Citrus Sinensis ID: 033478

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------12
Protein Sequence
MTTTWWSVARVNSLSQESFWLTLTCYHQEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIGVCGLSLFLCMCDLANQI
Secondary Structure (PSIPRED)
ccccccHHHHcccccccEEEEEccccHHccccEEccccccEEEEEccccEEEcccccccccccccccEEEEEcccccEEEEEEccccEEEcccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccEEEEEEEEccccccEEEEEEEccccHHHEEEEccccEEEEEcccccEEEcccccEEEcccccccEEEEEccccEEEEEEcccccEEEcccEcEEccccccccccccccccccccc
Coil and Loop (DISEMBL)
MTTTWWSVARVNSLSQESFWLTLTCYHQEMAQMVCGSCrrllayprgarhvkcsccqTVNFVLEAHQVGQVKCASCAVLlmypygapsvrcssccfvteigvcGLSLFLCMCDLANQI
Flexible Loop (DISEMBL)
MTTTWWSVARVNSLSQESFWLTLTCYHQEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIGVCGLSLFLCMCDLANQI
Low Complexity Region (SEG)
MTTTWWSVARVNSLSQESFWLTLTCYHQEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIGVCGLSLFLCMCDLANQI
Disordered region (IsUnstruct)
***TWWSVARVNSLSQESFWLTLTCYHQEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIGVCGLSLFLCMCDLA***
Disordered Region (DISOPRED)
*TTTWWSVARVNSLSQESFWLTLTCYHQEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIGVC***************
Disordered Region (DISEMBL)
MTTTWWSVARVNSLSQESFWLTLTCYHQEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIGVCGLSLFLCMCDLANQI
Disordered Region (DISPRO)
*TTTWWSVARVNSLSQESFWLTLTCYHQEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIGVCGLSLFLCMCDL****
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MTTTWWSVARVNSLSQESFWLTLTCYHQEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIGVCGLSLFLCMCDLANQI
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	118	2.2.26 [Sep-21-2011]
O65426	155	Protein LOL2 OS=Arabidops	yes	no	0.610	0.464	0.763	1e-26
Q704V3	163	Protein LOL5 OS=Oryza sat	no	no	0.635	0.460	0.693	2e-25
Q93ZB1	154	Protein LOL1 OS=Arabidops	no	no	0.618	0.474	0.616	3e-19
Q0J7V9	184	Protein LSD1 OS=Oryza sat	no	no	0.618	0.396	0.602	9e-19
Q6ASS2	186	Protein LOL3 OS=Oryza sat	no	no	0.627	0.397	0.513	4e-17
Q2QMB3	172	Protein LOL2 OS=Oryza sat	no	no	0.627	0.430	0.486	1e-16
P94077	189	Protein LSD1 OS=Arabidops	no	no	0.627	0.391	0.482	1e-15
Q84UR0	147	Protein LOL4 OS=Oryza sat	no	no	0.610	0.489	0.347	1e-09

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

 Score =  118 bits (296), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 55/72 (76%), Positives = 63/72 (87%)

Query: 29  EMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPS 88
           E AQMVCGSCRRLL+Y RG++HVKCS CQTVN VLEA+QVGQV C +C +LLMYPYGAP+
Sbjct: 57  EKAQMVCGSCRRLLSYLRGSKHVKCSSCQTVNLVLEANQVGQVNCNNCKLLLMYPYGAPA 116

Query: 89  VRCSSCCFVTEI 100
           VRCSSC  VT+I
Sbjct: 117 VRCSSCNSVTDI 128

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 =  114 bits (284), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 52/75 (69%), Positives = 64/75 (85%)

Query: 27  HQEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGA 86
           ++E+ QMVCGSCR LLAY RGA +V C+CCQT+N+VLEAH+VG+V C  CA LLMYP+GA
Sbjct: 65  NKEVGQMVCGSCRILLAYFRGAGYVHCTCCQTMNYVLEAHEVGKVHCGHCATLLMYPFGA 124

Query: 87  PSVRCSSCCFVTEIG 101
           P+V+CS C FVTEIG
Sbjct: 125 PAVKCSLCLFVTEIG 139

Involved in plant growth and disease resistance.

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score = 93.6 bits (231), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 45/73 (61%), Positives = 53/73 (72%)

Query: 29  EMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPS 88
           EMAQ+VCG C  LL Y RGA  V+CSCC TVN  LEA+QV  V C +C +LLMY YGA S
Sbjct: 70  EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCMMLLMYQYGARS 129

Query: 89  VRCSSCCFVTEIG 101
           V+C+ C FVT +G
Sbjct: 130 VKCAVCNFVTSVG 142

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 = 92.0 bits (227), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 44/73 (60%), Positives = 53/73 (72%)

Query: 29  EMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPS 88
           EMAQ+VCG C  LL Y RGA  V+CSCC TVN  +EA+QV  V C +C +LLMY YGA S
Sbjct: 101 EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLAMEANQVAHVNCGNCRMLLMYQYGARS 160

Query: 89  VRCSSCCFVTEIG 101
           V+C+ C FVT +G
Sbjct: 161 VKCAVCNFVTSVG 173

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

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score = 86.7 bits (213), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 38/74 (51%), Positives = 48/74 (64%)

Query: 29  EMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPS 88
           EMA ++CG CR LL Y R A  V+CSCC TVN V   + +  V C  C   LMYPYGAPS
Sbjct: 42  EMAHLICGGCRTLLMYTRNADTVRCSCCSTVNLVRPVNNIAHVSCGQCRTTLMYPYGAPS 101

Query: 89  VRCSSCCFVTEIGV 102
           V+C+ C ++T  G+
Sbjct: 102 VKCAICHYITNTGM 115

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

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score = 85.1 bits (209), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 36/74 (48%), Positives = 48/74 (64%)

Query: 29  EMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPS 88
           ++A ++CG CR LL Y R A  V+CSCC TVN V     +  + C  C  +LMYPYGAPS
Sbjct: 41  DIAHLICGGCRTLLMYTRNATSVRCSCCDTVNLVRPVSSIAHLNCGQCQTVLMYPYGAPS 100

Query: 89  VRCSSCCFVTEIGV 102
           V+C+ C F+T  G+
Sbjct: 101 VKCAICNFITNTGM 114

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 = 81.6 bits (200), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 41/85 (48%), Positives = 51/85 (60%), Gaps = 11/85 (12%)

Query: 28  QEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAH----------QVGQVKCASCA 77
            +MA ++CG CR +L Y RGA  V+CSCCQT N V  AH          QV Q+ C  C 
Sbjct: 46  HDMAHIICGGCRTMLMYTRGASSVRCSCCQTTNLV-PAHSNQVAHAPSSQVAQINCGHCR 104

Query: 78  VLLMYPYGAPSVRCSSCCFVTEIGV 102
             LMYPYGA SV+C+ C FVT + +
Sbjct: 105 TTLMYPYGASSVKCAVCQFVTNVNM 129

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 = 62.0 bits (149), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 44/72 (61%)

