Citrus Sinensis ID: 033883

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------11
Protein Sequence
MTGVTKESETLARKRPSMTSVVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPSVQGQDTGKWVIIDSGLCRILNSL
Secondary Structure (PSIPRED)
ccccccHHHHHcccHHHHHHHHHHHHHcccccEEEEEcccccccccEEEEEEcccHHHHHHHHHHHHHHHHHHcHHHHHcccccccccccccccEEEEEcccEEEEEcc
Secondary Structure Prediction (SSPRO)
ccccccHHHHHHHccHHHHHHHHHHHHHccccEEEEEccccccHEEEEEEEccccHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccEEEEEcccHEEEccc
Coil and Loop (DISEMBL)
mtgvtkesetlarkrpsmtsvvnptfdlkaddvkvipvgekcdwtdYMVIATGRSTWHVKNIAQAIIYKAKQRQrevgakqmmlpsvqgqdtgkwviiDSGLCRILNSL
Flexible Loop (DISEMBL)
mtgvtkesetlarkrpsmtsvvnptfdlkaddvkvipVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMmlpsvqgqdtgkwviiDSGLCRILNSL
Low Complexity Region (SEG)
MTGVTKESETLARKRPSMTSVVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPSVQGQDTGKWVIIDSGLCRILNSL
Disordered region (IsUnstruct)
*********************VNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQ**************VQGQDTGKWVIIDSGLCRIL***
Disordered Region (DISOPRED)
*******************SVVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPSVQGQDTGKWVIIDSGLCRILNSL
Disordered Region (DISEMBL)
******************TSVVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPSVQGQDTGKWVIIDSGLCRILNSL
Disordered Region (DISPRO)
*****K*SET*ARKRPSMTSVVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPSVQGQDTGKWVIIDSGLCRILNSL
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MTGVTKESETLARKRPSMTSVVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPSVQGQDTGKWVIIDSGLCRILNSL
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	109	2.2.26 [Sep-21-2011]
Q9CAF9	184	Protein Iojap-related, mi	yes	no	0.834	0.494	0.505	2e-21
P0AAT8	105	Ribosomal silencing facto	yes	no	0.669	0.695	0.341	3e-05
P0AAT6	105	Ribosomal silencing facto	N/A	no	0.669	0.695	0.341	3e-05
P0AAT7	105	Ribosomal silencing facto	yes	no	0.669	0.695	0.341	3e-05
Q96EH3	234	Mitochondrial assembly of	yes	no	0.853	0.397	0.289	0.0003
Q5NLX3	133	Ribosomal silencing facto	yes	no	0.623	0.511	0.32	0.0009

>sp|Q9CAF9|IOJAM_ARATH Protein Iojap-related, mitochondrial OS=Arabidopsis thaliana GN=At1g67620 PE=2 SV=1

 Score =  100 bits (250), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 50/99 (50%), Positives = 69/99 (69%), Gaps = 8/99 (8%)

Query: 3   GVTKESETLARKRPSMTSVVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNI 62
           G++  SE L     ++  V     D+KAD+V VIP    C W D+ VIATGRS WH++NI
Sbjct: 37  GISNVSEIL-----TLPEVEKILADVKADNVTVIPTHNHCFWADFTVIATGRSDWHLRNI 91

Query: 63  AQAIIYKAKQRQREVGAKQMMLPSVQGQDTGKWVIIDSG 101
           AQA++Y+AKQ+Q+  GAK +MLPSVQG ++ KW++ID G
Sbjct: 92  AQALVYRAKQKQK--GAKHVMLPSVQGYNS-KWIVIDYG 127

May be a ribosome silencing factor involved in organelle biogenesis and required for germination.
Arabidopsis thaliana (taxid: 3702)

>sp|P0AAT8|IOJAP_SHIFL Ribosomal silencing factor RsfS OS=Shigella flexneri GN=rsfS PE=3 SV=1

 Score = 47.4 bits (111), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 28/82 (34%), Positives = 45/82 (54%), Gaps = 9/82 (10%)

Query: 21  VVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAK 80
           V++   DLK  D+  + V  K   TD M+I TG S+ HV +IA  ++    Q  R  G  
Sbjct: 10  VIDKIDDLKGQDIIALDVQGKSSITDCMIICTGTSSRHVMSIADHVV----QESRAAG-- 63

Query: 81  QMMLP-SVQGQDTGKWVIIDSG 101
             +LP  V+G+++  W+++D G
Sbjct: 64  --LLPLGVEGENSADWIVVDLG 83

Shigella flexneri (taxid: 623)

>sp|P0AAT6|IOJAP_ECOLI Ribosomal silencing factor RsfS OS=Escherichia coli (strain K12) GN=rsfS PE=1 SV=1

 Score = 47.4 bits (111), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 28/82 (34%), Positives = 45/82 (54%), Gaps = 9/82 (10%)

Query: 21  VVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAK 80
           V++   DLK  D+  + V  K   TD M+I TG S+ HV +IA  ++    Q  R  G  
Sbjct: 10  VIDKIDDLKGQDIIALDVQGKSSITDCMIICTGTSSRHVMSIADHVV----QESRAAG-- 63

Query: 81  QMMLP-SVQGQDTGKWVIIDSG 101
             +LP  V+G+++  W+++D G
Sbjct: 64  --LLPLGVEGENSADWIVVDLG 83

Escherichia coli (strain K12) (taxid: 83333)

>sp|P0AAT7|IOJAP_ECOL6 Ribosomal silencing factor RsfS OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=rsfS PE=3 SV=1

 Score = 47.4 bits (111), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 28/82 (34%), Positives = 45/82 (54%), Gaps = 9/82 (10%)

Query: 21  VVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAK 80
           V++   DLK  D+  + V  K   TD M+I TG S+ HV +IA  ++    Q  R  G  
Sbjct: 10  VIDKIDDLKGQDIIALDVQGKSSITDCMIICTGTSSRHVMSIADHVV----QESRAAG-- 63

Query: 81  QMMLP-SVQGQDTGKWVIIDSG 101
             +LP  V+G+++  W+++D G
Sbjct: 64  --LLPLGVEGENSADWIVVDLG 83

Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) (taxid: 199310)

>sp|Q96EH3|MASU1_HUMAN Mitochondrial assembly of ribosomal large subunit protein 1 OS=Homo sapiens GN=MALSU1 PE=1 SV=1

 Score = 43.9 bits (102), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 33/114 (28%), Positives = 55/114 (48%), Gaps = 21/114 (18%)

Query: 3   GVTKESE-TLARKRPSMTSV--VNPTFDL----------KADDVKVIPVGEKCDWTDYMV 49
           G+ + +E T+   RP   +     P FD+           A D+ VI V  +  +TDY V
Sbjct: 66  GLEERAEGTVNEGRPESDAADHTGPKFDIDMMVSLLRQENARDICVIQVPPEMRYTDYFV 125

Query: 50  IATGRSTWHVKNIAQAII--YKAKQRQREVGAKQMMLPSVQGQDTGKWVIIDSG 101
           I +G ST H+  +A  ++  YK  + +R+   K      ++G+DT  W+ +D G
Sbjct: 126 IVSGTSTRHLHAMAFYVVKMYKHLKCKRDPHVK------IEGKDTDDWLCVDFG 173

Participates in the assembly and/or regulation of the stability of the large subunit of the mitochondrial ribosome.

Homo sapiens (taxid: 9606)

>sp|Q5NLX3|IOJAP_ZYMMO Ribosomal silencing factor RsfS OS=Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4) GN=rsfS PE=1 SV=1

 Score = 42.4 bits (98), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 7/75 (9%)

Query: 27  DLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPS 86
           D +A ++  IP+  K    DYMVIA+GRS+  V  +AQ +  + K       A    +  
Sbjct: 29  DDQALEIATIPLAGKSSIADYMVIASGRSSRQVTAMAQKLADRIK-------AATGYVSK 81

Query: 87  VQGQDTGKWVIIDSG 101
           ++G     WV++D+G
Sbjct: 82  IEGLPAADWVLLDAG 96

Functions as a ribosomal silencing factor. Interacts with ribosomal protein L14 (rplN), blocking formation of intersubunit bridge B8. Prevents association of the 30S and 50S ribosomal subunits and the formation of functional ribosomes, thus repressing translation.

Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4) (taxid: 264203)

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	109
255547874	200	conserved hypothetical protein [Ricinus	0.688	0.375	0.670	3e-26
351722821	177	uncharacterized protein LOC100500659 [Gl	0.669	0.412	0.733	6e-26
449450592	181	PREDICTED: protein Iojap-related, mitoch	0.660	0.397	0.716	1e-25
449530187	186	PREDICTED: protein Iojap-related, mitoch	0.660	0.387	0.716	1e-25
351722498	177	uncharacterized protein LOC100500386 [Gl	0.669	0.412	0.733	2e-25
224101567	186	predicted protein [Populus trichocarpa]	0.669	0.392	0.706	4e-25
357463073	175	hypothetical protein MTR_3g085720 [Medic	0.669	0.417	0.68	2e-24
225425859	186	PREDICTED: uncharacterized protein LOC10	0.642	0.376	0.693	2e-23
388496718	179	unknown [Lotus japonicus]	0.669	0.407	0.64	3e-23
343171958	177	Lojap-like protein, partial [Silene lati	0.669	0.412	0.6	8e-23

>gi|255547874|ref|XP_002514994.1| conserved hypothetical protein [Ricinus communis] gi|223546045|gb|EEF47548.1| conserved hypothetical protein [Ricinus communis]

 Score =  122 bits (306), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 55/82 (67%), Positives = 69/82 (84%), Gaps = 7/82 (8%)

Query: 27  DLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAK-------QRQREVGA 79
           D+KADDVKVIPV ++CDW DYMVIATGRSTWHVKNIAQA+IYKA         +Q++ GA
Sbjct: 64  DVKADDVKVIPVQKQCDWVDYMVIATGRSTWHVKNIAQALIYKAGFALLLSFSKQKQKGA 123

Query: 80  KQMMLPSVQGQDTGKWVIIDSG 101
           ++MMLPSV+GQ+ GKW+++DSG
Sbjct: 124 QRMMLPSVEGQEAGKWIVVDSG 145

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351722821|ref|NP_001237513.1| uncharacterized protein LOC100500659 [Glycine max] gi|255630873|gb|ACU15799.1| unknown [Glycine max]

 Score =  121 bits (303), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 55/75 (73%), Positives = 67/75 (89%), Gaps = 2/75 (2%)

Query: 27  DLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPS 86
           D+KAD+VKVIPV + CDW D+MV+ATGRSTWHVKNIAQA+IYKAKQ+QR  G ++MMLPS
Sbjct: 50  DVKADNVKVIPVPKHCDWADFMVLATGRSTWHVKNIAQALIYKAKQKQR--GVERMMLPS 107

Query: 87  VQGQDTGKWVIIDSG 101
           V+GQ  GKW++IDSG
Sbjct: 108 VEGQAGGKWIVIDSG 122

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449450592|ref|XP_004143046.1| PREDICTED: protein Iojap-related, mitochondrial-like [Cucumis sativus]

 Score =  120 bits (300), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 53/74 (71%), Positives = 66/74 (89%), Gaps = 2/74 (2%)

Query: 28  LKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPSV 87
           +KADDVKVIPV + CDW DYMV ATGRSTWHVKNIAQA+IY+ KQ+Q+  GA+Q++LPSV
Sbjct: 59  VKADDVKVIPVRKDCDWADYMVFATGRSTWHVKNIAQALIYQIKQKQK--GARQLVLPSV 116

Query: 88  QGQDTGKWVIIDSG 101
           +GQ+ GKW++IDSG
Sbjct: 117 EGQEEGKWIVIDSG 130

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449530187|ref|XP_004172077.1| PREDICTED: protein Iojap-related, mitochondrial-like [Cucumis sativus]

 Score =  120 bits (300), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 53/74 (71%), Positives = 66/74 (89%), Gaps = 2/74 (2%)

Query: 28  LKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPSV 87
           +KADDVKVIPV + CDW DYMV ATGRSTWHVKNIAQA+IY+ KQ+Q+  GA+Q++LPSV
Sbjct: 59  VKADDVKVIPVRKDCDWADYMVFATGRSTWHVKNIAQALIYQIKQKQK--GARQLVLPSV 116

Query: 88  QGQDTGKWVIIDSG 101
           +GQ+ GKW++IDSG
Sbjct: 117 EGQEEGKWIVIDSG 130

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351722498|ref|NP_001237246.1| uncharacterized protein LOC100500386 [Glycine max] gi|255630200|gb|ACU15455.1| unknown [Glycine max]

 Score =  119 bits (298), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 55/75 (73%), Positives = 65/75 (86%), Gaps = 2/75 (2%)

Query: 27  DLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPS 86
           D KAD VKVIPV + CDW D+MV+ATGRSTWHVKNIAQA+IYKAKQ+QR  G ++MMLPS
Sbjct: 50  DAKADGVKVIPVPKHCDWADFMVLATGRSTWHVKNIAQALIYKAKQKQR--GVERMMLPS 107

Query: 87  VQGQDTGKWVIIDSG 101
           V+GQ  GKW++IDSG
Sbjct: 108 VEGQAGGKWIVIDSG 122

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224101567|ref|XP_002312333.1| predicted protein [Populus trichocarpa] gi|222852153|gb|EEE89700.1| predicted protein [Populus trichocarpa]

 Score =  118 bits (296), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 53/75 (70%), Positives = 66/75 (88%), Gaps = 2/75 (2%)

Query: 27  DLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPS 86
           D++ADDVKVIP  +  +W DYMVIATGRSTWHVKNIAQA+IYKAKQ+Q+  GA++M LPS
Sbjct: 58  DVRADDVKVIPAKKHAEWADYMVIATGRSTWHVKNIAQALIYKAKQKQK--GAQRMTLPS 115

Query: 87  VQGQDTGKWVIIDSG 101
           V+GQ+ GKW++IDSG
Sbjct: 116 VEGQEGGKWIVIDSG 130

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357463073|ref|XP_003601818.1| hypothetical protein MTR_3g085720 [Medicago truncatula] gi|355490866|gb|AES72069.1| hypothetical protein MTR_3g085720 [Medicago truncatula] gi|388500568|gb|AFK38350.1| unknown [Medicago truncatula]

 Score =  116 bits (290), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 51/75 (68%), Positives = 67/75 (89%), Gaps = 2/75 (2%)

Query: 27  DLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPS 86
           D++ADDVK+IP  +  DWTD+MV+ATGRS+WHVKNIAQA+IY+AKQ+Q  +G ++MMLPS
Sbjct: 48  DVQADDVKIIPAPKHNDWTDFMVLATGRSSWHVKNIAQALIYQAKQKQ--IGVERMMLPS 105

Query: 87  VQGQDTGKWVIIDSG 101
           VQGQ+ GKW++IDSG
Sbjct: 106 VQGQEDGKWIVIDSG 120

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225425859|ref|XP_002266055.1| PREDICTED: uncharacterized protein LOC100249470 [Vitis vinifera]

 Score =  112 bits (281), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 52/75 (69%), Positives = 67/75 (89%), Gaps = 5/75 (6%)

Query: 27  DLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPS 86
           D+KADD++VIPV + CD   +MVIATGRS+WHVKNIAQA+IYKAKQ+Q+  GA++++LPS
Sbjct: 61  DVKADDIRVIPVRQHCD---FMVIATGRSSWHVKNIAQALIYKAKQKQK--GAQRILLPS 115

Query: 87  VQGQDTGKWVIIDSG 101
           V+GQ+ GKWVIIDSG
Sbjct: 116 VEGQEGGKWVIIDSG 130

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388496718|gb|AFK36425.1| unknown [Lotus japonicus]

 Score =  112 bits (280), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 48/75 (64%), Positives = 65/75 (86%), Gaps = 2/75 (2%)

Query: 27  DLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPS 86
           D+KADDVKV+P  + CDW D+MV+ATGRSTWHV+NIAQA++Y+AKQ+QR  G  + +LPS
Sbjct: 54  DVKADDVKVMPAPKHCDWADFMVLATGRSTWHVRNIAQALVYRAKQKQR--GVVRKILPS 111

Query: 87  VQGQDTGKWVIIDSG 101
           V+G++ GKW++IDSG
Sbjct: 112 VEGEEGGKWIVIDSG 126

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|343171958|gb|AEL98683.1| Lojap-like protein, partial [Silene latifolia]

 Score =  110 bits (276), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 45/75 (60%), Positives = 64/75 (85%), Gaps = 2/75 (2%)

Query: 27  DLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPS 86
           ++ ADDV+VIPV   CDWTDYMV ATGRSTWHV+NIA+A++YKAK++Q++  + +M+LPS
Sbjct: 53  EVHADDVRVIPVSHFCDWTDYMVFATGRSTWHVRNIAEALVYKAKRKQKD--SPRMLLPS 110

