Citrus Sinensis ID: 038665

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-
Protein Sequence
EEKKTVVVGSEAVEEVKSPSRSPLPLPKLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQIGQTVIIYRPSLTRMKLEEKKQQARRVYVRKESKLKPLLLKKAGVSRLSGRRRRGSSRFSSRASD
Secondary Structure (PSIPRED)
ccccccccccHHHHHcccccccccccccccHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHccEEEEEEccccHHHHHHHHHHHHHHHccEEEEEEccEEEEEEccccccccHHHHHHHHHHHHHHccccccHHHHHccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccEEEEccccEEccccccccccccccccHHHHHHHHHHHcccccEEEEEEEccccccHHHHHHHHHHHHHccEEEEEEcccccccHHHHHHHHHHHcccEEEEEEccEEEEEccccccHHHHHHHHHHHHHHHHccHcHcHHHHHcccccccccccccccccccccccc
Coil and Loop (DISEMBL)
EEKKTVVVGSEAveevkspsrsplplpkltvkEKKELASYAHSLGKklkcqlvgksgvtdGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQIGQTviiyrpsltrmkLEEKKQQARRVYVRKesklkplllkkagvsrlsgrrrrgssrfssrasd
Flexible Loop (DISEMBL)
eekktvvvgseaveevkspsrsplplpkltVKEKKELASYAHslgkklkcqlvgkSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEAtgsavvsqigqtviiyrpsltrmkleekkqqarrvyvrkesklkplllkkagvsrlsgrrrrgssrfssrasd
Low Complexity Region (SEG)
EEKKTVVVGSEAVEEVkspsrsplplpklTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQIGQTVIIYRPSLTRMKLEEKKQQARRVYVRKESklkplllkkAGVsrlsgrrrrgssrfssrasD
Disordered region (IsUnstruct)
**************************************SYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQIGQTVIIYRPSLT****************************************************
Disordered Region (DISOPRED)
***********************************ELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQIGQTVIIY*********************************************************
Disordered Region (DISEMBL)
**********************PLPLPKLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQIGQTVIIYRPSLTRMKL***********VRKESKLKPLLLKKAGV********************
Disordered Region (DISPRO)
*******V*SEAVEEV**PSRSPLPLPKLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQIGQTVIIYRPSLTRMKLEEKKQQARRVYVRKESKLK*LLLKK***********************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
EEKKTVVVGSEAVEEVKSPSRSPLPLPKLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQIGQTVIIYRPSLTxxxxxxxxxxxxxxxxxxxxxLKPLLLKKAGVSRLSGRRRRGSSRFSSRASD
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	171	2.2.26 [Sep-21-2011]
P54454	96	Probable RNA-binding prot	yes	no	0.502	0.895	0.370	2e-08
P0AGK7	97	RNA-binding protein YhbY	yes	no	0.473	0.835	0.333	1e-05
P0AGK4	97	RNA-binding protein YhbY	N/A	no	0.473	0.835	0.333	1e-05
P0AGK5	97	RNA-binding protein YhbY	yes	no	0.473	0.835	0.333	1e-05
P0AGK6	97	RNA-binding protein YhbY	N/A	no	0.473	0.835	0.333	1e-05
P71376	99	RNA-binding protein HI_13	yes	no	0.520	0.898	0.282	0.0007

>sp|P54454|YQEI_BACSU Probable RNA-binding protein YqeI OS=Bacillus subtilis (strain 168) GN=yqeI PE=4 SV=1

 Score = 58.5 bits (140), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 33/89 (37%), Positives = 51/89 (57%), Gaps = 3/89 (3%)

Query: 29  LTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGEL 88
           LT K+K+ L S AH L    +   VGK GV D ++    E LEA EL+K+ + + C  + 
Sbjct: 2   LTGKQKRFLRSKAHHLTPIFQ---VGKGGVNDNMIKQIAEALEARELIKVSVLQNCEEDK 58

Query: 89  EDVVKQLEEATGSAVVSQIGQTVIIYRPS 117
            DV + L + + S +V  IG T+++Y+ S
Sbjct: 59  NDVAEALVKGSRSQLVQTIGNTIVLYKES 87

Bacillus subtilis (strain 168) (taxid: 224308)

>sp|P0AGK7|YHBY_SHIFL RNA-binding protein YhbY OS=Shigella flexneri GN=yhbY PE=4 SV=1

 Score = 49.3 bits (116), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 32/96 (33%), Positives = 54/96 (56%), Gaps = 15/96 (15%)

Query: 28  KLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGE 87
            L+ K+K+ L   AH L   +   L+G +G+T+GV+    + LE +EL+K+KI       
Sbjct: 2   NLSTKQKQHLKGLAHPLKPVV---LLGSNGLTEGVLAEIEQALEHHELIKVKI------A 52

Query: 88  LED------VVKQLEEATGSAVVSQIGQTVIIYRPS 117
            ED      +V+ +   TG+  V  IG+T+++YRP+
Sbjct: 53  TEDRETKTLIVEAIVRETGACNVQVIGKTLVLYRPT 88

Shigella flexneri (taxid: 623)

>sp|P0AGK4|YHBY_ECOLI RNA-binding protein YhbY OS=Escherichia coli (strain K12) GN=yhbY PE=1 SV=1

 Score = 49.3 bits (116), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 32/96 (33%), Positives = 54/96 (56%), Gaps = 15/96 (15%)

Query: 28  KLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGE 87
            L+ K+K+ L   AH L   +   L+G +G+T+GV+    + LE +EL+K+KI       
Sbjct: 2   NLSTKQKQHLKGLAHPLKPVV---LLGSNGLTEGVLAEIEQALEHHELIKVKI------A 52

Query: 88  LED------VVKQLEEATGSAVVSQIGQTVIIYRPS 117
            ED      +V+ +   TG+  V  IG+T+++YRP+
Sbjct: 53  TEDRETKTLIVEAIVRETGACNVQVIGKTLVLYRPT 88

Escherichia coli (strain K12) (taxid: 83333)

>sp|P0AGK5|YHBY_ECOL6 RNA-binding protein YhbY OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=yhbY PE=4 SV=1

 Score = 49.3 bits (116), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 32/96 (33%), Positives = 54/96 (56%), Gaps = 15/96 (15%)

Query: 28  KLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGE 87
            L+ K+K+ L   AH L   +   L+G +G+T+GV+    + LE +EL+K+KI       
Sbjct: 2   NLSTKQKQHLKGLAHPLKPVV---LLGSNGLTEGVLAEIEQALEHHELIKVKI------A 52

Query: 88  LED------VVKQLEEATGSAVVSQIGQTVIIYRPS 117
            ED      +V+ +   TG+  V  IG+T+++YRP+
Sbjct: 53  TEDRETKTLIVEAIVRETGACNVQVIGKTLVLYRPT 88

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

>sp|P0AGK6|YHBY_ECO57 RNA-binding protein YhbY OS=Escherichia coli O157:H7 GN=yhbY PE=4 SV=1

 Score = 49.3 bits (116), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 32/96 (33%), Positives = 54/96 (56%), Gaps = 15/96 (15%)

Query: 28  KLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGE 87
            L+ K+K+ L   AH L   +   L+G +G+T+GV+    + LE +EL+K+KI       
Sbjct: 2   NLSTKQKQHLKGLAHPLKPVV---LLGSNGLTEGVLAEIEQALEHHELIKVKI------A 52

Query: 88  LED------VVKQLEEATGSAVVSQIGQTVIIYRPS 117
            ED      +V+ +   TG+  V  IG+T+++YRP+
Sbjct: 53  TEDRETKTLIVEAIVRETGACNVQVIGKTLVLYRPT 88

Escherichia coli O157:H7 (taxid: 83334)

>sp|P71376|Y1333_HAEIN RNA-binding protein HI_1333 OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) GN=HI_1333 PE=1 SV=1

 Score = 43.5 bits (101), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 26/92 (28%), Positives = 49/92 (53%), Gaps = 3/92 (3%)

