYSG---------- 50

Query: 55  GRFCGNRGKKIKLKTVTIQP-GKDQVVVLATTKTKKQNKPIALLHKSVMKHEIHRMAKVI 113
                N+      KTVT+QP GKDQ V+LATTKTKKQNKP ALLHKSVMK E  RMAK +
Sbjct: 51  ---LANK------KTVTVQPTGKDQSVLLATTKTKKQNKPAALLHKSVMKKEFRRMAKAV 101

Query: 114 ANRVGDNYYQPDLKNA 129
            N+V DNYY+PDLK A
Sbjct: 102 QNQVADNYYRPDLKKA 117

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356550472|ref|XP_003543611.1| PREDICTED: 60S ribosomal protein L28-2 [Glycine max]

 Score =  141 bits (356), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 76/131 (58%), Positives = 88/131 (67%), Gaps = 16/131 (12%)

Query: 1   MATVGGQLIWEIVKKNNCFLVKEFGRGSASAH-AVITCSVYKFGGRKIECSTFVFGRFCG 59
           M+TV GQLIWEIVKKNN FLVKEFGRG+ S   +    ++Y         +TF +     
Sbjct: 1   MSTVPGQLIWEIVKKNNSFLVKEFGRGTQSVQFSREPNNLY-------NLNTFKYSGLAN 53

Query: 60  NRGKKIKLKTVTIQP-GKDQVVVLATTKTKKQNKPIALLHKSVMKHEIHRMAKVIANRVG 118
                   KTVT+QP GKDQ V+LATTKTKKQNKP ALLHKSVMK E  RMAK + N+V 
Sbjct: 54  Q-------KTVTVQPAGKDQSVLLATTKTKKQNKPAALLHKSVMKKEFRRMAKAVQNQVA 106

Query: 119 DNYYQPDLKNA 129
           DNYY+PDLK A
Sbjct: 107 DNYYRPDLKRA 117

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351722416|ref|NP_001238011.1| uncharacterized protein LOC100499921 [Glycine max] gi|255627703|gb|ACU14196.1| unknown [Glycine max]

 Score =  139 bits (350), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 74/136 (54%), Positives = 90/136 (66%), Gaps = 26/136 (19%)

Query: 1   MATVGGQLIWEIVKKNNCFLVKEFGRGSAS------AHAVITCSVYKFGGRKIECSTFVF 54
           MATV GQL+WEIVKKNN FLVK+FGRG+ S      ++ +   + +K+ G          
Sbjct: 1   MATVPGQLVWEIVKKNNSFLVKQFGRGTQSVEFSRESNNLYNLNSFKYSG---------- 50

Query: 55  GRFCGNRGKKIKLKTVTIQP-GKDQVVVLATTKTKKQNKPIALLHKSVMKHEIHRMAKVI 113
                N+      KTVT+QP GKDQ V+LATTKTKKQNKP ALLHKSVMK E  RMAK +
Sbjct: 51  ---LANK------KTVTVQPEGKDQAVLLATTKTKKQNKPAALLHKSVMKKEFRRMAKAV 101

Query: 114 ANRVGDNYYQPDLKNA 129
            N+V +NYY+PDLK A
Sbjct: 102 ENQVAENYYRPDLKKA 117

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224054432|ref|XP_002298257.1| predicted protein [Populus trichocarpa] gi|118482187|gb|ABK93022.1| unknown [Populus trichocarpa] gi|222845515|gb|EEE83062.1| predicted protein [Populus trichocarpa]

 Score =  139 bits (350), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 77/130 (59%), Positives = 84/130 (64%), Gaps = 14/130 (10%)

Query: 1   MATVGGQLIWEIVKKNNCFLVKEFGRGSASAHAVITCSVYKFGGRKIECSTFVFGRFCGN 60
           MATV GQLIWEIVKKNN FLVK+FGRG+AS          +F             +  G 
Sbjct: 1   MATVPGQLIWEIVKKNNSFLVKQFGRGTAS---------LQFSKENNNLYNLNSYKHSGL 51

Query: 61  RGKKIKLKTVTIQPG-KDQVVVLATTKTKKQNKPIALLHKSVMKHEIHRMAKVIANRVGD 119
             KK    TVTIQP  KDQ VVLATTKTKKQNKP ALLHKSVMK E  RMAK + N+V D
Sbjct: 52  ANKK----TVTIQPADKDQAVVLATTKTKKQNKPAALLHKSVMKKEFSRMAKAVENQVAD 107

Query: 120 NYYQPDLKNA 129
           N Y+PDLK A
Sbjct: 108 NNYRPDLKRA 117

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255546219|ref|XP_002514169.1| 60S ribosomal protein L28, putative [Ricinus communis] gi|223546625|gb|EEF48123.1| 60S ribosomal protein L28, putative [Ricinus communis]

 Score =  137 bits (344), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 76/137 (55%), Positives = 89/137 (64%), Gaps = 26/137 (18%)

Query: 1   MATVGGQLIWEIVKKNNCFLVKEFGRGSAS------AHAVITCSVYKFGGRKIECSTFVF 54
           MATV GQLIWEIVK NN FLVKEFGRG+AS      ++ +   + YK  G          
Sbjct: 1   MATVPGQLIWEIVKTNNSFLVKEFGRGNASVQFSKESNNLYNLNSYKHSG---------- 50

