Citrus Sinensis ID: 032227

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-----
Protein Sequence
MPVPLAPYPTPPAPYTPPANGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVGASTSTTEQKFNT
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccEEEccccccEEEccccccEEEccccccccccccccccccEEEEcccccEEEEEccccEEEcccccccccccccccEEEEEccccccEEEEEccccEEEcccccccEEcccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccHHHEEEEccccEEEEEccccccEEEccccEEccccccccHHEEEEEccccEEEEEcccccEEEcccccEEEcccccccEEEEEccccEEEEEEccccccEEccEEEEEcccccccccccccccc
Coil and Loop (DISEMBL)
mpvplapyptppapytppangaqsqlvcsgcrnlllypvgaTSVCCAVcnavtavpppgtemaqLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVtavgaststteqkfnt
Flexible Loop (DISEMBL)
MPVPLAPYPTPPAPYTPPANGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAvgaststteqkfnt
Low Complexity Region (SEG)
MpvplapyptppapytppaNGAQSQLVCSGCRNLLLYPVGATSvccavcnavtavpppGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVGASTSTTEQKFNT
Disordered region (IsUnstruct)
************************QLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVG************
Disordered Region (DISOPRED)
******P******************LVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVT***************
Disordered Region (DISEMBL)
MPVPLAPYPTPPAPYTPPANGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVGA***********
Disordered Region (DISPRO)
*PVPLAPYPTPPAPYTPPANGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVG************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPVPLAPYPTPPAPYTPPANGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVGASTSTTEQKFNT
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	145	2.2.26 [Sep-21-2011]
Q93ZB1	154	Protein LOL1 OS=Arabidops	yes	no	0.889	0.837	0.924	4e-64
Q0J7V9	184	Protein LSD1 OS=Oryza sat	yes	no	0.965	0.760	0.886	4e-60
Q2QMB3	172	Protein LOL2 OS=Oryza sat	no	no	0.786	0.662	0.643	3e-37
Q6ASS2	186	Protein LOL3 OS=Oryza sat	no	no	0.786	0.612	0.620	3e-36
P94077	189	Protein LSD1 OS=Arabidops	no	no	0.779	0.597	0.596	2e-31
Q84UR0	147	Protein LOL4 OS=Oryza sat	no	no	0.758	0.748	0.477	9e-24
O65426	155	Protein LOL2 OS=Arabidops	no	no	0.524	0.490	0.571	9e-21
Q704V3	163	Protein LOL5 OS=Oryza sat	no	no	0.496	0.441	0.547	1e-17
Q69UP7	147	Protein LOL1 OS=Oryza sat	no	no	0.351	0.346	0.648	4e-12

>sp|Q93ZB1|LOL1_ARATH Protein LOL1 OS=Arabidopsis thaliana GN=LOL1 PE=2 SV=1

 Score =  243 bits (619), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 122/132 (92%), Positives = 126/132 (95%), Gaps = 3/132 (2%)

Query: 16  TPPANGA---QSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHT 72
           TPPANG+   QSQLVCSGCRNLL+YPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHT
Sbjct: 22  TPPANGSTSGQSQLVCSGCRNLLMYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHT 81

Query: 73  LLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAV 132
           LLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNC MLLMYQYGARSVKCAVCNFVT+V
Sbjct: 82  LLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCMMLLMYQYGARSVKCAVCNFVTSV 141

Query: 133 GASTSTTEQKFN 144
           G STSTT+ KFN
Sbjct: 142 GGSTSTTDSKFN 153

Positive regulator of reactive oxygen-induced cell death. May be involved in the repression of the copper/zinc superoxide dismutase CSD1 and CSD2 that detoxify accumulating superoxide before the reactive oxygen species (ROS) can trigger a cell death cascade. LSD1 and LOL1 have antagonistic effects on CSD1 and CSD2 accumulation to regulate oxidative stress-induced cell death.
Arabidopsis thaliana (taxid: 3702)

>sp|Q0J7V9|LSD1_ORYSJ Protein LSD1 OS=Oryza sativa subsp. japonica GN=LSD1 PE=2 SV=1

 Score =  229 bits (584), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 125/141 (88%), Positives = 132/141 (93%), Gaps = 1/141 (0%)

Query: 1   MPVPLAPYPTPPAPYTPPANGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGT 60
           MPVPLAPYPTPP P+TP  NGAQSQLVCSGCRNLL+YP GATSVCCAVC+ VTAVP PGT
Sbjct: 42  MPVPLAPYPTPPVPFTP-PNGAQSQLVCSGCRNLLMYPAGATSVCCAVCSTVTAVPAPGT 100

Query: 61  EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARS 120
           EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLA+EANQVAHVNCGNCRMLLMYQYGARS
Sbjct: 101 EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLAMEANQVAHVNCGNCRMLLMYQYGARS 160

Query: 121 VKCAVCNFVTAVGASTSTTEQ 141
           VKCAVCNFVT+VGAS  T ++
Sbjct: 161 VKCAVCNFVTSVGASPGTDQK 181

Negative regulator of programmed cell death and hypersensitive response (HR). Positive regulator of callus differentiation.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q2QMB3|LOL2_ORYSJ Protein LOL2 OS=Oryza sativa subsp. japonica GN=LOL2 PE=2 SV=1

 Score =  153 bits (387), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 74/115 (64%), Positives = 91/115 (79%), Gaps = 1/115 (0%)

Query: 23  QSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAV-PPPGTEMAQLVCGGCHTLLMYIRGAT 81
           QSQ+VC GCRN+LLYP GA SVCCAVC+AV++  P PG ++A L+CGGC TLLMY R AT
Sbjct: 2   QSQIVCHGCRNILLYPRGAPSVCCAVCHAVSSTAPSPGMDIAHLICGGCRTLLMYTRNAT 61

Query: 82  SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVGAST 136
           SV+CSCC TVNL    + +AH+NCG C+ +LMY YGA SVKCA+CNF+T  G +T
Sbjct: 62  SVRCSCCDTVNLVRPVSSIAHLNCGQCQTVLMYPYGAPSVKCAICNFITNTGMNT 116

Putative zinc finger that may be involved in programmed cell death and defense response.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q6ASS2|LOL3_ORYSJ Protein LOL3 OS=Oryza sativa subsp. japonica GN=LOL3 PE=2 SV=1

 Score =  150 bits (378), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 72/116 (62%), Positives = 87/116 (75%), Gaps = 2/116 (1%)

Query: 23  QSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPG--TEMAQLVCGGCHTLLMYIRGA 80
           QSQ+VC GCR++L YP GA SVCCA+C A+T VPPP    EMA L+CGGC TLLMY R A
Sbjct: 2   QSQIVCHGCRSVLRYPSGAPSVCCALCQAITTVPPPAPVMEMAHLICGGCRTLLMYTRNA 61

Query: 81  TSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVGAST 136
            +V+CSCC TVNL    N +AHV+CG CR  LMY YGA SVKCA+C+++T  G +T
Sbjct: 62  DTVRCSCCSTVNLVRPVNNIAHVSCGQCRTTLMYPYGAPSVKCAICHYITNTGMNT 117

Putative zinc finger that may be involved in programmed cell death and defense response.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|P94077|LSD1_ARATH Protein LSD1 OS=Arabidopsis thaliana GN=LSD1 PE=1 SV=1

 Score =  134 bits (336), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 74/124 (59%), Positives = 88/124 (70%), Gaps = 11/124 (8%)

Query: 23  QSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGT--EMAQLVCGGCHTLLMYIRGA 80
           Q QLVC GCRNLL+YP GA++V CA+CN +  VPPP    +MA ++CGGC T+LMY RGA
Sbjct: 7   QDQLVCHGCRNLLMYPRGASNVRCALCNTINMVPPPPPPHDMAHIICGGCRTMLMYTRGA 66

Query: 81  TSVQCSCCHTVNLA-LEANQVAH--------VNCGNCRMLLMYQYGARSVKCAVCNFVTA 131
           +SV+CSCC T NL    +NQVAH        +NCG+CR  LMY YGA SVKCAVC FVT 
Sbjct: 67  SSVRCSCCQTTNLVPAHSNQVAHAPSSQVAQINCGHCRTTLMYPYGASSVKCAVCQFVTN 126

Query: 132 VGAS 135
           V  S
Sbjct: 127 VNMS 130

Negative regulator of reactive oxygen-induced cell death, cold stress-induced cell death, pathogen-induced hypersensitive response (HR), basal disease resistance. May be involved in the induction of the copper/zinc superoxide dismutase CSD1 and CSD2 that detoxify accumulating superoxide before the reactive oxygen species (ROS) can trigger a cell death cascade. LSD1 and LOL1 have antagonistic effects on CSD1 and CSD2 accumulation to regulate oxidative stress-induced cell death. Antagonizes the function of BZIP10, a positive regulator of cell death, by interacting in the cytoplasm and preventing its nuclear localization. Controls lysigenous aerenchyma in hypocotyls under root hypoxia. Required for leaf acclimation in response to excess excitation energy.

Arabidopsis thaliana (taxid: 3702)

>sp|Q84UR0|LOL4_ORYSJ Protein LOL4 OS=Oryza sativa subsp. japonica GN=LOL4 PE=2 SV=1

 Score =  108 bits (271), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 53/111 (47%), Positives = 73/111 (65%), Gaps = 1/111 (0%)

Query: 23  QSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGT-EMAQLVCGGCHTLLMYIRGAT 81
           Q QL+CSGCR ++ Y  G   VCC  CN +TAV P    +M++L+C GC TLL Y RGA+
Sbjct: 2   QDQLICSGCRRVVQYRRGVAGVCCPGCNTLTAVNPSAVADMSELICSGCPTLLFYNRGAS 61

Query: 82  SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAV 132
           +++C  C+ +N    ANQ+AH+ CG CR  LM+  GA +V+CA C +V  V
Sbjct: 62  NIRCPSCNRLNSTRSANQIAHLTCGQCRTTLMHPPGASTVQCATCRYVNHV 112

Putative zinc finger that may be involved in programmed cell death and defense response.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|O65426|LOL2_ARATH Protein LOL2 OS=Arabidopsis thaliana GN=LOL2 PE=2 SV=1

 Score = 99.0 bits (245), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 44/77 (57%), Positives = 55/77 (71%)

Query: 61  EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARS 120
           E AQ+VCG C  LL Y+RG+  V+CS C TVNL LEANQV  VNC NC++LLMY YGA +
Sbjct: 57  EKAQMVCGSCRRLLSYLRGSKHVKCSSCQTVNLVLEANQVGQVNCNNCKLLLMYPYGAPA 116

Query: 121 VKCAVCNFVTAVGASTS 137
           V+C+ CN VT +  +  
Sbjct: 117 VRCSSCNSVTDISENNK 133

Putative zinc finger that may be involved in programmed cell death and defense response.