Query: 87  VQGQDTGKWVIIDSG 101
           + G++T  W++IDSG
Sbjct: 111 LDGEETANWIVIDSG 125

Source: Silene latifolia

Species: Silene latifolia

Genus: Silene

Family: Caryophyllaceae

Order: Caryophyllales

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	109
TAIR|locus:2008560	184	AT1G67620 "AT1G67620" [Arabido	0.834	0.494	0.505	4.9e-21
UNIPROTKB|Q8EHP7	109	SO_1170 "Iojap-like ribosome-a	0.678	0.678	0.407	1.4e-09
TIGR_CMR|SO_1170	109	SO_1170 "iojap domain protein"	0.678	0.678	0.407	1.4e-09
UNIPROTKB|Q9KTF0	105	VC_0952 "Putative uncharacteri	0.623	0.647	0.36	8.7e-08
TIGR_CMR|VC_0952	105	VC_0952 "conserved hypothetica	0.623	0.647	0.36	8.7e-08
UNIPROTKB|Q5LX03	128	SPO0219 "Iojap-related protein	0.623	0.531	0.386	1.1e-07
TIGR_CMR|SPO_0219	128	SPO_0219 "iojap-related protei	0.623	0.531	0.386	1.1e-07
UNIPROTKB|Q484R0	106	CPS_1717 "Iojap-related protei	0.660	0.679	0.291	1.4e-07
TIGR_CMR|CPS_1717	106	CPS_1717 "iojap-related protei	0.660	0.679	0.291	1.4e-07
UNIPROTKB|P0AAT6	105	rsfS "ribosomal silencing fact	0.669	0.695	0.341	2.9e-07

TAIR|locus:2008560 AT1G67620 "AT1G67620" [Arabidopsis thaliana (taxid:3702)]

 Score = 247 (92.0 bits), Expect = 4.9e-21, P = 4.9e-21
 Identities = 50/99 (50%), Positives = 70/99 (70%)

Query:     3 GVTKESETLARKRPSMTSVVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNI 62
             G++  SE L    P +  ++    D+KAD+V VIP    C W D+ VIATGRS WH++NI
Sbjct:    37 GISNVSEILTL--PEVEKILA---DVKADNVTVIPTHNHCFWADFTVIATGRSDWHLRNI 91

Query:    63 AQAIIYKAKQRQREVGAKQMMLPSVQGQDTGKWVIIDSG 101
             AQA++Y+AKQ+Q+  GAK +MLPSVQG ++ KW++ID G
Sbjct:    92 AQALVYRAKQKQK--GAKHVMLPSVQGYNS-KWIVIDYG 127

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0008150 "biological_process" evidence=ND

GO:0006457 "protein folding" evidence=RCA

GO:0009408 "response to heat" evidence=RCA

GO:0009644 "response to high light intensity" evidence=RCA

GO:0034976 "response to endoplasmic reticulum stress" evidence=RCA

GO:0042542 "response to hydrogen peroxide" evidence=RCA

UNIPROTKB|Q8EHP7 SO_1170 "Iojap-like ribosome-associated protein" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 139 (54.0 bits), Expect = 1.4e-09, P = 1.4e-09
 Identities = 33/81 (40%), Positives = 49/81 (60%)

Query:    21 VVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAK 80
             VV+   DLKA DV VI V  + + TDYMVI +G S  HVK IA+ ++ +AK      G  
Sbjct:    10 VVDKIDDLKARDVVVIDVSNQSNITDYMVICSGTSKTHVKAIAENLVIEAKA----AGIP 65

Query:    81 QMMLPSVQGQDTGKWVIIDSG 101
              +    ++G+D+ +WV++D G
Sbjct:    66 PI---GIEGRDSSEWVLVDMG 83

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|SO_1170 SO_1170 "iojap domain protein" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 139 (54.0 bits), Expect = 1.4e-09, P = 1.4e-09
 Identities = 33/81 (40%), Positives = 49/81 (60%)

Query:    21 VVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAK 80
             VV+   DLKA DV VI V  + + TDYMVI +G S  HVK IA+ ++ +AK      G  
Sbjct:    10 VVDKIDDLKARDVVVIDVSNQSNITDYMVICSGTSKTHVKAIAENLVIEAKA----AGIP 65

Query:    81 QMMLPSVQGQDTGKWVIIDSG 101
              +    ++G+D+ +WV++D G
Sbjct:    66 PI---GIEGRDSSEWVLVDMG 83

GO:0008150 "biological_process" evidence=ND

GO:0003674 "molecular_function" evidence=ND

UNIPROTKB|Q9KTF0 VC_0952 "Putative uncharacterized protein" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)]

 Score = 122 (48.0 bits), Expect = 8.7e-08, P = 8.7e-08
 Identities = 27/75 (36%), Positives = 44/75 (58%)

Query:    27 DLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPS 86
             D+KA D+  + V EK   TDYM++ TG S  HV +IA+ +  +AK      G + +    
Sbjct:    16 DMKAVDIVTLDVKEKSSVTDYMIVCTGTSKRHVASIAEHVANEAKLS----GLQPL---G 68

Query:    87 VQGQDTGKWVIIDSG 101
             + G++ G+WV++D G
Sbjct:    69 MNGENEGEWVVLDMG 83

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|VC_0952 VC_0952 "conserved hypothetical protein" [Vibrio cholerae O1 biovar El Tor (taxid:686)]

 Score = 122 (48.0 bits), Expect = 8.7e-08, P = 8.7e-08
 Identities = 27/75 (36%), Positives = 44/75 (58%)

Query:    27 DLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPS 86
             D+KA D+  + V EK   TDYM++ TG S  HV +IA+ +  +AK      G + +    
Sbjct:    16 DMKAVDIVTLDVKEKSSVTDYMIVCTGTSKRHVASIAEHVANEAKLS----GLQPL---G 68

Query:    87 VQGQDTGKWVIIDSG 101
             + G++ G+WV++D G
Sbjct:    69 MNGENEGEWVVLDMG 83

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q5LX03 SPO0219 "Iojap-related protein" [Ruegeria pomeroyi DSS-3 (taxid:246200)]

 Score = 121 (47.7 bits), Expect = 1.1e-07, P = 1.1e-07
 Identities = 29/75 (38%), Positives = 43/75 (57%)

Query:    27 DLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPS 86
             D KA+D+  I +  K    DYMVIA+GRST  V  +A+ ++ + K    E G        
Sbjct:    30 DDKAEDLVQIDLRGKTSMGDYMVIASGRSTRQVSAMAEKLVQRLKD---EFGLNS----K 82

Query:    87 VQGQDTGKWVIIDSG 101
             ++G+D G WV+ID+G
Sbjct:    83 IEGKDAGDWVLIDTG 97

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|SPO_0219 SPO_0219 "iojap-related protein" [Ruegeria pomeroyi DSS-3 (taxid:246200)]

 Score = 121 (47.7 bits), Expect = 1.1e-07, P = 1.1e-07
 Identities = 29/75 (38%), Positives = 43/75 (57%)

Query:    27 DLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPS 86
             D KA+D+  I +  K    DYMVIA+GRST  V  +A+ ++ + K    E G        
Sbjct:    30 DDKAEDLVQIDLRGKTSMGDYMVIASGRSTRQVSAMAEKLVQRLKD---EFGLNS----K 82

Query:    87 VQGQDTGKWVIIDSG 101
             ++G+D G WV+ID+G
Sbjct:    83 IEGKDAGDWVLIDTG 97

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q484R0 CPS_1717 "Iojap-related protein" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 120 (47.3 bits), Expect = 1.4e-07, P = 1.4e-07
 Identities = 23/79 (29%), Positives = 43/79 (54%)

Query:    21 VVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAK 80
             V+    D+K  D+  + + +K  + DYM+I +G S  HVK+IAQ++  + + +  E    
Sbjct:    10 VIEKLEDMKGRDIIALNISDKASFADYMIICSGNSNRHVKSIAQSVAMECRAQGTEPRG- 68

Query:    81 QMMLPSVQGQDTGKWVIID 99
                   ++G D G+W ++D
Sbjct:    69 ------MEGNDVGEWALVD 81

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|CPS_1717 CPS_1717 "iojap-related protein" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 120 (47.3 bits), Expect = 1.4e-07, P = 1.4e-07
 Identities = 23/79 (29%), Positives = 43/79 (54%)

Query:    21 VVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAK 80
             V+    D+K  D+  + + +K  + DYM+I +G S  HVK+IAQ++  + + +  E    
Sbjct:    10 VIEKLEDMKGRDIIALNISDKASFADYMIICSGNSNRHVKSIAQSVAMECRAQGTEPRG- 68