Query: 55  GRFCGNRGKKIKLKTVTIQPG-KDQVVVLATTKTKKQNKPIALLHKSVMKHEIHRMAKVI 113
                N+      KTV+IQPG KD  VVLATTKTKKQNKP + LHKSVM+ E  RMAK +
Sbjct: 51  ---LANK------KTVSIQPGGKDLSVVLATTKTKKQNKPASSLHKSVMRKEFRRMAKAV 101

Query: 114 ANRVGDNYYQPDLKNAV 130
           +N+VGDNYY+PDLK A 
Sbjct: 102 SNQVGDNYYRPDLKKAA 118

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225442353|ref|XP_002281233.1| PREDICTED: 60S ribosomal protein L28-2 [Vitis vinifera] gi|147863559|emb|CAN84039.1| hypothetical protein VITISV_024169 [Vitis vinifera] gi|297743118|emb|CBI35985.3| unnamed protein product [Vitis vinifera]

 Score =  135 bits (341), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 76/136 (55%), Positives = 87/136 (63%), Gaps = 25/136 (18%)

Query: 1   MATVGGQLIWEIVKKNNCFLVKEFGRGSAS------AHAVITCSVYKFGGRKIECSTFVF 54
           MATV GQLIWEIVKKN+ FLVKEFG G+AS      ++ +   + YK  G          
Sbjct: 1   MATVPGQLIWEIVKKNSSFLVKEFGNGTASVQFSKESNNLYNVNSYKHSG---------- 50

Query: 55  GRFCGNRGKKIKLKTVTIQPGKDQVVVLATTKTKKQNKPIALLHKSVMKHEIHRMAKVIA 114
                N       KTVTIQ GKD  VVLATTKTKKQNKP +LLHKS MK E  RMAK ++
Sbjct: 51  ---LANH------KTVTIQGGKDNAVVLATTKTKKQNKPGSLLHKSAMKKEFRRMAKAVS 101

Query: 115 NRVGDNYYQPDLKNAV 130
           N+VGDNYY+PDLK A 
Sbjct: 102 NQVGDNYYRPDLKKAA 117

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224073524|ref|XP_002304107.1| predicted protein [Populus trichocarpa] gi|224073532|ref|XP_002304108.1| predicted protein [Populus trichocarpa] gi|118481531|gb|ABK92708.1| unknown [Populus trichocarpa] gi|222841539|gb|EEE79086.1| predicted protein [Populus trichocarpa] gi|222841540|gb|EEE79087.1| predicted protein [Populus trichocarpa]

 Score =  135 bits (340), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 77/137 (56%), Positives = 88/137 (64%), Gaps = 26/137 (18%)

Query: 1   MATVGGQLIWEIVKKNNCFLVKEFGRGSAS------AHAVITCSVYKFGGRKIECSTFVF 54
           MATV GQLIWEIVKKNNCFLVK+FGRG+AS      ++ +   + YK  G          
Sbjct: 1   MATVPGQLIWEIVKKNNCFLVKQFGRGTASLRFSKESNNLYNLNSYKHSG---------- 50

Query: 55  GRFCGNRGKKIKLKTVTIQPG-KDQVVVLATTKTKKQNKPIALLHKSVMKHEIHRMAKVI 113
                N+      KTVTIQ G KDQ VVLAT+KTKKQNKP AL HKSVMK E  RMAK +
Sbjct: 51  ---LANK------KTVTIQAGDKDQAVVLATSKTKKQNKPAALFHKSVMKKEFRRMAKAV 101

Query: 114 ANRVGDNYYQPDLKNAV 130
            N+V  NYY+PDLK A 
Sbjct: 102 ENQVEGNYYRPDLKKAA 118

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449458189|ref|XP_004146830.1| PREDICTED: 60S ribosomal protein L28-2-like isoform 1 [Cucumis sativus] gi|449458191|ref|XP_004146831.1| PREDICTED: 60S ribosomal protein L28-2-like isoform 2 [Cucumis sativus] gi|449476678|ref|XP_004154804.1| PREDICTED: 60S ribosomal protein L28-2-like isoform 1 [Cucumis sativus] gi|449476681|ref|XP_004154805.1| PREDICTED: 60S ribosomal protein L28-2-like isoform 2 [Cucumis sativus]

 Score =  134 bits (338), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 73/137 (53%), Positives = 87/137 (63%), Gaps = 26/137 (18%)

Query: 1   MATVGGQLIWEIVKKNNCFLVKEFGRGSA------SAHAVITCSVYKFGGRKIECSTFVF 54
           MA V GQLIWEIVK+NN FLVKEFGRG+A       A+ +   + YK  G          
Sbjct: 1   MAAVPGQLIWEIVKRNNSFLVKEFGRGTAGVQFSKEANNLYNLNSYKHSG---------- 50

Query: 55  GRFCGNRGKKIKLKTVTIQPG-KDQVVVLATTKTKKQNKPIALLHKSVMKHEIHRMAKVI 113
                N+      KTVTIQPG KDQ ++LATTK+KKQNKP + LHKS+MK E  RMAK +
Sbjct: 51  ---LANK------KTVTIQPGGKDQSILLATTKSKKQNKPSSSLHKSLMKKEFRRMAKAV 101