Arabidopsis thaliana (taxid: 3702)

>sp|Q704V3|LOL5_ORYSJ Protein LOL5 OS=Oryza sativa subsp. japonica GN=LOL5 PE=2 SV=1

 Score = 88.6 bits (218), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 40/73 (54%), Positives = 53/73 (72%)

Query: 61  EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARS 120
           E+ Q+VCG C  LL Y RGA  V C+CC T+N  LEA++V  V+CG+C  LLMY +GA +
Sbjct: 67  EVGQMVCGSCRILLAYFRGAGYVHCTCCQTMNYVLEAHEVGKVHCGHCATLLMYPFGAPA 126

Query: 121 VKCAVCNFVTAVG 133
           VKC++C FVT +G
Sbjct: 127 VKCSLCLFVTEIG 139

Involved in plant growth and disease resistance.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q69UP7|LOL1_ORYSJ Protein LOL1 OS=Oryza sativa subsp. japonica GN=LOL1 PE=2 SV=1

 Score = 70.1 bits (170), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 35/54 (64%), Positives = 40/54 (74%)

Query: 5  LAPYPTPPAPYTPPANGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPP 58
          +A  P    P +  + GAQSQLVCSGCRNLL+YP GATS+CCAVC  VTAVP P
Sbjct: 27 MASTPWSSMPPSSHSLGAQSQLVCSGCRNLLMYPAGATSICCAVCGTVTAVPAP 80

Putative zinc finger that may be involved in programmed cell death and defense response.

Oryza sativa subsp. japonica (taxid: 39947)

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	145
297742122	230	unnamed protein product [Vitis vinifera]	0.993	0.626	0.930	2e-72
225427256	145	PREDICTED: protein LOL1-like [Vitis vini	0.993	0.993	0.930	5e-71
147810699	146	hypothetical protein VITISV_014138 [Viti	0.972	0.965	0.893	8e-66
255574680	147	conserved hypothetical protein [Ricinus	1.0	0.986	0.931	4e-65
388497348	145	unknown [Lotus japonicus]	1.0	1.0	0.951	3e-64
388492562	146	unknown [Lotus japonicus]	1.0	0.993	0.869	1e-63
351723389	145	uncharacterized protein LOC100306356 [Gl	1.0	1.0	0.944	4e-63
346472259	145	hypothetical protein [Amblyomma maculatu	0.979	0.979	0.875	7e-63
18398482	154	lsd one like 1 protein [Arabidopsis thal	0.889	0.837	0.924	2e-62
357476673	154	Zinc finger protein LSD1 [Medicago trunc	0.868	0.818	0.960	6e-62

>gi|297742122|emb|CBI33909.3| unnamed protein product [Vitis vinifera]

 Score =  276 bits (705), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 134/144 (93%), Positives = 138/144 (95%)

Query: 1   MPVPLAPYPTPPAPYTPPANGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGT 60
           MPVPLAPYPTPP P+T PANGAQSQLVCSGCRNLLLYPVGA SVCCAVCN VTAVP PGT
Sbjct: 86  MPVPLAPYPTPPVPFTQPANGAQSQLVCSGCRNLLLYPVGAKSVCCAVCNVVTAVPLPGT 145

Query: 61  EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARS 120
           EMAQLVCGGCHTLLMYIRGATSVQCSCCHT+NLALEANQVAHVNCGNCRMLLMYQYGARS
Sbjct: 146 EMAQLVCGGCHTLLMYIRGATSVQCSCCHTINLALEANQVAHVNCGNCRMLLMYQYGARS 205

Query: 121 VKCAVCNFVTAVGASTSTTEQKFN 144
           VKCAVCNFVT+VGASTS+TE KFN
Sbjct: 206 VKCAVCNFVTSVGASTSSTEHKFN 229

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225427256|ref|XP_002281099.1| PREDICTED: protein LOL1-like [Vitis vinifera]

 Score =  271 bits (694), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 134/144 (93%), Positives = 138/144 (95%)

Query: 1   MPVPLAPYPTPPAPYTPPANGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGT 60
           MPVPLAPYPTPP P+T PANGAQSQLVCSGCRNLLLYPVGA SVCCAVCN VTAVP PGT
Sbjct: 1   MPVPLAPYPTPPVPFTQPANGAQSQLVCSGCRNLLLYPVGAKSVCCAVCNVVTAVPLPGT 60

Query: 61  EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARS 120
           EMAQLVCGGCHTLLMYIRGATSVQCSCCHT+NLALEANQVAHVNCGNCRMLLMYQYGARS
Sbjct: 61  EMAQLVCGGCHTLLMYIRGATSVQCSCCHTINLALEANQVAHVNCGNCRMLLMYQYGARS 120

Query: 121 VKCAVCNFVTAVGASTSTTEQKFN 144
           VKCAVCNFVT+VGASTS+TE KFN
Sbjct: 121 VKCAVCNFVTSVGASTSSTEHKFN 144

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147810699|emb|CAN76365.1| hypothetical protein VITISV_014138 [Vitis vinifera]

 Score =  254 bits (649), Expect = 8e-66,   Method: Compositional matrix adjust.
 Identities = 126/141 (89%), Positives = 131/141 (92%)

Query: 1   MPVPLAPYPTPPAPYTPPANGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGT 60
           MPVPLAPYPTPP P+T PANGAQSQLVCSGCRNLLLYPVGA SVCCAVCN VTAVP PGT
Sbjct: 1   MPVPLAPYPTPPVPFTQPANGAQSQLVCSGCRNLLLYPVGAKSVCCAVCNVVTAVPLPGT 60

Query: 61  EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARS 120
           EMAQLVCGGCHTLLMYIRGATSVQCSCCHT+NLALEANQVAHVNCGNCRMLLMYQYGARS
Sbjct: 61  EMAQLVCGGCHTLLMYIRGATSVQCSCCHTINLALEANQVAHVNCGNCRMLLMYQYGARS 120

Query: 121 VKCAVCNFVTAVGASTSTTEQ 141
           VKCAVCNFVT+VG + +   Q
Sbjct: 121 VKCAVCNFVTSVGPTQTKHGQ 141

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255574680|ref|XP_002528249.1| conserved hypothetical protein [Ricinus communis] gi|223532335|gb|EEF34134.1| conserved hypothetical protein [Ricinus communis]

 Score =  252 bits (643), Expect = 4e-65,   Method: Compositional matrix adjust.
 Identities = 137/147 (93%), Positives = 141/147 (95%), Gaps = 2/147 (1%)

Query: 1   MPVPLAPYPTPPAPYT--PPANGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPP 58
           MPVPLAPYPTPP PYT    ANGAQSQLVCSGCRNLLLYP GATSVCCAVCNAVTAVPPP
Sbjct: 1   MPVPLAPYPTPPTPYTQPASANGAQSQLVCSGCRNLLLYPAGATSVCCAVCNAVTAVPPP 60

Query: 59  GTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGA 118
           GTEMAQLVCGGCHTLLMYIRGATSVQCSCCHT+NLA+EANQVAHVNCGNCRMLLMYQYGA
Sbjct: 61  GTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTINLAMEANQVAHVNCGNCRMLLMYQYGA 120

Query: 119 RSVKCAVCNFVTAVGASTSTTEQKFNT 145
           RSVKC+VCNFVTAVGASTSTTEQKFN+
Sbjct: 121 RSVKCSVCNFVTAVGASTSTTEQKFNS 147

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388497348|gb|AFK36740.1| unknown [Lotus japonicus]

 Score =  249 bits (636), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 138/145 (95%), Positives = 142/145 (97%)

Query: 1   MPVPLAPYPTPPAPYTPPANGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGT 60
           MPVPLAPYPTPPAPYTPP NGAQSQLVCSGCRNLL+YPVGATSVCCAVCNAVT+VPPPGT
Sbjct: 1   MPVPLAPYPTPPAPYTPPTNGAQSQLVCSGCRNLLVYPVGATSVCCAVCNAVTSVPPPGT 60

Query: 61  EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARS 120
           EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARS
Sbjct: 61  EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARS 120

Query: 121 VKCAVCNFVTAVGASTSTTEQKFNT 145
           VKCAVCNFVT+VG S STTEQKF+T
Sbjct: 121 VKCAVCNFVTSVGTSASTTEQKFST 145

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388492562|gb|AFK34347.1| unknown [Lotus japonicus]

 Score =  247 bits (631), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 127/146 (86%), Positives = 133/146 (91%), Gaps = 1/146 (0%)

Query: 1   MPVPLAPYPT-PPAPYTPPANGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPG 59
           MPVPLAPYPT PPA YT   NGAQSQL CSGCRNLLLYPVGAT+VCCAVCNAVTAVPPPG
Sbjct: 1   MPVPLAPYPTTPPALYTHAPNGAQSQLACSGCRNLLLYPVGATTVCCAVCNAVTAVPPPG 60

Query: 60  TEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGAR 119
           TEMAQLVCGGCHTL+MYIRGATSVQCSCCHTVNLALEANQVAHV CGNC+MLLMYQ+GA 
Sbjct: 61  TEMAQLVCGGCHTLIMYIRGATSVQCSCCHTVNLALEANQVAHVYCGNCKMLLMYQHGAG 120

Query: 120 SVKCAVCNFVTAVGASTSTTEQKFNT 145
           SVKCAVC+FVT V ASTS  EQK +T
Sbjct: 121 SVKCAVCSFVTLVEASTSINEQKIST 146

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351723389|ref|NP_001237533.1| uncharacterized protein LOC100306356 [Glycine max] gi|356563463|ref|XP_003549982.1| PREDICTED: protein LOL1-like [Glycine max] gi|255628291|gb|ACU14490.1| unknown [Glycine max]

 Score =  245 bits (626), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 137/145 (94%), Positives = 142/145 (97%)

Query: 1   MPVPLAPYPTPPAPYTPPANGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGT 60
           MPVPLAPYPTPPAPYTPPANG QSQLVCSGCRNLL++PVGATSVCCAVCNAVTAVPPPGT
Sbjct: 1   MPVPLAPYPTPPAPYTPPANGVQSQLVCSGCRNLLVFPVGATSVCCAVCNAVTAVPPPGT 60

