Citrus Sinensis ID: 033096

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------
Protein Sequence
MENREKESMENQEENEEAGPPPGWQPIPPPLPVPSPSEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIGVCGLSLFLCMCDLANQI
Secondary Structure (PSIPRED)
cccHHHHHHHHHHHccccccccccccccccccccccccccEEEEcccccEEEEEccccEEEcccccccccccccccEEEEEcccccEEEEEcccccEEEccccccEEEcccccccccEEEEcccccc
Secondary Structure Prediction (SSPRO)
cccccHHcHHccccccccccccccccccccccccccHHHHHEEcccccEEEEEcccccEEEccccccEEcccccccEEEEEccccEEEEEEccccccEEcccEEEEcccccccccHHHccccccccc
Coil and Loop (DISEMBL)
menrekesmenqeeneeagpppgwqpippplpvpspsemaQMVCGSCrrllayprgarhvkcsccqTVNFVLEAHQVGQVKCASCAVLlmypygapsvrcssccfvteigvcGLSLFLCMCDLANQI
Flexible Loop (DISEMBL)
menrekesMENQEeneeagpppgwqpIPPPLPVPSPSEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIGVCGLSLFLCMCDLANQI
Low Complexity Region (SEG)
MenrekesmenqeeneeAGpppgwqpippplpvpspSEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIGVCGLSLFLCMCDLANQI
Disordered region (IsUnstruct)
*****************************************MVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIGVCGLSLFLCMCDLA***
Disordered Region (DISOPRED)
***************************************AQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIGVCGLSLFLCMCDLAN**
Disordered Region (DISEMBL)
*********************PGWQPIPPPLPVPSPSEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIGVCGLSLFLCMCDLANQI
Disordered Region (DISPRO)
*********************PGWQPIPPPLPVPSPSEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIGVCGLSLFLCMCDLAN**
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MENREKESMENQEENEEAGPPPGWQPIPPPLPVPSPSEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIGVCGLSLFLCMCDLANQI
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	127	2.2.26 [Sep-21-2011]
O65426	155	Protein LOL2 OS=Arabidops	yes	no	0.724	0.593	0.628	1e-29
Q704V3	163	Protein LOL5 OS=Oryza sat	no	no	0.574	0.447	0.712	1e-25
Q93ZB1	154	Protein LOL1 OS=Arabidops	no	no	0.622	0.512	0.571	9e-21
Q0J7V9	184	Protein LSD1 OS=Oryza sat	no	no	0.614	0.423	0.594	2e-20
Q6ASS2	186	Protein LOL3 OS=Oryza sat	no	no	0.645	0.440	0.505	5e-19
Q2QMB3	172	Protein LOL2 OS=Oryza sat	no	no	0.614	0.453	0.493	2e-17
P94077	189	Protein LSD1 OS=Arabidops	no	no	0.582	0.391	0.493	5e-16
Q84UR0	147	Protein LOL4 OS=Oryza sat	no	no	0.574	0.496	0.342	1e-09

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

 Score =  128 bits (321), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 66/105 (62%), Positives = 79/105 (75%), Gaps = 13/105 (12%)

Query: 19  GPPPGWQP--IPPPLPV------PSPS-----EMAQMVCGSCRRLLAYPRGARHVKCSCC 65
           GPPPGW+   +PPP+        P+P+     E AQMVCGSCRRLL+Y RG++HVKCS C
Sbjct: 25  GPPPGWESAVLPPPIVTITAAVNPNPTTVEIPEKAQMVCGSCRRLLSYLRGSKHVKCSSC 84

Query: 66  QTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIG 110
           QTVN VLEA+QVGQV C +C +LLMYPYGAP+VRCSSC  VT+I 
Sbjct: 85  QTVNLVLEANQVGQVNCNNCKLLLMYPYGAPAVRCSSCNSVTDIS 129

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 (286), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 52/73 (71%), Positives = 62/73 (84%)

Query: 38  EMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPS 97
           E+ QMVCGSCR LLAY RGA +V C+CCQT+N+VLEAH+VG+V C  CA LLMYP+GAP+
Sbjct: 67  EVGQMVCGSCRILLAYFRGAGYVHCTCCQTMNYVLEAHEVGKVHCGHCATLLMYPFGAPA 126

Query: 98  VRCSSCCFVTEIG 110
           V+CS C FVTEIG
Sbjct: 127 VKCSLCLFVTEIG 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 = 99.0 bits (245), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 48/84 (57%), Positives = 58/84 (69%), Gaps = 5/84 (5%)

Query: 27  IPPPLPVPSPSEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCA 86
           +PPP      +EMAQ+VCG C  LL Y RGA  V+CSCC TVN  LEA+QV  V C +C 
Sbjct: 64  VPPP-----GTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCM 118

Query: 87  VLLMYPYGAPSVRCSSCCFVTEIG 110
           +LLMY YGA SV+C+ C FVT +G
Sbjct: 119 MLLMYQYGARSVKCAVCNFVTSVG 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 = 97.8 bits (242), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 47/79 (59%), Positives = 58/79 (73%), Gaps = 1/79 (1%)

Query: 33  VPSP-SEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMY 91
           VP+P +EMAQ+VCG C  LL Y RGA  V+CSCC TVN  +EA+QV  V C +C +LLMY
Sbjct: 95  VPAPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLAMEANQVAHVNCGNCRMLLMY 154

Query: 92  PYGAPSVRCSSCCFVTEIG 110
            YGA SV+C+ C FVT +G
Sbjct: 155 QYGARSVKCAVCNFVTSVG 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 = 92.8 bits (229), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 43/85 (50%), Positives = 54/85 (63%), Gaps = 3/85 (3%)

Query: 27  IPPPLPVPSPSEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCA 86
           +PPP PV    EMA ++CG CR LL Y R A  V+CSCC TVN V   + +  V C  C 
Sbjct: 34  VPPPAPV---MEMAHLICGGCRTLLMYTRNADTVRCSCCSTVNLVRPVNNIAHVSCGQCR 90

Query: 87  VLLMYPYGAPSVRCSSCCFVTEIGV 111
             LMYPYGAPSV+C+ C ++T  G+
Sbjct: 91  TTLMYPYGAPSVKCAICHYITNTGM 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 = 87.4 bits (215), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 39/79 (49%), Positives = 51/79 (64%), Gaps = 1/79 (1%)

Query: 34  PSPS-EMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYP 92
           PSP  ++A ++CG CR LL Y R A  V+CSCC TVN V     +  + C  C  +LMYP
Sbjct: 36  PSPGMDIAHLICGGCRTLLMYTRNATSVRCSCCDTVNLVRPVSSIAHLNCGQCQTVLMYP 95

Query: 93  YGAPSVRCSSCCFVTEIGV 111
           YGAPSV+C+ C F+T  G+
Sbjct: 96  YGAPSVKCAICNFITNTGM 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 = 83.2 bits (204), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 41/83 (49%), Positives = 51/83 (61%), Gaps = 9/83 (10%)

Query: 38  EMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFV-----LEAH----QVGQVKCASCAVL 88
           +MA ++CG CR +L Y RGA  V+CSCCQT N V       AH    QV Q+ C  C   
Sbjct: 47  DMAHIICGGCRTMLMYTRGASSVRCSCCQTTNLVPAHSNQVAHAPSSQVAQINCGHCRTT 106