Query: 114 ANRVGDNYYQPDLKNAV 130
            N+V DNYY+PDLK A 
Sbjct: 102 TNQVADNYYRPDLKKAA 118

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|89258491|gb|ABD65459.1| putative ribosomal protein L28 [Gossypium hirsutum]

 Score =  134 bits (338), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 74/137 (54%), Positives = 88/137 (64%), Gaps = 26/137 (18%)

Query: 1   MATVGGQLIWEIVKKNNCFLVKEFGRGSA------SAHAVITCSVYKFGGRKIECSTFVF 54
           MATV GQLIWE+VK+NNCFLVK+FGRG+A        + +   + YK  G          
Sbjct: 1   MATVPGQLIWEVVKRNNCFLVKQFGRGTAGVRFSKEPNNLYNVNSYKHSG---------- 50

Query: 55  GRFCGNRGKKIKLKTVTIQP-GKDQVVVLATTKTKKQNKPIALLHKSVMKHEIHRMAKVI 113
                N+      KTVTIQP GKDQ V+LATTK+KKQNKP +LLHKSVMK E  RMAK +
Sbjct: 51  ---LANK------KTVTIQPAGKDQSVLLATTKSKKQNKPSSLLHKSVMKKEFPRMAKAV 101

Query: 114 ANRVGDNYYQPDLKNAV 130
            N+V DNYY+PDL  A 
Sbjct: 102 KNQVTDNYYRPDLTKAA 118

Source: Gossypium hirsutum

Species: Gossypium hirsutum

Genus: Gossypium

Family: Malvaceae

Order: Malvales

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	131
TAIR|locus:2118289	143	AT4G29410 [Arabidopsis thalian	0.885	0.811	0.538	3.5e-27
TAIR|locus:2052010	143	AT2G19730 [Arabidopsis thalian	0.885	0.811	0.530	5.2e-26
POMBASE|SPAC1687.06c	134	rpl44 "60S ribosomal protein L	0.816	0.798	0.320	5.5e-06

TAIR|locus:2118289 AT4G29410 [Arabidopsis thaliana (taxid:3702)]

 Score = 305 (112.4 bits), Expect = 3.5e-27, P = 3.5e-27
 Identities = 70/130 (53%), Positives = 87/130 (66%)

Query:     1 MATVGGQLIWEIVKKNNCFLVKEFGRGSASAHAVITCSVYKFGGRKIECSTFVFGRFCGN 60
             MATV GQLIWEIVK+NNCFLVK+FGRG+A           K     +  +++   +  G 
Sbjct:     1 MATVPGQLIWEIVKRNNCFLVKQFGRGNAKVQ------FSKESNNLVNINSY---KHSGL 51

Query:    61 RGKKIKLKTVTIQP-GKDQVVVLATTKTKKQNKPIALLHKSVMKHEIHRMAKVIANRVGD 119
               KK    TVTIQ  GKDQ VVL TTKTK+QNKP   ++KS++K E  RM+KV+AN+V D
Sbjct:    52 ANKK----TVTIQAAGKDQGVVLGTTKTKRQNKPKLSVNKSILKKEFSRMSKVVANQVVD 107

Query:   120 NYYQPDLKNA 129
             NYY+PDLK A
Sbjct:   108 NYYRPDLKKA 117

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:0042254 "ribosome biogenesis" evidence=ISS

GO:0005886 "plasma membrane" evidence=IDA

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

GO:0009506 "plasmodesma" evidence=IDA

GO:0001510 "RNA methylation" evidence=RCA

GO:0009220 "pyrimidine ribonucleotide biosynthetic process" evidence=RCA

GO:0009909 "regulation of flower development" evidence=RCA

GO:0034968 "histone lysine methylation" evidence=RCA

TAIR|locus:2052010 AT2G19730 [Arabidopsis thaliana (taxid:3702)]

 Score = 294 (108.6 bits), Expect = 5.2e-26, P = 5.2e-26
 Identities = 69/130 (53%), Positives = 83/130 (63%)

Query:     1 MATVGGQLIWEIVKKNNCFLVKEFGRGSASAHAVITCSVYKFGGRKIECSTFVFGRFCGN 60
             MATV GQLIWEIVK NNCFLVK+FGRG++           +F       +     +  G 
Sbjct:     1 MATVPGQLIWEIVKNNNCFLVKQFGRGNSKV---------QFSKETNNLTNVHSYKHSGL 51

Query:    61 RGKKIKLKTVTIQPG-KDQVVVLATTKTKKQNKPIALLHKSVMKHEIHRMAKVIANRVGD 119
               KK    TVTIQ   KDQ VVLATTKTKKQNKP   ++KS++K E  RM+K +AN+V D
Sbjct:    52 ANKK----TVTIQAADKDQAVVLATTKTKKQNKPKLSVNKSILKKEFPRMSKAVANQVVD 107

Query:   120 NYYQPDLKNA 129
             NYY+PDLK A
Sbjct:   108 NYYRPDLKKA 117

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:0042254 "ribosome biogenesis" evidence=ISS