Query: 29  EMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPS 88
           +M++++C  C  LL Y RGA +++C  C  +N    A+Q+  + C  C   LM+P GA +
Sbjct: 41  DMSELICSGCPTLLFYNRGASNIRCPSCNRLNSTRSANQIAHLTCGQCRTTLMHPPGAST 100

Query: 89  VRCSSCCFVTEI 100
           V+C++C +V  +
Sbjct: 101 VQCATCRYVNHV 112

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	118
225470420	141	PREDICTED: protein LOL2 [Vitis vinifera]	0.686	0.574	0.864	1e-33
356521358	128	PREDICTED: protein LOL2-like [Glycine ma	0.610	0.562	0.875	2e-28
198400327	236	zinc finger protein LSD2-like protein [C	0.618	0.309	0.794	1e-27
125571157	1463	hypothetical protein OsJ_02587 [Oryza sa	0.635	0.051	0.693	2e-27
125526829	1413	hypothetical protein OsI_02839 [Oryza sa	0.635	0.053	0.693	2e-27
449457731	131	PREDICTED: protein LOL2-like [Cucumis sa	0.627	0.564	0.824	2e-27
357130480	939	PREDICTED: uncharacterized protein LOC10	0.635	0.079	0.68	1e-26
224077114	94	predicted protein [Populus trichocarpa]	0.584	0.734	0.826	4e-26
297803986	150	hypothetical protein ARALYDRAFT_492714 [	0.610	0.48	0.75	1e-25
15234540	155	lsd one like 2 protein [Arabidopsis thal	0.610	0.464	0.763	4e-25

>gi|225470420|ref|XP_002273964.1| PREDICTED: protein LOL2 [Vitis vinifera] gi|302144197|emb|CBI23324.3| unnamed protein product [Vitis vinifera]

 Score =  146 bits (369), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 70/81 (86%), Positives = 73/81 (90%)

Query: 29  EMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPS 88
           EMAQMVCGSCRRLL+YP+G RHV+CSCCQTVNFVLEAHQVGQVKC SCAVLLMYPYGAPS
Sbjct: 45  EMAQMVCGSCRRLLSYPQGTRHVECSCCQTVNFVLEAHQVGQVKCGSCAVLLMYPYGAPS 104

Query: 89  VRCSSCCFVTEIGVCGLSLFL 109
           VRCSSC FVTEIGV    L L
Sbjct: 105 VRCSSCRFVTEIGVHNRRLPL 125

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356521358|ref|XP_003529323.1| PREDICTED: protein LOL2-like [Glycine max]

 Score =  129 bits (325), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 63/72 (87%), Positives = 65/72 (90%)

Query: 31  AQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVR 90
           AQMVCGSCRRLL+YPRGA+HVKCSCCQTVN VLEA QVGQVKC SCAVLLMYPYGA  VR
Sbjct: 36  AQMVCGSCRRLLSYPRGAKHVKCSCCQTVNIVLEADQVGQVKCGSCAVLLMYPYGASQVR 95

Query: 91  CSSCCFVTEIGV 102
           CSSC FVTEIG 
Sbjct: 96  CSSCRFVTEIGA 107

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|198400327|gb|ACH87172.1| zinc finger protein LSD2-like protein [Camellia sinensis]

 Score =  127 bits (318), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 58/73 (79%), Positives = 64/73 (87%)

Query: 29  EMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPS 88
           EM QMVCGSC+ LL+YPRGAR V+C CCQTVN+ LE H+VGQVKC  CAVLLMYPYGAP 
Sbjct: 141 EMGQMVCGSCQELLSYPRGARLVRCLCCQTVNYCLEEHEVGQVKCGGCAVLLMYPYGAPF 200

Query: 89  VRCSSCCFVTEIG 101
           V+CSSCCFVTEIG
Sbjct: 201 VKCSSCCFVTEIG 213

Source: Camellia sinensis

Species: Camellia sinensis

Genus: Camellia

Family: Theaceae

Order: Ericales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|125571157|gb|EAZ12672.1| hypothetical protein OsJ_02587 [Oryza sativa Japonica Group]

 Score =  126 bits (316), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 52/75 (69%), Positives = 64/75 (85%)

Query: 27   HQEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGA 86
            ++E+ QMVCGSCR LLAY RGA +V C+CCQT+N+VLEAH+VG+V C  CA LLMYP+GA
Sbjct: 1365 NKEVGQMVCGSCRILLAYFRGAGYVHCTCCQTMNYVLEAHEVGKVHCGHCATLLMYPFGA 1424

Query: 87   PSVRCSSCCFVTEIG 101
            P+V+CS C FVTEIG
Sbjct: 1425 PAVKCSLCLFVTEIG 1439

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|125526829|gb|EAY74943.1| hypothetical protein OsI_02839 [Oryza sativa Indica Group]

 Score =  126 bits (316), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 52/75 (69%), Positives = 64/75 (85%)

Query: 27   HQEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGA 86
            ++E+ QMVCGSCR LLAY RGA +V C+CCQT+N+VLEAH+VG+V C  CA LLMYP+GA
Sbjct: 1315 NKEVGQMVCGSCRILLAYFRGAGYVHCTCCQTMNYVLEAHEVGKVHCGHCATLLMYPFGA 1374

Query: 87   PSVRCSSCCFVTEIG 101
            P+V+CS C FVTEIG
Sbjct: 1375 PAVKCSLCLFVTEIG 1389

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449457731|ref|XP_004146601.1| PREDICTED: protein LOL2-like [Cucumis sativus] gi|449508900|ref|XP_004163439.1| PREDICTED: protein LOL2-like [Cucumis sativus]

 Score =  125 bits (315), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 61/74 (82%), Positives = 67/74 (90%)

Query: 29  EMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPS 88
           +MAQMVCG+CRRLL Y +GAR+V+CSCC TVNFVLEAH+VGQVKC SCAVLLMYPYGA S
Sbjct: 36  DMAQMVCGTCRRLLKYLKGARYVQCSCCSTVNFVLEAHEVGQVKCGSCAVLLMYPYGASS 95

Query: 89  VRCSSCCFVTEIGV 102
           VRCSSC  VTEIGV
Sbjct: 96  VRCSSCTSVTEIGV 109

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357130480|ref|XP_003566876.1| PREDICTED: uncharacterized protein LOC100840817 [Brachypodium distachyon]

 Score =  124 bits (310), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 51/75 (68%), Positives = 61/75 (81%)

Query: 27  HQEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGA 86
           ++EM QMVCG CR LLAYPRGA HV+C+ C T+N VLEAH+VG+V C  C  LLMYP+GA
Sbjct: 840 NKEMGQMVCGCCRELLAYPRGAVHVQCAGCLTINLVLEAHEVGKVHCGRCETLLMYPFGA 899

