Citrus Sinensis ID: 030905

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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-------17
Protein Sequence
MAEVQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAASRSRRFGSRGGRSGGFYGGRGRGGGYGRGGRGGRSVGSGGGAGSGACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPNY
Secondary Structure (PSIPRED)
cccccccccEEEEEcccccEEEEEcccccccEEEEEEEEEcccccccccccEEEEEEEEccccccEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccEEEEEEEEEccccEEEEEEccccccEEEEHHHEccccccccccccEEEEEEEcccccccEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccEEcccccccccccccccccccccccccccccccccccccccccHcccccc
Coil and Loop (DISEMBL)
maevqrssgtvkwfsaqkgfgfiapedggedlFVHQTSiksegfrtlsegqtvefsvdvgedgrtkAVDVEAAsrsrrfgsrggrsggfyggrgrgggygrggrggrsvgsgggagsgacfncgrtghiarecysrgrgggrgygggrggggcyncgeeghfardcpny
Flexible Loop (DISEMBL)
maevqrssgtvkwfsaQKGFGFIAPEDGGEDLFVHQTSIKSegfrtlsegqtvefsvdvgedgrtkavdveaasrsrrfgsrggrsggfyggrgrgggygrGGRGGRSVGSGGGAGSGACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGeeghfardcpny
Low Complexity Region (SEG)
MAEVQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAAsrsrrfgsrggrsggfyggrgrgggygrggrggrsvgsgggagsgaCFNCGRTGHIArecysrgrgggrgygggrggggcyncgeegHFARDCPNY
Disordered region (IsUnstruct)
**********VKWFSAQKGFGFIAPEDGGEDLFVHQTSI*****************************************************************************SGACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGH********
Disordered Region (DISOPRED)
******S***VKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSV******************************************************************************************RGGGGCYNCGEEGHFARDCPN*
Disordered Region (DISEMBL)
**********VKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAASRSRRFGSRGGRSGGFYGGRGRGGGYGRGGRGGRSVGSGGGAGSGACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPNY
Disordered Region (DISPRO)
*****RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAASRSRR***************************************GACF*C*RTGHIARECYS******RG*********C*****EGHFARDCPN*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAEVQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAASRSRRFGSRGGRSGGFYGGRGRGGGYGRGGRGGRSVGSGGGAGSGACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPNY
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	169	2.2.26 [Sep-21-2011]
O65639	299	Cold shock protein 1 OS=A	yes	no	0.952	0.538	0.459	5e-27
Q94C69	301	Cold shock domain-contain	no	no	0.786	0.441	0.439	5e-25
Q38896	201	Cold shock domain-contain	no	no	0.958	0.805	0.491	9e-24
P27484	214	Glycine-rich protein 2 OS	N/A	no	0.414	0.327	0.75	3e-23
Q41188	203	Cold shock protein 2 OS=A	no	no	0.958	0.798	0.473	5e-18
P0A981	70	Cold shock-like protein C	yes	no	0.366	0.885	0.564	1e-14
P0A978	70	Cold shock-like protein C	N/A	no	0.366	0.885	0.564	1e-14
P0A979	70	Cold shock-like protein C	yes	no	0.366	0.885	0.564	1e-14
P0A980	70	Cold shock-like protein C	N/A	no	0.366	0.885	0.564	1e-14
P72188	64	Cold shock protein CapA (	N/A	no	0.349	0.921	0.610	3e-14

>sp|O65639|CSP1_ARATH Cold shock protein 1 OS=Arabidopsis thaliana GN=CSP1 PE=2 SV=1

 Score =  120 bits (300), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 79/172 (45%), Positives = 95/172 (55%), Gaps = 11/172 (6%)

Query: 6   RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRT 65
           RS+G V WF+A KG+GFI P+DG  +LFVHQ+SI SEG+R+L+ G  VEF++  G DG+T
Sbjct: 10  RSTGKVNWFNASKGYGFITPDDGSVELFVHQSSIVSEGYRSLTVGDAVEFAITQGSDGKT 69

Query: 66  KAVDVEAASRSRRFGSRGGRSGGFYGGRGRGGGYGRGGRGGRS----------VGSGGGA 115
           KAV+V A            R  G   G G  G Y  G  G  S           G     
Sbjct: 70  KAVNVTAPGGGSLKKENNSRGNGARRGGGGSGCYNCGELGHISKDCGIGGGGGGGERRSR 129

Query: 116 GSGACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCP 167
           G   C+NCG TGH AR+C S G G  RG   G G  GCY CG+ GH ARDC 
Sbjct: 130 GGEGCYNCGDTGHFARDCTSAGNGDQRGATKG-GNDGCYTCGDVGHVARDCT 180

Chaperone that binds to RNA, single- (ssDNA) and double-stranded (dsDNA) DNA, and unwinds nucleic acid duplex. Exhibits a DNA melting activity. May be involved in cold resistance. Prevents seed germination under dehydration or salt stress conditions.
Arabidopsis thaliana (taxid: 3702)

>sp|Q94C69|CSP3_ARATH Cold shock domain-containing protein 3 OS=Arabidopsis thaliana GN=CSP3 PE=2 SV=1

 Score =  113 bits (283), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 72/164 (43%), Positives = 92/164 (56%), Gaps = 31/164 (18%)

Query: 6   RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRT 65
           RS G V WFS  KG+GFI P+DGGE+LFVHQ+SI S+GFR+L+ G++VE+ + +G DG+T
Sbjct: 10  RSIGKVSWFSDGKGYGFITPDDGGEELFVHQSSIVSDGFRSLTLGESVEYEIALGSDGKT 69

Query: 66  KAVDVEAASRSRRFGSRGGRSGGFYGGRGRGGGYGRGGRGGRSVGSGGGAGSGACFNCGR 125
           KA++V A                        GG     +   S GSGG      CFNCG 
Sbjct: 70  KAIEVTAP-----------------------GGGSLNKKENSSRGSGGN-----CFNCGE 101

Query: 126 TGHIAREC---YSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDC 166
            GH+A++C         GG G     G G CY CG+ GHFARDC
Sbjct: 102 VGHMAKDCDGGSGGKSFGGGGGRRSGGEGECYMCGDVGHFARDC 145

Chaperone that binds to RNA, single- (ssDNA) and double-stranded (dsDNA) DNA, and unwinds nucleic acid duplex. Promotes freezing tolerance.

Arabidopsis thaliana (taxid: 3702)

>sp|Q38896|CSP4_ARATH Cold shock domain-containing protein 4 OS=Arabidopsis thaliana GN=CSP4 PE=1 SV=1

 Score =  109 bits (272), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 90/183 (49%), Positives = 105/183 (57%), Gaps = 21/183 (11%)

Query: 5   QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGR 64
            R  GTVKWF  QKGFGFI P DGG+DLFVHQ+SI+SEGFR+L+  ++VEF V+V   GR
Sbjct: 13  DRRKGTVKWFDTQKGFGFITPSDGGDDLFVHQSSIRSEGFRSLAAEESVEFDVEVDNSGR 72

Query: 65  TKAVDVEAASRSRRFGS----------RGGRSGGFYGGRGRGGGYGRGGRGGRSVGSGGG 114
            KA++V     +   G+           G   GG  GG   GG YG G  G  S G GGG
Sbjct: 73  PKAIEVSGPDGAPVQGNSGGGGSSGGRGGFGGGGGRGGGRGGGSYGGGYGGRGSGGRGGG 132

Query: 115 AGSGACFNCGRTGHIARECYSRGRGGGRGYGGGRGGG-----------GCYNCGEEGHFA 163
            G  +CF CG  GH+AREC   G G   G GGGR G             CY+CGE GHFA
Sbjct: 133 GGDNSCFKCGEPGHMARECSQGGGGYSGGGGGGRYGSGGGGGGGGGGLSCYSCGESGHFA 192

Query: 164 RDC 166
           RDC
Sbjct: 193 RDC 195

Arabidopsis thaliana (taxid: 3702)

>sp|P27484|GRP2_NICSY Glycine-rich protein 2 OS=Nicotiana sylvestris GN=GRP-2 PE=2 SV=1

 Score =  107 bits (268), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 54/72 (75%), Positives = 62/72 (86%), Gaps = 2/72 (2%)

Query: 1  MAEV--QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVD 58
          MAE   QR+ GTVKWFS QKGFGFI P+DGGEDLFVHQ+ I+SEGFR+L+EG+TVEF V+
Sbjct: 1  MAEESGQRAKGTVKWFSDQKGFGFITPDDGGEDLFVHQSGIRSEGFRSLAEGETVEFEVE 60

Query: 59 VGEDGRTKAVDV 70
           G DGRTKAVDV
Sbjct: 61 SGGDGRTKAVDV 72

Nicotiana sylvestris (taxid: 4096)

>sp|Q41188|CSP2_ARATH Cold shock protein 2 OS=Arabidopsis thaliana GN=CSP2 PE=1 SV=1

 Score = 90.5 bits (223), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 90/190 (47%), Positives = 109/190 (57%), Gaps = 28/190 (14%)

Query: 5   QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGR 64
           +R  G+VKWF  QKGFGFI P+DGG+DLFVHQ+SI+SEGFR+L+  + VEF V++  + R
Sbjct: 9   ERRKGSVKWFDTQKGFGFITPDDGGDDLFVHQSSIRSEGFRSLAAEEAVEFEVEIDNNNR 68

Query: 65  TKAVDVEAASRSRRFGSRGGRSGGFYGGRGRGGGYGRGGRGGRSVGSGGGAGSGA----- 119
            KA+DV     +   G+ GG S G  GG G G G GRG  GG   G GG  G G      
Sbjct: 69  PKAIDVSGPDGAPVQGNSGGGSSGGRGGFGGGRGGGRGSGGGYGGGGGGYGGRGGGGRGG 128

Query: 120 --CFNCGRTGHIAREC---------------------YSRGRGGGRGYGGGRGGGGCYNC 156
             C+ CG  GH+AR+C                        G  GG G GGG GGG CY+C
Sbjct: 129 SDCYKCGEPGHMARDCSEGGGGYGGGGGGYGGGGGYGGGGGGYGGGGRGGGGGGGSCYSC 188

Query: 157 GEEGHFARDC 166
           GE GHFARDC
Sbjct: 189 GESGHFARDC 198

Chaperone that binds to RNA, single- (ssDNA) and double-stranded (dsDNA) DNA, and unwinds nucleic acid duplex. Accelerates seed germination and seedling growth under cold stress, and contributes to enhancement of cold and freezing tolerance. Regulates flowering transition, and flower and seed development. Promotes seed germination under salt stress. May regulate respiratory oxygen uptake.

Arabidopsis thaliana (taxid: 3702)

>sp|P0A981|CSPG_SHIFL Cold shock-like protein CspG OS=Shigella flexneri GN=cspG PE=3 SV=1

 Score = 79.3 bits (194), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 35/62 (56%), Positives = 47/62 (75%)

Query: 6  RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRT 65
          + +G VKWF+A KGFGFI P+DG +D+FVH T+I+S  FRTL+E Q VEFS++ G+ G  
Sbjct: 4  KMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRGPA 63

Query: 66 KA 67
           A
Sbjct: 64 AA 65

Shigella flexneri (taxid: 623)

>sp|P0A978|CSPG_ECOLI Cold shock-like protein CspG OS=Escherichia coli (strain K12) GN=cspG PE=1 SV=1

 Score = 79.3 bits (194), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 35/62 (56%), Positives = 47/62 (75%)

Query: 6  RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRT 65
          + +G VKWF+A KGFGFI P+DG +D+FVH T+I+S  FRTL+E Q VEFS++ G+ G  
Sbjct: 4  KMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRGPA 63

Query: 66 KA 67
           A
Sbjct: 64 AA 65

Escherichia coli (strain K12) (taxid: 83333)

>sp|P0A979|CSPG_ECOL6 Cold shock-like protein CspG OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=cspG PE=3 SV=1

 Score = 79.3 bits (194), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 35/62 (56%), Positives = 47/62 (75%)

Query: 6  RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRT 65
          + +G VKWF+A KGFGFI P+DG +D+FVH T+I+S  FRTL+E Q VEFS++ G+ G  
Sbjct: 4  KMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRGPA 63

Query: 66 KA 67
           A
Sbjct: 64 AA 65

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

>sp|P0A980|CSPG_ECO57 Cold shock-like protein CspG OS=Escherichia coli O157:H7 GN=cspG PE=3 SV=1

 Score = 79.3 bits (194), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 35/62 (56%), Positives = 47/62 (75%)

Query: 6  RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRT 65
          + +G VKWF+A KGFGFI P+DG +D+FVH T+I+S  FRTL+E Q VEFS++ G+ G  
Sbjct: 4  KMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRGPA 63

Query: 66 KA 67
           A
Sbjct: 64 AA 65

Escherichia coli O157:H7 (taxid: 83334)

>sp|P72188|CAPA_PSEFR Cold shock protein CapA (Fragment) OS=Pseudomonas fragi GN=capA PE=2 SV=1

 Score = 78.2 bits (191), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 36/59 (61%), Positives = 47/59 (79%)

Query: 5  QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDG 63
          QR SGTVKWF+ +KGFGFI P+ GG+DLFVH  +I+S+GF++L EGQTV F  + G+ G
Sbjct: 3  QRQSGTVKWFNDEKGFGFITPQGGGDDLFVHFKAIESDGFKSLKEGQTVSFVAEKGQKG 61

Affects cell viability at low temperatures.

Pseudomonas fragi (taxid: 296)

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	169
255545420	184	cold shock protein, putative [Ricinus co	0.994	0.913	0.644	2e-36
224063128	184	predicted protein [Populus trichocarpa]	0.994	0.913	0.661	4e-36
449445142	181	PREDICTED: cold shock domain-containing	0.988	0.922	0.597	4e-35
356515858	176	PREDICTED: glycine-rich protein 2b-like	0.964	0.926	0.565	4e-34
356509444	170	PREDICTED: uncharacterized protein LOC10	0.917	0.911	0.556	2e-32
147812546	189	hypothetical protein VITISV_018906 [Viti	0.792	0.708	0.574	1e-31
255640679	170	unknown [Glycine max]	0.917	0.911	0.544	3e-31
413926631	188	hypothetical protein ZEAMMB73_047398 [Ze	0.899	0.808	0.601	9e-31
223946111	187	unknown [Zea mays]	0.893	0.807	0.589	7e-30
302822137	159	hypothetical protein SELMODRAFT_186937 [	0.899	0.955	0.527	1e-29

>gi|255545420|ref|XP_002513770.1| cold shock protein, putative [Ricinus communis] gi|223546856|gb|EEF48353.1| cold shock protein, putative [Ricinus communis]

 Score =  156 bits (395), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 116/180 (64%), Positives = 125/180 (69%), Gaps = 12/180 (6%)

Query: 1   MAEVQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG 60
           MAE +RS GTVKWFSAQKGFGFIAP+DGGEDLFVHQTSI+S+GFRTLSEGQ VEFSVD G
Sbjct: 1   MAENKRSIGTVKWFSAQKGFGFIAPDDGGEDLFVHQTSIQSDGFRTLSEGQPVEFSVDFG 60

Query: 61  EDGRTKAVDV--------EAASRSRRFGSRGGRSGGFYGGRGRGGGYGRGGRGGRSVGSG 112
           EDGRTKAVDV                +G RG   GG Y G GRG G     RG      G
Sbjct: 61  EDGRTKAVDVIPRSRRGGRGGFGRGFYGGRGRGGGGGYSGGGRGDGGVYVRRGRGGRSGG 120

Query: 113 GGAGSGACFNCGRTGHIARECYS----RGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPN 168
           GGAG  AC+NCGR GH+AR+CY      G GG R +GGG G G CYNCGEEGHFARDC N
Sbjct: 121 GGAGGSACYNCGRYGHLARDCYQGGGGGGGGGSRRFGGGGGSGACYNCGEEGHFARDCAN 180

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224063128|ref|XP_002301004.1| predicted protein [Populus trichocarpa] gi|222842730|gb|EEE80277.1| predicted protein [Populus trichocarpa]

 Score =  155 bits (393), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 119/180 (66%), Positives = 129/180 (71%), Gaps = 12/180 (6%)

Query: 1   MAEVQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG 60
           MAE +RS+GTVKWFSAQKGFGFIAP+DGGEDLFVHQTSI+S+GFRTLS+GQ VEFSV  G
Sbjct: 1   MAETKRSTGTVKWFSAQKGFGFIAPDDGGEDLFVHQTSIQSDGFRTLSDGQPVEFSVGSG 60

Query: 61  EDGRTKAVDVEAA---SRSRRFGSRGGRSGGFYGGRGRGGGYGRGGRGGRSVGSGGGAGS 117
           EDGR KA DV  A    R  R G  GG   G+Y GRGRGGGY RGG        GGG+  
Sbjct: 61  EDGRAKAADVVGASRSRRPPRGGRGGGGGRGYYSGRGRGGGYERGGHSRGRGYGGGGSSG 120

Query: 118 GACFNCGRTGHIARECYS---------RGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPN 168
           GACFNCGR GH+AR+CY           G G     GGG GGGGCYNCGEEGHFARDCPN
Sbjct: 121 GACFNCGRYGHLARDCYEGGDDGGRYGGGGGRRYSGGGGGGGGGCYNCGEEGHFARDCPN 180

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449445142|ref|XP_004140332.1| PREDICTED: cold shock domain-containing protein 4-like [Cucumis sativus]

 Score =  152 bits (385), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 107/179 (59%), Positives = 123/179 (68%), Gaps = 12/179 (6%)

Query: 1   MAEVQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG 60
           MAE++RS+GTV+WFSAQKGFGFIAP+D  +DLFVHQTSI+SEGFRTL +GQTVEF++D  
Sbjct: 1   MAELKRSTGTVRWFSAQKGFGFIAPDDATDDLFVHQTSIRSEGFRTLFDGQTVEFTIDYD 60

Query: 61  EDGRTKAVDVEAASRSRRFGSRGGRSGGFYGGRGRGGGYGRGGRGG--RSVGSGGGAGSG 118
           +D R KAVDV    RS R+G   G   G  G  GR GG GRG   G      SGGG G G
Sbjct: 61  QDQRAKAVDVTVIDRSTRYGGGRGGGRGRGGSYGRFGGGGRGFGRGRWNEGPSGGGRGGG 120

Query: 119 ACFNCGRTGHIARECYSRGRGGGRG---------YGGGRGGGGCYNCGEEGHFARDCPN 168
            C+NCGR GH+AR+CY RG GG            YGGG GG GCYNCG+ GH ARDC N
Sbjct: 121 ECYNCGRMGHLARDCY-RGNGGAPSGRRYDGGRGYGGGGGGRGCYNCGDTGHLARDCQN 178

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356515858|ref|XP_003526614.1| PREDICTED: glycine-rich protein 2b-like [Glycine max]

 Score =  149 bits (376), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 99/175 (56%), Positives = 118/175 (67%), Gaps = 12/175 (6%)

Query: 1   MAEVQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG 60
           MAE +RS+GTVKWF+A KGFGFI P+DG +DLFVH TSI+S+G+R+LS+GQ+VEF +D G
Sbjct: 1   MAETRRSTGTVKWFNAHKGFGFITPQDGTDDLFVHFTSIRSDGYRSLSDGQSVEFLLDYG 60

Query: 61  EDGRTKAVDVEAASRSRRFGSRGGRSGGFYGGRGRGGGYGRGGRGGRSVGSGGGAGSGAC 120
           +DGRT AVDV +A RSR  G   G  GG        GG   GG  GR  G G   G   C
Sbjct: 61  DDGRTMAVDVTSAVRSRLPGGFRGGGGG-----RGRGGGRYGGGEGRGRGFGRRGGGPEC 115

Query: 121 FNCGRTGHIARECY-------SRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPN 168
           +NCGR GH+AR+CY              R  GGG GGGGC+NCGEEGHFAR+CPN
Sbjct: 116 YNCGRIGHLARDCYHGQGGGGGDDGRNRRRGGGGGGGGGCFNCGEEGHFARECPN 170

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356509444|ref|XP_003523459.1| PREDICTED: uncharacterized protein LOC100815731 [Glycine max]

 Score =  143 bits (361), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 99/178 (55%), Positives = 119/178 (66%), Gaps = 23/178 (12%)

Query: 1   MAEVQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG 60
           MAE +RS+GTVKWF++QKGFGFI P+DG +DLFVH TSI+S+G+R+LSEGQ+VEF +D G
Sbjct: 1   MAESRRSTGTVKWFNSQKGFGFITPQDGTDDLFVHFTSIRSDGYRSLSEGQSVEFLLDYG 60

Query: 61  EDGRTKAVDVEAASRSRRFGSRGGRSGGFYGGRGRGGGYGRGGRGGRSVGSGGGAGSGAC 120
           +DGRT AVDV +A RSR                G  GG GRG  GGR  G G   G   C
Sbjct: 61  DDGRTMAVDVTSAVRSR-------------RPGGFRGGGGRGRGGGRGGGFGRRGGGPEC 107

Query: 121 FNCGRTGHIARECY----------SRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPN 168
           +NCGR GH+AR+CY            GR   RG GGG GG GC+NCGEEGHF R+CP+
Sbjct: 108 YNCGRIGHLARDCYHGQGGGGGVDGDGRNRRRGGGGGGGGRGCFNCGEEGHFVRECPD 165

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147812546|emb|CAN68380.1| hypothetical protein VITISV_018906 [Vitis vinifera]

 Score =  140 bits (354), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 81/141 (57%), Positives = 92/141 (65%), Gaps = 7/141 (4%)

Query: 1   MAEVQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG 60
           MAE +RS+GTVKWFS QKGFGFIAP+DGGEDLFVHQTSI+S+GFRTLSEG+TVEF+VD G
Sbjct: 1   MAESKRSTGTVKWFSGQKGFGFIAPDDGGEDLFVHQTSIRSDGFRTLSEGETVEFAVDHG 60

Query: 61  EDGRTKAVDVEAASRSRRFGSRGGRSGGFYGGRGRGGGYGRGGRGGRSVG-------SGG 113
           EDGRTKAV+V A   S   G                      G G    G         G
Sbjct: 61  EDGRTKAVEVTAVRGSYSSGVGVVVMVDTVAAVMVVVVVVVVGYGRGVRGGRRSGRTDDG 120

Query: 114 GAGSGACFNCGRTGHIARECY 134
             G GAC+NCGRTGH+AR+CY
Sbjct: 121 YGGGGACYNCGRTGHLARDCY 141

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255640679|gb|ACU20624.1| unknown [Glycine max]

 Score =  139 bits (351), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 97/178 (54%), Positives = 118/178 (66%), Gaps = 23/178 (12%)

Query: 1   MAEVQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG 60
           MAE +RS+G VKWF++QKGFGFI P+DG +DLFVH TSI+S+G+R+LSEGQ+VEF +D G
Sbjct: 1   MAESRRSTGMVKWFNSQKGFGFITPQDGTDDLFVHFTSIRSDGYRSLSEGQSVEFLLDYG 60

Query: 61  EDGRTKAVDVEAASRSRRFGSRGGRSGGFYGGRGRGGGYGRGGRGGRSVGSGGGAGSGAC 120
           +DGRT AVDV +A RSR                G  GG GRG  GGR  G G   G   C
Sbjct: 61  DDGRTMAVDVTSAVRSR-------------RPGGFRGGGGRGIGGGRGGGFGRRGGGPEC 107

Query: 121 FNCGRTGHIARECY----------SRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPN 168
           +NCGR GH+AR+CY            GR   RG GGG GG GC+NCGEEG+F R+CP+
Sbjct: 108 YNCGRIGHLARDCYHGQGGGGGVDGDGRNRRRGGGGGGGGRGCFNCGEEGYFVRECPD 165

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|413926631|gb|AFW66563.1| hypothetical protein ZEAMMB73_047398 [Zea mays]

 Score =  138 bits (347), Expect = 9e-31,   Method: Compositional matrix adjust.
 Identities = 101/168 (60%), Positives = 112/168 (66%), Gaps = 16/168 (9%)

Query: 1   MAEVQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG 60
           MA   R  GTVKWF+  KGFGFI+PEDG EDLFVHQ+SIKSEGFR+L+EG+ VEFSV  G
Sbjct: 1   MAAAARQRGTVKWFNDTKGFGFISPEDGSEDLFVHQSSIKSEGFRSLAEGEEVEFSVSEG 60

Query: 61  EDGRTKAVDVEAASRSRRFGSRGGRSGGFYGGRGRGGGYGRGGRGGRSVGSGGGAGSGAC 120
           +DGRTKAVDV             G  G F   RG GGG G GG  G     GGG G G C
Sbjct: 61  DDGRTKAVDV------------TGPDGSFV--RGGGGGGGGGGGYGGGGYGGGGGGGGGC 106

Query: 121 FNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPN 168
           F CG  GH+AR+C S G G G   GGG GGGGCYNCG+ GH ARDCP+
Sbjct: 107 FKCGEPGHMARDCSSGGGGYGG--GGGGGGGGCYNCGQAGHMARDCPS 152

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|223946111|gb|ACN27139.1| unknown [Zea mays]

 Score =  135 bits (339), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 99/168 (58%), Positives = 110/168 (65%), Gaps = 17/168 (10%)

Query: 1   MAEVQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG 60
           MA   R  GTVKWF+  KGFGFI+PEDG EDLFVHQ+SIKSEGFR+L+EG+ VEFSV  G
Sbjct: 1   MAAAARQRGTVKWFNDTKGFGFISPEDGSEDLFVHQSSIKSEGFRSLAEGEEVEFSVSEG 60

Query: 61  EDGRTKAVDVEAASRSRRFGSRGGRSGGFYGGRGRGGGYGRGGRGGRSVGSGGGAGSGAC 120
           +DGRTKAVDV             G  G F  G G G G   GG  G     GGG G G C
Sbjct: 61  DDGRTKAVDV------------TGPDGSFVRGGGGGYG---GGGYGGGGYGGGGGGGGGC 105

Query: 121 FNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPN 168
           F CG  GH+AR+C S G G G   GGG GGGGCYNCG+ GH ARDCP+
Sbjct: 106 FKCGEPGHMARDCSSGGGGYGG--GGGGGGGGCYNCGQAGHMARDCPS 151

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302822137|ref|XP_002992728.1| hypothetical protein SELMODRAFT_186937 [Selaginella moellendorffii] gi|300139469|gb|EFJ06209.1| hypothetical protein SELMODRAFT_186937 [Selaginella moellendorffii]

 Score =  134 bits (337), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 87/165 (52%), Positives = 107/165 (64%), Gaps = 13/165 (7%)