GO:0005886 "plasma membrane" evidence=IDA

GO:0022626 "cytosolic ribosome" evidence=IDA

GO:0005618 "cell wall" evidence=IDA

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

GO:0009507 "chloroplast" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

POMBASE|SPAC1687.06c rpl44 "60S ribosomal protein L28/L44 (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 105 (42.0 bits), Expect = 5.5e-06, P = 5.5e-06
 Identities = 41/128 (32%), Positives = 56/128 (43%)

Query:     3 TVGGQLIWEIVKKNNCFLVK--EFGRGSASAHAVITCSVYKFGGRKIECSTFVFGRFCGN 60
             +V   LIW++++ NN FLVK  EFG G       +  S     G+  +     F   C +
Sbjct:     2 SVSNDLIWQVIRDNNRFLVKRPEFG-GIQFNREPVNVS-----GKNAQR----FSGLCND 51

Query:    61 RGKKIKLKTVTIQPGKDQVVVLAT-TKTKKQNKPIALLHKSVMKHEIHRMA-KVIANRVG 118
                    K V +Q    + VVL T T  K   KP  L  K V+ +   R   K IA R+G
Sbjct:    52 -------KAVGVQANSPRGVVLITKTNPKNAQKPAKLFRKDVIANASSRKTYKSIAGRIG 104

Query:   119 DNYYQPDL 126
                Y+ DL
Sbjct:   105 RTGYRDDL 112


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        0.322   0.135   0.403    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      131       131   0.00091  102 3  11 22  0.37    31
                                                     29  0.42    33


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:  3
  No. of states in DFA:  590 (63 KB)
  Total size of DFA:  136 KB (2084 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:  11.74u 0.14s 11.88t   Elapsed:  00:00:01
  Total cpu time:  11.74u 0.14s 11.88t   Elapsed:  00:00:01
  Start:  Fri May 10 02:18:43 2013   End:  Fri May 10 02:18:44 2013

GO:0002181 "cytoplasmic translation" evidence=NAS

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

GO:0005829 "cytosol" evidence=IDA

GO:0006412 "translation" evidence=ISS

GO:0022625 "cytosolic large ribosomal subunit" 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)
Q9M0E2	RL282_ARATH	No assigned EC number	0.5220	0.8396	0.7692	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	131
pfam01778	114	pfam01778, Ribosomal_L28e, Ribosomal L28e protein	1e-12

>gnl|CDD|201967 pfam01778, Ribosomal_L28e, Ribosomal L28e protein family

 Score = 59.5 bits (145), Expect = 1e-12
 Identities = 38/125 (30%), Positives = 51/125 (40%), Gaps = 24/125 (19%)

Query: 8   LIWEIVKKNNCFLVKEFGRGSASAHAVITCSVYKFGGRKIECSTFVFGRFCG--NRGKKI 65
           LIWEI++KNNCFLVK             +   Y   G      +    ++ G  N     
Sbjct: 1   LIWEIIRKNNCFLVK-------RNGKTFSREPYNLTGL----CSR---KYSGLANS---- 42

Query: 66  KLKTVTIQPGKDQVVVLATTKTKKQNKPIALLHKSVMKHEIHRMAKVIANRVGDNYYQPD 125
             K VT+ P     VVL T K K+ +KP  L  K  +     +  K I   +   YY+PD
Sbjct: 43  --KYVTVVPTAKGGVVLVTKKPKRAHKPAKLWEKVTLSKNYRKALKQIKKAL--AYYRPD 98

Query: 126 LKNAV 130
           L    
Sbjct: 99  LIKKA 103

Length = 114

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	131
KOG3412	133	consensus 60S ribosomal protein L28 [Translation,	100.0
PTZ00197	146	60S ribosomal protein L28; Provisional	100.0
PF01778	117	Ribosomal_L28e: Ribosomal L28e protein family; Int	99.97
PLN00040	233	Protein MAK16 homolog; Provisional	99.9
KOG3064	303	consensus RNA-binding nuclear protein (MAK16) cont	94.73
COG5129	303	MAK16 Nuclear protein with HMG-like acidic region	91.68

>KOG3412 consensus 60S ribosomal protein L28 [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=7.5e-40  Score=247.44  Aligned_cols=110  Identities=40%  Similarity=0.684  Sum_probs=103.5

Q ss_pred             CCCCCccceEEEEecCceeEEeecCC-C---ccCcCccceeeeeeecccccccccceeceeecCcccccccceEEEEe-C
Q 040088            1 MATVGGQLIWEIVKKNNCFLVKEFGR-G---SASAHAVITCSVYKFGGRKIECSTFVFGRFCGNRGKKIKLKTVTIQP-G   75 (131)
Q Consensus         1 m~~~S~dL~W~iVrnnnsFLvK~~g~-~---s~s~~NL~n~~s~KysG~~~~~~~~~~~~l~~~~~~~~~~KaV~V~~-~   75 (131)
                      |+ ||+||+|||||||||||+|+.+. +   |.||.||.+++||+|||            |||       +|||||+| +
T Consensus         1 ma-~S~~L~W~VIRnNn~FL~k~r~~~k~~FstEpnNL~~vnS~rySG------------L~n-------kKtvgV~~aA   60 (133)
T KOG3412|consen    1 MA-TSGHLIWQVIRNNNAFLVKQRGNVKKQFSTEPNNLKNVNSYRYSG------------LAN-------KKTVGVIPAA   60 (133)
T ss_pred             CC-cccceeeeeeecCCceeeeeccccccccccCCccccccccccccc------------ccc-------cceeeeeecC
Confidence            66 89999999999999999998743 3   66789999999999999            999       99999999 6