Query: 89  LMYPYGAPSVRCSSCCFVTEIGV 111
           LMYPYGA SV+C+ C FVT + +
Sbjct: 107 LMYPYGASSVKCAVCQFVTNVNM 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 = 61.6 bits (148), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 45/73 (61%)

Query: 37  SEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAP 96
           ++M++++C  C  LL Y RGA +++C  C  +N    A+Q+  + C  C   LM+P GA 
Sbjct: 40  ADMSELICSGCPTLLFYNRGASNIRCPSCNRLNSTRSANQIAHLTCGQCRTTLMHPPGAS 99

Query: 97  SVRCSSCCFVTEI 109
           +V+C++C +V  +
Sbjct: 100 TVQCATCRYVNHV 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	127
225470420	141	PREDICTED: protein LOL2 [Vitis vinifera]	0.685	0.617	0.816	9e-35
449457731	131	PREDICTED: protein LOL2-like [Cucumis sa	0.779	0.755	0.737	2e-32
356521358	128	PREDICTED: protein LOL2-like [Glycine ma	0.826	0.820	0.726	2e-32
198400327	236	zinc finger protein LSD2-like protein [C	0.811	0.436	0.467	3e-29
15234540	155	lsd one like 2 protein [Arabidopsis thal	0.724	0.593	0.628	8e-28
224077114	94	predicted protein [Populus trichocarpa]	0.543	0.734	0.826	1e-25
297803986	150	hypothetical protein ARALYDRAFT_492714 [	0.645	0.546	0.698	1e-25
125571157	1463	hypothetical protein OsJ_02587 [Oryza sa	0.574	0.049	0.712	7e-25
125526829	1413	hypothetical protein OsI_02839 [Oryza sa	0.574	0.051	0.712	8e-25
115438514	855	Os01g0612700 [Oryza sativa Japonica Grou	0.574	0.085	0.712	1e-24

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

 Score =  151 bits (381), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 71/87 (81%), Positives = 77/87 (88%)

Query: 25  QPIPPPLPVPSPSEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCAS 84
           + + P   +  PSEMAQMVCGSCRRLL+YP+G RHV+CSCCQTVNFVLEAHQVGQVKC S
Sbjct: 32  ETVAPTTTLKQPSEMAQMVCGSCRRLLSYPQGTRHVECSCCQTVNFVLEAHQVGQVKCGS 91

Query: 85  CAVLLMYPYGAPSVRCSSCCFVTEIGV 111
           CAVLLMYPYGAPSVRCSSC FVTEIGV
Sbjct: 92  CAVLLMYPYGAPSVRCSSCRFVTEIGV 118

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  143 bits (361), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 76/103 (73%), Positives = 87/103 (84%), Gaps = 4/103 (3%)

Query: 13  EENEEAGPPPGWQPIPPPLPVPSPS----EMAQMVCGSCRRLLAYPRGARHVKCSCCQTV 68
           E++E+ GPPPGW+PI P LP+P P     +MAQMVCG+CRRLL Y +GAR+V+CSCC TV
Sbjct: 7   EKDEDDGPPPGWEPITPSLPLPPPPQLSSDMAQMVCGTCRRLLKYLKGARYVQCSCCSTV 66

Query: 69  NFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIGV 111
           NFVLEAH+VGQVKC SCAVLLMYPYGA SVRCSSC  VTEIGV
Sbjct: 67  NFVLEAHEVGQVKCGSCAVLLMYPYGASSVRCSSCTSVTEIGV 109

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  143 bits (360), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 77/106 (72%), Positives = 85/106 (80%), Gaps = 1/106 (0%)

Query: 7   ESMENQEENEEAGPPPGWQPIPPPLPVPSP-SEMAQMVCGSCRRLLAYPRGARHVKCSCC 65
           +S +  +E ++ GPPPGWQP+P   P P   S  AQMVCGSCRRLL+YPRGA+HVKCSCC
Sbjct: 2   QSQQTVKEEDDEGPPPGWQPLPAQPPPPPRPSGWAQMVCGSCRRLLSYPRGAKHVKCSCC 61

Query: 66  QTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIGV 111
           QTVN VLEA QVGQVKC SCAVLLMYPYGA  VRCSSC FVTEIG 
Sbjct: 62  QTVNIVLEADQVGQVKCGSCAVLLMYPYGASQVRCSSCRFVTEIGA 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 =  132 bits (333), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 72/154 (46%), Positives = 85/154 (55%), Gaps = 51/154 (33%)

Query: 8   SMENQEENEEAGPPPGWQPIPPP------------------------------------- 30
           +++ +EE+++ GPPPGWQ IPP                                      
Sbjct: 60  AVKKEEEDDDDGPPPGWQSIPPSQPPTITPAPTTPPPPPAVASGSGNAAHTQLQQQPPKQ 119

Query: 31  --------------LPVPSPSEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQ 76
                         LP     EM QMVCGSC+ LL+YPRGAR V+C CCQTVN+ LE H+
Sbjct: 120 EGSAKAARTQLQQELPKQEAVEMGQMVCGSCQELLSYPRGARLVRCLCCQTVNYCLEEHE 179

Query: 77  VGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIG 110
           VGQVKC  CAVLLMYPYGAP V+CSSCCFVTEIG
Sbjct: 180 VGQVKCGGCAVLLMYPYGAPFVKCSSCCFVTEIG 213

Source: Camellia sinensis

Species: Camellia sinensis

Genus: Camellia

Family: Theaceae

Order: Ericales

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 =  128 bits (321), Expect = 8e-28,   Method: Compositional matrix adjust.
 Identities = 66/105 (62%), Positives = 79/105 (75%), Gaps = 13/105 (12%)

Query: 19  GPPPGWQP--IPPPLPV------PSPS-----EMAQMVCGSCRRLLAYPRGARHVKCSCC 65
           GPPPGW+   +PPP+        P+P+     E AQMVCGSCRRLL+Y RG++HVKCS C
Sbjct: 25  GPPPGWESAVLPPPIVTITAAVNPNPTTVEIPEKAQMVCGSCRRLLSYLRGSKHVKCSSC 84

Query: 66  QTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIG 110
           QTVN VLEA+QVGQV C +C +LLMYPYGAP+VRCSSC  VT+I 
Sbjct: 85  QTVNLVLEANQVGQVNCNNCKLLLMYPYGAPAVRCSSCNSVTDIS 129

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  120 bits (302), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 57/69 (82%), Positives = 62/69 (89%)

Query: 42  MVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCS 101
           MVCGSCRRLL+YP+G RHV+C CCQ +NFVLEAH+VGQVKC SC VLLMYPYGA SVRCS
Sbjct: 1   MVCGSCRRLLSYPKGVRHVQCQCCQMINFVLEAHEVGQVKCGSCDVLLMYPYGASSVRCS 60

Query: 102 SCCFVTEIG 110
           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 (302), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 58/83 (69%), Positives = 67/83 (80%), Gaps = 1/83 (1%)