Query: 4   VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDG 63
            ++ SG VKWF++ KGFGFI P+DGGEDLFVHQ+SI ++GFR+L +G+ VEF++D  EDG
Sbjct: 5   TEKKSGKVKWFNSAKGFGFITPDDGGEDLFVHQSSIHADGFRSLKDGEAVEFTIDRSEDG 64

Query: 64  RTKAVDVEAASRSRRFGSRGGRSGGFYGGRGRGGGYGRGGRGGRSVGSGGGAGSGACFNC 123
           RTKA+DV             G  G F  G G   G G GGR G   G  GG     CF C
Sbjct: 65  RTKALDV------------TGPEGSFVQGAGADSGRGGGGRFGGGGGRSGGGRGDGCFKC 112

Query: 124 GRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPN 168
           G++GHI+R+C S G GGG   GGG GG  CYNC + GH A+DCPN
Sbjct: 113 GQSGHISRDCPSGGGGGGGR-GGGGGGRNCYNCQQSGHIAKDCPN 156

Source: Selaginella moellendorffii

Species: Selaginella moellendorffii

Genus: Selaginella

Family: Selaginellaceae

Order: Selaginellales

Class: Isoetopsida

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	169
TAIR|locus:2047092	201	GRP2B "glycine-rich protein 2B	0.414	0.348	0.614	2.5e-26
TAIR|locus:2827810	301	CSP3 "cold shock domain protei	0.396	0.222	0.597	4.1e-26
TAIR|locus:2121219	203	GRP2 "AT4G38680" [Arabidopsis	0.390	0.325	0.606	1.3e-25
TAIR|locus:2135139	299	CSDP1 "cold shock domain prote	0.396	0.224	0.597	1.7e-25
UNIPROTKB|Q61CX7	237	lin-28 "Protein lin-28" [Caeno	0.360	0.257	0.426	4.8e-16
TIGR_CMR|SPO_3625	68	SPO_3625 "cold shock protein C	0.396	0.985	0.492	1.3e-15
WB|WBGene00003014	227	lin-28 [Caenorhabditis elegans	0.349	0.259	0.423	2e-15
UNIPROTKB|P92186	227	lin-28 "Protein lin-28" [Caeno	0.349	0.259	0.423	2e-15
UNIPROTKB|P0A978	70	cspG [Escherichia coli K-12 (t	0.366	0.885	0.564	2.6e-15
UNIPROTKB|Q9KN00	70	cspA "Cold shock-like protein	0.396	0.957	0.544	2.6e-15

TAIR|locus:2047092 GRP2B "glycine-rich protein 2B" [Arabidopsis thaliana (taxid:3702)]

 Score = 235 (87.8 bits), Expect = 2.5e-26, Sum P(3) = 2.5e-26
 Identities = 43/70 (61%), Positives = 54/70 (77%)

Query:     1 MAEVQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG 60
             M+   R  GTVKWF  QKGFGFI P DGG+DLFVHQ+SI+SEGFR+L+  ++VEF V+V 
Sbjct:     9 MSGGDRRKGTVKWFDTQKGFGFITPSDGGDDLFVHQSSIRSEGFRSLAAEESVEFDVEVD 68

Query:    61 EDGRTKAVDV 70
               GR KA++V
Sbjct:    69 NSGRPKAIEV 78

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0003677 "DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009409 "response to cold" evidence=IEP

GO:0005634 "nucleus" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0009790 "embryo development" evidence=IMP

GO:0010154 "fruit development" evidence=IMP

TAIR|locus:2827810 CSP3 "cold shock domain protein 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 226 (84.6 bits), Expect = 4.1e-26, Sum P(3) = 4.1e-26
 Identities = 40/67 (59%), Positives = 55/67 (82%)

Query:     6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRT 65
             RS G V WFS  KG+GFI P+DGGE+LFVHQ+SI S+GFR+L+ G++VE+ + +G DG+T
Sbjct:    10 RSIGKVSWFSDGKGYGFITPDDGGEELFVHQSSIVSDGFRSLTLGESVEYEIALGSDGKT 69

Query:    66 KAVDVEA 72
             KA++V A
Sbjct:    70 KAIEVTA 76

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009409 "response to cold" evidence=IEP;IMP

GO:0005737 "cytoplasm" evidence=IDA

GO:0009631 "cold acclimation" evidence=IMP

GO:0032508 "DNA duplex unwinding" evidence=IDA

TAIR|locus:2121219 GRP2 "AT4G38680" [Arabidopsis thaliana (taxid:3702)]

 Score = 231 (86.4 bits), Expect = 1.3e-25, Sum P(3) = 1.3e-25
 Identities = 40/66 (60%), Positives = 53/66 (80%)

Query:     5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGR 64
             +R  G+VKWF  QKGFGFI P+DGG+DLFVHQ+SI+SEGFR+L+  + VEF V++  + R
Sbjct:     9 ERRKGSVKWFDTQKGFGFITPDDGGDDLFVHQSSIRSEGFRSLAAEEAVEFEVEIDNNNR 68

Query:    65 TKAVDV 70
              KA+DV
Sbjct:    69 PKAIDV 74

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0009409 "response to cold" evidence=IEP

GO:0003690 "double-stranded DNA binding" evidence=IDA

GO:0003697 "single-stranded DNA binding" evidence=IDA

GO:0003729 "mRNA binding" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=IMP

GO:0048316 "seed development" evidence=IMP

GO:0048443 "stamen development" evidence=IMP

GO:0009414 "response to water deprivation" evidence=IEP

GO:0032508 "DNA duplex unwinding" evidence=IDA

GO:0043457 "regulation of cellular respiration" evidence=IMP

GO:0005886 "plasma membrane" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0009631 "cold acclimation" evidence=IGI

GO:0005829 "cytosol" evidence=IDA

GO:0009269 "response to desiccation" evidence=IEP

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

TAIR|locus:2135139 CSDP1 "cold shock domain protein 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 221 (82.9 bits), Expect = 1.7e-25, Sum P(3) = 1.7e-25
 Identities = 40/67 (59%), Positives = 53/67 (79%)

Query:     6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRT 65
             RS+G V WF+A KG+GFI P+DG  +LFVHQ+SI SEG+R+L+ G  VEF++  G DG+T
Sbjct:    10 RSTGKVNWFNASKGYGFITPDDGSVELFVHQSSIVSEGYRSLTVGDAVEFAITQGSDGKT 69

Query:    66 KAVDVEA 72
             KAV+V A
Sbjct:    70 KAVNVTA 76

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0003677 "DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009409 "response to cold" evidence=IGI;IEP

GO:0003690 "double-stranded DNA binding" evidence=IDA

GO:0003697 "single-stranded DNA binding" evidence=IDA

GO:0003723 "RNA binding" evidence=IDA

GO:0009414 "response to water deprivation" evidence=IEP

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

GO:0010501 "RNA secondary structure unwinding" evidence=IDA

GO:0032508 "DNA duplex unwinding" evidence=IDA

GO:0009631 "cold acclimation" evidence=IGI

GO:0009165 "nucleotide biosynthetic process" evidence=RCA

UNIPROTKB|Q61CX7 lin-28 "Protein lin-28" [Caenorhabditis briggsae (taxid:6238)]

 Score = 157 (60.3 bits), Expect = 4.8e-16, Sum P(3) = 4.8e-16
 Identities = 26/61 (42%), Positives = 42/61 (68%)

Query:     6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRT 65
             R  G+ KWF+  KG+GF+  ++ GEDLFVHQ+++  +GFR+L EG+ V + +    +G+ 
Sbjct:    52 RYFGSCKWFNVSKGYGFVIDDNTGEDLFVHQSNLNMQGFRSLDEGERVSYYIQERSNGKG 111

Query:    66 K 66
             K
Sbjct:   112 K 112

GO:0001708 "cell fate specification" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

TIGR_CMR|SPO_3625 SPO_3625 "cold shock protein CspA" [Ruegeria pomeroyi DSS-3 (taxid:246200)]

 Score = 196 (74.1 bits), Expect = 1.3e-15, P = 1.3e-15
 Identities = 33/67 (49%), Positives = 50/67 (74%)

Query:     7 SSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTK 66
             ++GTVKWF++QKGFGFIAPE G +D+FVH ++++  G + L +GQ V F ++ G DGR  
Sbjct:     2 ANGTVKWFNSQKGFGFIAPEQGSKDVFVHISALERSGIQKLDDGQAVTFDIESGRDGRES 61

Query:    67 AVDVEAA 73
             A+++  A
Sbjct:    62 AINLALA 68

GO:0003677 "DNA binding" evidence=ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS

GO:0009409 "response to cold" evidence=ISS

WB|WBGene00003014 lin-28 [Caenorhabditis elegans (taxid:6239)]

 Score = 150 (57.9 bits), Expect = 2.0e-15, Sum P(3) = 2.0e-15
 Identities = 25/59 (42%), Positives = 40/59 (67%)

Query:     6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGR 64
             R  G+ KWF+  KG+GF+  +  GEDLFVHQ+++  +GFR+L EG+ V + +    +G+
Sbjct:    52 RYFGSCKWFNVSKGYGFVIDDITGEDLFVHQSNLNMQGFRSLDEGERVSYYIQERSNGK 110

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0018991 "oviposition" evidence=IMP

GO:0002009 "morphogenesis of an epithelium" evidence=IMP

GO:0040034 "regulation of development, heterochronic" evidence=IGI;IMP

GO:0005737 "cytoplasm" evidence=IDA

GO:0070883 "pre-miRNA binding" evidence=IPI

GO:0007549 "dosage compensation" evidence=IGI

UNIPROTKB|P92186 lin-28 "Protein lin-28" [Caenorhabditis elegans (taxid:6239)]

 Score = 150 (57.9 bits), Expect = 2.0e-15, Sum P(3) = 2.0e-15
 Identities = 25/59 (42%), Positives = 40/59 (67%)

Query:     6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGR 64
             R  G+ KWF+  KG+GF+  +  GEDLFVHQ+++  +GFR+L EG+ V + +    +G+
Sbjct:    52 RYFGSCKWFNVSKGYGFVIDDITGEDLFVHQSNLNMQGFRSLDEGERVSYYIQERSNGK 110

GO:0001708 "cell fate specification" evidence=IMP

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|P0A978 cspG [Escherichia coli K-12 (taxid:83333)]

 Score = 193 (73.0 bits), Expect = 2.6e-15, P = 2.6e-15
 Identities = 35/62 (56%), Positives = 47/62 (75%)

Query:     6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRT 65
             + +G VKWF+A KGFGFI P+DG +D+FVH T+I+S  FRTL+E Q VEFS++ G+ G  
Sbjct:     4 KMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRGPA 63

Query:    66 KA 67
              A
Sbjct:    64 AA 65

GO:0009409 "response to cold" evidence=IDA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0006950 "response to stress" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|Q9KN00 cspA "Cold shock-like protein CspA" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)]

 Score = 193 (73.0 bits), Expect = 2.6e-15, P = 2.6e-15
 Identities = 37/68 (54%), Positives = 52/68 (76%)

Query:     5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGR 64
             Q+ +G+VKWF+  KGFGFI+ ++GG+D+FVH  SI SEGF+TL+EGQ V F+V+ G+ G 
Sbjct:     3 QKMTGSVKWFNETKGFGFISQDNGGQDVFVHFKSIVSEGFKTLAEGQRVSFTVEQGKKG- 61

Query:    65 TKAVDVEA 72
              +A  V A
Sbjct:    62 PQAAQVTA 69

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS

GO:0009409 "response to cold" evidence=ISS

---

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

Your Input: fgenesh4_pg.C_LG_II000796 hypothetical protein (184 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	169
pfam00313	66	pfam00313, CSD, 'Cold-shock' DNA-binding domain	1e-23
cd04458	65	cd04458, CSP_CDS, Cold-Shock Protein (CSP) contain	2e-22
COG1278	67	COG1278, CspC, Cold shock proteins [Transcription]	4e-21
PRK09890	70	PRK09890, PRK09890, cold shock protein CspG; Provi	2e-19
PRK09507	69	PRK09507, cspE, cold shock protein CspE; Reviewed	6e-18
PRK10354	70	PRK10354, PRK10354, RNA chaperone/anti-terminator;	6e-17
TIGR02381	68	TIGR02381, cspD, cold shock domain protein CspD	7e-16
PRK10943	69	PRK10943, PRK10943, cold shock-like protein CspC;	2e-15
PRK09937	74	PRK09937, PRK09937, stationary phase/starvation in	2e-15
PRK14998	73	PRK14998, PRK14998, cold shock-like protein CspD;	3e-15
smart00357	64	smart00357, CSP, Cold shock protein domain	2e-14
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	4e-11
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	6e-10
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	6e-10
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	7e-10
COG5082	190	COG5082, AIR1, Arginine methyltransferase-interact	1e-07
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	8e-07
COG5082	190	COG5082, AIR1, Arginine methyltransferase-interact	1e-06
pfam00098	18	pfam00098, zf-CCHC, Zinc knuckle	1e-05
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	1e-05
smart00343	17	smart00343, ZnF_C2HC, zinc finger	3e-05
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	6e-05
PRK15463	70	PRK15463, PRK15463, cold shock-like protein CspF;	1e-04
pfam00098	18	pfam00098, zf-CCHC, Zinc knuckle	0.002

>gnl|CDD|201147 pfam00313, CSD, 'Cold-shock' DNA-binding domain

 Score = 87.3 bits (217), Expect = 1e-23
 Identities = 35/62 (56%), Positives = 47/62 (75%), Gaps = 1/62 (1%)

Query: 9  GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAV 68
          GTVKWF+A+KGFGFI PEDG +D+FVH ++I+ +GFR+L EGQ VEF +  G     +A 
Sbjct: 3  GTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQRVEFDIVEG-TKGPQAA 61

Query: 69 DV 70
          +V
Sbjct: 62 NV 63

Length = 66

>gnl|CDD|239905 cd04458, CSP_CDS, Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea

 Score = 84.6 bits (210), Expect = 2e-22
 Identities = 35/62 (56%), Positives = 48/62 (77%), Gaps = 1/62 (1%)

Query: 9  GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAV 68
          GTVKWF  +KGFGFI P+DGGED+FVH ++++ +GFR+L EG  VEF ++ G D   +AV
Sbjct: 3  GTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEG-DKGPQAV 61

Query: 69 DV 70
          +V
Sbjct: 62 NV 63

CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription. Length = 65

>gnl|CDD|224197 COG1278, CspC, Cold shock proteins [Transcription]

 Score = 81.0 bits (201), Expect = 4e-21
 Identities = 39/68 (57%), Positives = 49/68 (72%), Gaps = 1/68 (1%)

Query: 6  RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRT 65
           ++GTVKWF+A KGFGFI PEDGG+D+FVH ++I+  GFRTL EGQ VEF V+ G     
Sbjct: 1  MATGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRAGFRTLREGQKVEFEVEQG-RKGP 59

Query: 66 KAVDVEAA 73
           A +V A 
Sbjct: 60 SAANVRAL 67

Length = 67

>gnl|CDD|77467 PRK09890, PRK09890, cold shock protein CspG; Provisional

 Score = 77.1 bits (189), Expect = 2e-19
 Identities = 35/62 (56%), Positives = 47/62 (75%)

Query: 6  RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRT 65
          + +G VKWF+A KGFGFI P+DG +D+FVH T+I+S  FRTL+E Q VEFS++ G+ G  
Sbjct: 4  KMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRGPA 63

Query: 66 KA 67
           A
Sbjct: 64 AA 65

Length = 70

>gnl|CDD|169931 PRK09507, cspE, cold shock protein CspE; Reviewed

 Score = 73.1 bits (179), Expect = 6e-18
 Identities = 33/59 (55%), Positives = 44/59 (74%)

Query: 9  GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKA 67
          G VKWF+  KGFGFI PEDG +D+FVH ++I++ GF+TL+EGQ VEF +  G  G + A
Sbjct: 6  GNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAA 64

Length = 69

>gnl|CDD|182402 PRK10354, PRK10354, RNA chaperone/anti-terminator; Provisional

 Score = 70.8 bits (173), Expect = 6e-17
 Identities = 29/58 (50%), Positives = 46/58 (79%)

Query: 6  RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDG 63
          + +G VKWF+A KGFGFI P+DG +D+FVH ++I+++G+++L EGQ V F+++ G  G
Sbjct: 4  KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKG 61

Length = 70

>gnl|CDD|131434 TIGR02381, cspD, cold shock domain protein CspD

 Score = 68.0 bits (166), Expect = 7e-16
 Identities = 31/66 (46%), Positives = 40/66 (60%), Gaps = 2/66 (3%)

Query: 8  SGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGR--T 65
           G VKWF+  KGFGFI PE    D+F H ++I+ +G+RTL  GQ V+F V  G  G   T
Sbjct: 3  IGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDGYRTLKAGQKVQFEVVQGPKGAHAT 62

Query: 66 KAVDVE 71
            V +E
Sbjct: 63 HIVPIE 68

This model represents what appears to be a phylogenetically distinct clade, containing E. coli CspD (SP|P24245) and related proteobacterial proteins within the larger family of cold shock domain proteins described by Pfam model pfam00313. The gene symbol cspD may have been used idependently for other subfamilies of cold shock domain proteins, such as for B. subtilis CspD. These proteins typically are shorter than 70 amino acids. In E. coli, CspD is a stress response protein induced in stationary phase. This homodimer binds single-stranded DNA and appears to inhibit DNA replication [DNA metabolism, DNA replication, recombination, and repair, Cellular processes, Adaptations to atypical conditions]. Length = 68

>gnl|CDD|170841 PRK10943, PRK10943, cold shock-like protein CspC; Provisional

 Score = 67.0 bits (163), Expect = 2e-15
 Identities = 31/55 (56%), Positives = 41/55 (74%)

Query: 9  GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDG 63
          G VKWF+  KGFGFI P DG +D+FVH ++I+  GF+TL+EGQ VEF +  G+ G
Sbjct: 6  GQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKG 60

Length = 69

>gnl|CDD|77494 PRK09937, PRK09937, stationary phase/starvation inducible regulatory protein CspD; Provisional

 Score = 66.7 bits (162), Expect = 2e-15
 Identities = 37/69 (53%), Positives = 48/69 (69%), Gaps = 4/69 (5%)

Query: 9  GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKA- 67
          GTVKWF+  KGFGFI PE GGED+F H ++I+ +G+RTL  GQ+V+F V  G  G   + 
Sbjct: 4  GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKGNHASV 63

Query: 68 ---VDVEAA 73
             V+VEAA
Sbjct: 64 IVPVEVEAA 72

Length = 74

>gnl|CDD|184960 PRK14998, PRK14998, cold shock-like protein CspD; Provisional

 Score = 66.2 bits (161), Expect = 3e-15
 Identities = 34/63 (53%), Positives = 44/63 (69%)

Query: 8  SGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKA 67
          +GTVKWF+  KGFGFI PE GGED+F H ++I+ +G+RTL  GQ+V F V  G  G   +
Sbjct: 3  TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHAS 62

Query: 68 VDV 70
          V V
Sbjct: 63 VIV 65

Length = 73

>gnl|CDD|214633 smart00357, CSP, Cold shock protein domain

 Score = 63.8 bits (156), Expect = 2e-14
 Identities = 30/63 (47%), Positives = 41/63 (65%), Gaps = 4/63 (6%)

Query: 9  GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSV-DVGEDGRTKA 67
          G VKWF+  KGFGFI P+DGG+D+FVH + I+  G ++L EG  VEF V       + +A
Sbjct: 2  GVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQG-GLKSLREGDEVEFKVVSPEGGEKPEA 58

Query: 68 VDV 70
           +V
Sbjct: 59 ENV 61

RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor. Length = 64

>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional

 Score = 57.5 bits (139), Expect = 4e-11
 Identities = 29/56 (51%), Positives = 37/56 (66%), Gaps = 7/56 (12%)

Query: 113 GGAGSGACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPN 168
            G+G  +C+NCG+TGHI+REC +R +GG            CYNCG EGH +RDCPN
Sbjct: 73  PGSGPRSCYNCGQTGHISRECPNRAKGG-------AARRACYNCGGEGHISRDCPN 121

Length = 148

>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional

 Score = 54.4 bits (131), Expect = 6e-10
 Identities = 30/74 (40%), Positives = 38/74 (51%), Gaps = 8/74 (10%)

Query: 95  RGGGYGRGGRGGRSVGSGGGAGSGACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCY 154
           R GG G   R   +    G A +  C+ CG  GH++REC S          GGRG   CY
Sbjct: 5   RCGGVGHQSRECPNSAPAGAAKARPCYKCGEPGHLSRECPSAP--------GGRGERSCY 56

Query: 155 NCGEEGHFARDCPN 168
           NCG+ GH +R+CP 
Sbjct: 57  NCGKTGHLSRECPE 70

Length = 148

>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional

 Score = 54.4 bits (131), Expect = 6e-10
 Identities = 27/55 (49%), Positives = 34/55 (61%), Gaps = 7/55 (12%)

Query: 113 GGAGSGACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCP 167
           GGA   AC+NCG  GHI+R+C + G+  G       G   CYNCG+ GH +RDCP
Sbjct: 99  GGAARRACYNCGGEGHISRDCPNAGKRPG-------GDKTCYNCGQTGHLSRDCP 146

Length = 148

>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional

 Score = 54.0 bits (130), Expect = 7e-10
 Identities = 26/56 (46%), Positives = 34/56 (60%), Gaps = 8/56 (14%)

Query: 113 GGAGSGACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPN 168
           GG G  +C+NCG+TGH++REC             G G   CYNCG+ GH +R+CPN
Sbjct: 48  GGRGERSCYNCGKTGHLSRECPEA--------PPGSGPRSCYNCGQTGHISRECPN 95

Length = 148

>gnl|CDD|227414 COG5082, AIR1, Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

 Score = 48.7 bits (116), Expect = 1e-07
 Identities = 21/71 (29%), Positives = 27/71 (38%), Gaps = 24/71 (33%)

Query: 120 CFNCGRTGHIARECYSRGRGG-------------------GRGYGGGRGGGG-----CYN 155
           C+NCG TGH++R+C                           + Y    G G      CY+
Sbjct: 100 CYNCGETGHLSRDCNPSKDQQKSCFDCNSTRHSSEDCPSIWKHYVLNNGDGHPIKKFCYS 159

Query: 156 CGEEGHFARDC 166
           CG  GHF  DC
Sbjct: 160 CGSAGHFGDDC 170

Length = 190

>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional

 Score = 46.0 bits (109), Expect = 8e-07
 Identities = 19/49 (38%), Positives = 25/49 (51%), Gaps = 6/49 (12%)

Query: 120 CFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPN 168
           C+ CG  GH +REC +          G      CY CGE GH +R+CP+
Sbjct: 3   CYRCGGVGHQSRECPNSAP------AGAAKARPCYKCGEPGHLSRECPS 45

Length = 148

>gnl|CDD|227414 COG5082, AIR1, Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

 Score = 46.0 bits (109), Expect = 1e-06
 Identities = 23/54 (42%), Positives = 29/54 (53%), Gaps = 6/54 (11%)

Query: 119 ACFNCGRTGHIAREC-----YSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCP 167
            CFNCG+ GH+ R+C     Y+    G R     +    CYNCGE GH +RDC 
Sbjct: 62  VCFNCGQNGHLRRDCPHSICYNCSWDGHRSNHCPK-PKKCYNCGETGHLSRDCN 114

Length = 190

>gnl|CDD|189387 pfam00098, zf-CCHC, Zinc knuckle

 Score = 40.1 bits (95), Expect = 1e-05
 Identities = 13/18 (72%), Positives = 14/18 (77%)

Query: 151 GGCYNCGEEGHFARDCPN 168
             CYNCG+EGH ARDCP 
Sbjct: 1   RKCYNCGKEGHLARDCPE 18

The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger. Length = 18

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 43.6 bits (103), Expect = 1e-05
 Identities = 32/73 (43%), Positives = 32/73 (43%), Gaps = 20/73 (27%)

Query: 80  GSRGGRSGGFYGGRGRGGGYGRGGRGGRSVGSGGGAGSGACFNCGRTGHIARECYSRGRG 139
           G  GG  GG  GGRG GGG GRGG G      GG                      RGRG
Sbjct: 1   GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGR--------------------GRGRG 40

Query: 140 GGRGYGGGRGGGG 152
           GG G  GG GGGG
Sbjct: 41  GGGGGRGGGGGGG 53

Length = 293

>gnl|CDD|197667 smart00343, ZnF_C2HC, zinc finger

 Score = 39.0 bits (92), Expect = 3e-05
 Identities = 13/17 (76%), Positives = 15/17 (88%)

Query: 152 GCYNCGEEGHFARDCPN 168
            CYNCG+EGH ARDCP+
Sbjct: 1   KCYNCGKEGHIARDCPS 17

Length = 17

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 41.6 bits (98), Expect = 6e-05
 Identities = 23/44 (52%), Positives = 23/44 (52%)

Query: 75  RSRRFGSRGGRSGGFYGGRGRGGGYGRGGRGGRSVGSGGGAGSG 118
              R G RGG  GG  GG GRGGG G G   GR  G GG  G G
Sbjct: 7   GGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGG 50

Length = 293

>gnl|CDD|185360 PRK15463, PRK15463, cold shock-like protein CspF; Provisional

 Score = 38.3 bits (89), Expect = 1e-04
 Identities = 22/63 (34%), Positives = 32/63 (50%)

Query: 5  QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGR 64
          ++ +G VK F  + G G I P DG +D+ VH +++       L+ G  VEF    G  G 
Sbjct: 3  RKMTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRINGLRGP 62

Query: 65 TKA 67
          T A
Sbjct: 63 TAA 65

Length = 70

>gnl|CDD|189387 pfam00098, zf-CCHC, Zinc knuckle

 Score = 33.6 bits (78), Expect = 0.002
 Identities = 9/18 (50%), Positives = 13/18 (72%)