Q ss_pred             CCCeEEEEEeccCCCCCCcceeeeeeeccchhHHHHHHHHHhcCCCCChhhhhhh
Q 040088           76 KDQVVVLATTKTKKQNKPIALLHKSVMKHEIHRMAKVIANRVGDNYYQPDLKNAV  130 (131)
Q Consensus        76 ~~~gVvl~tkk~k~~~kPak~~~~~~~k~~~Rr~~k~I~~~v~~n~YRpDL~~aA  130 (131)
                      +++||+++++++|.+++|++++.++++++++|+++++|++++.+++|||||+++|
T Consensus        61 ~~kgvvv~~kk~K~aqkPAk~~~k~~~~k~~r~s~k~la~~i~~nkYR~Dl~~aa  115 (133)
T KOG3412|consen   61 DKKGVVVVTKKTKGAQKPAKSVVKSTLKKEPRRSLKSLANQIGDNKYRPDLRKAA  115 (133)
T ss_pred             CCceEEEEEeccccccCchhhhhHHHHhcccHHHHHHHHHHhhhcccchHHHHHH
Confidence            7789999999999999999999999999999999999999999999999999987

>PTZ00197 60S ribosomal protein L28; Provisional

Probab=100.00  E-value=2.7e-38  Score=243.04  Aligned_cols=104  Identities=25%  Similarity=0.384  Sum_probs=99.0

Q ss_pred             CCCccceEEEEecCceeEEeecCCC-ccCcCccceeeeeeecccccccccceeceeecCcccccccceEEEEeCCCCeEE
Q 040088            3 TVGGQLIWEIVKKNNCFLVKEFGRG-SASAHAVITCSVYKFGGRKIECSTFVFGRFCGNRGKKIKLKTVTIQPGKDQVVV   81 (131)
Q Consensus         3 ~~S~dL~W~iVrnnnsFLvK~~g~~-s~s~~NL~n~~s~KysG~~~~~~~~~~~~l~~~~~~~~~~KaV~V~~~~~~gVv   81 (131)
                      +.|+||||||||+|||||+|++|.. |.||+||+|+|||||||            |+|       .|+|||+ ++++||+
T Consensus         2 ~~S~dL~W~iVRnnnsFLvKr~g~~FSrEP~NL~n~nS~KysG------------L~n-------~KaVgV~-~~~kgVv   61 (146)
T PTZ00197          2 THSTDLQWLLVRQNSKFLQKRNGIRLSSDPFNNNANWTKRHCG------------FLN-------TKAAVVK-TKGDRIL   61 (146)
T ss_pred             CCchheeeeeeeccceeEEccCCCcccCCCCcccccccccccc------------ccc-------cceEEEE-ecCCEEE
Confidence            3799999999999999999998776 88999999999999999            999       9999999 7999999


Q ss_pred             EEEeccCCCCCCcceeeeeeeccchhHHHHHHHHHhcCCCCChhhhhhh
Q 040088           82 LATTKTKKQNKPIALLHKSVMKHEIHRMAKVIANRVGDNYYQPDLKNAV  130 (131)
Q Consensus        82 l~tkk~k~~~kPak~~~~~~~k~~~Rr~~k~I~~~v~~n~YRpDL~~aA  130 (131)
                      |+|++.+++++|++++.+++|++|+|++  .|++++.+  |||||+++|
T Consensus        62 v~tKk~k~~~kPak~~~~~tlkkg~Rr~--~V~~~v~~--YR~DL~~aA  106 (146)
T PTZ00197         62 VTTKDGSSNNKPKQMYKKTVMAAGVRAS--VVSRAVAA--VRPDLASVA  106 (146)
T ss_pred             EEEecCCCCCCCchheeEEeeccCccHH--HHHHHHHh--hCHHHHHHH
Confidence            9999999999999999999999999999  59999876  999999988

>PF01778 Ribosomal_L28e: Ribosomal L28e protein family; InterPro: IPR002672 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.97  E-value=2.9e-33  Score=205.22  Aligned_cols=103  Identities=34%  Similarity=0.617  Sum_probs=82.5

Q ss_pred             ceEEEEecCceeEEeecC--CC-ccCcCccceeeeeeecccccccccceeceeecCcccccccceEEEEeCCCCeEEEEE
Q 040088            8 LIWEIVKKNNCFLVKEFG--RG-SASAHAVITCSVYKFGGRKIECSTFVFGRFCGNRGKKIKLKTVTIQPGKDQVVVLAT   84 (131)
Q Consensus         8 L~W~iVrnnnsFLvK~~g--~~-s~s~~NL~n~~s~KysG~~~~~~~~~~~~l~~~~~~~~~~KaV~V~~~~~~gVvl~t   84 (131)
                      |+|||||+|||||+|+++  .. +.||+||+|+|||+|+|            |+|       .|+|||+|.++++|+|++
T Consensus         1 L~W~iir~~~~Fl~K~~~~~~~fs~ep~NL~~~~s~kysg------------Lan-------~k~v~V~~~~~g~v~l~~   61 (117)
T PF01778_consen    1 LQWEIIRNNNCFLVKRNGIGKTFSREPGNLTNLNSFKYSG------------LAN-------SKAVGVRPAPNGGVVLVT   61 (117)
T ss_dssp             HHHHHHTTT-TTEEEET--TEEEE--TT-SSSB-STTT-T------------TTS-------S--EECCCEGGGECCCEE
T ss_pred             CEEEEecCcceEEEEeCCCCCcccCCCCcccccccccccc------------ccc-------ceeEEEEECCCCcEEEEE
Confidence            799999999999999994  33 77899999999999999            999       999999997678999999