Query: 26  LPKLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCP 85
           +  L+ K+K+ L   AH L   +   ++G +G+T+GV+      L  +EL+K+K+     
Sbjct: 1   MTTLSTKQKQFLKGLAHHLNPVV---MLGGNGLTEGVLAEIENALNHHELIKVKVAGADR 57

Query: 86  GELEDVVKQLEEATGSAVVSQIGQTVIIYRPS 117
              + ++  +   T +A V  IG  +++YRPS
Sbjct: 58  ETKQLIINAIVRETKAAQVQTIGHILVLYRPS 89

Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (taxid: 71421)

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	171
449515613	279	PREDICTED: uncharacterized protein LOC10	0.812	0.498	0.7	2e-46
449461613	279	PREDICTED: uncharacterized protein LOC10	0.812	0.498	0.692	7e-46
356538720	260	PREDICTED: uncharacterized protein LOC10	0.807	0.530	0.662	1e-44
225427732	287	PREDICTED: uncharacterized protein LOC10	0.766	0.456	0.711	2e-44
147771494	239	hypothetical protein VITISV_005730 [Viti	0.766	0.548	0.711	3e-44
255637509	260	unknown [Glycine max]	0.807	0.530	0.655	4e-44
255543825	311	hypothetical protein RCOM_1449540 [Ricin	0.777	0.427	0.657	3e-43
224105319	99	predicted protein [Populus trichocarpa]	0.578	1.0	0.858	3e-41
388496390	282	unknown [Lotus japonicus]	0.666	0.404	0.745	1e-40
357473479	285	CRS1 / YhbY domain containing protein [M	0.684	0.410	0.683	2e-40

>gi|449515613|ref|XP_004164843.1| PREDICTED: uncharacterized protein LOC101225856 [Cucumis sativus]

 Score =  189 bits (481), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 98/140 (70%), Positives = 117/140 (83%), Gaps = 1/140 (0%)

Query: 26  LPKLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCP 85
           +P LT+KEKKELASYAH LGKKLK QLVGKSGVT G+ TSFIETLEANELLKIKI   CP
Sbjct: 136 IPSLTIKEKKELASYAHGLGKKLKSQLVGKSGVTPGLATSFIETLEANELLKIKILGNCP 195

Query: 86  GELEDVVKQLEEATGSAVVSQIGQTVIIYRPSLTRMKLEEKKQQARRVYVRKE-SKLKPL 144
            ELEDVV++L E+TGS VV+QIG+TVIIYRPS+T+MK EE+K++AR+VY+RKE  ++K +
Sbjct: 196 EELEDVVRKLAESTGSVVVNQIGRTVIIYRPSITKMKAEEEKRRARKVYMRKEPDRVKSI 255

Query: 145 LLKKAGVSRLSGRRRRGSSR 164
           L KK    R S R RRG+SR
Sbjct: 256 LQKKIETPRSSNRGRRGTSR 275

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449461613|ref|XP_004148536.1| PREDICTED: uncharacterized protein LOC101213060 [Cucumis sativus]

 Score =  188 bits (477), Expect = 7e-46,   Method: Compositional matrix adjust.
 Identities = 97/140 (69%), Positives = 117/140 (83%), Gaps = 1/140 (0%)

Query: 26  LPKLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCP 85
           +P LT+KEKKELASYAH LGKKLK QLVGKSGVT G+ TSFIETLEANELLKIKI   CP
Sbjct: 136 IPSLTIKEKKELASYAHGLGKKLKSQLVGKSGVTPGLATSFIETLEANELLKIKILGNCP 195

Query: 86  GELEDVVKQLEEATGSAVVSQIGQTVIIYRPSLTRMKLEEKKQQARRVYVRKE-SKLKPL 144
            ELEDVV++L E+TGS VV+QIG+TVIIYRPS+T+MK EE+K++AR+VY+RKE  ++K +
Sbjct: 196 EELEDVVRKLAESTGSVVVNQIGRTVIIYRPSITKMKAEEEKRRARKVYMRKEPDRVKSI 255

Query: 145 LLKKAGVSRLSGRRRRGSSR 164
           L KK    + S R RRG+SR
Sbjct: 256 LQKKIETPQSSNRGRRGTSR 275

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356538720|ref|XP_003537849.1| PREDICTED: uncharacterized protein LOC100779359 [Glycine max]

 Score =  184 bits (467), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 96/145 (66%), Positives = 115/145 (79%), Gaps = 7/145 (4%)

Query: 24  LPLPKLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRT 83
           L +P L+VKE+KELASYAHSLG KLK QLVGKSGVT  + TSFIETLEANELLKIKIHRT
Sbjct: 116 LEVPSLSVKERKELASYAHSLGDKLKTQLVGKSGVTPNLATSFIETLEANELLKIKIHRT 175

Query: 84  CPGELEDVVKQLEEATGSAVVSQIGQTVIIYRPSLTRMKLEEKKQQARRVYVRKESKLKP 143
           CPGEL+DVVKQLEEATGS  V QIG+T+IIYRPSL++MK EEKK+QAR + ++K+ K + 
Sbjct: 176 CPGELDDVVKQLEEATGSVAVGQIGRTLIIYRPSLSKMKAEEKKKQARNLILKKQVKQRL 235

Query: 144 LLLKKAGVSRL-------SGRRRRG 161
           +   K  V +L       SG++RR 
Sbjct: 236 VNKSKEQVPKLSWPGSSWSGKKRRA 260

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225427732|ref|XP_002265886.1| PREDICTED: uncharacterized protein LOC100243481 [Vitis vinifera] gi|297744749|emb|CBI38011.3| unnamed protein product [Vitis vinifera]

 Score =  183 bits (464), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 96/135 (71%), Positives = 112/135 (82%), Gaps = 4/135 (2%)

Query: 11  EAVEEVKSPSRSPLPLPKLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETL 70
           E+ E VK  SR   P+  LT+KEKKELASYAHSLGKKLKCQLVGK GVT  V ++FIE L
Sbjct: 131 ESEETVKETSR---PV-NLTIKEKKELASYAHSLGKKLKCQLVGKQGVTASVASAFIENL 186

Query: 71  EANELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQIGQTVIIYRPSLTRMKLEEKKQQA 130
           E+NELLKIKIH TCPGEL DVVKQLEE+TGS VV QIG++VI+YRPS+T++K EEK++QA
Sbjct: 187 ESNELLKIKIHGTCPGELPDVVKQLEESTGSVVVGQIGRSVILYRPSVTKLKAEEKRKQA 246

Query: 131 RRVYVRKESKLKPLL 145
           RRVYVRK +  KP L
Sbjct: 247 RRVYVRKGAIFKPKL 261

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147771494|emb|CAN73653.1| hypothetical protein VITISV_005730 [Vitis vinifera]

 Score =  183 bits (464), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 96/135 (71%), Positives = 112/135 (82%), Gaps = 4/135 (2%)

Query: 11  EAVEEVKSPSRSPLPLPKLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETL 70
           E+ E VK  SR   P+  LT+KEKKELASYAHSLGKKLKCQLVGK GVT  V ++FIE L
Sbjct: 100 ESEETVKETSR---PV-NLTIKEKKELASYAHSLGKKLKCQLVGKQGVTASVASAFIENL 155

Query: 71  EANELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQIGQTVIIYRPSLTRMKLEEKKQQA 130
           E+NELLKIKIH TCPGEL DVVKQLEE+TGS VV QIG++VI+YRPS+T++K EEK++QA
Sbjct: 156 ESNELLKIKIHGTCPGELPDVVKQLEESTGSVVVGQIGRSVILYRPSVTKLKAEEKRKQA 215

Query: 131 RRVYVRKESKLKPLL 145
           RRVYVRK +  KP L
Sbjct: 216 RRVYVRKGAIFKPKL 230

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255637509|gb|ACU19081.1| unknown [Glycine max]

 Score =  182 bits (462), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 95/145 (65%), Positives = 112/145 (77%), Gaps = 7/145 (4%)

Query: 24  LPLPKLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRT 83
           L +P L+VKE+KELASYAHSLG KLK QLVGKSGVT  + TSFIETLEANELLKIKIHRT
Sbjct: 116 LEVPSLSVKERKELASYAHSLGDKLKTQLVGKSGVTPNLATSFIETLEANELLKIKIHRT 175