Query: 118 GACFNCGRTGHIARECYS 135
             C+NCG+ GH+AR+C  
Sbjct: 1   RKCYNCGKEGHLARDCPE 18

The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger. Length = 18

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	169
COG1278	67	CspC Cold shock proteins [Transcription]	99.95
PRK10943	69	cold shock-like protein CspC; Provisional	99.94
PRK15464	70	cold shock-like protein CspH; Provisional	99.94
PRK15463	70	cold shock-like protein CspF; Provisional	99.93
PRK10354	70	RNA chaperone/anti-terminator; Provisional	99.93
PRK09890	70	cold shock protein CspG; Provisional	99.93
PRK09507	69	cspE cold shock protein CspE; Reviewed	99.93
PRK09937	74	stationary phase/starvation inducible regulatory p	99.93
TIGR02381	68	cspD cold shock domain protein CspD. This model re	99.92
PRK14998	73	cold shock-like protein CspD; Provisional	99.92
PF00313	66	CSD: 'Cold-shock' DNA-binding domain; InterPro: IP	99.89
cd04458	65	CSP_CDS Cold-Shock Protein (CSP) contains an S1-li	99.88
KOG3070	235	consensus Predicted RNA-binding protein containing	99.79
smart00357	64	CSP Cold shock protein domain. RNA-binding domain	99.16
PTZ00368	148	universal minicircle sequence binding protein (UMS	98.8
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	98.66
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	98.63
PTZ00368	148	universal minicircle sequence binding protein (UMS	98.55
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	98.29
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	98.21
KOG4400	261	consensus E3 ubiquitin ligase interacting with arg	98.16
KOG4400	261	consensus E3 ubiquitin ligase interacting with arg	98.07
PF14444	58	S1-like: S1-like	97.81
PF08206	58	OB_RNB: Ribonuclease B OB domain; InterPro: IPR013	97.75
PF13696	32	zf-CCHC_2: Zinc knuckle	97.7
PF07497	78	Rho_RNA_bind: Rho termination factor, RNA-binding	97.03
KOG0119	554	consensus Splicing factor 1/branch point binding p	96.72
smart00343	26	ZnF_C2HC zinc finger.	96.59
PF13917	42	zf-CCHC_3: Zinc knuckle	96.44
cd04459	68	Rho_CSD Rho_CSD: Rho protein cold-shock domain (CS	96.29
PF14787	36	zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB:	96.24
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	96.03
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	95.96
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	95.62
PF13696	32	zf-CCHC_2: Zinc knuckle	95.52
PF13917	42	zf-CCHC_3: Zinc knuckle	95.45
PRK11642	813	exoribonuclease R; Provisional	94.8
smart00343	26	ZnF_C2HC zinc finger.	94.74
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	94.74
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	94.33
PRK08582	139	hypothetical protein; Provisional	94.22
PF15288	40	zf-CCHC_6: Zinc knuckle	94.02
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	93.55
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	93.46
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	93.37
COG5222	427	Uncharacterized conserved protein, contains RING Z	93.08
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	93.04
PF14392	49	zf-CCHC_4: Zinc knuckle	92.79
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	92.78
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	92.54
PRK05054	644	exoribonuclease II; Provisional	92.53
PRK07252	120	hypothetical protein; Provisional	92.34
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	92.33
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	92.3
PRK12608	380	transcription termination factor Rho; Provisional	91.99
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	91.91
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	91.77
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	91.72
PF14392	49	zf-CCHC_4: Zinc knuckle	91.71
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	91.58
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	91.56
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	91.3
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	91.2
COG1158	422	Rho Transcription termination factor [Transcriptio	91.18
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	90.61
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	90.48
PF15288	40	zf-CCHC_6: Zinc knuckle	90.4
PRK09376	416	rho transcription termination factor Rho; Provisio	89.89
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	89.72
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	88.99
PRK05807	136	hypothetical protein; Provisional	88.96
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	88.96
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	88.91
PF14787	36	zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB:	88.88
PRK12678	672	transcription termination factor Rho; Provisional	87.84
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	87.51
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	86.51
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	86.43
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	86.41
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	85.93
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	85.52
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	84.54
COG5222	427	Uncharacterized conserved protein, contains RING Z	84.34
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	83.65
PRK08059	123	general stress protein 13; Validated	83.59
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	83.26
COG1098	129	VacB Predicted RNA binding protein (contains ribos	83.12
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	82.66
PF11604	70	CusF_Ec: Copper binding periplasmic protein CusF;	82.43
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	82.39
TIGR00767	415	rho transcription termination factor Rho. Members	81.97
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	81.57
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	81.3

>COG1278 CspC Cold shock proteins [Transcription]

Probab=99.95  E-value=9.9e-28  Score=157.60  Aligned_cols=67  Identities=60%  Similarity=1.072  Sum_probs=63.9

Q ss_pred             ccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcC
Q 030905            6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAA   73 (169)
Q Consensus         6 ~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~   73 (169)
                      |++|+|||||.+||||||+++++.+|||||+|+|+..++++|.+||+|+|+++++++| ++|.||+++
T Consensus         1 ~~~GtVKwfn~~KGfGFI~p~~G~~DvFVH~Sai~~~g~~~L~eGQ~V~f~~~~g~kg-p~A~nv~~~   67 (67)
T COG1278           1 MATGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRAGFRTLREGQKVEFEVEQGRKG-PSAANVRAL   67 (67)
T ss_pred             CCcceEEEeeCCCcceEcCCCCCCcCEEEEeeeeccCCCcccCCCCEEEEEEecCCCC-CceeEEEeC
Confidence            4689999999999999999999999999999999999999999999999999999999 899999863

>PRK10943 cold shock-like protein CspC; Provisional

Probab=99.94  E-value=1.3e-26  Score=154.61  Aligned_cols=69  Identities=51%  Similarity=0.983  Sum_probs=64.9

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAA   73 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~   73 (169)
                      ||+++|+|||||.+||||||+++++++|||||+|+|+..+++.|.+|++|+|+++++++| ++|++|+.+
T Consensus         1 ~~~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~g~~~l~~G~~V~f~~~~~~~g-~~A~~V~~~   69 (69)
T PRK10943          1 MAKIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKG-PAAVNVTAI   69 (69)
T ss_pred             CCccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHccccCCCCCCCCCEEEEEEEECCCC-ceeEEEEcC
Confidence            467999999999999999999999889999999999999889999999999999999998 799999853

>PRK15464 cold shock-like protein CspH; Provisional

Probab=99.94  E-value=1.8e-26  Score=154.17  Aligned_cols=69  Identities=33%  Similarity=0.517  Sum_probs=64.3

Q ss_pred             CCcccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEc
Q 030905            1 MAEVQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEA   72 (169)
Q Consensus         1 M~~~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~   72 (169)
                      |+  .+++|+|||||.+||||||+++++++|||||+++|+..+++.|.+|++|+|+++++++| ++|++|.+
T Consensus         1 m~--~~~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~g~~~l~~G~~V~f~v~~~~kG-~~A~~v~~   69 (70)
T PRK15464          1 MS--RKMTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRG-PTAANVYL   69 (70)
T ss_pred             CC--ccceEEEEEEECCCCeEEEccCCCCccEEEEehhehhcCCCCCCCCCEEEEEEEECCCC-ceeEEEEc
Confidence            65  34699999999999999999999999999999999988888999999999999999999 79999975

>PRK15463 cold shock-like protein CspF; Provisional

Probab=99.93  E-value=4.3e-26  Score=152.47  Aligned_cols=69  Identities=33%  Similarity=0.527  Sum_probs=64.5

Q ss_pred             CCcccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEc
Q 030905            1 MAEVQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEA   72 (169)
Q Consensus         1 M~~~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~   72 (169)
                      |+  .+++|+|||||.+||||||+++++++|||||+++|+..+++.|.+|++|+|+++++++| ++|++|++
T Consensus         1 m~--~~~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~g~~~l~~G~~V~f~v~~~~~G-~~A~~V~~   69 (70)
T PRK15463          1 MS--RKMTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRINGLRG-PTAANVYL   69 (70)
T ss_pred             CC--ccceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhcCCCCCCCCCEEEEEEEECCCC-ceeEEEEc
Confidence            66  34699999999999999999999999999999999988889999999999999999999 79999975

>PRK10354 RNA chaperone/anti-terminator; Provisional

Probab=99.93  E-value=7.5e-26  Score=151.41  Aligned_cols=70  Identities=46%  Similarity=0.969  Sum_probs=64.9

Q ss_pred             CCcccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcC
Q 030905            1 MAEVQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAA   73 (169)
Q Consensus         1 M~~~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~   73 (169)
                      |+  .+++|+|||||.+||||||+++++++|||||+|+|...+++.|.+|++|+|+++++++| ++|++|+.+
T Consensus         1 m~--~~~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f~~~~~~~G-~~A~~V~~~   70 (70)
T PRK10354          1 MS--GKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKG-PAAGNVTSL   70 (70)
T ss_pred             CC--ccceEEEEEEeCCCCcEEEecCCCCccEEEEEeeccccCCCCCCCCCEEEEEEEECCCC-ceeEEEEeC
Confidence            77  33599999999999999999999989999999999999889999999999999999999 899999863

>PRK09890 cold shock protein CspG; Provisional

Probab=99.93  E-value=8e-26  Score=151.25  Aligned_cols=69  Identities=54%  Similarity=0.983  Sum_probs=64.7

Q ss_pred             CCcccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEc
Q 030905            1 MAEVQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEA   72 (169)
Q Consensus         1 M~~~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~   72 (169)
                      |+  ++++|+|||||.+||||||+++++++|||||+|+|+..+++.|.+|++|+|+++++++| ++|++|..
T Consensus         1 m~--~~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~~~~~l~~G~~V~f~~~~~~~G-~~A~~V~~   69 (70)
T PRK09890          1 MS--NKMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRG-PAAANVVT   69 (70)
T ss_pred             CC--ccceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccCCCCCCCCCCEEEEEEEECCCC-ceeEEEEe
Confidence            66  45699999999999999999999989999999999999999999999999999999999 79999975

>PRK09507 cspE cold shock protein CspE; Reviewed

Probab=99.93  E-value=9.5e-26  Score=150.50  Aligned_cols=67  Identities=52%  Similarity=0.997  Sum_probs=63.8

Q ss_pred             cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEc
Q 030905            5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEA   72 (169)
Q Consensus         5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~   72 (169)
                      .+++|+|||||.+||||||+++++++|||||+|+|...+++.|.+|++|+|+++++++| ++|++|+.
T Consensus         2 ~~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f~~~~~~~G-~~A~~V~~   68 (69)
T PRK09507          2 SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKG-PSAANVIA   68 (69)
T ss_pred             CccceEEEEEeCCCCcEEEecCCCCeeEEEEeecccccCCCCCCCCCEEEEEEEECCCC-cccEEEEe
Confidence            36899999999999999999999989999999999998899999999999999999999 79999975

>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional

Probab=99.93  E-value=2.1e-25  Score=150.55  Aligned_cols=67  Identities=49%  Similarity=0.958  Sum_probs=63.7

Q ss_pred             cceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcCC
Q 030905            7 SSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAAS   74 (169)
Q Consensus         7 ~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~~   74 (169)
                      .+|+|||||.+||||||+++++++|||||+|+|+..+++.|.+|++|+|+++++++| ++|++|..++
T Consensus         2 ~~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~g~~~l~~G~~V~f~~~~~~~G-~~A~~V~~~~   68 (74)
T PRK09937          2 EKGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKG-NHASVIVPVE   68 (74)
T ss_pred             CCeEEEEEeCCCCeEEEeeCCCCccEEEEEeeccccCCCCCCCCCEEEEEEEECCCC-ceeeEEEECC
Confidence            479999999999999999999999999999999999999999999999999999999 6999999874

>TIGR02381 cspD cold shock domain protein CspD

Probab=99.92  E-value=2.7e-25  Score=147.95  Aligned_cols=66  Identities=44%  Similarity=0.838  Sum_probs=62.7

Q ss_pred             cceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcC
Q 030905            7 SSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAA   73 (169)
Q Consensus         7 ~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~   73 (169)
                      .+|+|||||.+||||||+++++++|||||+|+|+..+++.|.+|++|+|+++++++| ++|++|..+
T Consensus         2 ~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~g~~~l~~G~~V~f~~~~~~~G-~~A~~V~~~   67 (68)
T TIGR02381         2 AIGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDGYRTLKAGQKVQFEVVQGPKG-AHATHIVPI   67 (68)
T ss_pred             CCeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhcCCCCCCCCCEEEEEEEECCCC-ceeEEEEEC
Confidence            479999999999999999999889999999999998899999999999999999999 799999864

This model represents what appears to be a phylogenetically distinct clade, containing E. coli CspD and related proteobacterial proteins within the larger family of cold shock domain proteins described by pfam model pfam00313. The gene symbol cspD may have been used idependently for other subfamilies of cold shock domain proteins, such as for B. subtilis CspD. These proteins typically are shorter than 70 amino acids. In E. coli, CspD is a stress response protein induced in stationary phase. This homodimer binds single-stranded DNA and appears to inhibit DNA replication.

>PRK14998 cold shock-like protein CspD; Provisional

Probab=99.92  E-value=4.4e-25  Score=148.70  Aligned_cols=68  Identities=49%  Similarity=0.937  Sum_probs=64.0

Q ss_pred             cceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcCCC
Q 030905            7 SSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAASR   75 (169)
Q Consensus         7 ~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~~g   75 (169)
                      .+|+|||||.+||||||+++++++|||||+|+|+..+++.|.+|++|+|+++++++| ++|++|..++.
T Consensus         2 ~~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~g~~~l~~G~~V~f~~~~~~~G-~~A~~V~~~~~   69 (73)
T PRK14998          2 ETGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKG-NHASVIVPIEA   69 (73)
T ss_pred             CCeEEEEEeCCCceEEEecCCCCccEEEEeeeecccCCCCCCCCCEEEEEEEECCCC-ceeEEEEECcc
Confidence            479999999999999999999999999999999999999999999999999999999 69999987653

>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []

Probab=99.89  E-value=1e-22  Score=134.28  Aligned_cols=66  Identities=50%  Similarity=1.018  Sum_probs=59.8

Q ss_pred             cceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcC
Q 030905            7 SSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAA   73 (169)
Q Consensus         7 ~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~   73 (169)
                      |+|+|||||++||||||+++++.+|||||+++|....+..|.+|++|+|++..++++ ++|++|+++
T Consensus         1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~~~~~l~~G~~V~F~~~~~~~g-~~A~~V~~~   66 (66)
T PF00313_consen    1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGNGFRSLKEGDRVEFEVEEGKKG-PQAVNVRKI   66 (66)
T ss_dssp             EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSSSSTS--TTSEEEEEEEECTTS-EEEEEEEE-
T ss_pred             CeEEEEEEECCCCceEEEEcccceeEEeccccccccccccCCCCCEEEEEEEECCCC-CEEEEEECc
Confidence            689999999999999999999988999999999999888999999999999998887 899999864

During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....

>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea

Probab=99.88  E-value=3e-22  Score=131.72  Aligned_cols=65  Identities=54%  Similarity=1.112  Sum_probs=61.0

Q ss_pred             cceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEc
Q 030905            7 SSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEA   72 (169)
Q Consensus         7 ~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~   72 (169)
                      ++|+|||||++||||||+++++++|||||+++|...++..|.+|+.|+|+++.+.+| ++|++|+.
T Consensus         1 ~~G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~~~~~~~~G~~V~f~~~~~~~g-~~A~~V~~   65 (65)
T cd04458           1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKG-PQAVNVRL   65 (65)
T ss_pred             CcEEEEEEECCCCeEEEecCCCCcCEEEEhhHhhccCCCcCCCCCEEEEEEEECCCC-CeEEEeEC
Confidence            479999999999999999999889999999999998889999999999999999888 79999973

CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.

>KOG3070 consensus Predicted RNA-binding protein containing PIN domain and invovled in translation or RNA processing [Translation, ribosomal structure and biogenesis]

Probab=99.79  E-value=9.2e-19  Score=141.55  Aligned_cols=157  Identities=40%  Similarity=0.684  Sum_probs=105.5

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeecccc----CCcccCCCCCEEEEEEeeCCCCceeEEEEEcCCCcccc
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKS----EGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAASRSRRF   79 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~----~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~~g~~~~   79 (169)
                      ....+|+|||||..+|||||+++++.+|||||+++|..    .+|++|.+++.|.|+++...++ ..|++|+-+++.++.
T Consensus        54 ~~~~~G~~k~fnv~~G~gFi~~~d~~~D~fvhQs~i~~~~~~~~~rs~~~~e~v~f~~~~~~~g-~~a~~vt~p~g~~~~  132 (235)
T KOG3070|consen   54 GARVKGTVKWFNVGKGYGFITRDDGPEDVFVHQSAITKYTPSEGFRSLKEGEAVPFDIQEGNKG-TEAANVTGPDGVPVR  132 (235)
T ss_pred             cccccCcceeEeccCCcceecccCCCCceeEEeeeecccccccchhhcccCCCccceecccCcc-ceeeeecCCCCcccc
Confidence            46789999999999999999999999999999999999    8899999999999999999999 899999999999998


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCC---CCCCCCCCCCCCccccCcCCeecccCCCCCCCCCCCCCCCCCCcccccc
Q 030905           80 GSRGGRSGGFYGGRGRGGGYGRGGRGGR---SVGSGGGAGSGACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNC  156 (169)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~g~g---~~~gg~~~~~~~C~~Cg~~GH~a~~C~~~~~~~~~~~~g~~~~~~C~~C  156 (169)
                      ++......-.+...........+.-...   +...+.......|+.|+..+|.... +...      -.+......|+.|
T Consensus       133 ~s~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~-~~r~------~~g~r~~~~~~~~  205 (235)
T KOG3070|consen  133 GSKGAVKGNNERRVVGKSKVGHGGPIGQDDVRGEPGGEAVGVSGRACGGAGAAQRP-PVRK------CGGYRPASLCYTC  205 (235)
T ss_pred             cccccccccccccccccccCCCCCCcccccccccccccccccccccccccccccCC-CCcc------cccCCCccccccc
Confidence            7754222111100000000000000000   1111222233344778877764422 1100      0011135679999


Q ss_pred             CCCCccCCCCCC
Q 030905          157 GEEGHFARDCPN  168 (169)
Q Consensus       157 g~~GH~ardCp~  168 (169)
                      ++++|.+.+|++
T Consensus       206 ~~~g~~~~~~~e  217 (235)
T KOG3070|consen  206 GEPGHVADGCEE  217 (235)
T ss_pred             Cccccccccccc
Confidence            999999999876

>smart00357 CSP Cold shock protein domain

Probab=99.16  E-value=2.4e-10  Score=73.39  Aligned_cols=62  Identities=50%  Similarity=0.986  Sum_probs=50.7

Q ss_pred             ceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeC-CCCceeEEEEEc
Q 030905            8 SGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG-EDGRTKAVDVEA   72 (169)
Q Consensus         8 ~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~-~kGr~~A~~V~~   72 (169)
                      +|+|+|++  +|||||.+++..+|||||.++|.. .+..+.+|+.|.|.+... .+++++|..|+.
T Consensus         1 ~G~i~~~~--~g~gfv~~~~~~~~i~v~~~~~~~-~~~~~~~Gd~V~~~i~~~~~~~~~~a~~v~~   63 (64)
T smart00357        1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQG-GLKSLREGDEVEFKVVSPRGGGKPEAENVVK   63 (64)
T ss_pred             CeEEEEEc--CCeeEEecCCCCccEEEEhHHhhc-CCCcCCCCCEEEEEEEEccCCCCcEEEEEEe
Confidence            58999998  799999998765699999999876 556789999999999873 334478887764

RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.

>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional

Probab=98.80  E-value=3.5e-09  Score=80.02  Aligned_cols=47  Identities=49%  Similarity=1.206  Sum_probs=36.7

Q ss_pred             CCCCccccCcCCeecccCCCCCCCCCCCCCCCCCCccccccCCCCccCCCCCCC
Q 030905          116 GSGACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPNY  169 (169)
Q Consensus       116 ~~~~C~~Cg~~GH~a~~C~~~~~~~~~~~~g~~~~~~C~~Cg~~GH~ardCp~~  169 (169)
                      ....||+|++.+|++++||+....       ......||+|++.+||++|||++
T Consensus       102 ~~~~C~~Cg~~gH~~~~C~~~~~~-------~~~~~~C~~Cg~~gH~~~dCp~~  148 (148)
T PTZ00368        102 ARRACYNCGGEGHISRDCPNAGKR-------PGGDKTCYNCGQTGHLSRDCPDK  148 (148)
T ss_pred             cchhhcccCcCCcchhcCCCcccc-------CCCCCccccCCCcCcccccCCCC
Confidence            445799999999999999875211       11357899999999999999985

>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

Probab=98.66  E-value=1.4e-08  Score=79.46  Aligned_cols=54  Identities=39%  Similarity=0.861  Sum_probs=36.0

Q ss_pred             CCCCCccccCcCCeecccCCCCCC---CCCCCCCC-CCCCccccccCCCCccCCCC-CC
Q 030905          115 AGSGACFNCGRTGHIARECYSRGR---GGGRGYGG-GRGGGGCYNCGEEGHFARDC-PN  168 (169)
Q Consensus       115 ~~~~~C~~Cg~~GH~a~~C~~~~~---~~~~~~~g-~~~~~~C~~Cg~~GH~ardC-p~  168 (169)
                      .....||+|++.||.++|||...-   .--+++.. -...+.||+|++.||+++|| |+
T Consensus        58 ~~~~~C~nCg~~GH~~~DCP~~iC~~C~~~~H~s~~C~~~~~C~~Cg~~GH~~~dC~P~  116 (190)
T COG5082          58 EENPVCFNCGQNGHLRRDCPHSICYNCSWDGHRSNHCPKPKKCYNCGETGHLSRDCNPS  116 (190)
T ss_pred             ccccccchhcccCcccccCChhHhhhcCCCCcccccCCcccccccccccCccccccCcc
Confidence            456689999999999999991000   00001111 11247899999999999999 54

>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=98.63  E-value=1.6e-08  Score=50.18  Aligned_cols=17  Identities=71%  Similarity=1.679  Sum_probs=14.3

Q ss_pred             cccccCCCCccCCCCCC
Q 030905          152 GCYNCGEEGHFARDCPN  168 (169)
Q Consensus       152 ~C~~Cg~~GH~ardCp~  168 (169)
                      .||+|+++||+++|||+
T Consensus         2 ~C~~C~~~GH~~~~Cp~   18 (18)
T PF00098_consen    2 KCFNCGEPGHIARDCPK   18 (18)
T ss_dssp             BCTTTSCSSSCGCTSSS
T ss_pred             cCcCCCCcCcccccCcc
Confidence            58888888888888885

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....

>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional

Probab=98.55  E-value=7.8e-08  Score=72.64  Aligned_cols=44  Identities=52%  Similarity=1.312  Sum_probs=30.9

Q ss_pred             CCCccccCcCCeecccCCCCCCCCCCCCCCCCCCccccccCCCCccCCCCCC
Q 030905          117 SGACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPN  168 (169)
Q Consensus       117 ~~~C~~Cg~~GH~a~~C~~~~~~~~~~~~g~~~~~~C~~Cg~~GH~ardCp~  168 (169)
                      ...||+|++.+|++++||......        ....||+|++.+|++++||+
T Consensus        52 ~~~C~~Cg~~GH~~~~Cp~~~~~~--------~~~~C~~Cg~~GH~~~~C~~   95 (148)
T PTZ00368         52 ERSCYNCGKTGHLSRECPEAPPGS--------GPRSCYNCGQTGHISRECPN   95 (148)
T ss_pred             CcccCCCCCcCcCcccCCCcccCC--------CCcccCcCCCCCcccccCCC
Confidence            345777777777777776643211        24579999999999999986

>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

Probab=98.29  E-value=3.7e-07  Score=71.44  Aligned_cols=41  Identities=39%  Similarity=1.109  Sum_probs=29.5

Q ss_pred             CCCccccCcCCeecccC-CCCCCCCCCCCCCCCCCccccccCCCCccCCCCCC
Q 030905          117 SGACFNCGRTGHIAREC-YSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPN  168 (169)
Q Consensus       117 ~~~C~~Cg~~GH~a~~C-~~~~~~~~~~~~g~~~~~~C~~Cg~~GH~ardCp~  168 (169)
                      ...||+|++.||++++| |....           .+.||.|....|.+++||+
T Consensus        97 ~~~C~~Cg~~GH~~~dC~P~~~~-----------~~~C~~C~s~~H~s~~Cp~  138 (190)
T COG5082          97 PKKCYNCGETGHLSRDCNPSKDQ-----------QKSCFDCNSTRHSSEDCPS  138 (190)
T ss_pred             ccccccccccCccccccCccccc-----------CcceeccCCCccccccCcc
Confidence            36899999999999999 55432           3456666666666666664

>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=98.21  E-value=7e-07  Score=44.20  Aligned_cols=18  Identities=61%  Similarity=1.376  Sum_probs=16.5

Q ss_pred             CCccccCcCCeecccCCC
Q 030905          118 GACFNCGRTGHIARECYS  135 (169)
Q Consensus       118 ~~C~~Cg~~GH~a~~C~~  135 (169)
                      +.||+|++.||++++||+
T Consensus         1 ~~C~~C~~~GH~~~~Cp~   18 (18)
T PF00098_consen    1 RKCFNCGEPGHIARDCPK   18 (18)
T ss_dssp             SBCTTTSCSSSCGCTSSS
T ss_pred             CcCcCCCCcCcccccCcc
Confidence            379999999999999985

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....