Query:    81 QMMLPSVQGQDTGKWVIID 99
                   ++G D G+W ++D
Sbjct:    69 ------MEGNDVGEWALVD 81

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|P0AAT6 rsfS "ribosomal silencing factor" [Escherichia coli K-12 (taxid:83333)]

 Score = 117 (46.2 bits), Expect = 2.9e-07, P = 2.9e-07
 Identities = 28/82 (34%), Positives = 45/82 (54%)

Query:    21 VVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAK 80
             V++   DLK  D+  + V  K   TD M+I TG S+ HV +IA  ++    Q  R  G  
Sbjct:    10 VIDKIDDLKGQDIIALDVQGKSSITDCMIICTGTSSRHVMSIADHVV----QESRAAG-- 63

Query:    81 QMMLP-SVQGQDTGKWVIIDSG 101
               +LP  V+G+++  W+++D G
Sbjct:    64 --LLPLGVEGENSADWIVVDLG 83

GO:0017148 "negative regulation of translation" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0090071 "negative regulation of ribosome biogenesis" evidence=IDA

GO:0043023 "ribosomal large subunit binding" evidence=IDA

GO:0005737 "cytoplasm" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	109
pfam02410	99	pfam02410, Oligomerisation, Oligomerisation domain	4e-23
TIGR00090	99	TIGR00090, iojap_ybeB, iojap-like ribosome-associa	9e-20
COG0799	115	COG0799, COG0799, Uncharacterized homolog of plant	2e-18
PRK11538	105	PRK11538, PRK11538, ribosome-associated protein; P	2e-10

>gnl|CDD|217021 pfam02410, Oligomerisation, Oligomerisation domain

 Score = 85.3 bits (212), Expect = 4e-23
 Identities = 30/75 (40%), Positives = 41/75 (54%), Gaps = 7/75 (9%)

Query: 27  DLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPS 86
           D KA+D+ V+ V +K    DY VIATG ST HVK IA  +  + K+         +    
Sbjct: 11  DKKAEDIVVLDVSKKSSIADYFVIATGTSTRHVKAIADNVEEELKE-------AGLKPLG 63

Query: 87  VQGQDTGKWVIIDSG 101
           V+G D G WV++D G
Sbjct: 64  VEGLDEGDWVLLDYG 78

In yeasts, this domain is required for the oligomerisation of ATP synthase subunit 9 into a ring structure. Length = 99

>gnl|CDD|161702 TIGR00090, iojap_ybeB, iojap-like ribosome-associated protein

 Score = 76.7 bits (190), Expect = 9e-20
 Identities = 27/75 (36%), Positives = 39/75 (52%), Gaps = 7/75 (9%)

Query: 27  DLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPS 86
           D KA+D+ V+ V  K    DY VIA+G S+ HVK IA  +  + K          +    
Sbjct: 11  DKKAEDIVVLDVRGKSSIADYFVIASGTSSRHVKAIADNVEEELK-------EAGLKPLG 63

Query: 87  VQGQDTGKWVIIDSG 101
           V+G + G WV++D G
Sbjct: 64  VEGLEEGDWVLVDLG 78

This model describes a widely distributed family of bacterial proteins related to iojap from plants. It includes YbeB from E. coli. The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. More recent work in bacteria suggests that the bacterial iojap-related protein physically associates with ribosomes. The function remains unknown [Unknown function, General]. Length = 99

>gnl|CDD|223870 COG0799, COG0799, Uncharacterized homolog of plant Iojap protein [Function unknown]

 Score = 73.8 bits (182), Expect = 2e-18
 Identities = 29/75 (38%), Positives = 40/75 (53%), Gaps = 7/75 (9%)

Query: 27  DLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPS 86
           D KA+D+ V+ V  K   TDY VIATG S+ HVK IA  +  + K+              
Sbjct: 16  DKKAEDIVVLDVSGKSSLTDYFVIATGNSSRHVKAIADNVKEELKEAGEV-------PLR 68

Query: 87  VQGQDTGKWVIIDSG 101
           ++G   G+WV+ID G
Sbjct: 69  IEGLSEGEWVLIDLG 83

Length = 115

>gnl|CDD|183184 PRK11538, PRK11538, ribosome-associated protein; Provisional

 Score = 52.9 bits (127), Expect = 2e-10
 Identities = 26/81 (32%), Positives = 43/81 (53%), Gaps = 7/81 (8%)

Query: 21  VVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAK 80
           V++   DLK  D+  + V  K   TD M+I TG S+ HV +IA  ++    Q  R  G  
Sbjct: 10  VIDKIDDLKGQDIIALDVQGKSSITDCMIICTGTSSRHVMSIADHVV----QESRAAG-- 63

Query: 81  QMMLPSVQGQDTGKWVIIDSG 101
            ++   V+G++   W+++D G
Sbjct: 64  -LLPLGVEGENAADWIVVDLG 83

Length = 105

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	109
PRK11538	105	ribosome-associated protein; Provisional	100.0
COG0799	115	Uncharacterized homolog of plant Iojap protein [Fu	100.0
TIGR00090	99	iojap_ybeB iojap-like ribosome-associated protein.	100.0
PF02410	100	Oligomerisation: Oligomerisation domain; InterPro:	99.97
KOG3212	208	consensus Uncharacterized conserved protein relate	99.86
PRK09271	160	flavodoxin; Provisional	84.98

>PRK11538 ribosome-associated protein; Provisional

Probab=100.00  E-value=3.4e-33  Score=190.43  Aligned_cols=86  Identities=28%  Similarity=0.487  Sum_probs=79.8

Q ss_pred             hHHHHhcCCCHHHHHHHHHhCCCCCeEEEecCCCCCcccEEEEEEcCCHHHHHHHHHHHHHHHHHhhhhhccccCCCCCc
Q 033883            8 SETLARKRPSMTSVVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPSV   87 (109)
Q Consensus         8 ~~~l~~~~~~i~~i~~~l~dkKa~dI~vlDv~~~~~~aDyfVI~Ta~S~rh~~ala~~i~~~lk~~~~~~~~~~~~~~~v   87 (109)
                      ++++.+      .++++|+++||+||++|||++.|++|||||||||+|.||++|||++|.+.+++.+    .   .++++
T Consensus         3 ~~~~~~------~i~~~l~dkKa~DI~vlDv~~~~~~~Dy~VIatg~S~rh~~aia~~v~~~~k~~~----~---~~~~~   69 (105)
T PRK11538          3 GKALQD------FVIDKIDDLKGQDIIALDVQGKSSITDCMIICTGTSSRHVMSIADHVVQESRAAG----L---LPLGV   69 (105)
T ss_pred             HHHHHH------HHHHHHHHcCCCCeEEEECCCCCcccCEEEEEEeCCHHHHHHHHHHHHHHHHHcC----C---CCCcc
Confidence            355666      9999999999999999999999999999999999999999999999999998874    3   46799


Q ss_pred             ccCCCCCeEEEEcCCEEEE
Q 033883           88 QGQDTGKWVIIDSGLCRIL  106 (109)
Q Consensus        88 EG~~~~~WvllD~GdiVVh  106 (109)
                      ||.++++|+|+|||+||||
T Consensus        70 eG~~~~~WillD~g~ivVH   88 (105)
T PRK11538         70 EGENAADWIVVDLGDVIVH   88 (105)
T ss_pred             cCCCCCCEEEEeCCCEEEE
Confidence            9999999999999999999

>COG0799 Uncharacterized homolog of plant Iojap protein [Function unknown]

Probab=100.00  E-value=2.7e-33  Score=193.43  Aligned_cols=82  Identities=37%  Similarity=0.543  Sum_probs=77.3

Q ss_pred             HHHHHHHHHhCCCCCeEEEecCCCCCcccEEEEEEcCCHHHHHHHHHHHHHHHHHhhhhhccccCCCCCcccCCCCCeEE
Q 033883           18 MTSVVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPSVQGQDTGKWVI   97 (109)
Q Consensus        18 i~~i~~~l~dkKa~dI~vlDv~~~~~~aDyfVI~Ta~S~rh~~ala~~i~~~lk~~~~~~~~~~~~~~~vEG~~~~~Wvl   97 (109)
                      ++.++++|+|+||+||++|||+++|++|||||||||+|.||++|||+++.+++|+.+    .   .+.++||..+++|+|
T Consensus         7 ~~~i~~alddkKAeDIv~lDv~~~s~~tDyfVIatg~s~rhv~Aiad~i~~~~k~~g----~---~~~~~EG~~~~~Wvl   79 (115)
T COG0799           7 LEVIVEALDDKKAEDIVVLDVSGKSSLTDYFVIATGNSSRHVKAIADNVKEELKEAG----E---VPLRIEGLSEGEWVL   79 (115)
T ss_pred             HHHHHHHHHhccCCCeEEEEccCCcccccEEEEEEeCchHHHHHHHHHHHHHHHHcC----C---CcccccCCCcCCEEE
Confidence            349999999999999999999999999999999999999999999999999998774    3   467999999999999


