Citrus Sinensis ID: 026941

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230
Protein Sequence
MPLRGFHLIHNEIKKPNQTKQIKLSFFIFLFLFIYINHTITQLSIDFDFSNDSILLSLQGMQSQLVCSGCRSVLLYPRGATNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNVNMANARVPLPANRPNGTAIPGTLPSTSMTQTVVVENPMSVDESGKLVSNVVVGVSTEKK
Secondary Structure (PSIPRED)
ccccccccccccccccccccccEEEHHHHHHHHHHHHHHccccccccccccccccccccccccEEEcccccccEEccccccEEEcccccccccccccccccEEEEEcccccEEEEcccccEEEcccccccccccccccccEEEccccccEEEEcccccEEEcccccEEEEEcccccccccccccccccccccccccccccEEEEEEccccccccccEEEEEEEEEEEccc
Secondary Structure Prediction (SSPRO)
cccccEEEEEcccccccccccEEEHHHHHHHHHEHHHHccccccccccccccHHHHHHHcHHHHHEHccccEEEEcccccccEEccccccccccccccHHHcEEEEccccEEEEEcccccEEEcccccEEEcccccccEEEEEcccccEEEEEccccccEEcccEcEEcccccccccccccccccccccccccccccccccEEEEEccccccccccEEEEEEEEEccccc
Coil and Loop (DISEMBL)
mplrgfhlihneikkpnqtkqIKLSFFIFLFLFIYINHTITqlsidfdfsndSILLSLQGMQSQlvcsgcrsvllyprgatNVCCALCntitsvpipgmEMAQLICGGCRTllmytrgatsvrcscchtvnlapapnqfahiicghcrttlmyphgapsvkcAVCQYVTNvnmanarvplpanrpngtaipgtlpstsmtQTVVvenpmsvdesgkLVSNVVVGVSTEKK
Flexible Loop (DISEMBL)
mplrgfhlihneikkpnqtkQIKLSFFIFLFLFIYINHTITQLSIDFDFSNDSILLSLQGMQSQLVCSGCRSVLLYPRGATNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNVNMANARVPLPANRPNGTAIPGTLPSTSMTQTVVVENpmsvdesgklvsnvvvgvstekk
Low Complexity Region (SEG)
MPLRGFHLIHNEIKKPNQTKQIKLSffiflflfiYINHTITQLSIDFDFSNDSILLSLQGMQSQLVCSGCRSVLLYPRGATNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNVNMANARVPLPANRPNGTAIPGTLPSTSMTQTVVVENPMSVDESGKLVSNVVVGVSTEKK
Disordered region (IsUnstruct)
*****FHLIHNEIKKPNQTKQIKLSFFIFLFLFIYINHTITQLSIDFDFSNDSILLSLQGMQSQLVCSGCRSVLLYPRGATNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNVNMANARV****************************************************
Disordered Region (DISOPRED)
**LRGFH******************FFIFLFLFIYINHTITQLSIDFDFS*************QLVCSGCRSVLLYPRGATNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNV********************************VVENPMSVDESGKLVSNVVVGVST***
Disordered Region (DISEMBL)
MPLRGFHLIHNEIKKPNQTKQIKLSFFIFLFLFIYINHTITQLSIDFDFSNDSILLSLQGMQSQLVCSGCRSVLLYPRGATNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNVNMANARVPLPANRPNGTAIPGTLPSTSMTQTVVVENPMSVDESGKLVSNVVVGVSTEKK
Disordered Region (DISPRO)
*PLRGFHLIHNEIKKPNQTKQIKLSFFIFLFLFIYINHTITQLSIDFDFSNDSILLSLQGMQSQLVCSGCRSVLLYPRGATNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNVN***************************TQTVVVENPMSVDESGKLVSNVVVGVST***
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPLRGFHLIHNEIKKPNQTKQIKLSFFIFLFLFIYINHTITQLSIDFDFSNDSILLSLQGMQSQLVCSGCRSVLLYPRGATNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNVNMANARVPLPANRPNGTAIPGTLPSTSMTQTVVVENPMSVDESGKLVSNVVVGVSTEKK
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	230	2.2.26 [Sep-21-2011]
P94077	189	Protein LSD1 OS=Arabidops	yes	no	0.760	0.925	0.693	1e-60
Q6ASS2	186	Protein LOL3 OS=Oryza sat	yes	no	0.730	0.903	0.620	3e-53
Q2QMB3	172	Protein LOL2 OS=Oryza sat	no	no	0.734	0.982	0.627	3e-52
Q0J7V9	184	Protein LSD1 OS=Oryza sat	no	no	0.491	0.614	0.716	8e-43
Q93ZB1	154	Protein LOL1 OS=Arabidops	no	no	0.478	0.714	0.718	2e-40
Q84UR0	147	Protein LOL4 OS=Oryza sat	no	no	0.634	0.993	0.491	9e-38
Q704V3	163	Protein LOL5 OS=Oryza sat	no	no	0.4	0.564	0.451	3e-18
O65426	155	Protein LOL2 OS=Arabidops	no	no	0.473	0.703	0.437	4e-18
Q69UP7	147	Protein LOL1 OS=Oryza sat	no	no	0.165	0.258	0.684	1e-09

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

 Score =  232 bits (592), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 131/189 (69%), Positives = 146/189 (77%), Gaps = 14/189 (7%)

Query: 56  LSLQGMQSQLVCSGCRSVLLYPRGATNVCCALCNTITSVPIPGM--EMAQLICGGCRTLL 113
           + +  MQ QLVC GCR++L+YPRGA+NV CALCNTI  VP P    +MA +ICGGCRT+L
Sbjct: 1   MKVADMQDQLVCHGCRNLLMYPRGASNVRCALCNTINMVPPPPPPHDMAHIICGGCRTML 60

Query: 114 MYTRGATSVRCSCCHTVNLAPA-PNQFAH--------IICGHCRTTLMYPHGAPSVKCAV 164
           MYTRGA+SVRCSCC T NL PA  NQ AH        I CGHCRTTLMYP+GA SVKCAV
Sbjct: 61  MYTRGASSVRCSCCQTTNLVPAHSNQVAHAPSSQVAQINCGHCRTTLMYPYGASSVKCAV 120

Query: 165 CQYVTNVNMANARVPLPANRPNGTA---IPGTLPSTSMTQTVVVENPMSVDESGKLVSNV 221
           CQ+VTNVNM+N RVPLP NRPNGTA      T    S TQTVVVENPMSVDESGKLVSNV
Sbjct: 121 CQFVTNVNMSNGRVPLPTNRPNGTACPPSTSTSTPPSQTQTVVVENPMSVDESGKLVSNV 180

Query: 222 VVGVSTEKK 230
           VVGV+T+KK
Sbjct: 181 VVGVTTDKK 189

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

 Score =  208 bits (529), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 116/187 (62%), Positives = 128/187 (68%), Gaps = 19/187 (10%)

Query: 61  MQSQLVCSGCRSVLLYPRGATNVCCALCNTITSVPIPG--MEMAQLICGGCRTLLMYTRG 118
           MQSQ+VC GCRSVL YP GA +VCCALC  IT+VP P   MEMA LICGGCRTLLMYTR 
Sbjct: 1   MQSQIVCHGCRSVLRYPSGAPSVCCALCQAITTVPPPAPVMEMAHLICGGCRTLLMYTRN 60

Query: 119 ATSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNVNMANARV 178
           A +VRCSCC TVNL    N  AH+ CG CRTTLMYP+GAPSVKCA+C Y+TN  M N   
Sbjct: 61  ADTVRCSCCSTVNLVRPVNNIAHVSCGQCRTTLMYPYGAPSVKCAICHYITNTGM-NTVA 119

Query: 179 PLPANRPNGT--------------AIPGTLPSTSMTQ--TVVVENPMSVDESGKLVSNVV 222
           P P+  P  +              A P T   TS  Q  TVVVENPM+VDE GKLVSNVV
Sbjct: 120 PTPSPMPTSSGSSYNAPPSGSSYNAPPPTSAPTSRPQNVTVVVENPMTVDEKGKLVSNVV 179

Query: 223 VGVSTEK 229
           VGV+T K
Sbjct: 180 VGVTTGK 186

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 =  205 bits (521), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 108/172 (62%), Positives = 130/172 (75%), Gaps = 3/172 (1%)

Query: 61  MQSQLVCSGCRSVLLYPRGATNVCCALCNTITS-VPIPGMEMAQLICGGCRTLLMYTRGA 119
           MQSQ+VC GCR++LLYPRGA +VCCA+C+ ++S  P PGM++A LICGGCRTLLMYTR A
Sbjct: 1   MQSQIVCHGCRNILLYPRGAPSVCCAVCHAVSSTAPSPGMDIAHLICGGCRTLLMYTRNA 60

Query: 120 TSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNVNMANARVP 179
           TSVRCSCC TVNL    +  AH+ CG C+T LMYP+GAPSVKCA+C ++TN  M   R  
Sbjct: 61  TSVRCSCCDTVNLVRPVSSIAHLNCGQCQTVLMYPYGAPSVKCAICNFITNTGMNTMR-H 119

Query: 180 LPANRPNGTAIPGTLPST-SMTQTVVVENPMSVDESGKLVSNVVVGVSTEKK 230
           LP N  + TA   + P+T S   TVVVENPM+VD  GKLVSNVVVGV+T  K
Sbjct: 120 LPPNGTSYTAPSTSAPTTQSQNVTVVVENPMTVDAKGKLVSNVVVGVTTGGK 171

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

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  173 bits (439), Expect = 8e-43,   Method: Compositional matrix adjust.
 Identities = 81/113 (71%), Positives = 96/113 (84%)

Query: 60  GMQSQLVCSGCRSVLLYPRGATNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGA 119
           G QSQLVCSGCR++L+YP GAT+VCCA+C+T+T+VP PG EMAQL+CGGC TLLMY RGA
Sbjct: 61  GAQSQLVCSGCRNLLMYPAGATSVCCAVCSTVTAVPAPGTEMAQLVCGGCHTLLMYIRGA 120

Query: 120 TSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNVN 172
           TSV+CSCCHTVNLA   NQ AH+ CG+CR  LMY +GA SVKCAVC +VT+V 
Sbjct: 121 TSVQCSCCHTVNLAMEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTSVG 173

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

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  166 bits (419), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 79/110 (71%), Positives = 93/110 (84%)

Query: 62  QSQLVCSGCRSVLLYPRGATNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATS 121
           QSQLVCSGCR++L+YP GAT+VCCA+CN +T+VP PG EMAQL+CGGC TLLMY RGATS
Sbjct: 32  QSQLVCSGCRNLLMYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATS 91

Query: 122 VRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNV 171
           V+CSCCHTVNLA   NQ AH+ CG+C   LMY +GA SVKCAVC +VT+V
Sbjct: 92  VQCSCCHTVNLALEANQVAHVNCGNCMMLLMYQYGARSVKCAVCNFVTSV 141

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

 Score =  157 bits (396), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 84/171 (49%), Positives = 110/171 (64%), Gaps = 25/171 (14%)

