Citrus Sinensis ID: 032369

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140--
Protein Sequence
MPVPLAPYPTPPAPYTPPANGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVGVSNHIFFLV
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccEEEccccccEEEccccccEEEccccccccccccccccccEEEEcccccEEEEEccccEEEcccccccccccccccEEcEEccccccEEEEEccccEEEcccccccEEccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccHHHEEEEccccEEEEEccccccEEEccEccEccccccccHHEEEEEccccEEEEEcccccEEEcccccEEEcccccccEEEEEccccEEEEEEccccccEEccEEEEEccccccccEEEEc
Coil and Loop (DISEMBL)
mpvplapyptppapytppangaqsqlvcsgcrnlllypvgaTSVCCAVcnavtavpppgtemaqLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVGVSNHIFFLV
Flexible Loop (DISEMBL)
MPVPLAPYPTPPAPYTPPANGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVGVsnhifflv
Low Complexity Region (SEG)
MpvplapyptppapytppaNGAQSQLVCSGCRNLLLYPVGATSvccavcnavtavpppGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVGVSNHIFFLV
Disordered region (IsUnstruct)
************************QLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVGVSNHIFFL*
Disordered Region (DISOPRED)
******P*******************VCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVGVS*******
Disordered Region (DISEMBL)
MPVPLAPYPTPPAPYTPPANGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVGVSNHIFFLV
Disordered Region (DISPRO)
*PVPLAPYPTPPAPYTPPANGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVGVSNHIFFLV
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MPVPLAPYPTPPAPYTPPANGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVGVSNHIFFLV
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	142	2.2.26 [Sep-21-2011]
Q93ZB1	154	Protein LOL1 OS=Arabidops	yes	no	0.845	0.779	0.934	5e-59
Q0J7V9	184	Protein LSD1 OS=Oryza sat	yes	no	0.943	0.728	0.911	9e-59
Q2QMB3	172	Protein LOL2 OS=Oryza sat	no	no	0.795	0.656	0.640	1e-36
Q6ASS2	186	Protein LOL3 OS=Oryza sat	no	no	0.795	0.607	0.617	9e-36
P94077	189	Protein LSD1 OS=Arabidops	no	no	0.802	0.603	0.6	6e-32
Q84UR0	147	Protein LOL4 OS=Oryza sat	no	no	0.774	0.748	0.477	8e-24
O65426	155	Protein LOL2 OS=Arabidops	no	no	0.535	0.490	0.584	3e-21
Q704V3	163	Protein LOL5 OS=Oryza sat	no	no	0.528	0.460	0.539	7e-18
Q69UP7	147	Protein LOL1 OS=Oryza sat	no	no	0.352	0.340	0.648	4e-12

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

 Score =  225 bits (574), Expect = 5e-59,   Method: Compositional matrix adjust.
 Identities = 115/123 (93%), Positives = 118/123 (95%), Gaps = 3/123 (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 GVS 135
           G S
Sbjct: 142 GGS 144

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 =  224 bits (572), Expect = 9e-59,   Method: Compositional matrix adjust.
 Identities = 123/135 (91%), Positives = 128/135 (94%), Gaps = 1/135 (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 VKCAVCNFVTAVGVS 135
           VKCAVCNFVT+VG S
Sbjct: 161 VKCAVCNFVTSVGAS 175

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 =  151 bits (382), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 73/114 (64%), Positives = 91/114 (79%), Gaps = 1/114 (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  SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVGVS 135
           SV+CSCC TVNL    + +AH+NCG C+ +LMY YGA SVKCA+CNF+T  G++
Sbjct: 62  SVRCSCCDTVNLVRPVSSIAHLNCGQCQTVLMYPYGAPSVKCAICNFITNTGMN 115

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 =  148 bits (374), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 71/115 (61%), Positives = 87/115 (75%), Gaps = 2/115 (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  TSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVGVS 135
            +V+CSCC TVNL    N +AHV+CG CR  LMY YGA SVKCA+C+++T  G++
Sbjct: 62  DTVRCSCCSTVNLVRPVNNIAHVSCGQCRTTLMYPYGAPSVKCAICHYITNTGMN 116

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 =  135 bits (341), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 75/125 (60%), Positives = 90/125 (72%), Gaps = 11/125 (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 VGVSN 136
           V +SN
Sbjct: 127 VNMSN 131

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 = 8e-24,   Method: Compositional matrix adjust.
 Identities = 53/111 (47%), Positives = 73/111 (65%), Gaps = 1/111 (0%)

Query: 23  QSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPG-TEMAQLVCGGCHTLLMYIRGAT 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 =  100 bits (248), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 45/77 (58%), Positives = 56/77 (72%)

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 VKCAVCNFVTAVGVSNH 137
           V+C+ CN VT +  +N 
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 = 89.4 bits (220), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 41/76 (53%), Positives = 54/76 (71%)

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 VKCAVCNFVTAVGVSN 136
           VKC++C FVT +G  N
Sbjct: 127 VKCSLCLFVTEIGERN 142

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	142
297742122	230	unnamed protein product [Vitis vinifera]	0.950	0.586	0.933	8e-67
225427256	145	PREDICTED: protein LOL1-like [Vitis vini	0.950	0.931	0.933	1e-65
147810699	146	hypothetical protein VITISV_014138 [Viti	0.936	0.910	0.939	5e-65
346472259	145	hypothetical protein [Amblyomma maculatu	0.950	0.931	0.890	8e-61
388492562	146	unknown [Lotus japonicus]	0.971	0.945	0.870	1e-59
388497348	145	unknown [Lotus japonicus]	0.950	0.931	0.962	4e-59
158516901	142	LOL1 [Bambusa oldhamii]	0.922	0.922	0.879	5e-59
255574680	147	conserved hypothetical protein [Ricinus	0.950	0.918	0.927	9e-59
449461519	144	PREDICTED: protein LOL1-like isoform 1 [	0.943	0.930	0.947	2e-58
357476673	154	Zinc finger protein LSD1 [Medicago trunc	0.816	0.753	0.974	1e-57

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

 Score =  258 bits (658), Expect = 8e-67,   Method: Compositional matrix adjust.
 Identities = 126/135 (93%), Positives = 129/135 (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 VKCAVCNFVTAVGVS 135
           VKCAVCNFVT+VG S
Sbjct: 206 VKCAVCNFVTSVGAS 220

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 =  253 bits (647), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 126/135 (93%), Positives = 129/135 (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 VKCAVCNFVTAVGVS 135
           VKCAVCNFVT+VG S
Sbjct: 121 VKCAVCNFVTSVGAS 135

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 =  251 bits (642), Expect = 5e-65,   Method: Compositional matrix adjust.
 Identities = 125/133 (93%), Positives = 128/133 (96%)

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 VKCAVCNFVTAVG 133
           VKCAVCNFVT+VG
Sbjct: 121 VKCAVCNFVTSVG 133

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  238 bits (606), Expect = 8e-61,   Method: Compositional matrix adjust.
 Identities = 122/137 (89%), Positives = 130/137 (94%), Gaps = 2/137 (1%)