Q ss_pred             EEcCCEEEE
Q 033883           98 IDSGLCRIL  106 (109)
Q Consensus        98 lD~GdiVVh  106 (109)
                      +|+||||||
T Consensus        80 iD~GdivVH   88 (115)
T COG0799          80 IDLGDIVVH   88 (115)
T ss_pred             EecCcEEEE
Confidence            999999999

>TIGR00090 iojap_ybeB iojap-like ribosome-associated protein

Probab=100.00  E-value=1.3e-32  Score=185.59  Aligned_cols=82  Identities=34%  Similarity=0.506  Sum_probs=77.5

Q ss_pred             HHHHHHHHHhCCCCCeEEEecCCCCCcccEEEEEEcCCHHHHHHHHHHHHHHHHHhhhhhccccCCCCCcccCCCCCeEE
Q 033883           18 MTSVVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPSVQGQDTGKWVI   97 (109)
Q Consensus        18 i~~i~~~l~dkKa~dI~vlDv~~~~~~aDyfVI~Ta~S~rh~~ala~~i~~~lk~~~~~~~~~~~~~~~vEG~~~~~Wvl   97 (109)
                      ++.++++|+++||+||++|||++.+++|||||||||+|+||++|||++|.+.+|+.+    .   .++++||.++++|+|
T Consensus         2 ~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VI~Tg~S~rh~~aia~~v~~~~k~~~----~---~~~~~EG~~~~~Wil   74 (99)
T TIGR00090         2 LELIVEALDDKKAEDIVVLDVRGKSSIADYFVIASGTSSRHVKAIADNVEEELKEAG----L---KPLGVEGLEEGDWVL   74 (99)
T ss_pred             HHHHHHHHHHcCCCCEEEEECCCCCcccCEEEEEEeCCHHHHHHHHHHHHHHHHHcC----C---CcccccCCCCCCEEE
Confidence            468999999999999999999999999999999999999999999999999998874    3   467999999999999


Q ss_pred             EEcCCEEEE
Q 033883           98 IDSGLCRIL  106 (109)
Q Consensus        98 lD~GdiVVh  106 (109)
                      +|||+|+||
T Consensus        75 lD~g~ivVH   83 (99)
T TIGR00090        75 VDLGDVVVH   83 (99)
T ss_pred             EECCCEEEE
Confidence            999999999

This model describes a widely distributed family of bacterial proteins related to iojap from plants. It includes YbeB from E. coli. The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. More recent work in bacteria suggests that the bacterial iojap-related protein physically associates with ribosomes. The function remains unknown.

>PF02410 Oligomerisation: Oligomerisation domain; InterPro: IPR004394 The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells

Probab=99.97  E-value=9.1e-31  Score=176.32  Aligned_cols=82  Identities=35%  Similarity=0.586  Sum_probs=72.1

Q ss_pred             HHHHHHHHHhCCCCCeEEEecCCCCCcccEEEEEEcCCHHHHHHHHHHHHHHH-HHhhhhhccccCCCCCcccCCCCCeE
Q 033883           18 MTSVVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKA-KQRQREVGAKQMMLPSVQGQDTGKWV   96 (109)
Q Consensus        18 i~~i~~~l~dkKa~dI~vlDv~~~~~~aDyfVI~Ta~S~rh~~ala~~i~~~l-k~~~~~~~~~~~~~~~vEG~~~~~Wv   96 (109)
                      ++.++++|+++||+||++||+++.|++|||||||||+|+||++|+|++|.+.+ ++.+    .   .++++||.++++|+
T Consensus         2 ~~~i~~~l~~~k~~dI~v~dv~~~~~~~dy~II~T~~S~rh~~aia~~v~~~~~k~~~----~---~~~~~eG~~~~~W~   74 (100)
T PF02410_consen    2 LEEIVEALEDKKAEDIVVLDVREKSSWADYFIIATGRSERHVRAIADEVEKALKKEYG----E---RPLRIEGLDESDWV   74 (100)
T ss_dssp             HHHHHHHHHHTT-EEEEEEEGCTTBSS-SEEEEEEESSHHHHHHHHHHHHHHH-HHTT-----------EEESTTTTSEE
T ss_pred             HHHHHHHHHHcCCCCeEEEECCCCCcccCEEEEEEcCCHHHHHHHHHHHHHHHHHHcC----C---cccccCCCCCCCEE
Confidence            56899999999999999999999999999999999999999999999999999 4432    2   47899999999999


Q ss_pred             EEEcCCEEEE
Q 033883           97 IIDSGLCRIL  106 (109)
Q Consensus        97 llD~GdiVVh  106 (109)
                      ++|||+|+||
T Consensus        75 lvD~g~ivVH   84 (100)
T PF02410_consen   75 LVDYGDIVVH   84 (100)
T ss_dssp             EEEESSEEEE
T ss_pred             EEcccEEEEE
Confidence            9999999999

Maize has two RNA polymerases in plastids, but the plastid-encoded one, similar to bacterial RNA polymerases, is missing in iojap mutants. The role of iojap in chloroplast development, and the role of its bacterial orthologs modeled here, is unclear [, ]. This entry contains the bacterial protein YbeB (P0AAT6 from SWISSPROT), which has been shown to comigrate with the mature 50S ribosome subunit. Therefore it either represents a novel ribosome-associated protein or it is associated with a different oligomeric complex that comigrates with ribosomal particles [].; PDB: 2O5A_A 2ID1_B 3UPS_A.

>KOG3212 consensus Uncharacterized conserved protein related to IojAP [Function unknown]

Probab=99.86  E-value=1.9e-21  Score=144.01  Aligned_cols=86  Identities=36%  Similarity=0.573  Sum_probs=78.3

Q ss_pred             HHHHHHHHHhCCCCCeEEEecCCCCCcccEEEEEEcCCHHHHHHHHHHHHHHHHHhhhhhccccCCCCCcccCCCCCeEE
Q 033883           18 MTSVVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPSVQGQDTGKWVI   97 (109)
Q Consensus        18 i~~i~~~l~dkKa~dI~vlDv~~~~~~aDyfVI~Ta~S~rh~~ala~~i~~~lk~~~~~~~~~~~~~~~vEG~~~~~Wvl   97 (109)
                      ++.++++|.+.+|.||+|+-+.+.+.|+||+|||||+|.||++|+|+++...+|-+.. .|.   ..+++||.++++|++
T Consensus        71 ve~vv~lLrdenadDVfVi~vpeem~y~dh~VIcSgrs~rhl~aiAe~lv~m~Kik~~-kgd---~hvriegk~s~dW~v  146 (208)
T KOG3212|consen   71 VEEVVKLLRDENADDVFVIPVPEEMFYADHTVICSGRSDRHLRAIAEALVYMAKIKSQ-KGD---KHVRIEGKQSSDWIV  146 (208)
T ss_pred             HHHHHHHHHhcccCceEEEeccccceeeeeEEEEecCchHHHHHHHHHHHHHHHHhhc-CCC---cccccccccCCCeEE
Confidence            7899999999999999999999999999999999999999999999999999987621 133   466999999999999


Q ss_pred             EEcCCEEEEc
Q 033883           98 IDSGLCRILN  107 (109)
Q Consensus        98 lD~GdiVVh~  107 (109)
                      +|||.++||-
T Consensus       147 ~D~g~~vvH~  156 (208)
T KOG3212|consen  147 IDYGKFVVHA  156 (208)
T ss_pred             EEeceEEEEe
Confidence            9999999994

>PRK09271 flavodoxin; Provisional

Probab=84.98  E-value=5.1  Score=28.24  Aligned_cols=58  Identities=16%  Similarity=0.189  Sum_probs=34.8