Query: 87  PSVRCSSCCFVTEIG 101
           P+V+CS C FVTEIG
Sbjct: 900 PAVKCSLCLFVTEIG 914

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224077114|ref|XP_002305138.1| predicted protein [Populus trichocarpa] gi|222848102|gb|EEE85649.1| predicted protein [Populus trichocarpa]

 Score =  122 bits (305), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 57/69 (82%), Positives = 62/69 (89%)

Query: 33  MVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCS 92
           MVCGSCRRLL+YP+G RHV+C CCQ +NFVLEAH+VGQVKC SC VLLMYPYGA SVRCS
Sbjct: 1   MVCGSCRRLLSYPKGVRHVQCQCCQMINFVLEAHEVGQVKCGSCDVLLMYPYGASSVRCS 60

Query: 93  SCCFVTEIG 101
           SC FVTEIG
Sbjct: 61  SCRFVTEIG 69

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297803986|ref|XP_002869877.1| hypothetical protein ARALYDRAFT_492714 [Arabidopsis lyrata subsp. lyrata] gi|297315713|gb|EFH46136.1| hypothetical protein ARALYDRAFT_492714 [Arabidopsis lyrata subsp. lyrata]

 Score =  120 bits (301), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 54/72 (75%), Positives = 63/72 (87%)

Query: 29  EMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPS 88
           E AQM+CGSCRRLL+Y RG++HVKCS CQTVN VLEA+QVGQV C +C +LLMYPYGAPS
Sbjct: 56  EKAQMICGSCRRLLSYLRGSKHVKCSSCQTVNLVLEANQVGQVNCNNCKLLLMYPYGAPS 115

Query: 89  VRCSSCCFVTEI 100
           VRCSSC  +T+I
Sbjct: 116 VRCSSCNSITDI 127

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15234540|ref|NP_193892.1| lsd one like 2 protein [Arabidopsis thaliana] gi|75099427|sp|O65426.1|LOL2_ARATH RecName: Full=Protein LOL2; AltName: Full=Protein LSD ONE LIKE 2; Short=AtLOL2; AltName: Full=Putative zinc finger LOL2 gi|3080405|emb|CAA18725.1| Lsd1 like protein [Arabidopsis thaliana] gi|4455269|emb|CAB36805.1| Lsd1 like protein [Arabidopsis thaliana] gi|7268958|emb|CAB81268.1| Lsd1 like protein [Arabidopsis thaliana] gi|45476531|gb|AAS65931.1| At4g21610 [Arabidopsis thaliana] gi|46359821|gb|AAS88774.1| At4g21610 [Arabidopsis thaliana] gi|332659080|gb|AEE84480.1| lsd one like 2 protein [Arabidopsis thaliana]

 Score =  118 bits (296), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 55/72 (76%), Positives = 63/72 (87%)

Query: 29  EMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPS 88
           E AQMVCGSCRRLL+Y RG++HVKCS CQTVN VLEA+QVGQV C +C +LLMYPYGAP+
Sbjct: 57  EKAQMVCGSCRRLLSYLRGSKHVKCSSCQTVNLVLEANQVGQVNCNNCKLLLMYPYGAPA 116

Query: 89  VRCSSCCFVTEI 100
           VRCSSC  VT+I
Sbjct: 117 VRCSSCNSVTDI 128

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	118
TAIR|locus:2119622	155	LOL2 "AT4G21610" [Arabidopsis	0.610	0.464	0.763	9.4e-27
UNIPROTKB|Q704V3	163	LOL5 "Protein LOL5" [Oryza sat	0.635	0.460	0.693	1.9e-26
UNIPROTKB|Q0J7V9	184	LSD1 "Protein LSD1" [Oryza sat	0.618	0.396	0.602	3e-21
UNIPROTKB|F8RP38	176	F8RP38 "Zinc finger protein LS	0.627	0.420	0.540	5.7e-20
TAIR|locus:2128639	210	LSD1 "LESION SIMULATING DISEAS	0.576	0.323	0.472	4.9e-14
FB|FBgn0039300	84	RpS27 "Ribosomal protein S27"	0.483	0.678	0.338	0.00073

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

 Score = 301 (111.0 bits), Expect = 9.4e-27, P = 9.4e-27
 Identities = 55/72 (76%), Positives = 63/72 (87%)

Query:    29 EMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPS 88
             E AQMVCGSCRRLL+Y RG++HVKCS CQTVN VLEA+QVGQV C +C +LLMYPYGAP+
Sbjct:    57 EKAQMVCGSCRRLLSYLRGSKHVKCSSCQTVNLVLEANQVGQVNCNNCKLLLMYPYGAPA 116

Query:    89 VRCSSCCFVTEI 100
             VRCSSC  VT+I
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 = 298 (110.0 bits), Expect = 1.9e-26, P = 1.9e-26
 Identities = 52/75 (69%), Positives = 64/75 (85%)

Query:    27 HQEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGA 86
             ++E+ QMVCGSCR LLAY RGA +V C+CCQT+N+VLEAH+VG+V C  CA LLMYP+GA
Sbjct:    65 NKEVGQMVCGSCRILLAYFRGAGYVHCTCCQTMNYVLEAHEVGKVHCGHCATLLMYPFGA 124

Query:    87 PSVRCSSCCFVTEIG 101
             P+V+CS C FVTEIG
Sbjct:   125 PAVKCSLCLFVTEIG 139

GO:0005634 "nucleus" evidence=IDA

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

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

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

 Score = 249 (92.7 bits), Expect = 3.0e-21, P = 3.0e-21
 Identities = 44/73 (60%), Positives = 53/73 (72%)

Query:    29 EMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPS 88
             EMAQ+VCG C  LL Y RGA  V+CSCC TVN  +EA+QV  V C +C +LLMY YGA S
Sbjct:   101 EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLAMEANQVAHVNCGNCRMLLMYQYGARS 160

Query:    89 VRCSSCCFVTEIG 101
             V+C+ C FVT +G
Sbjct:   161 VKCAVCNFVTSVG 173

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 = 237 (88.5 bits), Expect = 5.7e-20, P = 5.7e-20
 Identities = 40/74 (54%), Positives = 52/74 (70%)

Query:    29 EMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPS 88
             +M+Q+ CG CR LL Y RGA  V+CSCC TVN    ++QV  V CA+C   LMYPYGAPS
Sbjct:    40 DMSQLYCGGCRTLLMYTRGATSVRCSCCHTVNLAPVSNQVAHVPCANCRTTLMYPYGAPS 99

Query:    89 VRCSSCCFVTEIGV 102
             V+C+ C ++T I +
Sbjct:   100 VKCAVCHYITNINM 113

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 = 181 (68.8 bits), Expect = 4.9e-14, P = 4.9e-14
 Identities = 34/72 (47%), Positives = 43/72 (59%)

Query:    32 QMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEA---HQVGQVKCASCAVLLMYPYGAPS 88
             Q+VC  CR LL YPRGA +V+C+ C T+N V      H +  + C  C  +LMY  GA S
Sbjct:     4 QLVCHGCRNLLMYPRGASNVRCALCNTINMVPPPPPPHDMAHIICGGCRTMLMYTRGASS 63