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 SVKCAVCNFVTAVGVSN 136
           SVKCAVCN+VT VG S+
Sbjct: 120 SVKCAVCNYVTPVGPSS 136

Source: Amblyomma maculatum

Species: Amblyomma maculatum

Genus: Amblyomma

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  234 bits (596), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 121/139 (87%), Positives = 126/139 (90%), Gaps = 1/139 (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 SVKCAVCNFVTAVGVSNHI 138
           SVKCAVC+FVT V  S  I
Sbjct: 121 SVKCAVCSFVTLVEASTSI 139

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  232 bits (591), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 130/135 (96%), Positives = 133/135 (98%)

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

Query: 61  EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARS 120
           EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARS
Sbjct: 61  EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARS 120

Query: 121 VKCAVCNFVTAVGVS 135
           VKCAVCNFVT+VG S
Sbjct: 121 VKCAVCNFVTSVGTS 135

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|158516901|gb|ABW70167.1| LOL1 [Bambusa oldhamii]

 Score =  232 bits (591), Expect = 5e-59,   Method: Compositional matrix adjust.
 Identities = 117/133 (87%), Positives = 126/133 (94%), Gaps = 2/133 (1%)

Query: 1   MPVPLAPYPTPPAPYTPPANGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGT 60
           MPVPLAP+PTP  P+TPP NGAQSQL+CSGCRNLL+Y  GATSVCCAVC+ +TAVP PGT
Sbjct: 1   MPVPLAPHPTP-VPFTPP-NGAQSQLICSGCRNLLMYSAGATSVCCAVCSTMTAVPAPGT 58

Query: 61  EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARS 120
           EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLA+EANQVAHVNCGNCR+LLMYQYGARS
Sbjct: 59  EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLAMEANQVAHVNCGNCRILLMYQYGARS 118

Query: 121 VKCAVCNFVTAVG 133
           VKCAVCNFVT+VG
Sbjct: 119 VKCAVCNFVTSVG 131

Source: Bambusa oldhamii

Species: Bambusa oldhamii

Genus: Bambusa

Family: Poaceae

Order: Poales

Class: Liliopsida

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 =  231 bits (588), Expect = 9e-59,   Method: Compositional matrix adjust.
 Identities = 127/137 (92%), Positives = 130/137 (94%), Gaps = 2/137 (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 RSVKCAVCNFVTAVGVS 135
           RSVKC+VCNFVTAVG S
Sbjct: 121 RSVKCSVCNFVTAVGAS 137

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449461519|ref|XP_004148489.1| PREDICTED: protein LOL1-like isoform 1 [Cucumis sativus] gi|449461521|ref|XP_004148490.1| PREDICTED: protein LOL1-like isoform 2 [Cucumis sativus] gi|449523109|ref|XP_004168567.1| PREDICTED: protein LOL1-like isoform 1 [Cucumis sativus] gi|449523111|ref|XP_004168568.1| PREDICTED: protein LOL1-like isoform 2 [Cucumis sativus]

 Score =  229 bits (585), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 127/134 (94%), Positives = 131/134 (97%)

Query: 2   PVPLAPYPTPPAPYTPPANGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTE 61
           PVPLAPYPTPPAPYT P+N  QSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTE
Sbjct: 3   PVPLAPYPTPPAPYTQPSNATQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTE 62

Query: 62  MAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSV 121
           MAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHV+CGNCRMLLMYQYGARSV
Sbjct: 63  MAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVSCGNCRMLLMYQYGARSV 122

Query: 122 KCAVCNFVTAVGVS 135
           KCAVCNFVT+VG+S
Sbjct: 123 KCAVCNFVTSVGMS 136

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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 =  227 bits (579), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 113/116 (97%), Positives = 115/116 (99%)

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

Query: 80  ATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVGVS 135
           ATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVT+VG S
Sbjct: 88  ATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTSVGAS 143

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	142
UNIPROTKB|Q0J7V9	184	LSD1 "Protein LSD1" [Oryza sat	0.816	0.630	0.827	1.5e-49
UNIPROTKB|F8RP38	176	F8RP38 "Zinc finger protein LS	0.802	0.647	0.631	7.2e-36
TAIR|locus:2128639	210	LSD1 "LESION SIMULATING DISEAS	0.535	0.361	0.487	6.8e-30
TAIR|locus:2119622	155	LOL2 "AT4G21610" [Arabidopsis	0.535	0.490	0.592	5.5e-22
UNIPROTKB|Q704V3	163	LOL5 "Protein LOL5" [Oryza sat	0.535	0.466	0.539	4.4e-20

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

 Score = 516 (186.7 bits), Expect = 1.5e-49, P = 1.5e-49
 Identities = 96/116 (82%), Positives = 99/116 (85%)

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

Query:    80 ATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVGVS 135
             ATSVQCSCCHTVNLA+EANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVT+VG S
Sbjct:   120 ATSVQCSCCHTVNLAMEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTSVGAS 175

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 = 387 (141.3 bits), Expect = 7.2e-36, P = 7.2e-36
 Identities = 72/114 (63%), Positives = 84/114 (73%)

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

Query:    83 VQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVGVSN 136
             V+CSCCHTVNLA  +NQVAHV C NCR  LMY YGA SVKCAVC+++T + +SN
Sbjct:    62 VRCSCCHTVNLAPVSNQVAHVPCANCRTTLMYPYGAPSVKCAVCHYITNINMSN 115

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 = 6.8e-30, Sum P(2) = 6.8e-30
 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 = 256 (95.2 bits), Expect = 5.5e-22, P = 5.5e-22
 Identities = 45/76 (59%), Positives = 56/76 (73%)

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 VKCAVCNFVTAVGVSN 136
             V+C+ CN VT +  +N
Sbjct:   117 VRCSSCNSVTDISENN 132

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 = 238 (88.8 bits), Expect = 4.4e-20, P = 4.4e-20
 Identities = 41/76 (53%), Positives = 54/76 (71%)

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 VKCAVCNFVTAVGVSN 136
             VKC++C FVT +G  N
Sbjct:   127 VKCSLCLFVTEIGERN 142