Query: 61  MQSQLVCSGCRSVLLYPRGATNVCCALCNTITSV-PIPGMEMAQLICGGCRTLLMYTRGA 119
           MQ QL+CSGCR V+ Y RG   VCC  CNT+T+V P    +M++LIC GC TLL Y RGA
Sbjct: 1   MQDQLICSGCRRVVQYRRGVAGVCCPGCNTLTAVNPSAVADMSELICSGCPTLLFYNRGA 60

Query: 120 TSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNVNMANARVP 179
           +++RC  C+ +N   + NQ AH+ CG CRTTLM+P GA +V+CA C+YV +V  A     
Sbjct: 61  SNIRCPSCNRLNSTRSANQIAHLTCGQCRTTLMHPPGASTVQCATCRYVNHVRDA----- 115

Query: 180 LPANRPNGTAIPGTLPSTSMTQTVVVENPMSVDESGKLVSNVVVGVSTEKK 230
               RP               QTV+VENP ++D+ GKLVSNVVVGV++ K+
Sbjct: 116 ----RP---------------QTVLVENPKTLDDKGKLVSNVVVGVTSWKR 147

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

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score = 92.0 bits (227), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 42/93 (45%), Positives = 56/93 (60%)

Query: 100 EMAQLICGGCRTLLMYTRGATSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPS 159
           E+ Q++CG CR LL Y RGA  V C+CC T+N     ++   + CGHC T LMYP GAP+
Sbjct: 67  EVGQMVCGSCRILLAYFRGAGYVHCTCCQTMNYVLEAHEVGKVHCGHCATLLMYPFGAPA 126

Query: 160 VKCAVCQYVTNVNMANARVPLPANRPNGTAIPG 192
           VKC++C +VT +   N R  L   +P  T   G
Sbjct: 127 VKCSLCLFVTEIGERNVRRRLSIEQPTRTNSSG 159

Involved in plant growth and disease resistance.

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score = 91.7 bits (226), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 49/112 (43%), Positives = 67/112 (59%), Gaps = 3/112 (2%)

Query: 69  GCRSVLLYPRGATNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATSVRCSCCH 128
           G  S +L P   T +  A+    T+V IP  E AQ++CG CR LL Y RG+  V+CS C 
Sbjct: 29  GWESAVLPPPIVT-ITAAVNPNPTTVEIP--EKAQMVCGSCRRLLSYLRGSKHVKCSSCQ 85

Query: 129 TVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNVNMANARVPL 180
           TVNL    NQ   + C +C+  LMYP+GAP+V+C+ C  VT+++  N R P 
Sbjct: 86  TVNLVLEANQVGQVNCNNCKLLLMYPYGAPAVRCSSCNSVTDISENNKRPPW 137

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

Arabidopsis thaliana (taxid: 3702)

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

 Score = 63.5 bits (153), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 26/38 (68%), Positives = 34/38 (89%)

Query: 60 GMQSQLVCSGCRSVLLYPRGATNVCCALCNTITSVPIP 97
          G QSQLVCSGCR++L+YP GAT++CCA+C T+T+VP P
Sbjct: 43 GAQSQLVCSGCRNLLMYPAGATSICCAVCGTVTAVPAP 80

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

Oryza sativa subsp. japonica (taxid: 39947)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	230
357519449	223	Lsd1-like protein [Medicago truncatula]	0.739	0.762	0.772	2e-73
305387471	176	zinc finger protein LSD1 [Pisum sativum]	0.739	0.965	0.784	3e-73
357519447	211	Lsd1-like protein [Medicago truncatula]	0.739	0.805	0.772	3e-73
359483998	264	PREDICTED: protein LSD1 [Vitis vinifera]	0.939	0.818	0.656	8e-73
296089240	259	unnamed protein product [Vitis vinifera]	0.913	0.810	0.674	2e-72
388505592	176	unknown [Medicago truncatula]	0.739	0.965	0.767	2e-72
388491514	175	unknown [Lotus japonicus]	0.734	0.965	0.784	3e-72
449490759	343	PREDICTED: protein LOL3-like [Cucumis sa	0.943	0.632	0.630	4e-72
449434208	410	PREDICTED: vacuolar protein sorting-asso	0.756	0.424	0.754	5e-72
388521485	175	unknown [Lotus japonicus]	0.734	0.965	0.778	1e-71

>gi|357519449|ref|XP_003630013.1| Lsd1-like protein [Medicago truncatula] gi|355524035|gb|AET04489.1| Lsd1-like protein [Medicago truncatula]

 Score =  281 bits (718), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 136/176 (77%), Positives = 154/176 (87%), Gaps = 6/176 (3%)

Query: 61  MQSQLVCSGCRSVLLYPRGATNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGAT 120
           MQSQLVC+GCR+ LLYPRGATNVCCALCNTIT+VP PGM+M+QL CGGCRTLLMYTRGAT
Sbjct: 48  MQSQLVCNGCRNTLLYPRGATNVCCALCNTITAVPPPGMDMSQLYCGGCRTLLMYTRGAT 107

Query: 121 SVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNVNMANARVPL 180
           SVRCSCCHTVNLAP  NQ AH+ CG+CRTTLMYP+GAPSVKCAVC Y+TN+NM+N R+P+
Sbjct: 108 SVRCSCCHTVNLAPVSNQVAHVPCGNCRTTLMYPYGAPSVKCAVCHYITNINMSNGRLPI 167

Query: 181 PANRPNGTAIPGTLPST------SMTQTVVVENPMSVDESGKLVSNVVVGVSTEKK 230
           P +RP+GT   G LPST      S +QTVVVENPMSVD SGKLVSNVVVGV+T+KK
Sbjct: 168 PGHRPHGTTDSGMLPSTSTSMPQSQSQTVVVENPMSVDSSGKLVSNVVVGVTTDKK 223

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|305387471|gb|ADM52200.1| zinc finger protein LSD1 [Pisum sativum]

 Score =  280 bits (717), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 138/176 (78%), Positives = 154/176 (87%), Gaps = 6/176 (3%)

Query: 61  MQSQLVCSGCRSVLLYPRGATNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGAT 120
           MQSQLVC+GCR++LLYPRGATNVCCALCNTI+ VP PGM+M+QL CGGCRTLLMYTRGAT
Sbjct: 1   MQSQLVCNGCRNMLLYPRGATNVCCALCNTISPVPPPGMDMSQLYCGGCRTLLMYTRGAT 60

Query: 121 SVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNVNMANARVPL 180
           SVRCSCCHTVNLAP  NQ AH+ C +CRTTLMYP+GAPSVKCAVC Y+TN+NM+N RVP+
Sbjct: 61  SVRCSCCHTVNLAPVSNQVAHVPCANCRTTLMYPYGAPSVKCAVCHYITNINMSNGRVPV 120

Query: 181 PANRPNGTAIPGTLPSTSMT------QTVVVENPMSVDESGKLVSNVVVGVSTEKK 230
           PANRP GT   GTLPSTS +      QTVVVENPMSVD SGKLVSNVVVGV+T+KK
Sbjct: 121 PANRPQGTTNLGTLPSTSTSMPQSQGQTVVVENPMSVDSSGKLVSNVVVGVTTDKK 176

Source: Pisum sativum

Species: Pisum sativum

Genus: Pisum

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357519447|ref|XP_003630012.1| Lsd1-like protein [Medicago truncatula] gi|355524034|gb|AET04488.1| Lsd1-like protein [Medicago truncatula]

 Score =  280 bits (716), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 136/176 (77%), Positives = 154/176 (87%), Gaps = 6/176 (3%)

Query: 61  MQSQLVCSGCRSVLLYPRGATNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGAT 120
           MQSQLVC+GCR+ LLYPRGATNVCCALCNTIT+VP PGM+M+QL CGGCRTLLMYTRGAT
Sbjct: 36  MQSQLVCNGCRNTLLYPRGATNVCCALCNTITAVPPPGMDMSQLYCGGCRTLLMYTRGAT 95

Query: 121 SVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNVNMANARVPL 180
           SVRCSCCHTVNLAP  NQ AH+ CG+CRTTLMYP+GAPSVKCAVC Y+TN+NM+N R+P+
Sbjct: 96  SVRCSCCHTVNLAPVSNQVAHVPCGNCRTTLMYPYGAPSVKCAVCHYITNINMSNGRLPI 155

Query: 181 PANRPNGTAIPGTLPST------SMTQTVVVENPMSVDESGKLVSNVVVGVSTEKK 230
           P +RP+GT   G LPST      S +QTVVVENPMSVD SGKLVSNVVVGV+T+KK
Sbjct: 156 PGHRPHGTTDSGMLPSTSTSMPQSQSQTVVVENPMSVDSSGKLVSNVVVGVTTDKK 211

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359483998|ref|XP_002276731.2| PREDICTED: protein LSD1 [Vitis vinifera]

 Score =  279 bits (713), Expect = 8e-73,   Method: Compositional matrix adjust.
 Identities = 149/227 (65%), Positives = 173/227 (76%), Gaps = 11/227 (4%)

Query: 6   FHLIHNEIKKPNQTKQIKLSFFIFLFLFIYINHTITQLSIDFDFSNDSILLSLQ-GMQSQ 64
           +  ++ +  K + TK    S  IF F               F+ S+     S Q  MQS 
Sbjct: 47  YPFLNLQFSKSDSTKSTTFSHRIFAF---------NSSPFPFNCSSSERKFSYQSAMQSH 97

Query: 65  LVCSGCRSVLLYPRGATNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATSVRC 124
           L+C+GCRS+L+YPRGATNVCCALCN++TSVP PG+EMAQLICGGCRTLLMYTRGATSVRC
Sbjct: 98  LMCNGCRSILVYPRGATNVCCALCNSVTSVPPPGLEMAQLICGGCRTLLMYTRGATSVRC 157

Query: 125 SCCHTVNLAPAP-NQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNVNMANARVPLPAN 183
           SCCHTVNLAPAP NQ AH+ CG+CRTTLMYP+GAPSVKCAVC YVT+V M N RVP+P +
Sbjct: 158 SCCHTVNLAPAPSNQVAHVNCGNCRTTLMYPYGAPSVKCAVCHYVTSVGMVNVRVPIPVH 217

Query: 184 RPNGTAIPGTLPSTSMTQTVVVENPMSVDESGKLVSNVVVGVSTEKK 230
           RPN  AI  + PSTS +QTVVV+NPMSVDESGKLVSNVVVGV+TEKK
Sbjct: 218 RPNAAAISASTPSTSSSQTVVVKNPMSVDESGKLVSNVVVGVTTEKK 264

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296089240|emb|CBI39012.3| unnamed protein product [Vitis vinifera]

 Score =  278 bits (710), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 149/221 (67%), Positives = 170/221 (76%), Gaps = 11/221 (4%)

Query: 12  EIKKPNQTKQIKLSFFIFLFLFIYINHTITQLSIDFDFSNDSILLSLQ-GMQSQLVCSGC 70
           +  K + TK    S  IF F               F+ S+     S Q  MQS L+C+GC
Sbjct: 48  QFSKSDSTKSTTFSHRIFAF---------NSSPFPFNCSSSERKFSYQSAMQSHLMCNGC 98