Query:    89 VRCSSCCFVTEI 100
             VRCS CC  T +
Sbjct:    64 VRCS-CCQTTNL 74

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

FB|FBgn0039300 RpS27 "Ribosomal protein S27" [Drosophila melanogaster (taxid:7227)]

 Score = 85 (35.0 bits), Expect = 0.00073, P = 0.00072
 Identities = 20/59 (33%), Positives = 27/59 (45%)

Query:    39 RRLLAYPRGA-RHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCF 96
             +RL+ +P      VKC  C  +  V  +H  G V CA CA +L  P G  +     C F
Sbjct:    22 KRLVQHPNSYFMDVKCPGCYRITTVF-SHAQGVVVCAGCATILCQPTGGRAKLTEGCSF 79


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.330   0.134   0.477    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      118       118   0.00091  102 3  11 21  0.36    30
                                                     29  0.47    32


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  6
  No. of states in DFA:  562 (60 KB)
  Total size of DFA:  145 KB (2089 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  11.07u 0.11s 11.18t   Elapsed:  00:00:00
  Total cpu time:  11.07u 0.11s 11.18t   Elapsed:  00:00:00
  Start:  Mon May 20 23:00:26 2013   End:  Mon May 20 23:00:26 2013

GO:0022627 "cytosolic small ribosomal subunit" evidence=ISS

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

GO:0006412 "translation" evidence=IEA

GO:0005811 "lipid particle" evidence=IDA

GO:0005840 "ribosome" evidence=IDA

---

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)
O65426	LOL2_ARATH	No assigned EC number	0.7638	0.6101	0.4645	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: GSVIVG00011208001 SubName- Full=Chromosome undetermined scaffold_2316, whole genome shotgun sequence; (96 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	118
TIGR01053	31	TIGR01053, LSD1, zinc finger domain, LSD1 subclass	5e-08
pfam06943	25	pfam06943, zf-LSD1, LSD1 zinc finger	1e-06
pfam06943	25	pfam06943, zf-LSD1, LSD1 zinc finger	9e-05

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

 Score = 45.1 bits (107), Expect = 5e-08
 Identities = 21/31 (67%), Positives = 24/31 (77%)

Query: 32 QMVCGSCRRLLAYPRGARHVKCSCCQTVNFV 62
          Q+VCG CR LL YPRGA  V+C+ CQTVN 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 = 41.4 bits (98), Expect = 1e-06
 Identities = 16/25 (64%), Positives = 18/25 (72%)

Query: 35 CGSCRRLLAYPRGARHVKCSCCQTV 59
          CG CR LL YPRGA  V+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 = 36.8 bits (86), Expect = 9e-05
 Identities = 16/25 (64%), Positives = 17/25 (68%)

Query: 73 CASCAVLLMYPYGAPSVRCSSCCFV 97
          C  C  LLMYP GAPSVRC+ C  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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	118
TIGR01053	31	LSD1 zinc finger domain, LSD1 subclass. This model	99.56
PF06943	25	zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zin	99.51
TIGR01053	31	LSD1 zinc finger domain, LSD1 subclass. This model	99.48
PF06943	25	zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zin	99.4
PF10122	51	Mu-like_Com: Mu-like prophage protein Com; InterPr	95.38
KOG1546	362	consensus Metacaspase involved in regulation of ap	95.14
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	93.89
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	93.75
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	93.59
PF10122	51	Mu-like_Com: Mu-like prophage protein Com; InterPr	93.57
PF09788	256	Tmemb_55A: Transmembrane protein 55A; InterPro: IP	93.37
PLN00209	86	ribosomal protein S27; Provisional	93.31
PF01667	55	Ribosomal_S27e: Ribosomal protein S27; InterPro: I	93.2
PTZ00083	85	40S ribosomal protein S27; Provisional	93.02
PRK00415	59	rps27e 30S ribosomal protein S27e; Reviewed	92.64
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	92.14
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	91.53
COG2051	67	RPS27A Ribosomal protein S27E [Translation, riboso	90.71
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	90.4
PF11331	46	DUF3133: Protein of unknown function (DUF3133); In	90.1
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	90.03
PF12773	50	DZR: Double zinc ribbon	89.42
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	89.05
KOG1779	84	consensus 40s ribosomal protein S27 [Translation,	86.32
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	86.17
PF09788	256	Tmemb_55A: Transmembrane protein 55A; InterPro: IP	85.34
PF04810	40	zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro:	83.46

>TIGR01053 LSD1 zinc finger domain, LSD1 subclass

Probab=99.56  E-value=1.5e-15  Score=89.63  Aligned_cols=31  Identities=68%  Similarity=1.339  Sum_probs=23.1

Q ss_pred             eeeeccccceeeecCCCCeEEcCCCCccccc
Q 033478           32 QMVCGSCRRLLAYPRGARHVKCSCCQTVNFV   62 (118)
Q Consensus        32 QLvCggCr~lL~YprGA~sVrC~~C~tVn~v   62 (118)
                      |++|++||++|+||+||++|||+.|++||.+
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=99.51  E-value=5.9e-15  Score=84.15  Aligned_cols=25  Identities=68%  Similarity=1.578  Sum_probs=19.7

Q ss_pred             eccccceeeecCCCCeEEcCCCCcc
Q 033478           35 CGSCRRLLAYPRGARHVKCSCCQTV   59 (118)
Q Consensus        35 CggCr~lL~YprGA~sVrC~~C~tV   59 (118)
                      |+|||++|+||+||+||||+.|++|
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            6778888888888888888888775

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=99.48  E-value=1.3e-14  Score=85.74  Aligned_cols=31  Identities=55%  Similarity=1.019  Sum_probs=29.5

Q ss_pred             EEEcCCCCeeeEeeCCCCeEECCCCCcccee
Q 033478           70 QVKCASCAVLLMYPYGAPSVRCSSCCFVTEI  100 (118)
Q Consensus        70 ~v~Cg~Crt~LmyP~GA~SVrCs~C~tVT~V  100 (118)
                      |++|++||++|+||+||++|||+.|++||.|
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            5899999999999999999999999999975

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=1.5e-13  Score=78.44  Aligned_cols=25  Identities=64%  Similarity=1.334  Sum_probs=24.3

Q ss_pred             cCCCCeeeEeeCCCCeEECCCCCcc
Q 033478           73 CASCAVLLMYPYGAPSVRCSSCCFV   97 (118)
Q Consensus        73 Cg~Crt~LmyP~GA~SVrCs~C~tV   97 (118)
                      |++||++||||+||+||||+.|++|
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            8999999999999999999999987

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 [].