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	0.9349	0.8450	0.7792	yes	no
Q0J7V9	LSD1_ORYSJ	No assigned EC number	0.9111	0.9436	0.7282	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: 4344713 LSD1 zinc finger domain containing protein, expressed (201 aa) (Oryza sativa Japonica)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	142
TIGR01053	31	TIGR01053, LSD1, zinc finger domain, LSD1 subclass	6e-07
pfam06943	25	pfam06943, zf-LSD1, LSD1 zinc finger	1e-06
pfam06943	25	pfam06943, zf-LSD1, LSD1 zinc finger	9e-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 = 42.8 bits (101), 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 = 42.2 bits (100), Expect = 1e-06
 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 = 39.9 bits (94), Expect = 9e-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	142
TIGR01053	31	LSD1 zinc finger domain, LSD1 subclass. This model	99.5
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	99.4
PF09788	256	Tmemb_55A: Transmembrane protein 55A; InterPro: IP	97.7
PF10122	51	Mu-like_Com: Mu-like prophage protein Com; InterPr	95.07
PF10122	51	Mu-like_Com: Mu-like prophage protein Com; InterPr	94.44
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	93.61
PF01667	55	Ribosomal_S27e: Ribosomal protein S27; InterPro: I	92.0
PLN00209	86	ribosomal protein S27; Provisional	91.03
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	90.86
PF11331	46	DUF3133: Protein of unknown function (DUF3133); In	90.86
PTZ00083	85	40S ribosomal protein S27; Provisional	90.73
PF11331	46	DUF3133: Protein of unknown function (DUF3133); In	89.86
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	89.78
PF09788	256	Tmemb_55A: Transmembrane protein 55A; InterPro: IP	89.51
PRK00415	59	rps27e 30S ribosomal protein S27e; Reviewed	89.01
PLN00209	86	ribosomal protein S27; Provisional	88.95
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	88.6
PTZ00083	85	40S ribosomal protein S27; Provisional	88.48
PF01667	55	Ribosomal_S27e: Ribosomal protein S27; InterPro: I	87.89
COG2051	67	RPS27A Ribosomal protein S27E [Translation, riboso	86.74
PRK00415	59	rps27e 30S ribosomal protein S27e; Reviewed	86.55
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	85.9
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	85.05
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	84.26
KOG1779	84	consensus 40s ribosomal protein S27 [Translation,	83.56
KOG4684	275	consensus Uncharacterized conserved protein, conta	83.11
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	81.91
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	81.28
COG2051	67	RPS27A Ribosomal protein S27E [Translation, riboso	81.08

>TIGR01053 LSD1 zinc finger domain, LSD1 subclass

Probab=99.50  E-value=1e-14  Score=88.20  Aligned_cols=31  Identities=61%  Similarity=1.243  Sum_probs=23.1

Q ss_pred             eeeccCccceeecccCCCeEecCCCCccccC
Q 032369           25 QLVCSGCRNLLLYPVGATSVCCAVCNAVTAV   55 (142)
Q Consensus        25 QlvC~gCr~lL~YprGA~~VrC~~C~tvn~v   55 (142)
                      |++|++||++|+||+||++|||+.|++||.+
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            6777777777777777777777777777753

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=3.7e-14  Score=82.63  Aligned_cols=25  Identities=64%  Similarity=1.364  Sum_probs=15.9

Q ss_pred             ccCccceeecccCCCeEecCCCCcc
Q 032369           28 CSGCRNLLLYPVGATSVCCAVCNAV   52 (142)
Q Consensus        28 C~gCr~lL~YprGA~~VrC~~C~tv   52 (142)
                      |+|||++|+||+||+||||+.|++|
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 [].

>TIGR01053 LSD1 zinc finger domain, LSD1 subclass

Probab=99.43  E-value=5e-14  Score=85.17  Aligned_cols=30  Identities=73%  Similarity=1.381  Sum_probs=19.7

Q ss_pred             eEEeCCccceEEeecCCCeEECCCCccccc
Q 032369           64 QLVCGGCHTLLMYIRGATSVQCSCCHTVNL   93 (142)
Q Consensus        64 ql~Cg~Cr~lLmYp~GA~sVrC~~C~tVn~   93 (142)
                      |++|++||++|+||+||.+|||+.|++||.
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            456666666666666666666666666664

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=99.40  E-value=1.2e-13  Score=80.45  Aligned_cols=25  Identities=80%  Similarity=1.666  Sum_probs=15.0

Q ss_pred             eCCccceEEeecCCCeEECCCCccc
Q 032369           67 CGGCHTLLMYIRGATSVQCSCCHTV   91 (142)
Q Consensus        67 Cg~Cr~lLmYp~GA~sVrC~~C~tV   91 (142)
                      ||+||++||||+||+||||+.|++|
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            5566666666666666666666554

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=97.70  E-value=0.00034  Score=59.66  Aligned_cols=111  Identities=23%  Similarity=0.531  Sum_probs=85.2

Q ss_pred             cceeeccCccceeeccc--CCCeEecCCCCccccCCCCCCceeeEEeCCccceEEeecCCCeEECCC--Cccc-ccccc-
Q 032369           23 QSQLVCSGCRNLLLYPV--GATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSC--CHTV-NLALE-   96 (142)
Q Consensus        23 ~sQlvC~gCr~lL~Ypr--GA~~VrC~~C~tvn~vpp~~~~~aql~Cg~Cr~lLmYp~GA~sVrC~~--C~tV-n~v~~-   96 (142)
                      +.-+.|.=|+.++--..  ----|+|..||-.|...++.....-++|- |.-||+=...++-+-|+.  |..| |+.+. 
T Consensus        63 ~p~v~CrVCq~~I~i~gk~~QhVVkC~~CnEATPIr~aPpGKKYVRCP-CNCLLICk~sS~rIaCPRp~CkRiI~L~~~~  141 (256)
T PF09788_consen   63 APVVTCRVCQSLIDIEGKMHQHVVKCSVCNEATPIRNAPPGKKYVRCP-CNCLLICKSSSQRIACPRPNCKRIINLGPSH  141 (256)
T ss_pred             CceEEeecCCceecccCccceeeEECCCCCccccccCCCCCCeeEecC-CceEEEeecccccccCCCCCCcceEEeCCcc
Confidence            35678999998876542  22348999999988865444556677774 788999999999999987  9876 44332 


Q ss_pred             ----------ccceeEEEcCCcceEEEeecCC--CeEeCCcCcceeeecc
Q 032369           97 ----------ANQVAHVNCGNCRMLLMYQYGA--RSVKCAVCNFVTAVGV  134 (142)
Q Consensus        97 ----------a~q~~~v~Cg~C~t~LmYP~GA--~sVkCa~C~~VT~i~~  134 (142)
                                ......++||+|+.+.+++.=.  ...||+.|+.|..|+.
T Consensus       142 ~~p~~~~~~~~p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKvSSVG~  191 (256)
T PF09788_consen  142 QGPVTPPVPTQPGSCRVICGHCSNTFLFNTLTSNTLARCPHCRKVSSVGP  191 (256)
T ss_pred             CCCCCCCCCCCCCceeEECCCCCCcEeccCCCCCccccCCCCceeccccc
Confidence                      2355789999999999999766  5669999999999985

>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=95.07  E-value=0.01  Score=39.94  Aligned_cols=34  Identities=26%  Similarity=0.637  Sum_probs=23.1

Q ss_pred             eeEEeCCccceEEeecC--CCeEECCCCcccccccc
Q 032369           63 AQLVCGGCHTLLMYIRG--ATSVQCSCCHTVNLALE   96 (142)
Q Consensus        63 aql~Cg~Cr~lLmYp~G--A~sVrC~~C~tVn~v~~   96 (142)
                      -.+.|++|+.+|+.--+  -..+||+.|.++|.+..
T Consensus         3 ~eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a   38 (51)
T PF10122_consen    3 KEIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRA   38 (51)
T ss_pred             cceeccchhHHHhhhcCccEEEEECCCCCccceEec
Confidence            35677778777777433  34777888888877653