Query: 84  CPGELEDVVKQLEEATGSAVVSQIGQTVIIYRPSLTRMKLEEKKQQARRVYVRKESKLKP 143
           CPGEL+DVVKQLEEATGS  V QIG+T IIYRPS ++MK EEKK+QAR +  +K+ K + 
Sbjct: 176 CPGELDDVVKQLEEATGSVAVGQIGRTFIIYRPSFSKMKAEEKKKQARNLIFKKQVKQRL 235

Query: 144 LLLKKAGVSRL-------SGRRRRG 161
           +   K  V +L       SG++RR 
Sbjct: 236 VNKSKEQVPKLSWPGSSWSGKKRRA 260

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255543825|ref|XP_002512975.1| hypothetical protein RCOM_1449540 [Ricinus communis] gi|223547986|gb|EEF49478.1| hypothetical protein RCOM_1449540 [Ricinus communis]

 Score =  179 bits (455), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 96/146 (65%), Positives = 115/146 (78%), Gaps = 13/146 (8%)

Query: 21  RSPLPLPKLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLE--------- 71
           R+   +P LTVKEKKELASYA+SLGKKLK QLVGKSGVTD V TSFIETL+         
Sbjct: 155 RNGFKVPNLTVKEKKELASYANSLGKKLKSQLVGKSGVTDNVATSFIETLKQMSXRIVWC 214

Query: 72  ANELL----KIKIHRTCPGELEDVVKQLEEATGSAVVSQIGQTVIIYRPSLTRMKLEEKK 127
           A  +L    +IKIHRTCPGELEDVV++L+EATGS VV QIG+TVIIYRPSL++M+ EEK+
Sbjct: 215 AKPVLECSEQIKIHRTCPGELEDVVQRLQEATGSVVVGQIGRTVIIYRPSLSKMEAEEKR 274

Query: 128 QQARRVYVRKESKLKPLLLKKAGVSR 153
           +QARR+YVRKE KLKP+ L    ++R
Sbjct: 275 RQARRIYVRKEPKLKPISLILQHIAR 300

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224105319|ref|XP_002313766.1| predicted protein [Populus trichocarpa] gi|222850174|gb|EEE87721.1| predicted protein [Populus trichocarpa]

 Score =  173 bits (438), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 85/99 (85%), Positives = 91/99 (91%)

Query: 29  LTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGEL 88
           LTVKEKKELASYAH LGKKLK QL+GKSG TD V TSFIETLEANELLKIKIHRTCPGEL
Sbjct: 1   LTVKEKKELASYAHGLGKKLKSQLIGKSGFTDNVATSFIETLEANELLKIKIHRTCPGEL 60

Query: 89  EDVVKQLEEATGSAVVSQIGQTVIIYRPSLTRMKLEEKK 127
           EDVV++LEEATGS VV QIG+TVIIYRPSLT+MK EEK+
Sbjct: 61  EDVVRRLEEATGSVVVGQIGRTVIIYRPSLTKMKAEEKR 99

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388496390|gb|AFK36261.1| unknown [Lotus japonicus]

 Score =  171 bits (432), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 85/114 (74%), Positives = 97/114 (85%)

Query: 24  LPLPKLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRT 83
           L +P LTVKEKKELAS+AHSL KKLK QLVGKSGVT  + TSFIETLEANELLKIK+HRT
Sbjct: 167 LEVPSLTVKEKKELASFAHSLWKKLKSQLVGKSGVTSNLATSFIETLEANELLKIKVHRT 226

Query: 84  CPGELEDVVKQLEEATGSAVVSQIGQTVIIYRPSLTRMKLEEKKQQARRVYVRK 137
           CPGELED VKQLEE TGS  VSQIG+T+IIY+PSLT++K EEKK+ + + Y  K
Sbjct: 227 CPGELEDAVKQLEELTGSVTVSQIGRTLIIYKPSLTKLKAEEKKKTSSQPYSEK 280

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357473479|ref|XP_003607024.1| CRS1 / YhbY domain containing protein [Medicago truncatula] gi|355508079|gb|AES89221.1| CRS1 / YhbY domain containing protein [Medicago truncatula]

 Score =  170 bits (431), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 80/117 (68%), Positives = 102/117 (87%)

Query: 24  LPLPKLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRT 83
           L +P L+VKE+KEL SYAHSLGKKL  QLVGKSGVT  +VT+F + LEANELLKIKIH +
Sbjct: 140 LEVPSLSVKERKELGSYAHSLGKKLSTQLVGKSGVTPNLVTAFSDNLEANELLKIKIHGS 199

Query: 84  CPGELEDVVKQLEEATGSAVVSQIGQTVIIYRPSLTRMKLEEKKQQARRVYVRKESK 140
           CPGELEDVVKQLEE+TGS  V QIG+T+I+YRPSL+++K+EEKK+Q R++++ K++K
Sbjct: 200 CPGELEDVVKQLEESTGSVTVGQIGRTLILYRPSLSKLKVEEKKKQVRKLFLEKQNK 256

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	171
TAIR|locus:2120282	296	AT4G39040 [Arabidopsis thalian	0.631	0.364	0.694	1.9e-35
TAIR|locus:2050150	222	AT2G21350 [Arabidopsis thalian	0.584	0.450	0.7	2.5e-33
UNIPROTKB|Q81LQ2	97	BA_4560 "Putative RNA-binding	0.497	0.876	0.318	2.9e-09
TIGR_CMR|BA_4560	97	BA_4560 "conserved hypothetica	0.497	0.876	0.318	2.9e-09
UNIPROTKB|Q71ZI1	96	LMOf2365_1508 "Putative unchar	0.538	0.958	0.294	4.7e-09
UNIPROTKB|P0AGK4	97	yhbY "predicted RNA-binding pr	0.508	0.896	0.347	1.2e-08
UNIPROTKB|Q74DQ2	98	yhbY "RNA-binding protein YhbY	0.549	0.959	0.306	6.8e-08
UNIPROTKB|Q97P93	103	SP_1748 "Putative uncharacteri	0.538	0.893	0.316	6.8e-08
TIGR_CMR|GSU_1263	98	GSU_1263 "conserved hypothetic	0.549	0.959	0.306	6.8e-08
UNIPROTKB|Q8EHM4	99	yhbY "Putative RNA-binding pro	0.520	0.898	0.347	1.1e-07

TAIR|locus:2120282 AT4G39040 [Arabidopsis thaliana (taxid:3702)]

 Score = 383 (139.9 bits), Expect = 1.9e-35, P = 1.9e-35
 Identities = 75/108 (69%), Positives = 89/108 (82%)

Query:    30 TVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELE 89
             ++KEKKELASYAHSLG KLKCQLVGKSGVTD VV SF+ETLE NELLK+KI +T P ELE
Sbjct:   154 SIKEKKELASYAHSLGDKLKCQLVGKSGVTDSVVFSFLETLEKNELLKVKIRKTSPDELE 213

Query:    90 DVVKQLEEATGSAVVSQIGQTVIIYRPSLTRMKLEEKKQQARRVYVRK 137
             D V+ LEEATGS  V QIG+TVI+YRPS T+MK E KK++  R+ + +
Sbjct:   214 DAVQHLEEATGSVAVGQIGRTVILYRPSPTKMKAEAKKKEVERMSITR 261

GO:0003723 "RNA binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=IDA

GO:0009073 "aromatic amino acid family biosynthetic process" evidence=RCA

GO:0016117 "carotenoid biosynthetic process" evidence=RCA

GO:0016226 "iron-sulfur cluster assembly" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA

TAIR|locus:2050150 AT2G21350 [Arabidopsis thaliana (taxid:3702)]

 Score = 363 (132.8 bits), Expect = 2.5e-33, P = 2.5e-33
 Identities = 70/100 (70%), Positives = 85/100 (85%)