Query: 61  EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARS 120
           EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLL YQYGARS
Sbjct: 61  EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLAYQYGARS 120

Query: 121 VKCAVCNFVTAVGASTSTTEQKFNT 145
           VKCAVCNFVT+VGA+ STTEQKF+T
Sbjct: 121 VKCAVCNFVTSVGATASTTEQKFST 145

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|346472259|gb|AEO35974.1| hypothetical protein [Amblyomma maculatum]

 Score =  244 bits (624), Expect = 7e-63,   Method: Compositional matrix adjust.
 Identities = 127/145 (87%), Positives = 134/145 (92%), Gaps = 3/145 (2%)

Query: 1   MPVPLAPYPTPPA-PYTPPANGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPG 59
           MPVPLAPYPTPPA P+T P NG QSQLVCSGCRNLLLYP+GA+SVCCA+CNAVT VPPPG
Sbjct: 1   MPVPLAPYPTPPAVPFTAP-NGGQSQLVCSGCRNLLLYPLGASSVCCAICNAVTPVPPPG 59

Query: 60  TEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGAR 119
           TEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLAL+ANQVAHVNCG+CRMLLMYQYGAR
Sbjct: 60  TEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALDANQVAHVNCGSCRMLLMYQYGAR 119

Query: 120 SVKCAVCNFVTAVGASTSTTEQKFN 144
           SVKCAVCN+VT VG S S  EQK N
Sbjct: 120 SVKCAVCNYVTPVGPS-SGNEQKVN 143

Source: Amblyomma maculatum

Species: Amblyomma maculatum

Genus: Amblyomma

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|18398482|ref|NP_564405.1| lsd one like 1 protein [Arabidopsis thaliana] gi|186479127|ref|NP_001117399.1| lsd one like 1 protein [Arabidopsis thaliana] gi|75163743|sp|Q93ZB1.1|LOL1_ARATH RecName: Full=Protein LOL1; AltName: Full=Protein LSD ONE LIKE 1; Short=AtLOL1; AltName: Full=Putative zinc finger LOL1 gi|16323143|gb|AAL15306.1| At1g32540/T9G5_1 [Arabidopsis thaliana] gi|21436015|gb|AAM51585.1| At1g32540/T9G5_1 [Arabidopsis thaliana] gi|33867796|gb|AAQ55219.1| LSD1-like [Arabidopsis thaliana] gi|332193377|gb|AEE31498.1| lsd one like 1 protein [Arabidopsis thaliana] gi|332193379|gb|AEE31500.1| lsd one like 1 protein [Arabidopsis thaliana]

 Score =  243 bits (619), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 122/132 (92%), Positives = 126/132 (95%), Gaps = 3/132 (2%)

Query: 16  TPPANGA---QSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHT 72
           TPPANG+   QSQLVCSGCRNLL+YPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHT
Sbjct: 22  TPPANGSTSGQSQLVCSGCRNLLMYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHT 81

Query: 73  LLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAV 132
           LLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNC MLLMYQYGARSVKCAVCNFVT+V
Sbjct: 82  LLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCMMLLMYQYGARSVKCAVCNFVTSV 141

Query: 133 GASTSTTEQKFN 144
           G STSTT+ KFN
Sbjct: 142 GGSTSTTDSKFN 153

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357476673|ref|XP_003608622.1| Zinc finger protein LSD1 [Medicago truncatula] gi|217075072|gb|ACJ85896.1| unknown [Medicago truncatula] gi|217075520|gb|ACJ86120.1| unknown [Medicago truncatula] gi|355509677|gb|AES90819.1| Zinc finger protein LSD1 [Medicago truncatula] gi|388499772|gb|AFK37952.1| unknown [Medicago truncatula] gi|388500106|gb|AFK38119.1| unknown [Medicago truncatula]

 Score =  241 bits (616), Expect = 6e-62,   Method: Compositional matrix adjust.
 Identities = 122/127 (96%), Positives = 125/127 (98%), Gaps = 1/127 (0%)

Query: 20  NGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRG 79
           NGAQSQLVCSGCRNLL+YPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRG
Sbjct: 28  NGAQSQLVCSGCRNLLMYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRG 87

Query: 80  ATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVGASTSTT 139
           ATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVT+VGAS STT
Sbjct: 88  ATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTSVGASASTT 147

Query: 140 E-QKFNT 145
           E QKF+T
Sbjct: 148 EPQKFST 154

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

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	145
UNIPROTKB|Q0J7V9	184	LSD1 "Protein LSD1" [Oryza sat	0.841	0.663	0.813	1.1e-50
UNIPROTKB|F8RP38	176	F8RP38 "Zinc finger protein LS	0.779	0.642	0.628	5.1e-35
TAIR|locus:2128639	210	LSD1 "LESION SIMULATING DISEAS	0.524	0.361	0.487	4.7e-29
TAIR|locus:2119622	155	LOL2 "AT4G21610" [Arabidopsis	0.496	0.464	0.611	1.9e-21
UNIPROTKB|Q704V3	163	LOL5 "Protein LOL5" [Oryza sat	0.503	0.447	0.547	9.2e-20

UNIPROTKB|Q0J7V9 LSD1 "Protein LSD1" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 527 (190.6 bits), Expect = 1.1e-50, P = 1.1e-50
 Identities = 100/123 (81%), Positives = 104/123 (84%)

Query:    20 NGAQSQLVCSGCRNLLLYPVGATSXXXXXXXXXXXXXXXGTEMAQLVCGGCHTLLMYIRG 79
             NGAQSQLVCSGCRNLL+YP GATS               GTEMAQLVCGGCHTLLMYIRG
Sbjct:    60 NGAQSQLVCSGCRNLLMYPAGATSVCCAVCSTVTAVPAPGTEMAQLVCGGCHTLLMYIRG 119

Query:    80 ATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVGASTSTT 139
             ATSVQCSCCHTVNLA+EANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVT+VGAS  T 
Sbjct:   120 ATSVQCSCCHTVNLAMEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTSVGASPGT- 178

Query:   140 EQK 142
             +QK
Sbjct:   179 DQK 181

GO:0005634 "nucleus" evidence=TAS

GO:0031348 "negative regulation of defense response" evidence=IMP

GO:0034051 "negative regulation of plant-type hypersensitive response" evidence=IMP

GO:0045595 "regulation of cell differentiation" evidence=IMP

UNIPROTKB|F8RP38 F8RP38 "Zinc finger protein LSD1" [Pisum sativum (taxid:3888)]

 Score = 379 (138.5 bits), Expect = 5.1e-35, P = 5.1e-35
 Identities = 71/113 (62%), Positives = 82/113 (72%)

Query:    23 QSQLVCSGCRNLLLYPVGATSXXXXXXXXXXXXXXXGTEMAQLVCGGCHTLLMYIRGATS 82
             QSQLVC+GCRN+LLYP GAT+               G +M+QL CGGC TLLMY RGATS
Sbjct:     2 QSQLVCNGCRNMLLYPRGATNVCCALCNTISPVPPPGMDMSQLYCGGCRTLLMYTRGATS 61

Query:    83 VQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVGAS 135
             V+CSCCHTVNLA  +NQVAHV C NCR  LMY YGA SVKCAVC+++T +  S
Sbjct:    62 VRCSCCHTVNLAPVSNQVAHVPCANCRTTLMYPYGAPSVKCAVCHYITNINMS 114

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IMP

GO:0060548 "negative regulation of cell death" evidence=IMP

TAIR|locus:2128639 LSD1 "LESION SIMULATING DISEASE" [Arabidopsis thaliana (taxid:3702)]

 Score = 196 (74.1 bits), Expect = 4.7e-29, Sum P(2) = 4.7e-29
 Identities = 38/78 (48%), Positives = 49/78 (62%)

Query:    23 QSQLVCSGCRNLLLYPVGATSXXXXXXXXXXXXXXXGT--EMAQLVCGGCHTLLMYIRGA 80
             Q QLVC GCRNLL+YP GA++                   +MA ++CGGC T+LMY RGA
Sbjct:     2 QDQLVCHGCRNLLMYPRGASNVRCALCNTINMVPPPPPPHDMAHIICGGCRTMLMYTRGA 61

Query:    81 TSVQCSCCHTVNLALEAN 98
             +SV+CSCC T NL  E++
Sbjct:    62 SSVRCSCCQTTNLVPESS 79

GO:0005576 "extracellular region" evidence=ISM

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=TAS

GO:0009862 "systemic acquired resistance, salicylic acid mediated signaling pathway" evidence=IEP

GO:0005515 "protein binding" evidence=IPI

GO:0002240 "response to molecule of oomycetes origin" evidence=IMP

GO:0009626 "plant-type hypersensitive response" evidence=IMP

GO:0001666 "response to hypoxia" evidence=IMP

GO:0010310 "regulation of hydrogen peroxide metabolic process" evidence=IMP

GO:0010602 "regulation of 1-aminocyclopropane-1-carboxylate metabolic process" evidence=IMP

GO:0010618 "aerenchyma formation" evidence=IMP

GO:0010104 "regulation of ethylene mediated signaling pathway" evidence=IMP

GO:0043067 "regulation of programmed cell death" evidence=IGI

GO:0043069 "negative regulation of programmed cell death" evidence=IGI

GO:0000303 "response to superoxide" evidence=IMP;RCA

GO:0006914 "autophagy" evidence=RCA

GO:0008219 "cell death" evidence=IMP;RCA

GO:0009651 "response to salt stress" evidence=RCA

GO:0009733 "response to auxin stimulus" evidence=RCA

GO:0009737 "response to abscisic acid stimulus" evidence=RCA

GO:0009743 "response to carbohydrate stimulus" evidence=RCA

GO:0009751 "response to salicylic acid stimulus" evidence=RCA

GO:0009863 "salicylic acid mediated signaling pathway" evidence=RCA

GO:0009873 "ethylene mediated signaling pathway" evidence=RCA

TAIR|locus:2119622 LOL2 "AT4G21610" [Arabidopsis thaliana (taxid:3702)]

 Score = 251 (93.4 bits), Expect = 1.9e-21, P = 1.9e-21
 Identities = 44/72 (61%), Positives = 54/72 (75%)

Query:    61 EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARS 120
             E AQ+VCG C  LL Y+RG+  V+CS C TVNL LEANQV  VNC NC++LLMY YGA +
Sbjct:    57 EKAQMVCGSCRRLLSYLRGSKHVKCSSCQTVNLVLEANQVGQVNCNNCKLLLMYPYGAPA 116