>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=94.44  E-value=0.013  Score=39.36  Aligned_cols=36  Identities=25%  Similarity=0.597  Sum_probs=30.3

Q ss_pred             eEEEcCCcceEEEee--cCCCeEeCCcCcceeeecccc
Q 032369          101 AHVNCGNCRMLLMYQ--YGARSVKCAVCNFVTAVGVSN  136 (142)
Q Consensus       101 ~~v~Cg~C~t~LmYP--~GA~sVkCa~C~~VT~i~~~~  136 (142)
                      ..++|++|+-+|+--  +.....||+.|.+++.|+..+
T Consensus         3 ~eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a~~   40 (51)
T PF10122_consen    3 KEIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRATS   40 (51)
T ss_pred             cceeccchhHHHhhhcCccEEEEECCCCCccceEeccC
Confidence            358999999999995  555689999999999997654

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

Probab=93.61  E-value=0.049  Score=37.57  Aligned_cols=53  Identities=26%  Similarity=0.590  Sum_probs=41.2

Q ss_pred             ceeeEEeCCccceEEeecC-CCeEECCCCccccccccccceeEEEcCCcceEEEeecCCCeEeCCcCcce
Q 032369           61 EMAQLVCGGCHTLLMYIRG-ATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFV  129 (142)
Q Consensus        61 ~~aql~Cg~Cr~lLmYp~G-A~sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~GA~sVkCa~C~~V  129 (142)
                      ++.-.+|.+|...| .|.+ +....|+.|..+..         .+|..||.+      +..++|+.|.|.
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 99999999976554         469999976      467899999875

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

Probab=92.00  E-value=0.15  Score=34.49  Aligned_cols=43  Identities=19%  Similarity=0.414  Sum_probs=28.3

Q ss_pred             eEECCCCccccccccccceeEEEcCCcceEEEeecCCCeEeCCc
Q 032369           82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAV  125 (142)
Q Consensus        82 sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~GA~sVkCa~  125 (142)
                      .|||+.|..++.+= .+....+.|.+|.++|.-|.|-..-.=+.
T Consensus         7 ~VkCp~C~~~q~vF-Sha~t~V~C~~Cg~~L~~PtGGKa~l~~~   49 (55)
T PF01667_consen    7 DVKCPGCYNIQTVF-SHAQTVVKCVVCGTVLAQPTGGKARLTEG   49 (55)
T ss_dssp             EEE-TTT-SEEEEE-TT-SS-EE-SSSTSEEEEE-SSSEEESSS
T ss_pred             EEECCCCCCeeEEE-ecCCeEEEcccCCCEecCCCCcCeEEeCC
Confidence            58999999888774 35567789999999999999976644333

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=91.03  E-value=0.36  Score=35.56  Aligned_cols=46  Identities=24%  Similarity=0.631  Sum_probs=30.9

Q ss_pred             eEECCCCccccccccccceeEEEcCCcceEEEeecCCCeEeCCcCcc
Q 032369           82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNF  128 (142)
Q Consensus        82 sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~GA~sVkCa~C~~  128 (142)
                      .|+|+.|..++.+= .+-...|.|..|.++|..|.|-....=..|.|
T Consensus        36 ~VkCp~C~n~q~VF-ShA~t~V~C~~Cg~~L~~PTGGKa~l~~gc~f   81 (86)
T PLN00209         36 DVKCQGCFNITTVF-SHSQTVVVCGSCQTVLCQPTGGKARLTEGCSF   81 (86)
T ss_pred             EEECCCCCCeeEEE-ecCceEEEccccCCEeeccCCCCeEecCCceE
Confidence            46777777777654 34556778888888888888876654444443

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=90.86  E-value=0.21  Score=29.89  Aligned_cols=30  Identities=27%  Similarity=0.678  Sum_probs=15.7

Q ss_pred             EECCCCccccccccc---cceeEEEcCCcceEE
Q 032369           83 VQCSCCHTVNLALEA---NQVAHVNCGNCRMLL  112 (142)
Q Consensus        83 VrC~~C~tVn~v~~a---~q~~~v~Cg~C~t~L  112 (142)
                      ++|+.|++.+.+.++   ..-..++|++|...+
T Consensus         3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~   35 (38)
T TIGR02098         3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW   35 (38)
T ss_pred             EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence            556666665554421   112256666666554

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.

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

Probab=90.86  E-value=0.26  Score=32.33  Aligned_cols=38  Identities=29%  Similarity=0.691  Sum_probs=21.7

Q ss_pred             CCCeEecCCCCccccCCCC----CCceeeEEeCCccceEEee
Q 032369           40 GATSVCCAVCNAVTAVPPP----GTEMAQLVCGGCHTLLMYI   77 (142)
Q Consensus        40 GA~~VrC~~C~tvn~vpp~----~~~~aql~Cg~Cr~lLmYp   77 (142)
                      ||+-|-|..|..+=..|..    .....+|.||.|...|.|.
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            5666666666655555432    1225566677776666653

>PTZ00083 40S ribosomal protein S27; Provisional

Probab=90.73  E-value=0.41  Score=35.21  Aligned_cols=44  Identities=23%  Similarity=0.542  Sum_probs=29.0

Q ss_pred             eEECCCCccccccccccceeEEEcCCcceEEEeecCCCeEeCCcC
Q 032369           82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVC  126 (142)
Q Consensus        82 sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~GA~sVkCa~C  126 (142)
                      .|+|+.|..++.+= .+-...|.|.+|.++|.-|.|-....=.-|
T Consensus        35 ~VkCp~C~n~q~VF-ShA~t~V~C~~Cg~~L~~PTGGKa~l~~gc   78 (85)
T PTZ00083         35 DVKCPGCSQITTVF-SHAQTVVLCGGCSSQLCQPTGGKAKLTEGC   78 (85)
T ss_pred             EEECCCCCCeeEEE-ecCceEEEccccCCEeeccCCCCeEecCCc
Confidence            46777777776654 244566788888888888887665443333

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

Probab=89.86  E-value=0.41  Score=31.43  Aligned_cols=37  Identities=27%  Similarity=0.594  Sum_probs=25.7

Q ss_pred             CCCeEECCCCcccccccc-----ccceeEEEcCCcceEEEee
Q 032369           79 GATSVQCSCCHTVNLALE-----ANQVAHVNCGNCRMLLMYQ  115 (142)
Q Consensus        79 GA~sVrC~~C~tVn~v~~-----a~q~~~v~Cg~C~t~LmYP  115 (142)
                      ||+-|-|..|..+=..+.     ...+.+++||.|...|.|-
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            666666666665544432     2348899999999999874

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=89.78  E-value=0.31  Score=29.76  Aligned_cols=11  Identities=27%  Similarity=0.549  Sum_probs=4.9