Query:    30 TVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELE 89
             + KEK++LASYAH LG KLK QLVGKSGVTD VV SF+ETLE NELLK+KIHRTCPGELE
Sbjct:   120 SAKEKRKLASYAHHLGDKLKSQLVGKSGVTDSVVLSFVETLEKNELLKVKIHRTCPGELE 179

Query:    90 DVVKQLEEATGSAVVSQIGQTVIIYRPSLTRMKLEEKKQQ 129
             D++ +LEEATGS  V QI +TVI+YRPS T++K +E K++
Sbjct:   180 DMILRLEEATGSVSVGQIARTVILYRPSPTKLKADEDKKR 219

GO:0003723 "RNA binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

UNIPROTKB|Q81LQ2 BA_4560 "Putative RNA-binding protein, YhbY family" [Bacillus anthracis (taxid:1392)]

 Score = 136 (52.9 bits), Expect = 2.9e-09, P = 2.9e-09
 Identities = 28/88 (31%), Positives = 50/88 (56%)

Query:    30 TVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELE 89
             T K+K+ L + AH L    +   VGK GV + ++    +TLEA EL K+ + + C  +  
Sbjct:     3 TGKQKRFLRAQAHHLTPIFQ---VGKGGVNENMIKQIADTLEARELFKVSVLQNCEFDRR 59

Query:    90 DVVKQLEEATGSAVVSQIGQTVIIYRPS 117
             +V ++L +   + +V  IG T+++Y+ S
Sbjct:    60 EVAEELAKGARAEIVQVIGSTIVLYKES 87

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|BA_4560 BA_4560 "conserved hypothetical protein TIGR00253" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 136 (52.9 bits), Expect = 2.9e-09, P = 2.9e-09
 Identities = 28/88 (31%), Positives = 50/88 (56%)

Query:    30 TVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELE 89
             T K+K+ L + AH L    +   VGK GV + ++    +TLEA EL K+ + + C  +  
Sbjct:     3 TGKQKRFLRAQAHHLTPIFQ---VGKGGVNENMIKQIADTLEARELFKVSVLQNCEFDRR 59

Query:    90 DVVKQLEEATGSAVVSQIGQTVIIYRPS 117
             +V ++L +   + +V  IG T+++Y+ S
Sbjct:    60 EVAEELAKGARAEIVQVIGSTIVLYKES 87

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q71ZI1 LMOf2365_1508 "Putative uncharacterized protein" [Listeria monocytogenes serotype 4b str. F2365 (taxid:265669)]

 Score = 134 (52.2 bits), Expect = 4.7e-09, P = 4.7e-09
 Identities = 28/95 (29%), Positives = 55/95 (57%)

Query:    30 TVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELE 89
             T  +K+ L   AH++    +   VGK  V+  ++    E LEA EL+KI I + C  + +
Sbjct:     3 TATQKRFLRKEAHNIQPIFQ---VGKGSVSPNLIIHVKEALEARELIKISILQNCEEDKQ 59

Query:    90 DVVKQLEEATGSAVVSQIGQTVIIYRPSLTRMKLE 124
              V +++   +G+ +V  IG+T+I+Y+ S+ + +++
Sbjct:    60 TVAEKISARSGAEIVQVIGRTIILYKTSVNKQQIK 94

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|P0AGK4 yhbY "predicted RNA-binding protein" [Escherichia coli K-12 (taxid:83333)]

 Score = 130 (50.8 bits), Expect = 1.2e-08, P = 1.2e-08
 Identities = 32/92 (34%), Positives = 55/92 (59%)

Query:    30 TVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELE 89
             + K+K+ L   AH L   +   L+G +G+T+GV+    + LE +EL+K+KI  T   E +
Sbjct:     4 STKQKQHLKGLAHPLKPVV---LLGSNGLTEGVLAEIEQALEHHELIKVKI-ATEDRETK 59

Query:    90 D-VVKQLEEATGSAVVSQIGQTVIIYRPSLTR 120
               +V+ +   TG+  V  IG+T+++YRP+  R
Sbjct:    60 TLIVEAIVRETGACNVQVIGKTLVLYRPTKER 91

GO:0005737 "cytoplasm" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|Q74DQ2 yhbY "RNA-binding protein YhbY" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 123 (48.4 bits), Expect = 6.8e-08, P = 6.8e-08
 Identities = 30/98 (30%), Positives = 53/98 (54%)

Query:    30 TVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELE 89
             T K+K+ L    HSL   +    +GK  +++ +V    E LE +EL+K+KI  +C  +  
Sbjct:     3 TGKQKRHLRGLGHSLAPVIT---IGKGEISEALVKETDEALEHHELIKVKILESCLLDRH 59

Query:    90 DVVKQLEEATGSAVVSQIGQTVIIYRPSLTRMKLEEKK 127
             +  ++L  A G+ V   +G+T +++R +    KLE  K
Sbjct:    60 EAAEELASACGAEVAQVLGRTFLLFRRA-QEPKLELPK 96

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q97P93 SP_1748 "Putative uncharacterized protein" [Streptococcus pneumoniae TIGR4 (taxid:170187)]

 Score = 123 (48.4 bits), Expect = 6.8e-08, P = 6.8e-08
 Identities = 31/98 (31%), Positives = 56/98 (57%)

Query:    30 TVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELE 89
             T K++  L S AH+L   ++   +GK+G+ D + TS  + L+A EL+K+ + +     + 
Sbjct:     4 TSKQRAFLNSQAHTLKPIIQ---IGKNGLNDQIKTSVRQALDARELIKVTLLQNTDENIH 60

Query:    90 DVVKQLEEATGSAVVSQIGQTVIIYRPSLTRMKLEEKK 127
             +V + LEE  G   V +IG+ +I+++ S    K E +K
Sbjct:    61 EVAEILEEEIGVDTVQKIGRILILFKQS---SKKENRK 95

GO:0005515 "protein binding" evidence=IPI

TIGR_CMR|GSU_1263 GSU_1263 "conserved hypothetical protein TIGR00253" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 123 (48.4 bits), Expect = 6.8e-08, P = 6.8e-08
 Identities = 30/98 (30%), Positives = 53/98 (54%)

Query:    30 TVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELE 89
             T K+K+ L    HSL   +    +GK  +++ +V    E LE +EL+K+KI  +C  +  
Sbjct:     3 TGKQKRHLRGLGHSLAPVIT---IGKGEISEALVKETDEALEHHELIKVKILESCLLDRH 59

Query:    90 DVVKQLEEATGSAVVSQIGQTVIIYRPSLTRMKLEEKK 127
             +  ++L  A G+ V   +G+T +++R +    KLE  K
Sbjct:    60 EAAEELASACGAEVAQVLGRTFLLFRRA-QEPKLELPK 96

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q8EHM4 yhbY "Putative RNA-binding protein YhbY" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 121 (47.7 bits), Expect = 1.1e-07, P = 1.1e-07
 Identities = 33/95 (34%), Positives = 54/95 (56%)

Query:    30 TVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELE 89
             T K+K+ L   AH+L   +   L+G +G+T+GV+      L  +EL+K+K+  +   EL+
Sbjct:     4 TTKQKQHLKGLAHNLKPVV---LLGANGLTEGVLAEIESALAYHELIKVKV-ASADRELK 59

Query:    90 D-VVKQLEEATGSAVVSQIGQTVIIYRPSLTRMKL 123
             + +V  +   T SA V  IG  ++IYR S   MK+
Sbjct:    60 NAIVDAIVRETQSAKVQLIGHILVIYRQS-PEMKI 93

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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	171
pfam01985	84	pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain	3e-22
smart01103	84	smart01103, CRS1_YhbY, Escherichia coli YhbY is as	8e-20
COG1534	97	COG1534, COG1534, Predicted RNA-binding protein co	1e-15
TIGR00253	95	TIGR00253, RNA_bind_YhbY, putative RNA-binding pro	1e-11
PRK10343	97	PRK10343, PRK10343, RNA-binding protein YhbY; Prov	6e-07

>gnl|CDD|190184 pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain

 Score = 84.8 bits (211), Expect = 3e-22
 Identities = 32/87 (36%), Positives = 57/87 (65%), Gaps = 3/87 (3%)