Query: 28  PPPLPVPSPSEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAV 87
           P P  V  P E AQM+CGSCRRLL+Y RG++HVKCS CQTVN VLEA+QVGQV C +C +
Sbjct: 47  PNPTTVEIP-EKAQMICGSCRRLLSYLRGSKHVKCSSCQTVNLVLEANQVGQVNCNNCKL 105

Query: 88  LLMYPYGAPSVRCSSCCFVTEIG 110
           LLMYPYGAPSVRCSSC  +T+I 
Sbjct: 106 LLMYPYGAPSVRCSSCNSITDIS 128

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  118 bits (296), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 52/73 (71%), Positives = 62/73 (84%)

Query: 38   EMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPS 97
            E+ QMVCGSCR LLAY RGA +V C+CCQT+N+VLEAH+VG+V C  CA LLMYP+GAP+
Sbjct: 1367 EVGQMVCGSCRILLAYFRGAGYVHCTCCQTMNYVLEAHEVGKVHCGHCATLLMYPFGAPA 1426

Query: 98   VRCSSCCFVTEIG 110
            V+CS C FVTEIG
Sbjct: 1427 VKCSLCLFVTEIG 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 =  118 bits (296), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 52/73 (71%), Positives = 62/73 (84%)

Query: 38   EMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPS 97
            E+ QMVCGSCR LLAY RGA +V C+CCQT+N+VLEAH+VG+V C  CA LLMYP+GAP+
Sbjct: 1317 EVGQMVCGSCRILLAYFRGAGYVHCTCCQTMNYVLEAHEVGKVHCGHCATLLMYPFGAPA 1376

Query: 98   VRCSSCCFVTEIG 110
            V+CS C FVTEIG
Sbjct: 1377 VKCSLCLFVTEIG 1389

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115438514|ref|NP_001043558.1| Os01g0612700 [Oryza sativa Japonica Group] gi|113533089|dbj|BAF05472.1| Os01g0612700 [Oryza sativa Japonica Group]

 Score =  117 bits (294), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 52/73 (71%), Positives = 62/73 (84%)

Query: 38  EMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPS 97
           E+ QMVCGSCR LLAY RGA +V C+CCQT+N+VLEAH+VG+V C  CA LLMYP+GAP+
Sbjct: 759 EVGQMVCGSCRILLAYFRGAGYVHCTCCQTMNYVLEAHEVGKVHCGHCATLLMYPFGAPA 818

Query: 98  VRCSSCCFVTEIG 110
           V+CS C FVTEIG
Sbjct: 819 VKCSLCLFVTEIG 831

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

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	127
TAIR|locus:2119622	155	LOL2 "AT4G21610" [Arabidopsis	0.566	0.464	0.763	9.4e-27
UNIPROTKB|Q704V3	163	LOL5 "Protein LOL5" [Oryza sat	0.574	0.447	0.712	3.2e-26
UNIPROTKB|Q0J7V9	184	LSD1 "Protein LSD1" [Oryza sat	0.582	0.402	0.594	2.4e-21
UNIPROTKB|F8RP38	176	F8RP38 "Zinc finger protein LS	0.582	0.420	0.540	5.7e-20
TAIR|locus:2128639	210	LSD1 "LESION SIMULATING DISEAS	0.535	0.323	0.472	4.9e-14
FB|FBgn0039300	84	RpS27 "Ribosomal protein S27"	0.448	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:    38 EMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPS 97
             E AQMVCGSCRRLL+Y RG++HVKCS CQTVN VLEA+QVGQV C +C +LLMYPYGAP+
Sbjct:    57 EKAQMVCGSCRRLLSYLRGSKHVKCSSCQTVNLVLEANQVGQVNCNNCKLLLMYPYGAPA 116

Query:    98 VRCSSCCFVTEI 109
             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 = 296 (109.3 bits), Expect = 3.2e-26, P = 3.2e-26
 Identities = 52/73 (71%), Positives = 62/73 (84%)

Query:    38 EMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPS 97
             E+ QMVCGSCR LLAY RGA +V C+CCQT+N+VLEAH+VG+V C  CA LLMYP+GAP+
Sbjct:    67 EVGQMVCGSCRILLAYFRGAGYVHCTCCQTMNYVLEAHEVGKVHCGHCATLLMYPFGAPA 126

Query:    98 VRCSSCCFVTEIG 110
             V+CS C FVTEIG
Sbjct:   127 VKCSLCLFVTEIG 139

GO:0005634 "nucleus" evidence=IDA

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

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

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

 Score = 250 (93.1 bits), Expect = 2.4e-21, P = 2.4e-21
 Identities = 44/74 (59%), Positives = 54/74 (72%)

Query:    37 SEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAP 96
             +EMAQ+VCG C  LL Y RGA  V+CSCC TVN  +EA+QV  V C +C +LLMY YGA 
Sbjct:   100 TEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLAMEANQVAHVNCGNCRMLLMYQYGAR 159

Query:    97 SVRCSSCCFVTEIG 110
             SV+C+ C FVT +G
Sbjct:   160 SVKCAVCNFVTSVG 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:    38 EMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPS 97
             +M+Q+ CG CR LL Y RGA  V+CSCC TVN    ++QV  V CA+C   LMYPYGAPS
Sbjct:    40 DMSQLYCGGCRTLLMYTRGATSVRCSCCHTVNLAPVSNQVAHVPCANCRTTLMYPYGAPS 99

Query:    98 VRCSSCCFVTEIGV 111
             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:    41 QMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEA---HQVGQVKCASCAVLLMYPYGAPS 97
             Q+VC  CR LL YPRGA +V+C+ C T+N V      H +  + C  C  +LMY  GA S
Sbjct:     4 QLVCHGCRNLLMYPRGASNVRCALCNTINMVPPPPPPHDMAHIICGGCRTMLMYTRGASS 63

Query:    98 VRCSSCCFVTEI 109
             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:    48 RRLLAYPRGA-RHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCF 105
             +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        0.332   0.138   0.475    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      127        94   0.00091  102 3  11 21  0.37    29
                                                     29  0.42    31


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:  496 (53 KB)
  Total size of DFA:  109 KB (2075 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:  9.17u 0.09s 9.26t   Elapsed:  00:00:01
  Total cpu time:  9.17u 0.09s 9.26t   Elapsed:  00:00:01
  Start:  Fri May 10 14:14:46 2013   End:  Fri May 10 14:14:47 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

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	127
TIGR01053	31	TIGR01053, LSD1, zinc finger domain, LSD1 subclass	1e-09
pfam06943	25	pfam06943, zf-LSD1, LSD1 zinc finger	1e-07
pfam06943	25	pfam06943, zf-LSD1, LSD1 zinc finger	1e-05
TIGR01053	31	TIGR01053, LSD1, zinc finger domain, LSD1 subclass	0.002

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

 Score = 49.4 bits (118), Expect = 1e-09
 Identities = 21/31 (67%), Positives = 24/31 (77%)

Query: 41 QMVCGSCRRLLAYPRGARHVKCSCCQTVNFV 71
          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 = 44.5 bits (106), Expect = 1e-07
 Identities = 16/25 (64%), Positives = 18/25 (72%)

Query: 44 CGSCRRLLAYPRGARHVKCSCCQTV 68
          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 = 39.1 bits (92), Expect = 1e-05
 Identities = 16/25 (64%), Positives = 17/25 (68%)