Q ss_pred             ECCCCcccccc
Q 032369           84 QCSCCHTVNLA   94 (142)
Q Consensus        84 rC~~C~tVn~v   94 (142)
                      +|+.|++.-.+
T Consensus         4 ~CP~C~~~f~v   14 (37)
T PF13719_consen    4 TCPNCQTRFRV   14 (37)
T ss_pred             ECCCCCceEEc
Confidence            44444444433

>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=89.51  E-value=0.55  Score=40.40  Aligned_cols=66  Identities=21%  Similarity=0.587  Sum_probs=45.0

Q ss_pred             ccceeecccCCCeEecCC--CCcc-ccCCC---C-------CCceeeEEeCCccceEEeecCC--CeEECCCCccccccc
Q 032369           31 CRNLLLYPVGATSVCCAV--CNAV-TAVPP---P-------GTEMAQLVCGGCHTLLMYIRGA--TSVQCSCCHTVNLAL   95 (142)
Q Consensus        31 Cr~lL~YprGA~~VrC~~--C~tv-n~vpp---~-------~~~~aql~Cg~Cr~lLmYp~GA--~sVrC~~C~tVn~v~   95 (142)
                      |.-||+=..-++-+-|++  |..| |+.|.   +       ...+..++||+|+...+++.=.  +-.||+.|..|+.+.
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  7654 44432   1       2467889999999999999755  556999999999885


Q ss_pred             c
Q 032369           96 E   96 (142)
Q Consensus        96 ~   96 (142)
                      .
T Consensus       191 ~  191 (256)
T PF09788_consen  191 P  191 (256)
T ss_pred             c
Confidence            3

>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed

Probab=89.01  E-value=0.26  Score=33.95  Aligned_cols=38  Identities=21%  Similarity=0.461  Sum_probs=24.1

Q ss_pred             eEECCCCccccccccccceeEEEcCCcceEEEeecCCCe
Q 032369           82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARS  120 (142)
Q Consensus        82 sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~GA~s  120 (142)
                      .|||+.|..++.+= .+-...+.|..|.++|.-|.|-..
T Consensus        11 ~VkCp~C~n~q~vF-sha~t~V~C~~Cg~~L~~PtGGKa   48 (59)
T PRK00415         11 KVKCPDCGNEQVVF-SHASTVVRCLVCGKTLAEPTGGKA   48 (59)
T ss_pred             EEECCCCCCeEEEE-ecCCcEEECcccCCCcccCCCcce
Confidence            46666676666543 234456777777777777777543

>PLN00209 ribosomal protein S27; Provisional

Probab=88.95  E-value=0.35  Score=35.63  Aligned_cols=40  Identities=30%  Similarity=0.546  Sum_probs=30.7

Q ss_pred             eEecCCCCccccCCCCCCceeeEEeCCccceEEeecCCCeEE
Q 032369           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQ   84 (142)
Q Consensus        43 ~VrC~~C~tvn~vpp~~~~~aql~Cg~Cr~lLmYp~GA~sVr   84 (142)
                      .|+|..|..++.+=  ++....+.|.+|.++|..|.|--...
T Consensus        36 ~VkCp~C~n~q~VF--ShA~t~V~C~~Cg~~L~~PTGGKa~l   75 (86)
T PLN00209         36 DVKCQGCFNITTVF--SHSQTVVVCGSCQTVLCQPTGGKARL   75 (86)
T ss_pred             EEECCCCCCeeEEE--ecCceEEEccccCCEeeccCCCCeEe
Confidence            58888888888763  45677888888888888888866543

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

Probab=88.60  E-value=0.58  Score=29.32  Aligned_cols=25  Identities=24%  Similarity=0.515  Sum_probs=11.0

Q ss_pred             EEeCCccceEEeecCCCeEECCCCc
Q 032369           65 LVCGGCHTLLMYIRGATSVQCSCCH   89 (142)
Q Consensus        65 l~Cg~Cr~lLmYp~GA~sVrC~~C~   89 (142)
                      ..|.+|...+.+..+...++|+.|+
T Consensus         4 y~C~~CG~~~~~~~~~~~~~Cp~CG   28 (46)
T PRK00398          4 YKCARCGREVELDEYGTGVRCPYCG   28 (46)
T ss_pred             EECCCCCCEEEECCCCCceECCCCC
Confidence            3444444444444444444444443

>PTZ00083 40S ribosomal protein S27; Provisional

Probab=88.48  E-value=0.4  Score=35.25  Aligned_cols=39  Identities=28%  Similarity=0.603  Sum_probs=29.4

Q ss_pred             eEecCCCCccccCCCCCCceeeEEeCCccceEEeecCCCeE
Q 032369           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSV   83 (142)
Q Consensus        43 ~VrC~~C~tvn~vpp~~~~~aql~Cg~Cr~lLmYp~GA~sV   83 (142)
                      .|+|..|..++.+=  ++....+.|.+|.++|..|.|--..
T Consensus        35 ~VkCp~C~n~q~VF--ShA~t~V~C~~Cg~~L~~PTGGKa~   73 (85)
T PTZ00083         35 DVKCPGCSQITTVF--SHAQTVVLCGGCSSQLCQPTGGKAK   73 (85)
T ss_pred             EEECCCCCCeeEEE--ecCceEEEccccCCEeeccCCCCeE
Confidence            47888888888763  4557778888888888888886544

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

Probab=87.89  E-value=0.47  Score=32.14  Aligned_cols=38  Identities=24%  Similarity=0.417  Sum_probs=23.9

Q ss_pred             eEecCCCCccccCCCCCCceeeEEeCCccceEEeecCCCe
Q 032369           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATS   82 (142)
Q Consensus        43 ~VrC~~C~tvn~vpp~~~~~aql~Cg~Cr~lLmYp~GA~s   82 (142)
                      .|+|..|..++.+=  ++....+.|.+|.++|..|.|-..
T Consensus         7 ~VkCp~C~~~q~vF--Sha~t~V~C~~Cg~~L~~PtGGKa   44 (55)
T PF01667_consen    7 DVKCPGCYNIQTVF--SHAQTVVKCVVCGTVLAQPTGGKA   44 (55)
T ss_dssp             EEE-TTT-SEEEEE--TT-SS-EE-SSSTSEEEEE-SSSE
T ss_pred             EEECCCCCCeeEEE--ecCCeEEEcccCCCEecCCCCcCe
Confidence            47888888888762  455677888888888888887654

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.