Query: 29  LTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGEL 88
           LT K+++ L S AH L   ++   +GK+G+T+GVV    E LE +EL+K+K+      + 
Sbjct: 1   LTGKQRRYLRSLAHHLKPVVQ---IGKNGLTEGVVEEIDEALEKHELIKVKVLGNDREDR 57

Query: 89  EDVVKQLEEATGSAVVSQIGQTVIIYR 115
           +++ ++L E TG+ +V  IG+T+++YR
Sbjct: 58  KEIAEELAEKTGAELVQVIGRTIVLYR 84

Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome. Length = 84

>gnl|CDD|198171 smart01103, CRS1_YhbY, Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly

 Score = 78.3 bits (194), Expect = 8e-20
 Identities = 32/87 (36%), Positives = 57/87 (65%), Gaps = 3/87 (3%)

Query: 29  LTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGEL 88
           LT K+K+ L S AH L   ++   +GK+G+T+GV+    E LE +EL+K+K+      + 
Sbjct: 1   LTGKQKRYLRSLAHHLKPVVQ---IGKNGLTEGVLEEIDEALEKHELIKVKVLGNDREDR 57

Query: 89  EDVVKQLEEATGSAVVSQIGQTVIIYR 115
           +++ ++L E TG+ +V  IG+T+++YR
Sbjct: 58  KEIAEELAEETGAELVQVIGKTIVLYR 84

GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome. Length = 84

>gnl|CDD|224451 COG1534, COG1534, Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]

 Score = 68.0 bits (167), Expect = 1e-15
 Identities = 34/97 (35%), Positives = 59/97 (60%), Gaps = 3/97 (3%)

Query: 28  KLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGE 87
            LT K+K+ L S AH L   +    +GK+G+T+GV+      LEA EL+K+K+ +    +
Sbjct: 1   MLTGKQKRFLRSKAHHLKPIV---QIGKNGLTEGVIKEIDRALEARELIKVKVLQNARED 57

Query: 88  LEDVVKQLEEATGSAVVSQIGQTVIIYRPSLTRMKLE 124
            +++ + L E TG+ +V  IG+T+++YR S  + K+ 
Sbjct: 58  KKEIAEALAEETGAELVQVIGKTLVLYRESKEKRKIS 94

Length = 97

>gnl|CDD|129355 TIGR00253, RNA_bind_YhbY, putative RNA-binding protein, YhbY family

 Score = 57.6 bits (139), Expect = 1e-11
 Identities = 34/96 (35%), Positives = 56/96 (58%), Gaps = 3/96 (3%)

Query: 29  LTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGEL 88
           LT K+K+ L   AH L   +   LVGK+G+T+GV+    + LE  EL+K+K+      + 
Sbjct: 1   LTGKQKRHLRGKAHHLKPVV---LVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDK 57

Query: 89  EDVVKQLEEATGSAVVSQIGQTVIIYRPSLTRMKLE 124
             + + L + TG+  V  IG+T+++YRP+  R  +E
Sbjct: 58  TLIAEALVKETGACNVQVIGKTIVLYRPTKERKIIE 93

A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins [Unknown function, General]. Length = 95

>gnl|CDD|182393 PRK10343, PRK10343, RNA-binding protein YhbY; Provisional

 Score = 45.1 bits (106), Expect = 6e-07
 Identities = 31/92 (33%), Positives = 53/92 (57%), Gaps = 3/92 (3%)

Query: 29  LTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGEL 88
           L+ K+K+ L   AH L   +   L+G +G+T+GV+    + LE +EL+K+KI        
Sbjct: 3   LSTKQKQHLKGLAHPLKPVV---LLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETK 59

Query: 89  EDVVKQLEEATGSAVVSQIGQTVIIYRPSLTR 120
             +V+ +   TG+  V  IG+T+++YRP+  R
Sbjct: 60  TLIVEAIVRETGACNVQVIGKTLVLYRPTKER 91

Length = 97

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	171
PRK10343	97	RNA-binding protein YhbY; Provisional	100.0
TIGR00253	95	RNA_bind_YhbY putative RNA-binding protein, YhbY f	100.0
COG1534	97	Predicted RNA-binding protein containing KH domain	100.0
PF01985	84	CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR	99.97
KOG1990	564	consensus Poly(A)-specific exoribonuclease PARN [R	97.44
KOG1990	564	consensus Poly(A)-specific exoribonuclease PARN [R	95.21

>PRK10343 RNA-binding protein YhbY; Provisional

Probab=100.00  E-value=1.3e-36  Score=228.55  Aligned_cols=90  Identities=33%  Similarity=0.544  Sum_probs=87.5

Q ss_pred             CCCCHHHHHHHHHhhhhcCCcccceecCCCCCCHHHHHHHHHHHHhCCeEeEEEcCCChhhHHHHHHHHHHHhCCeEEeE
Q 038665           27 PKLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQ  106 (171)
Q Consensus        27 ~~LT~kqRk~LR~~AH~LkP~i~~V~IGK~GLTe~VI~eI~~aL~~hELIKVKil~n~~~d~~e~ae~La~~tgaevVq~  106 (171)
                      |+||++||+|||++||+|+|+   |+|||+||||+|+++|+++|++||||||+|++++++++++++++||+.|+|++||+
T Consensus         1 m~Lt~kqr~~LR~~ah~l~Pv---v~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~   77 (97)
T PRK10343          1 MNLSTKQKQHLKGLAHPLKPV---VLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQV   77 (97)
T ss_pred             CCCCHHHHHHHHHhcCCCCCe---EEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEee
Confidence            679999999999999999995   79999999999999999999999999999999999999999999999999999999


Q ss_pred             EccEEEEEcCCCC
Q 038665          107 IGQTVIIYRPSLT  119 (171)
Q Consensus       107 IG~t~ILYR~s~~  119 (171)
                      ||+++||||++++
T Consensus        78 IG~~~vlYR~~~~   90 (97)
T PRK10343         78 IGKTLVLYRPTKE   90 (97)
T ss_pred             eCcEEEEEecCCC
Confidence            9999999999864

>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family

Probab=100.00  E-value=5.2e-36  Score=224.21  Aligned_cols=91  Identities=36%  Similarity=0.557  Sum_probs=87.7

Q ss_pred             CCHHHHHHHHHhhhhcCCcccceecCCCCCCHHHHHHHHHHHHhCCeEeEEEcCCChhhHHHHHHHHHHHhCCeEEeEEc
Q 038665           29 LTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQIG  108 (171)
Q Consensus        29 LT~kqRk~LR~~AH~LkP~i~~V~IGK~GLTe~VI~eI~~aL~~hELIKVKil~n~~~d~~e~ae~La~~tgaevVq~IG  108 (171)
                      ||++||++||++||+|+|+   |+|||+||||+|+++|+++|++||||||+|++++++|++++|++||+.|||++||+||
T Consensus         1 Lt~kqr~~Lr~~ah~l~p~---v~IGK~Glt~~vi~ei~~aL~~hELIKVkvl~~~~~~~~e~a~~i~~~~~a~~Vq~iG   77 (95)
T TIGR00253         1 LTGKQKRHLRGKAHHLKPV---VLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQVIG   77 (95)
T ss_pred             CCHHHHHHHHHHhCCCCCe---EEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEEEEc
Confidence            7999999999999999995   7999999999999999999999999999999999999999999999999999999999


Q ss_pred             cEEEEEcCCCCccc
Q 038665          109 QTVIIYRPSLTRMK  122 (171)
Q Consensus       109 ~t~ILYR~s~~~~k  122 (171)
                      ++++|||+++++++
T Consensus        78 ~~~vlYR~~~~~~~   91 (95)
T TIGR00253        78 KTIVLYRPTKERKI   91 (95)
T ss_pred             cEEEEEecCCccCC
Confidence            99999999987543

A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins.

