Citrus Sinensis ID: 034324

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------10
Protein Sequence
MPVPLAPYPTPPAPYTPPANGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEGI
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccEEEccccccEEEEcccccEEEccccccccccccccccEEEEEEcccccEEEEEccccEEEcccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccHHHEEEcccccEEEEEccccccEEEccccEEEccccccccEEEEEEcccEEEEEEccccccccccHHHHHHHHHHHc
Coil and Loop (DISEMBL)
mpvplapyptppapytppangaqsqlvcsgcrnlllypvgaTSVCCAVcnavtavpppgtemaqLVCGGCHTLLMYIRGAtsvqcscchtvNLALEGI
Flexible Loop (DISEMBL)
MPVPLAPYPTPPAPYTPPANGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEGI
Low Complexity Region (SEG)
MpvplapyptppapytppaNGAQSQLVCSGCRNLLLYPVGATSvccavcnavtavpppGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEGI
Disordered region (IsUnstruct)
************************QLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLAL***
Disordered Region (DISOPRED)
*************************LVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEG*
Disordered Region (DISEMBL)
MPVPLAPYPTPPAPYTPPANGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEGI
Disordered Region (DISPRO)
*PVPLAPYPTPPAPYTPPANGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEGI
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooohhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPVPLAPYPTPPAPYTPPANGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEGI
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	98	2.2.26 [Sep-21-2011]
Q93ZB1	154	Protein LOL1 OS=Arabidops	yes	no	0.826	0.525	0.940	8e-38
Q0J7V9	184	Protein LSD1 OS=Oryza sat	yes	no	0.969	0.516	0.885	2e-36
Q2QMB3	172	Protein LOL2 OS=Oryza sat	no	no	0.724	0.412	0.708	2e-22
Q6ASS2	186	Protein LOL3 OS=Oryza sat	no	no	0.724	0.381	0.671	4e-21
P94077	189	Protein LSD1 OS=Arabidops	no	no	0.724	0.375	0.630	9e-19
Q84UR0	147	Protein LOL4 OS=Oryza sat	no	no	0.714	0.476	0.478	1e-12
Q69UP7	147	Protein LOL1 OS=Oryza sat	no	no	0.520	0.346	0.648	5e-12
O65426	155	Protein LOL2 OS=Arabidops	no	no	0.704	0.445	0.4	6e-07
Q704V3	163	Protein LOL5 OS=Oryza sat	no	no	0.693	0.417	0.434	2e-05

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

 Score =  155 bits (392), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 79/84 (94%), Positives = 81/84 (96%), Gaps = 3/84 (3%)

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

Query: 73  LLMYIRGATSVQCSCCHTVNLALE 96
           LLMYIRGATSVQCSCCHTVNLALE
Sbjct: 82  LLMYIRGATSVQCSCCHTVNLALE 105

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 =  150 bits (379), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 85/96 (88%), Positives = 88/96 (91%), Gaps = 1/96 (1%)

Query: 1   MPVPLAPYPTPPAPYTPPANGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGT 60
           MPVPLAPYPTPP P   P NGAQSQLVCSGCRNLL+YP GATSVCCAVC+ VTAVP PGT
Sbjct: 42  MPVPLAPYPTPPVP-FTPPNGAQSQLVCSGCRNLLMYPAGATSVCCAVCSTVTAVPAPGT 100

Query: 61  EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALE 96
           EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLA+E
Sbjct: 101 EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLAME 136

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

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  104 bits (259), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 51/72 (70%), Positives = 60/72 (83%), Gaps = 1/72 (1%)

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

Query: 82 SVQCSCCHTVNL 93
          SV+CSCC TVNL
Sbjct: 62 SVRCSCCDTVNL 73

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

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score = 99.8 bits (247), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 49/73 (67%), Positives = 57/73 (78%), Gaps = 2/73 (2%)

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

Query: 81 TSVQCSCCHTVNL 93
           +V+CSCC TVNL
Sbjct: 62 DTVRCSCCSTVNL 74

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 = 92.0 bits (227), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 46/73 (63%), Positives = 57/73 (78%), Gaps = 2/73 (2%)

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

Query: 81 TSVQCSCCHTVNL 93
          +SV+CSCC T NL
Sbjct: 67 SSVRCSCCQTTNL 79

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 = 71.6 bits (174), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/71 (47%), Positives = 48/71 (67%), Gaps = 1/71 (1%)

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

Query: 82 SVQCSCCHTVN 92
          +++C  C+ +N
Sbjct: 62 NIRCPSCNRLN 72

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

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score = 69.7 bits (169), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 35/54 (64%), Positives = 40/54 (74%)

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

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

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score = 52.8 bits (125), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 28/70 (40%), Positives = 40/70 (57%), Gaps = 1/70 (1%)

Query: 22  AQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGAT 81
            ++Q+VC  CR LL Y  G+  V C+ C  V  V     ++ Q+ C  C  LLMY  GA 
Sbjct: 57  EKAQMVCGSCRRLLSYLRGSKHVKCSSCQTVNLVLE-ANQVGQVNCNNCKLLLMYPYGAP 115

Query: 82  SVQCSCCHTV 91
           +V+CS C++V
Sbjct: 116 AVRCSSCNSV 125

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 = 47.4 bits (111), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 30/69 (43%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 20  NGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRG 79
           N    Q+VC  CR LL Y  GA  V C  C  +  V     E+ ++ CG C TLLMY  G
Sbjct: 65  NKEVGQMVCGSCRILLAYFRGAGYVHCTCCQTMNYV-LEAHEVGKVHCGHCATLLMYPFG 123

Query: 80  ATSVQCSCC 88
           A +V+CS C
Sbjct: 124 APAVKCSLC 132

Involved in plant growth and disease resistance.