Q ss_pred             CCCcccchHHHHhcCCCHHHHHHHHHhCCCCCeEEEecCCCC------C--cccEEEEEEcC-----CHHHHHHHHHHHH
Q 033883            1 MTGVTKESETLARKRPSMTSVVNPTFDLKADDVKVIPVGEKC------D--WTDYMVIATGR-----STWHVKNIAQAII   67 (109)
Q Consensus         1 ~~~~~~~~~~l~~~~~~i~~i~~~l~dkKa~dI~vlDv~~~~------~--~aDyfVI~Ta~-----S~rh~~ala~~i~   67 (109)
                      |||.|   +.+++      .+++.|.+. +.++.+.++....      .  -+|.++|+|.+     -+..++...+.+.
T Consensus        10 ~tGnT---e~~A~------~ia~~l~~~-g~~v~~~~~~~~~~~~~~~~~~~~d~vilgt~T~~~G~~p~~~~~f~~~l~   79 (160)
T PRK09271         10 LSGNT---REVAR------EIEERCEEA-GHEVDWVETDVQTLAEYPLDPEDYDLYLLGTWTDNAGRTPPEMKRFIAELA   79 (160)
T ss_pred             CCchH---HHHHH------HHHHHHHhC-CCeeEEEecccccccccccCcccCCEEEEECcccCCCcCCHHHHHHHHHHH
Confidence            45554   57777      888888764 4467777764421      1  24889999843     2334666655554


Q ss_pred             H
Q 033883           68 Y   68 (109)
Q Consensus        68 ~   68 (109)
                      +
T Consensus        80 ~   80 (160)
T PRK09271         80 E   80 (160)
T ss_pred             H
Confidence            3

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	109
3ups_A	136	Crystal Structure Of Iojap-Like Protein From Zymomo		7e-04

>pdb|3UPS|A Chain A, Crystal Structure Of Iojap-Like Protein From Zymomonas Mobilis Length = 136

Iteration: 1
 Score = 38.9 bits (89), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 7/75 (9%)
Query: 27  DLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPS 86
           D +A ++  IP+  K    DY VIA+GRS+  V   AQ +  + K       A    +  
Sbjct: 32  DDQALEIATIPLAGKSSIADYXVIASGRSSRQVTAXAQKLADRIK-------AATGYVSK 84
Query: 87  VQGQDTGKWVIIDSG 101
           ++G     WV++D+G
Sbjct: 85  IEGLPAADWVLLDAG 99

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	109
3ups_A	136	Iojap-like protein; PSI-biology, MCSG, midwest cen	2e-19
2id1_A	130	Hypothetical protein; alpha-beta protein, structur	6e-19
2o5a_A	125	BH1328 protein; BHR21, NESG, structural genomics,	8e-18

>3ups_A Iojap-like protein; PSI-biology, MCSG, midwest center for structural genomics, U function, structural genomics; HET: MSE; 1.75A {Zymomonas mobilis subsp} Length = 136

 Score = 76.2 bits (188), Expect = 2e-19
 Identities = 26/106 (24%), Positives = 45/106 (42%), Gaps = 13/106 (12%)

Query: 2   TGVTKESETLARKRPSMTS------VVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRS 55
           +       +  + + S         V +   D +A ++  IP+  K    DYMVIA+GRS
Sbjct: 1   SNAMPAPSSPRKNQTSFDPEMLLKLVTDSLDDDQALEIATIPLAGKSSIADYMVIASGRS 60

Query: 56  TWHVKNIAQAIIYKAKQRQREVGAKQMMLPSVQGQDTGKWVIIDSG 101
           +  V  +AQ +  + K     V         ++G     WV++D+G
Sbjct: 61  SRQVTAMAQKLADRIKAATGYV-------SKIEGLPAADWVLLDAG 99

>2id1_A Hypothetical protein; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative; 3.00A {Chromobacterium violaceum} SCOP: d.218.1.12 Length = 130

 Score = 75.0 bits (185), Expect = 6e-19
 Identities = 19/75 (25%), Positives = 38/75 (50%), Gaps = 7/75 (9%)

Query: 27  DLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPS 86
           D+K  D+  +   +       M++ATG S   VK +A ++  K K+   ++         
Sbjct: 16  DIKGKDIIELDTSKLTSLFQRMIVATGDSNRQVKALANSVQVKLKEAGVDI-------VG 68

Query: 87  VQGQDTGKWVIIDSG 101
            +G ++G+WV++D+G
Sbjct: 69  SEGHESGEWVLVDAG 83

>2o5a_A BH1328 protein; BHR21, NESG, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium; 2.70A {Bacillus halodurans} SCOP: d.218.1.12 Length = 125

 Score = 71.8 bits (177), Expect = 8e-18
 Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 7/75 (9%)

Query: 27  DLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPS 86
           D KA+ V  + +       D+ +I  G S   V+ IA  +   A+++  E+         
Sbjct: 16  DKKAEQVVALNMKGISLIADFFLICHGNSEKQVQAIAHELKKVAQEQGIEI-------KR 68

Query: 87  VQGQDTGKWVIIDSG 101
           ++G +  +WV+ID G
Sbjct: 69  LEGYEQARWVLIDLG 83

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	109
3ups_A	136	Iojap-like protein; PSI-biology, MCSG, midwest cen	100.0
2o5a_A	125	BH1328 protein; BHR21, NESG, structural genomics,	100.0
2id1_A	130	Hypothetical protein; alpha-beta protein, structur	100.0
5nul_A	138	Flavodoxin; electron transport, flavoprotein, FMN;	80.09

>3ups_A Iojap-like protein; PSI-biology, MCSG, midwest center for structural genomics, U function, structural genomics; HET: MSE; 1.75A {Zymomonas mobilis subsp}

Probab=100.00  E-value=5e-34  Score=201.25  Aligned_cols=89  Identities=30%  Similarity=0.487  Sum_probs=82.0

Q ss_pred             ccchHHHHhcCCCHHHHHHHHHhCCCCCeEEEecCCCCCcccEEEEEEcCCHHHHHHHHHHHHHHHHHhhhhhccccCCC
Q 033883            5 TKESETLARKRPSMTSVVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMML   84 (109)
Q Consensus         5 ~~~~~~l~~~~~~i~~i~~~l~dkKa~dI~vlDv~~~~~~aDyfVI~Ta~S~rh~~ala~~i~~~lk~~~~~~~~~~~~~   84 (109)
                      +.++++|.+      .++++|+++||+||++|||++++++|||||||||+|+||++|||++|.+.+|+.+    .   .+
T Consensus        16 ~~~~~~l~~------~i~~al~dkKa~DI~vlDv~~~s~~~DyfVIatg~S~rqv~Aiad~v~~~lk~~g----~---~~   82 (136)
T 3ups_A           16 SFDPEMLLK------LVTDSLDDDQALEIATIPLAGKSSIADYMVIASGRSSRQVTAMAQKLADRIKAAT----G---YV   82 (136)
T ss_dssp             -CCHHHHHH------HHHHHHHHTTCEEEEEEECTTTCSSCSEEEEEECSSHHHHHHHHHHHHHHHHHHH----C---CC
T ss_pred             CCCHHHHHH------HHHHHHHHcCCCCeEEEECCCCCcccCEEEEEEcCCHHHHHHHHHHHHHHHHHcC----C---cc
Confidence            344666777      9999999999999999999999999999999999999999999999999999875    3   47


Q ss_pred             CCcccCCCCCeEEEEcCCEEEE
Q 033883           85 PSVQGQDTGKWVIIDSGLCRIL  106 (109)
Q Consensus        85 ~~vEG~~~~~WvllD~GdiVVh  106 (109)
                      +++||.++++|+|+||||||||
T Consensus        83 ~~~EG~~~~~WvLlD~GdVvVH  104 (136)
T 3ups_A           83 SKIEGLPAADWVLLDAGDIIIH  104 (136)
T ss_dssp             CEEESCSSCSEEEEECSSEEEE
T ss_pred             CcccCCCCCCEEEEeCCCEEEE
Confidence            8999999999999999999999

>2o5a_A BH1328 protein; BHR21, NESG, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium; 2.70A {Bacillus halodurans} SCOP: d.218.1.12

Probab=100.00  E-value=3.8e-34  Score=199.42  Aligned_cols=86  Identities=24%  Similarity=0.379  Sum_probs=78.5