>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]

Probab=98.16  E-value=1.1e-06  Score=72.21  Aligned_cols=40  Identities=45%  Similarity=1.217  Sum_probs=35.5

Q ss_pred             CCccccCcCCeecccCCCCCCCCCCCCCCCCCCccccccCCCCccCCCCCCC
Q 030905          118 GACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPNY  169 (169)
Q Consensus       118 ~~C~~Cg~~GH~a~~C~~~~~~~~~~~~g~~~~~~C~~Cg~~GH~ardCp~~  169 (169)
                      ..||+|++.||++.+||.+.            ...||.|++.+|+++|||++
T Consensus       144 ~~Cy~Cg~~GH~s~~C~~~~------------~~~c~~c~~~~h~~~~C~~~  183 (261)
T KOG4400|consen  144 AKCYSCGEQGHISDDCPENK------------GGTCFRCGKVGHGSRDCPSK  183 (261)
T ss_pred             CccCCCCcCCcchhhCCCCC------------CCccccCCCcceecccCCcc
Confidence            67999999999999999751            56799999999999999974

>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]

Probab=98.07  E-value=2.8e-06  Score=69.85  Aligned_cols=53  Identities=47%  Similarity=1.105  Sum_probs=39.1

Q ss_pred             CCCCccccCcCCeecccCCCCCCCCC-----------CCCC--------CCCCCccccccCCCCccCCCCCCC
Q 030905          116 GSGACFNCGRTGHIARECYSRGRGGG-----------RGYG--------GGRGGGGCYNCGEEGHFARDCPNY  169 (169)
Q Consensus       116 ~~~~C~~Cg~~GH~a~~C~~~~~~~~-----------~~~~--------g~~~~~~C~~Cg~~GH~ardCp~~  169 (169)
                      ....||+|++.||++++|+.......           +...        .... ..||+|++.|||+++||++
T Consensus        91 ~~~~c~~C~~~gH~~~~c~~~~~~~~~~~~~~~c~~~gh~~~~~~~~~~~~~~-~~Cy~Cg~~GH~s~~C~~~  162 (261)
T KOG4400|consen   91 IAAACFNCGEGGHIERDCPEAGKEGSSETSCYSCGKTGHRGCPDADPVDGPKP-AKCYSCGEQGHISDDCPEN  162 (261)
T ss_pred             cchhhhhCCCCccchhhCCcccCcccccceeeccCCCccccCcccccccCCCC-CccCCCCcCCcchhhCCCC
Confidence            46689999999999999998765330           0001        1112 6699999999999999953

>PF14444 S1-like: S1-like

Probab=97.81  E-value=7.6e-05  Score=47.69  Aligned_cols=53  Identities=23%  Similarity=0.329  Sum_probs=42.9

Q ss_pred             ccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCC--CceeEE
Q 030905            6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGED--GRTKAV   68 (169)
Q Consensus         6 ~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~k--Gr~~A~   68 (169)
                      .++|.|+.+.  ..||||.     +||||+.+.+...   .|++||+|..+...++.  .+|.|.
T Consensus         3 ~~~GvVTkl~--~~yG~ID-----e~vFF~~~vv~G~---~P~vGdrV~v~A~~n~~~~~kW~A~   57 (58)
T PF14444_consen    3 VFTGVVTKLC--DDYGFID-----EDVFFQTDVVKGN---VPKVGDRVLVEAIYNPNMPFKWNAT   57 (58)
T ss_pred             eEEEEEEEEe--CCcceEc-----ccEEEEcccEecC---CCccCCEEEEEEEeCCCCCccceee
Confidence            4689999997  5899997     7899999998864   57999999999987753  245554

>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies

Probab=97.75  E-value=9.5e-05  Score=47.31  Aligned_cols=40  Identities=35%  Similarity=0.788  Sum_probs=30.8

Q ss_pred             CCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCC
Q 030905           17 QKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGE   61 (169)
Q Consensus        17 ~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~   61 (169)
                      .+||||+.+++..+|||+...++...     ..||.|...+....
T Consensus         7 ~~GfGFv~~~~~~~DifIp~~~l~~A-----~~gD~V~v~i~~~~   46 (58)
T PF08206_consen    7 PKGFGFVIPDDGGEDIFIPPRNLNGA-----MDGDKVLVRITPPS   46 (58)
T ss_dssp             SSS-EEEEECT-TEEEEE-HHHHTTS------TT-EEEEEEEESS
T ss_pred             cCCCEEEEECCCCCCEEECHHHHCCC-----CCCCEEEEEEecCC
Confidence            79999999999889999999999754     69999999998843

; PDB: 2ID0_D 2IX1_A 2IX0_A.

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=97.70  E-value=1.2e-05  Score=45.42  Aligned_cols=20  Identities=45%  Similarity=1.160  Sum_probs=17.4

Q ss_pred             CccccccCCCCccCCCCCCC
Q 030905          150 GGGCYNCGEEGHFARDCPNY  169 (169)
Q Consensus       150 ~~~C~~Cg~~GH~ardCp~~  169 (169)
                      .-.|+.|++.|||.+|||.|
T Consensus         8 ~Y~C~~C~~~GH~i~dCP~~   27 (32)
T PF13696_consen    8 GYVCHRCGQKGHWIQDCPTN   27 (32)
T ss_pred             CCEeecCCCCCccHhHCCCC
Confidence            45799999999999999975

>PF07497 Rho_RNA_bind: Rho termination factor, RNA-binding domain; InterPro: IPR011113 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts

Probab=97.03  E-value=0.0018  Score=44.08  Aligned_cols=66  Identities=24%  Similarity=0.449  Sum_probs=41.7

Q ss_pred             ceEEEEeeCCCCeeEEecC-----CCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCC-c-eeEEEEEcCCCccc
Q 030905            8 SGTVKWFSAQKGFGFIAPE-----DGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDG-R-TKAVDVEAASRSRR   78 (169)
Q Consensus         8 ~G~Vk~~~~~kGfGFI~~~-----~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kG-r-~~A~~V~~~~g~~~   78 (169)
                      .|.+--  ..+|||||..+     .+.+||||..+.|+..+   |+.|+.|+=.+.....+ | +..+.|..+++.++
T Consensus         4 ~GvLei--~~dGyGFLR~~~~~y~~~~~DvYVs~~qIrrf~---LR~GD~V~G~vr~p~~~ek~~aL~~V~~VNg~~p   76 (78)
T PF07497_consen    4 EGVLEI--LPDGYGFLRSPDNNYLPSPDDVYVSPSQIRRFG---LRTGDLVEGQVRPPREGEKYFALLRVESVNGRPP   76 (78)
T ss_dssp             EEEEEE---TTS-EEEE-GGGTTS-STTSEEE-CCCCCCTT-----TTEEEEEEEE--STTSSSEEECEECEETTECT
T ss_pred             EEEEEE--CCCCcEEeECCCcCCCCCCCCEEECHHHHHHcC---CCCCCEEEEEEeCCCCCCcceeeEEEEeECCcCC
Confidence            455542  34799999987     35689999999999864   88999999888876444 2 34566777776543

It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [].; GO: 0003723 RNA binding, 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....

>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]

Probab=96.72  E-value=0.0011  Score=58.74  Aligned_cols=45  Identities=38%  Similarity=0.705  Sum_probs=36.7

Q ss_pred             CCCCccccCcCCeecccCCCCCCCCCCCCCCCCCCccccccCCCCccCCCCCCC
Q 030905          116 GSGACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPNY  169 (169)
Q Consensus       116 ~~~~C~~Cg~~GH~a~~C~~~~~~~~~~~~g~~~~~~C~~Cg~~GH~ardCp~~  169 (169)
                      ....|.+|+..+|...+||..-..-         ...|+.|+..+|+++||+.+
T Consensus       260 d~~~c~~cg~~~H~q~~cp~r~~~~---------~n~c~~cg~~gH~~~dc~~~  304 (554)
T KOG0119|consen  260 DNRACRNCGSTGHKQYDCPGRIPNT---------TNVCKICGPLGHISIDCKVN  304 (554)
T ss_pred             ccccccccCCCccccccCCcccccc---------cccccccCCcccccccCCCc
Confidence            4468999999999999999862211         23799999999999999864

>smart00343 ZnF_C2HC zinc finger

Probab=96.59  E-value=0.00095  Score=35.66  Aligned_cols=17  Identities=76%  Similarity=1.765  Sum_probs=14.0

Q ss_pred             cccccCCCCccCCCCCC
Q 030905          152 GCYNCGEEGHFARDCPN  168 (169)
Q Consensus       152 ~C~~Cg~~GH~ardCp~  168 (169)
                      .|++|++.+|++++||+
T Consensus         1 ~C~~CG~~GH~~~~C~~   17 (26)
T smart00343        1 KCYNCGKEGHIARDCPK   17 (26)
T ss_pred             CCccCCCCCcchhhCCc
Confidence            38888889998888873

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=96.44  E-value=0.0016  Score=39.14  Aligned_cols=18  Identities=39%  Similarity=1.167  Sum_probs=15.1

Q ss_pred             CccccccCCCCccCCCCC
Q 030905          150 GGGCYNCGEEGHFARDCP  167 (169)
Q Consensus       150 ~~~C~~Cg~~GH~ardCp  167 (169)
                      ...|.+|++.|||+.+||
T Consensus         4 ~~~CqkC~~~GH~tyeC~   21 (42)
T PF13917_consen    4 RVRCQKCGQKGHWTYECP   21 (42)
T ss_pred             CCcCcccCCCCcchhhCC
Confidence            466888888888888888

>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD)

Probab=96.29  E-value=0.011  Score=39.13  Aligned_cols=41  Identities=29%  Similarity=0.558  Sum_probs=34.2

Q ss_pred             CCeeEEecC-----CCCccEEEEeeccccCCcccCCCCCEEEEEEeeCC
Q 030905           18 KGFGFIAPE-----DGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGE   61 (169)
Q Consensus        18 kGfGFI~~~-----~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~   61 (169)
                      .|||||...     .+.+||||..+.|+..+   |+.|+.|+=.+....
T Consensus        10 ~g~GFLR~~~~~y~~~~~DvyVs~~~Irr~~---LR~GD~V~G~vr~p~   55 (68)
T cd04459          10 DGFGFLRSSGYNYLPGPDDIYVSPSQIRRFN---LRTGDTVVGQIRPPK   55 (68)
T ss_pred             CCceEEecCCcCCCCCCCCEEECHHHHHHhC---CCCCCEEEEEEeCCC
Confidence            499999976     35689999999999864   899999998877643

Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.

>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A

Probab=96.24  E-value=0.0023  Score=36.91  Aligned_cols=18  Identities=39%  Similarity=0.929  Sum_probs=10.9

Q ss_pred             ccccccCCCCccCCCCCC
Q 030905          151 GGCYNCGEEGHFARDCPN  168 (169)
Q Consensus       151 ~~C~~Cg~~GH~ardCp~  168 (169)
                      ..|++|++..|||+||-+
T Consensus         3 ~~CprC~kg~Hwa~~C~s   20 (36)
T PF14787_consen    3 GLCPRCGKGFHWASECRS   20 (36)
T ss_dssp             -C-TTTSSSCS-TTT---
T ss_pred             ccCcccCCCcchhhhhhh
Confidence            469999999999999954

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=96.03  E-value=0.026  Score=36.22  Aligned_cols=55  Identities=22%  Similarity=0.384  Sum_probs=34.7

Q ss_pred             cceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEE
Q 030905            7 SSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAV   68 (169)
Q Consensus         7 ~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~   68 (169)
                      .+-+|+..+   .+|++...+..++||+|.+.+..    .+++||.|+.-+-.+.++++.|+
T Consensus         5 ~~L~V~~~~---~~g~fL~~~~~~~vlLp~~e~~~----~~~~Gd~v~VFvY~D~~~rl~AT   59 (61)
T PF13509_consen    5 NTLKVVDKN---EFGYFLDDGEGKEVLLPKSEVPE----PLKVGDEVEVFVYLDKEGRLVAT   59 (61)
T ss_dssp             ----EEEE----SSEEEEEETT-EEEEEEGGG----------TTSEEEEEEEE-TTS-EEEE
T ss_pred             cceEEEEEe---CCEEEEECCCCCEEEechHHcCC----CCCCCCEEEEEEEECCCCCEEEe
Confidence            455677776   46777666666899999999974    48999999999999999988875

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=95.96  E-value=0.015  Score=48.72  Aligned_cols=22  Identities=32%  Similarity=0.951  Sum_probs=19.0

Q ss_pred             CCCccccCcCCeecccCCCCCC
Q 030905          117 SGACFNCGRTGHIARECYSRGR  138 (169)
Q Consensus       117 ~~~C~~Cg~~GH~a~~C~~~~~  138 (169)
                      ...||.|++.|||+++||....
T Consensus       160 q~~cyrcGkeghwskEcP~~~~  181 (346)
T KOG0109|consen  160 QSGCYRCGKEGHWSKECPVDRT  181 (346)
T ss_pred             HHHheeccccccccccCCccCC
Confidence            3479999999999999998665

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=95.62  E-value=0.0044  Score=51.79  Aligned_cols=21  Identities=33%  Similarity=0.472  Sum_probs=18.3

Q ss_pred             cceEEEEeeCCCCeeEEecCC
Q 030905            7 SSGTVKWFSAQKGFGFIAPED   27 (169)
Q Consensus         7 ~~G~Vk~~~~~kGfGFI~~~~   27 (169)
                      ..|||..-|..|.|||+..++
T Consensus        25 ~ygkVlECDIvKNYgFVHiEd   45 (346)
T KOG0109|consen   25 QYGKVLECDIVKNYGFVHIED   45 (346)
T ss_pred             hhCceEeeeeecccceEEeec
Confidence            468999999999999988765

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=95.52  E-value=0.0063  Score=34.35  Aligned_cols=20  Identities=30%  Similarity=0.871  Sum_probs=17.8

Q ss_pred             CCCccccCcCCeecccCCCC
Q 030905          117 SGACFNCGRTGHIARECYSR  136 (169)
Q Consensus       117 ~~~C~~Cg~~GH~a~~C~~~  136 (169)
                      .-.|+.|++.||+.++||..
T Consensus         8 ~Y~C~~C~~~GH~i~dCP~~   27 (32)
T PF13696_consen    8 GYVCHRCGQKGHWIQDCPTN   27 (32)
T ss_pred             CCEeecCCCCCccHhHCCCC
Confidence            34799999999999999984

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=95.45  E-value=0.0078  Score=36.11  Aligned_cols=20  Identities=35%  Similarity=0.805  Sum_probs=18.1

Q ss_pred             CCCCccccCcCCeecccCCC
Q 030905          116 GSGACFNCGRTGHIARECYS  135 (169)
Q Consensus       116 ~~~~C~~Cg~~GH~a~~C~~  135 (169)
                      ....|.+|++.||+..+|++
T Consensus         3 ~~~~CqkC~~~GH~tyeC~~   22 (42)
T PF13917_consen    3 ARVRCQKCGQKGHWTYECPN   22 (42)
T ss_pred             CCCcCcccCCCCcchhhCCC
Confidence            56689999999999999994

>PRK11642 exoribonuclease R; Provisional

Probab=94.80  E-value=0.086  Score=50.10  Aligned_cols=62  Identities=26%  Similarity=0.334  Sum_probs=45.8

Q ss_pred             ccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEee-CCCCceeEEEEEcCC
Q 030905            6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDV-GEDGRTKAVDVEAAS   74 (169)
Q Consensus         6 ~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~-~~kGr~~A~~V~~~~   74 (169)
                      .+.|+|..  ..+||||+.+++..+|||+.-..+..     .-.||+|...+.. +.++++.|.=|.++.
T Consensus        84 ~~~G~v~~--~~~GfgFv~~e~~~~difI~~~~l~~-----A~~GD~V~v~i~~~~~~~r~eg~Vv~Ile  146 (813)
T PRK11642         84 LLKGTVIG--HRDGYGFLRVEGRKDDLYLSSEQMKT-----CIHGDQVLAQPLGADRKGRREARIVRVLV  146 (813)
T ss_pred             eEEEEEEE--CCCccEEEEECCCCCCEEEChHHHcc-----CCCCCEEEEEEccCCCCCCcEEEEEEEEe
Confidence            46788884  46999999998766899998887754     3689999988765 234556666555554

>smart00343 ZnF_C2HC zinc finger

Probab=94.74  E-value=0.014  Score=31.05  Aligned_cols=18  Identities=56%  Similarity=1.392  Sum_probs=16.0

Q ss_pred             CccccCcCCeecccCCCC
Q 030905          119 ACFNCGRTGHIARECYSR  136 (169)
Q Consensus       119 ~C~~Cg~~GH~a~~C~~~  136 (169)
                      .|++|+..+|++++||..
T Consensus         1 ~C~~CG~~GH~~~~C~~~   18 (26)
T smart00343        1 KCYNCGKEGHIARDCPKX   18 (26)
T ss_pred             CCccCCCCCcchhhCCcc
Confidence            499999999999999843

>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=94.74  E-value=0.12  Score=33.63  Aligned_cols=54  Identities=20%  Similarity=0.212  Sum_probs=43.3

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccC----CcccCCCCCEEEEEEeeC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSE----GFRTLSEGQTVEFSVDVG   60 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~----~~~~l~~G~~V~F~~~~~   60 (169)
                      .+.+.|+|+..++   ||++..-..+-+.|+|+++|...    ....+.+||.|.+.+..-
T Consensus         5 G~iv~g~V~~v~~---~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~v   62 (74)
T PF00575_consen    5 GDIVEGKVTSVED---FGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKV   62 (74)
T ss_dssp             TSEEEEEEEEEET---TEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEE
T ss_pred             CCEEEEEEEEEEC---CEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEE
Confidence            4678999999986   66666655668999999999863    346789999999988764

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....

>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases

Probab=94.33  E-value=0.15  Score=47.32  Aligned_cols=63  Identities=30%  Similarity=0.450  Sum_probs=46.4

Q ss_pred             cccceEEEEeeCCCCeeEEecCC-CCccEEEEeeccccCCcccCCCCCEEEEEEee-CCCCceeEEEEEcCC
Q 030905            5 QRSSGTVKWFSAQKGFGFIAPED-GGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDV-GEDGRTKAVDVEAAS   74 (169)
Q Consensus         5 ~~~~G~Vk~~~~~kGfGFI~~~~-~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~-~~kGr~~A~~V~~~~   74 (169)
                      ..++|+|+.=  .+||||+.+++ ..+|||+.-..+..     .-.||.|...+.. ..++++.|.=|.++.
T Consensus        15 ~~~~G~i~~~--~~gfgFv~~~~~~~~difI~~~~~~~-----a~~GD~V~v~i~~~~~~~~~~g~v~~il~   79 (654)
T TIGR00358        15 DLVKGVVKAH--NKGFGFLRPDDDDKKDYFIPPPQMKK-----VMHGDLVEACPLSQPQRGRFEAEVERILE   79 (654)
T ss_pred             CeEEEEEEEC--CCccEEEEeCCCCCCcEEEchHHhCc-----CCCCCEEEEEEeecCCCCCceEEEEEEec
Confidence            3578999963  69999999986 35799999887754     4689999998754 345555666555554

This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.

>PRK08582 hypothetical protein; Provisional

Probab=94.22  E-value=0.51  Score=35.30  Aligned_cols=69  Identities=22%  Similarity=0.304  Sum_probs=48.9

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeC-CCCceeEEEEEcCCCc
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVG-EDGRTKAVDVEAASRS   76 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~-~kGr~~A~~V~~~~g~   76 (169)
                      ...+.|+|+...   .||++..-+...+-|+|++.|...-+    ..+.+||.|+..|... .+++ ..+.+..+...
T Consensus         6 G~iv~G~V~~I~---~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~~gk-I~LSlk~~~~~   79 (139)
T PRK08582          6 GSKLQGKVTGIT---NFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGK-IGLSIKKAKDR   79 (139)
T ss_pred             CCEEEEEEEEEE---CCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECCCCc-EEEEEEecccC
Confidence            457899999865   47776665555899999999975422    4588999999887764 3564 55666655443

>PF15288 zf-CCHC_6: Zinc knuckle

Probab=94.02  E-value=0.031  Score=33.12  Aligned_cols=16  Identities=50%  Similarity=1.277  Sum_probs=8.0

Q ss_pred             cccccCCCCccC--CCCC
Q 030905          152 GCYNCGEEGHFA--RDCP  167 (169)
Q Consensus       152 ~C~~Cg~~GH~a--rdCp  167 (169)
                      +|.+||..||++  +.||
T Consensus         3 kC~~CG~~GH~~t~k~CP   20 (40)
T PF15288_consen    3 KCKNCGAFGHMRTNKRCP   20 (40)
T ss_pred             cccccccccccccCccCC
Confidence            355555555544  3444

>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain

Probab=93.55  E-value=0.68  Score=31.77  Aligned_cols=56  Identities=23%  Similarity=0.191  Sum_probs=39.6

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeecccc-------CCcccCCCCCEEEEEEeeC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKS-------EGFRTLSEGQTVEFSVDVG   60 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~-------~~~~~l~~G~~V~F~~~~~   60 (169)
                      ...+.|+|+...+.-.==||...+ +.+-|+|++++..       .--..|++||.|...+...
T Consensus         8 G~iy~g~V~~i~~~~~GaFV~l~~-g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~   70 (88)
T cd04453           8 GNIYLGRVKKIVPGLQAAFVDIGL-GKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKE   70 (88)
T ss_pred             CCEEEEEEEEeccCCcEEEEEeCC-CCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEe
Confidence            457899999986432233555554 4799999999954       1124589999999998864

RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th

>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=93.46  E-value=0.43  Score=30.59  Aligned_cols=55  Identities=16%  Similarity=0.140  Sum_probs=40.2

Q ss_pred             cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC----cccCCCCCEEEEEEeeCCC
Q 030905            5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDVGED   62 (169)
Q Consensus         5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~~~k   62 (169)
                      +.+.|+|+...+   ||.+..-...-+-|+|+++|....    ...+++||.|++.+..-..
T Consensus         2 ~~~~g~V~~v~~---~G~~V~l~~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~   60 (70)
T cd05698           2 LKTHGTIVKVKP---NGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDP   60 (70)
T ss_pred             CEEEEEEEEEec---CcEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcC
Confidence            357899999864   666555444479999999997532    1348899999999887543

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=93.37  E-value=0.63  Score=30.48  Aligned_cols=60  Identities=17%  Similarity=0.142  Sum_probs=42.9

Q ss_pred             cccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeCCCCc
Q 030905            3 EVQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVGEDGR   64 (169)
Q Consensus         3 ~~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~~kGr   64 (169)
                      ..+.+.|+|+...+.  ||.+..-..+.+-|+|+|++...-.    ..+++||.|...+..-.+++
T Consensus         3 ~G~iv~G~V~~i~~~--~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~~~   66 (72)
T cd05704           3 EGAVTLGMVTKVIPH--SGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKDGK   66 (72)
T ss_pred             CCCEEEEEEEEeeCC--cEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecCCE
Confidence            356789999997543  5555555455799999999976432    33688999998887765554

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=93.08  E-value=0.039  Score=46.45  Aligned_cols=20  Identities=45%  Similarity=1.285  Sum_probs=17.7

Q ss_pred             CccccccCCCCccCCCCCCC
Q 030905          150 GGGCYNCGEEGHFARDCPNY  169 (169)
Q Consensus       150 ~~~C~~Cg~~GH~ardCp~~  169 (169)
                      +-.||+||+.|||..+||-|
T Consensus       176 gY~CyRCGqkgHwIqnCpTN  195 (427)
T COG5222         176 GYVCYRCGQKGHWIQNCPTN  195 (427)
T ss_pred             ceeEEecCCCCchhhcCCCC
Confidence            45699999999999999865

>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain

Probab=93.04  E-value=0.51  Score=28.85  Aligned_cols=51  Identities=25%  Similarity=0.361  Sum_probs=37.1

Q ss_pred             cceEEEEeeCCCCee-EEecCCCCccEEEEeeccccCC----cccCCCCCEEEEEEeeCC
Q 030905            7 SSGTVKWFSAQKGFG-FIAPEDGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDVGE   61 (169)
Q Consensus         7 ~~G~Vk~~~~~kGfG-FI~~~~~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~~~   61 (169)
                      +.|+|+..+   .+| ||..+ ...+.|+|.+.+....    ...+++||.|.+.+..-.
T Consensus         1 v~g~V~~v~---~~g~~v~l~-~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d   56 (65)
T cd00164           1 VTGKVVSIT---KFGVFVELE-DGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVD   56 (65)
T ss_pred             CEEEEEEEE---eeeEEEEec-CCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEc
Confidence            368899997   344 45544 4479999999997531    245899999999987643

Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.

>PF14392 zf-CCHC_4: Zinc knuckle

Probab=92.79  E-value=0.036  Score=34.08  Aligned_cols=17  Identities=41%  Similarity=1.202  Sum_probs=10.0

Q ss_pred             ccccccCCCCccCCCCC
Q 030905          151 GGCYNCGEEGHFARDCP  167 (169)
Q Consensus       151 ~~C~~Cg~~GH~ardCp  167 (169)
                      ..|+.|+..||.+++||
T Consensus        32 ~~C~~C~~~gH~~~~C~   48 (49)
T PF14392_consen   32 RFCFHCGRIGHSDKECP   48 (49)
T ss_pred             hhhcCCCCcCcCHhHcC
Confidence            34666666666666665

>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains

Probab=92.78  E-value=0.41  Score=32.01  Aligned_cols=55  Identities=20%  Similarity=0.189  Sum_probs=42.3

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeCC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVGE   61 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~~   61 (169)
                      .+.+.|+|+...+   ||++..-..+-+.|+|++++....+    ..+++||.|++.+..-.
T Consensus        15 G~i~~g~V~~v~~---~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id   73 (83)
T cd04461          15 GMVVHGYVRNITP---YGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVD   73 (83)
T ss_pred             CCEEEEEEEEEee---ceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEc
Confidence            4678899998864   8887775555899999999965532    34788999999987644

Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=92.54  E-value=0.48  Score=30.97  Aligned_cols=52  Identities=15%  Similarity=0.102  Sum_probs=36.3

Q ss_pred             ccc-eEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC----cccCCCCCEEEEEEee
Q 030905            6 RSS-GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDV   59 (169)
Q Consensus         6 ~~~-G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~   59 (169)
                      .+. |+|+...  ..||.+..-..+-+-|+|+|.|....    ...+++||.|++.+..
T Consensus         3 v~~~g~V~~v~--~~~G~~V~l~~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~   59 (71)
T cd05696           3 VVDSVKVTKVE--PDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIG   59 (71)
T ss_pred             EeeeeEEEEEc--cCceEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEE
Confidence            345 8999875  34666544433479999999996432    2458999999998764

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>PRK05054 exoribonuclease II; Provisional

Probab=92.53  E-value=0.38  Score=44.64  Aligned_cols=61  Identities=25%  Similarity=0.395  Sum_probs=43.2

Q ss_pred             cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcCC
Q 030905            5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAAS   74 (169)
Q Consensus         5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~~   74 (169)
                      ..+.|+|+.  ..+||||+.+++ .+|||++-..+...     -.||.|...+... +++..|.=+..+.
T Consensus        20 ~~~~G~~~~--~~~gfgFv~~~~-~~difI~~~~l~~a-----~~GD~V~v~i~~~-~~r~~g~v~~il~   80 (644)
T PRK05054         20 PRVEGVVKA--TEKGFGFLEVDA-QKSYFIPPPQMKKV-----MHGDRIIAVIHTE-KDREIAEPEELIE   80 (644)
T ss_pred             CeEEEEEEE--CCCccEEEEECC-CCcEEEChHHHccC-----CCCCEEEEEEecC-CCCcEEEEEEEEe
Confidence            457788885  469999998855 46999999888653     5799999887643 3444554444433

>PRK07252 hypothetical protein; Provisional

Probab=92.34  E-value=1.6  Score=31.85  Aligned_cols=70  Identities=19%  Similarity=0.276  Sum_probs=48.8

Q ss_pred             CCcccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeCC--CCceeEEEEEcCC
Q 030905            1 MAEVQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVGE--DGRTKAVDVEAAS   74 (169)
Q Consensus         1 M~~~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~~--kGr~~A~~V~~~~   74 (169)
                      |.....+.|+|+...+   ||++..-....+-|+|+++|...-+    ..+.+||.|+..+..-.  +++ ..+.+..+.
T Consensus         1 ~kvG~iv~G~V~~V~~---~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~r-i~lSlk~~~   76 (120)
T PRK07252          1 MKIGDKLKGTITGIKP---YGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGK-ASLSLRTLE   76 (120)
T ss_pred             CCCCCEEEEEEEEEeC---cEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCE-EEEEEeecc
Confidence            3445678999999864   8877766555799999999975432    34789999999988743  443 334444443

>TIGR02062 RNase_B exoribonuclease II

Probab=92.33  E-value=0.45  Score=44.10  Aligned_cols=61  Identities=25%  Similarity=0.401  Sum_probs=43.5

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAA   73 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~   73 (169)
                      ...+.|+|+.  ..+||||+.+++ .+|||+.-..+...     -.||.|...+.... ++..|.=+..+
T Consensus        16 ~~~~~G~i~~--~~kGfgFv~~~~-~~difI~~~~l~~A-----~~GD~V~v~i~~~~-~r~~~~v~~iv   76 (639)
T TIGR02062        16 TPRVEGVVKA--TEKGFGFLEVDA-QKSYFIPPPQMKKV-----MHGDKIIAVIHSEK-ERESAEPEELI   76 (639)
T ss_pred             CceEEEEEEE--CCCccEEEEECC-CCcEEEChHHHccC-----CCCCEEEEEEecCC-CCcEEEEEEEE
Confidence            3457799985  469999997665 46999999888653     57999998876543 44455444444

This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.