Query:   121 VKCAVCNFVTAV 132
             V+C+ CN VT +
Sbjct:   117 VRCSSCNSVTDI 128

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0009617 "response to bacterium" evidence=IEP

UNIPROTKB|Q704V3 LOL5 "Protein LOL5" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 235 (87.8 bits), Expect = 9.2e-20, P = 9.2e-20
 Identities = 40/73 (54%), Positives = 53/73 (72%)

Query:    61 EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARS 120
             E+ Q+VCG C  LL Y RGA  V C+CC T+N  LEA++V  V+CG+C  LLMY +GA +
Sbjct:    67 EVGQMVCGSCRILLAYFRGAGYVHCTCCQTMNYVLEAHEVGKVHCGHCATLLMYPFGAPA 126

Query:   121 VKCAVCNFVTAVG 133
             VKC++C FVT +G
Sbjct:   127 VKCSLCLFVTEIG 139

GO:0005634 "nucleus" evidence=IDA

GO:0031349 "positive regulation of defense response" evidence=IMP

GO:0045927 "positive regulation of growth" evidence=IMP

---

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)
Q93ZB1	LOL1_ARATH	No assigned EC number	0.9242	0.8896	0.8376	yes	no
Q0J7V9	LSD1_ORYSJ	No assigned EC number	0.8865	0.9655	0.7608	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	145
TIGR01053	31	TIGR01053, LSD1, zinc finger domain, LSD1 subclass	6e-07
pfam06943	25	pfam06943, zf-LSD1, LSD1 zinc finger	9e-07
pfam06943	25	pfam06943, zf-LSD1, LSD1 zinc finger	7e-06
TIGR01053	31	TIGR01053, LSD1, zinc finger domain, LSD1 subclass	4e-05
pfam06943	25	pfam06943, zf-LSD1, LSD1 zinc finger	2e-04
TIGR01053	31	TIGR01053, LSD1, zinc finger domain, LSD1 subclass	4e-04

>gnl|CDD|130125 TIGR01053, LSD1, zinc finger domain, LSD1 subclass

 Score = 43.2 bits (102), Expect = 6e-07
 Identities = 22/30 (73%), Positives = 26/30 (86%)

Query: 64 QLVCGGCHTLLMYIRGATSVQCSCCHTVNL 93
          Q+VCGGC TLLMY RGA+SV+C+ C TVNL
Sbjct: 1  QVVCGGCRTLLMYPRGASSVRCALCQTVNL 30

This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC. Length = 31

>gnl|CDD|191646 pfam06943, zf-LSD1, LSD1 zinc finger

 Score = 42.6 bits (101), Expect = 9e-07
 Identities = 18/25 (72%), Positives = 21/25 (84%)

Query: 67 CGGCHTLLMYIRGATSVQCSCCHTV 91
          CGGC TLLMY RGA SV+C+ C+TV
Sbjct: 1  CGGCRTLLMYPRGAPSVRCALCNTV 25

This family consists of several plant specific LSD1 zinc finger domains. Arabidopsis lsd1 mutants are hyper-responsive to cell death initiators and fail to limit the extent of cell death. Superoxide is a necessary and sufficient signal for cell death propagation. LSD1 monitors a superoxide-dependent signal and negatively regulates a plant cell death pathway. LSD1 protein contains three zinc finger domains, defined by CxxCxRxxLMYxxGASxVxCxxC. It has been suggested that LSD1 defines a zinc finger protein subclass and that LSD1 regulates transcription, via either repression of a pro-death pathway or activation of an anti-death pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. Length = 25

>gnl|CDD|191646 pfam06943, zf-LSD1, LSD1 zinc finger

 Score = 40.3 bits (95), Expect = 7e-06
 Identities = 17/25 (68%), Positives = 19/25 (76%)

Query: 28 CSGCRNLLLYPVGATSVCCAVCNAV 52
          C GCR LL+YP GA SV CA+CN V
Sbjct: 1  CGGCRTLLMYPRGAPSVRCALCNTV 25

This family consists of several plant specific LSD1 zinc finger domains. Arabidopsis lsd1 mutants are hyper-responsive to cell death initiators and fail to limit the extent of cell death. Superoxide is a necessary and sufficient signal for cell death propagation. LSD1 monitors a superoxide-dependent signal and negatively regulates a plant cell death pathway. LSD1 protein contains three zinc finger domains, defined by CxxCxRxxLMYxxGASxVxCxxC. It has been suggested that LSD1 defines a zinc finger protein subclass and that LSD1 regulates transcription, via either repression of a pro-death pathway or activation of an anti-death pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. Length = 25

>gnl|CDD|130125 TIGR01053, LSD1, zinc finger domain, LSD1 subclass

 Score = 38.2 bits (89), Expect = 4e-05
 Identities = 19/31 (61%), Positives = 23/31 (74%)

Query: 25 QLVCSGCRNLLLYPVGATSVCCAVCNAVTAV 55
          Q+VC GCR LL+YP GA+SV CA+C  V  V
Sbjct: 1  QVVCGGCRTLLMYPRGASSVRCALCQTVNLV 31

This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC. Length = 31

>gnl|CDD|191646 pfam06943, zf-LSD1, LSD1 zinc finger

 Score = 36.4 bits (85), Expect = 2e-04
 Identities = 17/25 (68%), Positives = 19/25 (76%)

Query: 105 CGNCRMLLMYQYGARSVKCAVCNFV 129
           CG CR LLMY  GA SV+CA+CN V
Sbjct: 1   CGGCRTLLMYPRGAPSVRCALCNTV 25

This family consists of several plant specific LSD1 zinc finger domains. Arabidopsis lsd1 mutants are hyper-responsive to cell death initiators and fail to limit the extent of cell death. Superoxide is a necessary and sufficient signal for cell death propagation. LSD1 monitors a superoxide-dependent signal and negatively regulates a plant cell death pathway. LSD1 protein contains three zinc finger domains, defined by CxxCxRxxLMYxxGASxVxCxxC. It has been suggested that LSD1 defines a zinc finger protein subclass and that LSD1 regulates transcription, via either repression of a pro-death pathway or activation of an anti-death pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. Length = 25

>gnl|CDD|130125 TIGR01053, LSD1, zinc finger domain, LSD1 subclass

 Score = 35.5 bits (82), Expect = 4e-04
 Identities = 18/31 (58%), Positives = 20/31 (64%)

Query: 102 HVNCGNCRMLLMYQYGARSVKCAVCNFVTAV 132
            V CG CR LLMY  GA SV+CA+C  V  V
Sbjct: 1   QVVCGGCRTLLMYPRGASSVRCALCQTVNLV 31

This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC. Length = 31

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	145
TIGR01053	31	LSD1 zinc finger domain, LSD1 subclass. This model	99.51
PF06943	25	zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zin	99.45
TIGR01053	31	LSD1 zinc finger domain, LSD1 subclass. This model	99.43
PF06943	25	zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zin	99.39
PF09788	256	Tmemb_55A: Transmembrane protein 55A; InterPro: IP	97.77
PF10122	51	Mu-like_Com: Mu-like prophage protein Com; InterPr	95.93
PF10122	51	Mu-like_Com: Mu-like prophage protein Com; InterPr	94.77
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	93.88
PF01667	55	Ribosomal_S27e: Ribosomal protein S27; InterPro: I	93.56
PLN00209	86	ribosomal protein S27; Provisional	92.75
PTZ00083	85	40S ribosomal protein S27; Provisional	92.62
PRK00415	59	rps27e 30S ribosomal protein S27e; Reviewed	91.87
PF11331	46	DUF3133: Protein of unknown function (DUF3133); In	91.46
KOG1779	84	consensus 40s ribosomal protein S27 [Translation,	91.11
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	90.1
COG2051	67	RPS27A Ribosomal protein S27E [Translation, riboso	90.07
PLN00209	86	ribosomal protein S27; Provisional	89.45
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	89.2
PTZ00083	85	40S ribosomal protein S27; Provisional	89.05
PF09788	256	Tmemb_55A: Transmembrane protein 55A; InterPro: IP	88.86
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	88.83
PF01667	55	Ribosomal_S27e: Ribosomal protein S27; InterPro: I	88.0
PF11331	46	DUF3133: Protein of unknown function (DUF3133); In	87.99
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	87.51
PRK00415	59	rps27e 30S ribosomal protein S27e; Reviewed	87.17
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	85.92
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	83.33
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	82.95
COG2051	67	RPS27A Ribosomal protein S27E [Translation, riboso	81.77
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	80.15

>TIGR01053 LSD1 zinc finger domain, LSD1 subclass

Probab=99.51  E-value=8.7e-15  Score=88.74  Aligned_cols=31  Identities=61%  Similarity=1.243  Sum_probs=23.9

Q ss_pred             eeeccCccceeecccCCCeeecCCCCcccCC
Q 032227           25 QLVCSGCRNLLLYPVGATSVCCAVCNAVTAV   55 (145)
Q Consensus        25 QlvC~gCr~lL~YprGA~~VrC~~C~tvn~v   55 (145)
                      |++|++||++|+||+||++|||+.|++||.+
T Consensus         1 q~~C~~C~t~L~yP~gA~~vrCs~C~~vt~v   31 (31)
T TIGR01053         1 QVVCGGCRTLLMYPRGASSVRCALCQTVNLV   31 (31)
T ss_pred             CcCcCCCCcEeecCCCCCeEECCCCCeEecC
Confidence            6778888888888888888888888877753

This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC

>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=99.45  E-value=3e-14  Score=83.21  Aligned_cols=25  Identities=64%  Similarity=1.364  Sum_probs=16.8

Q ss_pred             ccCccceeecccCCCeeecCCCCcc
Q 032227           28 CSGCRNLLLYPVGATSVCCAVCNAV   52 (145)
Q Consensus        28 C~gCr~lL~YprGA~~VrC~~C~tv   52 (145)
                      |+|||++|+||+||++|||+.|++|
T Consensus         1 C~~Cr~~L~yp~GA~sVrCa~C~~V   25 (25)
T PF06943_consen    1 CGGCRTLLMYPRGAPSVRCACCHTV   25 (25)
T ss_pred             CCCCCceEEcCCCCCCeECCccCcC
Confidence            5666666666666666666666664

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].