>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=95.38  E-value=0.0087  Score=39.30  Aligned_cols=35  Identities=17%  Similarity=0.541  Sum_probs=24.8

Q ss_pred             EEEcCCCCeeeEee--CCCCeEECCCCCccceeccCC
Q 033478           70 QVKCASCAVLLMYP--YGAPSVRCSSCCFVTEIGVCG  104 (118)
Q Consensus        70 ~v~Cg~Crt~LmyP--~GA~SVrCs~C~tVT~V~~~n  104 (118)
                      .++|++|+.+|.-.  ...-.++|+-|.++|.|...+
T Consensus         4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a~~   40 (51)
T PF10122_consen    4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRATS   40 (51)
T ss_pred             ceeccchhHHHhhhcCccEEEEECCCCCccceEeccC
Confidence            47788888888775  333478888888888877544

>KOG1546 consensus Metacaspase involved in regulation of apoptosis [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=95.14  E-value=0.0082  Score=52.00  Aligned_cols=30  Identities=37%  Similarity=0.702  Sum_probs=27.5

Q ss_pred             EEcCCCCeeeEeeCCCCeEECCCCCccceecc
Q 033478           71 VKCASCAVLLMYPYGAPSVRCSSCCFVTEIGV  102 (118)
Q Consensus        71 v~Cg~Crt~LmyP~GA~SVrCs~C~tVT~V~~  102 (118)
                      +.|. |++.++.|+||+. ||+.||++|.+..
T Consensus         5 ~~~~-~~~p~~~pp~ar~-q~~~~~~~~~~~~   34 (362)
T KOG1546|consen    5 VGCN-CQRPMAPPPGARY-QCAGCHAVTQIAQ   34 (362)
T ss_pred             ccCC-CCCCCCCCCCCcc-cccccceeeeecc
Confidence            5676 9999999999999 9999999999983

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=93.89  E-value=0.064  Score=31.95  Aligned_cols=27  Identities=33%  Similarity=0.842  Sum_probs=15.5

Q ss_pred             EEcCCCCeeeEeeC-----CCCeEECCCCCcc
Q 033478           71 VKCASCAVLLMYPY-----GAPSVRCSSCCFV   97 (118)
Q Consensus        71 v~Cg~Crt~LmyP~-----GA~SVrCs~C~tV   97 (118)
                      +.|.+|.+..-+|.     +...|||+.|+++
T Consensus         3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~   34 (37)
T PF13719_consen    3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHV   34 (37)
T ss_pred             EECCCCCceEEcCHHHcccCCcEEECCCCCcE
Confidence            44555555554443     4567777777665

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

Probab=93.75  E-value=0.14  Score=31.16  Aligned_cols=32  Identities=25%  Similarity=0.473  Sum_probs=22.0

Q ss_pred             EEEcCCCCeeeEeeCCCCeEECCCCCccceec
Q 033478           70 QVKCASCAVLLMYPYGAPSVRCSSCCFVTEIG  101 (118)
Q Consensus        70 ~v~Cg~Crt~LmyP~GA~SVrCs~C~tVT~V~  101 (118)
                      ...|++|+..+.+..+...++|+-|++--.+.
T Consensus         3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~   34 (46)
T PRK00398          3 EYKCARCGREVELDEYGTGVRCPYCGYRILFK   34 (46)
T ss_pred             EEECCCCCCEEEECCCCCceECCCCCCeEEEc
Confidence            45677777777777777777777777644443

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=93.59  E-value=0.094  Score=30.48  Aligned_cols=30  Identities=27%  Similarity=0.732  Sum_probs=16.1

Q ss_pred             EEcCCCCcccccccc---ceeeEEEcCCCCeee
Q 033478           51 VKCSCCQTVNFVLEA---HQVGQVKCASCAVLL   80 (118)
Q Consensus        51 VrC~~C~tVn~v~~a---~q~a~v~Cg~Crt~L   80 (118)
                      +.|+.|.+.+.++++   .+...+.|++|+..+
T Consensus         3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~   35 (38)
T TIGR02098         3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW   35 (38)
T ss_pred             EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence            566677766555531   122356666666554

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.

>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=93.57  E-value=0.038  Score=36.31  Aligned_cols=33  Identities=36%  Similarity=0.794  Sum_probs=28.3

Q ss_pred             ceeeeccccceeeecCCCC--eEEcCCCCcccccc
Q 033478           31 AQMVCGSCRRLLAYPRGAR--HVKCSCCQTVNFVL   63 (118)
Q Consensus        31 sQLvCggCr~lL~YprGA~--sVrC~~C~tVn~v~   63 (118)
                      -.+.|+.|..+|+.--++.  .++|+.|.++|.+.
T Consensus         3 ~eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~   37 (51)
T PF10122_consen    3 KEIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVR   37 (51)
T ss_pred             cceeccchhHHHhhhcCccEEEEECCCCCccceEe
Confidence            4678999999999875665  88999999999876

>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=93.37  E-value=0.1  Score=43.49  Aligned_cols=41  Identities=20%  Similarity=0.380  Sum_probs=33.9

Q ss_pred             ceeeEEEcCCCCeeeEeeCCC--CeEECCCCCccceeccCCcc
Q 033478           66 HQVGQVKCASCAVLLMYPYGA--PSVRCSSCCFVTEIGVCGLS  106 (118)
Q Consensus        66 ~q~a~v~Cg~Crt~LmyP~GA--~SVrCs~C~tVT~V~~~n~r  106 (118)
                      ..+..++|++|+...+++.=.  ...||+.|+.|..|...-.|
T Consensus       153 p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKvSSVG~~faR  195 (256)
T PF09788_consen  153 PGSCRVICGHCSNTFLFNTLTSNTLARCPHCRKVSSVGPRFAR  195 (256)
T ss_pred             CCceeEECCCCCCcEeccCCCCCccccCCCCceeccccchHhh
Confidence            356889999999999998755  56799999999999875444

>PLN00209 ribosomal protein S27; Provisional

Probab=93.31  E-value=0.085  Score=37.85  Aligned_cols=40  Identities=33%  Similarity=0.630  Sum_probs=33.1

Q ss_pred             eEEcCCCCccccccccceeeEEEcCCCCeeeEeeCCCCeEE
Q 033478           50 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVR   90 (118)
Q Consensus        50 sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~SVr   90 (118)
                      .|+|+.|..++.+= ++....|.|..|++.|..|.|-...-
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            58999999998875 35577899999999999999976543

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

Probab=93.20  E-value=0.085  Score=34.84  Aligned_cols=39  Identities=33%  Similarity=0.692  Sum_probs=26.7

Q ss_pred             eEEcCCCCccccccccceeeEEEcCCCCeeeEeeCCCCeE
Q 033478           50 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSV   89 (118)
Q Consensus        50 sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~SV   89 (118)
                      .|+|+.|..++.+= ++....+.|.+|++.|.-|.|-..-
T Consensus         7 ~VkCp~C~~~q~vF-Sha~t~V~C~~Cg~~L~~PtGGKa~   45 (55)
T PF01667_consen    7 DVKCPGCYNIQTVF-SHAQTVVKCVVCGTVLAQPTGGKAR   45 (55)
T ss_dssp             EEE-TTT-SEEEEE-TT-SS-EE-SSSTSEEEEE-SSSEE
T ss_pred             EEECCCCCCeeEEE-ecCCeEEEcccCCCEecCCCCcCeE
Confidence            58999999998874 3556779999999999999986643

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.