>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=7.3e-34  Score=213.96  Aligned_cols=93  Identities=37%  Similarity=0.576  Sum_probs=89.7

Q ss_pred             CCCHHHHHHHHHhhhhcCCcccceecCCCCCCHHHHHHHHHHHHhCCeEeEEEcCCChhhHHHHHHHHHHHhCCeEEeEE
Q 038665           28 KLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQI  107 (171)
Q Consensus        28 ~LT~kqRk~LR~~AH~LkP~i~~V~IGK~GLTe~VI~eI~~aL~~hELIKVKil~n~~~d~~e~ae~La~~tgaevVq~I  107 (171)
                      +||++|+++||++||+++|+   |||||+||||+||+||+++|++||||||+|++++.+|++++|+.||+.+||++||+|
T Consensus         1 ~Lt~kq~~~Lrs~Ah~l~pi---v~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVqvi   77 (97)
T COG1534           1 MLTGKQKRFLRSKAHHLKPI---VQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQVI   77 (97)
T ss_pred             CCcHHHHHHHHHhhccCCce---EEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEeeee
Confidence            58999999999999999996   699999999999999999999999999999999999999999999999999999999


Q ss_pred             ccEEEEEcCCCCccch
Q 038665          108 GQTVIIYRPSLTRMKL  123 (171)
Q Consensus       108 G~t~ILYR~s~~~~k~  123 (171)
                      |+++||||++.++.++
T Consensus        78 G~~~vlyr~~~e~~~i   93 (97)
T COG1534          78 GKTLVLYRESKEKRKI   93 (97)
T ss_pred             eeEEEEEecCcccccc
Confidence            9999999988887765

>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain

Probab=99.97  E-value=4.9e-32  Score=196.65  Aligned_cols=84  Identities=42%  Similarity=0.694  Sum_probs=75.0

Q ss_pred             CCHHHHHHHHHhhhhcCCcccceecCCCCCCHHHHHHHHHHHHhCCeEeEEEcCCChhhHHHHHHHHHHHhCCeEEeEEc
Q 038665           29 LTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQIG  108 (171)
Q Consensus        29 LT~kqRk~LR~~AH~LkP~i~~V~IGK~GLTe~VI~eI~~aL~~hELIKVKil~n~~~d~~e~ae~La~~tgaevVq~IG  108 (171)
                      ||++|+++||++||+|+|+   |+|||+||||+|+++|+++|++||||||+|++++++|+++++++||+.|||++||+||
T Consensus         1 Lt~ke~~~Lr~~a~~l~p~---v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~~~~~~~~~~~~~~l~~~t~~~~V~~iG   77 (84)
T PF01985_consen    1 LTSKERKFLRKLAHHLKPV---VQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQVIG   77 (84)
T ss_dssp             --HHHHHHHHHHHTTC--S---EEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEEEET
T ss_pred             CCHHHHHHHHHHhcCCCCe---EEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEEEEC
Confidence            7999999999999999996   6999999999999999999999999999999999999999999999999999999999


Q ss_pred             cEEEEEc
Q 038665          109 QTVIIYR  115 (171)
Q Consensus       109 ~t~ILYR  115 (171)
                      +++||||
T Consensus        78 ~~~vlyR   84 (84)
T PF01985_consen   78 RTIVLYR   84 (84)
T ss_dssp             TEEEEEE
T ss_pred             CEEEEEC
Confidence            9999998

The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterised members of the family: Zea mays (Maize) CRS1 (Q9FYT6 from SWISSPROT), CAF1 (Q84N49 from SWISSPROT) and CAF2 (Q84N48 from SWISSPROT) proteins and the Escherichia coli protein YhbY (P0AGK4 from SWISSPROT). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [, ]. The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue []. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants []. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing []. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes []. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [].; GO: 0003723 RNA binding; PDB: 1RQ8_A 1JO0_B 1LN4_A.

>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]

Probab=97.44  E-value=0.00014  Score=68.93  Aligned_cols=105  Identities=22%  Similarity=0.309  Sum_probs=91.1

Q ss_pred             eccCCCCCCCCCCCCCHHHHHHHHHhhhhcCCcccceecCCCCCCHHHHHHHHHHHHhCCeEeEEEcCCCh-hhHHHHHH
Q 038665           15 EVKSPSRSPLPLPKLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCP-GELEDVVK   93 (171)
Q Consensus        15 ~~~~~~r~~~~~~~LT~kqRk~LR~~AH~LkP~i~~V~IGK~GLTe~VI~eI~~aL~~hELIKVKil~n~~-~d~~e~ae   93 (171)
                      ..+.+...+-....+|.+++.+++.++..+++.   +..|..|+.++++..++.+|+++|++|+.+..... ....+.+.
T Consensus       369 ~~~~~~~~~~~~e~~t~ee~~~~~k~g~k~~~~---~~~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~  445 (564)
T KOG1990|consen  369 DPKIPAELRYDPESITEEERLMLRKVGLKMKRR---LLSGRRGVFDGVIENMHLHWKSRELVKVICKEKNLPSQVKQYAS  445 (564)
T ss_pred             ccccccccccchhhcChHHHHHHHHHHHhhccc---cccCCcccccceeecchhhhhhcccceeeeccccccHHHHHHHH
Confidence            345555555566779999999999999999997   59999999999999999999999999999999654 89999999


Q ss_pred             HHHHHhCCeEEeEEcc----EEEEEcCCCCccc
Q 038665           94 QLEEATGSAVVSQIGQ----TVIIYRPSLTRMK  122 (171)
Q Consensus        94 ~La~~tgaevVq~IG~----t~ILYR~s~~~~k  122 (171)
                      .++...|..+|....+    .+++||+......
T Consensus       446 ~le~esg~~~v~~~~~~~~~ai~~yr~k~y~~p  478 (564)
T KOG1990|consen  446 ALERESGGILVSIDKNPKGYAIIAYRGKNYDRP  478 (564)
T ss_pred             HHHHHhCCceeeeccCCchhhHHHhhhhhccCC
Confidence            9999999999999954    4799998765544

>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]

Probab=95.21  E-value=0.021  Score=54.32  Aligned_cols=96  Identities=19%  Similarity=0.081  Sum_probs=84.9

Q ss_pred             CCCCCCCCCHHHHHHHHHhhhhcCCcccceecCCCCCCHHHHHHHHHHHHhCCeEeEEEcCCChhhHHHHHHHHHHHhCC
Q 038665           22 SPLPLPKLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGS  101 (171)
Q Consensus        22 ~~~~~~~LT~kqRk~LR~~AH~LkP~i~~V~IGK~GLTe~VI~eI~~aL~~hELIKVKil~n~~~d~~e~ae~La~~tga  101 (171)
                      ..+.++.+..++-.+||..+-.+.-.     +++.|+|..+++.|.+-|+.+|++.++|.-..-..+....+.+...|++
T Consensus         7 ~~~~~~~~~~~~~~~l~~~~~~~~~~-----~~~~~~~~~~~~~~y~k~k~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~   81 (564)
T KOG1990|consen    7 LSLAELTVDEADLRRLRLVATGMTSA-----PWKAGSTFDTVEAIYLKWKDNEEVYLKFQFGLCLFMKRSHEALEMSTGG   81 (564)
T ss_pred             hhHHHhhcCHHHHHHHhhhhccceec-----ccccccchhhhHHHHHHHHhhhhhheeeccccchhHHHhhhHhhccCCC
Confidence            56777889999999999999999874     5999999999999999999999999999999888999999999999999


Q ss_pred             -eEEeEEccEEEEEcCCCCccc
Q 038665          102 -AVVSQIGQTVIIYRPSLTRMK  122 (171)
Q Consensus       102 -evVq~IG~t~ILYR~s~~~~k  122 (171)
                       -+||..|-....|++.-...+
T Consensus        82 n~~~~~~g~~~s~~~~~~~~~~  103 (564)
T KOG1990|consen   82 NFVVWSRGDSISSPEFLCQRSP  103 (564)
T ss_pred             ceeeeecCccccCCccceeecc
Confidence             789999999999844443333

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	171
1rq8_A	104	Solution Structure Of The Hypothetical Protein Sav1		4e-07
1ln4_A	104	Crystal Structure Of E. Coli Yhby Length = 104		6e-06
1jo0_A	98	Structure Of Hi1333, A Hypothetical Protein From Ha		2e-04