Query: 82  CASCAVLLMYPYGAPSVRCSSCCFV 106
           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

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

 Score = 33.2 bits (76), Expect = 0.002
 Identities = 17/31 (54%), Positives = 19/31 (61%)

Query: 79  QVKCASCAVLLMYPYGAPSVRCSSCCFVTEI 109
           QV C  C  LLMYP GA SVRC+ C  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	127
TIGR01053	31	LSD1 zinc finger domain, LSD1 subclass. This model	99.54
PF06943	25	zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zin	99.49
TIGR01053	31	LSD1 zinc finger domain, LSD1 subclass. This model	99.46
PF06943	25	zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zin	99.35
PF09788	256	Tmemb_55A: Transmembrane protein 55A; InterPro: IP	97.08
PF10122	51	Mu-like_Com: Mu-like prophage protein Com; InterPr	95.07
KOG1546	362	consensus Metacaspase involved in regulation of ap	94.98
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	94.35
PLN00209	86	ribosomal protein S27; Provisional	94.22
PF01667	55	Ribosomal_S27e: Ribosomal protein S27; InterPro: I	94.18
PF10122	51	Mu-like_Com: Mu-like prophage protein Com; InterPr	94.12
PTZ00083	85	40S ribosomal protein S27; Provisional	94.07
PRK00415	59	rps27e 30S ribosomal protein S27e; Reviewed	93.84
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	93.71
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	92.91
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	92.45
PF11331	46	DUF3133: Protein of unknown function (DUF3133); In	92.37
PLN00162	761	transport protein sec23; Provisional	92.28
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	92.22
COG2051	67	RPS27A Ribosomal protein S27E [Translation, riboso	92.08
KOG1779	84	consensus 40s ribosomal protein S27 [Translation,	91.38
PF12773	50	DZR: Double zinc ribbon	91.01
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	89.04
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	88.32
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	86.22
PF04810	40	zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro:	85.03
PF04690	170	YABBY: YABBY protein; InterPro: IPR006780 YABBY pr	84.14
PF04810	40	zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro:	83.29
PF11331	46	DUF3133: Protein of unknown function (DUF3133); In	83.29
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	82.17
PF09788	256	Tmemb_55A: Transmembrane protein 55A; InterPro: IP	80.41

>TIGR01053 LSD1 zinc finger domain, LSD1 subclass

Probab=99.54  E-value=3.1e-15  Score=89.25  Aligned_cols=31  Identities=68%  Similarity=1.339  Sum_probs=22.8

Q ss_pred             eeeeccccceeeecCCCCeEEcCCCCCcccc
Q 033096           41 QMVCGSCRRLLAYPRGARHVKCSCCQTVNFV   71 (127)
Q Consensus        41 QLvCggCr~lL~YprGA~sVrCs~C~tVn~v   71 (127)
                      |++|++||++|+||+||++|||+.|++||.+
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            5677777777777777777777777777753

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=99.49  E-value=1.4e-14  Score=83.46  Aligned_cols=25  Identities=68%  Similarity=1.578  Sum_probs=20.4

Q ss_pred             eccccceeeecCCCCeEEcCCCCCc
Q 033096           44 CGSCRRLLAYPRGARHVKCSCCQTV   68 (127)
Q Consensus        44 CggCr~lL~YprGA~sVrCs~C~tV   68 (127)
                      |+|||++|+||+||+||||+.|++|
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            7788888888888888888888876

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=99.46  E-value=2.5e-14  Score=85.31  Aligned_cols=31  Identities=55%  Similarity=1.019  Sum_probs=29.6

Q ss_pred             eEEcCCCCeeeeeeCCCCeEeCCCCCCceee
Q 033096           79 QVKCASCAVLLMYPYGAPSVRCSSCCFVTEI  109 (127)
Q Consensus        79 ~v~Cg~Crt~L~yP~GA~SVrCa~C~tVT~V  109 (127)
                      |++|++||++|+||+||++|||+.|++||.|
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            6899999999999999999999999999976

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=99.35  E-value=4.1e-13  Score=77.34  Aligned_cols=25  Identities=64%  Similarity=1.334  Sum_probs=24.3

Q ss_pred             cCCCCeeeeeeCCCCeEeCCCCCCc
Q 033096           82 CASCAVLLMYPYGAPSVRCSSCCFV  106 (127)
Q Consensus        82 Cg~Crt~L~yP~GA~SVrCa~C~tV  106 (127)
                      |++||++||||+||+||||+.|++|
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 [].

>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=97.08  E-value=0.0021  Score=54.04  Aligned_cols=36  Identities=22%  Similarity=0.524  Sum_probs=30.0

Q ss_pred             ceeeEEcCCCCeeeeeeCCC--CeEeCCCCCCceeecc
Q 033096           76 QVGQVKCASCAVLLMYPYGA--PSVRCSSCCFVTEIGV  111 (127)
Q Consensus        76 e~a~v~Cg~Crt~L~yP~GA--~SVrCa~C~tVT~V~~  111 (127)
                      .+..++|++|+...+++.=.  ...||++|+.|+.|..
T Consensus       154 ~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKvSSVG~  191 (256)
T PF09788_consen  154 GSCRVICGHCSNTFLFNTLTSNTLARCPHCRKVSSVGP  191 (256)
T ss_pred             CceeEECCCCCCcEeccCCCCCccccCCCCceeccccc
Confidence            45688999999999998644  5679999999999984

>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=0.014  Score=38.74  Aligned_cols=34  Identities=18%  Similarity=0.553  Sum_probs=20.8

Q ss_pred             eEEcCCCCeeeeee--CCCCeEeCCCCCCceeeccC
Q 033096           79 QVKCASCAVLLMYP--YGAPSVRCSSCCFVTEIGVC  112 (127)
Q Consensus        79 ~v~Cg~Crt~L~yP--~GA~SVrCa~C~tVT~V~~~  112 (127)
                      .++|++|+.+|+..  ...-.|+|+-|.+++.|.+.
T Consensus         4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a~   39 (51)
T PF10122_consen    4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRAT   39 (51)
T ss_pred             ceeccchhHHHhhhcCccEEEEECCCCCccceEecc
Confidence            45667777666664  33346677777777766543

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

Probab=94.98  E-value=0.01  Score=51.93  Aligned_cols=30  Identities=37%  Similarity=0.701  Sum_probs=27.5

Q ss_pred             eEEcCCCCeeeeeeCCCCeEeCCCCCCceeec
Q 033096           79 QVKCASCAVLLMYPYGAPSVRCSSCCFVTEIG  110 (127)
Q Consensus        79 ~v~Cg~Crt~L~yP~GA~SVrCa~C~tVT~V~  110 (127)
                      .+.|. |++.++.|+||+. ||+.||+||.+.
T Consensus         4 ~~~~~-~~~p~~~pp~ar~-q~~~~~~~~~~~   33 (362)
T KOG1546|consen    4 LVGCN-CQRPMAPPPGARY-QCAGCHAVTQIA   33 (362)
T ss_pred             cccCC-CCCCCCCCCCCcc-cccccceeeeec
Confidence            45676 9999999999999 999999999987

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=94.35  E-value=0.045  Score=32.98  Aligned_cols=30  Identities=30%  Similarity=0.723  Sum_probs=19.8