>PTZ00083 40S ribosomal protein S27; Provisional

Probab=93.02  E-value=0.1  Score=37.36  Aligned_cols=40  Identities=30%  Similarity=0.606  Sum_probs=32.8

Q ss_pred             eEEcCCCCccccccccceeeEEEcCCCCeeeEeeCCCCeEE
Q 033478           50 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVR   90 (118)
Q Consensus        50 sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~SVr   90 (118)
                      .|+|+.|..++.+= ++....|.|.+|++.|.-|.|-...-
T Consensus        35 ~VkCp~C~n~q~VF-ShA~t~V~C~~Cg~~L~~PTGGKa~l   74 (85)
T PTZ00083         35 DVKCPGCSQITTVF-SHAQTVVLCGGCSSQLCQPTGGKAKL   74 (85)
T ss_pred             EEECCCCCCeeEEE-ecCceEEEccccCCEeeccCCCCeEe
Confidence            58999999998875 35577799999999999999976543

>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed

Probab=92.64  E-value=0.083  Score=35.48  Aligned_cols=38  Identities=32%  Similarity=0.639  Sum_probs=27.6

Q ss_pred             eEEcCCCCccccccccceeeEEEcCCCCeeeEeeCCCCe
Q 033478           50 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPS   88 (118)
Q Consensus        50 sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~S   88 (118)
                      .|+|+.|..++.+= ++-...+.|..|++.|.-|.|-..
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            47888888887654 244566888888888888887543

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=92.14  E-value=0.22  Score=29.61  Aligned_cols=15  Identities=47%  Similarity=0.840  Sum_probs=8.9

Q ss_pred             eCCCCeEECCCCCcc
Q 033478           83 PYGAPSVRCSSCCFV   97 (118)
Q Consensus        83 P~GA~SVrCs~C~tV   97 (118)
                      |++...|+|+.|+.+
T Consensus        20 p~~g~~v~C~~C~~~   34 (36)
T PF13717_consen   20 PPKGRKVRCSKCGHV   34 (36)
T ss_pred             CCCCcEEECCCCCCE
Confidence            445556666666653

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=91.53  E-value=0.43  Score=27.64  Aligned_cols=30  Identities=23%  Similarity=0.540  Sum_probs=22.9

Q ss_pred             EEEcCCCCeeeEeeC-----CCCeEECCCCCccce
Q 033478           70 QVKCASCAVLLMYPY-----GAPSVRCSSCCFVTE   99 (118)
Q Consensus        70 ~v~Cg~Crt~LmyP~-----GA~SVrCs~C~tVT~   99 (118)
                      .+.|.+|++...++.     +...|+|+.|+++-.
T Consensus         2 ~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~   36 (38)
T TIGR02098         2 RIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY   36 (38)
T ss_pred             EEECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence            578999999888884     234799999987644

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=90.71  E-value=0.3  Score=33.75  Aligned_cols=38  Identities=32%  Similarity=0.624  Sum_probs=28.0

Q ss_pred             eEEcCCCCccccccccceeeEEEcCCCCeeeEeeCCCCe
Q 033478           50 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPS   88 (118)
Q Consensus        50 sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~S   88 (118)
                      .|+|+.|...+-+= ++....+.|..|++.|..|.|-.+
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            47888887776654 344666888888888888888654

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

Probab=90.40  E-value=0.31  Score=32.83  Aligned_cols=53  Identities=28%  Similarity=0.603  Sum_probs=41.1

Q ss_pred             ccceeeeccccceeeecCC-CCeEEcCCCCccccccccceeeEEEcCCCCeeeEeeCCCCeEECCCCCcc
Q 033478           29 EMAQMVCGSCRRLLAYPRG-ARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFV   97 (118)
Q Consensus        29 ~~sQLvCggCr~lL~YprG-A~sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~SVrCs~C~tV   97 (118)
                      .+.-.+|.+|...| .|++ |+.--|+.|..+..         .+|..||.+      +...+|+.|.+.
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            34556899999888 5666 99999999987654         568999876      356788888764

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

Probab=90.10  E-value=0.36  Score=30.91  Aligned_cols=38  Identities=24%  Similarity=0.572  Sum_probs=27.0

Q ss_pred             CCCCeEEcCCCCccccccc-----cceeeEEEcCCCCeeeEee
Q 033478           46 RGARHVKCSCCQTVNFVLE-----AHQVGQVKCASCAVLLMYP   83 (118)
Q Consensus        46 rGA~sVrC~~C~tVn~v~~-----a~q~a~v~Cg~Crt~LmyP   83 (118)
                      .||+-|-|..|..+=..|.     .....++.||.|...|.|-
T Consensus         2 GGAPFv~C~~C~~lLqlP~~~~~~~k~~~klrCGaCs~vl~~s   44 (46)
T PF11331_consen    2 GGAPFVVCSSCFELLQLPAKFSLSKKNQQKLRCGACSEVLSFS   44 (46)
T ss_pred             CCCCEeECccHHHHHcCCCccCCCccceeEEeCCCCceeEEEe
Confidence            3677777777776666653     2337789999999888764

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=90.03  E-value=0.33  Score=28.86  Aligned_cols=30  Identities=27%  Similarity=0.583  Sum_probs=20.4

Q ss_pred             EEcCCCCcccccccc---ceeeEEEcCCCCeee
Q 033478           51 VKCSCCQTVNFVLEA---HQVGQVKCASCAVLL   80 (118)
Q Consensus        51 VrC~~C~tVn~v~~a---~q~a~v~Cg~Crt~L   80 (118)
                      ++|+.|++.-.+++.   ..-..++|+.|+...
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            677888877777642   445677888887653

>PF12773 DZR: Double zinc ribbon

Probab=89.42  E-value=0.2  Score=30.31  Aligned_cols=40  Identities=25%  Similarity=0.464  Sum_probs=25.9

Q ss_pred             cCCCCccccccccceeeEEEcCCCCeeeEeeCCCCeEECCCCCccce
Q 033478           53 CSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTE   99 (118)
Q Consensus        53 C~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~SVrCs~C~tVT~   99 (118)
                      |+.|.+.+..      ....|..|++.|. +.....+.|+.|.+.+.
T Consensus         1 Cp~Cg~~~~~------~~~fC~~CG~~l~-~~~~~~~~C~~Cg~~~~   40 (50)
T PF12773_consen    1 CPHCGTPNPD------DAKFCPHCGTPLP-PPDQSKKICPNCGAENP   40 (50)
T ss_pred             CCCcCCcCCc------cccCChhhcCChh-hccCCCCCCcCCcCCCc
Confidence            5666666532      2467777777777 55566677888877643

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

Probab=89.05  E-value=0.58  Score=28.46  Aligned_cols=25  Identities=24%  Similarity=0.623  Sum_probs=11.4