>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain

Probab=92.30  E-value=0.63  Score=29.14  Aligned_cols=53  Identities=28%  Similarity=0.349  Sum_probs=39.0

Q ss_pred             cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeC
Q 030905            5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVG   60 (169)
Q Consensus         5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~   60 (169)
                      ..+.|+|+...+   ||++..-+...+.|+|++++.....    ..+++||.|+..+..-
T Consensus         2 ~~~~g~V~~i~~---~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~   58 (69)
T cd05692           2 SVVEGTVTRLKP---FGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSI   58 (69)
T ss_pred             CEEEEEEEEEEe---eeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEE
Confidence            357889998764   7776665555799999999975422    3478999999887553

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>PRK12608 transcription termination factor Rho; Provisional

Probab=91.99  E-value=0.33  Score=42.30  Aligned_cols=70  Identities=21%  Similarity=0.341  Sum_probs=49.0

Q ss_pred             ccccceEEEEeeCCCCeeEEecC-----CCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcCCCccc
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPE-----DGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAASRSRR   78 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~-----~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~~g~~~   78 (169)
                      .....|++--..  .||||+...     .+.+||||..+.|+..+   |+.|+.|.-.... +-+...-..|.-+.+.|+
T Consensus        16 ~~~~~g~l~~~~--~g~gflr~~~~~~~~~~~d~yv~~~~i~~~~---l~~Gd~V~~~~r~-~~~~~~LgrV~~~~G~p~   89 (380)
T PRK12608         16 TEEVLGVLEILG--DGFGFLRSARRNYLPSPDDVFVPPALIRRFN---LRTGDVVEGVARP-RERYRVLVRVDSVNGTDP   89 (380)
T ss_pred             CCcceEEEEEcC--CCceEeecCccCCCCCCCCeeeCHHHHHHhC---CCCCCEEEeccCC-CCChhheEEEeccCCcCc
Confidence            345677777554  499999985     45689999999999864   8899999987665 333223345555555554


Q ss_pred             c
Q 030905           79 F   79 (169)
Q Consensus        79 ~   79 (169)
                      .
T Consensus        90 d   90 (380)
T PRK12608         90 E   90 (380)
T ss_pred             h
Confidence            3

>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=91.91  E-value=0.72  Score=29.59  Aligned_cols=54  Identities=17%  Similarity=0.148  Sum_probs=40.4

Q ss_pred             cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeCC
Q 030905            5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVGE   61 (169)
Q Consensus         5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~~   61 (169)
                      +.++|+|+...   .||.+..-+.+-+-|+|++.+....+    ..+++||.|++.+..-+
T Consensus         2 ~~v~g~V~~v~---~~Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id   59 (69)
T cd05697           2 QVVKGTIRKLR---PSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVE   59 (69)
T ss_pred             CEEEEEEEEEe---ccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEE
Confidence            35789999986   36777665445899999999975422    35889999999987653

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>smart00316 S1 Ribosomal protein S1-like RNA-binding domain

Probab=91.77  E-value=0.48  Score=29.59  Aligned_cols=55  Identities=18%  Similarity=0.210  Sum_probs=40.4

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC----cccCCCCCEEEEEEeeCC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDVGE   61 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~~~   61 (169)
                      ...+.|+|+..+.   +|++..-....+.|+|.+++....    ...+++||.|.+.+..-.
T Consensus         3 G~~v~g~V~~v~~---~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~   61 (72)
T smart00316        3 GDVVEGTVTEITP---FGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVD   61 (72)
T ss_pred             CCEEEEEEEEEEc---cEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEe
Confidence            3567899999976   455554443578999999997641    134899999999887653

>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=91.72  E-value=1.1  Score=29.01  Aligned_cols=56  Identities=9%  Similarity=-0.146  Sum_probs=39.9

Q ss_pred             cccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC----cccCCCCCEEEEEEeeCC
Q 030905            3 EVQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDVGE   61 (169)
Q Consensus         3 ~~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~~~   61 (169)
                      ..+.+.|+|+....   ||.+..-+.+-+-|+|+++|....    ...+++||.|+..+..-.
T Consensus         3 ~G~iv~g~V~~v~~---~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d   62 (73)
T cd05706           3 VGDILPGRVTKVND---RYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVD   62 (73)
T ss_pred             CCCEEEEEEEEEeC---CeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEe
Confidence            34678999999753   555544444489999999997542    134789999999887643

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>PF14392 zf-CCHC_4: Zinc knuckle

Probab=91.71  E-value=0.066  Score=32.89  Aligned_cols=20  Identities=45%  Similarity=0.997  Sum_probs=17.2

Q ss_pred             CCCCccccCcCCeecccCCC
Q 030905          116 GSGACFNCGRTGHIARECYS  135 (169)
Q Consensus       116 ~~~~C~~Cg~~GH~a~~C~~  135 (169)
                      -+..|++|+..||...+||.
T Consensus        30 lp~~C~~C~~~gH~~~~C~k   49 (49)
T PF14392_consen   30 LPRFCFHCGRIGHSDKECPK   49 (49)
T ss_pred             cChhhcCCCCcCcCHhHcCC
Confidence            34479999999999999984

>TIGR02063 RNase_R ribonuclease R

Probab=91.58  E-value=0.58  Score=43.81  Aligned_cols=62  Identities=26%  Similarity=0.431  Sum_probs=44.0

Q ss_pred             ccceEEEEeeCCCCeeEEecCC-CCccEEEEeeccccCCcccCCCCCEEEEEEeeCC--CCceeEEEEEcCC
Q 030905            6 RSSGTVKWFSAQKGFGFIAPED-GGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGE--DGRTKAVDVEAAS   74 (169)
Q Consensus         6 ~~~G~Vk~~~~~kGfGFI~~~~-~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~--kGr~~A~~V~~~~   74 (169)
                      .+.|+|+.  ..+||||+.+++ ..+|||+....+..     ...||.|...+....  ++++.|.=|.+++
T Consensus        68 ~~~G~i~~--~~~g~gFv~~~~~~~~di~I~~~~~~~-----a~~GD~Vlv~I~~~~~~~~~~eg~Vv~Il~  132 (709)
T TIGR02063        68 LVKGTVIA--HRDGFGFLRPEDDDEDDIFIPPRQMNG-----AMHGDRVLVRITGKPDGGDRFEARVIKILE  132 (709)
T ss_pred             eEEEEEEE--CCCccEEEEECCCCCCcEEEChHHhCc-----CCCCCEEEEEEecccCCCCCceEEEEEEEe
Confidence            46788875  478999999886 35799998776643     578999999986542  3445665445443

This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.

>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=91.56  E-value=1.3  Score=29.35  Aligned_cols=52  Identities=21%  Similarity=0.165  Sum_probs=40.5

Q ss_pred             ccccceEEEEeeCCCCeeEEecCC-CCccEEEEeeccccCCcccCCCCCEEEEEEeeC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPED-GGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG   60 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~-~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~   60 (169)
                      .+.++|+|+..-   -||++..-. .+-+-|+|.+++...  ..+.+||.|...+..-
T Consensus         5 G~~v~g~V~si~---d~G~~v~~g~~gv~Gfl~~~~~~~~--~~~~~Gq~v~~~V~~v   57 (74)
T cd05694           5 GMVLSGCVSSVE---DHGYILDIGIPGTTGFLPKKDAGNF--SKLKVGQLLLCVVEKV   57 (74)
T ss_pred             CCEEEEEEEEEe---CCEEEEEeCCCCcEEEEEHHHCCcc--cccCCCCEEEEEEEEE
Confidence            467899999985   577766543 346899999999865  5689999999997643

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain

Probab=91.30  E-value=1.4  Score=28.31  Aligned_cols=54  Identities=22%  Similarity=0.231  Sum_probs=38.8

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc-----ccCCCCCEEEEEEeeC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF-----RTLSEGQTVEFSVDVG   60 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~-----~~l~~G~~V~F~~~~~   60 (169)
                      .+.+.|+|+...+   ||+...-+.+.+-|+|+++|.....     ..++.||.|+..+..-
T Consensus         4 g~~~~g~V~~i~~---~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~i   62 (72)
T cd05689           4 GTRLFGKVTNLTD---YGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDI   62 (72)
T ss_pred             CCEEEEEEEEEEe---eEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEe
Confidence            4568899998754   8887665545899999999963211     2467888888877654

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=91.20  E-value=0.92  Score=29.98  Aligned_cols=54  Identities=17%  Similarity=-0.018  Sum_probs=39.5

Q ss_pred             ccccceEEEEeeCCCCeeE-EecCCCCccEEEEeeccccCCc-------ccCCCCCEEEEEEeeCC
Q 030905            4 VQRSSGTVKWFSAQKGFGF-IAPEDGGEDLFVHQTSIKSEGF-------RTLSEGQTVEFSVDVGE   61 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGF-I~~~~~~~dvF~H~s~i~~~~~-------~~l~~G~~V~F~~~~~~   61 (169)
                      ...+.|+|+...   .||. +... .+-+-|+|+++|.....       ..+++||.|++.+..-+
T Consensus         4 G~~V~g~V~~i~---~~G~fV~l~-~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id   65 (74)
T cd05705           4 GQLLRGYVSSVT---KQGVFFRLS-SSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVN   65 (74)
T ss_pred             CCEEEEEEEEEe---CCcEEEEeC-CCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEE
Confidence            467899999985   4554 4544 35799999999876531       35699999999887643

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>COG1158 Rho Transcription termination factor [Transcription]

Probab=91.18  E-value=0.35  Score=41.72  Aligned_cols=67  Identities=33%  Similarity=0.541  Sum_probs=49.8

Q ss_pred             ceEEEEeeCCCCeeEEecCC-----CCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCC-ceeE-EEEEcCCCcccc
Q 030905            8 SGTVKWFSAQKGFGFIAPED-----GGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDG-RTKA-VDVEAASRSRRF   79 (169)
Q Consensus         8 ~G~Vk~~~~~kGfGFI~~~~-----~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kG-r~~A-~~V~~~~g~~~~   79 (169)
                      .|++--..  .||||+.+.+     +.+||||.-|.|....   |+.||.|+=.+.....| |+.| +.|..+++.++.
T Consensus        55 ~GvLeil~--dGfGFLR~~~~~yl~~~~DiYvSpSQIRrf~---LrtGD~v~G~vR~Pke~Ery~aLl~ve~vN~~~pe  128 (422)
T COG1158          55 DGVLEILP--DGFGFLRSADSSYLPGPDDIYVSPSQIRRFN---LRTGDTVEGKVRPPKEGERYFALLKVEAVNGDDPE  128 (422)
T ss_pred             eeEEEecc--CCcceeecCccccCCCCCceEECHHHHhhcc---CccCCEEeeeecCCCcccceeeeEEEeecCCCCHH
Confidence            35555443  7999999865     4589999999999864   88999999998877665 3444 567777766643

>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain

Probab=90.61  E-value=1.2  Score=27.93  Aligned_cols=53  Identities=25%  Similarity=0.265  Sum_probs=40.1

Q ss_pred             ccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeCC
Q 030905            6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVGE   61 (169)
Q Consensus         6 ~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~~   61 (169)
                      .+.|+|....+   ||++..-....+-|+|++++...-+    ..++.||.|...+....
T Consensus         3 ~~~g~V~~v~~---~G~~v~l~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d   59 (68)
T cd04472           3 IYEGKVVKIKD---FGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVD   59 (68)
T ss_pred             EEEEEEEEEEE---eEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEEC
Confidence            57889998875   8888775555899999999976432    24689999998877643

PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.

>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain

Probab=90.48  E-value=1.5  Score=28.60  Aligned_cols=54  Identities=20%  Similarity=0.201  Sum_probs=39.6

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCC-CccEEEEeeccccCCcc----cCCCCCEEEEEEeeC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDG-GEDLFVHQTSIKSEGFR----TLSEGQTVEFSVDVG   60 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~-~~dvF~H~s~i~~~~~~----~l~~G~~V~F~~~~~   60 (169)
                      ...+.|+|+...+   ||++..-++ ..+-|+|++++...-+.    .+++||.|...+..-
T Consensus         4 g~~~~g~V~~i~~---fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~v   62 (73)
T cd05686           4 YQIFKGEVASVTE---YGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGR   62 (73)
T ss_pred             CCEEEEEEEEEEe---eeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEE
Confidence            4568899999864   887666533 35899999999765432    257899999887654

pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.

>PF15288 zf-CCHC_6: Zinc knuckle

Probab=90.40  E-value=0.13  Score=30.40  Aligned_cols=20  Identities=35%  Similarity=0.740  Sum_probs=16.7

Q ss_pred             CCccccCcCCeec--ccCCCCC
Q 030905          118 GACFNCGRTGHIA--RECYSRG  137 (169)
Q Consensus       118 ~~C~~Cg~~GH~a--~~C~~~~  137 (169)
                      ..|.+||.+||.+  +.||...
T Consensus         2 ~kC~~CG~~GH~~t~k~CP~~~   23 (40)
T PF15288_consen    2 VKCKNCGAFGHMRTNKRCPMYC   23 (40)
T ss_pred             ccccccccccccccCccCCCCC
Confidence            5799999999987  6788754

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=89.89  E-value=0.87  Score=40.11  Aligned_cols=67  Identities=28%  Similarity=0.541  Sum_probs=48.4

Q ss_pred             cceEEEEeeCCCCeeEEecCC-----CCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCC-c-eeEEEEEcCCCccc
Q 030905            7 SSGTVKWFSAQKGFGFIAPED-----GGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDG-R-TKAVDVEAASRSRR   78 (169)
Q Consensus         7 ~~G~Vk~~~~~kGfGFI~~~~-----~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kG-r-~~A~~V~~~~g~~~   78 (169)
                      ..|++--..  .|||||.+.+     +.+||||-.+.|+..+   |+.|+.|+=.+.....+ | +.-+.|..+++.++
T Consensus        51 ~~g~le~~~--~g~gflr~~~~~y~~~~~d~yvs~~~ir~~~---lr~gd~v~g~~r~~~~~e~~~~l~~v~~vng~~~  124 (416)
T PRK09376         51 GEGVLEILP--DGFGFLRSPDANYLPGPDDIYVSPSQIRRFN---LRTGDTVEGKIRPPKEGERYFALLKVETVNGEDP  124 (416)
T ss_pred             EEEEEEEcC--CCCeEEeCCCcCCCCCCCCeeeCHHHHHhcC---CCCCCEEEEEeeCCCCCCCccceEEEeeeCCCCH
Confidence            556665443  3999999853     4589999999999864   88999999888865433 2 34567777776553

>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain

Probab=89.72  E-value=0.73  Score=29.42  Aligned_cols=53  Identities=15%  Similarity=0.171  Sum_probs=37.9

Q ss_pred             cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcc--cCCCCCEEEEEEeeCC
Q 030905            5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFR--TLSEGQTVEFSVDVGE   61 (169)
Q Consensus         5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~--~l~~G~~V~F~~~~~~   61 (169)
                      ..++|+|+..++   +|++..-+ +-+.|+|.+.+......  ...+|+.+.+.+..-.
T Consensus         2 ~iv~g~V~~v~~---~G~~v~l~-g~~gfip~s~~~~~~~~~~~~~vG~~i~~~i~~vd   56 (67)
T cd04465           2 EIVEGKVTEKVK---GGLIVDIE-GVRAFLPASQVDLRPVEDLDEYVGKELKFKIIEID   56 (67)
T ss_pred             CEEEEEEEEEEC---CeEEEEEC-CEEEEEEHHHCCCcccCChHHhCCCEEEEEEEEEe
Confidence            357899999964   66666653 57899999999754321  1247999999887643

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=88.99  E-value=1.6  Score=27.84  Aligned_cols=52  Identities=19%  Similarity=0.153  Sum_probs=37.3

Q ss_pred             ccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeC
Q 030905            6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVG   60 (169)
Q Consensus         6 ~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~   60 (169)
                      .+.|+|+...   .||.+..-...-+-|+|++.|.....    ..+++||.|+..+..-
T Consensus         3 ~v~g~V~~v~---~~Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~   58 (68)
T cd05707           3 VVRGFVKNIA---NNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSI   58 (68)
T ss_pred             EEEEEEEEEE---CccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEE
Confidence            4789999985   35555444444799999999965422    3478999999987654

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>PRK05807 hypothetical protein; Provisional

Probab=88.96  E-value=3.2  Score=30.87  Aligned_cols=66  Identities=21%  Similarity=0.287  Sum_probs=46.5

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeC-CCCceeEEEEEcCC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVG-EDGRTKAVDVEAAS   74 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~-~kGr~~A~~V~~~~   74 (169)
                      ...+.|+|+...   .||++..-+ ..+-|+|++.|...-+    ..+++||.|+..+... .+++ ..+.+..+.
T Consensus         6 G~vv~G~Vt~i~---~~GafV~L~-~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~~gk-I~LSlk~~~   76 (136)
T PRK05807          6 GSILEGTVVNIT---NFGAFVEVE-GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGK-ISLSIKQAM   76 (136)
T ss_pred             CCEEEEEEEEEE---CCeEEEEEC-CEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECCCCc-EEEEEEecc
Confidence            567899999975   477766654 3689999999965322    4579999999887653 4564 555565543

>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide

Probab=88.96  E-value=3.6  Score=26.99  Aligned_cols=55  Identities=25%  Similarity=0.364  Sum_probs=39.6

Q ss_pred             ccceEEEEeeCCCCeeEEecCC---CCccEEEEeeccccCCc-----ccCCCCCEEEEEEeeCCCC
Q 030905            6 RSSGTVKWFSAQKGFGFIAPED---GGEDLFVHQTSIKSEGF-----RTLSEGQTVEFSVDVGEDG   63 (169)
Q Consensus         6 ~~~G~Vk~~~~~kGfGFI~~~~---~~~dvF~H~s~i~~~~~-----~~l~~G~~V~F~~~~~~kG   63 (169)
                      .+.|+|+...+   ||+...-+   .+.+-|+|+++|...-+     ..++.||.|...+...+++
T Consensus         3 ~~~g~V~~v~~---~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd~~   65 (79)
T cd05684           3 IYKGKVTSIMD---FGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQNG   65 (79)
T ss_pred             EEEEEEEEEEe---eeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEeCC
Confidence            46788888864   67666544   24789999999975432     2468999999887765555

The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.

>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain

Probab=88.91  E-value=2.8  Score=26.73  Aligned_cols=53  Identities=15%  Similarity=0.208  Sum_probs=39.2

Q ss_pred             ccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeCC
Q 030905            6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVGE   61 (169)
Q Consensus         6 ~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~~   61 (169)
                      .+.|+|+...   .+|++..-...-+-|+|++++....+    ..+++||.|++.+..-.
T Consensus         3 ~v~g~V~~v~---~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d   59 (73)
T cd05691           3 IVTGKVTEVD---AKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVD   59 (73)
T ss_pred             EEEEEEEEEE---CCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEe
Confidence            4789999985   46666654445789999999876432    34689999999987654

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A

Probab=88.88  E-value=0.25  Score=28.51  Aligned_cols=21  Identities=43%  Similarity=0.811  Sum_probs=13.3

Q ss_pred             CCccccCcCCeecccCCCCCC
Q 030905          118 GACFNCGRTGHIARECYSRGR  138 (169)
Q Consensus       118 ~~C~~Cg~~GH~a~~C~~~~~  138 (169)
                      ..|++|+...|+|.+|.+..+
T Consensus         3 ~~CprC~kg~Hwa~~C~sk~d   23 (36)
T PF14787_consen    3 GLCPRCGKGFHWASECRSKTD   23 (36)
T ss_dssp             -C-TTTSSSCS-TTT---TCC
T ss_pred             ccCcccCCCcchhhhhhhhhc
Confidence            479999999999999987654

>PRK12678 transcription termination factor Rho; Provisional

Probab=87.84  E-value=1.2  Score=41.16  Aligned_cols=66  Identities=18%  Similarity=0.434  Sum_probs=47.7

Q ss_pred             cceEEEEeeCCCCeeEEecC---CCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCC-------ce-eEEEEEcCCC
Q 030905            7 SSGTVKWFSAQKGFGFIAPE---DGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDG-------RT-KAVDVEAASR   75 (169)
Q Consensus         7 ~~G~Vk~~~~~kGfGFI~~~---~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kG-------r~-~A~~V~~~~g   75 (169)
                      +.|++--.   .+||||...   .+..||||..+.|+..+   |..|+.|+=.+.....+       |+ .-+.|..+++
T Consensus       296 ~~GiLdi~---dg~gFlR~~~y~~~~~Dvyvs~~qirr~~---Lr~Gd~v~G~vr~p~~~e~~~~r~k~~~l~~v~~vNg  369 (672)
T PRK12678        296 VAGILDVL---DNYAFVRTSGYLPGPNDVYVSMNQVRKNG---LRKGDAVTGAVRAPREGEQGNQRQKFNPLVRLDSVNG  369 (672)
T ss_pred             eeEEEEec---CCeeEeeCCCCCCCCCCeeeCHHHHHHcC---CCCCCEEEEeecCCCCCccccccceeeeeeeEeeeCC
Confidence            55666655   399999976   45689999999999875   88999999887764433       22 2356666776


Q ss_pred             ccc
Q 030905           76 SRR   78 (169)
Q Consensus        76 ~~~   78 (169)
                      .++
T Consensus       370 ~~~  372 (672)
T PRK12678        370 MSP  372 (672)
T ss_pred             CCh
Confidence            553

>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease

Probab=87.51  E-value=2.7  Score=27.73  Aligned_cols=50  Identities=16%  Similarity=0.189  Sum_probs=39.0

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG   60 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~   60 (169)
                      ...+.|+|....   -||+...-+...+-|+|.+++.    ..++.||.|...+..-
T Consensus        17 G~~~~g~V~~i~---~~G~fV~l~~~~~Glv~~se~~----~~~~iGd~v~v~I~~i   66 (77)
T cd04473          17 GKLYKGKVNGVA---KYGVFVDLNDHVRGLIHRSNLL----RDYEVGDEVIVQVTDI   66 (77)
T ss_pred             CCEEEEEEEeEe---cceEEEEECCCcEEEEEchhcc----CcCCCCCEEEEEEEEE
Confidence            456889998864   4887777655589999999985    3589999999887654

The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.

>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain

Probab=86.51  E-value=2.8  Score=26.72  Aligned_cols=53  Identities=13%  Similarity=0.016  Sum_probs=38.6

Q ss_pred             cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC----cccCCCCCEEEEEEeeC
Q 030905            5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDVG   60 (169)
Q Consensus         5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~~   60 (169)
                      ..++|+|+....  ..=||.... ..+-|+|++++....    ...+++||.|++.+..-
T Consensus         2 ~iv~g~V~~i~~--~~~~v~l~~-~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~   58 (70)
T cd05687           2 DIVKGTVVSVDD--DEVLVDIGY-KSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRV   58 (70)
T ss_pred             CEEEEEEEEEeC--CEEEEEeCC-CceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEE
Confidence            357899999865  245555543 478999999997542    13489999999998763

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain

Probab=86.43  E-value=3.1  Score=26.24  Aligned_cols=52  Identities=33%  Similarity=0.355  Sum_probs=37.8

Q ss_pred             ccceEEEEeeCCCCeeEEecCCCCccEEEEeecccc-CC----cccCCCCCEEEEEEeeC
Q 030905            6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKS-EG----FRTLSEGQTVEFSVDVG   60 (169)
Q Consensus         6 ~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~-~~----~~~l~~G~~V~F~~~~~   60 (169)
                      .+.|+|+...   -||+...-+...+-|+|+++|.. ..    ...+++||.|...+..-
T Consensus         3 ~~~g~V~~i~---~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~i   59 (69)
T cd05690           3 VVSGKIKSIT---DFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNI   59 (69)
T ss_pred             EEEEEEEEEE---eeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEE
Confidence            5788998875   48877665555899999999973 11    13468899998877653

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=86.41  E-value=3.5  Score=27.00  Aligned_cols=51  Identities=12%  Similarity=-0.007  Sum_probs=37.1

Q ss_pred             ccceEEEEeeCCCCee-EEecCCCCccEEEEeeccccCC------cccCCCCCEEEEEEeeC
Q 030905            6 RSSGTVKWFSAQKGFG-FIAPEDGGEDLFVHQTSIKSEG------FRTLSEGQTVEFSVDVG   60 (169)
Q Consensus         6 ~~~G~Vk~~~~~kGfG-FI~~~~~~~dvF~H~s~i~~~~------~~~l~~G~~V~F~~~~~   60 (169)
                      .++|+|+...   -|| ||+..+ +-+-|+|+++|....      ...+++||.|++.+..-
T Consensus         3 ~V~g~V~~i~---~~g~~V~l~~-~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~i   60 (73)
T cd05703           3 EVTGFVNNVS---KEFVWLTISP-DVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGV   60 (73)
T ss_pred             EEEEEEEEEe---CCEEEEEeCC-CcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEE
Confidence            4789999985   344 455544 479999999996431      24589999999997753

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain

Probab=85.93  E-value=2.7  Score=26.97  Aligned_cols=51  Identities=12%  Similarity=0.066  Sum_probs=37.9

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG   60 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~   60 (169)
                      ...++|+|...+.  .+=||.. +. -+-|++.+.+...  ..+++|+.|.+.+..-
T Consensus         4 g~iV~G~V~~~~~--~~~~vdi-g~-~eg~lp~~e~~~~--~~~~~Gd~v~v~v~~v   54 (67)
T cd04455           4 GEIVTGIVKRVDR--GNVIVDL-GK-VEAILPKKEQIPG--ESYRPGDRIKAYVLEV   54 (67)
T ss_pred             CCEEEEEEEEEcC--CCEEEEc-CC-eEEEeeHHHCCCC--CcCCCCCEEEEEEEEE
Confidence            4567999999976  2334444 33 6889999999754  4579999999988764

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.