Q ss_pred             eEEcCCCCeeeeee-----CCCCeEeCCCCCCcee
Q 033096           79 QVKCASCAVLLMYP-----YGAPSVRCSSCCFVTE  108 (127)
Q Consensus        79 ~v~Cg~Crt~L~yP-----~GA~SVrCa~C~tVT~  108 (127)
                      .+.|.+|.+.+-+|     .+...|||+.|+++=.
T Consensus         2 ~i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~   36 (37)
T PF13719_consen    2 IITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR   36 (37)
T ss_pred             EEECCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence            35666666666655     3466888888877643

>PLN00209 ribosomal protein S27; Provisional

Probab=94.22  E-value=0.053  Score=39.33  Aligned_cols=40  Identities=33%  Similarity=0.623  Sum_probs=33.6

Q ss_pred             eEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCeEe
Q 033096           59 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVR   99 (127)
Q Consensus        59 sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SVr   99 (127)
                      .|+|+.|..++.+.. +....+.|..|++.|..|.|....-
T Consensus        36 ~VkCp~C~n~q~VFS-hA~t~V~C~~Cg~~L~~PTGGKa~l   75 (86)
T PLN00209         36 DVKCQGCFNITTVFS-HSQTVVVCGSCQTVLCQPTGGKARL   75 (86)
T ss_pred             EEECCCCCCeeEEEe-cCceEEEccccCCEeeccCCCCeEe
Confidence            589999999998874 5567899999999999999977643

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

Probab=94.18  E-value=0.044  Score=36.59  Aligned_cols=39  Identities=33%  Similarity=0.684  Sum_probs=27.7

Q ss_pred             eEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCeE
Q 033096           59 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSV   98 (127)
Q Consensus        59 sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SV   98 (127)
                      .|+|+.|..++.+.. +....+.|..|++.|.-|.|-..-
T Consensus         7 ~VkCp~C~~~q~vFS-ha~t~V~C~~Cg~~L~~PtGGKa~   45 (55)
T PF01667_consen    7 DVKCPGCYNIQTVFS-HAQTVVKCVVCGTVLAQPTGGKAR   45 (55)
T ss_dssp             EEE-TTT-SEEEEET-T-SS-EE-SSSTSEEEEE-SSSEE
T ss_pred             EEECCCCCCeeEEEe-cCCeEEEcccCCCEecCCCCcCeE
Confidence            489999999998874 456788999999999999987653

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.

>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=94.12  E-value=0.029  Score=37.24  Aligned_cols=35  Identities=34%  Similarity=0.775  Sum_probs=29.1

Q ss_pred             cceeeeccccceeeecCCCC--eEEcCCCCCcccccC
Q 033096           39 MAQMVCGSCRRLLAYPRGAR--HVKCSCCQTVNFVLE   73 (127)
Q Consensus        39 ~sQLvCggCr~lL~YprGA~--sVrCs~C~tVn~v~~   73 (127)
                      +-.+.|+.|..||..--++.  .+.|+.|.|||.+..
T Consensus         2 ~~eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a   38 (51)
T PF10122_consen    2 LKEIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRA   38 (51)
T ss_pred             CcceeccchhHHHhhhcCccEEEEECCCCCccceEec
Confidence            34689999999999865555  789999999998763

>PTZ00083 40S ribosomal protein S27; Provisional

Probab=94.07  E-value=0.06  Score=38.95  Aligned_cols=40  Identities=30%  Similarity=0.599  Sum_probs=33.5

Q ss_pred             eEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCeEe
Q 033096           59 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVR   99 (127)
Q Consensus        59 sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SVr   99 (127)
                      .|+|+.|..++.+.. +....+.|..|++.|.-|.|....-
T Consensus        35 ~VkCp~C~n~q~VFS-hA~t~V~C~~Cg~~L~~PTGGKa~l   74 (85)
T PTZ00083         35 DVKCPGCSQITTVFS-HAQTVVLCGGCSSQLCQPTGGKAKL   74 (85)
T ss_pred             EEECCCCCCeeEEEe-cCceEEEccccCCEeeccCCCCeEe
Confidence            589999999998874 4567899999999999999977643

>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed

Probab=93.84  E-value=0.045  Score=37.18  Aligned_cols=38  Identities=32%  Similarity=0.631  Sum_probs=30.6

Q ss_pred             eEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCe
Q 033096           59 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPS   97 (127)
Q Consensus        59 sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~S   97 (127)
                      .|+|+.|..++.+.. +-...+.|..|++.|.-|.|-..
T Consensus        11 ~VkCp~C~n~q~vFs-ha~t~V~C~~Cg~~L~~PtGGKa   48 (59)
T PRK00415         11 KVKCPDCGNEQVVFS-HASTVVRCLVCGKTLAEPTGGKA   48 (59)
T ss_pred             EEECCCCCCeEEEEe-cCCcEEECcccCCCcccCCCcce
Confidence            488999999887763 44567889999999999988654

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

Probab=93.71  E-value=0.095  Score=32.33  Aligned_cols=30  Identities=27%  Similarity=0.505  Sum_probs=22.0

Q ss_pred             eEEcCCCCeeeeeeCCCCeEeCCCCCCcee
Q 033096           79 QVKCASCAVLLMYPYGAPSVRCSSCCFVTE  108 (127)
Q Consensus        79 ~v~Cg~Crt~L~yP~GA~SVrCa~C~tVT~  108 (127)
                      ...|.+|+..+.+......++|+.|++--.
T Consensus         3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~   32 (46)
T PRK00398          3 EYKCARCGREVELDEYGTGVRCPYCGYRIL   32 (46)
T ss_pred             EEECCCCCCEEEECCCCCceECCCCCCeEE
Confidence            456888888888877777788888876433

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=92.91  E-value=0.13  Score=30.24  Aligned_cols=13  Identities=31%  Similarity=0.721  Sum_probs=6.7

Q ss_pred             EEcCCCCCccccc
Q 033096           60 VKCSCCQTVNFVL   72 (127)
Q Consensus        60 VrCs~C~tVn~v~   72 (127)
                      +.|+.|.+.+.++
T Consensus         3 ~~CP~C~~~~~v~   15 (38)
T TIGR02098         3 IQCPNCKTSFRVV   15 (38)
T ss_pred             EECCCCCCEEEeC
Confidence            4555555554444

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.