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	98
297742122	230	unnamed protein product [Vitis vinifera]	0.989	0.421	0.917	2e-44
225427256	145	PREDICTED: protein LOL1-like [Vitis vini	0.989	0.668	0.917	2e-43
147810699	146	hypothetical protein VITISV_014138 [Viti	0.989	0.664	0.917	2e-43
388492562	146	unknown [Lotus japonicus]	0.989	0.664	0.908	2e-41
346472259	145	hypothetical protein [Amblyomma maculatu	0.969	0.655	0.896	6e-40
158516901	142	LOL1 [Bambusa oldhamii]	0.959	0.661	0.854	1e-37
388497348	145	unknown [Lotus japonicus]	0.979	0.662	0.968	4e-37
449461519	144	PREDICTED: protein LOL1-like isoform 1 [	0.979	0.666	0.947	8e-37
255574680	147	conserved hypothetical protein [Ricinus	0.979	0.653	0.918	1e-36
351723389	145	uncharacterized protein LOC100306356 [Gl	0.979	0.662	0.968	1e-36

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

 Score =  182 bits (463), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 89/97 (91%), Positives = 91/97 (93%)

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

Query: 61  EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEG 97
           EMAQLVCGGCHTLLMYIRGATSVQCSCCHT+NLALE 
Sbjct: 146 EMAQLVCGGCHTLLMYIRGATSVQCSCCHTINLALEA 182

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  179 bits (455), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 89/97 (91%), Positives = 91/97 (93%)

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

Query: 61 EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEG 97
          EMAQLVCGGCHTLLMYIRGATSVQCSCCHT+NLALE 
Sbjct: 61 EMAQLVCGGCHTLLMYIRGATSVQCSCCHTINLALEA 97

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  179 bits (453), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 89/97 (91%), Positives = 91/97 (93%)

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

Query: 61 EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEG 97
          EMAQLVCGGCHTLLMYIRGATSVQCSCCHT+NLALE 
Sbjct: 61 EMAQLVCGGCHTLLMYIRGATSVQCSCCHTINLALEA 97

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  172 bits (437), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 89/98 (90%), Positives = 91/98 (92%), Gaps = 1/98 (1%)

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

Query: 60 TEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEG 97
          TEMAQLVCGGCHTL+MYIRGATSVQCSCCHTVNLALE 
Sbjct: 61 TEMAQLVCGGCHTLIMYIRGATSVQCSCCHTVNLALEA 98

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  167 bits (424), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 87/97 (89%), Positives = 92/97 (94%), Gaps = 2/97 (2%)

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

Query: 60 TEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALE 96
          TEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLAL+
Sbjct: 60 TEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALD 96

Source: Amblyomma maculatum

Species: Amblyomma maculatum

Genus: Amblyomma

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  160 bits (404), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 82/96 (85%), Positives = 89/96 (92%), Gaps = 2/96 (2%)

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

Query: 61 EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALE 96
          EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLA+E
Sbjct: 59 EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLAME 94

Source: Bambusa oldhamii

Species: Bambusa oldhamii

Genus: Bambusa

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  158 bits (399), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 93/96 (96%), Positives = 95/96 (98%)

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

Query: 61 EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALE 96
          EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALE
Sbjct: 61 EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALE 96

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  157 bits (397), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 91/96 (94%), Positives = 92/96 (95%)

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

Query: 62 MAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEG 97
          MAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALE 
Sbjct: 63 MAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEA 98

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  157 bits (396), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 90/98 (91%), Positives = 92/98 (93%), Gaps = 2/98 (2%)

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

Query: 59 GTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALE 96
          GTEMAQLVCGGCHTLLMYIRGATSVQCSCCHT+NLA+E
Sbjct: 61 GTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTINLAME 98

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  156 bits (395), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 93/96 (96%), Positives = 95/96 (98%)

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

Query: 61 EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALE 96
          EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALE
Sbjct: 61 EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALE 96

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	98
UNIPROTKB|Q0J7V9	184	LSD1 "Protein LSD1" [Oryza sat	0.785	0.418	0.766	5e-28
UNIPROTKB|F8RP38	176	F8RP38 "Zinc finger protein LS	0.734	0.409	0.638	1.7e-20
TAIR|locus:2128639	210	LSD1 "LESION SIMULATING DISEAS	0.755	0.352	0.5	2e-15
TAIR|locus:2119622	155	LOL2 "AT4G21610" [Arabidopsis	0.367	0.232	0.611	8.7e-08
UNIPROTKB|Q704V3	163	LOL5 "Protein LOL5" [Oryza sat	0.367	0.220	0.555	2.9e-07

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

 Score = 313 (115.2 bits), Expect = 5.0e-28, P = 5.0e-28
 Identities = 59/77 (76%), Positives = 61/77 (79%)

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

Query:    80 ATSVQCSCCHTVNLALE 96
             ATSVQCSCCHTVNLA+E
Sbjct:   120 ATSVQCSCCHTVNLAME 136

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 = 242 (90.2 bits), Expect = 1.7e-20, P = 1.7e-20
 Identities = 46/72 (63%), Positives = 52/72 (72%)