Query: 71  RSVLLYPRGATNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATSVRCSCCHTV 130
           RS+L+YPRGATNVCCALCN++TSVP PG+EMAQLICGGCRTLLMYTRGATSVRCSCCHTV
Sbjct: 99  RSILVYPRGATNVCCALCNSVTSVPPPGLEMAQLICGGCRTLLMYTRGATSVRCSCCHTV 158

Query: 131 NLAPAP-NQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNVNMANARVPLPANRPNGTA 189
           NLAPAP NQ AH+ CG+CRTTLMYP+GAPSVKCAVC YVT+V M N RVP+P +RPN  A
Sbjct: 159 NLAPAPSNQVAHVNCGNCRTTLMYPYGAPSVKCAVCHYVTSVGMVNVRVPIPVHRPNAAA 218

Query: 190 IPGTLPSTSMTQTVVVENPMSVDESGKLVSNVVVGVSTEKK 230
           I  + PSTS +QTVVV+NPMSVDESGKLVSNVVVGV+TEKK
Sbjct: 219 ISASTPSTSSSQTVVVKNPMSVDESGKLVSNVVVGVTTEKK 259

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388505592|gb|AFK40862.1| unknown [Medicago truncatula]

 Score =  278 bits (710), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 135/176 (76%), Positives = 153/176 (86%), Gaps = 6/176 (3%)

Query: 61  MQSQLVCSGCRSVLLYPRGATNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGAT 120
           MQSQLVC+GCR+ LLYPRGATNVCCALCNTIT+VP PGM+M+QL CGGCRTLLMYTRGAT
Sbjct: 1   MQSQLVCNGCRNTLLYPRGATNVCCALCNTITAVPPPGMDMSQLYCGGCRTLLMYTRGAT 60

Query: 121 SVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNVNMANARVPL 180
           SVRCSCCHTVNLAP  NQ AH+ CG+CRTTLMYP+GAPSVKC VC Y+TN+NM+N R+P+
Sbjct: 61  SVRCSCCHTVNLAPVSNQVAHVPCGNCRTTLMYPYGAPSVKCVVCHYITNINMSNGRLPI 120

Query: 181 PANRPNGTAIPGTLPST------SMTQTVVVENPMSVDESGKLVSNVVVGVSTEKK 230
           P +RP+GT   G LPST      S +QTVVVENPMSVD SGKLVSNVVVGV+T+KK
Sbjct: 121 PGHRPHGTTDSGMLPSTSTSMPQSQSQTVVVENPMSVDSSGKLVSNVVVGVTTDKK 176

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388491514|gb|AFK33823.1| unknown [Lotus japonicus]

 Score =  276 bits (707), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 138/176 (78%), Positives = 154/176 (87%), Gaps = 7/176 (3%)

Query: 61  MQSQLVCSGCRSVLLYPRGATNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGAT 120
           MQSQLVC+GCRS+LLYPRGATNVCCALCNTIT+VP PGM+M+QL CGGCRTLLMYTRGA 
Sbjct: 1   MQSQLVCNGCRSILLYPRGATNVCCALCNTITAVPPPGMDMSQLYCGGCRTLLMYTRGAA 60

Query: 121 SVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNVNMANARVPL 180
           SVRCSCCHTVNLAPA NQ AH+ CG+CRTTLMYP+GAPSVKCA+C Y+TNVNM+N R+ +
Sbjct: 61  SVRCSCCHTVNLAPA-NQVAHVPCGNCRTTLMYPYGAPSVKCALCHYITNVNMSNGRLQV 119

Query: 181 PANRPNGTAIPGTLPST------SMTQTVVVENPMSVDESGKLVSNVVVGVSTEKK 230
           P +RPNGT   G LPST      S TQTVVVENPMSVD SGKLVSNVVVGV+T+KK
Sbjct: 120 PMHRPNGTTNSGALPSTSTSMPQSQTQTVVVENPMSVDSSGKLVSNVVVGVTTDKK 175

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449490759|ref|XP_004158699.1| PREDICTED: protein LOL3-like [Cucumis sativus]

 Score =  276 bits (707), Expect = 4e-72,   Method: Compositional matrix adjust.
 Identities = 140/222 (63%), Positives = 167/222 (75%), Gaps = 5/222 (2%)

Query: 14  KKPNQTKQIKLSFFIFLFLFIYINHTITQLSIDFDFSNDSILLSLQGMQSQLVCSGCRSV 73
           K+    K+ +         + Y+N+ +    ++  F    +L     MQSQLVCSGCRS+
Sbjct: 122 KQAKVIKEFQKQSAQLDMTWTYVNYCLILNLVEEKFKLLKLLCIEAAMQSQLVCSGCRSI 181

Query: 74  LLYPRGATNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATSVRCSCCHTVNLA 133
           LLYP GATNVCCALCNT+TSVP PG +MAQLICGGCRTLLMY RGATSVRCSCCHTVNLA
Sbjct: 182 LLYPGGATNVCCALCNTVTSVPPPGTDMAQLICGGCRTLLMYARGATSVRCSCCHTVNLA 241

Query: 134 PAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNVNMANARVPLPANRPNGTAIPGT 193
           PA NQ AH+ CG+CRTTL++P+GAPSVKCA+C YVTNV ++N RVP+P +R NGT   G 
Sbjct: 242 PATNQVAHVNCGNCRTTLVFPYGAPSVKCAICHYVTNVGISNVRVPIPVHRRNGTISSGM 301

Query: 194 LP-----STSMTQTVVVENPMSVDESGKLVSNVVVGVSTEKK 230
            P     S S +QTVVVENPMSVDESGKLVSNVVVGV+T+K+
Sbjct: 302 PPSSSVRSQSQSQTVVVENPMSVDESGKLVSNVVVGVTTDKR 343

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449434208|ref|XP_004134888.1| PREDICTED: vacuolar protein sorting-associated protein 2 homolog 2-like [Cucumis sativus]

 Score =  276 bits (706), Expect = 5e-72,   Method: Compositional matrix adjust.
 Identities = 135/179 (75%), Positives = 153/179 (85%), Gaps = 5/179 (2%)

Query: 57  SLQGMQSQLVCSGCRSVLLYPRGATNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYT 116
           S + MQSQLVCSGCRS+LLYP GATNVCCALCNT+TSVP PG +MAQLICGGCRTLLMY 
Sbjct: 232 SGEAMQSQLVCSGCRSILLYPGGATNVCCALCNTVTSVPPPGTDMAQLICGGCRTLLMYA 291

Query: 117 RGATSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNVNMANA 176
           RGATSVRCSCCHTVNLAPA NQ AH+ CG+CRTTL++P+GAPSVKCA+C YVTNV ++N 
Sbjct: 292 RGATSVRCSCCHTVNLAPATNQVAHVNCGNCRTTLVFPYGAPSVKCAICHYVTNVGISNV 351

Query: 177 RVPLPANRPNGTAIPGTLP-----STSMTQTVVVENPMSVDESGKLVSNVVVGVSTEKK 230
           RVP+P +R NGT   G  P     S S +QTVVVENPMSVDESGKLVSNVVVGV+T+K+
Sbjct: 352 RVPIPVHRRNGTISSGMPPSSSVRSQSQSQTVVVENPMSVDESGKLVSNVVVGVTTDKR 410

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388521485|gb|AFK48804.1| unknown [Lotus japonicus]

 Score =  275 bits (702), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 137/176 (77%), Positives = 154/176 (87%), Gaps = 7/176 (3%)

Query: 61  MQSQLVCSGCRSVLLYPRGATNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGAT 120
           MQSQLVC+GCRS+LLYPRGATNVCCALCNTIT+VP PGM+M+QL CGGCRTLLM+TRGA 
Sbjct: 1   MQSQLVCNGCRSILLYPRGATNVCCALCNTITAVPPPGMDMSQLYCGGCRTLLMHTRGAA 60

Query: 121 SVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNVNMANARVPL 180
           SVRCSCCHTVNLAPA NQ AH+ CG+CRTTLMYP+GAPSVKCA+C Y+TNVNM+N R+ +
Sbjct: 61  SVRCSCCHTVNLAPA-NQVAHVPCGNCRTTLMYPYGAPSVKCALCHYITNVNMSNGRLQV 119

Query: 181 PANRPNGTAIPGTLPST------SMTQTVVVENPMSVDESGKLVSNVVVGVSTEKK 230
           P +RPNGT   G LPST      S TQTVVVENPMSVD SGKLVSNVVVGV+T+KK
Sbjct: 120 PMHRPNGTTNSGALPSTSTSMPQSQTQTVVVENPMSVDSSGKLVSNVVVGVTTDKK 175

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	230
UNIPROTKB|F8RP38	176	F8RP38 "Zinc finger protein LS	0.739	0.965	0.784	5.1e-74
UNIPROTKB|Q0J7V9	184	LSD1 "Protein LSD1" [Oryza sat	0.486	0.608	0.723	1.9e-44
TAIR|locus:2128639	210	LSD1 "LESION SIMULATING DISEAS	0.704	0.771	0.578	3.9e-44
TAIR|locus:2119622	155	LOL2 "AT4G21610" [Arabidopsis	0.469	0.696	0.441	1.3e-20
UNIPROTKB|Q704V3	163	LOL5 "Protein LOL5" [Oryza sat	0.426	0.601	0.438	1.7e-20
TAIR|locus:1009023119	305	AT1G30814 "AT1G30814" [Arabido	0.378	0.285	0.282	1.5e-05

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

 Score = 747 (268.0 bits), Expect = 5.1e-74, P = 5.1e-74
 Identities = 138/176 (78%), Positives = 154/176 (87%)

Query:    61 MQSQLVCSGCRSVLLYPRGATNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGAT 120
             MQSQLVC+GCR++LLYPRGATNVCCALCNTI+ VP PGM+M+QL CGGCRTLLMYTRGAT
Sbjct:     1 MQSQLVCNGCRNMLLYPRGATNVCCALCNTISPVPPPGMDMSQLYCGGCRTLLMYTRGAT 60

Query:   121 SVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNVNMANARVPL 180
             SVRCSCCHTVNLAP  NQ AH+ C +CRTTLMYP+GAPSVKCAVC Y+TN+NM+N RVP+
Sbjct:    61 SVRCSCCHTVNLAPVSNQVAHVPCANCRTTLMYPYGAPSVKCAVCHYITNINMSNGRVPV 120

Query:   181 PANRPNGTAIPGTLPSTSMT------QTVVVENPMSVDESGKLVSNVVVGVSTEKK 230
             PANRP GT   GTLPSTS +      QTVVVENPMSVD SGKLVSNVVVGV+T+KK
Sbjct:   121 PANRPQGTTNLGTLPSTSTSMPQSQGQTVVVENPMSVDSSGKLVSNVVVGVTTDKK 176

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IMP

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

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

 Score = 468 (169.8 bits), Expect = 1.9e-44, P = 1.9e-44
 Identities = 81/112 (72%), Positives = 96/112 (85%)