Q ss_pred             eccCCCCCCcceeeeeeeccchhHHHHHHHHHhcCCCCChhhhhhh
Q 040088           85 TKTKKQNKPIALLHKSVMKHEIHRMAKVIANRVGDNYYQPDLKNAV  130 (131)
Q Consensus        85 kk~k~~~kPak~~~~~~~k~~~Rr~~k~I~~~v~~n~YRpDL~~aA  130 (131)
                      |+.+..++|++++.++++++++|++++.|++.+.. +|||||+.+|
T Consensus        62 K~~~~~~~P~k~~~~~~l~k~~r~a~~~I~~~~~~-~yr~dL~~~a  106 (117)
T PF01778_consen   62 KKPKRANKPAKSWEKVTLSKNSRKALKSIKKQLAK-KYRPDLRKAA  106 (117)
T ss_dssp             E-----TTTT--EEEEEESSCHHHHHHHHHHHTSS-THHHHHCCHH
T ss_pred             ccccccCCCcceeEEEecCccHHHHHHHHHHHHHh-cCCHHHHHHH
Confidence            99999999999999999999999999999999998 8999999887

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 L28e forms part of the 60S ribosomal subunit []. This family is found in eukaryotes. In rat there are 9 or 10 copies of the L28 gene. The L28 protein contains a possible internal duplication of 9 residues [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1D_O 4A1B_O 4A18_O 4A19_O 3IZR_b.

>PLN00040 Protein MAK16 homolog; Provisional

Probab=99.90  E-value=7.3e-24  Score=173.14  Aligned_cols=95  Identities=16%  Similarity=0.232  Sum_probs=88.9

Q ss_pred             CCccceEEEEecCce-eEEeecCCC-ccCcCccceeeeeeecccccccccceeceeecCcccccccceEEEEeCCCCeEE
Q 040088            4 VGGQLIWEIVKKNNC-FLVKEFGRG-SASAHAVITCSVYKFGGRKIECSTFVFGRFCGNRGKKIKLKTVTIQPGKDQVVV   81 (131)
Q Consensus         4 ~S~dL~W~iVrnnns-FLvK~~g~~-s~s~~NL~n~~s~KysG~~~~~~~~~~~~l~~~~~~~~~~KaV~V~~~~~~gVv   81 (131)
                      ||+||+|+|||+||| |++|+.+.. +.+|+||+|+||++|+|            |+|       ++++||.|. +++|+
T Consensus         2 ~SddLiW~IIr~~~csF~vK~~~~~Fcrnp~Nltglcsrkycg------------LAN-------sKyatV~~~-~G~v~   61 (233)
T PLN00040          2 QHDEVIWQVINHNHCSFKAKIDTGNFCRNKYNVTGLCNRSSCP------------LAN-------SRYATIREE-DGRFY   61 (233)
T ss_pred             CccchhhhhhcCcceeEEEccCCCcccCCCCcccccccccccc------------ccc-------ceeeEEEEc-CCEEE
Confidence            799999999999999 889877554 66789999999999999            999       999999996 78899


Q ss_pred             EEEeccCCCCCCcceeeeeeeccchhHHHHHHHHHhc
Q 040088           82 LATTKTKKQNKPIALLHKSVMKHEIHRMAKVIANRVG  118 (131)
Q Consensus        82 l~tkk~k~~~kPak~~~~~~~k~~~Rr~~k~I~~~v~  118 (131)
                      |++|+.+.+++|+++..++++++++|++++.|.+.+.
T Consensus        62 L~~Kt~erah~Pak~w~kv~Lskn~rkalk~I~~~L~   98 (233)
T PLN00040         62 LYMKTIERAHMPNKLWEKVKLSRNYEKALEQIDKHLA   98 (233)
T ss_pred             EEEecccccCCcccceEEEecCCCHHHHHHHHHHHHh
Confidence            9999999999999999999999999999999999876

>KOG3064 consensus RNA-binding nuclear protein (MAK16) containing a distinct C4 Zn-finger [RNA processing and modification]

Probab=94.73  E-value=0.017  Score=49.36  Aligned_cols=94  Identities=13%  Similarity=0.236  Sum_probs=73.1