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

Query:    83 VQCSCCHTVNLA 94
             V+CSCCHTVNLA
Sbjct:    62 VRCSCCHTVNLA 73

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 = 194 (73.4 bits), Expect = 2.0e-15, P = 2.0e-15
 Identities = 38/76 (50%), Positives = 47/76 (61%)

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

Query:    81 TSVQCSCCHTVNLALE 96
             +SV+CSCC T NL  E
Sbjct:    62 SSVRCSCCQTTNLVPE 77

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 = 122 (48.0 bits), Expect = 8.7e-08, P = 8.7e-08
 Identities = 22/36 (61%), Positives = 26/36 (72%)

Query:    61 EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALE 96
             E AQ+VCG C  LL Y+RG+  V+CS C TVNL LE
Sbjct:    57 EKAQMVCGSCRRLLSYLRGSKHVKCSSCQTVNLVLE 92

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 = 117 (46.2 bits), Expect = 2.9e-07, P = 2.9e-07
 Identities = 20/36 (55%), Positives = 24/36 (66%)

Query:    61 EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALE 96
             E+ Q+VCG C  LL Y RGA  V C+CC T+N  LE
Sbjct:    67 EVGQMVCGSCRILLAYFRGAGYVHCTCCQTMNYVLE 102

GO:0005634 "nucleus" evidence=IDA

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

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

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q93ZB1	LOL1_ARATH	No assigned EC number	0.9404	0.8265	0.5259	yes	no
Q0J7V9	LSD1_ORYSJ	No assigned EC number	0.8854	0.9693	0.5163	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!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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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	98
TIGR01053	31	TIGR01053, LSD1, zinc finger domain, LSD1 subclass	3e-07
pfam06943	25	pfam06943, zf-LSD1, LSD1 zinc finger	7e-07
pfam06943	25	pfam06943, zf-LSD1, LSD1 zinc finger	5e-06
TIGR01053	31	TIGR01053, LSD1, zinc finger domain, LSD1 subclass	2e-05

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

 Score = 42.4 bits (100), Expect = 3e-07
 Identities = 22/30 (73%), Positives = 26/30 (86%)

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

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

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

 Score = 41.4 bits (98), Expect = 7e-07
 Identities = 18/25 (72%), Positives = 21/25 (84%)

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

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

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

 Score = 39.5 bits (93), Expect = 5e-06
 Identities = 17/25 (68%), Positives = 19/25 (76%)

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

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

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

 Score = 37.8 bits (88), Expect = 2e-05
 Identities = 19/31 (61%), Positives = 23/31 (74%)

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

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	98
TIGR01053	31	LSD1 zinc finger domain, LSD1 subclass. This model	99.58
PF06943	25	zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zin	99.54
TIGR01053	31	LSD1 zinc finger domain, LSD1 subclass. This model	99.53
PF06943	25	zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zin	99.47
PF10122	51	Mu-like_Com: Mu-like prophage protein Com; InterPr	95.75
PF10122	51	Mu-like_Com: Mu-like prophage protein Com; InterPr	95.56
PF09788	256	Tmemb_55A: Transmembrane protein 55A; InterPro: IP	93.88
PLN00209	86	ribosomal protein S27; Provisional	92.93
PTZ00083	85	40S ribosomal protein S27; Provisional	92.5
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	92.46
PF01667	55	Ribosomal_S27e: Ribosomal protein S27; InterPro: I	92.23
PF11331	46	DUF3133: Protein of unknown function (DUF3133); In	92.01
PRK00415	59	rps27e 30S ribosomal protein S27e; Reviewed	91.59
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	91.3
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	90.74
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	90.68
KOG1546	362	consensus Metacaspase involved in regulation of ap	90.23
COG2051	67	RPS27A Ribosomal protein S27E [Translation, riboso	89.97
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	89.04
PF09788	256	Tmemb_55A: Transmembrane protein 55A; InterPro: IP	86.73
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	86.11
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	85.51
KOG1779	84	consensus 40s ribosomal protein S27 [Translation,	84.39
PF12773	50	DZR: Double zinc ribbon	84.08
PF04810	40	zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro:	81.76
COG4357	105	Zinc finger domain containing protein (CHY type) [	80.46
PF07754	24	DUF1610: Domain of unknown function (DUF1610); Int	80.28

>TIGR01053 LSD1 zinc finger domain, LSD1 subclass

Probab=99.58  E-value=7.3e-16  Score=88.02  Aligned_cols=30  Identities=60%  Similarity=1.247  Sum_probs=21.0

Q ss_pred             eEEcCCCCeeeeecCCCCeEecCCCCcccc
Q 034324           25 QLVCSGCRNLLLYPVGATSVCCAVCNAVTA   54 (98)
Q Consensus        25 QlvC~gCr~lL~Yp~GA~~VrC~~C~tVn~   54 (98)
                      |++|++||++|+||+||++|||+.|++||.
T Consensus         1 q~~C~~C~t~L~yP~gA~~vrCs~C~~vt~   30 (31)
T TIGR01053         1 QVVCGGCRTLLMYPRGASSVRCALCQTVNL   30 (31)
T ss_pred             CcCcCCCCcEeecCCCCCeEECCCCCeEec
Confidence            566777777777777777777777777664

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

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

Probab=99.54  E-value=3.5e-15  Score=82.12  Aligned_cols=25  Identities=64%  Similarity=1.364  Sum_probs=17.6