>TIGR01053 LSD1 zinc finger domain, LSD1 subclass

Probab=99.43  E-value=5.6e-14  Score=85.20  Aligned_cols=30  Identities=73%  Similarity=1.381  Sum_probs=21.0

Q ss_pred             eEEeCcccceEeeecCCceEECCCCCcccc
Q 032227           64 QLVCGGCHTLLMYIRGATSVQCSCCHTVNL   93 (145)
Q Consensus        64 ql~CGgCr~lLmYP~GA~sVrC~~C~tVn~   93 (145)
                      |++|++||++|+||+||.+|||+.|++||.
T Consensus         1 q~~C~~C~t~L~yP~gA~~vrCs~C~~vt~   30 (31)
T TIGR01053         1 QVVCGGCRTLLMYPRGASSVRCALCQTVNL   30 (31)
T ss_pred             CcCcCCCCcEeecCCCCCeEECCCCCeEec
Confidence            566777777777777777777777777664

This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC

>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=99.39  E-value=1.3e-13  Score=80.51  Aligned_cols=25  Identities=80%  Similarity=1.666  Sum_probs=15.8

Q ss_pred             eCcccceEeeecCCceEECCCCCcc
Q 032227           67 CGGCHTLLMYIRGATSVQCSCCHTV   91 (145)
Q Consensus        67 CGgCr~lLmYP~GA~sVrC~~C~tV   91 (145)
                      ||+||++||||+||+||||+.|++|
T Consensus         1 C~~Cr~~L~yp~GA~sVrCa~C~~V   25 (25)
T PF06943_consen    1 CGGCRTLLMYPRGAPSVRCACCHTV   25 (25)
T ss_pred             CCCCCceEEcCCCCCCeECCccCcC
Confidence            5666666666666666666666654

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].

>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate

Probab=97.77  E-value=0.00023  Score=60.80  Aligned_cols=112  Identities=23%  Similarity=0.534  Sum_probs=86.7

Q ss_pred             ccceeeccCccceeeccc--CCCeeecCCCCcccCCCCCCCcceeEEeCcccceEeeecCCceEECCC--CCcc-ccccc
Q 032227           22 AQSQLVCSGCRNLLLYPV--GATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSC--CHTV-NLALE   96 (145)
Q Consensus        22 ~~sQlvC~gCr~lL~Ypr--GA~~VrC~~C~tvn~vpp~~~q~aql~CGgCr~lLmYP~GA~sVrC~~--C~tV-n~v~~   96 (145)
                      .+--+.|.=|+.++--.-  ----|+|..||-.|...++.....-+.|- |+-||+-...++-+-|+.  |..| |+.+.
T Consensus        62 ~~p~v~CrVCq~~I~i~gk~~QhVVkC~~CnEATPIr~aPpGKKYVRCP-CNCLLICk~sS~rIaCPRp~CkRiI~L~~~  140 (256)
T PF09788_consen   62 GAPVVTCRVCQSLIDIEGKMHQHVVKCSVCNEATPIRNAPPGKKYVRCP-CNCLLICKSSSQRIACPRPNCKRIINLGPS  140 (256)
T ss_pred             CCceEEeecCCceecccCccceeeEECCCCCccccccCCCCCCeeEecC-CceEEEeecccccccCCCCCCcceEEeCCc
Confidence            345688999998876542  22358999999999876555556677774 788999999999999988  9877 44332


Q ss_pred             -----------cceeEEEEcCCcCeEEEEecCC--ceEeCCCCCceeeccC
Q 032227           97 -----------ANQVAHVNCGNCRMLLMYQYGA--RSVKCAVCNFVTAVGA  134 (145)
Q Consensus        97 -----------~~q~~~v~Cg~Crt~LmyP~GA--~sVkCa~C~~VT~i~~  134 (145)
                                 ......++||+|+.+.+++.=.  .-.||+-|+.|..|+.
T Consensus       141 ~~~p~~~~~~~~p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKvSSVG~  191 (256)
T PF09788_consen  141 HQGPVTPPVPTQPGSCRVICGHCSNTFLFNTLTSNTLARCPHCRKVSSVGP  191 (256)
T ss_pred             cCCCCCCCCCCCCCceeEECCCCCCcEeccCCCCCccccCCCCceeccccc
Confidence                       2355789999999999999766  5569999999999974

>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ]

Probab=95.93  E-value=0.0029  Score=42.68  Aligned_cols=39  Identities=28%  Similarity=0.613  Sum_probs=26.5

Q ss_pred             EEEcCCcCeEEEEe--cCCceEeCCCCCceeeccCCCCccc
Q 032227          102 HVNCGNCRMLLMYQ--YGARSVKCAVCNFVTAVGASTSTTE  140 (145)
Q Consensus       102 ~v~Cg~Crt~LmyP--~GA~sVkCa~C~~VT~i~~~~~~~~  140 (145)
                      .++|++|+.+|+.-  +.....||+.|.+++.|++.+...|
T Consensus         4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a~~~~~~   44 (51)
T PF10122_consen    4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRATSPEPE   44 (51)
T ss_pred             ceeccchhHHHhhhcCccEEEEECCCCCccceEeccCCCCC
Confidence            46777777777774  4445777888888777776654443

>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ]

Probab=94.77  E-value=0.014  Score=39.33  Aligned_cols=34  Identities=26%  Similarity=0.591  Sum_probs=26.5

Q ss_pred             eeEEeCcccceEeee--cCCceEECCCCCccccccc
Q 032227           63 AQLVCGGCHTLLMYI--RGATSVQCSCCHTVNLALE   96 (145)
Q Consensus        63 aql~CGgCr~lLmYP--~GA~sVrC~~C~tVn~v~~   96 (145)
                      -.+.|++|+.+|+.-  ..-..+||+.|.++|.+..
T Consensus         3 ~eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a   38 (51)
T PF10122_consen    3 KEIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRA   38 (51)
T ss_pred             cceeccchhHHHhhhcCccEEEEECCCCCccceEec
Confidence            367899999998885  3335889999999998754

>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional

Probab=93.88  E-value=0.042  Score=38.01  Aligned_cols=53  Identities=26%  Similarity=0.590  Sum_probs=41.2

Q ss_pred             cceeEEeCcccceEeeecC-CceEECCCCCccccccccceeEEEEcCCcCeEEEEecCCceEeCCCCCce
Q 032227           61 EMAQLVCGGCHTLLMYIRG-ATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFV  129 (145)
Q Consensus        61 q~aql~CGgCr~lLmYP~G-A~sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~GA~sVkCa~C~~V  129 (145)
                      ++.-.+|-+|...| .|.+ +..+.|+.|..+..         .+|..||.+      +..++|+.|+|.
T Consensus         4 ~~~~~~CtSCg~~i-~~~~~~~~F~CPnCG~~~I---------~RC~~CRk~------~~~Y~CP~CGF~   57 (59)
T PRK14890          4 MMEPPKCTSCGIEI-APREKAVKFLCPNCGEVII---------YRCEKCRKQ------SNPYTCPKCGFE   57 (59)
T ss_pred             cccCccccCCCCcc-cCCCccCEeeCCCCCCeeE---------eechhHHhc------CCceECCCCCCc
Confidence            34455799999888 5666 99999999976533         569999986      467899999885

>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=93.56  E-value=0.083  Score=35.92  Aligned_cols=42  Identities=19%  Similarity=0.426  Sum_probs=27.8

Q ss_pred             eEECCCCCccccccccceeEEEEcCCcCeEEEEecCCceEeCC
Q 032227           82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCA  124 (145)
Q Consensus        82 sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~GA~sVkCa  124 (145)
                      .|+|+.|..++.+-+.. ...+.|.+|.++|..|.|-..-.=.
T Consensus         7 ~VkCp~C~~~q~vFSha-~t~V~C~~Cg~~L~~PtGGKa~l~~   48 (55)
T PF01667_consen    7 DVKCPGCYNIQTVFSHA-QTVVKCVVCGTVLAQPTGGKARLTE   48 (55)
T ss_dssp             EEE-TTT-SEEEEETT--SS-EE-SSSTSEEEEE-SSSEEESS
T ss_pred             EEECCCCCCeeEEEecC-CeEEEcccCCCEecCCCCcCeEEeC
Confidence            58999999998875433 3479999999999999997654433

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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.

>PLN00209 ribosomal protein S27; Provisional

Probab=92.75  E-value=0.19  Score=37.12  Aligned_cols=46  Identities=24%  Similarity=0.611  Sum_probs=32.9

Q ss_pred             eEECCCCCccccccccceeEEEEcCCcCeEEEEecCCceEeCCCCCc
Q 032227           82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNF  128 (145)
Q Consensus        82 sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~GA~sVkCa~C~~  128 (145)
                      .|+|+.|..++.+-+. -...+.|..|.++|..|.|-....=.-|.|
T Consensus        36 ~VkCp~C~n~q~VFSh-A~t~V~C~~Cg~~L~~PTGGKa~l~~gc~f   81 (86)
T PLN00209         36 DVKCQGCFNITTVFSH-SQTVVVCGSCQTVLCQPTGGKARLTEGCSF   81 (86)
T ss_pred             EEECCCCCCeeEEEec-CceEEEccccCCEeeccCCCCeEecCCceE
Confidence            5788888888776543 334788999999999998877655444443

>PTZ00083 40S ribosomal protein S27; Provisional

Probab=92.62  E-value=0.21  Score=36.85  Aligned_cols=44  Identities=23%  Similarity=0.520  Sum_probs=31.3

Q ss_pred             eEECCCCCccccccccceeEEEEcCCcCeEEEEecCCceEeCCCC
Q 032227           82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVC  126 (145)
Q Consensus        82 sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~GA~sVkCa~C  126 (145)
                      .|+|+.|..++.+-+.. ...+.|.+|.++|.-|.|-....=.-|
T Consensus        35 ~VkCp~C~n~q~VFShA-~t~V~C~~Cg~~L~~PTGGKa~l~~gc   78 (85)
T PTZ00083         35 DVKCPGCSQITTVFSHA-QTVVLCGGCSSQLCQPTGGKAKLTEGC   78 (85)
T ss_pred             EEECCCCCCeeEEEecC-ceEEEccccCCEeeccCCCCeEecCCc
Confidence            47888888887765433 347888888888888888766543333

>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed

Probab=91.87  E-value=0.12  Score=35.76  Aligned_cols=38  Identities=21%  Similarity=0.436  Sum_probs=26.3