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

Probab=86.74  E-value=0.8  Score=32.42  Aligned_cols=39  Identities=21%  Similarity=0.436  Sum_probs=27.5

Q ss_pred             eEECCCCccccccccccceeEEEcCCcceEEEeecCCCeE
Q 032369           82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSV  121 (142)
Q Consensus        82 sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~GA~sV  121 (142)
                      .|+|+.|...+.+- ++-...++|..|.++|..|.|-.+.
T Consensus        19 ~VkCpdC~N~q~vF-shast~V~C~~CG~~l~~PTGGka~   57 (67)
T COG2051          19 RVKCPDCGNEQVVF-SHASTVVTCLICGTTLAEPTGGKAK   57 (67)
T ss_pred             EEECCCCCCEEEEe-ccCceEEEecccccEEEecCCCeEE
Confidence            47777777766553 3445668888888888888886543

>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed

Probab=86.55  E-value=0.4  Score=33.01  Aligned_cols=34  Identities=24%  Similarity=0.331  Sum_probs=15.6

Q ss_pred             EecCCCCccccCCCCCCceeeEEeCCccceEEeecC
Q 032369           44 VCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRG   79 (142)
Q Consensus        44 VrC~~C~tvn~vpp~~~~~aql~Cg~Cr~lLmYp~G   79 (142)
                      |+|+.|..++.+=  ++....+.|..|.++|..|.|
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            4555555544331  223344455555555555544

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=85.90  E-value=0.85  Score=27.83  Aligned_cols=28  Identities=32%  Similarity=0.771  Sum_probs=19.1

Q ss_pred             EEcCCcceEEEeec-----CCCeEeCCcCccee
Q 032369          103 VNCGNCRMLLMYQY-----GARSVKCAVCNFVT  130 (142)
Q Consensus       103 v~Cg~C~t~LmYP~-----GA~sVkCa~C~~VT  130 (142)
                      ++|-+|.+..-.|.     +...|||+.|+++=
T Consensus         3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f   35 (37)
T PF13719_consen    3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF   35 (37)
T ss_pred             EECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence            56777777776554     45677777777653

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=85.05  E-value=0.78  Score=27.33  Aligned_cols=31  Identities=23%  Similarity=0.592  Sum_probs=17.9

Q ss_pred             EecCCCCccccCCCC--CCceeeEEeCCccceE
Q 032369           44 VCCAVCNAVTAVPPP--GTEMAQLVCGGCHTLL   74 (142)
Q Consensus        44 VrC~~C~tvn~vpp~--~~~~aql~Cg~Cr~lL   74 (142)
                      +.|+.|.+...++++  ..+-..+.|+.|...+
T Consensus         3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~   35 (38)
T TIGR02098         3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW   35 (38)
T ss_pred             EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence            678888887766532  1122356666666554

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.

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

Probab=84.26  E-value=1.6  Score=27.26  Aligned_cols=30  Identities=20%  Similarity=0.445  Sum_probs=12.2

Q ss_pred             EECCCCccccccccccceeEEEcCCcceEEEe
Q 032369           83 VQCSCCHTVNLALEANQVAHVNCGNCRMLLMY  114 (142)
Q Consensus        83 VrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmY  114 (142)
                      .+|+.|+......+..+  .++|-.|...++|
T Consensus         4 y~C~~CG~~~~~~~~~~--~~~Cp~CG~~~~~   33 (46)
T PRK00398          4 YKCARCGREVELDEYGT--GVRCPYCGYRILF   33 (46)
T ss_pred             EECCCCCCEEEECCCCC--ceECCCCCCeEEE
Confidence            34444444433322222  3444444444444

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

Probab=83.56  E-value=2.3  Score=31.23  Aligned_cols=43  Identities=21%  Similarity=0.539  Sum_probs=23.4

Q ss_pred             EECCCCccccccccccceeEEEcCCcceEEEeecCCCeEeCCcC
Q 032369           83 VQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVC  126 (142)
Q Consensus        83 VrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~GA~sVkCa~C  126 (142)
                      |||+.|-.+|-+-+ +-+.-+.|++|.+.|.-|.|-..+.=..|
T Consensus        35 VkC~gc~~iT~vfS-HaqtvVvc~~c~~il~~~tggra~ls~~c   77 (84)
T KOG1779|consen   35 VKCPGCFKITTVFS-HAQTVVVCEGCSTILCQPTGGKAKLSEGC   77 (84)
T ss_pred             EEcCCceEEEEEee-cCceEEEcCCCceEEEEecCCcEEecCCC
Confidence            44555544444332 23344667777777777776665544444

>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]

Probab=83.11  E-value=1.2  Score=38.43  Aligned_cols=95  Identities=24%  Similarity=0.553  Sum_probs=62.9

Q ss_pred             cCCCeEecCCCCccccCCCCCCceeeEEeCCccceE---EeecCCCeEECCC-------------------Ccc-ccccc
Q 032369           39 VGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLL---MYIRGATSVQCSC-------------------CHT-VNLAL   95 (142)
Q Consensus        39 rGA~~VrC~~C~tvn~vpp~~~~~aql~Cg~Cr~lL---mYp~GA~sVrC~~-------------------C~t-Vn~v~   95 (142)
                      -+++-|-|..|+..-.+- --+|.-.+.|+.|..--   --|.|-..|||++                   |.. ||+.+
T Consensus        76 g~~PmvtCRVCq~~i~~e-gk~~QHVVKC~~CnEATPIrnAPpGKKYVRCPCNCLLICK~sSqRIACPRpnCkRiInL~p  154 (275)
T KOG4684|consen   76 GQFPMVTCRVCQVAISLE-GKNQQHVVKCHSCNEATPIRNAPPGKKYVRCPCNCLLICKASSQRIACPRPNCKRIINLDP  154 (275)
T ss_pred             CCCceEeehhhhHHhccc-cccceeeEeecccCccccCCCCCCCCceeecCCcEEEEEecccceeccCCCCcceeeecCC
Confidence            456678888887765542 23555666788886532   3567778888874                   222 23221


Q ss_pred             ---------cccceeEEEcCCcceEEEeec-CCCeEeCCcCcceeeecc
Q 032369           96 ---------EANQVAHVNCGNCRMLLMYQY-GARSVKCAVCNFVTAVGV  134 (142)
Q Consensus        96 ---------~a~q~~~v~Cg~C~t~LmYP~-GA~sVkCa~C~~VT~i~~  134 (142)
                               .+...-.|+||.|+-+.+|-. --...+|+-|+.|..|+.
T Consensus       155 ~~~~p~~P~~~P~gcRV~CgHC~~tFLfnt~tnaLArCPHCrKvSsvGs  203 (275)
T KOG4684|consen  155 LIEKPRDPGTAPTGCRVKCGHCNETFLFNTLTNALARCPHCRKVSSVGS  203 (275)
T ss_pred             CCCCCCCCCCCCcceEEEecCccceeehhhHHHHHhcCCcccchhhhhh
Confidence                     123456899999998888743 225679999999999975

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=81.91  E-value=1.5  Score=26.80  Aligned_cols=11  Identities=18%  Similarity=0.507  Sum_probs=4.8

Q ss_pred             ECCCCcccccc
Q 032369           84 QCSCCHTVNLA   94 (142)
Q Consensus        84 rC~~C~tVn~v   94 (142)
                      .|+.|++.-.+
T Consensus         4 ~Cp~C~~~y~i   14 (36)
T PF13717_consen    4 TCPNCQAKYEI   14 (36)
T ss_pred             ECCCCCCEEeC
Confidence            44444444433