Q ss_pred             cCCCCeeeeecCCCCeEecCCCCcc
Q 034324           28 CSGCRNLLLYPVGATSVCCAVCNAV   52 (98)
Q Consensus        28 C~gCr~lL~Yp~GA~~VrC~~C~tV   52 (98)
                      |+|||++|+||+||+||||+.|++|
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            6677777777777777777777665

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=99.53  E-value=3e-15  Score=85.48  Aligned_cols=31  Identities=71%  Similarity=1.338  Sum_probs=29.6

Q ss_pred             EEEeCCcCceEEeecCCCeEECCCCCccccc
Q 034324           64 QLVCGGCHTLLMYIRGATSVQCSCCHTVNLA   94 (98)
Q Consensus        64 ql~Cg~Cr~lL~yP~GA~sVrC~~C~~Vt~v   94 (98)
                      |++|++||++|+||+||++|||+.|++||.|
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            6899999999999999999999999999975

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=99.47  E-value=2.5e-14  Score=78.75  Aligned_cols=25  Identities=80%  Similarity=1.666  Sum_probs=24.3

Q ss_pred             eCCcCceEEeecCCCeEECCCCCcc
Q 034324           67 CGGCHTLLMYIRGATSVQCSCCHTV   91 (98)
Q Consensus        67 Cg~Cr~lL~yP~GA~sVrC~~C~~V   91 (98)
                      ||+||++||||+||+||||+.|++|
T Consensus         1 C~~Cr~~L~yp~GA~sVrCa~C~~V   25 (25)
T PF06943_consen    1 CGGCRTLLMYPRGAPSVRCACCHTV   25 (25)
T ss_pred             CCCCCceEEcCCCCCCeECCccCcC
Confidence            8999999999999999999999987

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

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

Probab=95.75  E-value=0.0048  Score=39.05  Aligned_cols=32  Identities=28%  Similarity=0.632  Sum_probs=16.7

Q ss_pred             EEEeCCcCceEEee--cCCCeEECCCCCcccccc
Q 034324           64 QLVCGGCHTLLMYI--RGATSVQCSCCHTVNLAL   95 (98)
Q Consensus        64 ql~Cg~Cr~lL~yP--~GA~sVrC~~C~~Vt~v~   95 (98)
                      .+.|++|+.+|+.-  ..-..++|+-|.++|.++
T Consensus         4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~   37 (51)
T PF10122_consen    4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVR   37 (51)
T ss_pred             ceeccchhHHHhhhcCccEEEEECCCCCccceEe
Confidence            34555555555553  222355566666655554

>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=95.56  E-value=0.0068  Score=38.38  Aligned_cols=36  Identities=19%  Similarity=0.488  Sum_probs=30.2

Q ss_pred             CceeEEcCCCCeeeeecCCCC--eEecCCCCccccCCC
Q 034324           22 AQSQLVCSGCRNLLLYPVGAT--SVCCAVCNAVTAVPP   57 (98)
Q Consensus        22 ~~sQlvC~gCr~lL~Yp~GA~--~VrC~~C~tVn~vp~   57 (98)
                      |+-++.|+.|..||...-++.  .+.|+.|.++|.+.+
T Consensus         1 m~~eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a   38 (51)
T PF10122_consen    1 MLKEIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRA   38 (51)
T ss_pred             CCcceeccchhHHHhhhcCccEEEEECCCCCccceEec
Confidence            345789999999999975665  889999999998764

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

Probab=93.88  E-value=0.11  Score=41.85  Aligned_cols=36  Identities=19%  Similarity=0.536  Sum_probs=30.6

Q ss_pred             CceeEEEeCCcCceEEeecCC--CeEECCCCCcccccc
Q 034324           60 TEMAQLVCGGCHTLLMYIRGA--TSVQCSCCHTVNLAL   95 (98)
Q Consensus        60 ~~~aql~Cg~Cr~lL~yP~GA--~sVrC~~C~~Vt~v~   95 (98)
                      ..+.-++||+|+...+++.=.  ...||+.|+.|..|-
T Consensus       153 p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKvSSVG  190 (256)
T PF09788_consen  153 PGSCRVICGHCSNTFLFNTLTSNTLARCPHCRKVSSVG  190 (256)
T ss_pred             CCceeEECCCCCCcEeccCCCCCccccCCCCceecccc
Confidence            357889999999999999755  567999999998875

>PLN00209 ribosomal protein S27; Provisional

Probab=92.93  E-value=0.097  Score=36.20  Aligned_cols=40  Identities=30%  Similarity=0.546  Sum_probs=32.3

Q ss_pred             eEecCCCCccccCCCCCCceeEEEeCCcCceEEeecCCCeEE
Q 034324           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQ   84 (98)
Q Consensus        43 ~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~GA~sVr   84 (98)
                      .|+|+.|..++.+=  ++....+.|.+|.++|..|.|-....
T Consensus        36 ~VkCp~C~n~q~VF--ShA~t~V~C~~Cg~~L~~PTGGKa~l   75 (86)
T PLN00209         36 DVKCQGCFNITTVF--SHSQTVVVCGSCQTVLCQPTGGKARL   75 (86)
T ss_pred             EEECCCCCCeeEEE--ecCceEEEccccCCEeeccCCCCeEe
Confidence            58999999998774  35568899999999999999876543

>PTZ00083 40S ribosomal protein S27; Provisional

Probab=92.50  E-value=0.12  Score=35.61  Aligned_cols=40  Identities=28%  Similarity=0.575  Sum_probs=31.7