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=92.45  E-value=0.19  Score=30.30  Aligned_cols=28  Identities=32%  Similarity=0.695  Sum_probs=16.6

Q ss_pred             eEEcCCCCeeeee-----eCCCCeEeCCCCCCc
Q 033096           79 QVKCASCAVLLMY-----PYGAPSVRCSSCCFV  106 (127)
Q Consensus        79 ~v~Cg~Crt~L~y-----P~GA~SVrCa~C~tV  106 (127)
                      .+.|.+|.+...+     |.+...|+|+.|+.+
T Consensus         2 ~i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~   34 (36)
T PF13717_consen    2 IITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHV   34 (36)
T ss_pred             EEECCCCCCEEeCCHHHCCCCCcEEECCCCCCE
Confidence            3455555555443     455667777777764

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

Probab=92.37  E-value=0.14  Score=33.21  Aligned_cols=38  Identities=24%  Similarity=0.572  Sum_probs=27.6

Q ss_pred             CCCCeEEcCCCCCcccccC-----ccceeeEEcCCCCeeeeee
Q 033096           55 RGARHVKCSCCQTVNFVLE-----AHQVGQVKCASCAVLLMYP   92 (127)
Q Consensus        55 rGA~sVrCs~C~tVn~v~~-----~~e~a~v~Cg~Crt~L~yP   92 (127)
                      .||+.|-|..|..+=.+|.     ...+..+.||.|...|.|-
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            4788888888877766663     2236788899999888763

>PLN00162 transport protein sec23; Provisional

Probab=92.28  E-value=0.15  Score=47.43  Aligned_cols=64  Identities=23%  Similarity=0.389  Sum_probs=47.1

Q ss_pred             hhhhhhhhcCCCCCCCCCCC-----------------CC---CCCCccccceeeecccccee----eecCCCCeEEcCCC
Q 033096           10 ENQEENEEAGPPPGWQPIPP-----------------PL---PVPSPSEMAQMVCGSCRRLL----AYPRGARHVKCSCC   65 (127)
Q Consensus        10 ~~~~~~~~~~~~~gw~~~~~-----------------~~---~~p~~~~~sQLvCggCr~lL----~YprGA~sVrCs~C   65 (127)
                      +-+|-|+.+|.|.-|..+|-                 |.   +..|-.+..-+.|..||..|    .+..+...++|..|
T Consensus         2 ~~~~~e~~~gvR~s~n~~P~t~~~~~~~~iPlg~v~tPl~~~~~vp~v~~~pvRC~~CraylNPf~~~d~~~~~W~C~~C   81 (761)
T PLN00162          2 DFAELEAIDGVRMSWNVWPSSKIEASKCVIPLAALYTPLKPLPELPVLPYDPLRCRTCRAVLNPYCRVDFQAKIWICPFC   81 (761)
T ss_pred             chhhhcccCceEeeeecCCCCHHHHhcCCCCeEEEEecCCcCCCCCcCCCCCCccCCCcCEECCceEEecCCCEEEccCC
Confidence            34455566999999998875                 11   12233445678999999987    35568899999999


Q ss_pred             CCcccccC
Q 033096           66 QTVNFVLE   73 (127)
Q Consensus        66 ~tVn~v~~   73 (127)
                      ...|.+|+
T Consensus        82 ~~~N~~P~   89 (761)
T PLN00162         82 FQRNHFPP   89 (761)
T ss_pred             CCCCCCch
Confidence            99998874

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=92.22  E-value=0.33  Score=28.49  Aligned_cols=31  Identities=23%  Similarity=0.514  Sum_probs=23.4

Q ss_pred             eEEcCCCCeeeeeeC-----CCCeEeCCCCCCceee
Q 033096           79 QVKCASCAVLLMYPY-----GAPSVRCSSCCFVTEI  109 (127)
Q Consensus        79 ~v~Cg~Crt~L~yP~-----GA~SVrCa~C~tVT~V  109 (127)
                      .+.|.+|++...++.     +...|+|+.|+++-.+
T Consensus         2 ~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~~   37 (38)
T TIGR02098         2 RIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWYA   37 (38)
T ss_pred             EEECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEEe
Confidence            577999999888884     2347999999886543

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=92.08  E-value=0.21  Score=34.90  Aligned_cols=39  Identities=31%  Similarity=0.586  Sum_probs=30.7

Q ss_pred             eEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCeE
Q 033096           59 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSV   98 (127)
Q Consensus        59 sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SV   98 (127)
                      .|+|+.|...+-+.. +-...+.|..|+++|..|.|-.+.
T Consensus        19 ~VkCpdC~N~q~vFs-hast~V~C~~CG~~l~~PTGGka~   57 (67)
T COG2051          19 RVKCPDCGNEQVVFS-HASTVVTCLICGTTLAEPTGGKAK   57 (67)
T ss_pred             EEECCCCCCEEEEec-cCceEEEecccccEEEecCCCeEE
Confidence            488999988887763 445678899999999999887653

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

Probab=91.38  E-value=0.24  Score=35.88  Aligned_cols=40  Identities=30%  Similarity=0.620  Sum_probs=33.1

Q ss_pred             eEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCeEe
Q 033096           59 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVR   99 (127)
Q Consensus        59 sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SVr   99 (127)
                      -|+|+.|--||-+.+ +...-+.|.+|.+.|.-|.|.+.+-
T Consensus        34 ~VkC~gc~~iT~vfS-HaqtvVvc~~c~~il~~~tggra~l   73 (84)
T KOG1779|consen   34 DVKCPGCFKITTVFS-HAQTVVVCEGCSTILCQPTGGKAKL   73 (84)
T ss_pred             EEEcCCceEEEEEee-cCceEEEcCCCceEEEEecCCcEEe
Confidence            489999999998875 4455788999999999999988764

>PF12773 DZR: Double zinc ribbon

Probab=91.01  E-value=0.12  Score=31.76  Aligned_cols=39  Identities=26%  Similarity=0.480  Sum_probs=27.7

Q ss_pred             cCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCeEeCCCCCCce
Q 033096           62 CSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVT  107 (127)
Q Consensus        62 Cs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SVrCa~C~tVT  107 (127)
                      |+.|.+.+.      .....|.+|++.|. ......+.|+.|++.+
T Consensus         1 Cp~Cg~~~~------~~~~fC~~CG~~l~-~~~~~~~~C~~Cg~~~   39 (50)
T PF12773_consen    1 CPHCGTPNP------DDAKFCPHCGTPLP-PPDQSKKICPNCGAEN   39 (50)
T ss_pred             CCCcCCcCC------ccccCChhhcCChh-hccCCCCCCcCCcCCC
Confidence            566777653      23566888888888 5566677888888863

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

Probab=89.04  E-value=0.56  Score=28.84  Aligned_cols=27  Identities=22%  Similarity=0.575  Sum_probs=15.0

Q ss_pred             eeeeccccceeeecCCCCeEEcCCCCC
Q 033096           41 QMVCGSCRRLLAYPRGARHVKCSCCQT   67 (127)
Q Consensus        41 QLvCggCr~lL~YprGA~sVrCs~C~t   67 (127)
                      ...|..|...+.|......++|+.|.+
T Consensus         3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~   29 (46)
T PRK00398          3 EYKCARCGREVELDEYGTGVRCPYCGY   29 (46)
T ss_pred             EEECCCCCCEEEECCCCCceECCCCCC
Confidence            345566666665555555555555543

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=88.32  E-value=0.5  Score=28.39  Aligned_cols=30  Identities=27%  Similarity=0.583  Sum_probs=17.7

Q ss_pred             EEcCCCCCcccccCc---cceeeEEcCCCCeee
Q 033096           60 VKCSCCQTVNFVLEA---HQVGQVKCASCAVLL   89 (127)
Q Consensus        60 VrCs~C~tVn~v~~~---~e~a~v~Cg~Crt~L   89 (127)
                      ++|+.|++.-.+++.   ..-..+.|+.|+...
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            567777766665531   334466677776543

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

Probab=86.22  E-value=0.75  Score=31.33  Aligned_cols=52  Identities=29%  Similarity=0.607  Sum_probs=38.3