Query:    60 GMQSQLVCSGCRSVLLYPRGATNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGA 119
             G QSQLVCSGCR++L+YP GAT+VCCA+C+T+T+VP PG EMAQL+CGGC TLLMY RGA
Sbjct:    61 GAQSQLVCSGCRNLLMYPAGATSVCCAVCSTVTAVPAPGTEMAQLVCGGCHTLLMYIRGA 120

Query:   120 TSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNV 171
             TSV+CSCCHTVNLA   NQ AH+ CG+CR  LMY +GA SVKCAVC +VT+V
Sbjct:   121 TSVQCSCCHTVNLAMEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTSV 172

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

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

 Score = 465 (168.7 bits), Expect = 3.9e-44, P = 3.9e-44
 Identities = 100/173 (57%), Positives = 121/173 (69%)

Query:    63 SQLVCSGCRSVLLYPRGATNVCCALCNTITSVPIPGMEMA-QLICGGCRTLLMYTRGATS 121
             + ++C GCR++L+Y RGA++V C+ C T   VP     +    I    +T L+   G  +
Sbjct:    44 AHIICGGCRTMLMYTRGASSVRCSCCQTTNLVPESSFTLLFDNILKVLKTKLLDGPGGLA 103

Query:   122 VRCSCCHTVNLAPAPN-QFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNVNMANARVPL 180
                   H+  +A AP+ Q A I CGHCRTTLMYP+GA SVKCAVCQ+VTNVNM+N RVPL
Sbjct:   104 ------HSNQVAHAPSSQVAQINCGHCRTTLMYPYGASSVKCAVCQFVTNVNMSNGRVPL 157

Query:   181 PANRPNGTAIP-GTLPST--SMTQTVVVENPMSVDESGKLVSNVVVGVSTEKK 230
             P NRPNGTA P  T  ST  S TQTVVVENPMSVDESGKLVSNVVVGV+T+KK
Sbjct:   158 PTNRPNGTACPPSTSTSTPPSQTQTVVVENPMSVDESGKLVSNVVVGVTTDKK 210

GO:0005576 "extracellular region" evidence=ISM

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

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

GO:0005515 "protein binding" evidence=IPI

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

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

GO:0001666 "response to hypoxia" evidence=IMP

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

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

GO:0010618 "aerenchyma formation" evidence=IMP

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

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

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

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

GO:0006914 "autophagy" evidence=RCA

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

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

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

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

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

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

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

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

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

 Score = 243 (90.6 bits), Expect = 1.3e-20, P = 1.3e-20
 Identities = 49/111 (44%), Positives = 67/111 (60%)

Query:    69 GCRSVLLYPRGATNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATSVRCSCCH 128
             G  S +L P   T +  A+    T+V IP  E AQ++CG CR LL Y RG+  V+CS C 
Sbjct:    29 GWESAVLPPPIVT-ITAAVNPNPTTVEIP--EKAQMVCGSCRRLLSYLRGSKHVKCSSCQ 85

Query:   129 TVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNVNMANARVP 179
             TVNL    NQ   + C +C+  LMYP+GAP+V+C+ C  VT+++  N R P
Sbjct:    86 TVNLVLEANQVGQVNCNNCKLLLMYPYGAPAVRCSSCNSVTDISENNKRPP 136

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 = 242 (90.2 bits), Expect = 1.7e-20, P = 1.7e-20
 Identities = 43/98 (43%), Positives = 57/98 (58%)

Query:    95 PIPGMEMAQLICGGCRTLLMYTRGATSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYP 154
             P    E+ Q++CG CR LL Y RGA  V C+CC T+N     ++   + CGHC T LMYP
Sbjct:    62 PYLNKEVGQMVCGSCRILLAYFRGAGYVHCTCCQTMNYVLEAHEVGKVHCGHCATLLMYP 121

Query:   155 HGAPSVKCAVCQYVTNVNMANARVPLPANRPNGTAIPG 192
              GAP+VKC++C +VT +   N R  L   +P  T   G
Sbjct:   122 FGAPAVKCSLCLFVTEIGERNVRRRLSIEQPTRTNSSG 159

GO:0005634 "nucleus" evidence=IDA

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

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

TAIR|locus:1009023119 AT1G30814 "AT1G30814" [Arabidopsis thaliana (taxid:3702)]

 Score = 123 (48.4 bits), Expect = 1.5e-05, P = 1.5e-05
 Identities = 26/92 (28%), Positives = 47/92 (51%)

Query:    79 GATNVCCALCNTITSVPIPGMEMA-QLICGGCRTLLMYTRG-ATSVRCSCCHTVNLAPAP 136
             G   + C  C+ +   P  G  +A +  C  C+  L +    A + RC CC T++  P P
Sbjct:    32 GGKIIECPNCH-VQFTPTLGNWIADKFACKSCKANLSFRNSTAKTARCPCC-TIS-RPVP 88

Query:   137 NQFAHIICGHCRTTLMYPHGAPSVKCAVCQYV 168
             N F  ++CG C  ++++     +VKC+ C+++
Sbjct:    89 NNFTMLVCGGCPVSVVHQKRDKTVKCSECKHI 120


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.322   0.133   0.414    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      230       221   0.00095  112 3  11 22  0.49    32
                                                     32  0.40    36


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:  573 (61 KB)
  Total size of DFA:  164 KB (2096 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:  20.40u 0.10s 20.50t   Elapsed:  00:00:01
  Total cpu time:  20.40u 0.10s 20.50t   Elapsed:  00:00:01
  Start:  Mon May 20 18:33:41 2013   End:  Mon May 20 18:33:42 2013

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

---

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)
P94077	LSD1_ARATH	No assigned EC number	0.6931	0.7608	0.9259	yes	no
Q6ASS2	LOL3_ORYSJ	No assigned EC number	0.6203	0.7304	0.9032	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: gw1.XI.999.1 hypothetical protein (179 aa) (Populus trichocarpa)

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	230
pfam06943	25	pfam06943, zf-LSD1, LSD1 zinc finger	4e-10
TIGR01053	31	TIGR01053, LSD1, zinc finger domain, LSD1 subclass	5e-10
pfam06943	25	pfam06943, zf-LSD1, LSD1 zinc finger	2e-07
pfam06943	25	pfam06943, zf-LSD1, LSD1 zinc finger	2e-07
TIGR01053	31	TIGR01053, LSD1, zinc finger domain, LSD1 subclass	1e-06
TIGR01053	31	TIGR01053, LSD1, zinc finger domain, LSD1 subclass	6e-06

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

 Score = 53.0 bits (128), Expect = 4e-10
 Identities = 20/25 (80%), Positives = 22/25 (88%)

Query: 106 CGGCRTLLMYTRGATSVRCSCCHTV 130
           CGGCRTLLMY RGA SVRC+ 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|130125 TIGR01053, LSD1, zinc finger domain, LSD1 subclass

 Score = 52.8 bits (127), Expect = 5e-10
 Identities = 23/30 (76%), Positives = 27/30 (90%)

Query: 103 QLICGGCRTLLMYTRGATSVRCSCCHTVNL 132
           Q++CGGCRTLLMY RGA+SVRC+ C TVNL
Sbjct: 1   QVVCGGCRTLLMYPRGASSVRCALCQTVNL 30

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

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

 Score = 45.7 bits (109), Expect = 2e-07
 Identities = 18/25 (72%), Positives = 20/25 (80%)

Query: 144 CGHCRTTLMYPHGAPSVKCAVCQYV 168
           CG CRT LMYP GAPSV+CA+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|191646 pfam06943, zf-LSD1, LSD1 zinc finger

 Score = 45.7 bits (109), Expect = 2e-07
 Identities = 17/25 (68%), Positives = 22/25 (88%)

Query: 67 CSGCRSVLLYPRGATNVCCALCNTI 91
          C GCR++L+YPRGA +V CALCNT+
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 = 43.6 bits (103), Expect = 1e-06
 Identities = 19/31 (61%), Positives = 26/31 (83%)

Query: 64 QLVCSGCRSVLLYPRGATNVCCALCNTITSV 94
          Q+VC GCR++L+YPRGA++V CALC T+  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|130125 TIGR01053, LSD1, zinc finger domain, LSD1 subclass

 Score = 41.7 bits (98), Expect = 6e-06
 Identities = 19/31 (61%), Positives = 23/31 (74%)

Query: 141 HIICGHCRTTLMYPHGAPSVKCAVCQYVTNV 171
            ++CG CRT LMYP GA SV+CA+CQ V  V
Sbjct: 1   QVVCGGCRTLLMYPRGASSVRCALCQTVNLV 31

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	230
PF09788	256	Tmemb_55A: Transmembrane protein 55A; InterPro: IP	99.48
TIGR01053	31	LSD1 zinc finger domain, LSD1 subclass. This model	99.3
PF06943	25	zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zin	99.26
TIGR01053	31	LSD1 zinc finger domain, LSD1 subclass. This model	99.26
PF06943	25	zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zin	99.2
KOG4684	275	consensus Uncharacterized conserved protein, conta	98.97
KOG1546	362	consensus Metacaspase involved in regulation of ap	95.02
PF10122	51	Mu-like_Com: Mu-like prophage protein Com; InterPr	94.41
PF10122	51	Mu-like_Com: Mu-like prophage protein Com; InterPr	94.2
PF09788	256	Tmemb_55A: Transmembrane protein 55A; InterPro: IP	94.02
PF11331	46	DUF3133: Protein of unknown function (DUF3133); In	92.9
PF01667	55	Ribosomal_S27e: Ribosomal protein S27; InterPro: I	92.21
PTZ00083	85	40S ribosomal protein S27; Provisional	91.57
PLN00209	86	ribosomal protein S27; Provisional	91.55
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	91.5
PRK00415	59	rps27e 30S ribosomal protein S27e; Reviewed	91.25
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	91.11
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	90.62
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	89.8
KOG1779	84	consensus 40s ribosomal protein S27 [Translation,	89.41
COG2051	67	RPS27A Ribosomal protein S27E [Translation, riboso	89.02
PF11331	46	DUF3133: Protein of unknown function (DUF3133); In	89.01
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	88.5
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	88.14
PLN00209	86	ribosomal protein S27; Provisional	87.75
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	87.33
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	86.05
PTZ00083	85	40S ribosomal protein S27; Provisional	85.71
PF01667	55	Ribosomal_S27e: Ribosomal protein S27; InterPro: I	85.55
PRK00415	59	rps27e 30S ribosomal protein S27e; Reviewed	84.22
KOG1779	84	consensus 40s ribosomal protein S27 [Translation,	83.91
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	83.65
PF04690	170	YABBY: YABBY protein; InterPro: IPR006780 YABBY pr	82.49
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	80.38

>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=99.48  E-value=1.4e-13  Score=123.89  Aligned_cols=114  Identities=23%  Similarity=0.501  Sum_probs=100.5