Q ss_pred             hHHHHhcCCCHHHHHHHHHhCCCCCeEEEecCCCCCcccEEEEEEcCCHHHHHHHHHHHHHHHHHhhhhhccccCCCCCc
Q 033883            8 SETLARKRPSMTSVVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPSV   87 (109)
Q Consensus         8 ~~~l~~~~~~i~~i~~~l~dkKa~dI~vlDv~~~~~~aDyfVI~Ta~S~rh~~ala~~i~~~lk~~~~~~~~~~~~~~~v   87 (109)
                      +++|++      .++++|+++||+||++|||++++++|||||||||+|+||++|||++|.+.+|+.|    .   .++++
T Consensus         3 ~~~l~~------~i~~al~dkKa~DI~vlDv~~~s~~~DyfVIatg~S~rqv~Aiad~v~~~lk~~g----~---~~~~~   69 (125)
T 2o5a_A            3 NQELLQ------LAVNAVDDKKAEQVVALNMKGISLIADFFLICHGNSEKQVQAIAHELKKVAQEQG----I---EIKRL   69 (125)
T ss_dssp             CHHHHH------HHHHHHHHTTCEEEEEEECBTTBC--CEEEEEEESSHHHHHHHHHHHHHHHHHTT----C---CCCEE
T ss_pred             HHHHHH------HHHHHHHHcCCCCeEEEEcCCCCcccCEEEEEEcCCHHHHHHHHHHHHHHHHHcC----C---ccccc
Confidence            456666      9999999999999999999999999999999999999999999999999999874    3   47899


Q ss_pred             ccCCCCCeEEEEcCCEEEE
Q 033883           88 QGQDTGKWVIIDSGLCRIL  106 (109)
Q Consensus        88 EG~~~~~WvllD~GdiVVh  106 (109)
                      ||.++++|+|+||||||||
T Consensus        70 EG~~~~~WvLlD~GdVvVH   88 (125)
T 2o5a_A           70 EGYEQARWVLIDLGDVVVH   88 (125)
T ss_dssp             ESTTTTSEEEEECSSEEEE
T ss_pred             cCCCCCCEEEEeCCCEEEE
Confidence            9999999999999999999

>2id1_A Hypothetical protein; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative; 3.00A {Chromobacterium violaceum} SCOP: d.218.1.12

Probab=100.00  E-value=6.1e-34  Score=199.50  Aligned_cols=86  Identities=22%  Similarity=0.426  Sum_probs=80.8

Q ss_pred             hHHHHhcCCCHHHHHHHHHhCCCCCeEEEecCCCCCcccEEEEEEcCCHHHHHHHHHHHHHHHHHhhhhhccccCCCCCc
Q 033883            8 SETLARKRPSMTSVVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPSV   87 (109)
Q Consensus         8 ~~~l~~~~~~i~~i~~~l~dkKa~dI~vlDv~~~~~~aDyfVI~Ta~S~rh~~ala~~i~~~lk~~~~~~~~~~~~~~~v   87 (109)
                      +++|++      .++++|+|+||+||++|||++++++|||||||||+|+||++|||++|++.+|+.+    .   .++++
T Consensus         3 ~~~l~~------~i~~al~dkKa~DI~vlDv~~~s~~~DyfVIaTg~S~rqv~Aiad~v~~~lk~~g----~---~~~~~   69 (130)
T 2id1_A            3 IQEISK------LAIEALEDIKGKDIIELDTSKLTSLFQRMIVATGDSNRQVKALANSVQVKLKEAG----V---DIVGS   69 (130)
T ss_dssp             HHHHHH------HHHHHHHHTTCEEEEEEEGGGTCSSCSEEEEEECSSHHHHHHHHHHHHHHHHHTT----C---CCCBC
T ss_pred             HHHHHH------HHHHHHHHcCCCCeEEEEcCCCCcccCEEEEEEcCCHHHHHHHHHHHHHHHHHcC----C---cCccc
Confidence            456777      9999999999999999999999999999999999999999999999999999874    3   47899


Q ss_pred             ccCCCCCeEEEEcCCEEEE
Q 033883           88 QGQDTGKWVIIDSGLCRIL  106 (109)
Q Consensus        88 EG~~~~~WvllD~GdiVVh  106 (109)
                      ||.++++|+|+||||||||
T Consensus        70 EG~~~~~WvLlD~GdVvVH   88 (130)
T 2id1_A           70 EGHESGEWVLVDAGDVVVH   88 (130)
T ss_dssp             CSTTTSSEEEEEETTEEEE
T ss_pred             cCCCCCCEEEEecCCEEEE
Confidence            9999999999999999999

>5nul_A Flavodoxin; electron transport, flavoprotein, FMN; HET: FMN; 1.60A {Clostridium beijerinckii} SCOP: c.23.5.1 PDB: 2flv_A* 2fvx_A* 1fld_A* 3nll_A* 1fvx_A* 1fla_A* 4nll_A* 5nll_A* 2fox_A* 5ull_A* 2fdx_A* 2fax_A* 6nul_A* 1fln_A* 4nul_A*

Probab=80.09  E-value=3.1  Score=26.76  Aligned_cols=40  Identities=18%  Similarity=0.276  Sum_probs=30.9

Q ss_pred             hHHHHhcCCCHHHHHHHHHhCCCCCeEEEecCCCC----CcccEEEEEEcC
Q 033883            8 SETLARKRPSMTSVVNPTFDLKADDVKVIPVGEKC----DWTDYMVIATGR   54 (109)
Q Consensus         8 ~~~l~~~~~~i~~i~~~l~dkKa~dI~vlDv~~~~----~~aDyfVI~Ta~   54 (109)
                      ++.+++      .+++.|.+. +.++.++|+.+..    .-+|.+||++..
T Consensus        12 T~~iA~------~ia~~l~~~-g~~v~~~~~~~~~~~~l~~~d~iiig~pt   55 (138)
T 5nul_A           12 TEKMAE------LIAKGIIES-GKDVNTINVSDVNIDELLNEDILILGCSA   55 (138)
T ss_dssp             HHHHHH------HHHHHHHHT-TCCCEEEEGGGCCHHHHTTCSEEEEEECC
T ss_pred             HHHHHH------HHHHHHHHC-CCeEEEEEhhhCCHHHHhhCCEEEEEcCc
Confidence            457888      888888875 5679999998753    246899999875

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	109
d2o5aa1	113	d.218.1.12 (A:2-114) Uncharacterized protein BH132	2e-15
d2id1a1	120	d.218.1.12 (A:1-120) Hypothetical protein CV0518 {	4e-15

>d2o5aa1 d.218.1.12 (A:2-114) Uncharacterized protein BH1328 {Bacillus halodurans [TaxId: 86665]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Nucleotidyltransferase
superfamily: Nucleotidyltransferase
family: Iojap/YbeB-like
domain: Uncharacterized protein BH1328
species: Bacillus halodurans [TaxId: 86665]

 Score = 64.1 bits (156), Expect = 2e-15
 Identities = 18/75 (24%), Positives = 35/75 (46%), Gaps = 7/75 (9%)

Query: 27  DLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPS 86
           D KA+ V  + +       D+ +I  G S   V+ IA  +   A++       + + +  
Sbjct: 15  DKKAEQVVALNMKGISLIADFFLICHGNSEKQVQAIAHELKKVAQE-------QGIEIKR 67

Query: 87  VQGQDTGKWVIIDSG 101
           ++G +  +WV+ID G
Sbjct: 68  LEGYEQARWVLIDLG 82

>d2id1a1 d.218.1.12 (A:1-120) Hypothetical protein CV0518 {Chromobacterium violaceum [TaxId: 536]} Length = 120

class: Alpha and beta proteins (a+b)
fold: Nucleotidyltransferase
superfamily: Nucleotidyltransferase
family: Iojap/YbeB-like
domain: Hypothetical protein CV0518
species: Chromobacterium violaceum [TaxId: 536]

 Score = 63.4 bits (154), Expect = 4e-15
 Identities = 17/75 (22%), Positives = 37/75 (49%), Gaps = 7/75 (9%)

Query: 27  DLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPS 86
           D+K  D+  +   +       M++ATG S   VK +A ++         ++    + +  
Sbjct: 16  DIKGKDIIELDTSKLTSLFQRMIVATGDSNRQVKALANSVQ-------VKLKEAGVDIVG 68

Query: 87  VQGQDTGKWVIIDSG 101
            +G ++G+WV++D+G
Sbjct: 69  SEGHESGEWVLVDAG 83

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	109
d2o5aa1	113	Uncharacterized protein BH1328 {Bacillus haloduran	100.0
d2id1a1	120	Hypothetical protein CV0518 {Chromobacterium viola	99.98
d1e5da1	152	Rubredoxin oxygen:oxidoreductase (ROO), C-terminal	85.57
d5nula_	138	Flavodoxin {Clostridium beijerinckii [TaxId: 1520]	80.65

>d2o5aa1 d.218.1.12 (A:2-114) Uncharacterized protein BH1328 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a+b)
fold: Nucleotidyltransferase
superfamily: Nucleotidyltransferase
family: Iojap/YbeB-like
domain: Uncharacterized protein BH1328
species: Bacillus halodurans [TaxId: 86665]