Q ss_pred             eeeccccceeeecCCCCeEEcCCCC
Q 033478           33 MVCGSCRRLLAYPRGARHVKCSCCQ   57 (118)
Q Consensus        33 LvCggCr~lL~YprGA~sVrC~~C~   57 (118)
                      ..|..|...+.+..+....+|+.|.
T Consensus         4 y~C~~CG~~~~~~~~~~~~~Cp~CG   28 (46)
T PRK00398          4 YKCARCGREVELDEYGTGVRCPYCG   28 (46)
T ss_pred             EECCCCCCEEEECCCCCceECCCCC
Confidence            3444444444444444444444443

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

Probab=86.32  E-value=1.4  Score=31.60  Aligned_cols=41  Identities=29%  Similarity=0.606  Sum_probs=32.4

Q ss_pred             eEEcCCCCccccccccceeeEEEcCCCCeeeEeeCCCCeEEC
Q 033478           50 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRC   91 (118)
Q Consensus        50 sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~SVrC   91 (118)
                      -|+|+.|--||.+-+ +...-+.|++|.+.|.-|.|-..+-=
T Consensus        34 ~VkC~gc~~iT~vfS-HaqtvVvc~~c~~il~~~tggra~ls   74 (84)
T KOG1779|consen   34 DVKCPGCFKITTVFS-HAQTVVVCEGCSTILCQPTGGKAKLS   74 (84)
T ss_pred             EEEcCCceEEEEEee-cCceEEEcCCCceEEEEecCCcEEec
Confidence            488999988888763 44566899999999999998876643

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=86.17  E-value=0.83  Score=27.14  Aligned_cols=29  Identities=21%  Similarity=0.591  Sum_probs=21.0

Q ss_pred             EEcCCCCccccccc---cceeeEEEcCCCCee
Q 033478           51 VKCSCCQTVNFVLE---AHQVGQVKCASCAVL   79 (118)
Q Consensus        51 VrC~~C~tVn~v~~---a~q~a~v~Cg~Crt~   79 (118)
                      +.|+.|++.-.+++   ...-..+.|+.|+..
T Consensus         3 i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~   34 (36)
T PF13717_consen    3 ITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHV   34 (36)
T ss_pred             EECCCCCCEEeCCHHHCCCCCcEEECCCCCCE
Confidence            67888888877764   245667888888764

>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=85.34  E-value=1.7  Score=36.49  Aligned_cols=73  Identities=22%  Similarity=0.534  Sum_probs=57.4

Q ss_pred             cceeeeccccceeeecCC--CCeEEcCCCCccccccc-cceeeEEEcCCCCeeeEeeCCCCeEECCC--CCccceeccC
Q 033478           30 MAQMVCGSCRRLLAYPRG--ARHVKCSCCQTVNFVLE-AHQVGQVKCASCAVLLMYPYGAPSVRCSS--CCFVTEIGVC  103 (118)
Q Consensus        30 ~sQLvCggCr~lL~YprG--A~sVrC~~C~tVn~v~~-a~q~a~v~Cg~Crt~LmyP~GA~SVrCs~--C~tVT~V~~~  103 (118)
                      +.-+.|.=|+.++--.--  =--|+|..|+-.|+..+ ....-.++| -|..+|+....++.|-|+.  |+.|......
T Consensus        63 ~p~v~CrVCq~~I~i~gk~~QhVVkC~~CnEATPIr~aPpGKKYVRC-PCNCLLICk~sS~rIaCPRp~CkRiI~L~~~  140 (256)
T PF09788_consen   63 APVVTCRVCQSLIDIEGKMHQHVVKCSVCNEATPIRNAPPGKKYVRC-PCNCLLICKSSSQRIACPRPNCKRIINLGPS  140 (256)
T ss_pred             CceEEeecCCceecccCccceeeEECCCCCccccccCCCCCCeeEec-CCceEEEeecccccccCCCCCCcceEEeCCc
Confidence            356789999987755432  22489999999998764 456778999 7899999999999999988  9998877655

>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=83.46  E-value=1.1  Score=26.90  Aligned_cols=20  Identities=15%  Similarity=0.237  Sum_probs=11.1

Q ss_pred             eCCCCeEECCCCCccceecc
Q 033478           83 PYGAPSVRCSSCCFVTEIGV  102 (118)
Q Consensus        83 P~GA~SVrCs~C~tVT~V~~  102 (118)
                      -.+..+-+|+.|.+.|.++.
T Consensus        19 ~~~~~~w~C~~C~~~N~lp~   38 (40)
T PF04810_consen   19 DDGGKTWICNFCGTKNPLPP   38 (40)
T ss_dssp             ETTTTEEEETTT--EEE--G
T ss_pred             cCCCCEEECcCCCCcCCCCC
Confidence            34667777777777777764

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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....

---

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	118
1qxf_A	66	GR2, 30S ribosomal protein S27E; structural genomi	93.98
3j20_W	63	30S ribosomal protein S27E; archaea, archaeal, KIN	93.5
2xzm_6	81	RPS27E; ribosome, translation; 3.93A {Tetrahymena	92.91
3u5c_b	82	RP61, YS20, 40S ribosomal protein S27-A; translati	91.17
3iz6_X	86	40S ribosomal protein S27 (S27E); eukaryotic ribos	88.96
1gh9_A	71	8.3 kDa protein (gene MTH1184); beta+alpha complex	87.52
2ppt_A	155	Thioredoxin-2; thiredoxin, zinc finger, oxidoreduc	80.82

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

Probab=93.98  E-value=0.034  Score=37.16  Aligned_cols=39  Identities=28%  Similarity=0.601  Sum_probs=31.9

Q ss_pred             eEEcCCCCccccccccceeeEEEcCCCCeeeEeeCCCCeE
Q 033478           50 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSV   89 (118)
Q Consensus        50 sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~SV   89 (118)
                      .|+|+.|..++.+=+ +....+.|.+|++.|.-|.|-..-
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            589999999988753 446679999999999999987653

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

Probab=93.50  E-value=0.046  Score=36.22  Aligned_cols=38  Identities=32%  Similarity=0.686  Sum_probs=30.7

Q ss_pred             eEEcCCCCccccccccceeeEEEcCCCCeeeEeeCCCCe
Q 033478           50 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPS   88 (118)
Q Consensus        50 sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~S   88 (118)
                      .|+|+.|..++.+= ++....+.|.+|++.|.-|.|-..
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            58999999888874 355667899999999999988654

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

Probab=92.91  E-value=0.065  Score=37.00  Aligned_cols=40  Identities=25%  Similarity=0.658  Sum_probs=31.9