Q ss_pred             ceeeccccceeeeecCCC--CeeecCCCCcccccCCCCCceeEEEeCCcceeEEeecCCCeEeCCC--CCcceecCC---
Q 026941           63 SQLVCSGCRSVLLYPRGA--TNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATSVRCSC--CHTVNLAPA---  135 (230)
Q Consensus        63 sQlvC~gCr~lL~YP~GA--~~VrCa~C~tVt~Vpp~~~q~~qLvCggCr~lL~YP~GA~sVrC~~--C~tVn~Vp~---  135 (230)
                      .-+.|+.|+.++......  -.|+|..|++.|+..++++++.+++|. |+.||+....++.+-|+.  |..|....+   
T Consensus        64 p~v~CrVCq~~I~i~gk~~QhVVkC~~CnEATPIr~aPpGKKYVRCP-CNCLLICk~sS~rIaCPRp~CkRiI~L~~~~~  142 (256)
T PF09788_consen   64 PVVTCRVCQSLIDIEGKMHQHVVKCSVCNEATPIRNAPPGKKYVRCP-CNCLLICKSSSQRIACPRPNCKRIINLGPSHQ  142 (256)
T ss_pred             ceEEeecCCceecccCccceeeEECCCCCccccccCCCCCCeeEecC-CceEEEeecccccccCCCCCCcceEEeCCccC
Confidence            578999999999998766  369999999999999999999999997 999999999999999996  998875432   


Q ss_pred             ---------CCceeEEEcCCCCeeeeccCCC--CeEeCCCCCcceeeccCCCC
Q 026941          136 ---------PNQFAHIICGHCRTTLMYPHGA--PSVKCAVCQYVTNVNMANAR  177 (230)
Q Consensus       136 ---------~~q~a~V~Cg~Crt~LmyP~GA--~sVrCa~C~~VT~V~~~n~R  177 (230)
                               .+.+..++||+|+.+++++.=.  ..+||++|++|++|+...+|
T Consensus       143 ~p~~~~~~~~p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKvSSVG~~faR  195 (256)
T PF09788_consen  143 GPVTPPVPTQPGSCRVICGHCSNTFLFNTLTSNTLARCPHCRKVSSVGPRFAR  195 (256)
T ss_pred             CCCCCCCCCCCCceeEECCCCCCcEeccCCCCCccccCCCCceeccccchHhh
Confidence                     2367899999999999999744  67899999999999977776

>TIGR01053 LSD1 zinc finger domain, LSD1 subclass

Probab=99.30  E-value=9.8e-13  Score=84.88  Aligned_cols=30  Identities=77%  Similarity=1.488  Sum_probs=15.9

Q ss_pred             EEEeCCcceeEEeecCCCeEeCCCCCccee
Q 026941          103 QLICGGCRTLLMYTRGATSVRCSCCHTVNL  132 (230)
Q Consensus       103 qLvCggCr~lL~YP~GA~sVrC~~C~tVn~  132 (230)
                      |++|++||++|+||+||++|||+.|++||.
T Consensus         1 q~~C~~C~t~L~yP~gA~~vrCs~C~~vt~   30 (31)
T TIGR01053         1 QVVCGGCRTLLMYPRGASSVRCALCQTVNL   30 (31)
T ss_pred             CcCcCCCCcEeecCCCCCeEECCCCCeEec
Confidence            345555555555555555555555555543

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=99.26  E-value=2.4e-12  Score=79.90  Aligned_cols=25  Identities=88%  Similarity=1.799  Sum_probs=14.1

Q ss_pred             eCCcceeEEeecCCCeEeCCCCCcc
Q 026941          106 CGGCRTLLMYTRGATSVRCSCCHTV  130 (230)
Q Consensus       106 CggCr~lL~YP~GA~sVrC~~C~tV  130 (230)
                      |++||++||||+||++|||+.|++|
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            4555555555555555555555554

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=99.26  E-value=2.5e-12  Score=82.97  Aligned_cols=31  Identities=61%  Similarity=1.243  Sum_probs=29.3

Q ss_pred             EEEcCCCCeeeeccCCCCeEeCCCCCcceee
Q 026941          141 HIICGHCRTTLMYPHGAPSVKCAVCQYVTNV  171 (230)
Q Consensus       141 ~V~Cg~Crt~LmyP~GA~sVrCa~C~~VT~V  171 (230)
                      |++|++||++|+||+||++|||+.|++||.|
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            5799999999999999999999999999975

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=99.20  E-value=9e-12  Score=77.38  Aligned_cols=25  Identities=72%  Similarity=1.483  Sum_probs=24.2

Q ss_pred             cCCCCeeeeccCCCCeEeCCCCCcc
Q 026941          144 CGHCRTTLMYPHGAPSVKCAVCQYV  168 (230)
Q Consensus       144 Cg~Crt~LmyP~GA~sVrCa~C~~V  168 (230)
                      |++||++||||+||++|||+.|++|
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            8999999999999999999999986

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 [].

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

Probab=98.97  E-value=6.4e-10  Score=99.85  Aligned_cols=113  Identities=21%  Similarity=0.475  Sum_probs=94.9

Q ss_pred             eeeccccceeeeecCCC--CeeecCCCCcccccCCCCCceeEEEeCCcceeEEeecCCCeEeCC--CCCcceecCC----
Q 026941           64 QLVCSGCRSVLLYPRGA--TNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATSVRCS--CCHTVNLAPA----  135 (230)
Q Consensus        64 QlvC~gCr~lL~YP~GA--~~VrCa~C~tVt~Vpp~~~q~~qLvCggCr~lL~YP~GA~sVrC~--~C~tVn~Vp~----  135 (230)
                      -+.|+.|+.++..-.--  -.|.|..||+.|+..++++...+++|. |+.||+.....+..-|+  .|..|....+    
T Consensus        80 mvtCRVCq~~i~~egk~~QHVVKC~~CnEATPIrnAPpGKKYVRCP-CNCLLICK~sSqRIACPRpnCkRiInL~p~~~~  158 (275)
T KOG4684|consen   80 MVTCRVCQVAISLEGKNQQHVVKCHSCNEATPIRNAPPGKKYVRCP-CNCLLICKASSQRIACPRPNCKRIINLDPLIEK  158 (275)
T ss_pred             eEeehhhhHHhccccccceeeEeecccCccccCCCCCCCCceeecC-CcEEEEEecccceeccCCCCcceeeecCCCCCC
Confidence            47899999998874333  369999999999999889999999997 99999999999999998  8988764321    


Q ss_pred             ------CCceeEEEcCCCCeeeeccC-CCCeEeCCCCCcceeeccCCCC
Q 026941          136 ------PNQFAHIICGHCRTTLMYPH-GAPSVKCAVCQYVTNVNMANAR  177 (230)
Q Consensus       136 ------~~q~a~V~Cg~Crt~LmyP~-GA~sVrCa~C~~VT~V~~~n~R  177 (230)
                            ++.+-+|.||+|+.++++.. -....+|++|++|.+|+-..+|
T Consensus       159 p~~P~~~P~gcRV~CgHC~~tFLfnt~tnaLArCPHCrKvSsvGsrfar  207 (275)
T KOG4684|consen  159 PRDPGTAPTGCRVKCGHCNETFLFNTLTNALARCPHCRKVSSVGSRFAR  207 (275)
T ss_pred             CCCCCCCCcceEEEecCccceeehhhHHHHHhcCCcccchhhhhhHHhh
Confidence                  24668999999999999985 2367899999999999865554

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

Probab=95.02  E-value=0.025  Score=53.98  Aligned_cols=30  Identities=33%  Similarity=0.724  Sum_probs=28.0

Q ss_pred             EEEcCCCCeeeeccCCCCeEeCCCCCcceeec
Q 026941          141 HIICGHCRTTLMYPHGAPSVKCAVCQYVTNVN  172 (230)
Q Consensus       141 ~V~Cg~Crt~LmyP~GA~sVrCa~C~~VT~V~  172 (230)
                      .+.|. |+++++.|+||+. +|+.|++||.++
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            46787 9999999999999 999999999997

>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=94.41  E-value=0.023  Score=40.92  Aligned_cols=33  Identities=30%  Similarity=0.662  Sum_probs=27.6

Q ss_pred             eEEEcCCCCeeeeccC--CCCeEeCCCCCcceeec
Q 026941          140 AHIICGHCRTTLMYPH--GAPSVKCAVCQYVTNVN  172 (230)
Q Consensus       140 a~V~Cg~Crt~LmyP~--GA~sVrCa~C~~VT~V~  172 (230)
                      -.++|++|+.+|.--.  ....+||+.|.+++.|.
T Consensus         3 ~eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~   37 (51)
T PF10122_consen    3 KEIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVR   37 (51)
T ss_pred             cceeccchhHHHhhhcCccEEEEECCCCCccceEe
Confidence            3589999999999863  44589999999999996

>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=94.20  E-value=0.021  Score=41.12  Aligned_cols=34  Identities=29%  Similarity=0.686  Sum_probs=27.2

Q ss_pred             eEEEeCCcceeEEeecCC--CeEeCCCCCcceecCC
Q 026941          102 AQLICGGCRTLLMYTRGA--TSVRCSCCHTVNLAPA  135 (230)
Q Consensus       102 ~qLvCggCr~lL~YP~GA--~sVrC~~C~tVn~Vp~  135 (230)
                      ..++|++|+.+|+.--++  ..++||.|.++|.+..
T Consensus         3 ~eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a   38 (51)
T PF10122_consen    3 KEIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRA   38 (51)
T ss_pred             cceeccchhHHHhhhcCccEEEEECCCCCccceEec
Confidence            468899999999885444  4889999999998764

>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=94.02  E-value=0.12  Score=47.48  Aligned_cols=92  Identities=26%  Similarity=0.500  Sum_probs=59.0

Q ss_pred             hhcceeeEEEEeeeecCCcccccCcCccceeeccccceeeee---cCCCCeeecC-----------------C--C-Ccc
Q 026941           35 YINHTITQLSIDFDFSNDSILLSLQGMQSQLVCSGCRSVLLY---PRGATNVCCA-----------------L--C-NTI   91 (230)
Q Consensus        35 ~~~~~~~~~~~~~~f~~~~~l~~~~~mqsQlvC~gCr~lL~Y---P~GA~~VrCa-----------------~--C-~tV   91 (230)
                      .|+-.+=|-.||++=..+         |--..|..|.+---.   |.|-..|||+                 +  | ..|
T Consensus        65 ~v~CrVCq~~I~i~gk~~---------QhVVkC~~CnEATPIr~aPpGKKYVRCPCNCLLICk~sS~rIaCPRp~CkRiI  135 (256)
T PF09788_consen   65 VVTCRVCQSLIDIEGKMH---------QHVVKCSVCNEATPIRNAPPGKKYVRCPCNCLLICKSSSQRIACPRPNCKRII  135 (256)
T ss_pred             eEEeecCCceecccCccc---------eeeEECCCCCccccccCCCCCCeeEecCCceEEEeecccccccCCCCCCcceE
Confidence            345566677777764433         344556656553332   4455555554                 4  6 334