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

Probab=81.28  E-value=1.3  Score=30.86  Aligned_cols=50  Identities=28%  Similarity=0.687  Sum_probs=39.6

Q ss_pred             EEeCCccceEEeecCCCeEECCCCccccccccccceeEEEcCCcceEEEeecCCCeEeCCcCcce
Q 032369           65 LVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFV  129 (142)
Q Consensus        65 l~Cg~Cr~lLmYp~GA~sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~GA~sVkCa~C~~V  129 (142)
                      -+|.+|...|.--.++.+..|+.|.-+..         .+|..||.+      ...++|+.|.|.
T Consensus        10 ~~CtSCg~~i~p~e~~v~F~CPnCGe~~I---------~Rc~~CRk~------g~~Y~Cp~CGF~   59 (61)
T COG2888          10 PVCTSCGREIAPGETAVKFPCPNCGEVEI---------YRCAKCRKL------GNPYRCPKCGFE   59 (61)
T ss_pred             ceeccCCCEeccCCceeEeeCCCCCceee---------ehhhhHHHc------CCceECCCcCcc
Confidence            58999999998888999999999985544         478888875      346788888875

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

Probab=81.08  E-value=1.8  Score=30.68  Aligned_cols=38  Identities=24%  Similarity=0.337  Sum_probs=24.7

Q ss_pred             eEecCCCCccccCCCCCCceeeEEeCCccceEEeecCCCe
Q 032369           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATS   82 (142)
Q Consensus        43 ~VrC~~C~tvn~vpp~~~~~aql~Cg~Cr~lLmYp~GA~s   82 (142)
                      .|+|..|...+-+=  ++....+.|..|.++|..|-|-..
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            47777777666552  334556777777777777777543

---

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	142
3j20_W	63	30S ribosomal protein S27E; archaea, archaeal, KIN	92.13
1qxf_A	66	GR2, 30S ribosomal protein S27E; structural genomi	92.11
2xzm_6	81	RPS27E; ribosome, translation; 3.93A {Tetrahymena	91.11
1qxf_A	66	GR2, 30S ribosomal protein S27E; structural genomi	90.1
3j20_W	63	30S ribosomal protein S27E; archaea, archaeal, KIN	89.2
2xzm_6	81	RPS27E; ribosome, translation; 3.93A {Tetrahymena	88.55
3u5c_b	82	RP61, YS20, 40S ribosomal protein S27-A; translati	87.97
3u5c_b	82	RP61, YS20, 40S ribosomal protein S27-A; translati	83.91
3iz6_X	86	40S ribosomal protein S27 (S27E); eukaryotic ribos	83.2
3iz6_X	86	40S ribosomal protein S27 (S27E); eukaryotic ribos	80.11

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

Probab=92.13  E-value=0.091  Score=35.64  Aligned_cols=38  Identities=21%  Similarity=0.496  Sum_probs=28.1

Q ss_pred             eEECCCCccccccccccceeEEEcCCcceEEEeecCCCe
Q 032369           82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARS  120 (142)
Q Consensus        82 sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~GA~s  120 (142)
                      .|||+.|..++.+= .+-...+.|.+|.++|..|.|-..
T Consensus        15 ~VkCp~C~~~q~VF-Sha~t~V~C~~Cgt~L~~PTGGKa   52 (63)
T 3j20_W           15 RVKCIDCGNEQIVF-SHPATKVRCLICGATLVEPTGGKG   52 (63)
T ss_dssp             EEECSSSCCEEEEE-SSCSSCEECSSSCCEEEECCSSSC
T ss_pred             EEECCCCCCeeEEE-ecCCeEEEccCcCCEEecCCCCcE
Confidence            57777777777663 345567888888888988888654

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

Probab=92.11  E-value=0.092  Score=35.97  Aligned_cols=39  Identities=18%  Similarity=0.415  Sum_probs=30.5

Q ss_pred             eEECCCCccccccccccceeEEEcCCcceEEEeecCCCeE
Q 032369           82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSV  121 (142)
Q Consensus        82 sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~GA~sV  121 (142)
                      .|||+.|..++.+=+ +-...+.|.+|.++|..|.|-..-
T Consensus         7 ~VKCp~C~niq~VFS-hA~tvV~C~~Cg~~L~~PTGGKA~   45 (66)
T 1qxf_A            7 KVKCPDCEHEQVIFD-HPSTIVKCIICGRTVAEPTGGKGN   45 (66)
T ss_dssp             EEECTTTCCEEEEES-SCSSCEECSSSCCEEEECCSSSCE
T ss_pred             EEECCCCCCceEEEe-cCceEEEcccCCCEEeecCCccee
Confidence            588999988887643 455678999999999999986543

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

Probab=91.11  E-value=0.25  Score=34.95  Aligned_cols=45  Identities=22%  Similarity=0.570  Sum_probs=28.1

Q ss_pred             eEECCCCccccccccccceeEEEcCCcceEEEeecCCCeEeCCcCc
Q 032369           82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCN  127 (142)
Q Consensus        82 sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~GA~sVkCa~C~  127 (142)
                      .|+|+.|..++.+-+ +-...|.|.+|.++|..|.|-..-.=.-|.
T Consensus        32 ~VkCp~C~n~q~VFS-hA~t~V~C~~Cg~~L~~PTGGKA~l~egc~   76 (81)
T 2xzm_6           32 DVKCAQCQNIQMIFS-NAQSTIICEKCSAILCKPTGGKVQIQAGCA   76 (81)
T ss_dssp             EEECSSSCCEEEEET-TCSSCEECSSSCCEEEEECSSCEEECSSCE
T ss_pred             EeECCCCCCeeEEEe-cCccEEEccCCCCEEeecCCCCeEecCCcc
Confidence            356666666665532 344567788888888888776654434443

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

Probab=90.10  E-value=0.18  Score=34.57  Aligned_cols=39  Identities=15%  Similarity=0.237  Sum_probs=30.5

Q ss_pred             eEecCCCCccccCCCCCCceeeEEeCCccceEEeecCCCeE
Q 032369           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSV   83 (142)
Q Consensus        43 ~VrC~~C~tvn~vpp~~~~~aql~Cg~Cr~lLmYp~GA~sV   83 (142)
                      .|+|+.|..++.+=  +.....+.|.+|.++|..|.|-..-
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            58899998888763  4556778899999999999886543

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

Probab=89.20  E-value=0.22  Score=33.71  Aligned_cols=37  Identities=22%  Similarity=0.333  Sum_probs=24.4

Q ss_pred             eEecCCCCccccCCCCCCceeeEEeCCccceEEeecCCC
Q 032369           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGAT   81 (142)
Q Consensus        43 ~VrC~~C~tvn~vpp~~~~~aql~Cg~Cr~lLmYp~GA~   81 (142)
                      .|+|..|..++.+=  ++....+.|.+|.++|..|.|-.
T Consensus        15 ~VkCp~C~~~q~VF--Sha~t~V~C~~Cgt~L~~PTGGK   51 (63)
T 3j20_W           15 RVKCIDCGNEQIVF--SHPATKVRCLICGATLVEPTGGK   51 (63)
T ss_dssp             EEECSSSCCEEEEE--SSCSSCEECSSSCCEEEECCSSS
T ss_pred             EEECCCCCCeeEEE--ecCCeEEEccCcCCEEecCCCCc
Confidence            46777777776652  44456677777777777777654