Q ss_pred             CCccceEEEEecCce-eEEeecCCCccCc--CccceeeeeeecccccccccceeceeecCcccccccceEEEEeCCCCeE
Q 040088            4 VGGQLIWEIVKKNNC-FLVKEFGRGSASA--HAVITCSVYKFGGRKIECSTFVFGRFCGNRGKKIKLKTVTIQPGKDQVV   80 (131)
Q Consensus         4 ~S~dL~W~iVrnnns-FLvK~~g~~s~s~--~NL~n~~s~KysG~~~~~~~~~~~~l~~~~~~~~~~KaV~V~~~~~~gV   80 (131)
                      ||++.+|++|.++.| |-+|-.+ .+|=.  .|||++-...-.-            |+|       .+--+|.. +++.+
T Consensus         2 q~DeviW~vin~~~CS~k~kte~-~~fCRNeyNvTGLCnR~SCP------------LAN-------SrYATVre-~~g~~   60 (303)
T KOG3064|consen    2 QSDEVIWQVINKSFCSYKIKTET-QTFCRNEYNVTGLCNRSSCP------------LAN-------SRYATVRE-ENGVL   60 (303)
T ss_pred             cchHHHHHHhchhhcceeeeccc-cchhccccccceeeccccCc------------Ccc-------ccceeEee-cCCEE
Confidence            799999999976665 4455432 35544  5999988877777            999       88888885 55666


Q ss_pred             EEEEeccCCCCCCcceeeeeeeccchhHHHHHHHHHhc
Q 040088           81 VLATTKTKKQNKPIALLHKSVMKHEIHRMAKVIANRVG  118 (131)
Q Consensus        81 vl~tkk~k~~~kPak~~~~~~~k~~~Rr~~k~I~~~v~  118 (131)
                      -|-.|..-.+.-|.++..++-++++.-+++..|-..+-
T Consensus        61 yLymKt~ERaH~P~klwErikLSkNyekALeQIde~Ll   98 (303)
T KOG3064|consen   61 YLYMKTIERAHMPRKLWERIKLSKNYEKALEQIDEQLL   98 (303)
T ss_pred             EEEEechhhhcCcHHHHHHHhcchhHHHHHHHHHHHHh
Confidence            77777777889999999999999999898888876543

>COG5129 MAK16 Nuclear protein with HMG-like acidic region [General function prediction only]

Probab=91.68  E-value=0.093  Score=44.53  Aligned_cols=93  Identities=13%  Similarity=0.231  Sum_probs=73.0

Q ss_pred             CCccceEEEEecCce-eEEeecCCCccCc--CccceeeeeeecccccccccceeceeecCcccccccceEEEEeCCCCeE
Q 040088            4 VGGQLIWEIVKKNNC-FLVKEFGRGSASA--HAVITCSVYKFGGRKIECSTFVFGRFCGNRGKKIKLKTVTIQPGKDQVV   80 (131)
Q Consensus         4 ~S~dL~W~iVrnnns-FLvK~~g~~s~s~--~NL~n~~s~KysG~~~~~~~~~~~~l~~~~~~~~~~KaV~V~~~~~~gV   80 (131)
                      ||+..+|+++-.|-| |-+|-.++ .|-+  .|++++-..--.-            |+|       .+-.+|.+ +++.+
T Consensus         1 msDE~~Wqv~g~~fCS~rik~e~q-nfCRNeyNVTGLC~RqSCP------------LAN-------SrYATVr~-dngkL   59 (303)
T COG5129           1 MSDESLWQVSGENFCSFRIKTEEQ-NFCRNEYNVTGLCDRQSCP------------LAN-------SRYATVRA-DNGKL   59 (303)
T ss_pred             CchhHHHHHccccccceeeecchh-hhhhcccccceeeccccCc------------Ccc-------CcceEEEe-cCCEE
Confidence            689999998877766 44665433 3333  6999887766666            999       88888885 66788


Q ss_pred             EEEEeccCCCCCCcceeeeeeeccchhHHHHHHHHHh
Q 040088           81 VLATTKTKKQNKPIALLHKSVMKHEIHRMAKVIANRV  117 (131)
Q Consensus        81 vl~tkk~k~~~kPak~~~~~~~k~~~Rr~~k~I~~~v  117 (131)
                      -|-+|.+-...-|+++..++.++++.-++++.|-..+
T Consensus        60 yLymKtpERaH~P~klwerIkLSkNY~kAL~QIde~L   96 (303)
T COG5129          60 YLYMKTPERAHVPRKLWERIKLSKNYEKALKQIDESL   96 (303)
T ss_pred             EEEecChhhccCcHHHHHHHHhhhhHHHHHHHHHHHH
Confidence            8888988899999999999999999988888886543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	131
3izr_b	147	Localization Of The Large Subunit Ribosomal Protein		5e-27

>pdb|3IZR|BB Chain b, Localization Of The Large Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 147

Iteration: 1
 Score =  115 bits (289), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 66/134 (49%), Positives = 77/134 (57%), Gaps = 27/134 (20%)
Query: 1   MATVGGQLIWEIVKKNNCFLVKEFGRGSA------SAHAVITCSVYKFGGRKIECSTFVF 54
           MATV   LIWEIVKKNNCFLVK+FG  +A        + +     YK  G          
Sbjct: 1   MATVPEPLIWEIVKKNNCFLVKQFGNSNAKVQFTKEPNNLYNVHSYKHSG---------- 50
Query: 55  GRFCGNRGKKIKLKTVTIQPG--KDQVVVLATTKTKKQNKPIALLHKSVMKHEIHRMAKV 112
                N+      KTVTIQP   KD  VVL+TTKTKKQN P  L HKSVM+ E  +MAK 
Sbjct: 51  ---LANK------KTVTIQPSGVKDAAVVLSTTKTKKQNAPAKLYHKSVMRKEFRKMAKA 101
Query: 113 IANRVGDNYYQPDL 126
           + N+V DNYY+PDL
Sbjct: 102 VKNQVSDNYYRPDL 115