Q ss_pred             eEecCCCCccccCCCCCCceeEEEeCCcCceEEeecCCCeEE
Q 034324           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQ   84 (98)
Q Consensus        43 ~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~GA~sVr   84 (98)
                      .|+|+.|..++.+=  ++....+.|.+|.++|.-|.|-....
T Consensus        35 ~VkCp~C~n~q~VF--ShA~t~V~C~~Cg~~L~~PTGGKa~l   74 (85)
T PTZ00083         35 DVKCPGCSQITTVF--SHAQTVVLCGGCSSQLCQPTGGKAKL   74 (85)
T ss_pred             EEECCCCCCeeEEE--ecCceEEEccccCCEeeccCCCCeEe
Confidence            58899999988774  34567899999999999999876543

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

Probab=92.46  E-value=0.22  Score=29.38  Aligned_cols=27  Identities=22%  Similarity=0.475  Sum_probs=15.9

Q ss_pred             EEEeCCcCceEEeecCCCeEECCCCCc
Q 034324           64 QLVCGGCHTLLMYIRGATSVQCSCCHT   90 (98)
Q Consensus        64 ql~Cg~Cr~lL~yP~GA~sVrC~~C~~   90 (98)
                      ...|.+|+..+.+..+...++|+-|++
T Consensus         3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~   29 (46)
T PRK00398          3 EYKCARCGREVELDEYGTGVRCPYCGY   29 (46)
T ss_pred             EEECCCCCCEEEECCCCCceECCCCCC
Confidence            345666666666665555666666654

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

Probab=92.23  E-value=0.13  Score=32.75  Aligned_cols=38  Identities=24%  Similarity=0.417  Sum_probs=25.6

Q ss_pred             eEecCCCCccccCCCCCCceeEEEeCCcCceEEeecCCCe
Q 034324           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATS   82 (98)
Q Consensus        43 ~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~GA~s   82 (98)
                      .|+|+.|..++.+=  .+....+.|.+|.++|.-|.|-..
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            58999999988773  345678999999999999988654

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.

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

Probab=92.01  E-value=0.2  Score=30.92  Aligned_cols=39  Identities=28%  Similarity=0.646  Sum_probs=27.2

Q ss_pred             CCCCeEecCCCCccccCCCC----CCceeEEEeCCcCceEEee
Q 034324           39 VGATSVCCAVCNAVTAVPPP----GTEMAQLVCGGCHTLLMYI   77 (98)
Q Consensus        39 ~GA~~VrC~~C~tVn~vp~~----~~~~aql~Cg~Cr~lL~yP   77 (98)
                      .||+-|-|..|..+=.+|..    .....++.||.|...|.|-
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            36677777777666555532    2347899999999999874

>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed

Probab=91.59  E-value=0.11  Score=33.64  Aligned_cols=37  Identities=22%  Similarity=0.311  Sum_probs=24.0

Q ss_pred             eEecCCCCccccCCCCCCceeEEEeCCcCceEEeecCCC
Q 034324           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGAT   81 (98)
Q Consensus        43 ~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~GA~   81 (98)
                      .|+|+.|..++.+=  ++....+.|..|.++|.-|.|-.
T Consensus        11 ~VkCp~C~n~q~vF--sha~t~V~C~~Cg~~L~~PtGGK   47 (59)
T PRK00415         11 KVKCPDCGNEQVVF--SHASTVVRCLVCGKTLAEPTGGK   47 (59)
T ss_pred             EEECCCCCCeEEEE--ecCCcEEECcccCCCcccCCCcc
Confidence            46777777777542  23346677777777777777643

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

Probab=91.30  E-value=0.33  Score=28.57  Aligned_cols=28  Identities=21%  Similarity=0.455  Sum_probs=20.2

Q ss_pred             eeEEcCCCCeeeeecCCCCeEecCCCCc
Q 034324           24 SQLVCSGCRNLLLYPVGATSVCCAVCNA   51 (98)
Q Consensus        24 sQlvC~gCr~lL~Yp~GA~~VrC~~C~t   51 (98)
                      -...|..|...+.+..+...++|+.|.+
T Consensus         2 ~~y~C~~CG~~~~~~~~~~~~~Cp~CG~   29 (46)
T PRK00398          2 AEYKCARCGREVELDEYGTGVRCPYCGY   29 (46)
T ss_pred             CEEECCCCCCEEEECCCCCceECCCCCC
Confidence            3457777777777777777777777765

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=90.74  E-value=0.27  Score=27.62  Aligned_cols=32  Identities=22%  Similarity=0.571  Sum_probs=17.8

Q ss_pred             EecCCCCccccCCCC--CCceeEEEeCCcCceEE
Q 034324           44 VCCAVCNAVTAVPPP--GTEMAQLVCGGCHTLLM   75 (98)
Q Consensus        44 VrC~~C~tVn~vp~~--~~~~aql~Cg~Cr~lL~   75 (98)
                      +.|+.|.+.+.++.+  ..+...+.|+.|+..+.
T Consensus         3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~   36 (38)
T TIGR02098         3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY   36 (38)
T ss_pred             EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence            567777776665431  11223566666666553

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.