Probab=100.00  E-value=4.1e-33  Score=189.47  Aligned_cols=86  Identities=24%  Similarity=0.379  Sum_probs=78.2

Q ss_pred             hHHHHhcCCCHHHHHHHHHhCCCCCeEEEecCCCCCcccEEEEEEcCCHHHHHHHHHHHHHHHHHhhhhhccccCCCCCc
Q 033883            8 SETLARKRPSMTSVVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPSV   87 (109)
Q Consensus         8 ~~~l~~~~~~i~~i~~~l~dkKa~dI~vlDv~~~~~~aDyfVI~Ta~S~rh~~ala~~i~~~lk~~~~~~~~~~~~~~~v   87 (109)
                      +++|.+      .++++|+++||+||++|||++.|++|||||||||+|+||++|||++|.+.+|+++    .   .++++
T Consensus         2 ~~el~~------~i~~~l~dkKa~dI~vldv~~~~~~~D~~VIatg~S~rh~~aia~~v~~~~k~~~----~---~~~~~   68 (113)
T d2o5aa1           2 NQELLQ------LAVNAVDDKKAEQVVALNMKGISLIADFFLICHGNSEKQVQAIAHELKKVAQEQG----I---EIKRL   68 (113)
T ss_dssp             CHHHHH------HHHHHHHHTTCEEEEEEECBTTBC--CEEEEEEESSHHHHHHHHHHHHHHHHHTT----C---CCCEE
T ss_pred             HHHHHH------HHHHHHHHcCCCCeEEEECCCCCcccCEEEEEEeCCHHHHHHHHHHHHHHHHHhc----c---ccccc
Confidence            456666      9999999999999999999999999999999999999999999999999999875    3   46799


Q ss_pred             ccCCCCCeEEEEcCCEEEE
Q 033883           88 QGQDTGKWVIIDSGLCRIL  106 (109)
Q Consensus        88 EG~~~~~WvllD~GdiVVh  106 (109)
                      ||.++++|+|+|||+||||
T Consensus        69 eG~~~~~WvliD~gdvvVH   87 (113)
T d2o5aa1          69 EGYEQARWVLIDLGDVVVH   87 (113)
T ss_dssp             ESTTTTSEEEEECSSEEEE
T ss_pred             cCCCCCCEEEeeCCCEEEE
Confidence            9999999999999999999

>d2id1a1 d.218.1.12 (A:1-120) Hypothetical protein CV0518 {Chromobacterium violaceum [TaxId: 536]}

class: Alpha and beta proteins (a+b)
fold: Nucleotidyltransferase
superfamily: Nucleotidyltransferase
family: Iojap/YbeB-like
domain: Hypothetical protein CV0518
species: Chromobacterium violaceum [TaxId: 536]

Probab=99.98  E-value=2.2e-32  Score=187.51  Aligned_cols=86  Identities=22%  Similarity=0.426  Sum_probs=80.2

Q ss_pred             hHHHHhcCCCHHHHHHHHHhCCCCCeEEEecCCCCCcccEEEEEEcCCHHHHHHHHHHHHHHHHHhhhhhccccCCCCCc
Q 033883            8 SETLARKRPSMTSVVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPSV   87 (109)
Q Consensus         8 ~~~l~~~~~~i~~i~~~l~dkKa~dI~vlDv~~~~~~aDyfVI~Ta~S~rh~~ala~~i~~~lk~~~~~~~~~~~~~~~v   87 (109)
                      .++|.+      .++++|+++||+||++|||++.+++|||||||||+|+||++|+|++|.+.+|+.+    .   .++++
T Consensus         3 ~~~l~~------~i~~~l~d~Ka~DI~vldv~~~~~~~D~~VI~Tg~S~rh~~aia~~i~~~lk~~~----~---~~~~~   69 (120)
T d2id1a1           3 IQEISK------LAIEALEDIKGKDIIELDTSKLTSLFQRMIVATGDSNRQVKALANSVQVKLKEAG----V---DIVGS   69 (120)
T ss_dssp             HHHHHH------HHHHHHHHTTCEEEEEEEGGGTCSSCSEEEEEECSSHHHHHHHHHHHHHHHHHTT----C---CCCBC
T ss_pred             HHHHHH------HHHHHHHHcCCCCeEEEECCCCCccccEEEEEEecCHHHHHHHHHHHHHHHHHcC----C---ccccc
Confidence            456666      9999999999999999999999999999999999999999999999999999874    3   47799


Q ss_pred             ccCCCCCeEEEEcCCEEEE
Q 033883           88 QGQDTGKWVIIDSGLCRIL  106 (109)
Q Consensus        88 EG~~~~~WvllD~GdiVVh  106 (109)
                      ||.++++|+|+|||+||||
T Consensus        70 eG~~~~~WillD~gdivVH   88 (120)
T d2id1a1          70 EGHESGEWVLVDAGDVVVH   88 (120)
T ss_dssp             CSTTTSSEEEEEETTEEEE
T ss_pred             cCCCCCCEEEEecCceEEE
Confidence            9999999999999999999

>d1e5da1 c.23.5.1 (A:251-402) Rubredoxin oxygen:oxidoreductase (ROO), C-terminal domain {Desulfovibrio gigas [TaxId: 879]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Flavoproteins
family: Flavodoxin-related
domain: Rubredoxin oxygen:oxidoreductase (ROO), C-terminal domain
species: Desulfovibrio gigas [TaxId: 879]

Probab=85.57  E-value=0.51  Score=29.80  Aligned_cols=45  Identities=18%  Similarity=0.097  Sum_probs=34.7

Q ss_pred             CCCcccchHHHHhcCCCHHHHHHHHHhCCCCCeEEEecCCCC--------CcccEEEEEEcCC
Q 033883            1 MTGVTKESETLARKRPSMTSVVNPTFDLKADDVKVIPVGEKC--------DWTDYMVIATGRS   55 (109)
Q Consensus         1 ~~~~~~~~~~l~~~~~~i~~i~~~l~dkKa~dI~vlDv~~~~--------~~aDyfVI~Ta~S   55 (109)
                      |||.|   +.+++      .|++.|.+. +-++.++|+++..        .-+|.+||+|..-
T Consensus        12 ~tGnT---e~~A~------~Ia~~l~~~-g~ev~~~~~~~~~~~~~~~~l~~~d~vi~Gspt~   64 (152)
T d1e5da1          12 MWHST---EKMAR------VLAESFRDE-GCTVKLMWCKACHHSQIMSEISDAGAVIVGSPTH   64 (152)
T ss_dssp             SSSHH---HHHHH------HHHHHHHHT-TCEEEEEETTTSCHHHHHHHHHTCSEEEEECCCB
T ss_pred             CCcHH---HHHHH------HHHHHHhhC-CCEEEEeecccCChhhhccchhhCCEEEEecccc
Confidence            45554   47888      888999886 6689999998754        2479999998774

>d5nula_ c.23.5.1 (A:) Flavodoxin {Clostridium beijerinckii [TaxId: 1520]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Flavoproteins
family: Flavodoxin-related
domain: Flavodoxin
species: Clostridium beijerinckii [TaxId: 1520]

Probab=80.65  E-value=1.4  Score=27.09  Aligned_cols=45  Identities=20%  Similarity=0.278  Sum_probs=33.5

Q ss_pred             CCCcccchHHHHhcCCCHHHHHHHHHhCCCCCeEEEecCCCCC----cccEEEEEEcCC
Q 033883            1 MTGVTKESETLARKRPSMTSVVNPTFDLKADDVKVIPVGEKCD----WTDYMVIATGRS   55 (109)
Q Consensus         1 ~~~~~~~~~~l~~~~~~i~~i~~~l~dkKa~dI~vlDv~~~~~----~aDyfVI~Ta~S   55 (109)
                      |||.   ++.+++      .+++.|.+ ++.++.++++.+...    -+|.+||+|.+-
T Consensus         8 ~tGn---T~~vA~------~ia~~l~~-~g~~v~~~~~~~~~~~~l~~~~~~i~g~pt~   56 (138)
T d5nula_           8 GTGN---TEKMAE------LIAKGIIE-SGKDVNTINVSDVNIDELLNEDILILGCSAM   56 (138)
T ss_dssp             SSSH---HHHHHH------HHHHHHHH-TTCCCEEEEGGGCCHHHHTTCSEEEEEECCB
T ss_pred             cChH---HHHHHH------HHHHHHHh-cCCcceecccccccccccccCCeEEEEEecc
Confidence            4554   457888      88888877 666899999987642    478999998763