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	131
3iz5_B	261	60S ribosomal protein L2 (L2P); eukaryotic ribosom	3e-16
4a18_O	134	RPL28, ribosomal protein L22; ribosome, eukaryotic	2e-09

>4a18_O RPL28, ribosomal protein L22; ribosome, eukaryotic initiation factor 6, EIF6, transla large ribosomal subunit, rRNA; 3.52A {Tetrahymena thermophila} PDB: 4a19_O 4a1b_O 4a1d_O Length = 134

 Score = 51.3 bits (122), Expect = 2e-09
 Identities = 23/124 (18%), Positives = 39/124 (31%), Gaps = 21/124 (16%)

Query: 7   QLIWEIVKKNNCFLVKEFGRG-SASAHAVITCSVYKFGGRKIECSTFVFGRFCGNRGKKI 65
           QL+WEIVK NN FLVK  G   +    +V   +     G                     
Sbjct: 3   QLVWEIVKNNNAFLVKNNGVAFTTDPFSVTGRNTQVGLGF-------------------T 43

Query: 66  KLKTVTIQPGKDQVVVLATTKTKKQNKPIALLHKSVMKHEIHRMAKVIANRVGDNYYQPD 125
               V ++ G  Q +   + +  + +K             +    + +A  +   +    
Sbjct: 44  HRHGVALKGGAKQAIAT-SLRKNQSHKVKKTGTIEAETLTVKGGVQRVAKVIRGRFQSKG 102

Query: 126 LKNA 129
           LK  
Sbjct: 103 LKQF 106

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	131
3iz5_b	147	60S ribosomal protein L28 (L28E); eukaryotic ribos	100.0
4a18_O	134	RPL28, ribosomal protein L22; ribosome, eukaryotic	100.0

>4a18_O RPL28, ribosomal protein L22; ribosome, eukaryotic initiation factor 6, EIF6, transla large ribosomal subunit, rRNA; 3.52A {Tetrahymena thermophila} PDB: 4a19_O 4a1b_O 4a1d_O

Probab=100.00  E-value=8.2e-35  Score=219.35  Aligned_cols=101  Identities=33%  Similarity=0.473  Sum_probs=94.6

Q ss_pred             CCccceEEEEecCceeEEeecCCC-ccCcCccceeeeeeecccccccccceeceeecCcccccccceEEEEeCCCCeEEE
Q 040088            4 VGGQLIWEIVKKNNCFLVKEFGRG-SASAHAVITCSVYKFGGRKIECSTFVFGRFCGNRGKKIKLKTVTIQPGKDQVVVL   82 (131)
Q Consensus         4 ~S~dL~W~iVrnnnsFLvK~~g~~-s~s~~NL~n~~s~KysG~~~~~~~~~~~~l~~~~~~~~~~KaV~V~~~~~~gVvl   82 (131)
                      || ||||||||+|||||+|++|.. |.||+||+|+|||+|+|            |+|       .|+|||+|++++|  |
T Consensus         1 MS-dL~W~ivrnnnsFLvKr~g~~FS~eP~NL~n~~S~kysG------------Lan-------~KavgV~~~~~gg--v   58 (134)
T 4a18_O            1 MS-QLVWEIVKNNNAFLVKNNGVAFTTDPFSVTGRNTQVGLG------------FTH-------RHGVALKGGAKQA--I   58 (134)
T ss_dssp             CH-HHHHHHHTTTCTTEEEETTEEEECCTTCSSSBCSTTTCT------------TTS-------SCCEEEEEEGGGE--E
T ss_pred             Cc-ceeehhhcCcceEEEeeCCccccCCCCCccceecccccc------------ccc-------cceeEEEEcCCCc--E
Confidence            67 999999999999999999766 88999999999999999            999       9999999976667  8


Q ss_pred             EEeccCCCCCCc----ceeeee-eeccchhHHHHHHHHHhcCCCCChhhhhhh
Q 040088           83 ATTKTKKQNKPI----ALLHKS-VMKHEIHRMAKVIANRVGDNYYQPDLKNAV  130 (131)
Q Consensus        83 ~tkk~k~~~kPa----k~~~~~-~~k~~~Rr~~k~I~~~v~~n~YRpDL~~aA  130 (131)
                      +|++++.+++|+    +++.++ ++++++|+++++|+++++++    ||+++|
T Consensus        59 ~~Kk~k~~~kPa~~~~k~~~~~~~~~k~~Rk~~k~I~~~~~~~----DL~~aA  107 (134)
T 4a18_O           59 ATSLRKNQSHKVKKTGTIEAETLTVKGGVQRVAKVIRGRFQSK----GLKQFA  107 (134)
T ss_dssp             EEEEECCCCCCSSCCSCSSEEEEEESSTHHHHHHHHHHHCCSH----HHHHHH
T ss_pred             EEecCcccCCCCccccceeEEEeccccchHHHHHHHHHHHhhc----hHHHHH
Confidence            899999999999    999999 99999999999999999974    999987

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

No hit with probability above 80.00