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

Probab=90.68  E-value=0.23  Score=32.25  Aligned_cols=53  Identities=21%  Similarity=0.477  Sum_probs=40.7

Q ss_pred             CceeEEcCCCCeeeeecCC-CCeEecCCCCccccCCCCCCceeEEEeCCcCceEEeecCCCeEECCCCCcc
Q 034324           22 AQSQLVCSGCRNLLLYPVG-ATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTV   91 (98)
Q Consensus        22 ~~sQlvC~gCr~lL~Yp~G-A~~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~GA~sVrC~~C~~V   91 (98)
                      ++.-.+|.+|...| .+++ ++..-|+.|..+...          .|..||.+      +...+|+.|.+.
T Consensus         4 ~~~~~~CtSCg~~i-~~~~~~~~F~CPnCG~~~I~----------RC~~CRk~------~~~Y~CP~CGF~   57 (59)
T PRK14890          4 MMEPPKCTSCGIEI-APREKAVKFLCPNCGEVIIY----------RCEKCRKQ------SNPYTCPKCGFE   57 (59)
T ss_pred             cccCccccCCCCcc-cCCCccCEeeCCCCCCeeEe----------echhHHhc------CCceECCCCCCc
Confidence            44556899999988 4555 999999999876543          48899986      367889999875

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

Probab=90.23  E-value=0.1  Score=43.79  Aligned_cols=30  Identities=30%  Similarity=0.627  Sum_probs=26.0

Q ss_pred             EEeCCcCceEEeecCCCeEECCCCCccccccc
Q 034324           65 LVCGGCHTLLMYIRGATSVQCSCCHTVNLALE   96 (98)
Q Consensus        65 l~Cg~Cr~lL~yP~GA~sVrC~~C~~Vt~v~~   96 (98)
                      +.|. |++.|+.|.||++ +|+.||++|.+.+
T Consensus         5 ~~~~-~~~p~~~pp~ar~-q~~~~~~~~~~~~   34 (362)
T KOG1546|consen    5 VGCN-CQRPMAPPPGARY-QCAGCHAVTQIAQ   34 (362)
T ss_pred             ccCC-CCCCCCCCCCCcc-cccccceeeeecc
Confidence            4565 9999999999999 9999999998763

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

Probab=89.97  E-value=0.37  Score=32.05  Aligned_cols=38  Identities=24%  Similarity=0.337  Sum_probs=28.5

Q ss_pred             eEecCCCCccccCCCCCCceeEEEeCCcCceEEeecCCCe
Q 034324           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATS   82 (98)
Q Consensus        43 ~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~GA~s   82 (98)
                      .|+|..|...+.+=  ++....+.|..|..+|..|.|-..
T Consensus        19 ~VkCpdC~N~q~vF--shast~V~C~~CG~~l~~PTGGka   56 (67)
T COG2051          19 RVKCPDCGNEQVVF--SHASTVVTCLICGTTLAEPTGGKA   56 (67)
T ss_pred             EEECCCCCCEEEEe--ccCceEEEecccccEEEecCCCeE
Confidence            48888888877663  234577889999999999888654

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=89.04  E-value=0.5  Score=27.08  Aligned_cols=14  Identities=29%  Similarity=0.726  Sum_probs=8.2

Q ss_pred             EecCCCCccccCCC
Q 034324           44 VCCAVCNAVTAVPP   57 (98)
Q Consensus        44 VrC~~C~tVn~vp~   57 (98)
                      ++|+.|++.-.++.
T Consensus         3 i~CP~C~~~f~v~~   16 (37)
T PF13719_consen    3 ITCPNCQTRFRVPD   16 (37)
T ss_pred             EECCCCCceEEcCH
Confidence            45666666655543

>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=86.73  E-value=5.8  Score=32.17  Aligned_cols=71  Identities=21%  Similarity=0.479  Sum_probs=50.9

Q ss_pred             CceeEEcCCCCeeeeecCC--CCeEecCCCCccccCCCCCCceeEEEeCCcCceEEeecCCCeEECCC--CCcccc
Q 034324           22 AQSQLVCSGCRNLLLYPVG--ATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSC--CHTVNL   93 (98)
Q Consensus        22 ~~sQlvC~gCr~lL~Yp~G--A~~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~GA~sVrC~~--C~~Vt~   93 (98)
                      .+.-+.|.=|+.++.-.--  =--|+|..|+-.|....+....-.+.| -|.-||+--..++.+-|+.  |..|-.
T Consensus        62 ~~p~v~CrVCq~~I~i~gk~~QhVVkC~~CnEATPIr~aPpGKKYVRC-PCNCLLICk~sS~rIaCPRp~CkRiI~  136 (256)
T PF09788_consen   62 GAPVVTCRVCQSLIDIEGKMHQHVVKCSVCNEATPIRNAPPGKKYVRC-PCNCLLICKSSSQRIACPRPNCKRIIN  136 (256)
T ss_pred             CCceEEeecCCceecccCccceeeEECCCCCccccccCCCCCCeeEec-CCceEEEeecccccccCCCCCCcceEE
Confidence            3457889999988765432  234899999999986554456777888 6777777777777777776  765543

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=86.11  E-value=0.81  Score=26.20  Aligned_cols=27  Identities=30%  Similarity=0.699  Sum_probs=14.3

Q ss_pred             EEeCCcCceEEeec-----CCCeEECCCCCcc
Q 034324           65 LVCGGCHTLLMYIR-----GATSVQCSCCHTV   91 (98)
Q Consensus        65 l~Cg~Cr~lL~yP~-----GA~sVrC~~C~~V   91 (98)
                      +.|-+|.+..-.+.     +...|||+.|+++
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            34555555555443     3455666655554

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=85.51  E-value=1.3  Score=24.80  Aligned_cols=30  Identities=23%  Similarity=0.568  Sum_probs=21.5

Q ss_pred             EEEeCCcCceEEeec-----CCCeEECCCCCcccc
Q 034324           64 QLVCGGCHTLLMYIR-----GATSVQCSCCHTVNL   93 (98)
Q Consensus        64 ql~Cg~Cr~lL~yP~-----GA~sVrC~~C~~Vt~   93 (98)
                      .+.|-+|++...++.     +...|+|+.|+++-.
T Consensus         2 ~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~   36 (38)
T TIGR02098         2 RIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY   36 (38)
T ss_pred             EEECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence            467888888888774     234788888887643

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.