Q ss_pred             cceeeeccccceeeecCC-CCeEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCeEeCCCCCCc
Q 033096           39 MAQMVCGSCRRLLAYPRG-ARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFV  106 (127)
Q Consensus        39 ~sQLvCggCr~lL~YprG-A~sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SVrCa~C~tV  106 (127)
                      +.-.+|.+|...| .|++ |+.--|+.|..+..         .+|..||..-      ...+|+.|++.
T Consensus         5 ~~~~~CtSCg~~i-~~~~~~~~F~CPnCG~~~I---------~RC~~CRk~~------~~Y~CP~CGF~   57 (59)
T PRK14890          5 MEPPKCTSCGIEI-APREKAVKFLCPNCGEVII---------YRCEKCRKQS------NPYTCPKCGFE   57 (59)
T ss_pred             ccCccccCCCCcc-cCCCccCEeeCCCCCCeeE---------eechhHHhcC------CceECCCCCCc
Confidence            4455799999888 4555 89999999987653         3488888753      46788888764

>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=85.03  E-value=0.7  Score=28.12  Aligned_cols=30  Identities=30%  Similarity=0.656  Sum_probs=11.6

Q ss_pred             eecccccee----eecCCCCeEEcCCCCCccccc
Q 033096           43 VCGSCRRLL----AYPRGARHVKCSCCQTVNFVL   72 (127)
Q Consensus        43 vCggCr~lL----~YprGA~sVrCs~C~tVn~v~   72 (127)
                      .|..|+..|    .+..+.....|..|++.|.++
T Consensus         4 rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~lp   37 (40)
T PF04810_consen    4 RCRRCRAYLNPFCQFDDGGKTWICNFCGTKNPLP   37 (40)
T ss_dssp             B-TTT--BS-TTSEEETTTTEEEETTT--EEE--
T ss_pred             ccCCCCCEECCcceEcCCCCEEECcCCCCcCCCC
Confidence            455555443    244455555555555555444

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 ....

>PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ]

Probab=84.14  E-value=0.77  Score=36.57  Aligned_cols=38  Identities=29%  Similarity=0.473  Sum_probs=25.7

Q ss_pred             eEEcCCCCCccccc----CccceeeEEcCCCCeeeeeeCCCC
Q 033096           59 HVKCSCCQTVNFVL----EAHQVGQVKCASCAVLLMYPYGAP   96 (127)
Q Consensus        59 sVrCs~C~tVn~v~----~~~e~a~v~Cg~Crt~L~yP~GA~   96 (127)
                      .|+|.-|+||=+|.    ....+-.|+||+|-.+|.+--++.
T Consensus        12 YVhCnFC~TiLaVsVP~ssL~~~VTVRCGHCtNLLSVNm~~~   53 (170)
T PF04690_consen   12 YVHCNFCNTILAVSVPCSSLLKTVTVRCGHCTNLLSVNMRAL   53 (170)
T ss_pred             EEEcCCcCeEEEEecchhhhhhhhceeccCccceeeeecccc
Confidence            47777788777664    134556778888888887655444

>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=83.29  E-value=1.2  Score=27.08  Aligned_cols=31  Identities=19%  Similarity=0.502  Sum_probs=16.0

Q ss_pred             EcCCCCeee----eeeCCCCeEeCCCCCCceeecc
Q 033096           81 KCASCAVLL----MYPYGAPSVRCSSCCFVTEIGV  111 (127)
Q Consensus        81 ~Cg~Crt~L----~yP~GA~SVrCa~C~tVT~V~~  111 (127)
                      +|.+|++.|    .+-.+..+-.|..|.+.|.++.
T Consensus         4 rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~lp~   38 (40)
T PF04810_consen    4 RCRRCRAYLNPFCQFDDGGKTWICNFCGTKNPLPP   38 (40)
T ss_dssp             B-TTT--BS-TTSEEETTTTEEEETTT--EEE--G
T ss_pred             ccCCCCCEECCcceEcCCCCEEECcCCCCcCCCCC
Confidence            445555443    2335778889999999888864

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 ....

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

Probab=83.29  E-value=0.63  Score=30.12  Aligned_cols=31  Identities=35%  Similarity=0.674  Sum_probs=23.4

Q ss_pred             eEEcCCCCeeeeeeCC-------CCeEeCCCCCCceee
Q 033096           79 QVKCASCAVLLMYPYG-------APSVRCSSCCFVTEI  109 (127)
Q Consensus        79 ~v~Cg~Crt~L~yP~G-------A~SVrCa~C~tVT~V  109 (127)
                      -++|.+|..+|.+|.+       ...+||..|..|-.+
T Consensus         6 Fv~C~~C~~lLqlP~~~~~~~k~~~klrCGaCs~vl~~   43 (46)
T PF11331_consen    6 FVVCSSCFELLQLPAKFSLSKKNQQKLRCGACSEVLSF   43 (46)
T ss_pred             EeECccHHHHHcCCCccCCCccceeEEeCCCCceeEEE
Confidence            5778888888888853       457788888877654

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=82.17  E-value=1.6  Score=26.21  Aligned_cols=29  Identities=21%  Similarity=0.591  Sum_probs=18.4

Q ss_pred             EEcCCCCCcccccC---ccceeeEEcCCCCee
Q 033096           60 VKCSCCQTVNFVLE---AHQVGQVKCASCAVL   88 (127)
Q Consensus        60 VrCs~C~tVn~v~~---~~e~a~v~Cg~Crt~   88 (127)
                      +.|+.|++.-.+++   ...-..+.|+.|+..
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            56777777766653   234456777777754

>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=80.41  E-value=2  Score=36.47  Aligned_cols=36  Identities=19%  Similarity=0.547  Sum_probs=30.1

Q ss_pred             cccceeeeccccceeeecCCC--CeEEcCCCCCccccc
Q 033096           37 SEMAQMVCGSCRRLLAYPRGA--RHVKCSCCQTVNFVL   72 (127)
Q Consensus        37 ~~~sQLvCggCr~lL~YprGA--~sVrCs~C~tVn~v~   72 (127)
                      ..+..++|+.|+...+|+.=.  +-.||+.|..+.+|-
T Consensus       153 p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKvSSVG  190 (256)
T PF09788_consen  153 PGSCRVICGHCSNTFLFNTLTSNTLARCPHCRKVSSVG  190 (256)
T ss_pred             CCceeEECCCCCCcEeccCCCCCccccCCCCceecccc
Confidence            457899999999999998644  567999999998874

---

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	127
1qxf_A	66	GR2, 30S ribosomal protein S27E; structural genomi	94.79
3j20_W	63	30S ribosomal protein S27E; archaea, archaeal, KIN	94.48
2xzm_6	81	RPS27E; ribosome, translation; 3.93A {Tetrahymena	94.02
3u5c_b	82	RP61, YS20, 40S ribosomal protein S27-A; translati	93.3
3iz6_X	86	40S ribosomal protein S27 (S27E); eukaryotic ribos	92.11
1gh9_A	71	8.3 kDa protein (gene MTH1184); beta+alpha complex	86.26
2yrc_A	59	Protein transport protein SEC23A; zinc binding, co	85.14