Q ss_pred             cccCC---C-------CCceeEEEeCCcceeEEeecCC--CeEeCCCCCcceecCC
Q 026941           92 TSVPI---P-------GMEMAQLICGGCRTLLMYTRGA--TSVRCSCCHTVNLAPA  135 (230)
Q Consensus        92 t~Vpp---~-------~~q~~qLvCggCr~lL~YP~GA--~sVrC~~C~tVn~Vp~  135 (230)
                      |..+.   |       ...+--++||+|+...+++.=.  +..|||.|+.|++|..
T Consensus       136 ~L~~~~~~p~~~~~~~~p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKvSSVG~  191 (256)
T PF09788_consen  136 NLGPSHQGPVTPPVPTQPGSCRVICGHCSNTFLFNTLTSNTLARCPHCRKVSSVGP  191 (256)
T ss_pred             EeCCccCCCCCCCCCCCCCceeEECCCCCCcEeccCCCCCccccCCCCceeccccc
Confidence            44432   1       2357889999999999999755  6789999999999853

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

Probab=92.90  E-value=0.11  Score=36.54  Aligned_cols=38  Identities=29%  Similarity=0.693  Sum_probs=25.6

Q ss_pred             CCCeeecCCCCcccccCCC----CCceeEEEeCCcceeEEee
Q 026941           79 GATNVCCALCNTITSVPIP----GMEMAQLICGGCRTLLMYT  116 (230)
Q Consensus        79 GA~~VrCa~C~tVt~Vpp~----~~q~~qLvCggCr~lL~YP  116 (230)
                      ||+.|-|..|..+-.+|..    .....+|.||.|-.+|.|.
T Consensus         3 GAPFv~C~~C~~lLqlP~~~~~~~k~~~klrCGaCs~vl~~s   44 (46)
T PF11331_consen    3 GAPFVVCSSCFELLQLPAKFSLSKKNQQKLRCGACSEVLSFS   44 (46)
T ss_pred             CCCEeECccHHHHHcCCCccCCCccceeEEeCCCCceeEEEe
Confidence            6677777777666666432    2236788888888888774

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

Probab=92.21  E-value=0.13  Score=37.35  Aligned_cols=40  Identities=25%  Similarity=0.467  Sum_probs=25.6

Q ss_pred             eEeCCCCCcceecCCCCceeEEEcCCCCeeeeccCCCCeEe
Q 026941          121 SVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVK  161 (230)
Q Consensus       121 sVrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP~GA~sVr  161 (230)
                      .|+|+.|..++.|=+-++. .|.|..|.+.|.-|.|-.+--
T Consensus         7 ~VkCp~C~~~q~vFSha~t-~V~C~~Cg~~L~~PtGGKa~l   46 (55)
T PF01667_consen    7 DVKCPGCYNIQTVFSHAQT-VVKCVVCGTVLAQPTGGKARL   46 (55)
T ss_dssp             EEE-TTT-SEEEEETT-SS--EE-SSSTSEEEEE-SSSEEE
T ss_pred             EEECCCCCCeeEEEecCCe-EEEcccCCCEecCCCCcCeEE
Confidence            5888888888877554444 788999999998888865543

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=91.57  E-value=0.31  Score=38.45  Aligned_cols=38  Identities=32%  Similarity=0.680  Sum_probs=20.5

Q ss_pred             eeecCCCCcccccCCCCCceeEEEeCCcceeEEeecCCCe
Q 026941           82 NVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATS  121 (230)
Q Consensus        82 ~VrCa~C~tVt~Vpp~~~q~~qLvCggCr~lL~YP~GA~s  121 (230)
                      -|+|+.|..++.+=  ++....+.|.+|.++|..|.|--.
T Consensus        35 ~VkCp~C~n~q~VF--ShA~t~V~C~~Cg~~L~~PTGGKa   72 (85)
T PTZ00083         35 DVKCPGCSQITTVF--SHAQTVVLCGGCSSQLCQPTGGKA   72 (85)
T ss_pred             EEECCCCCCeeEEE--ecCceEEEccccCCEeeccCCCCe
Confidence            36666665555552  344455555555555555555443

>PLN00209 ribosomal protein S27; Provisional

Probab=91.55  E-value=0.3  Score=38.57  Aligned_cols=39  Identities=31%  Similarity=0.615  Sum_probs=21.8

Q ss_pred             eeecCCCCcccccCCCCCceeEEEeCCcceeEEeecCCCeE
Q 026941           82 NVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATSV  122 (230)
Q Consensus        82 ~VrCa~C~tVt~Vpp~~~q~~qLvCggCr~lL~YP~GA~sV  122 (230)
                      -|+|+.|..++.+=  ++....+.|.+|.++|..|.|--..
T Consensus        36 ~VkCp~C~n~q~VF--ShA~t~V~C~~Cg~~L~~PTGGKa~   74 (86)
T PLN00209         36 DVKCQGCFNITTVF--SHSQTVVVCGSCQTVLCQPTGGKAR   74 (86)
T ss_pred             EEECCCCCCeeEEE--ecCceEEEccccCCEeeccCCCCeE
Confidence            36666666666552  3444556666666666666654443

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=91.50  E-value=0.23  Score=31.97  Aligned_cols=30  Identities=20%  Similarity=0.519  Sum_probs=15.9

Q ss_pred             EeCCCCCcceecCCC---CceeEEEcCCCCeee
Q 026941          122 VRCSCCHTVNLAPAP---NQFAHIICGHCRTTL  151 (230)
Q Consensus       122 VrC~~C~tVn~Vp~~---~q~a~V~Cg~Crt~L  151 (230)
                      +.||.|++...++++   ..-..++|++|+..+
T Consensus         3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~   35 (38)
T TIGR02098         3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW   35 (38)
T ss_pred             EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence            556666666655532   112256666666554

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

>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed

Probab=91.25  E-value=0.19  Score=37.09  Aligned_cols=37  Identities=24%  Similarity=0.464  Sum_probs=21.4

Q ss_pred             eEeCCCCCcceecCCCCceeEEEcCCCCeeeeccCCCC
Q 026941          121 SVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAP  158 (230)
Q Consensus       121 sVrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP~GA~  158 (230)
                      .|+|+.|..++.+=+-.+. .|.|..|.++|.-|.|-.
T Consensus        11 ~VkCp~C~n~q~vFsha~t-~V~C~~Cg~~L~~PtGGK   47 (59)
T PRK00415         11 KVKCPDCGNEQVVFSHAST-VVRCLVCGKTLAEPTGGK   47 (59)
T ss_pred             EEECCCCCCeEEEEecCCc-EEECcccCCCcccCCCcc
Confidence            3566666666654433333 566666666666666543

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=91.11  E-value=0.24  Score=32.56  Aligned_cols=27  Identities=37%  Similarity=0.864  Sum_probs=14.1

Q ss_pred             EEcCCCCeeeecc-----CCCCeEeCCCCCcc
Q 026941          142 IICGHCRTTLMYP-----HGAPSVKCAVCQYV  168 (230)
Q Consensus       142 V~Cg~Crt~LmyP-----~GA~sVrCa~C~~V  168 (230)
                      +.|.+|.+.+-+|     .+...|||+.|+.+
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            4455555554443     23456666666654

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=90.62  E-value=0.26  Score=32.40  Aligned_cols=30  Identities=20%  Similarity=0.495  Sum_probs=17.1

Q ss_pred             EeCCCCCcceecCCC---CceeEEEcCCCCeee
Q 026941          122 VRCSCCHTVNLAPAP---NQFAHIICGHCRTTL  151 (230)
Q Consensus       122 VrC~~C~tVn~Vp~~---~q~a~V~Cg~Crt~L  151 (230)
                      +.||.|++.-.++++   ..-..++|+.|+...
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            456666666666542   234466666666543

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

Probab=89.80  E-value=0.34  Score=35.91  Aligned_cols=52  Identities=25%  Similarity=0.571  Sum_probs=40.4

Q ss_pred             eeEEEeCCcceeEEeecC-CCeEeCCCCCcceecCCCCceeEEEcCCCCeeeeccCCCCeEeCCCCCcc
Q 026941          101 MAQLICGGCRTLLMYTRG-ATSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYV  168 (230)
Q Consensus       101 ~~qLvCggCr~lL~YP~G-A~sVrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP~GA~sVrCa~C~~V  168 (230)
                      +.-.+|..|...| .|.+ +....||.|..+.         ..+|..||..      +..++|+.|++.
T Consensus         5 ~~~~~CtSCg~~i-~~~~~~~~F~CPnCG~~~---------I~RC~~CRk~------~~~Y~CP~CGF~   57 (59)
T PRK14890          5 MEPPKCTSCGIEI-APREKAVKFLCPNCGEVI---------IYRCEKCRKQ------SNPYTCPKCGFE   57 (59)
T ss_pred             ccCccccCCCCcc-cCCCccCEeeCCCCCCee---------EeechhHHhc------CCceECCCCCCc
Confidence            3445799999988 5666 9999999996553         4579999986      367899999874

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

Probab=89.41  E-value=0.66  Score=36.49  Aligned_cols=39  Identities=31%  Similarity=0.600  Sum_probs=18.2

Q ss_pred             eeecCCCCcccccCCCCCceeEEEeCCcceeEEeecCCCeE
Q 026941           82 NVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATSV  122 (230)
Q Consensus        82 ~VrCa~C~tVt~Vpp~~~q~~qLvCggCr~lL~YP~GA~sV  122 (230)
                      .|+|+.|-.||-+=  .+...-++|+||.+.|.-|.|-..+
T Consensus        34 ~VkC~gc~~iT~vf--SHaqtvVvc~~c~~il~~~tggra~   72 (84)
T KOG1779|consen   34 DVKCPGCFKITTVF--SHAQTVVVCEGCSTILCQPTGGKAK   72 (84)
T ss_pred             EEEcCCceEEEEEe--ecCceEEEcCCCceEEEEecCCcEE
Confidence            35555555555542  2223344555555555555444443

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

Probab=89.02  E-value=0.67  Score=35.18  Aligned_cols=35  Identities=29%  Similarity=0.533  Sum_probs=15.9

Q ss_pred             EeCCCCCcceecCCCCceeEEEcCCCCeeeeccCCC
Q 026941          122 VRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGA  157 (230)
Q Consensus       122 VrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP~GA  157 (230)
                      |+|+.|.....+=+-++. .++|..|.++|..|.|-
T Consensus        20 VkCpdC~N~q~vFshast-~V~C~~CG~~l~~PTGG   54 (67)
T COG2051          20 VKCPDCGNEQVVFSHAST-VVTCLICGTTLAEPTGG   54 (67)
T ss_pred             EECCCCCCEEEEeccCce-EEEecccccEEEecCCC
Confidence            445545444433332222 44555555555555543

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

Probab=89.01  E-value=0.43  Score=33.60  Aligned_cols=37  Identities=32%  Similarity=0.659  Sum_probs=25.7

Q ss_pred             cCCCeEeCCCCCcceecCCC-----CceeEEEcCCCCeeeec
Q 026941          117 RGATSVRCSCCHTVNLAPAP-----NQFAHIICGHCRTTLMY  153 (230)
Q Consensus       117 ~GA~sVrC~~C~tVn~Vp~~-----~q~a~V~Cg~Crt~Lmy  153 (230)
                      .||+-|-|..|..+-.+|..     ....+++||.|...|.|
T Consensus         2 GGAPFv~C~~C~~lLqlP~~~~~~~k~~~klrCGaCs~vl~~   43 (46)
T PF11331_consen    2 GGAPFVVCSSCFELLQLPAKFSLSKKNQQKLRCGACSEVLSF   43 (46)
T ss_pred             CCCCEeECccHHHHHcCCCccCCCccceeEEeCCCCceeEEE
Confidence            36777777777766666531     23668888888888776