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

Probab=84.39  E-value=1.7  Score=29.99  Aligned_cols=44  Identities=30%  Similarity=0.562  Sum_probs=30.8

Q ss_pred             eEecCCCCccccCCCCCCceeEEEeCCcCceEEeecCCCeEECCCC
Q 034324           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCC   88 (98)
Q Consensus        43 ~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~GA~sVrC~~C   88 (98)
                      .|+|+.|-.||.+=.  +...-++|.+|.+.|.-|.|-..+.=..|
T Consensus        34 ~VkC~gc~~iT~vfS--HaqtvVvc~~c~~il~~~tggra~ls~~c   77 (84)
T KOG1779|consen   34 DVKCPGCFKITTVFS--HAQTVVVCEGCSTILCQPTGGKAKLSEGC   77 (84)
T ss_pred             EEEcCCceEEEEEee--cCceEEEcCCCceEEEEecCCcEEecCCC
Confidence            478888888887642  33456788888888888888776543333

>PF12773 DZR: Double zinc ribbon

Probab=84.08  E-value=0.49  Score=27.74  Aligned_cols=29  Identities=24%  Similarity=0.380  Sum_probs=17.1

Q ss_pred             EEEeCCcCceEEeecCCCeEECCCCCcccc
Q 034324           64 QLVCGGCHTLLMYIRGATSVQCSCCHTVNL   93 (98)
Q Consensus        64 ql~Cg~Cr~lL~yP~GA~sVrC~~C~~Vt~   93 (98)
                      ...|..|++.|. ......+.|+.|.+.+.
T Consensus        12 ~~fC~~CG~~l~-~~~~~~~~C~~Cg~~~~   40 (50)
T PF12773_consen   12 AKFCPHCGTPLP-PPDQSKKICPNCGAENP   40 (50)
T ss_pred             ccCChhhcCChh-hccCCCCCCcCCcCCCc
Confidence            456666666666 44444556666666544

>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=81.76  E-value=0.98  Score=26.21  Aligned_cols=30  Identities=27%  Similarity=0.727  Sum_probs=11.4

Q ss_pred             EcCCCCeee----eecCCCCeEecCCCCccccCC
Q 034324           27 VCSGCRNLL----LYPVGATSVCCAVCNAVTAVP   56 (98)
Q Consensus        27 vC~gCr~lL----~Yp~GA~~VrC~~C~tVn~vp   56 (98)
                      .|..|+..|    .+..+...-.|..|++.|.+|
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            455555544    233445555555555555543

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 ....

>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]

Probab=80.46  E-value=0.36  Score=34.48  Aligned_cols=27  Identities=26%  Similarity=0.615  Sum_probs=24.8

Q ss_pred             EEcCCCCeeeeecCCCCeEecCCCCcc
Q 034324           26 LVCSGCRNLLLYPVGATSVCCAVCNAV   52 (98)
Q Consensus        26 lvC~gCr~lL~Yp~GA~~VrC~~C~tV   52 (98)
                      ++||-||.+|.+..=-..++|+.|++-
T Consensus        63 iiCGvC~~~LT~~EY~~~~~Cp~C~sp   89 (105)
T COG4357          63 IICGVCRKLLTRAEYGMCGSCPYCQSP   89 (105)
T ss_pred             EEhhhhhhhhhHHHHhhcCCCCCcCCC
Confidence            899999999999988888999999874

>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species

Probab=80.28  E-value=1.5  Score=23.82  Aligned_cols=22  Identities=27%  Similarity=0.678  Sum_probs=13.2

Q ss_pred             eCCcCceEEeecC-CCeEECCCCC
Q 034324           67 CGGCHTLLMYIRG-ATSVQCSCCH   89 (98)
Q Consensus        67 Cg~Cr~lL~yP~G-A~sVrC~~C~   89 (98)
                      |.+|...|. |++ +..+.|+.|.
T Consensus         1 C~sC~~~i~-~r~~~v~f~CPnCG   23 (24)
T PF07754_consen    1 CTSCGRPIA-PREQAVPFPCPNCG   23 (24)
T ss_pred             CccCCCccc-CcccCceEeCCCCC
Confidence            445555554 666 6667777664

It is likely to bind zinc via its four well-conserved cysteine residues.