Q ss_pred             eEECCCCCccccccccceeEEEEcCCcCeEEEEecCCce
Q 032227           82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARS  120 (145)
Q Consensus        82 sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~GA~s  120 (145)
                      .|+|+.|..++.+-+. -...+.|..|.++|.-|.|-..
T Consensus        11 ~VkCp~C~n~q~vFsh-a~t~V~C~~Cg~~L~~PtGGKa   48 (59)
T PRK00415         11 KVKCPDCGNEQVVFSH-ASTVVRCLVCGKTLAEPTGGKA   48 (59)
T ss_pred             EEECCCCCCeEEEEec-CCcEEECcccCCCcccCCCcce
Confidence            4777777777765433 2336788888888888887544

>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function

Probab=91.46  E-value=0.2  Score=32.96  Aligned_cols=37  Identities=30%  Similarity=0.726  Sum_probs=18.8

Q ss_pred             CCCeeecCCCCcccCCCCC----CCcceeEEeCcccceEee
Q 032227           40 GATSVCCAVCNAVTAVPPP----GTEMAQLVCGGCHTLLMY   76 (145)
Q Consensus        40 GA~~VrC~~C~tvn~vpp~----~~q~aql~CGgCr~lLmY   76 (145)
                      ||+-|-|..|..+-..|..    .....+|.||.|...|.|
T Consensus         3 GAPFv~C~~C~~lLqlP~~~~~~~k~~~klrCGaCs~vl~~   43 (46)
T PF11331_consen    3 GAPFVVCSSCFELLQLPAKFSLSKKNQQKLRCGACSEVLSF   43 (46)
T ss_pred             CCCEeECccHHHHHcCCCccCCCccceeEEeCCCCceeEEE
Confidence            5555555555555544421    112445566666655555

>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]

Probab=91.11  E-value=0.47  Score=34.96  Aligned_cols=45  Identities=22%  Similarity=0.537  Sum_probs=30.2

Q ss_pred             eEECCCCCccccccccceeEEEEcCCcCeEEEEecCCceEeCCCCC
Q 032227           82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCN  127 (145)
Q Consensus        82 sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~GA~sVkCa~C~  127 (145)
                      -|||+.|..||-+-+..|. -+.|++|.+.|.-|.|-..+.=..|.
T Consensus        34 ~VkC~gc~~iT~vfSHaqt-vVvc~~c~~il~~~tggra~ls~~cs   78 (84)
T KOG1779|consen   34 DVKCPGCFKITTVFSHAQT-VVVCEGCSTILCQPTGGKAKLSEGCS   78 (84)
T ss_pred             EEEcCCceEEEEEeecCce-EEEcCCCceEEEEecCCcEEecCCCc
Confidence            3667777666666544444 67888888888888887766544443

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=90.10  E-value=0.26  Score=29.51  Aligned_cols=30  Identities=27%  Similarity=0.678  Sum_probs=15.0

Q ss_pred             EECCCCCcccccccc---ceeEEEEcCCcCeEE
Q 032227           83 VQCSCCHTVNLALEA---NQVAHVNCGNCRMLL  112 (145)
Q Consensus        83 VrC~~C~tVn~v~~~---~q~~~v~Cg~Crt~L  112 (145)
                      ++|+.|++.+.+.++   ..-..++|++|+..+
T Consensus         3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~   35 (38)
T TIGR02098         3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW   35 (38)
T ss_pred             EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence            456666665544321   111256666666554

This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.

>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]

Probab=90.07  E-value=0.39  Score=34.07  Aligned_cols=39  Identities=21%  Similarity=0.428  Sum_probs=28.3

Q ss_pred             eEECCCCCccccccccceeEEEEcCCcCeEEEEecCCceE
Q 032227           82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSV  121 (145)
Q Consensus        82 sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~GA~sV  121 (145)
                      -|+|+-|.....+-. +-...++|..|.++|..|.|-.+.
T Consensus        19 ~VkCpdC~N~q~vFs-hast~V~C~~CG~~l~~PTGGka~   57 (67)
T COG2051          19 RVKCPDCGNEQVVFS-HASTVVTCLICGTTLAEPTGGKAK   57 (67)
T ss_pred             EEECCCCCCEEEEec-cCceEEEecccccEEEecCCCeEE
Confidence            578888887766543 333478888899999999886543

>PLN00209 ribosomal protein S27; Provisional

Probab=89.45  E-value=0.29  Score=36.16  Aligned_cols=40  Identities=30%  Similarity=0.546  Sum_probs=29.9

Q ss_pred             eeecCCCCcccCCCCCCCcceeEEeCcccceEeeecCCceEE
Q 032227           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQ   84 (145)
Q Consensus        43 ~VrC~~C~tvn~vpp~~~q~aql~CGgCr~lLmYP~GA~sVr   84 (145)
                      .|+|+.|..++.+  =++....+.|.+|.++|..|.|--...
T Consensus        36 ~VkCp~C~n~q~V--FShA~t~V~C~~Cg~~L~~PTGGKa~l   75 (86)
T PLN00209         36 DVKCQGCFNITTV--FSHSQTVVVCGSCQTVLCQPTGGKARL   75 (86)
T ss_pred             EEECCCCCCeeEE--EecCceEEEccccCCEeeccCCCCeEe
Confidence            4888888888876  245566788888888888888865543

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=89.20  E-value=0.43  Score=29.23  Aligned_cols=12  Identities=42%  Similarity=1.018  Sum_probs=6.3

Q ss_pred             CceEeCCCCCce
Q 032227          118 ARSVKCAVCNFV  129 (145)
Q Consensus       118 A~sVkCa~C~~V  129 (145)
                      ...|||+.|+++
T Consensus        23 ~~~vrC~~C~~~   34 (37)
T PF13719_consen   23 GRKVRCPKCGHV   34 (37)
T ss_pred             CcEEECCCCCcE
Confidence            445555555544

>PTZ00083 40S ribosomal protein S27; Provisional

Probab=89.05  E-value=0.33  Score=35.81  Aligned_cols=39  Identities=28%  Similarity=0.603  Sum_probs=28.5

Q ss_pred             eeecCCCCcccCCCCCCCcceeEEeCcccceEeeecCCceE
Q 032227           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSV   83 (145)
Q Consensus        43 ~VrC~~C~tvn~vpp~~~q~aql~CGgCr~lLmYP~GA~sV   83 (145)
                      .|+|+.|..++.+  =++....+.|.+|.++|..|.|--..
T Consensus        35 ~VkCp~C~n~q~V--FShA~t~V~C~~Cg~~L~~PTGGKa~   73 (85)
T PTZ00083         35 DVKCPGCSQITTV--FSHAQTVVLCGGCSSQLCQPTGGKAK   73 (85)
T ss_pred             EEECCCCCCeeEE--EecCceEEEccccCCEeeccCCCCeE
Confidence            4788888888776  24556678888888888888876543

>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate

Probab=88.86  E-value=0.64  Score=40.12  Aligned_cols=65  Identities=22%  Similarity=0.598  Sum_probs=44.0

Q ss_pred             ccceeecccCCCeeecCC--CCcc-cCCCC---C-------CCcceeEEeCcccceEeeecCC--ceEECCCCCcccccc
Q 032227           31 CRNLLLYPVGATSVCCAV--CNAV-TAVPP---P-------GTEMAQLVCGGCHTLLMYIRGA--TSVQCSCCHTVNLAL   95 (145)
Q Consensus        31 Cr~lL~YprGA~~VrC~~--C~tv-n~vpp---~-------~~q~aql~CGgCr~lLmYP~GA--~sVrC~~C~tVn~v~   95 (145)
                      |.-||+=..-++-|-|++  |..| |+.+.   +       ...+..++||+|+...+|+.=.  .-.||+.|+.|..+.
T Consensus       111 CNCLLICk~sS~rIaCPRp~CkRiI~L~~~~~~p~~~~~~~~p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKvSSVG  190 (256)
T PF09788_consen  111 CNCLLICKSSSQRIACPRPNCKRIINLGPSHQGPVTPPVPTQPGSCRVICGHCSNTFLFNTLTSNTLARCPHCRKVSSVG  190 (256)
T ss_pred             CceEEEeecccccccCCCCCCcceEEeCCccCCCCCCCCCCCCCceeEECCCCCCcEeccCCCCCccccCCCCceecccc
Confidence            334555555555555555  6544 44332   1       2467889999999999999655  456999999998885

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=88.83  E-value=0.36  Score=29.56  Aligned_cols=9  Identities=33%  Similarity=0.896  Sum_probs=4.4

Q ss_pred             EEEcCCcCe
Q 032227          102 HVNCGNCRM  110 (145)
Q Consensus       102 ~v~Cg~Crt  110 (145)
                      .++|+.|+.
T Consensus        25 ~vrC~~C~~   33 (37)
T PF13719_consen   25 KVRCPKCGH   33 (37)
T ss_pred             EEECCCCCc
Confidence            455555544

>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=88.00  E-value=0.42  Score=32.48  Aligned_cols=38  Identities=24%  Similarity=0.417  Sum_probs=22.8

Q ss_pred             eeecCCCCcccCCCCCCCcceeEEeCcccceEeeecCCce
Q 032227           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATS   82 (145)
Q Consensus        43 ~VrC~~C~tvn~vpp~~~q~aql~CGgCr~lLmYP~GA~s   82 (145)
                      .|+|+.|..++.+  =++....+.|.+|.++|..|.|-..
T Consensus         7 ~VkCp~C~~~q~v--FSha~t~V~C~~Cg~~L~~PtGGKa   44 (55)
T PF01667_consen    7 DVKCPGCYNIQTV--FSHAQTVVKCVVCGTVLAQPTGGKA   44 (55)
T ss_dssp             EEE-TTT-SEEEE--ETT-SS-EE-SSSTSEEEEE-SSSE
T ss_pred             EEECCCCCCeeEE--EecCCeEEEcccCCCEecCCCCcCe
Confidence            4788888888766  2445567788888888888877544

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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.