Q ss_pred             eEEcCCCCccccccccceeeEEEcCCCCeeeEeeCCCCeEE
Q 033478           50 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVR   90 (118)
Q Consensus        50 sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~SVr   90 (118)
                      .|+|+.|..++.+=+ +....|.|.+|++.|.-|.|-..--
T Consensus        32 ~VkCp~C~n~q~VFS-hA~t~V~C~~Cg~~L~~PTGGKA~l   71 (81)
T 2xzm_6           32 DVKCAQCQNIQMIFS-NAQSTIICEKCSAILCKPTGGKVQI   71 (81)
T ss_dssp             EEECSSSCCEEEEET-TCSSCEECSSSCCEEEEECSSCEEE
T ss_pred             EeECCCCCCeeEEEe-cCccEEEccCCCCEEeecCCCCeEe
Confidence            589999999888753 4566789999999999999876543

>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=91.17  E-value=0.072  Score=36.89  Aligned_cols=41  Identities=32%  Similarity=0.663  Sum_probs=32.1

Q ss_pred             eEEcCCCCccccccccceeeEEEcCCCCeeeEeeCCCCeEEC
Q 033478           50 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRC   91 (118)
Q Consensus        50 sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~SVrC   91 (118)
                      .|+|+.|..++.+= ++....|.|.+|++.|.-|.|-..--=
T Consensus        34 ~VkCp~C~~~q~VF-Sha~t~V~C~~Cg~~L~~PTGGKa~l~   74 (82)
T 3u5c_b           34 DVKCPGCLNITTVF-SHAQTAVTCESCSTILCTPTGGKAKLS   74 (82)
T ss_dssp             EEECTTSCSCEEEE-SBCSSCCCCSSSCCCCEECCSSBCEEC
T ss_pred             EEECCCCCCeeEEE-ecCCeEEEccccCCEEeccCCCCeEec
Confidence            58999999988875 344667889999999999998765443

>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=88.96  E-value=0.095  Score=36.57  Aligned_cols=49  Identities=29%  Similarity=0.556  Sum_probs=32.0

Q ss_pred             eeeecCCC-CeEEcCCCCccccccccceeeEEEcCCCCeeeEeeCCCCeEE
Q 033478           41 LLAYPRGA-RHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVR   90 (118)
Q Consensus        41 lL~YprGA-~sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~SVr   90 (118)
                      |..=|++- -.|+|+.|..++.+= ++....|.|.+|++.|.-|.|-..--
T Consensus        26 Lv~~PnS~Fm~VkCp~C~~~~~VF-ShA~t~V~C~~CgtvL~~PTGGKa~l   75 (86)
T 3iz6_X           26 LVQSPNSFFMDVKCQGCFNITTVF-SHSQTVVVCPGCQTVLCQPTGGKARL   75 (86)
T ss_dssp             -------CEEEEECTTTCCEEEEE-TTCSSCCCCSSSCCCCSCCCSSSCCC
T ss_pred             eccCCCCcEeEEECCCCCCeeEEE-ecCCcEEEccCCCCEeecCCCCCEEe
Confidence            33334443 348999999988775 34466688999999999998876543

>1gh9_A 8.3 kDa protein (gene MTH1184); beta+alpha complex structure, structural genomics, PSI, protein structure initiative; NMR {Methanothermobacterthermautotrophicus} SCOP: g.41.6.1

Probab=87.52  E-value=0.72  Score=30.57  Aligned_cols=34  Identities=21%  Similarity=0.382  Sum_probs=29.1

Q ss_pred             eeEEEcCCCCeeeEeeCCCCeEECCCCCccceeccC
Q 033478           68 VGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIGVC  103 (118)
Q Consensus        68 ~a~v~Cg~Crt~LmyP~GA~SVrCs~C~tVT~V~~~  103 (118)
                      +.-+.|. |+..+..-.|+.+.+|+ |....++...
T Consensus         2 Y~vv~C~-C~~~~~~~~~~kT~~C~-CG~~~~~~k~   35 (71)
T 1gh9_A            2 YIIFRCD-CGRALYSREGAKTRKCV-CGRTVNVKDR   35 (71)
T ss_dssp             EEEEEET-TSCCEEEETTCSEEEET-TTEEEECCSS
T ss_pred             eEEEECC-CCCEEEEcCCCcEEECC-CCCeeeeceE
Confidence            3457899 99999999999999998 9998887643

>2ppt_A Thioredoxin-2; thiredoxin, zinc finger, oxidoreductase; 1.92A {Rhodobacter capsulatus}

Probab=80.82  E-value=0.4  Score=32.98  Aligned_cols=31  Identities=26%  Similarity=0.500  Sum_probs=23.0

Q ss_pred             eEEcCCCCccccccccceeeEEEcCCCCeee
Q 033478           50 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLL   80 (118)
Q Consensus        50 sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~L   80 (118)
                      ++.|+.|.++|.+|+......-.||.|+..|
T Consensus        14 ~~~c~~c~~~~~~~~~r~~~~~~~~~~~~~~   44 (155)
T 2ppt_A           14 RLTCLACGQANKVPSDRLAAGPKCGICGAGL   44 (155)
T ss_dssp             EEECTTTCCEEEEEGGGTTSCCBCTTTCCBS
T ss_pred             eEECccccccccCCcccccCCCCCCcCCccc
Confidence            5888888888888765444556788888776

---

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	118
d1qxfa_	58	Ribosomal protein S27e {Archaeon Archaeoglobus ful	94.11
d1pd0a5	85	Sec24 {Baker's yeast (Saccharomyces cerevisiae) [T	82.69

>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=94.11  E-value=0.015  Score=36.39  Aligned_cols=38  Identities=29%  Similarity=0.610  Sum_probs=31.4

Q ss_pred             eEEcCCCCccccccccceeeEEEcCCCCeeeEeeCCCCe
Q 033478           50 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPS   88 (118)
Q Consensus        50 sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~S   88 (118)
                      .|+|+.|..++.+= ++....+.|..|++.|..|.|-..
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            58999999998775 344677999999999999998764

>d1pd0a5 g.41.10.1 (A:216-300) Sec24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-finger domain of Sec23/24
family: Zn-finger domain of Sec23/24
domain: Sec24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=82.69  E-value=0.5  Score=29.83  Aligned_cols=32  Identities=19%  Similarity=0.589  Sum_probs=22.3

Q ss_pred             EEcCCCCeee----EeeCCCCeEECCCCCccceecc
Q 033478           71 VKCASCAVLL----MYPYGAPSVRCSSCCFVTEIGV  102 (118)
Q Consensus        71 v~Cg~Crt~L----myP~GA~SVrCs~C~tVT~V~~  102 (118)
                      ++|.+||.-|    -+-.+...-+|..|+..|.++.
T Consensus        14 ~RC~~C~ayiNP~~~~~~~g~~w~C~~C~~~N~~p~   49 (85)
T d1pd0a5          14 VRCRRCRSYMNPFVTFIEQGRRWRCNFCRLANDVPM   49 (85)
T ss_dssp             CBCSSSCCBCCTTCEEETTTTEEECTTTCCEEECCG
T ss_pred             ccccCCcCEECCceEEeCCCCEEECCCCCcccCCCH
Confidence            4566666544    2345678899999999998864