>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=85.52  E-value=3.5  Score=26.50  Aligned_cols=55  Identities=18%  Similarity=0.138  Sum_probs=38.0

Q ss_pred             cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccC--C----cccCCCCCEEEEEEeeCCC
Q 030905            5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSE--G----FRTLSEGQTVEFSVDVGED   62 (169)
Q Consensus         5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~--~----~~~l~~G~~V~F~~~~~~k   62 (169)
                      ..+.|+|+.....  .=|+..+. +-+-++|++++...  .    ...+++||.|...+..-.+
T Consensus         2 ~iV~g~V~~i~~~--gi~v~l~~-~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~   62 (70)
T cd05702           2 DLVKAKVKSVKPT--QLNVQLAD-NVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHD   62 (70)
T ss_pred             CEEEEEEEEEECC--cEEEEeCC-CcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeC
Confidence            3578999998652  23444444 57999999999653  1    2447899999988765433

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain

Probab=84.54  E-value=5.1  Score=27.65  Aligned_cols=51  Identities=22%  Similarity=0.203  Sum_probs=36.7

Q ss_pred             ccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc---------------ccCCCCCEEEEEEeeC
Q 030905            6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF---------------RTLSEGQTVEFSVDVG   60 (169)
Q Consensus         6 ~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~---------------~~l~~G~~V~F~~~~~   60 (169)
                      .+.|+|+..+.   +|++..-+. .+.|+|++++....+               ..++.||.|...+..-
T Consensus         2 vv~g~V~~i~~---~GifV~l~~-v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~v   67 (99)
T cd04460           2 VVEGEVVEVVD---FGAFVRIGP-VDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAV   67 (99)
T ss_pred             EEEEEEEEEEe---ccEEEEEcC-eEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEE
Confidence            36788888864   566555443 789999999975433               3468999999988754

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.

>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=84.34  E-value=0.47  Score=40.12  Aligned_cols=20  Identities=30%  Similarity=0.966  Sum_probs=17.8

Q ss_pred             CccccCcCCeecccCCCCCC
Q 030905          119 ACFNCGRTGHIARECYSRGR  138 (169)
Q Consensus       119 ~C~~Cg~~GH~a~~C~~~~~  138 (169)
                      .||+||+.||+-++||...+
T Consensus       178 ~CyRCGqkgHwIqnCpTN~D  197 (427)
T COG5222         178 VCYRCGQKGHWIQNCPTNQD  197 (427)
T ss_pred             eEEecCCCCchhhcCCCCCC
Confidence            59999999999999997654

>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain

Probab=83.65  E-value=4.9  Score=25.83  Aligned_cols=54  Identities=13%  Similarity=0.044  Sum_probs=39.5

Q ss_pred             ccccceEEEEeeCCCCeeEEecCC--CCccEEEEeeccccCCc----ccCCCCCEEEEEEeeC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPED--GGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVG   60 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~--~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~   60 (169)
                      ...+.|+|+...   .||.+..-.  .+.+-|+|++.|...-+    ..++.||.|+..+..-
T Consensus         4 G~~~~g~V~~v~---~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~   63 (76)
T cd04452           4 GELVVVTVKSIA---DMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRV   63 (76)
T ss_pred             CCEEEEEEEEEE---ccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEE
Confidence            356789999885   488766543  23689999999976532    2478999999887754

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c

>PRK08059 general stress protein 13; Validated

Probab=83.59  E-value=11  Score=27.28  Aligned_cols=68  Identities=22%  Similarity=0.250  Sum_probs=47.1

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeC--CCCceeEEEEEcCCC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVG--EDGRTKAVDVEAASR   75 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~--~kGr~~A~~V~~~~g   75 (169)
                      ...+.|+|+...+   ||++..-....+-|+|++++...-.    ..+.+||.|...+..-  .+++ ....+..+..
T Consensus         8 G~iv~G~V~~i~~---~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~-i~lslk~~~~   81 (123)
T PRK08059          8 GSVVTGKVTGIQP---YGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGK-ISLSIRATEE   81 (123)
T ss_pred             CCEEEEEEEEEec---ceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCe-EEEEEEEccc
Confidence            4678899998764   7777765555799999999965322    3468999999988764  2453 4444554443

>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain

Probab=83.26  E-value=10  Score=24.66  Aligned_cols=54  Identities=17%  Similarity=0.263  Sum_probs=37.4

Q ss_pred             cccceEEEEeeCCCCeeEEecCCC-CccEEEEeeccccCC---------------cccCCCCCEEEEEEeeCC
Q 030905            5 QRSSGTVKWFSAQKGFGFIAPEDG-GEDLFVHQTSIKSEG---------------FRTLSEGQTVEFSVDVGE   61 (169)
Q Consensus         5 ~~~~G~Vk~~~~~kGfGFI~~~~~-~~dvF~H~s~i~~~~---------------~~~l~~G~~V~F~~~~~~   61 (169)
                      ..+.|+|+....   ||++..-.. +.+-|+|++++....               ...+++||.|.-.+....
T Consensus         3 ~~~~g~V~~v~~---~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd   72 (83)
T cd04471           3 EEFDGVISGVTS---FGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVD   72 (83)
T ss_pred             CEEEEEEEeEEe---eeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEec
Confidence            457788888854   787776553 467899999986431               135677888887776553

RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.

>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]

Probab=83.12  E-value=2.4  Score=31.32  Aligned_cols=70  Identities=21%  Similarity=0.333  Sum_probs=49.0

Q ss_pred             ccccceEEEEeeCCCCee-EEecCCCCccEEEEeeccccCC----cccCCCCCEEEEEEee-CCCCceeEEEEEcCCCcc
Q 030905            4 VQRSSGTVKWFSAQKGFG-FIAPEDGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDV-GEDGRTKAVDVEAASRSR   77 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfG-FI~~~~~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~-~~kGr~~A~~V~~~~g~~   77 (169)
                      ...++|+|+-.   +-|| |+..++ ++.=+||||.|...-    ...|.+||.|.-.+.. +.+|+ .-..|+.+..+|
T Consensus         6 G~~l~GkItgI---~~yGAFV~l~~-g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide~GK-isLSIr~~~e~p   80 (129)
T COG1098           6 GSKLKGKITGI---TPYGAFVELEG-GKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDENGK-ISLSIRKLEEEP   80 (129)
T ss_pred             cceEEEEEEee---EecceEEEecC-CCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeeccCCC-cceehHHhhhCc
Confidence            45678888865   4577 555554 478899999998642    2578999999987664 56786 556676665544


Q ss_pred             c
Q 030905           78 R   78 (169)
Q Consensus        78 ~   78 (169)
                      .
T Consensus        81 e   81 (129)
T COG1098          81 E   81 (129)
T ss_pred             c
Confidence            4

>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa

Probab=82.66  E-value=5  Score=24.80  Aligned_cols=52  Identities=21%  Similarity=0.190  Sum_probs=37.6

Q ss_pred             ccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeC
Q 030905            6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVG   60 (169)
Q Consensus         6 ~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~   60 (169)
                      .+.|+|+...+   ||....-....+-|+|.+++....+    ..+++||.|...+..-
T Consensus         3 ~~~g~V~~i~~---~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~v   58 (68)
T cd05685           3 VLEGVVTNVTD---FGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISI   58 (68)
T ss_pred             EEEEEEEEEec---ccEEEEcCCCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEE
Confidence            47889998864   6655554445789999999975422    2478999999887754

The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.

>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil

Probab=82.43  E-value=2.3  Score=27.97  Aligned_cols=29  Identities=24%  Similarity=0.456  Sum_probs=20.9

Q ss_pred             cccCCCCCEEEEEEeeCCCCceeEEEEEc
Q 030905           44 FRTLSEGQTVEFSVDVGEDGRTKAVDVEA   72 (169)
Q Consensus        44 ~~~l~~G~~V~F~~~~~~kGr~~A~~V~~   72 (169)
                      +..|++||+|.|+++....+.+.-+.|+.
T Consensus        40 l~~l~~Gd~V~F~~~~~~~~~~~I~~i~~   68 (70)
T PF11604_consen   40 LAGLKPGDKVRFTFERTDDGSYVITAIEP   68 (70)
T ss_dssp             ESS-STT-EEEEEEEEETTCEEEEEEEEE
T ss_pred             hhcCCCCCEEEEEEEECCCCcEEEEEEEE
Confidence            46799999999999998887455555543

CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.

>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]

Probab=82.39  E-value=6  Score=33.09  Aligned_cols=61  Identities=26%  Similarity=0.368  Sum_probs=45.3

Q ss_pred             cccceEEEEeeCCCCee-EEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEE
Q 030905            5 QRSSGTVKWFSAQKGFG-FIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVE   71 (169)
Q Consensus         5 ~~~~G~Vk~~~~~kGfG-FI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~   71 (169)
                      ...+..|+.++   .|| |+..+..++.|++|.+....   ..+++||.|++-|-.+.+.++.|+-..
T Consensus         7 ~~~~l~V~~~~---~~g~fL~~~~~~~~ilL~k~~~~~---~e~evGdev~vFiY~D~~~rl~aTt~~   68 (287)
T COG2996           7 QINSLEVVEFS---DFGYFLDAGEDGTTILLPKSEPEE---DELEVGDEVTVFIYVDSEDRLIATTRE   68 (287)
T ss_pred             ceEEEEEEEee---ceeEEEecCCCceEEeccccCCcC---CccccCcEEEEEEEECCCCceeheeec
Confidence            34566777765   455 44445555589999998865   468999999999999999988886544

>TIGR00767 rho transcription termination factor Rho

Probab=81.97  E-value=1.5  Score=38.63  Aligned_cols=50  Identities=26%  Similarity=0.536  Sum_probs=38.3

Q ss_pred             ccceEEEEeeCCCCeeEEecC-----CCCccEEEEeeccccCCcccCCCCCEEEEEEeeC
Q 030905            6 RSSGTVKWFSAQKGFGFIAPE-----DGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG   60 (169)
Q Consensus         6 ~~~G~Vk~~~~~kGfGFI~~~-----~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~   60 (169)
                      ...|.+--..  .||||+...     .+.+||||-.+.|+..+   |+.||.|+=.+...
T Consensus        50 ~~~g~le~~~--~g~gflr~~~~~~~~~~~d~yvs~~~i~~~~---lr~gd~v~g~~R~~  104 (415)
T TIGR00767        50 FGEGVLEILP--DGFGFLRSPDSSYLPGPDDIYVSPSQIRRFN---LRTGDTIEGQIRSP  104 (415)
T ss_pred             EEEEEEEEcC--CCCeEEeCCCcCCCCCCCCeeeCHHHHHhcC---CCCCCEEEEEEecc
Confidence            3456665443  499999985     35689999999999864   88999999776643

Members of this family differ in the specificity of RNA binding.

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=81.57  E-value=8.3  Score=34.01  Aligned_cols=71  Identities=20%  Similarity=0.193  Sum_probs=53.7

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC----------------cccCCCCCEEEEEEeeC---CCCc
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG----------------FRTLSEGQTVEFSVDVG---EDGR   64 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~----------------~~~l~~G~~V~F~~~~~---~kGr   64 (169)
                      ...+.|+|+...+.-.--||.-..+ +.-|+|++++...-                ...|++||.|..++...   .||.
T Consensus        26 GnIY~GrV~~i~p~l~aAFVdiG~~-k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke~~~~Kgp  104 (414)
T TIGR00757        26 GNIYKGRVTRILPSLQAAFVDIGLE-KNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVKEPRGNKGA  104 (414)
T ss_pred             CCEEEEEEeeecCCCceEEEEcCCC-ceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEeeCCcCCCCC
Confidence            3568999999988777899998765 78999999985310                11489999999999986   4675


Q ss_pred             eeEEEEEcCCC
Q 030905           65 TKAVDVEAASR   75 (169)
Q Consensus        65 ~~A~~V~~~~g   75 (169)
                      ....+|++++.
T Consensus       105 ~lT~~Isl~Gr  115 (414)
T TIGR00757       105 RLTTDISLPGR  115 (414)
T ss_pred             eEEEEEEeccc
Confidence            45567776653

The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.

>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain

Probab=81.30  E-value=7.3  Score=25.89  Aligned_cols=55  Identities=13%  Similarity=0.035  Sum_probs=37.9

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccC----C----cccCCCCCEEEEEEeeCC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSE----G----FRTLSEGQTVEFSVDVGE   61 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~----~----~~~l~~G~~V~F~~~~~~   61 (169)
                      ...+.|+|+...+   +|.+..-...-+-|+|+++|...    .    ...|++||.|.+.+..-.
T Consensus         7 GdiV~g~V~~i~~---~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~   69 (86)
T cd05789           7 GDVVIGRVTEVGF---KRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVD   69 (86)
T ss_pred             CCEEEEEEEEECC---CEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEEC
Confidence            3567899999643   44444334447899999999631    1    124899999999988753

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	169
3cam_A	67	Crystal Structure Of The Cold Shock Domain Protein		1e-14
3i2z_B	71	Structure Of Cold Shock Protein E From Salmonella T		2e-14
2l15_A	70	Solution Structure Of Cold Shock Protein Cspa Using		1e-13
3mef_A	69	Major Cold-Shock Protein From Escherichia Coli Solu		2e-13
1mjc_A	69	Crystal Structure Of Cspa, The Major Cold Shock Pro		2e-13
3a0j_A	73	Crystal Structure Of Cold Shock Protein 1 From Ther		8e-12
1g6p_A	66	Solution Nmr Structure Of The Cold Shock Protein Fr		1e-11
2i5l_X	67	Crystal Structure Of Bacillus Subtilis Cold Shock P		8e-11
1hz9_A	66	Bacillus Caldolyticus Cold-Shock Protein Mutants To		1e-10
1hzc_A	66	Bacillus Caldolyticus Cold-Shock Protein Mutants To		1e-10
1c9o_A	66	Crystal Structure Analysis Of The Bacillus Caldolyt		1e-10
1hza_A	67	Bacillus Caldolyticus Cold-Shock Protein Mutants To		2e-10
1i5f_A	66	Bacillus Caldolyticus Cold-Shock Protein Mutants To		2e-10
1hzb_A	66	Bacillus Caldolyticus Cold-Shock Protein Mutants To		2e-10
1h95_A	79	Solution Structure Of The Single-Stranded Dna-Bindi		2e-10
2es2_A	67	Crystal Structure Analysis Of The Bacillus Subtilis		5e-10
2i5m_X	67	Crystal Structure Of Bacillus Subtilis Cold Shock P		5e-10
2lss_A	70	Solution Structure Of The R. Rickettsii Cold Shock-		3e-09
3ulj_A	90	Crystal Structure Of Apo Lin28b Cold Shock Domain L		5e-09
4a4i_A	90	Crystal Structure Of The Human Lin28b Cold Shock Do		1e-08
3trz_A	148	Mouse Lin28a In Complex With Let-7d Microrna Pre-El		2e-07
3ts0_A	146	Mouse Lin28a In Complex With Let-7f-1 Microrna Pre-		2e-07
2bh8_A	101	Combinatorial Protein 1b11 Length = 101		2e-06

>pdb|3CAM|A Chain A, Crystal Structure Of The Cold Shock Domain Protein From Neisseria Meningitidis Length = 67

Iteration: 1
 Score = 75.5 bits (184), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 35/66 (53%), Positives = 48/66 (72%), Gaps = 1/66 (1%)
Query: 7  SSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTK 66
          ++G VKWF+  KGFGFI P++GGEDLF H ++I  EGF+TL EGQ V F V  G  G+ +
Sbjct: 2  ATGIVKWFNDAKGFGFITPDEGGEDLFAHFSAINXEGFKTLKEGQRVSFDVTTGPKGK-Q 60
Query: 67 AVDVEA 72
          A +++A
Sbjct: 61 AANIQA 66

>pdb|3I2Z|B Chain B, Structure Of Cold Shock Protein E From Salmonella Typhimurium Length = 71

Iteration: 1
 Score = 75.1 bits (183), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 33/66 (50%), Positives = 47/66 (71%)
Query: 2  AEVQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGE 61
          + + +  G VKWF+  KGFGFI PEDG +D+FVH ++I++ GF+TL+EGQ VEF +  G 
Sbjct: 1  SHMSKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGA 60
Query: 62 DGRTKA 67
           G + A
Sbjct: 61 KGPSAA 66

>pdb|2L15|A Chain A, Solution Structure Of Cold Shock Protein Cspa Using Combined Nmr And Cs-Rosetta Method Length = 70

Iteration: 1
 Score = 72.0 bits (175), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 29/58 (50%), Positives = 46/58 (79%)
Query: 6  RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDG 63
          + +G VKWF+A KGFGFI P+DG +D+FVH ++I+++G+++L EGQ V F+++ G  G
Sbjct: 4  KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKG 61

>pdb|3MEF|A Chain A, Major Cold-Shock Protein From Escherichia Coli Solution Nmr Structure Length = 69

Iteration: 1
 Score = 72.0 bits (175), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 29/58 (50%), Positives = 46/58 (79%)
Query: 6  RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDG 63
          + +G VKWF+A KGFGFI P+DG +D+FVH ++I+++G+++L EGQ V F+++ G  G
Sbjct: 3  KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKG 60

>pdb|1MJC|A Chain A, Crystal Structure Of Cspa, The Major Cold Shock Protein Of Escherichia Coli Length = 69

Iteration: 1
 Score = 72.0 bits (175), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 29/58 (50%), Positives = 46/58 (79%)
Query: 6  RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDG 63
          + +G VKWF+A KGFGFI P+DG +D+FVH ++I+++G+++L EGQ V F+++ G  G
Sbjct: 3  KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKG 60

>pdb|3A0J|A Chain A, Crystal Structure Of Cold Shock Protein 1 From Thermus Thermophilus Hb8 Length = 73

Iteration: 1
 Score = 66.2 bits (160), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 34/65 (52%), Positives = 47/65 (72%), Gaps = 2/65 (3%)
Query: 7  SSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGR-T 65
            G VKWF+A+KG+GFI  E G  D+FVH T+I ++GFRTL+EG  V F V+ G +G+  
Sbjct: 2  QKGRVKWFNAEKGYGFIERE-GDTDVFVHYTAINAKGFRTLNEGDIVTFDVEPGRNGKGP 60
Query: 66 KAVDV 70
          +AV+V
Sbjct: 61 QAVNV 65

>pdb|1G6P|A Chain A, Solution Nmr Structure Of The Cold Shock Protein From The Hyperthermophilic Bacterium Thermotoga Maritima Length = 66

Iteration: 1
 Score = 65.9 bits (159), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 31/59 (52%), Positives = 43/59 (72%), Gaps = 1/59 (1%)
Query: 9  GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKA 67
          G VKWF ++KG+GFI  ++GG D+FVH ++I+ EGF+TL EGQ VEF +  G+ G   A
Sbjct: 3  GKVKWFDSKKGYGFITKDEGG-DVFVHWSAIEMEGFKTLKEGQVVEFEIQEGKKGPQAA 60

>pdb|2I5L|X Chain X, Crystal Structure Of Bacillus Subtilis Cold Shock Protein Variant Bs-Cspb M1rE3KK65I Length = 67

Iteration: 1
 Score = 63.2 bits (152), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 35/68 (51%), Positives = 46/68 (67%), Gaps = 2/68 (2%)
Query: 6  RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRT 65
          R  G VKWF+++KGFGFI  E G +D+FVH ++I+ EGF+TL EGQ V F +  G  G  
Sbjct: 1  RLKGKVKWFNSEKGFGFIEVE-GQDDVFVHFSAIQGEGFKTLEEGQAVSFEIVEGNRGPQ 59
Query: 66 KA-VDVEA 72
           A V +EA
Sbjct: 60 AANVTIEA 67

>pdb|1HZ9|A Chain A, Bacillus Caldolyticus Cold-Shock Protein Mutants To Study Determinants Of Protein Stability Length = 66

Iteration: 1
 Score = 62.4 bits (150), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 32/59 (54%), Positives = 40/59 (67%), Gaps = 1/59 (1%)
Query: 9  GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKA 67
          G VKWF+ +KG+GFI  E GG D+FVH T+I+ EGF+TL EGQ V F +  G  G   A
Sbjct: 4  GKVKWFNNEKGYGFIEVE-GGSDVFVHFTAIQGEGFKTLEEGQAVSFEIVQGNRGPQAA 61

>pdb|1HZC|A Chain A, Bacillus Caldolyticus Cold-Shock Protein Mutants To Study Determinants Of Protein Stability Length = 66

Iteration: 1
 Score = 62.4 bits (150), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 32/59 (54%), Positives = 40/59 (67%), Gaps = 1/59 (1%)
Query: 9  GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKA 67
          G VKWF+ +KG+GFI  E GG D+FVH T+I+ EGF+TL EGQ V F +  G  G   A
Sbjct: 4  GKVKWFNNEKGYGFIEVE-GGSDVFVHFTAIQGEGFKTLEEGQAVSFEIVQGNRGPQAA 61

>pdb|1C9O|A Chain A, Crystal Structure Analysis Of The Bacillus Caldolyticus Cold Shock Protein Bc-Csp Length = 66

Iteration: 1
 Score = 62.0 bits (149), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 32/59 (54%), Positives = 40/59 (67%), Gaps = 1/59 (1%)
Query: 9  GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKA 67
          G VKWF+ +KG+GFI  E GG D+FVH T+I+ EGF+TL EGQ V F +  G  G   A
Sbjct: 4  GKVKWFNNEKGYGFIEVE-GGSDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGNRGPQAA 61

>pdb|1HZA|A Chain A, Bacillus Caldolyticus Cold-Shock Protein Mutants To Study Determinants Of Protein Stability Length = 67

Iteration: 1
 Score = 62.0 bits (149), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 32/59 (54%), Positives = 40/59 (67%), Gaps = 1/59 (1%)
Query: 9  GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKA 67
          G VKWF+ +KG+GFI  E GG D+FVH T+I+ EGF+TL EGQ V F +  G  G   A
Sbjct: 4  GKVKWFNNEKGYGFIEVE-GGSDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGNRGPQAA 61

>pdb|1I5F|A Chain A, Bacillus Caldolyticus Cold-Shock Protein Mutants To Study Determinants Of Protein Stability Length = 66

Iteration: 1
 Score = 62.0 bits (149), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 32/59 (54%), Positives = 40/59 (67%), Gaps = 1/59 (1%)
Query: 9  GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKA 67
          G VKWF+ +KG+GFI  E GG D+FVH T+I+ EGF+TL EGQ V F +  G  G   A
Sbjct: 4  GKVKWFNNEKGYGFIEVE-GGSDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGNRGPQAA 61

>pdb|1HZB|A Chain A, Bacillus Caldolyticus Cold-Shock Protein Mutants To Study Determinants Of Protein Stability Length = 66

Iteration: 1
 Score = 62.0 bits (149), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 32/59 (54%), Positives = 40/59 (67%), Gaps = 1/59 (1%)
Query: 9  GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKA 67
          G VKWF+ +KG+GFI  E GG D+FVH T+I+ EGF+TL EGQ V F +  G  G   A
Sbjct: 4  GKVKWFNNEKGYGFIEVE-GGSDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGNRGPQAA 61

>pdb|1H95|A Chain A, Solution Structure Of The Single-Stranded Dna-Binding Cold Shock Domain (Csd) Of Human Y-Box Protein 1 (Yb1) Determined By Nmr (10 Lowest Energy Structures) Length = 79

Iteration: 1
 Score = 61.6 bits (148), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 30/59 (50%), Positives = 39/59 (66%), Gaps = 4/59 (6%)
Query: 9  GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDVGEDG 63
          GTVKWF+ + G+GFI   D  ED+FVHQT+IK        R++ +G+TVEF V  GE G
Sbjct: 11 GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKG 69

>pdb|2ES2|A Chain A, Crystal Structure Analysis Of The Bacillus Subtilis Cold Shock Protein Bs-Cspb In Complex With Hexathymidine Length = 67

Iteration: 1
 Score = 60.5 bits (145), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 31/59 (52%), Positives = 41/59 (69%), Gaps = 1/59 (1%)
Query: 9  GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKA 67
          G VKWF+++KGFGFI  E G +D+FVH ++I+ EGF+TL EGQ V F +  G  G   A
Sbjct: 4  GKVKWFNSEKGFGFIEVE-GQDDVFVHFSAIQGEGFKTLEEGQAVSFEIVEGNRGPQAA 61

>pdb|2I5M|X Chain X, Crystal Structure Of Bacillus Subtilis Cold Shock Protein Cspb Variant A46k S48r Length = 67

Iteration: 1
 Score = 60.1 bits (144), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 31/59 (52%), Positives = 41/59 (69%), Gaps = 1/59 (1%)
Query: 9  GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKA 67
          G VKWF+++KGFGFI  E G +D+FVH ++I+ EGF+TL EGQ V F +  G  G   A
Sbjct: 4  GKVKWFNSEKGFGFIEVE-GQDDVFVHFSAIQGEGFKTLEEGQKVRFEIVEGNRGPQAA 61

>pdb|2LSS|A Chain A, Solution Structure Of The R. Rickettsii Cold Shock-like Protein Length = 70

Iteration: 1
 Score = 57.8 bits (138), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 25/62 (40%), Positives = 44/62 (70%), Gaps = 1/62 (1%)
Query: 9  GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAV 68
          G VKW+++ K FGFI  ++GG+D+FVH++++ + G  +L EGQ V F ++  + G+  AV
Sbjct: 7  GKVKWYNSTKNFGFIEQDNGGKDVFVHKSAVDAAGLHSLEEGQDVIFDLE-EKQGKAYAV 65
Query: 69 DV 70
          ++
Sbjct: 66 NL 67