>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function

Probab=87.99  E-value=0.67  Score=30.52  Aligned_cols=37  Identities=27%  Similarity=0.594  Sum_probs=23.3

Q ss_pred             CCceEECCCCCccccccc-----cceeEEEEcCCcCeEEEEe
Q 032227           79 GATSVQCSCCHTVNLALE-----ANQVAHVNCGNCRMLLMYQ  115 (145)
Q Consensus        79 GA~sVrC~~C~tVn~v~~-----~~q~~~v~Cg~Crt~LmyP  115 (145)
                      ||+-|-|..|.-+=..+.     ...+..++||.|...|.|-
T Consensus         3 GAPFv~C~~C~~lLqlP~~~~~~~k~~~klrCGaCs~vl~~s   44 (46)
T PF11331_consen    3 GAPFVVCSSCFELLQLPAKFSLSKKNQQKLRCGACSEVLSFS   44 (46)
T ss_pred             CCCEeECccHHHHHcCCCccCCCccceeEEeCCCCceeEEEe
Confidence            555555555554433321     2236699999999999874

>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional

Probab=87.51  E-value=0.74  Score=28.93  Aligned_cols=23  Identities=22%  Similarity=0.605  Sum_probs=8.6

Q ss_pred             cCCcCeEEEEecCCceEeCCCCC
Q 032227          105 CGNCRMLLMYQYGARSVKCAVCN  127 (145)
Q Consensus       105 Cg~Crt~LmyP~GA~sVkCa~C~  127 (145)
                      |++|...+.+......++|+.|+
T Consensus         6 C~~CG~~~~~~~~~~~~~Cp~CG   28 (46)
T PRK00398          6 CARCGREVELDEYGTGVRCPYCG   28 (46)
T ss_pred             CCCCCCEEEECCCCCceECCCCC
Confidence            33333333333333333333333

>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed

Probab=87.17  E-value=0.35  Score=33.45  Aligned_cols=34  Identities=24%  Similarity=0.331  Sum_probs=15.7

Q ss_pred             eecCCCCcccCCCCCCCcceeEEeCcccceEeeecC
Q 032227           44 VCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRG   79 (145)
Q Consensus        44 VrC~~C~tvn~vpp~~~q~aql~CGgCr~lLmYP~G   79 (145)
                      |+|+.|..++.+=  ++....+.|..|.++|..|.|
T Consensus        12 VkCp~C~n~q~vF--sha~t~V~C~~Cg~~L~~PtG   45 (59)
T PRK00415         12 VKCPDCGNEQVVF--SHASTVVRCLVCGKTLAEPTG   45 (59)
T ss_pred             EECCCCCCeEEEE--ecCCcEEECcccCCCcccCCC
Confidence            4555555554331  222334455555555555544

>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional

Probab=85.92  E-value=1.3  Score=27.76  Aligned_cols=26  Identities=23%  Similarity=0.471  Sum_probs=12.7

Q ss_pred             EEeCcccceEeeecCCceEECCCCCc
Q 032227           65 LVCGGCHTLLMYIRGATSVQCSCCHT   90 (145)
Q Consensus        65 l~CGgCr~lLmYP~GA~sVrC~~C~t   90 (145)
                      ..|.+|...+.+..+...++|+.|++
T Consensus         4 y~C~~CG~~~~~~~~~~~~~Cp~CG~   29 (46)
T PRK00398          4 YKCARCGREVELDEYGTGVRCPYCGY   29 (46)
T ss_pred             EECCCCCCEEEECCCCCceECCCCCC
Confidence            34555555555544444445544443

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=83.33  E-value=1.8  Score=26.50  Aligned_cols=13  Identities=15%  Similarity=0.406  Sum_probs=7.4

Q ss_pred             EECCCCCcccccc
Q 032227           83 VQCSCCHTVNLAL   95 (145)
Q Consensus        83 VrC~~C~tVn~v~   95 (145)
                      +.|+.|++.-.+.
T Consensus         3 i~Cp~C~~~y~i~   15 (36)
T PF13717_consen    3 ITCPNCQAKYEID   15 (36)
T ss_pred             EECCCCCCEEeCC
Confidence            4566666665553

>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]

Probab=82.95  E-value=1.1  Score=31.40  Aligned_cols=50  Identities=28%  Similarity=0.654  Sum_probs=40.1

Q ss_pred             EEeCcccceEeeecCCceEECCCCCccccccccceeEEEEcCCcCeEEEEecCCceEeCCCCCce
Q 032227           65 LVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFV  129 (145)
Q Consensus        65 l~CGgCr~lLmYP~GA~sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~GA~sVkCa~C~~V  129 (145)
                      -+|-+|...|.--.++.+..|+.|.-+.         -.+|..||.+      ...++|+.|.|.
T Consensus        10 ~~CtSCg~~i~p~e~~v~F~CPnCGe~~---------I~Rc~~CRk~------g~~Y~Cp~CGF~   59 (61)
T COG2888          10 PVCTSCGREIAPGETAVKFPCPNCGEVE---------IYRCAKCRKL------GNPYRCPKCGFE   59 (61)
T ss_pred             ceeccCCCEeccCCceeEeeCCCCCcee---------eehhhhHHHc------CCceECCCcCcc
Confidence            5899999999888899999999998542         4578889875      345789999885

>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]

Probab=81.77  E-value=1.5  Score=31.13  Aligned_cols=38  Identities=24%  Similarity=0.337  Sum_probs=23.9

Q ss_pred             eeecCCCCcccCCCCCCCcceeEEeCcccceEeeecCCce
Q 032227           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATS   82 (145)
Q Consensus        43 ~VrC~~C~tvn~vpp~~~q~aql~CGgCr~lLmYP~GA~s   82 (145)
                      .|+|..|..++-+=  ++....+.|..|.++|..|-|-..
T Consensus        19 ~VkCpdC~N~q~vF--shast~V~C~~CG~~l~~PTGGka   56 (67)
T COG2051          19 RVKCPDCGNEQVVF--SHASTVVTCLICGTTLAEPTGGKA   56 (67)
T ss_pred             EEECCCCCCEEEEe--ccCceEEEecccccEEEecCCCeE
Confidence            47777777666542  333456677777777777776543

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=80.15  E-value=1.9  Score=26.42  Aligned_cols=13  Identities=23%  Similarity=0.657  Sum_probs=6.2

Q ss_pred             eecCCCCcccCCC
Q 032227           44 VCCAVCNAVTAVP   56 (145)
Q Consensus        44 VrC~~C~tvn~vp   56 (145)
                      +.|..|++.-.++
T Consensus         3 i~Cp~C~~~y~i~   15 (36)
T PF13717_consen    3 ITCPNCQAKYEID   15 (36)
T ss_pred             EECCCCCCEEeCC
Confidence            3455555554443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	145
1qxf_A	66	GR2, 30S ribosomal protein S27E; structural genomi	93.9
3j20_W	63	30S ribosomal protein S27E; archaea, archaeal, KIN	93.43
2xzm_6	81	RPS27E; ribosome, translation; 3.93A {Tetrahymena	93.18
3u5c_b	82	RP61, YS20, 40S ribosomal protein S27-A; translati	90.82
1qxf_A	66	GR2, 30S ribosomal protein S27E; structural genomi	90.4
3j20_W	63	30S ribosomal protein S27E; archaea, archaeal, KIN	89.49
2xzm_6	81	RPS27E; ribosome, translation; 3.93A {Tetrahymena	89.04
3iz6_X	86	40S ribosomal protein S27 (S27E); eukaryotic ribos	87.3
3u5c_b	82	RP61, YS20, 40S ribosomal protein S27-A; translati	84.99
3iz6_X	86	40S ribosomal protein S27 (S27E); eukaryotic ribos	81.76

>1qxf_A GR2, 30S ribosomal protein S27E; structural genomics, beta sheet, PSI, protein structure initiative; NMR {Archaeoglobus fulgidus} SCOP: g.41.8.4

Probab=93.90  E-value=0.04  Score=37.91  Aligned_cols=41  Identities=17%  Similarity=0.361  Sum_probs=32.4

Q ss_pred             ceEECCCCCccccccccceeEEEEcCCcCeEEEEecCCceEe
Q 032227           81 TSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVK  122 (145)
Q Consensus        81 ~sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~GA~sVk  122 (145)
                      -.|||+.|..++.+-+..|. .+.|.+|.++|..|.|-.+-.
T Consensus         6 m~VKCp~C~niq~VFShA~t-vV~C~~Cg~~L~~PTGGKA~l   46 (66)
T 1qxf_A            6 VKVKCPDCEHEQVIFDHPST-IVKCIICGRTVAEPTGGKGNI   46 (66)
T ss_dssp             EEEECTTTCCEEEEESSCSS-CEECSSSCCEEEECCSSSCEE
T ss_pred             EEEECCCCCCceEEEecCce-EEEcccCCCEEeecCCcceee
Confidence            35899999999887554343 789999999999999976543

>3j20_W 30S ribosomal protein S27E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=93.43  E-value=0.054  Score=36.88  Aligned_cols=39  Identities=21%  Similarity=0.485  Sum_probs=29.5

Q ss_pred             eEECCCCCccccccccceeEEEEcCCcCeEEEEecCCceE
Q 032227           82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSV  121 (145)
Q Consensus        82 sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~GA~sV  121 (145)
                      .|||+.|..++.+-+. -...+.|.+|.++|..|.|-..-
T Consensus        15 ~VkCp~C~~~q~VFSh-a~t~V~C~~Cgt~L~~PTGGKa~   53 (63)
T 3j20_W           15 RVKCIDCGNEQIVFSH-PATKVRCLICGATLVEPTGGKGI   53 (63)
T ss_dssp             EEECSSSCCEEEEESS-CSSCEECSSSCCEEEECCSSSCE
T ss_pred             EEECCCCCCeeEEEec-CCeEEEccCcCCEEecCCCCcEE
Confidence            5888888888877543 33478899999999999886543

>2xzm_6 RPS27E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_6

Probab=93.18  E-value=0.11  Score=36.91  Aligned_cols=45  Identities=22%  Similarity=0.570  Sum_probs=30.8

Q ss_pred             eEECCCCCccccccccceeEEEEcCCcCeEEEEecCCceEeCCCCC
Q 032227           82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCN  127 (145)
Q Consensus        82 sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~GA~sVkCa~C~  127 (145)
                      .|+|+.|..++.+-+..| ..|.|.+|.++|..|.|-.+-.=.-|.
T Consensus        32 ~VkCp~C~n~q~VFShA~-t~V~C~~Cg~~L~~PTGGKA~l~egc~   76 (81)
T 2xzm_6           32 DVKCAQCQNIQMIFSNAQ-STIICEKCSAILCKPTGGKVQIQAGCA   76 (81)
T ss_dssp             EEECSSSCCEEEEETTCS-SCEECSSSCCEEEEECSSCEEECSSCE
T ss_pred             EeECCCCCCeeEEEecCc-cEEEccCCCCEEeecCCCCeEecCCcc
Confidence            467888887777654333 368888888888888887665444343

>3u5c_b RP61, YS20, 40S ribosomal protein S27-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_X 3u5g_b