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

Probab=94.79  E-value=0.02  Score=38.68  Aligned_cols=39  Identities=28%  Similarity=0.601  Sum_probs=33.0

Q ss_pred             eEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCeE
Q 033096           59 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSV   98 (127)
Q Consensus        59 sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SV   98 (127)
                      .|+|+.|..++.+.. +....+.|..|++.|.-|.|-.+.
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            599999999998874 445688999999999999997653

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

Probab=94.48  E-value=0.024  Score=37.98  Aligned_cols=39  Identities=31%  Similarity=0.687  Sum_probs=32.3

Q ss_pred             eEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCeE
Q 033096           59 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSV   98 (127)
Q Consensus        59 sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SV   98 (127)
                      .|+|+.|..++.+.+ +....+.|..|++.|.-|.|-..-
T Consensus        15 ~VkCp~C~~~q~VFS-ha~t~V~C~~Cgt~L~~PTGGKa~   53 (63)
T 3j20_W           15 RVKCIDCGNEQIVFS-HPATKVRCLICGATLVEPTGGKGI   53 (63)
T ss_dssp             EEECSSSCCEEEEES-SCSSCEECSSSCCEEEECCSSSCE
T ss_pred             EEECCCCCCeeEEEe-cCCeEEEccCcCCEEecCCCCcEE
Confidence            589999999998874 446688999999999999987643

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

Probab=94.02  E-value=0.042  Score=38.41  Aligned_cols=40  Identities=25%  Similarity=0.658  Sum_probs=32.6

Q ss_pred             eEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCeEe
Q 033096           59 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVR   99 (127)
Q Consensus        59 sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SVr   99 (127)
                      .|+|+.|..++.+.. +....+.|..|++.|..|.|..+.-
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            589999999998874 4456788999999999999876543

>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=93.30  E-value=0.037  Score=38.78  Aligned_cols=41  Identities=32%  Similarity=0.656  Sum_probs=33.2

Q ss_pred             eEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCeEeC
Q 033096           59 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRC  100 (127)
Q Consensus        59 sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SVrC  100 (127)
                      .|+|+.|..++.|.. +....+.|.+|++.|.-|.|-..--=
T Consensus        34 ~VkCp~C~~~q~VFS-ha~t~V~C~~Cg~~L~~PTGGKa~l~   74 (82)
T 3u5c_b           34 DVKCPGCLNITTVFS-HAQTAVTCESCSTILCTPTGGKAKLS   74 (82)
T ss_dssp             EEECTTSCSCEEEES-BCSSCCCCSSSCCCCEECCSSBCEEC
T ss_pred             EEECCCCCCeeEEEe-cCCeEEEccccCCEEeccCCCCeEec
Confidence            589999999998874 44567889999999999998765443

>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=92.11  E-value=0.049  Score=38.44  Aligned_cols=40  Identities=30%  Similarity=0.606  Sum_probs=32.6

Q ss_pred             eEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCeEe
Q 033096           59 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVR   99 (127)
Q Consensus        59 sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SVr   99 (127)
                      .|+|+.|..++.+.. +....+.|.+|++.|.-|.|-.+--
T Consensus        36 ~VkCp~C~~~~~VFS-hA~t~V~C~~CgtvL~~PTGGKa~l   75 (86)
T 3iz6_X           36 DVKCQGCFNITTVFS-HSQTVVVCPGCQTVLCQPTGGKARL   75 (86)
T ss_dssp             EEECTTTCCEEEEET-TCSSCCCCSSSCCCCSCCCSSSCCC
T ss_pred             EEECCCCCCeeEEEe-cCCcEEEccCCCCEeecCCCCCEEe
Confidence            499999999998874 4456788999999999999876543

>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=86.26  E-value=0.79  Score=30.70  Aligned_cols=34  Identities=21%  Similarity=0.382  Sum_probs=29.1

Q ss_pred             eeeEEcCCCCeeeeeeCCCCeEeCCCCCCceeeccC
Q 033096           77 VGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIGVC  112 (127)
Q Consensus        77 ~a~v~Cg~Crt~L~yP~GA~SVrCa~C~tVT~V~~~  112 (127)
                      +.-+.|. |+..+..-.|+.+.+|+ |++..+|...
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            3567899 99999999999999998 9998888644

>2yrc_A Protein transport protein SEC23A; zinc binding, copii, coat protein complex-II, endoplasmic reticulum, golgi, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2yrd_A

Probab=85.14  E-value=0.54  Score=30.31  Aligned_cols=39  Identities=26%  Similarity=0.421  Sum_probs=29.4

Q ss_pred             Cccccceeeecc--cccee----eecCCCCeEEcCCCCCcccccC
Q 033096           35 SPSEMAQMVCGS--CRRLL----AYPRGARHVKCSCCQTVNFVLE   73 (127)
Q Consensus        35 ~~~~~sQLvCgg--Cr~lL----~YprGA~sVrCs~C~tVn~v~~   73 (127)
                      .|.+..-+.|..  ||..|    .+..|+...+|..|...|.+++
T Consensus         3 ~~~~~~pvRC~r~~CraylNP~~~~~~~~~~W~C~~C~~~N~~P~   47 (59)
T 2yrc_A            3 SGSSGEPVLCSRTTCRAVLNPLCQVDYRAKLWACNFCYQRNQFPP   47 (59)
T ss_dssp             CSSCCCCCBCSCTTTCCBCCTTSEEEGGGTEEECSSSCCEEECCS
T ss_pred             ccCCCCCcccCCCCCCeEECCceEEECCCCEEEcccCCCcCCCCH
Confidence            355666778887  88876    4666778888888888888774

---

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	127
d1qxfa_	58	Ribosomal protein S27e {Archaeon Archaeoglobus ful	94.85
d1pd0a5	85	Sec24 {Baker's yeast (Saccharomyces cerevisiae) [T	82.97

>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=94.85  E-value=0.0085  Score=37.98  Aligned_cols=38  Identities=29%  Similarity=0.636  Sum_probs=32.5

Q ss_pred             eEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCe
Q 033096           59 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPS   97 (127)
Q Consensus        59 sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~S   97 (127)
                      .|+|+.|..++-+.+ +....+.|..|++.|..|.|...
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            589999999998874 44678999999999999999764

>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=82.97  E-value=0.51  Score=30.15  Aligned_cols=34  Identities=24%  Similarity=0.548  Sum_probs=27.5

Q ss_pred             ceeeecccccee----eecCCCCeEEcCCCCCcccccC
Q 033096           40 AQMVCGSCRRLL----AYPRGARHVKCSCCQTVNFVLE   73 (127)
Q Consensus        40 sQLvCggCr~lL----~YprGA~sVrCs~C~tVn~v~~   73 (127)
                      .=+.|..||..|    .+..+...+.|..|++.|.+++
T Consensus        12 ~i~RC~~C~ayiNP~~~~~~~g~~w~C~~C~~~N~~p~   49 (85)
T d1pd0a5          12 LIVRCRRCRSYMNPFVTFIEQGRRWRCNFCRLANDVPM   49 (85)
T ss_dssp             CCCBCSSSCCBCCTTCEEETTTTEEECTTTCCEEECCG
T ss_pred             CCccccCCcCEECCceEEeCCCCEEECCCCCcccCCCH
Confidence            446699999877    3777888899999999998774