>pdb|1RQ8|A Chain A, Solution Structure Of The Hypothetical Protein Sav1595 From Staphylococcus Aureus, A Putative Rna Binding Protein Length = 104

Iteration: 1
 Score = 50.8 bits (120), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 28/88 (31%), Positives = 51/88 (57%), Gaps = 3/88 (3%)
Query: 30  TVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELE 89
           T K+K+ L S AH++    +   +GK G+ + ++    +TLE  EL+K+ + +    + +
Sbjct: 3   TGKQKRYLRSLAHNIDPIFQ---IGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKK 59
Query: 90  DVVKQLEEATGSAVVSQIGQTVIIYRPS 117
           ++ + L EAT S +V  IG  ++IYR S
Sbjct: 60  ELAETLSEATRSELVQVIGSMIVIYRES 87

>pdb|1LN4|A Chain A, Crystal Structure Of E. Coli Yhby Length = 104

Iteration: 1
 Score = 47.0 bits (110), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 31/94 (32%), Positives = 53/94 (56%), Gaps = 15/94 (15%)
Query: 30  TVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELE 89
           + K+K+ L   AH L   +   L+G +G+T+GV+    + LE +EL+K+KI        E
Sbjct: 4   STKQKQHLKGLAHPLKPVV---LLGSNGLTEGVLAEIEQALEHHELIKVKI------ATE 54
Query: 90  D------VVKQLEEATGSAVVSQIGQTVIIYRPS 117
           D      +V+ +   TG+  V  IG+T+++YRP+
Sbjct: 55  DRETKTLIVEAIVRETGACNVQVIGKTLVLYRPT 88

>pdb|1JO0|A Chain A, Structure Of Hi1333, A Hypothetical Protein From Haemophilus Influenzae With Structural Similarity To Rna-binding Proteins Length = 98

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 30/103 (29%), Positives = 51/103 (49%), Gaps = 9/103 (8%)
Query: 30  TVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELE 89
           + K+K+ L   AH L       ++G +G+T+GV+      L  +EL+K+K+        +
Sbjct: 4   STKQKQFLKGLAHHLNP---VVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQ 60
Query: 90  DVVKQLEEATGSAVVSQIGQTVIIYRPSLTRMKLEEKKQQARR 132
            ++  +   T +A V  IG  +++YRPS      EE K Q  R
Sbjct: 61  LIINAIVRETKAAQVQTIGHILVLYRPS------EEAKIQLPR 97
  Database: pdbaa

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	171
1rq8_A	104	Conserved hypothetical protein; structural genomic	7e-24
1jo0_A	98	Hypothetical protein HI1333; structural genomics,	1e-22

>1rq8_A Conserved hypothetical protein; structural genomics, SAV1595, YHBY, UPF0044, unknown function; NMR {Staphylococcus aureus} SCOP: d.68.4.1 Length = 104

 Score = 88.9 bits (221), Expect = 7e-24
 Identities = 30/106 (28%), Positives = 56/106 (52%), Gaps = 3/106 (2%)

Query: 29  LTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGEL 88
           LT K+K+ L S AH++        +GK G+ + ++    +TLE  EL+K+ + +    + 
Sbjct: 2   LTGKQKRYLRSLAHNIDPIF---QIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDK 58

Query: 89  EDVVKQLEEATGSAVVSQIGQTVIIYRPSLTRMKLEEKKQQARRVY 134
           +++ + L EAT S +V  IG  ++IYR S    ++E   +     +
Sbjct: 59  KELAETLSEATRSELVQVIGSMIVIYRESKENKEIELPLEHHHHHH 104

>1jo0_A Hypothetical protein HI1333; structural genomics, YHBY_HAEI structure 2 function project, S2F, unknown function; 1.37A {Haemophilus influenzae} SCOP: d.68.4.1 PDB: 1ln4_A Length = 98

 Score = 85.4 bits (212), Expect = 1e-22
 Identities = 26/89 (29%), Positives = 48/89 (53%), Gaps = 3/89 (3%)

Query: 29  LTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGEL 88
           L+ K+K+ L   AH L   +   ++G +G+T+GV+      L  +EL+K+K+        
Sbjct: 3   LSTKQKQFLKGLAHHLNPVV---MLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETK 59

Query: 89  EDVVKQLEEATGSAVVSQIGQTVIIYRPS 117
           + ++  +   T +A V  IG  +++YRPS
Sbjct: 60  QLIINAIVRETKAAQVQTIGHILVLYRPS 88

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	171
1rq8_A	104	Conserved hypothetical protein; structural genomic	100.0
1jo0_A	98	Hypothetical protein HI1333; structural genomics,	100.0

>1rq8_A Conserved hypothetical protein; structural genomics, SAV1595, YHBY, UPF0044, unknown function; NMR {Staphylococcus aureus} SCOP: d.68.4.1

Probab=100.00  E-value=1.5e-36  Score=229.40  Aligned_cols=94  Identities=32%  Similarity=0.503  Sum_probs=90.2

Q ss_pred             CCCHHHHHHHHHhhhhcCCcccceecCCCCCCHHHHHHHHHHHHhCCeEeEEEcCCChhhHHHHHHHHHHHhCCeEEeEE
Q 038665           28 KLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQI  107 (171)
Q Consensus        28 ~LT~kqRk~LR~~AH~LkP~i~~V~IGK~GLTe~VI~eI~~aL~~hELIKVKil~n~~~d~~e~ae~La~~tgaevVq~I  107 (171)
                      |||++||+|||++||+|+|+   |+|||+||||+|+++|+++|++||||||+|+++|++|++++|++||+.|||++||+|
T Consensus         1 mLt~kqr~~LR~~ah~Lkpv---v~IGK~GlTe~vi~ei~~aL~~hELIKVkvl~~~~~d~~e~a~~la~~t~a~vVq~I   77 (104)
T 1rq8_A            1 MLTGKQKRYLRSLAHNIDPI---FQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQVI   77 (104)
T ss_dssp             CCCHHHHHHHHHHTTSSCCS---CEECSSSCCHHHHHHHHHHHHHSSEEEEEECCCCHHHHHHHHHHHHHHHTEEEEEEE
T ss_pred             CCCHHHHHHHHHHhcCCCCe---EEECCCCCCHHHHHHHHHHHHHCCcEEEEEeCCCHHHHHHHHHHHHHHhCCEEEEEE
Confidence            69999999999999999996   699999999999999999999999999999999999999999999999999999999


Q ss_pred             ccEEEEEcCCCCccchH
Q 038665          108 GQTVIIYRPSLTRMKLE  124 (171)
Q Consensus       108 G~t~ILYR~s~~~~k~~  124 (171)
                      |+++||||+++++++++
T Consensus        78 G~~~VLYR~~~~~~~i~   94 (104)
T 1rq8_A           78 GSMIVIYRESKENKEIE   94 (104)
T ss_dssp             TTEEEEEECCCSCCSCC
T ss_pred             CCEEEEEeCCCCCCcee
Confidence            99999999998777653

>1jo0_A Hypothetical protein HI1333; structural genomics, YHBY_HAEI structure 2 function project, S2F, unknown function; 1.37A {Haemophilus influenzae} SCOP: d.68.4.1 PDB: 1ln4_A

Probab=100.00  E-value=3.4e-36  Score=224.84  Aligned_cols=89  Identities=29%  Similarity=0.496  Sum_probs=86.7