>pdb|3ULJ|A Chain A, Crystal Structure Of Apo Lin28b Cold Shock Domain Length = 90

Iteration: 1
 Score = 57.0 bits (136), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 29/69 (42%), Positives = 40/69 (57%), Gaps = 7/69 (10%)
Query: 2  AEVQRSSGTVKWFSAQKGFGFIA-------PEDGGEDLFVHQTSIKSEGFRTLSEGQTVE 54
           +V R SG  KWF+ + GFGFI+       P +   D+FVHQ+ +  EGFR+L EG+ VE
Sbjct: 4  PQVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVE 63
Query: 55 FSVDVGEDG 63
          F+      G
Sbjct: 64 FTFKKSSKG 72

>pdb|4A4I|A Chain A, Crystal Structure Of The Human Lin28b Cold Shock Domain Length = 90

Iteration: 1
 Score = 55.8 bits (133), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 28/62 (45%), Positives = 40/62 (64%), Gaps = 7/62 (11%)
Query: 2  AEVQRSSGTVKWFSAQKGFGFIA-------PEDGGEDLFVHQTSIKSEGFRTLSEGQTVE 54
          ++V R +G  KWF+ + GFGFI+       P D   D+FVHQ+ +  EGFR+L EG+ VE
Sbjct: 4  SQVLRGTGHCKWFNVRMGFGFISMINREGSPLDIPVDVFVHQSKLFMEGFRSLKEGEPVE 63
Query: 55 FS 56
          F+
Sbjct: 64 FT 65

>pdb|3TRZ|A Chain A, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element Length = 148

Iteration: 1
 Score = 51.6 bits (122), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 24/62 (38%), Positives = 37/62 (59%), Gaps = 7/62 (11%)
Query: 2  AEVQRSSGTVKWFSAQKGFGFIAPE-------DGGEDLFVHQTSIKSEGFRTLSEGQTVE 54
           ++   +G  KWF+ + GFGF++         D   D+FVHQ+ +  EGFR+L EG+ VE
Sbjct: 5  PQLLHGAGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEGFRSLKEGEAVE 64
Query: 55 FS 56
          F+
Sbjct: 65 FT 66

>pdb|3TS0|A Chain A, Mouse Lin28a In Complex With Let-7f-1 Microrna Pre-Element Length = 146

Iteration: 1
 Score = 51.6 bits (122), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 24/62 (38%), Positives = 37/62 (59%), Gaps = 7/62 (11%)
Query: 2  AEVQRSSGTVKWFSAQKGFGFIAPE-------DGGEDLFVHQTSIKSEGFRTLSEGQTVE 54
           ++   +G  KWF+ + GFGF++         D   D+FVHQ+ +  EGFR+L EG+ VE
Sbjct: 3  PQLLHGAGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEGFRSLKEGEAVE 62
Query: 55 FS 56
          F+
Sbjct: 63 FT 64

>pdb|2BH8|A Chain A, Combinatorial Protein 1b11 Length = 101

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 19/30 (63%), Positives = 25/30 (83%)
Query: 6  RSSGTVKWFSAQKGFGFIAPEDGGEDLFVH 35
          + +G VKWF+A KGFGFI P+DG +D+FVH
Sbjct: 16 KMTGIVKWFNADKGFGFITPDDGSKDVFVH 45

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	169
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	100.0
3ulj_A	90	LIN28B, DNA-binding protein; beta barrel, cold sho	99.95
3cam_A	67	Cold-shock domain family protein; cold shock prote	99.94
3i2z_B	71	RNA chaperone, negative regulator of CSPA transcri	99.94
1h95_A	79	CSD, Y-box binding protein; translation factor, tr	99.93
1c9o_A	66	CSPB, cold-shock protein; beta barrel, homodimer,	99.93
3a0j_A	73	Cold shock protein; OB-fold, cytoplasm, transcript	99.93
1g6p_A	66	Cold shock protein TMCSP; greek-KEY, beta barrel,	99.92
2kcm_A	74	Cold shock domain family protein; nucleic acid bin	99.92
2lss_A	70	Cold shock-like protein; CSD, CSP, oligonucleotide	99.87
2k5n_A	74	Putative cold-shock protein; GFT protein structure	99.92
1wfq_A	89	UNR protein; beta-barrel, translational regulation	99.92
2yty_A	88	Cold shock domain-containing protein E1; cell-free	99.9
3aqq_A	147	Calcium-regulated heat stable protein 1; compact b	99.87
1x65_A	89	UNR protein; cell-free protein synthesis, beta-bar	99.87
2ytx_A	97	Cold shock domain-containing protein E1; cell-free	99.87
2ytv_A	79	Cold shock domain-containing protein E1; cell-free	99.85
2bh8_A	101	1B11; transcription, molecular evolution, unique a	99.72
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	99.47
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	99.45
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	99.44
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	99.42
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	99.42
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	99.39
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	99.38
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	99.35
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	99.03
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	98.98
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	98.85
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	98.73
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	98.53
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	98.44
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	98.19
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	98.19
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	98.11
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	98.06
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	97.89
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	97.83
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	97.69
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	97.68
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	97.61
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	97.59
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	97.58
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	97.57
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	97.55
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	97.55
1a62_A	130	RHO; transcription termination, termination, RNA b	97.31
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	97.25
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	96.46
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	94.79
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	94.79
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	94.66
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	93.97
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	93.15
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	92.88
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	92.8
3l0o_A	427	Transcription termination factor RHO; helicase, RH	91.97
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	91.97
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	91.56
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	91.07
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	90.05
2qcp_X	80	Cation efflux system protein CUSF; silver-binding,	89.84
2l55_A	82	SILB,silver efflux protein, MFP component of the c	89.79
2vb2_X	88	Copper protein, cation efflux system protein CUSF;	89.67
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	88.84
3ice_A	422	Transcription termination factor RHO; transcriptio	87.36
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	87.11
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	84.52
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	83.9
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	82.94
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	82.49
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	81.93
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	81.67
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	80.47

>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A*

Probab=100.00  E-value=7.3e-42  Score=258.28  Aligned_cols=126  Identities=33%  Similarity=0.679  Sum_probs=112.2

Q ss_pred             cccccceEEEEeeCCCCeeEEecC-------CCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcCCC
Q 030905            3 EVQRSSGTVKWFSAQKGFGFIAPE-------DGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAASR   75 (169)
Q Consensus         3 ~~~~~~G~Vk~~~~~kGfGFI~~~-------~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~~g   75 (169)
                      +.++++|+|||||.+||||||+++       ++++|||||+|+|...+|++|.+|++|+|+++++++| ++|++|+.+++
T Consensus         6 ~l~~~~G~Vkwfn~~kGfGFI~~~~~~g~p~~~g~DvFvH~s~i~~~g~~~l~eG~~V~f~~~~g~kG-~~A~~V~~pgg   84 (148)
T 3ts2_A            6 QLLHGAGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEGFRSLKEGEAVEFTFKKSAKG-LESIRVTGPGG   84 (148)
T ss_dssp             CCEEEEEEEEEEETTTTEEEEEEEEETTEEEEEEEEEEEEGGGBCSSSSCCCCTTCEEEEEEEEETTE-EEEEEEESGGG
T ss_pred             ccccceeEEEEEECCCCeeEEeeCccccccCCCCccEEEEhHHhcccCCccCCCCCEEEEEEEEcccc-chhhcccccCC
Confidence            467899999999999999999987       3678999999999999999999999999999999999 89999999999


Q ss_pred             ccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcCCeecccCCCCCCCCCCCCCCCCCCccccc
Q 030905           76 SRRFGSRGGRSGGFYGGRGRGGGYGRGGRGGRSVGSGGGAGSGACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYN  155 (169)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~g~~~gg~~~~~~~C~~Cg~~GH~a~~C~~~~~~~~~~~~g~~~~~~C~~  155 (169)
                      .+++++.+.+                             .....||+|++.||+|++||.+..           ...||+
T Consensus        85 ~pv~GS~rrp-----------------------------~~~~~C~~Cg~~GH~a~~C~~~~~-----------~~~C~~  124 (148)
T 3ts2_A           85 VFCIGSERRP-----------------------------KGGDRCYNCGGLDHHAKECKLPPQ-----------PKKCHF  124 (148)
T ss_dssp             CCCCCCTTSC-----------------------------CCSCCCTTTCCSSCCGGGCCSCCC-----------CCCCTT
T ss_pred             cccccccccc-----------------------------CCCCcccEeCCccchhhhCCCCCC-----------CCcccc
Confidence            9998776422                             124589999999999999998542           578999


Q ss_pred             cCCCCccCCCCCCC
Q 030905          156 CGEEGHFARDCPNY  169 (169)
Q Consensus       156 Cg~~GH~ardCp~~  169 (169)
                      |+++||+++|||++
T Consensus       125 Cg~~GH~~r~Cp~~  138 (148)
T 3ts2_A          125 CQSINHMVASCPLK  138 (148)
T ss_dssp             TCCSSCCGGGCTTT
T ss_pred             cCCcCCEeccCcCC
Confidence            99999999999974

>3ulj_A LIN28B, DNA-binding protein; beta barrel, cold shock domain fold, nucleic acid binding, D binding protein; 1.06A {Silurana} PDB: 4a4i_A

Probab=99.95  E-value=2.3e-28  Score=169.69  Aligned_cols=78  Identities=40%  Similarity=0.763  Sum_probs=72.2

Q ss_pred             ccccceEEEEeeCCCCeeEEe-------cCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcCCCc
Q 030905            4 VQRSSGTVKWFSAQKGFGFIA-------PEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAASRS   76 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~-------~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~~g~   76 (169)
                      .+|.+|+|||||..||||||+       ++++++|||||+|+|+..+|++|.+||+|+|+++++++| ++|+||+.+++.
T Consensus         6 ~~r~tG~VKWFn~~KGfGFI~~~~~~~~p~dgg~DvFVH~s~i~~~g~~~L~eG~~V~f~v~~g~kG-~~A~~Vtg~~G~   84 (90)
T 3ulj_A            6 VLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEFTFKKSSKG-FESLRVTGPGGN   84 (90)
T ss_dssp             CEEEEEEEEEEETTTTEEEEEEEEETTEEEEEEEEEEEEGGGBCCSSSCCCCTTCEEEEEEEEETTE-EEEEEEECGGGC
T ss_pred             ccccceEEEEeeCCCCeEEeEecCcCcCCCCCCccEEEEeehhcccCCCccCCCCEEEEEEEECCCC-cEEEEEECCCCc
Confidence            578899999999999999998       456678999999999999999999999999999999999 799999999999


Q ss_pred             cccCCC
Q 030905           77 RRFGSR   82 (169)
Q Consensus        77 ~~~~~~   82 (169)
                      |++++.
T Consensus        85 p~~gse   90 (90)
T 3ulj_A           85 PCLGNE   90 (90)
T ss_dssp             CCCCCC
T ss_pred             cccCCC
Confidence            998763

>3cam_A Cold-shock domain family protein; cold shock protein, chain SWAP, STRU genomics, oxford protein production facility, OPPF, gene RE; 2.60A {Neisseria meningitidis MC58}

Probab=99.94  E-value=9.9e-27  Score=153.46  Aligned_cols=67  Identities=54%  Similarity=1.033  Sum_probs=63.0

Q ss_pred             ccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcC
Q 030905            6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAA   73 (169)
Q Consensus         6 ~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~   73 (169)
                      |.+|+|||||.+||||||+++++++|||||+|+|+..+++.|.+||+|+|+++++++| ++|++|+++
T Consensus         1 m~~G~Vk~fn~~kGfGFI~~~~gg~dvFvH~s~i~~~g~~~l~~G~~V~f~~~~~~kG-~~A~~V~~~   67 (67)
T 3cam_A            1 MATGIVKWFNDAKGFGFITPDEGGEDLFAHFSAINMEGFKTLKEGQRVSFDVTTGPKG-KQAANIQAA   67 (67)
T ss_dssp             CEEEEEEEEETTTTEEEEEETTSCCCEEEEGGGBCGGGGSSCCTTCEEEEEEEEETTE-EEEEEEEEC
T ss_pred             CCCEEEEEEECCCCeEEEecCCCCccEEEEHHHccccCCCCCCCCCEEEEEEEECCCC-ccceEEEeC
Confidence            4589999999999999999999889999999999999999999999999999999999 699999863

>3i2z_B RNA chaperone, negative regulator of CSPA transcription; beta barrel, DNA binding protein/transcription, cytoplasm, gene regulation; 1.10A {Salmonella typhimurium} SCOP: b.40.4.5 PDB: 2l15_A 1mjc_A 3mef_A

Probab=99.94  E-value=1.5e-26  Score=154.17  Aligned_cols=69  Identities=51%  Similarity=0.982  Sum_probs=64.2

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAA   73 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~   73 (169)
                      |++++|+|||||.+||||||+++++++|||||+|+|...+++.|.+||+|+|+++++++| ++|++|+++
T Consensus         3 m~~~~G~Vk~fn~~kGfGFI~~~~g~~dvFvH~s~i~~~g~~~l~~G~~V~f~~~~~~kG-~~A~~V~~~   71 (71)
T 3i2z_B            3 MSKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKG-PSAANVTAL   71 (71)
T ss_dssp             --CEEEEEEEEETTTTEEEEEETTCCCCEEEEGGGBCCSSCCCCCTTCEEEEEEEEETTE-EEEEEEEEC
T ss_pred             cccccEEEEEEECCCCcEEEecCCCCccEEEEhHHcccccCcCCCCCCEEEEEEEECCCC-CEeEEEEeC
Confidence            468999999999999999999999989999999999999999999999999999999999 899999864

>1h95_A CSD, Y-box binding protein; translation factor, transcription factor, OB-fold, 5- stranded anti-parallel beta-barrel, single stranded DNA binding; NMR {Homo sapiens} SCOP: b.40.4.5

Probab=99.93  E-value=1.4e-26  Score=157.36  Aligned_cols=70  Identities=46%  Similarity=0.827  Sum_probs=64.7

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccC----CcccCCCCCEEEEEEeeCCCCceeEEEEEcCC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSE----GFRTLSEGQTVEFSVDVGEDGRTKAVDVEAAS   74 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~----~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~~   74 (169)
                      +++.+|+|||||.+||||||+++++++|||||+|+|+..    ++++|.+||+|+|+++++++| ++|++|+.++
T Consensus         6 ~~~~~G~Vkwfn~~kGfGFI~~~~gg~DvFvH~s~i~~~~~~~g~~~l~~G~~V~f~~~~~~kG-~~A~~V~~p~   79 (79)
T 1h95_A            6 ATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKG-AEAANVTGPG   79 (79)
T ss_dssp             EEEEEEEEEEEETTTTEEEEEEGGGTEEEEEEGGGBCSCCCSCCSCSCCSSCEEEEEEEECSSS-EEEESBCCCC
T ss_pred             ccccceEEEEEECCCCcEEEecCCCCccEEEEhHHccccccccccccCCCCCEEEEEEEECCCC-ceeEEEECcC
Confidence            467899999999999999999999889999999999976    689999999999999999999 6999998764

>1c9o_A CSPB, cold-shock protein; beta barrel, homodimer, transcription; 1.17A {Bacillus caldolyticus} SCOP: b.40.4.5 PDB: 2hax_A 1hz9_A 1hzb_A 1i5f_A 1hza_A 1hzc_A 3pf4_A 1csq_A 1nmf_A 1nmg_A 1csp_A 2f52_A 2es2_A 3pf5_A 2i5m_X 2i5l_X

Probab=99.93  E-value=3.8e-26  Score=150.25  Aligned_cols=66  Identities=48%  Similarity=0.883  Sum_probs=62.4

Q ss_pred             ccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcC
Q 030905            6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAA   73 (169)
Q Consensus         6 ~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~   73 (169)
                      |.+|+|||||.+||||||+++++ +|||||+|+|+..++++|.+||+|+|+++++++| ++|++|+++
T Consensus         1 m~~G~Vk~fn~~kGfGFI~~~~g-~dvFvH~s~i~~~g~~~l~~G~~V~f~~~~~~kG-~~A~~V~~~   66 (66)
T 1c9o_A            1 MQRGKVKWFNNEKGYGFIEVEGG-SDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGNRG-PQAANVVKL   66 (66)
T ss_dssp             CEEEEEEEEETTTTEEEEEETTE-EEEEEEGGGBCSSSCCCCCTTCEEEEEEEEETTE-EEEEEEEEC
T ss_pred             CCceEEEEEECCCCeEEEecCCC-ccEEEEHHHccccCCCCCCCCCEEEEEEEECCCC-cEeEEEEeC
Confidence            46899999999999999999998 9999999999999999999999999999999999 899999864

>3a0j_A Cold shock protein; OB-fold, cytoplasm, transcription, structural genomics, NPPSFA; 1.65A {Thermus thermophilus}

Probab=99.93  E-value=6.8e-26  Score=151.82  Aligned_cols=68  Identities=49%  Similarity=0.896  Sum_probs=63.6

Q ss_pred             ccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCC--CCceeEEEEEcCCC
Q 030905            6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGE--DGRTKAVDVEAASR   75 (169)
Q Consensus         6 ~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~--kGr~~A~~V~~~~g   75 (169)
                      |.+|+|||||.+||||||+++++ +|||||+|+|+..+++.|.+||+|+|++++++  +| ++|++|++++.
T Consensus         1 m~~G~Vk~fn~~kGfGFI~~~~g-~dvFvH~s~i~~~g~~~l~~G~~V~f~~~~~~~~kG-~~A~~V~~~~~   70 (73)
T 3a0j_A            1 MQKGRVKWFNAEKGYGFIEREGD-TDVFVHYTAINAKGFRTLNEGDIVTFDVEPGRNGKG-PQAVNVTVVEP   70 (73)
T ss_dssp             CEEEEEEEEETTTTEEEEECTTS-CCEEEEGGGBCSSSCSSCCTTCEEEEEEECCSCCSS-SEEEEEEEEEC
T ss_pred             CCCEEEEEEECCCCEEEEecCCC-CcEEEEhhhccccCCCCCCCCCEEEEEEEECCCCCC-CEEEEEEeCCC
Confidence            45899999999999999999987 99999999999999999999999999999998  88 79999998753

>1g6p_A Cold shock protein TMCSP; greek-KEY, beta barrel, OB-fold, structural genomics; NMR {Thermotoga maritima} SCOP: b.40.4.5

Probab=99.92  E-value=9.8e-26  Score=148.27  Aligned_cols=66  Identities=47%  Similarity=0.941  Sum_probs=62.2

Q ss_pred             cceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcCC
Q 030905            7 SSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAAS   74 (169)
Q Consensus         7 ~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~~   74 (169)
                      |+|+|||||.+||||||+++++ +|||||+|+|+..+++.|.+||+|+|+++++++| ++|++|++++
T Consensus         1 m~G~Vk~fn~~kGfGFI~~~~g-~dvFvH~s~i~~~g~~~l~~G~~V~f~~~~~~~G-~~A~~V~~~~   66 (66)
T 1g6p_A            1 MRGKVKWFDSKKGYGFITKDEG-GDVFVHWSAIEMEGFKTLKEGQVVEFEIQEGKKG-PQAAHVKVVE   66 (66)
T ss_dssp             CCEEEEEEETTTTEEEEEETTS-CBCBBCSSSSCCSSCCCCCSSSEEEEEEECSSSC-CEEEEEEEEC
T ss_pred             CcEEEEEEECCCCEEEEecCCC-ceEEEEhHHccccCCCCCCCCCEEEEEEEECCCC-CEEEEEEECC
Confidence            5799999999999999999976 8999999999999999999999999999999999 8999998753

>2kcm_A Cold shock domain family protein; nucleic acid binding protein, beta barrel, structural genomi 2, protein structure initiative; NMR {Shewanella oneidensis}

Probab=99.92  E-value=1.1e-25  Score=151.12  Aligned_cols=67  Identities=27%  Similarity=0.421  Sum_probs=63.2

Q ss_pred             cceEEEEeeCCCCeeEEecCCCCccEEEEeeccc-cCCcccCCCCCEEEEEEeeCCCCceeEEEEEcCCC
Q 030905            7 SSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIK-SEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAASR   75 (169)
Q Consensus         7 ~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~-~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~~g   75 (169)
                      ++|+|||||.+||||||+++++ +|||||+|+|+ ..+|+.|.+||+|+|+++++++| ++|++|++++.
T Consensus         1 ~~G~Vkwfn~~KGfGFI~~~dG-~DvFvH~s~i~~~~g~~~l~~G~~V~F~~~~g~kG-~~A~~V~~~~~   68 (74)
T 2kcm_A            1 MKGKVVSYLAAKKYGFIQGDDG-ESYFLHFSELLDKKDEGKLVKGSMVHFDPTPTPKG-LAAKAISLPLE   68 (74)
T ss_dssp             CEEEEEEEETTTTEEEEEETTS-CEECCCGGGSSCSGGGTTCCTTSEEEEEEECTTTS-CEEEEEECCSC
T ss_pred             CCEEEEEEECCCCEEEEecCCC-ceEEEEhhhcccCCCCCCCCCCCEEEEEEEECCCC-ceeEEEEEcCc
Confidence            5799999999999999999998 99999999999 88899999999999999999999 69999998763

>2lss_A Cold shock-like protein; CSD, CSP, oligonucleotide binding F fold, RNA binding protein, DNA binding protein; NMR {Rickettsia rickettsii}

Probab=99.87  E-value=4e-27  Score=156.63  Aligned_cols=69  Identities=38%  Similarity=0.792  Sum_probs=65.0

Q ss_pred             CCcccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEc
Q 030905            1 MAEVQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEA   72 (169)
Q Consensus         1 M~~~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~   72 (169)
                      |+  ++++|+|||||.+||||||+++++++|||||+|+|+..+++.|.+||+|+|+++++++| ++|++|++
T Consensus         1 m~--~~~~G~Vk~fn~~kGfGFI~~~~gg~dvFvH~s~i~~~g~~~l~~G~~V~f~~~~~~~g-~~A~~V~~   69 (70)
T 2lss_A            1 MA--TNIVGKVKWYNSTKNFGFIEQDNGGKDVFVHKSAVDAAGLHSLEEGQDVIFDLEEKQGK-AYAVNLRI   69 (70)
Confidence            66  78999999999999999999999889999999999999999999999999999999998 79999974

>2k5n_A Putative cold-shock protein; GFT protein structure, PSI, nesgc, OB fold, cold shock structural genomics; NMR {Pectobacterium atrosepticum}

Probab=99.92  E-value=3.8e-25  Score=148.45  Aligned_cols=67  Identities=24%  Similarity=0.449  Sum_probs=62.3

Q ss_pred             cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcCCC
Q 030905            5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAASR   75 (169)
Q Consensus         5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~~g   75 (169)
                      ||++|+|||||.+||||||+++++.+| |||+|+|+..+  .|.+||+|+|+++++++| ++|++|+++..
T Consensus         1 M~~~G~Vkwfn~~KGfGFI~~~dg~~d-FvH~s~i~~~g--~l~~G~~V~F~~~~g~kG-~~A~~V~~~~~   67 (74)
T 2k5n_A            1 MAMNGTITTWFKDKGFGFIKDENGDNR-YFHVIKVANPD--LIKKDAAVTFEPTTNNKG-LSAYAVKVVPL   67 (74)
T ss_dssp             CCEEEEEEEEETTTTEEEEEESSSCEE-EEEGGGBSSGG--GCCTTCEEEEEEEECSSS-EEEEEEEECCS
T ss_pred             CCcceEEEEEECCCCeEEEecCCCCce-EEEHhHcccCC--CCCCCCEEEEEEEeCCCC-ceeEEEEeCCC
Confidence            568999999999999999999998777 99999999886  799999999999999999 89999998764

>1wfq_A UNR protein; beta-barrel, translational regulation, RNA chaperone, RNA/DN binding, QB fold, greek-KEY topology, structur genomics; NMR {Homo sapiens} SCOP: b.40.4.5

Probab=99.92  E-value=3.4e-25  Score=153.63  Aligned_cols=69  Identities=26%  Similarity=0.458  Sum_probs=64.1

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCC-CceeEEEEEcCCC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGED-GRTKAVDVEAASR   75 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~k-Gr~~A~~V~~~~g   75 (169)
                      .++++|+|||||  ||||||+++++++|||||+++|+.. ++.|.+||+|+|+++++++ ||++|++|++++.
T Consensus        16 ~~~~~G~Vkwf~--KGfGFI~~ddgg~DVFvH~s~i~~~-~~~L~~G~~V~F~v~~~~k~Gk~~A~~V~~~~~   85 (89)
T 1wfq_A           16 ALRETGVIEKLL--TSYGFIQCSERQARLFFHCSQYNGN-LQDLKVGDDVEFEVSSDRRTGKPIAVKLVKISG   85 (89)
T ss_dssp             CCEEEEEEEEEC--SSEEEEEETTTTEEEEEETTTCSSC-TTTCCTTCCEEEEEEECSSSCCEEEEEEEESSC
T ss_pred             ccccceEEEEEe--CCeeEEecCCCCccEEEEhHHhhCc-cCCCCCCCEEEEEEEECCCCCCcEEEEEEECCc
Confidence            478899999996  9999999999889999999999987 7899999999999999998 8889999998854

>2yty_A Cold shock domain-containing protein E1; cell-free protein synthesis, beta-barrel, translational REGU RNA chaperone, RNA/DNA binding, QB fold; NMR {Homo sapiens}

Probab=99.90  E-value=3.6e-24  Score=148.17  Aligned_cols=69  Identities=26%  Similarity=0.485  Sum_probs=64.1

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcCCC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAASR   75 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~~g   75 (169)
                      .++++|+||||+  ||||||+++++++|||||+|+|+.. ++.|.+||+|+|+++++++|+++|++|++++.
T Consensus        16 ~~~~~G~Vk~f~--kGfGFI~~ddgg~DvFvH~S~i~~~-~~~L~~G~~V~F~~~~g~~Gk~~A~~V~~~~~   84 (88)
T 2yty_A           16 SKRLLGYVATLK--DNFGFIETANHDKEIFFHYSEFSGD-VDSLELGDMVEYSLSKGKGNKVSAEKVNKTSG   84 (88)
T ss_dssp             CCCEEEEEEEEC--SSEEEEECSSSSCEEEEETTTCCSC-TTTCCTTCEEEECCCCCSCSCCBCCSCEECCC
T ss_pred             CCceeEEEEEEE--CCccEEecCCCCceEEEEEhhhccc-cCcCCCCCEEEEEEEECCCCCeEeEEEEECCC
Confidence            578899999998  8999999999889999999999987 78999999999999999999889999998753