---

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	98
1qxf_A	66	GR2, 30S ribosomal protein S27E; structural genomi	92.97
3j20_W	63	30S ribosomal protein S27E; archaea, archaeal, KIN	92.5
2xzm_6	81	RPS27E; ribosome, translation; 3.93A {Tetrahymena	92.13
3u5c_b	82	RP61, YS20, 40S ribosomal protein S27-A; translati	89.37
3iz6_X	86	40S ribosomal protein S27 (S27E); eukaryotic ribos	86.4

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

Probab=92.97  E-value=0.051  Score=35.02  Aligned_cols=38  Identities=16%  Similarity=0.262  Sum_probs=30.1

Q ss_pred             eEecCCCCccccCCCCCCceeEEEeCCcCceEEeecCCCe
Q 034324           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATS   82 (98)
Q Consensus        43 ~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~GA~s   82 (98)
                      .|+|+.|..++.+=  ++....+.|.+|.++|..|.|-..
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            58999999888764  234577899999999999988654

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

Probab=92.50  E-value=0.063  Score=34.28  Aligned_cols=38  Identities=21%  Similarity=0.328  Sum_probs=27.5

Q ss_pred             eEecCCCCccccCCCCCCceeEEEeCCcCceEEeecCCCe
Q 034324           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATS   82 (98)
Q Consensus        43 ~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~GA~s   82 (98)
                      .|+|+.|..++.+=  .+....+.|.+|.++|..|.|-..
T Consensus        15 ~VkCp~C~~~q~VF--Sha~t~V~C~~Cgt~L~~PTGGKa   52 (63)
T 3j20_W           15 RVKCIDCGNEQIVF--SHPATKVRCLICGATLVEPTGGKG   52 (63)
T ss_dssp             EEECSSSCCEEEEE--SSCSSCEECSSSCCEEEECCSSSC
T ss_pred             EEECCCCCCeeEEE--ecCCeEEEccCcCCEEecCCCCcE
Confidence            47888888877763  344567888888888888887543

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

Probab=92.13  E-value=0.079  Score=35.30  Aligned_cols=39  Identities=21%  Similarity=0.524  Sum_probs=28.0

Q ss_pred             eEecCCCCccccCCCCCCceeEEEeCCcCceEEeecCCCeE
Q 034324           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSV   83 (98)
Q Consensus        43 ~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~GA~sV   83 (98)
                      .|+|+.|..++.+=  ++....+.|.+|.++|..|.|-..-
T Consensus        32 ~VkCp~C~n~q~VF--ShA~t~V~C~~Cg~~L~~PTGGKA~   70 (81)
T 2xzm_6           32 DVKCAQCQNIQMIF--SNAQSTIICEKCSAILCKPTGGKVQ   70 (81)
T ss_dssp             EEECSSSCCEEEEE--TTCSSCEECSSSCCEEEEECSSCEE
T ss_pred             EeECCCCCCeeEEE--ecCccEEEccCCCCEEeecCCCCeE
Confidence            47888888777763  2445678888888888888876543

>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=89.37  E-value=0.089  Score=35.12  Aligned_cols=40  Identities=25%  Similarity=0.468  Sum_probs=26.8

Q ss_pred             eEecCCCCccccCCCCCCceeEEEeCCcCceEEeecCCCeEE
Q 034324           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQ   84 (98)
Q Consensus        43 ~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~GA~sVr   84 (98)
                      .|+|+.|..++.+=  .+....+.|.+|.++|..|.|-..-.
T Consensus        34 ~VkCp~C~~~q~VF--Sha~t~V~C~~Cg~~L~~PTGGKa~l   73 (82)
T 3u5c_b           34 DVKCPGCLNITTVF--SHAQTAVTCESCSTILCTPTGGKAKL   73 (82)
T ss_dssp             EEECTTSCSCEEEE--SBCSSCCCCSSSCCCCEECCSSBCEE
T ss_pred             EEECCCCCCeeEEE--ecCCeEEEccccCCEEeccCCCCeEe
Confidence            47777777777653  23346677888888888887765433

>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=86.40  E-value=0.11  Score=34.92  Aligned_cols=37  Identities=32%  Similarity=0.600  Sum_probs=22.9

Q ss_pred             EecCCCCccccCCCCCCceeEEEeCCcCceEEeecCCCe
Q 034324           44 VCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATS   82 (98)
Q Consensus        44 VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~GA~s   82 (98)
                      |+|..|..++.+=  .+....+.|.+|.++|.-|.|-..
T Consensus        37 VkCp~C~~~~~VF--ShA~t~V~C~~CgtvL~~PTGGKa   73 (86)
T 3iz6_X           37 VKCQGCFNITTVF--SHSQTVVVCPGCQTVLCQPTGGKA   73 (86)
T ss_dssp             EECTTTCCEEEEE--TTCSSCCCCSSSCCCCSCCCSSSC
T ss_pred             EECCCCCCeeEEE--ecCCcEEEccCCCCEeecCCCCCE
Confidence            6677777666653  233455667777777777766543

---

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	98
d1qxfa_	58	Ribosomal protein S27e {Archaeon Archaeoglobus ful	93.58

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

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

Probab=93.58  E-value=0.017  Score=34.82  Aligned_cols=38  Identities=16%  Similarity=0.262  Sum_probs=30.9

Q ss_pred             eEecCCCCccccCCCCCCceeEEEeCCcCceEEeecCCCe
Q 034324           43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATS   82 (98)
Q Consensus        43 ~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~GA~s   82 (98)
                      .|+|+.|..++.+=  ++....+.|..|.++|..|.|-..
T Consensus         7 ~VkC~~C~n~~ivF--sha~t~V~C~~Cg~~L~~PtGGKa   44 (58)
T d1qxfa_           7 KVKCPDCEHEQVIF--DHPSTIVKCIICGRTVAEPTGGKG   44 (58)
T ss_dssp             EEECTTTCCEEEEE--SSCSSCEECSSSCCEEEECCSSSC
T ss_pred             EeECCCCCCeEEEE--ecCceEEEccccCCEEeccCCCeE
Confidence            58999999998764  344678999999999999998653