Q ss_pred             CCCHHHHHHHHHhhhhcCCcccceecCCCCCCHHHHHHHHHHHHhCCeEeEEEcCCChhhHHHHHHHHHHHhCCeEEeEE
Q 038665           28 KLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQI  107 (171)
Q Consensus        28 ~LT~kqRk~LR~~AH~LkP~i~~V~IGK~GLTe~VI~eI~~aL~~hELIKVKil~n~~~d~~e~ae~La~~tgaevVq~I  107 (171)
                      +||++||+|||++||+|+|+   |+|||+||||+|+++|+++|++||||||+|+++|++|++++|++||+.|||++||+|
T Consensus         2 ~Lt~kqr~~Lr~~ah~l~pv---v~IGk~GlT~~vi~ei~~aL~~~ELIKVkvl~~~~~~~~e~a~~la~~t~a~~Vq~I   78 (98)
T 1jo0_A            2 TLSTKQKQFLKGLAHHLNPV---VMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLIINAIVRETKAAQVQTI   78 (98)
T ss_dssp             CCCHHHHHHHHHHHTTBCCS---EEECTTCSCHHHHHHHHHHHHHHSEEEEEETTCCHHHHHHHHHHHHHHHCCEEEEEE
T ss_pred             CCCHHHHHHHHHHhcCCCCe---EEECCCCCCHHHHHHHHHHHHHCCeEEEEEeCCCHHHHHHHHHHHHHHhCCEEEEEE
Confidence            69999999999999999996   699999999999999999999999999999999999999999999999999999999


Q ss_pred             ccEEEEEcCCCC
Q 038665          108 GQTVIIYRPSLT  119 (171)
Q Consensus       108 G~t~ILYR~s~~  119 (171)
                      |+++||||++++
T Consensus        79 G~~~vLyR~~~~   90 (98)
T 1jo0_A           79 GHILVLYRPSEE   90 (98)
T ss_dssp             TTEEEEECCCSS
T ss_pred             CCEEEEEccCCC
Confidence            999999999855

---

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	171
d1rq8a_	96	d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphy	4e-22
d1jo0a_	97	d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus i	8e-22

>d1rq8a_ d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]} Length = 96

class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: YhbY-like
family: YhbY-like
domain: Hypothetical protein SAV1595
species: Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]

 Score = 83.2 bits (206), Expect = 4e-22
 Identities = 30/96 (31%), Positives = 55/96 (57%), Gaps = 3/96 (3%)

Query: 29  LTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGEL 88
           LT K+K+ L S AH++    +   +GK G+ + ++    +TLE  EL+K+ + +    + 
Sbjct: 2   LTGKQKRYLRSLAHNIDPIFQ---IGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDK 58

Query: 89  EDVVKQLEEATGSAVVSQIGQTVIIYRPSLTRMKLE 124
           +++ + L EAT S +V  IG  ++IYR S    ++E
Sbjct: 59  KELAETLSEATRSELVQVIGSMIVIYRESKENKEIE 94

>d1jo0a_ d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus influenzae [TaxId: 727]} Length = 97

class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: YhbY-like
family: YhbY-like
domain: YhbY homologue HI1333
species: Haemophilus influenzae [TaxId: 727]

 Score = 82.4 bits (204), Expect = 8e-22
 Identities = 26/89 (29%), Positives = 47/89 (52%), Gaps = 3/89 (3%)

Query: 29  LTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGEL 88
           L+ K+K+ L   AH L   +    +G +G+T+GV+      L  +EL+K+K+        
Sbjct: 3   LSTKQKQFLKGLAHHLNPVVM---LGGNGLTEGVLAEIENALNHHELIKVKVAGADRETK 59

Query: 89  EDVVKQLEEATGSAVVSQIGQTVIIYRPS 117
           + ++  +   T +A V  IG  +++YRPS
Sbjct: 60  QLIINAIVRETKAAQVQTIGHILVLYRPS 88

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	171
d1rq8a_	96	Hypothetical protein SAV1595 {Staphylococcus aureu	100.0
d1jo0a_	97	YhbY homologue HI1333 {Haemophilus influenzae [Tax	100.0

>d1rq8a_ d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]}

class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: YhbY-like
family: YhbY-like
domain: Hypothetical protein SAV1595
species: Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]

Probab=100.00  E-value=1.2e-35  Score=218.32  Aligned_cols=93  Identities=31%  Similarity=0.496  Sum_probs=90.4

Q ss_pred             CCCHHHHHHHHHhhhhcCCcccceecCCCCCCHHHHHHHHHHHHhCCeEeEEEcCCChhhHHHHHHHHHHHhCCeEEeEE
Q 038665           28 KLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQI  107 (171)
Q Consensus        28 ~LT~kqRk~LR~~AH~LkP~i~~V~IGK~GLTe~VI~eI~~aL~~hELIKVKil~n~~~d~~e~ae~La~~tgaevVq~I  107 (171)
                      |||++||++||++||+|+|+   |+|||+||||+|+++|+++|++||||||+|++++++|+++++++||+.|||++||+|
T Consensus         1 mLt~kqr~~LR~~ah~l~p~---v~IGk~Glt~~vi~ei~~~l~~~ELIKvk~~~~~~~~~~~~~~~l~~~t~a~~V~~i   77 (96)
T d1rq8a_           1 MLTGKQKRYLRSLAHNIDPI---FQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQVI   77 (96)
T ss_dssp             CCCHHHHHHHHHHTTSSCCS---CEECSSSCCHHHHHHHHHHHHHSSEEEEEECCCCHHHHHHHHHHHHHHHTEEEEEEE
T ss_pred             CcCHHHHHHHHHHhcCCCCE---EEECCCCCCHHHHHHHHHHHHhCCeeEEEecCCCHHHHHHHHHHHHHHhCCEEEEEE
Confidence            69999999999999999996   699999999999999999999999999999999999999999999999999999999


Q ss_pred             ccEEEEEcCCCCccch
Q 038665          108 GQTVIIYRPSLTRMKL  123 (171)
Q Consensus       108 G~t~ILYR~s~~~~k~  123 (171)
                      |+++||||++++++++
T Consensus        78 G~~~vlyR~~~~~~ki   93 (96)
T d1rq8a_          78 GSMIVIYRESKENKEI   93 (96)
T ss_dssp             TTEEEEEECCCSCCSC
T ss_pred             CCEEEEEeCCCCCCCC
Confidence            9999999999988875

>d1jo0a_ d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: YhbY-like
family: YhbY-like
domain: YhbY homologue HI1333
species: Haemophilus influenzae [TaxId: 727]

Probab=100.00  E-value=1.1e-34  Score=213.41  Aligned_cols=89  Identities=29%  Similarity=0.496  Sum_probs=86.4

Q ss_pred             CCCHHHHHHHHHhhhhcCCcccceecCCCCCCHHHHHHHHHHHHhCCeEeEEEcCCChhhHHHHHHHHHHHhCCeEEeEE
Q 038665           28 KLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQI  107 (171)
Q Consensus        28 ~LT~kqRk~LR~~AH~LkP~i~~V~IGK~GLTe~VI~eI~~aL~~hELIKVKil~n~~~d~~e~ae~La~~tgaevVq~I  107 (171)
                      +||++||+|||++||+|+|+   |+|||+||||+|+++|+++|++||||||+|++++++|+++++++||+.|||++||+|
T Consensus         2 tLt~kqr~~LR~~ah~lkp~---v~IGk~Glt~~vi~ei~~al~~~ELIKvki~~~~~~~~~~~~~~l~~~t~~~vV~~i   78 (97)
T d1jo0a_           2 TLSTKQKQFLKGLAHHLNPV---VMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLIINAIVRETKAAQVQTI   78 (97)
T ss_dssp             CCCHHHHHHHHHHHTTBCCS---EEECTTCSCHHHHHHHHHHHHHHSEEEEEETTCCHHHHHHHHHHHHHHHCCEEEEEE
T ss_pred             CCCHHHHHHHHHHhcCCCCE---EEECCCCCCHHHHHHHHHHHHhCCeEEEEEcCCCHHHHHHHHHHHHHHhCCEEEEEE
Confidence            69999999999999999996   699999999999999999999999999999999999999999999999999999999


Q ss_pred             ccEEEEEcCCCC
Q 038665          108 GQTVIIYRPSLT  119 (171)
Q Consensus       108 G~t~ILYR~s~~  119 (171)
                      |+++||||++++
T Consensus        79 G~~~ilYR~~~~   90 (97)
T d1jo0a_          79 GHILVLYRPSEE   90 (97)
T ss_dssp             TTEEEEECCCSS
T ss_pred             CCEEEEEcCCCC
Confidence            999999999864