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

Probab=88.50  E-value=0.59  Score=31.51  Aligned_cols=28  Identities=21%  Similarity=0.596  Sum_probs=17.7

Q ss_pred             EEEcCCCCeeeeccCCCCeEeCCCCCcc
Q 026941          141 HIICGHCRTTLMYPHGAPSVKCAVCQYV  168 (230)
Q Consensus       141 ~V~Cg~Crt~LmyP~GA~sVrCa~C~~V  168 (230)
                      ...|++|...+.+..+...++|+.|+.-
T Consensus         3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~   30 (46)
T PRK00398          3 EYKCARCGREVELDEYGTGVRCPYCGYR   30 (46)
T ss_pred             EEECCCCCCEEEECCCCCceECCCCCCe
Confidence            3466666666666666656666666653

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

Probab=88.14  E-value=0.85  Score=30.76  Aligned_cols=25  Identities=28%  Similarity=0.608  Sum_probs=11.5

Q ss_pred             EEeCCcceeEEeecCCCeEeCCCCC
Q 026941          104 LICGGCRTLLMYTRGATSVRCSCCH  128 (230)
Q Consensus       104 LvCggCr~lL~YP~GA~sVrC~~C~  128 (230)
                      .+|+.|...+.+..+...++|+.|+
T Consensus         4 y~C~~CG~~~~~~~~~~~~~Cp~CG   28 (46)
T PRK00398          4 YKCARCGREVELDEYGTGVRCPYCG   28 (46)
T ss_pred             EECCCCCCEEEECCCCCceECCCCC
Confidence            3444444444444444444444444

>PLN00209 ribosomal protein S27; Provisional

Probab=87.75  E-value=0.49  Score=37.37  Aligned_cols=19  Identities=37%  Similarity=0.945  Sum_probs=9.4

Q ss_pred             EEEcCCCCeeeeccCCCCe
Q 026941          141 HIICGHCRTTLMYPHGAPS  159 (230)
Q Consensus       141 ~V~Cg~Crt~LmyP~GA~s  159 (230)
                      .|.|..|.++|..|.|-.+
T Consensus        55 ~V~C~~Cg~~L~~PTGGKa   73 (86)
T PLN00209         55 VVVCGSCQTVLCQPTGGKA   73 (86)
T ss_pred             EEEccccCCEeeccCCCCe
Confidence            4455555555555554443

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=87.33  E-value=0.87  Score=29.91  Aligned_cols=14  Identities=14%  Similarity=0.444  Sum_probs=7.4

Q ss_pred             EeCCCCCcceecCC
Q 026941          122 VRCSCCHTVNLAPA  135 (230)
Q Consensus       122 VrC~~C~tVn~Vp~  135 (230)
                      +.|+.|++.-.+++
T Consensus         3 i~Cp~C~~~y~i~d   16 (36)
T PF13717_consen    3 ITCPNCQAKYEIDD   16 (36)
T ss_pred             EECCCCCCEEeCCH
Confidence            45555555555543

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=86.05  E-value=0.92  Score=29.80  Aligned_cols=28  Identities=25%  Similarity=0.581  Sum_probs=18.5

Q ss_pred             EEEcCCCCeeeecc-----CCCCeEeCCCCCcc
Q 026941          141 HIICGHCRTTLMYP-----HGAPSVKCAVCQYV  168 (230)
Q Consensus       141 ~V~Cg~Crt~LmyP-----~GA~sVrCa~C~~V  168 (230)
                      .+.|.+|++...+|     .+...|+|+.|+.+
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            56777777776543     45567777777654

>PTZ00083 40S ribosomal protein S27; Provisional

Probab=85.71  E-value=0.93  Score=35.77  Aligned_cols=45  Identities=24%  Similarity=0.596  Sum_probs=29.7

Q ss_pred             eEeCCCCCcceecCCCCceeEEEcCCCCeeeeccCCCCeEeCCCCC
Q 026941          121 SVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQ  166 (230)
Q Consensus       121 sVrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP~GA~sVrCa~C~  166 (230)
                      .|+|+.|..++.|=+-++. .|.|..|.++|.-|.|-.+.-=..|.
T Consensus        35 ~VkCp~C~n~q~VFShA~t-~V~C~~Cg~~L~~PTGGKa~l~~gc~   79 (85)
T PTZ00083         35 DVKCPGCSQITTVFSHAQT-VVLCGGCSSQLCQPTGGKAKLTEGCS   79 (85)
T ss_pred             EEECCCCCCeeEEEecCce-EEEccccCCEeeccCCCCeEecCCce
Confidence            4677777777766554444 67788888888888776655444443

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

Probab=85.55  E-value=0.83  Score=33.27  Aligned_cols=38  Identities=26%  Similarity=0.460  Sum_probs=21.0

Q ss_pred             eeecCCCCcccccCCCCCceeEEEeCCcceeEEeecCCCe
Q 026941           82 NVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATS  121 (230)
Q Consensus        82 ~VrCa~C~tVt~Vpp~~~q~~qLvCggCr~lL~YP~GA~s  121 (230)
                      .|+|+.|..++-+=  ++....+.|.+|.++|..|.|--.
T Consensus         7 ~VkCp~C~~~q~vF--Sha~t~V~C~~Cg~~L~~PtGGKa   44 (55)
T PF01667_consen    7 DVKCPGCYNIQTVF--SHAQTVVKCVVCGTVLAQPTGGKA   44 (55)
T ss_dssp             EEE-TTT-SEEEEE--TT-SS-EE-SSSTSEEEEE-SSSE
T ss_pred             EEECCCCCCeeEEE--ecCCeEEEcccCCCEecCCCCcCe
Confidence            47777777666662  233456777777777777777543

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.

>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed

Probab=84.22  E-value=0.66  Score=34.33  Aligned_cols=34  Identities=24%  Similarity=0.326  Sum_probs=15.7

Q ss_pred             eecCCCCcccccCCCCCceeEEEeCCcceeEEeecC
Q 026941           83 VCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRG  118 (230)
Q Consensus        83 VrCa~C~tVt~Vpp~~~q~~qLvCggCr~lL~YP~G  118 (230)
                      |+|+.|..++.+=  ++-...+.|..|.++|..|.|
T Consensus        12 VkCp~C~n~q~vF--sha~t~V~C~~Cg~~L~~PtG   45 (59)
T PRK00415         12 VKCPDCGNEQVVF--SHASTVVRCLVCGKTLAEPTG   45 (59)
T ss_pred             EECCCCCCeEEEE--ecCCcEEECcccCCCcccCCC
Confidence            5555554444331  122244555555555555554

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

Probab=83.91  E-value=1.3  Score=34.80  Aligned_cols=39  Identities=26%  Similarity=0.560  Sum_probs=21.2

Q ss_pred             EeCCCCCcceecCCCCceeEEEcCCCCeeeeccCCCCeEe
Q 026941          122 VRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVK  161 (230)
Q Consensus       122 VrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP~GA~sVr  161 (230)
                      |+|+.|-.+|.+=+-.|+ -|.|++|.+.|.-|.|-.+..
T Consensus        35 VkC~gc~~iT~vfSHaqt-vVvc~~c~~il~~~tggra~l   73 (84)
T KOG1779|consen   35 VKCPGCFKITTVFSHAQT-VVVCEGCSTILCQPTGGKAKL   73 (84)
T ss_pred             EEcCCceEEEEEeecCce-EEEcCCCceEEEEecCCcEEe
Confidence            455555555554443344 456666666666666555443

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=83.65  E-value=2.3  Score=27.29  Aligned_cols=29  Identities=28%  Similarity=0.619  Sum_probs=18.1

Q ss_pred             EEEcCCCCeeeeccC-----CCCeEeCCCCCcce
Q 026941          141 HIICGHCRTTLMYPH-----GAPSVKCAVCQYVT  169 (230)
Q Consensus       141 ~V~Cg~Crt~LmyP~-----GA~sVrCa~C~~VT  169 (230)
                      .+.|.+|.+...++.     +...++|+.|+.+-
T Consensus         2 ~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~   35 (38)
T TIGR02098         2 RIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW   35 (38)
T ss_pred             EEECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence            466777777766663     22367777777653

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.

>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=82.49  E-value=2.3  Score=37.01  Aligned_cols=35  Identities=26%  Similarity=0.582  Sum_probs=15.8

Q ss_pred             CceeEEEcCCCCeeeeccC------CCCeEeCCCCCcceee
Q 026941          137 NQFAHIICGHCRTTLMYPH------GAPSVKCAVCQYVTNV  171 (230)
Q Consensus       137 ~q~a~V~Cg~Crt~LmyP~------GA~sVrCa~C~~VT~V  171 (230)
                      .+..+|.|+-|.|.|.+--      ..-+|||.+|...-+|
T Consensus         8 E~lCYVhCnFC~TiLaVsVP~ssL~~~VTVRCGHCtNLLSV   48 (170)
T PF04690_consen    8 EQLCYVHCNFCNTILAVSVPCSSLLKTVTVRCGHCTNLLSV   48 (170)
T ss_pred             CcEEEEEcCCcCeEEEEecchhhhhhhhceeccCccceeee
Confidence            3444455555555444321      2234555555554444

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

Probab=80.38  E-value=1.9  Score=32.30  Aligned_cols=50  Identities=22%  Similarity=0.595  Sum_probs=40.2

Q ss_pred             EEeCCcceeEEeecCCCeEeCCCCCcceecCCCCceeEEEcCCCCeeeeccCCCCeEeCCCCCcc
Q 026941          104 LICGGCRTLLMYTRGATSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYV  168 (230)
Q Consensus       104 LvCggCr~lL~YP~GA~sVrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP~GA~sVrCa~C~~V  168 (230)
                      -+|..|...|.--.++...-||.|.-+         ...+|..||.+      ...++|+.|.+.
T Consensus        10 ~~CtSCg~~i~p~e~~v~F~CPnCGe~---------~I~Rc~~CRk~------g~~Y~Cp~CGF~   59 (61)
T COG2888          10 PVCTSCGREIAPGETAVKFPCPNCGEV---------EIYRCAKCRKL------GNPYRCPKCGFE   59 (61)
T ss_pred             ceeccCCCEeccCCceeEeeCCCCCce---------eeehhhhHHHc------CCceECCCcCcc
Confidence            589999999988889999999999633         35689999975      346789988864

---

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	230
1qxf_A	66	GR2, 30S ribosomal protein S27E; structural genomi	93.41
3j20_W	63	30S ribosomal protein S27E; archaea, archaeal, KIN	92.53
2xzm_6	81	RPS27E; ribosome, translation; 3.93A {Tetrahymena	91.75
1qxf_A	66	GR2, 30S ribosomal protein S27E; structural genomi	89.7
3u5c_b	82	RP61, YS20, 40S ribosomal protein S27-A; translati	89.4
3iz6_X	86	40S ribosomal protein S27 (S27E); eukaryotic ribos	89.26
3j20_W	63	30S ribosomal protein S27E; archaea, archaeal, KIN	88.62
2xzm_6	81	RPS27E; ribosome, translation; 3.93A {Tetrahymena	85.55