Probab=90.82  E-value=0.11  Score=37.03  Aligned_cols=44  Identities=20%  Similarity=0.477  Sum_probs=28.9

Q ss_pred             eEECCCCCccccccccceeEEEEcCCcCeEEEEecCCceEeCCCC
Q 032227           82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVC  126 (145)
Q Consensus        82 sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~GA~sVkCa~C  126 (145)
                      .|+|+.|..++.+-+..| ..+.|.+|.++|..|.|-..-.=.-|
T Consensus        34 ~VkCp~C~~~q~VFSha~-t~V~C~~Cg~~L~~PTGGKa~l~egc   77 (82)
T 3u5c_b           34 DVKCPGCLNITTVFSHAQ-TAVTCESCSTILCTPTGGKAKLSEGT   77 (82)
T ss_dssp             EEECTTSCSCEEEESBCS-SCCCCSSSCCCCEECCSSBCEECSSC
T ss_pred             EEECCCCCCeeEEEecCC-eEEEccccCCEEeccCCCCeEecCCc
Confidence            477777777776644333 36778888888888877665544444

>1qxf_A GR2, 30S ribosomal protein S27E; structural genomics, beta sheet, PSI, protein structure initiative; NMR {Archaeoglobus fulgidus} SCOP: g.41.8.4

Probab=90.40  E-value=0.15  Score=35.01  Aligned_cols=39  Identities=15%  Similarity=0.237  Sum_probs=29.9

Q ss_pred             eeecCCCCcccCCCCCCCcceeEEeCcccceEeeecCCceE
Q 032227           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSV   83 (145)
Q Consensus        43 ~VrC~~C~tvn~vpp~~~q~aql~CGgCr~lLmYP~GA~sV   83 (145)
                      .|+|+.|..++.+=  +.....+.|.+|.++|..|.|-..-
T Consensus         7 ~VKCp~C~niq~VF--ShA~tvV~C~~Cg~~L~~PTGGKA~   45 (66)
T 1qxf_A            7 KVKCPDCEHEQVIF--DHPSTIVKCIICGRTVAEPTGGKGN   45 (66)
T ss_dssp             EEECTTTCCEEEEE--SSCSSCEECSSSCCEEEECCSSSCE
T ss_pred             EEECCCCCCceEEE--ecCceEEEcccCCCEEeecCCccee
Confidence            58899998888762  4456678899999999988886543

>3j20_W 30S ribosomal protein S27E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=89.49  E-value=0.2  Score=34.12  Aligned_cols=37  Identities=22%  Similarity=0.333  Sum_probs=23.7

Q ss_pred             eeecCCCCcccCCCCCCCcceeEEeCcccceEeeecCCc
Q 032227           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGAT   81 (145)
Q Consensus        43 ~VrC~~C~tvn~vpp~~~q~aql~CGgCr~lLmYP~GA~   81 (145)
                      .|+|+.|..++.+  =++....+.|.+|.++|..|.|-.
T Consensus        15 ~VkCp~C~~~q~V--FSha~t~V~C~~Cgt~L~~PTGGK   51 (63)
T 3j20_W           15 RVKCIDCGNEQIV--FSHPATKVRCLICGATLVEPTGGK   51 (63)
T ss_dssp             EEECSSSCCEEEE--ESSCSSCEECSSSCCEEEECCSSS
T ss_pred             EEECCCCCCeeEE--EecCCeEEEccCcCCEEecCCCCc
Confidence            4677777776665  234455667777777777777654

>2xzm_6 RPS27E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_6

Probab=89.04  E-value=0.22  Score=35.32  Aligned_cols=38  Identities=21%  Similarity=0.551  Sum_probs=24.1

Q ss_pred             eeecCCCCcccCCCCCCCcceeEEeCcccceEeeecCCce
Q 032227           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATS   82 (145)
Q Consensus        43 ~VrC~~C~tvn~vpp~~~q~aql~CGgCr~lLmYP~GA~s   82 (145)
                      .|+|+.|..++.+=  ++....+.|.+|.++|..|.|--.
T Consensus        32 ~VkCp~C~n~q~VF--ShA~t~V~C~~Cg~~L~~PTGGKA   69 (81)
T 2xzm_6           32 DVKCAQCQNIQMIF--SNAQSTIICEKCSAILCKPTGGKV   69 (81)
T ss_dssp             EEECSSSCCEEEEE--TTCSSCEECSSSCCEEEEECSSCE
T ss_pred             EeECCCCCCeeEEE--ecCccEEEccCCCCEEeecCCCCe
Confidence            46777777766652  344556677777777777776544

>3iz6_X 40S ribosomal protein S27 (S27E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=87.30  E-value=0.14  Score=36.72  Aligned_cols=44  Identities=23%  Similarity=0.550  Sum_probs=29.0

Q ss_pred             eEECCCCCccccccccceeEEEEcCCcCeEEEEecCCceEeCCCC
Q 032227           82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVC  126 (145)
Q Consensus        82 sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~GA~sVkCa~C  126 (145)
                      .|+|+.|..++.+-+..+ ..+.|.+|.++|..|.|-.+-.=.-|
T Consensus        36 ~VkCp~C~~~~~VFShA~-t~V~C~~CgtvL~~PTGGKa~l~egc   79 (86)
T 3iz6_X           36 DVKCQGCFNITTVFSHSQ-TVVVCPGCQTVLCQPTGGKARLTEGC   79 (86)
T ss_dssp             EEECTTTCCEEEEETTCS-SCCCCSSSCCCCSCCCSSSCCCSCBC
T ss_pred             EEECCCCCCeeEEEecCC-cEEEccCCCCEeecCCCCCEEecCCc
Confidence            477777777776644333 36778888888888887665444444

>3u5c_b RP61, YS20, 40S ribosomal protein S27-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_X 3u5g_b

Probab=84.99  E-value=0.26  Score=35.04  Aligned_cols=39  Identities=26%  Similarity=0.493  Sum_probs=25.3

Q ss_pred             eeecCCCCcccCCCCCCCcceeEEeCcccceEeeecCCceE
Q 032227           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSV   83 (145)
Q Consensus        43 ~VrC~~C~tvn~vpp~~~q~aql~CGgCr~lLmYP~GA~sV   83 (145)
                      .|+|..|..++.+=  ++....+.|.+|.++|..|.|-..-
T Consensus        34 ~VkCp~C~~~q~VF--Sha~t~V~C~~Cg~~L~~PTGGKa~   72 (82)
T 3u5c_b           34 DVKCPGCLNITTVF--SHAQTAVTCESCSTILCTPTGGKAK   72 (82)
T ss_dssp             EEECTTSCSCEEEE--SBCSSCCCCSSSCCCCEECCSSBCE
T ss_pred             EEECCCCCCeeEEE--ecCCeEEEccccCCEEeccCCCCeE
Confidence            47777777777652  3445566777777777777775543

>3iz6_X 40S ribosomal protein S27 (S27E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=81.76  E-value=0.32  Score=34.86  Aligned_cols=38  Identities=32%  Similarity=0.588  Sum_probs=24.1

Q ss_pred             eeecCCCCcccCCCCCCCcceeEEeCcccceEeeecCCce
Q 032227           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATS   82 (145)
Q Consensus        43 ~VrC~~C~tvn~vpp~~~q~aql~CGgCr~lLmYP~GA~s   82 (145)
                      .|+|..|..++.+=  ++....+.|.+|.++|..|.|--.
T Consensus        36 ~VkCp~C~~~~~VF--ShA~t~V~C~~CgtvL~~PTGGKa   73 (86)
T 3iz6_X           36 DVKCQGCFNITTVF--SHSQTVVVCPGCQTVLCQPTGGKA   73 (86)
T ss_dssp             EEECTTTCCEEEEE--TTCSSCCCCSSSCCCCSCCCSSSC
T ss_pred             EEECCCCCCeeEEE--ecCCcEEEccCCCCEeecCCCCCE
Confidence            37777777777652  344456667777777777766543

---

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

ID	Length	Definition	Probability
Query	145
d1qxfa_	58	Ribosomal protein S27e {Archaeon Archaeoglobus ful	93.22
d1qxfa_	58	Ribosomal protein S27e {Archaeon Archaeoglobus ful	91.2

>d1qxfa_ g.41.8.4 (A:) Ribosomal protein S27e {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein S27e
domain: Ribosomal protein S27e
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=93.22  E-value=0.029  Score=36.04  Aligned_cols=38  Identities=18%  Similarity=0.432  Sum_probs=29.4

Q ss_pred             eEECCCCCccccccccceeEEEEcCCcCeEEEEecCCce
Q 032227           82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARS  120 (145)
Q Consensus        82 sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~GA~s  120 (145)
                      .|||+.|..++.+-+..+ ..+.|..|.++|..|.|-..
T Consensus         7 ~VkC~~C~n~~ivFsha~-t~V~C~~Cg~~L~~PtGGKa   44 (58)
T d1qxfa_           7 KVKCPDCEHEQVIFDHPS-TIVKCIICGRTVAEPTGGKG   44 (58)
T ss_dssp             EEECTTTCCEEEEESSCS-SCEECSSSCCEEEECCSSSC
T ss_pred             EeECCCCCCeEEEEecCc-eEEEccccCCEEeccCCCeE
Confidence            588888988887754333 37899999999999988654

>d1qxfa_ g.41.8.4 (A:) Ribosomal protein S27e {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein S27e
domain: Ribosomal protein S27e
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=91.20  E-value=0.055  Score=34.67  Aligned_cols=38  Identities=16%  Similarity=0.262  Sum_probs=29.7

Q ss_pred             eeecCCCCcccCCCCCCCcceeEEeCcccceEeeecCCce
Q 032227           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATS   82 (145)
Q Consensus        43 ~VrC~~C~tvn~vpp~~~q~aql~CGgCr~lLmYP~GA~s   82 (145)
                      .|+|+.|..++.+=  ++....+.|..|.++|..|.|-..
T Consensus         7 ~VkC~~C~n~~ivF--sha~t~V~C~~Cg~~L~~PtGGKa   44 (58)
T d1qxfa_           7 KVKCPDCEHEQVIF--DHPSTIVKCIICGRTVAEPTGGKG   44 (58)
T ss_dssp             EEECTTTCCEEEEE--SSCSSCEECSSSCCEEEECCSSSC
T ss_pred             EeECCCCCCeEEEE--ecCceEEEccccCCEEeccCCCeE
Confidence            58899999888762  455668889999999999888654