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

Probab=88.55  E-value=0.27  Score=34.79  Aligned_cols=39  Identities=21%  Similarity=0.524  Sum_probs=25.8

Q ss_pred             eEecCCCCccccCCCCCCceeeEEeCCccceEEeecCCCeE
Q 032369           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSV   83 (142)
Q Consensus        43 ~VrC~~C~tvn~vpp~~~~~aql~Cg~Cr~lLmYp~GA~sV   83 (142)
                      .|+|..|..++.+=  ++....+.|.+|.++|..|.|--.-
T Consensus        32 ~VkCp~C~n~q~VF--ShA~t~V~C~~Cg~~L~~PTGGKA~   70 (81)
T 2xzm_6           32 DVKCAQCQNIQMIF--SNAQSTIICEKCSAILCKPTGGKVQ   70 (81)
T ss_dssp             EEECSSSCCEEEEE--TTCSSCEECSSSCCEEEEECSSCEE
T ss_pred             EeECCCCCCeeEEE--ecCccEEEccCCCCEEeecCCCCeE
Confidence            46777777777652  3445667777777777777775543

>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=87.97  E-value=0.22  Score=35.32  Aligned_cols=44  Identities=18%  Similarity=0.462  Sum_probs=25.5

Q ss_pred             eEECCCCccccccccccceeEEEcCCcceEEEeecCCCeEeCCcC
Q 032369           82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVC  126 (142)
Q Consensus        82 sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~GA~sVkCa~C  126 (142)
                      .|+|+.|..++.+=+ +-...|.|.+|.++|..|.|-..-.=..|
T Consensus        34 ~VkCp~C~~~q~VFS-ha~t~V~C~~Cg~~L~~PTGGKa~l~egc   77 (82)
T 3u5c_b           34 DVKCPGCLNITTVFS-HAQTAVTCESCSTILCTPTGGKAKLSEGT   77 (82)
T ss_dssp             EEECTTSCSCEEEES-BCSSCCCCSSSCCCCEECCSSBCEECSSC
T ss_pred             EEECCCCCCeeEEEe-cCCeEEEccccCCEEeccCCCCeEecCCc
Confidence            456666666665432 33445667777777777777655444444

>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=83.91  E-value=0.31  Score=34.53  Aligned_cols=40  Identities=25%  Similarity=0.468  Sum_probs=26.6

Q ss_pred             eEecCCCCccccCCCCCCceeeEEeCCccceEEeecCCCeEE
Q 032369           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQ   84 (142)
Q Consensus        43 ~VrC~~C~tvn~vpp~~~~~aql~Cg~Cr~lLmYp~GA~sVr   84 (142)
                      .|+|..|..++.+=  ++....+.|.+|.++|..|.|-..-.
T Consensus        34 ~VkCp~C~~~q~VF--Sha~t~V~C~~Cg~~L~~PTGGKa~l   73 (82)
T 3u5c_b           34 DVKCPGCLNITTVF--SHAQTAVTCESCSTILCTPTGGKAKL   73 (82)
T ss_dssp             EEECTTSCSCEEEE--SBCSSCCCCSSSCCCCEECCSSBCEE
T ss_pred             EEECCCCCCeeEEE--ecCCeEEEccccCCEEeccCCCCeEe
Confidence            47777777777652  34456677777777777777755443

>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=83.20  E-value=0.28  Score=35.04  Aligned_cols=44  Identities=20%  Similarity=0.528  Sum_probs=26.6

Q ss_pred             eEECCCCccccccccccceeEEEcCCcceEEEeecCCCeEeCCcC
Q 032369           82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVC  126 (142)
Q Consensus        82 sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~GA~sVkCa~C  126 (142)
                      .|+|+.|..++.+=+ +-...|.|.+|.++|.-|.|-.+-.=..|
T Consensus        36 ~VkCp~C~~~~~VFS-hA~t~V~C~~CgtvL~~PTGGKa~l~egc   79 (86)
T 3iz6_X           36 DVKCQGCFNITTVFS-HSQTVVVCPGCQTVLCQPTGGKARLTEGC   79 (86)
T ss_dssp             EEECTTTCCEEEEET-TCSSCCCCSSSCCCCSCCCSSSCCCSCBC
T ss_pred             EEECCCCCCeeEEEe-cCCcEEEccCCCCEeecCCCCCEEecCCc
Confidence            366777766665532 34445677777777777777655444444

>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=80.11  E-value=0.39  Score=34.32  Aligned_cols=38  Identities=32%  Similarity=0.588  Sum_probs=24.5

Q ss_pred             eEecCCCCccccCCCCCCceeeEEeCCccceEEeecCCCe
Q 032369           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATS   82 (142)
Q Consensus        43 ~VrC~~C~tvn~vpp~~~~~aql~Cg~Cr~lLmYp~GA~s   82 (142)
                      .|+|..|..++.+=  ++....+.|.+|.++|..|.|-..
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  344556677777777777776544

---

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	142
d1qxfa_	58	Ribosomal protein S27e {Archaeon Archaeoglobus ful	91.08
d1qxfa_	58	Ribosomal protein S27e {Archaeon Archaeoglobus ful	91.04

>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=91.08  E-value=0.066  Score=34.18  Aligned_cols=38  Identities=18%  Similarity=0.445  Sum_probs=28.6

Q ss_pred             eEECCCCccccccccccceeEEEcCCcceEEEeecCCCe
Q 032369           82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARS  120 (142)
Q Consensus        82 sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~GA~s  120 (142)
                      .|||+.|..++.+=+ +-...+.|..|.++|..|.|-..
T Consensus         7 ~VkC~~C~n~~ivFs-ha~t~V~C~~Cg~~L~~PtGGKa   44 (58)
T d1qxfa_           7 KVKCPDCEHEQVIFD-HPSTIVKCIICGRTVAEPTGGKG   44 (58)
T ss_dssp             EEECTTTCCEEEEES-SCSSCEECSSSCCEEEECCSSSC
T ss_pred             EeECCCCCCeEEEEe-cCceEEEccccCCEEeccCCCeE
Confidence            578888888876642 44556888899999999988654

>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=91.04  E-value=0.062  Score=34.31  Aligned_cols=38  Identities=16%  Similarity=0.262  Sum_probs=30.3

Q ss_pred             eEecCCCCccccCCCCCCceeeEEeCCccceEEeecCCCe
Q 032369           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATS   82 (142)
Q Consensus        43 ~VrC~~C~tvn~vpp~~~~~aql~Cg~Cr~lLmYp~GA~s   82 (142)
                      .|+|..|..++.+=  ++....+.|..|.++|..|.|-..
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            58899999888763  455778899999999999988654