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

Probab=93.41  E-value=0.053  Score=39.85  Aligned_cols=39  Identities=21%  Similarity=0.386  Sum_probs=31.2

Q ss_pred             eEeCCCCCcceecCCCCceeEEEcCCCCeeeeccCCCCeE
Q 026941          121 SVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSV  160 (230)
Q Consensus       121 sVrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP~GA~sV  160 (230)
                      .|+|+.|..++.|=+-++. .|.|..|.++|--|.|-.+-
T Consensus         7 ~VKCp~C~niq~VFShA~t-vV~C~~Cg~~L~~PTGGKA~   45 (66)
T 1qxf_A            7 KVKCPDCEHEQVIFDHPST-IVKCIICGRTVAEPTGGKGN   45 (66)
T ss_dssp             EEECTTTCCEEEEESSCSS-CEECSSSCCEEEECCSSSCE
T ss_pred             EEECCCCCCceEEEecCce-EEEcccCCCEEeecCCccee
Confidence            5899999988887665555 78999999999999876543

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

Probab=92.53  E-value=0.081  Score=38.49  Aligned_cols=37  Identities=24%  Similarity=0.488  Sum_probs=22.4

Q ss_pred             eEeCCCCCcceecCCCCceeEEEcCCCCeeeeccCCCC
Q 026941          121 SVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAP  158 (230)
Q Consensus       121 sVrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP~GA~  158 (230)
                      .|+|+.|..++.|=+-.+. .|.|.+|.+.|--|.|-.
T Consensus        15 ~VkCp~C~~~q~VFSha~t-~V~C~~Cgt~L~~PTGGK   51 (63)
T 3j20_W           15 RVKCIDCGNEQIVFSHPAT-KVRCLICGATLVEPTGGK   51 (63)
T ss_dssp             EEECSSSCCEEEEESSCSS-CEECSSSCCEEEECCSSS
T ss_pred             EEECCCCCCeeEEEecCCe-EEEccCcCCEEecCCCCc
Confidence            4666666666655443333 567777777777776643

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

Probab=91.75  E-value=0.16  Score=38.60  Aligned_cols=38  Identities=26%  Similarity=0.581  Sum_probs=20.5

Q ss_pred             eeecCCCCcccccCCCCCceeEEEeCCcceeEEeecCCCe
Q 026941           82 NVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATS  121 (230)
Q Consensus        82 ~VrCa~C~tVt~Vpp~~~q~~qLvCggCr~lL~YP~GA~s  121 (230)
                      -|+|+.|..++.|=  ++....+.|.+|.++|..|.|--.
T Consensus        32 ~VkCp~C~n~q~VF--ShA~t~V~C~~Cg~~L~~PTGGKA   69 (81)
T 2xzm_6           32 DVKCAQCQNIQMIF--SNAQSTIICEKCSAILCKPTGGKV   69 (81)
T ss_dssp             EEECSSSCCEEEEE--TTCSSCEECSSSCCEEEEECSSCE
T ss_pred             EeECCCCCCeeEEE--ecCccEEEccCCCCEEeecCCCCe
Confidence            35666665555552  233445555555555555555443

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

Probab=89.70  E-value=0.21  Score=36.63  Aligned_cols=38  Identities=16%  Similarity=0.261  Sum_probs=24.3

Q ss_pred             eeecCCCCcccccCCCCCceeEEEeCCcceeEEeecCCCe
Q 026941           82 NVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATS  121 (230)
Q Consensus        82 ~VrCa~C~tVt~Vpp~~~q~~qLvCggCr~lL~YP~GA~s  121 (230)
                      .|+|+.|..++-+=  +.....+.|.+|.++|..|.|-..
T Consensus         7 ~VKCp~C~niq~VF--ShA~tvV~C~~Cg~~L~~PTGGKA   44 (66)
T 1qxf_A            7 KVKCPDCEHEQVIF--DHPSTIVKCIICGRTVAEPTGGKG   44 (66)
T ss_dssp             EEECTTTCCEEEEE--SSCSSCEECSSSCCEEEECCSSSC
T ss_pred             EEECCCCCCceEEE--ecCceEEEcccCCCEEeecCCcce
Confidence            36777776666652  233456777777777777777543

>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=89.40  E-value=0.16  Score=38.62  Aligned_cols=44  Identities=30%  Similarity=0.539  Sum_probs=23.1

Q ss_pred             cCCC-CeeecCCCCcccccCCCCCceeEEEeCCcceeEEeecCCCeE
Q 026941           77 PRGA-TNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATSV  122 (230)
Q Consensus        77 P~GA-~~VrCa~C~tVt~Vpp~~~q~~qLvCggCr~lL~YP~GA~sV  122 (230)
                      |++- .-|+|+.|..++-|=  ++....+.|.+|.++|..|.|--.-
T Consensus        28 PnS~Fm~VkCp~C~~~q~VF--Sha~t~V~C~~Cg~~L~~PTGGKa~   72 (82)
T 3u5c_b           28 PRSYFLDVKCPGCLNITTVF--SHAQTAVTCESCSTILCTPTGGKAK   72 (82)
T ss_dssp             CCCCEEEEECTTSCSCEEEE--SBCSSCCCCSSSCCCCEECCSSBCE
T ss_pred             CCCcEEEEECCCCCCeeEEE--ecCCeEEEccccCCEEeccCCCCeE
Confidence            4443 246666666666552  3334455566666666655554433

>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=89.26  E-value=0.19  Score=38.53  Aligned_cols=43  Identities=26%  Similarity=0.588  Sum_probs=22.2

Q ss_pred             EeCCCCCcceecCCCCceeEEEcCCCCeeeeccCCCCeEeCCCC
Q 026941          122 VRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVC  165 (230)
Q Consensus       122 VrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP~GA~sVrCa~C  165 (230)
                      |+|+.|..++.|=+-++. .|.|.+|.+.|--|.|-.+--=..|
T Consensus        37 VkCp~C~~~~~VFShA~t-~V~C~~CgtvL~~PTGGKa~l~egc   79 (86)
T 3iz6_X           37 VKCQGCFNITTVFSHSQT-VVVCPGCQTVLCQPTGGKARLTEGC   79 (86)
T ss_dssp             EECTTTCCEEEEETTCSS-CCCCSSSCCCCSCCCSSSCCCSCBC
T ss_pred             EECCCCCCeeEEEecCCc-EEEccCCCCEeecCCCCCEEecCCc
Confidence            555555555554433333 4556666666666655544433333

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

Probab=88.62  E-value=0.31  Score=35.44  Aligned_cols=42  Identities=24%  Similarity=0.380  Sum_probs=25.5

Q ss_pred             cCCC-CeeecCCCCcccccCCCCCceeEEEeCCcceeEEeecCCC
Q 026941           77 PRGA-TNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGAT  120 (230)
Q Consensus        77 P~GA-~~VrCa~C~tVt~Vpp~~~q~~qLvCggCr~lL~YP~GA~  120 (230)
                      |++. .-|+|+.|..++-+=  ++....+.|.+|.++|..|.|--
T Consensus         9 PnS~Fm~VkCp~C~~~q~VF--Sha~t~V~C~~Cgt~L~~PTGGK   51 (63)
T 3j20_W            9 PRSRFLRVKCIDCGNEQIVF--SHPATKVRCLICGATLVEPTGGK   51 (63)
T ss_dssp             CSCCEEEEECSSSCCEEEEE--SSCSSCEECSSSCCEEEECCSSS
T ss_pred             CCCcEEEEECCCCCCeeEEE--ecCCeEEEccCcCCEEecCCCCc
Confidence            4444 247777776666652  23345677777777777777643

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

Probab=85.55  E-value=0.57  Score=35.53  Aligned_cols=44  Identities=30%  Similarity=0.610  Sum_probs=23.7

Q ss_pred             eEeCCCCCcceecCCCCceeEEEcCCCCeeeeccCCCCeEeCCCC
Q 026941          121 SVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVC  165 (230)
Q Consensus       121 sVrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP~GA~sVrCa~C  165 (230)
                      .|+|+.|..++.|=+-++. .|.|.+|.+.|--|.|-.+--=..|
T Consensus        32 ~VkCp~C~n~q~VFShA~t-~V~C~~Cg~~L~~PTGGKA~l~egc   75 (81)
T 2xzm_6           32 DVKCAQCQNIQMIFSNAQS-TIICEKCSAILCKPTGGKVQIQAGC   75 (81)
T ss_dssp             EEECSSSCCEEEEETTCSS-CEECSSSCCEEEEECSSCEEECSSC
T ss_pred             EeECCCCCCeeEEEecCcc-EEEccCCCCEEeecCCCCeEecCCc
Confidence            3555555555555443333 5666666666666666554433333

---

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	230
d1qxfa_	58	Ribosomal protein S27e {Archaeon Archaeoglobus ful	92.62
d1qxfa_	58	Ribosomal protein S27e {Archaeon Archaeoglobus ful	89.49

>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=92.62  E-value=0.042  Score=37.70  Aligned_cols=38  Identities=21%  Similarity=0.415  Sum_probs=28.7

Q ss_pred             eEeCCCCCcceecCCCCceeEEEcCCCCeeeeccCCCCe
Q 026941          121 SVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPS  159 (230)
Q Consensus       121 sVrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP~GA~s  159 (230)
                      .|+|+.|..++.+=+-++. .|.|..|.++|..|.|-.+
T Consensus         7 ~VkC~~C~n~~ivFsha~t-~V~C~~Cg~~L~~PtGGKa   44 (58)
T d1qxfa_           7 KVKCPDCEHEQVIFDHPST-IVKCIICGRTVAEPTGGKG   44 (58)
T ss_dssp             EEECTTTCCEEEEESSCSS-CEECSSSCCEEEECCSSSC
T ss_pred             EeECCCCCCeEEEEecCce-EEEccccCCEEeccCCCeE
Confidence            5788888888876554444 7888888888888887653

>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=89.49  E-value=0.11  Score=35.55  Aligned_cols=37  Identities=16%  Similarity=0.265  Sum_probs=23.8

Q ss_pred             eeecCCCCcccccCCCCCceeEEEeCCcceeEEeecCCC
Q 026941           82 NVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGAT  120 (230)
Q Consensus        82 ~VrCa~C~tVt~Vpp~~~q~~qLvCggCr~lL~YP~GA~  120 (230)
                      .|+|+.|..++-+=  ++....+.|..|.++|..|.|--
T Consensus         7 ~VkC~~C~n~~ivF--sha~t~V~C~~Cg~~L~~PtGGK   43 (58)
T d1qxfa_           7 KVKCPDCEHEQVIF--DHPSTIVKCIICGRTVAEPTGGK   43 (58)
T ss_dssp             EEECTTTCCEEEEE--SSCSSCEECSSSCCEEEECCSSS
T ss_pred             EeECCCCCCeEEEE--ecCceEEEccccCCEEeccCCCe
Confidence            36777776666652  23345677777777777777754