>3aqq_A Calcium-regulated heat stable protein 1; compact beta-barrel, cold shock domain, ssDNA binding, DNA B protein; 2.80A {Homo sapiens}

Probab=99.87  E-value=2.5e-22  Score=150.63  Aligned_cols=72  Identities=31%  Similarity=0.503  Sum_probs=63.6

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeC---CCCceeEEEEEcCCCccc
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG---EDGRTKAVDVEAASRSRR   78 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~---~kGr~~A~~V~~~~g~~~   78 (169)
                      .+|++|+|||||.+||||||+++++++|||||+++|+..  ..|.+||+|+|+++++   .+| ++|++|++++..+.
T Consensus        60 g~m~~GtVKwFn~~KGfGFI~~ddGg~DVFVH~Sai~~~--~~L~eGq~V~Fev~~~~~~~~g-~qA~nV~~~~~~p~  134 (147)
T 3aqq_A           60 GPVYKGVCKCFCRSKGHGFITPADGGPDIFLHISDVEGE--YVPVEGDEVTYKMCSIPPKNEK-LQAVEVVITHLAPG  134 (147)
T ss_dssp             SCCEEEEEEEEETTTTEEEEEESSSCSCEEEEGGGEESS--BCCCTTCEEEEEEEEC--CCSC-EEEEEEEEEECCSS
T ss_pred             CCccceEEEEEeCCCCeEEeccCCCCccEEEEeeeecCC--CcCCCCCEEEEEEEeccCCCCC-ceEEEEEeCCCCCC
Confidence            478899999999999999999999889999999999865  4899999999999874   344 89999999876553

>1x65_A UNR protein; cell-free protein synthesis, beta-barrel, translational REGU RNA chaperone, RNA/DNA binding, QB fold, greek-KEY topology protein; NMR {Homo sapiens}

Probab=99.87  E-value=1.6e-23  Score=145.07  Aligned_cols=69  Identities=28%  Similarity=0.425  Sum_probs=62.4

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCC--CceeEEEEEcCCCc
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGED--GRTKAVDVEAASRS   76 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~k--Gr~~A~~V~~~~g~   76 (169)
                      .++++|+||||+  ||||||+++++++|||||+|+|.. + +.|.+||+|+|+++++++  |+++|++|+++...
T Consensus         6 ~~r~~G~Vk~f~--KGfGFI~~~~gg~DvFvH~s~i~~-~-~~L~~G~~V~F~v~~g~kg~G~~~A~~V~~~~~~   76 (89)
T 1x65_A            6 SGREMGVIAAMR--DGFGFIKCVDRDVRMFFHFSEILD-G-NQLHIADEVEFTVVPDMLSAQRNHAIRIKKLPKG   76 (89)
T ss_dssp             CCCEEEEEEECC--TTBCEEEESSSSSCCCCBTTGGGG-S-CCCCTTCCEEECCBCCSSSCCCCBCCSCEECCBT
T ss_pred             CcceeEEEEEEe--CCcceeecCCCCccEEEEhhhccC-C-CCCCCCCEEEEEEEeCCCcCCCceeeEEEECCCC
Confidence            478999999996  999999999988999999999997 5 789999999999999986  56899999987653

>2ytx_A Cold shock domain-containing protein E1; cell-free protein synthesis, beta-barrel, translational REGU RNA chaperone, RNA/DNA binding, QB fold; NMR {Homo sapiens}

Probab=99.87  E-value=1.9e-22  Score=141.91  Aligned_cols=73  Identities=27%  Similarity=0.429  Sum_probs=64.7

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcCCCccccC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAASRSRRFG   80 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~~g~~~~~   80 (169)
                      .++.+|+||||  +||||||+++++++|||||+|+|... ++.|.+||+|+|++++.+++ ++|++|++++..++..
T Consensus        16 ~~~~~G~Vkwf--~KGfGFI~~ddg~~DvFvH~s~i~~~-~~~L~~G~~V~F~v~~~~~g-~~A~~V~~~~~~~~~~   88 (97)
T 2ytx_A           16 QARCQGVVCAM--KEAFGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIKDRNGK-EVATDVRLLPQGTVIF   88 (97)
T ss_dssp             CCCEEEEECCC--CSSEEEEECSSSCCCEEEETTTCCSC-TTSCCSCCEEEEEECCCSSS-CBEEEEEECCCSSCCC
T ss_pred             CcceeEEEEEE--eCCceEEecCCCCceEEEEehHhccc-cCCCCCCCEEEEEEEcCCCC-cEEEEEEECCCCccce
Confidence            57889999999  89999999999889999999999987 78999999999999876665 8999999987655443

>2ytv_A Cold shock domain-containing protein E1; cell-free protein synthesis, beta-barrel, translational REGU RNA chaperone, RNA/DNA binding, QB fold; NMR {Homo sapiens}

Probab=99.85  E-value=9.9e-22  Score=133.35  Aligned_cols=67  Identities=34%  Similarity=0.530  Sum_probs=60.9

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCC-CccEEEEeeccccCCcccCCCCCEEEEEEeeCCC-CceeEEEEEcCC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDG-GEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGED-GRTKAVDVEAAS   74 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~-~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~k-Gr~~A~~V~~~~   74 (169)
                      .|+.+|+|+||  +||||||+++++ ++|||||+++|+ .+ ..|.+||+|+|+++++++ |+++|++|++++
T Consensus         6 ~~~~~G~V~~~--~KGfGFI~~ddg~g~DvFvH~s~i~-~g-~~l~~G~~V~F~v~~~~k~G~~~A~~V~~~~   74 (79)
T 2ytv_A            6 SGLRRATVECV--KDQFGFINYEVGDSKKLFFHVKEVQ-DG-IELQAGDEVEFSVILNQRTGKCSACNVWRVS   74 (79)
T ss_dssp             CSBCCEEEEEC--CSSEEEESCCCSSSSSEEEETTTCC-SS-CCCCTTCEEECBCEECSSSCCEECCSCEECS
T ss_pred             CCcccEEEEEe--cccceeEeCCCCCCCcEEEEhHHcC-CC-CcCCCCCEEEEEEEECCCCCCceeEEEEECC
Confidence            58899999999  599999999987 689999999999 66 899999999999999988 855999999875

>2bh8_A 1B11; transcription, molecular evolution, unique architecture, transcription regulation, phosphorylation; 1.9A {Escherichia coli}

Probab=99.72  E-value=8.8e-18  Score=118.79  Aligned_cols=60  Identities=40%  Similarity=0.686  Sum_probs=54.0

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc--ccCCCCCEEEEEEeeCC-CC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF--RTLSEGQTVEFSVDVGE-DG   63 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~--~~l~~G~~V~F~~~~~~-kG   63 (169)
                      .++++|+|||||.+||||||+++++++|||||+|+|...++  ..|.+|+.|+|++.... .|
T Consensus        14 ~~~~~G~Vk~fn~~kGfGFI~~~~gg~dvfvH~s~l~~~~~~~~~l~~Ge~V~g~V~~i~~fG   76 (101)
T 2bh8_A           14 SGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAGSSGAAVRGNPQQGDRVEGKIKSITDFG   76 (101)
T ss_dssp             --CEEEEEEEEEGGGTEEEEEESSSSCEEEEECCCSCSSSCCCCCCCTTCEEEEEEEECCSEE
T ss_pred             cccceeEEEEEECCCCCEEEEeCCCCcEEEEEEEEEecCCccccCCCCCCEEEEEEEEeCCcE
Confidence            46789999999999999999999988999999999999888  89999999999999865 45

>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}

Probab=99.47  E-value=2.2e-14  Score=84.38  Aligned_cols=39  Identities=46%  Similarity=1.094  Sum_probs=35.1

Q ss_pred             CCccccCcCCeecccCCCCCCCCCCCCCCCCCCccccccCCCCccCCCCCC
Q 030905          118 GACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPN  168 (169)
Q Consensus       118 ~~C~~Cg~~GH~a~~C~~~~~~~~~~~~g~~~~~~C~~Cg~~GH~ardCp~  168 (169)
                      ..||+|++.||++++||.+.            ...||+|+++||+++|||+
T Consensus         1 i~C~~Cg~~GH~a~~C~~~~------------~~~C~~Cg~~GH~~~~C~~   39 (39)
T 2a51_A            1 LTCFNCGKPGHTARMCRQPR------------QEGCWNCGSKEHRFAQCPK   39 (39)
T ss_dssp             CBCTTTCCBSSCTTTCCSCC------------CSSCTTTCCSSSCTTTSCC
T ss_pred             CeeeccCCCCcccccCCCCC------------CCccccCCCCCCccCcCcC
Confidence            36999999999999999853            4679999999999999996

>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}

Probab=99.45  E-value=3.6e-14  Score=82.54  Aligned_cols=37  Identities=35%  Similarity=1.162  Sum_probs=33.7

Q ss_pred             CCccccCcCCeecccCCCCCCCCCCCCCCCCCCccccccCCCCccCCCCCC
Q 030905          118 GACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPN  168 (169)
Q Consensus       118 ~~C~~Cg~~GH~a~~C~~~~~~~~~~~~g~~~~~~C~~Cg~~GH~ardCp~  168 (169)
                      ..||+|+++||++++||.+              ..||+|+++||+|+|||+
T Consensus         1 ~~C~~Cg~~GH~~~~C~~~--------------~~C~~Cg~~GH~a~~C~~   37 (37)
T 2bl6_A            1 QTCYNCGKPGHLSSQCRAP--------------KVCFKCKQPGHFSKQCRS   37 (37)
T ss_dssp             CCBSSSCCSSCCTTTSSCB--------------TTCSSCCCTTGGGGTTCC
T ss_pred             CcccccCCCCcchhhCcCc--------------CeEccCCCcCCccCcCcC
Confidence            3699999999999999973              569999999999999996

>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1

Probab=99.44  E-value=6.1e-14  Score=86.51  Aligned_cols=43  Identities=40%  Similarity=1.012  Sum_probs=37.6

Q ss_pred             CCCCCccccCcCCeecccCCCCCCCCCCCCCCCCCCccccccCCCCccCCCCCCC
Q 030905          115 AGSGACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPNY  169 (169)
Q Consensus       115 ~~~~~C~~Cg~~GH~a~~C~~~~~~~~~~~~g~~~~~~C~~Cg~~GH~ardCp~~  169 (169)
                      .....||+|++.||++++||.+.            ...||+|+++||+++|||++
T Consensus         4 ~r~~~C~~Cg~~GH~a~~C~~~~------------~~~C~~Cg~~GH~~~~C~~~   46 (49)
T 2ec7_A            4 RKVIRCWNCGKEGHSARQCRAPR------------RQGCWKCGKTGHVMAKCPER   46 (49)
T ss_dssp             CCCCBCTTTCCBTCCTTTCCCSS------------CCSCSSSCCSSCCGGGCCSS
T ss_pred             CCcCeeeecCCCCcChhhCcCCC------------CCeeCcCCCcCCccCCCcCC
Confidence            34568999999999999999853            46799999999999999974

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}

Probab=99.42  E-value=1.2e-13  Score=88.86  Aligned_cols=47  Identities=30%  Similarity=0.797  Sum_probs=38.5

Q ss_pred             CCCCccccCcCCeecccCCCCCCCCCCCCCCCCCCccccccCCCCccCCCCCCC
Q 030905          116 GSGACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPNY  169 (169)
Q Consensus       116 ~~~~C~~Cg~~GH~a~~C~~~~~~~~~~~~g~~~~~~C~~Cg~~GH~ardCp~~  169 (169)
                      ....||+|+++||++++||......       .....||+|+++||+|+|||+.
T Consensus         3 ~~~~C~~Cg~~GH~a~~C~~~~~~~-------~~~~~C~~Cg~~GH~ar~C~~~   49 (61)
T 2ihx_A            3 ARGLCYTCGSPGHYQAQCPKKRKSG-------NSRERCQLCNGMGHNAKQCRKR   49 (61)
T ss_dssp             CTTBCSSSCCBTCCGGGCTTTTSSS-------CCCSBCTTTCCBSSCGGGCCCC
T ss_pred             CCCcccccCCCCeehhhCcCCcCCC-------CCCCeeCCCCCCCCCcCCCcCC
Confidence            4568999999999999999865311       1247799999999999999974

>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.42  E-value=1.2e-13  Score=89.45  Aligned_cols=43  Identities=30%  Similarity=0.686  Sum_probs=37.3

Q ss_pred             CCCCCccccCcCCeecccCCCCCCCCCCCCCCCCCCccccccCCCCccCCCCCC
Q 030905          115 AGSGACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPN  168 (169)
Q Consensus       115 ~~~~~C~~Cg~~GH~a~~C~~~~~~~~~~~~g~~~~~~C~~Cg~~GH~ardCp~  168 (169)
                      .....||+|++.||++++||.+.           ....||+|+++||+|+|||+
T Consensus         5 ~r~~~C~~Cg~~GH~a~~C~~~~-----------~~~~C~~Cg~~GH~ar~Cp~   47 (63)
T 2cqf_A            5 SSGDRCYNCGGLDHHAKECKLPP-----------QPKKCHFCQSISHMVASCPL   47 (63)
T ss_dssp             CSCCCCSSSCCSSSCTTTCCSCC-----------CSSCCTTTCCSSSCTTTCTG
T ss_pred             CCCCcccccCCCCcChhhCCCCC-----------CCCccCCcCCcCCccCcCCC
Confidence            34568999999999999999753           15789999999999999996

>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A

Probab=99.39  E-value=1.5e-13  Score=86.54  Aligned_cols=43  Identities=44%  Similarity=1.097  Sum_probs=37.5

Q ss_pred             CCCCCccccCcCCeecccCCCCCCCCCCCCCCCCCCccccccCCCCccCCCCCCC
Q 030905          115 AGSGACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPNY  169 (169)
Q Consensus       115 ~~~~~C~~Cg~~GH~a~~C~~~~~~~~~~~~g~~~~~~C~~Cg~~GH~ardCp~~  169 (169)
                      .....||+|++.||++++||.+.            ...||+|+++||+++|||+.
T Consensus        10 ~~~~~C~~Cg~~GH~a~~C~~~~------------~~~C~~Cg~~GH~~~~C~~~   52 (55)
T 1a1t_A           10 RKTVKCFNCGKEGHIAKNCRAPR------------KKGCWKCGKEGHQMKDCTER   52 (55)
T ss_dssp             GGTCBCTTTCCBSSCGGGCSSCS------------CCBCTTTCCBSSCGGGCSSS
T ss_pred             CCCcceeeeCCCCcChhhcCCCC------------CCEeCCCCCcCCccCCCcCc
Confidence            34568999999999999999853            46799999999999999973

>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A

Probab=99.38  E-value=1.1e-13  Score=88.80  Aligned_cols=48  Identities=31%  Similarity=0.832  Sum_probs=18.5

Q ss_pred             CCccccCcCCeecccCCCCCCCCCCCCCCCCCCccccccCCCCccCCCCCCC
Q 030905          118 GACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPNY  169 (169)
Q Consensus       118 ~~C~~Cg~~GH~a~~C~~~~~~~~~~~~g~~~~~~C~~Cg~~GH~ardCp~~  169 (169)
                      ..||+|+++||+|++||.......    .......||+|+++||+|+|||+.
T Consensus         2 ~~Cf~Cg~~GH~a~~C~~~~~~~~----~~~~~~~C~~Cg~~GH~ar~C~~~   49 (60)
T 1cl4_A            2 GSCFKCGKKGHFAKNCHEHAHNNA----EPKVPGLCPRCKRGKHWANECKSK   49 (60)
T ss_dssp             -------------------------------CCCSCSSCSSCSSCSTTCCCT
T ss_pred             CccccCCCCCcCHhhCcCCCCCcc----ccCCCcceeECCCCCCccCcCCCc
Confidence            369999999999999998643211    011357899999999999999974

>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}

Probab=99.35  E-value=4.1e-13  Score=89.63  Aligned_cols=44  Identities=30%  Similarity=0.662  Sum_probs=37.7

Q ss_pred             CCCCCccccCcCCeecccCCCCCCCCCCCCCCCCCCccccccCCCCccCCCCCCC
Q 030905          115 AGSGACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPNY  169 (169)
Q Consensus       115 ~~~~~C~~Cg~~GH~a~~C~~~~~~~~~~~~g~~~~~~C~~Cg~~GH~ardCp~~  169 (169)
                      .....||+|++.||++++|+....           ...||+|+++||+|+|||+.
T Consensus        22 ~r~~~C~~Cg~~GH~a~~C~~~~~-----------~~~C~~Cg~~GH~ar~Cp~~   65 (74)
T 2li8_A           22 SKGDRCYNCGGLDHHAKECKLPPQ-----------PKKCHFCQSISHMVASCPLK   65 (74)
T ss_dssp             STTSCCTTTCCSSSCTTTCSSCCC-----------CCCCTTTCCTTSCGGGCTTG
T ss_pred             CCCCcccccCCcCcCcccCCCCCC-----------CCccCCcCCcCCccCcCcCC
Confidence            355689999999999999997531           57899999999999999963

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}

Probab=99.03  E-value=2.8e-10  Score=82.58  Aligned_cols=53  Identities=30%  Similarity=0.423  Sum_probs=38.8

Q ss_pred             CCCccccCcCCeecccCCCCCCCCC-----CC---CCCCCCCccccccCCCCccCCCCCCC
Q 030905          117 SGACFNCGRTGHIARECYSRGRGGG-----RG---YGGGRGGGGCYNCGEEGHFARDCPNY  169 (169)
Q Consensus       117 ~~~C~~Cg~~GH~a~~C~~~~~~~~-----~~---~~g~~~~~~C~~Cg~~GH~ardCp~~  169 (169)
                      ...||+|++.||++++||.......     ..   .........||+|++.||||+|||++
T Consensus        64 ~~~C~~Cg~~GH~~~~Cp~~~~~y~~~~~~~~~~~~~~~~~~~~Cy~Cg~~GH~a~dCp~~  124 (124)
T 2lli_A           64 KVQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEK  124 (124)
T ss_dssp             CCSSSSSCSSCCCTTTCCCSTTSCCSSSCCCCCCCSCCCCCCCCTTTTSSSCTTTTTSCCC
T ss_pred             CccCCCCCcCCcchhhCCCccccccccCccccccccccCCCCCCcCCCCCCCcCcccCcCC
Confidence            4689999999999999997643100     00   01122467899999999999999985

>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}

Probab=98.98  E-value=1.2e-10  Score=79.19  Aligned_cols=54  Identities=30%  Similarity=0.487  Sum_probs=36.0

Q ss_pred             CCCCccccCcCCeecccCCCCCCC----CCCCCC----CCCCCccccccCCCCccCCCCCCC
Q 030905          116 GSGACFNCGRTGHIARECYSRGRG----GGRGYG----GGRGGGGCYNCGEEGHFARDCPNY  169 (169)
Q Consensus       116 ~~~~C~~Cg~~GH~a~~C~~~~~~----~~~~~~----g~~~~~~C~~Cg~~GH~ardCp~~  169 (169)
                      ....||+|++.||++++||....-    ..+...    -....+.||+|++.|||++|||+.
T Consensus         4 k~~~C~~Cg~~GH~~~~Cp~~~rcY~c~~~gh~~~~c~~p~~~~~CYnCG~~GH~~rdC~~~   65 (83)
T 3nyb_B            4 KKVQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEK   65 (83)
T ss_dssp             ---CCSSSCCSSSCGGGCGGGTCCCCBC-------------CCCBCSSSSCBSSCGGGCSSC
T ss_pred             ccCCCCCCCCCCCccccCCCcccccccccCCcccccccCCCCCCeecccCCCCcCcccCCcc
Confidence            456899999999999999975320    000000    012357899999999999999973

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}

Probab=98.85  E-value=1.4e-09  Score=78.84  Aligned_cols=40  Identities=25%  Similarity=0.585  Sum_probs=31.2

Q ss_pred             CCccccCcCCeecccCCCCCCCCCCCCCCCCCCccccccCCCCccCCCCCC
Q 030905          118 GACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPN  168 (169)
Q Consensus       118 ~~C~~Cg~~GH~a~~C~~~~~~~~~~~~g~~~~~~C~~Cg~~GH~ardCp~  168 (169)
                      ..||+|++.||++++||...           ....||+|++.||+++|||+
T Consensus        43 ~~C~~Cg~~GH~~~~C~~~~-----------~~~~C~~Cg~~GH~~~~Cp~   82 (124)
T 2lli_A           43 IQCSKCDEVGHYRSQCPHKW-----------KKVQCTLCKSKKHSKERCPS   82 (124)
T ss_dssp             SCSSSSSCSSSSTTTSCCCC-----------CCCSSSSSCSSCCCTTTCCC
T ss_pred             ccccccCCCCCccccCcCcc-----------cCccCCCCCcCCcchhhCCC
Confidence            46777777777777777643           14679999999999999996

>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}

Probab=98.73  E-value=6.7e-09  Score=69.08  Aligned_cols=41  Identities=27%  Similarity=0.528  Sum_probs=22.1

Q ss_pred             CCeecccCCCCCCCCCCCCCCCCCCccccccCCCCccCCCCCC
Q 030905          126 TGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPN  168 (169)
Q Consensus       126 ~GH~a~~C~~~~~~~~~~~~g~~~~~~C~~Cg~~GH~ardCp~  168 (169)
                      +||+++||+.+......  ....+...||+|+++||++++||+
T Consensus         2 ~gh~~rdc~~~~~~~~~--~~~~r~~~C~~Cg~~GH~a~~C~~   42 (74)
T 2li8_A            2 SGLVPRGSHMPKGKSMQ--KRRSKGDRCYNCGGLDHHAKECKL   42 (74)
T ss_dssp             ----------CCCCCCC--SCCSTTSCCTTTCCSSSCTTTCSS
T ss_pred             CccccCcCCCCCcCccc--cccCCCCcccccCCcCcCcccCCC
Confidence            69999999987653211  123356789999999999999985

>1dsq_A Nucleic acid binding protein P14; CCHC type zinc finger, virus/viral protein; NMR {Mouse mammary tumor virus} SCOP: g.40.1.1

Probab=98.53  E-value=3.1e-08  Score=52.84  Aligned_cols=20  Identities=45%  Similarity=1.167  Sum_probs=16.1

Q ss_pred             CccccccCCCCccCCCCCCC
Q 030905          150 GGGCYNCGEEGHFARDCPNY  169 (169)
Q Consensus       150 ~~~C~~Cg~~GH~ardCp~~  169 (169)
                      ...||+|+++||||+|||+.
T Consensus         2 ~~~Cf~CG~~GH~ardC~~~   21 (26)
T 1dsq_A            2 GPVCFSCGKTGHIKRDCKEE   21 (26)
T ss_dssp             CCBCTTTCCBSSCTTTTTCC
T ss_pred             CCeeEeCCCCCcccccCCCc
Confidence            35689999999999999863

>1a6b_B Momulv, zinc finger protein NCP10; nucleocapsid protein, intercalation, nucleic acid, retrovirus, viral protein/DNA complex; HET: DNA; NMR {Synthetic} SCOP: g.40.1.1

Probab=98.44  E-value=9.5e-08  Score=56.07  Aligned_cols=20  Identities=45%  Similarity=1.082  Sum_probs=16.2

Q ss_pred             CccccccCCCCccCCCCCCC
Q 030905          150 GGGCYNCGEEGHFARDCPNY  169 (169)
Q Consensus       150 ~~~C~~Cg~~GH~ardCp~~  169 (169)
                      ...||+|++.||||+|||++
T Consensus        10 ~~~C~~Cgk~GH~ardCP~~   29 (40)
T 1a6b_B           10 RDQCAYCKEKGHWAKDCPKK   29 (40)
T ss_dssp             SSSCSSSCCTTCCTTSCSSS
T ss_pred             CCeeeECCCCCcchhhCcCC
Confidence            56788888888888888864

>1nc8_A Nucleocapsid protein; HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus 2} SCOP: g.40.1.1 PDB: 2di2_A

Probab=98.19  E-value=5.6e-07  Score=49.06  Aligned_cols=19  Identities=53%  Similarity=1.080  Sum_probs=14.4

Q ss_pred             CccccccCCCCccCCCCCC
Q 030905          150 GGGCYNCGEEGHFARDCPN  168 (169)
Q Consensus       150 ~~~C~~Cg~~GH~ardCp~  168 (169)
                      ...||+|+++||+++|||.
T Consensus         6 ~~~C~nCgk~GH~ar~C~~   24 (29)
T 1nc8_A            6 VIRCWNCGKEGHSARQCRA   24 (29)
T ss_dssp             CCBCTTTSCBSSCGGGCCS
T ss_pred             CCEEEECCccccCHhHCcc
Confidence            4568888888888888864

>1u6p_A GAG polyprotein; MLV, A-minor K-turn, stem loop, bulge, G-U mismatch, G-A MIS U mismatch, A-C mismatch, zinc finger, NC, viral protein-RN; HET: AP7; NMR {Moloney murine leukemia virus} SCOP: g.40.1.1 PDB: 1wwd_A 1wwe_A 1wwf_A 1wwg_A

Probab=98.19  E-value=4.2e-07  Score=57.12  Aligned_cols=19  Identities=47%  Similarity=1.176  Sum_probs=11.5

Q ss_pred             CccccccCCCCccCCCCCC
Q 030905          150 GGGCYNCGEEGHFARDCPN  168 (169)
Q Consensus       150 ~~~C~~Cg~~GH~ardCp~  168 (169)
                      ...||+|++.||||+|||+
T Consensus        23 ~~~C~~Cge~GH~ardCp~   41 (56)
T 1u6p_A           23 RDQCAYCKEKGHWAKDCPK   41 (56)
T ss_dssp             TTBCSSSCCBSSCGGGCTT
T ss_pred             CCcceeCCCCCcccccCcC
Confidence            3456666666666666654

>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.11  E-value=8.3e-07  Score=55.56  Aligned_cols=17  Identities=41%  Similarity=1.400  Sum_probs=10.4

Q ss_pred             ccccccCCCCccCCCCC
Q 030905          151 GGCYNCGEEGHFARDCP  167 (169)
Q Consensus       151 ~~C~~Cg~~GH~ardCp  167 (169)
                      ..||+|+++|||++|||
T Consensus         8 ~~C~kCGk~GH~~k~Cp   24 (55)
T 2ysa_A            8 YTCFRCGKPGHYIKNCP   24 (55)
T ss_dssp             CCCTTTCCTTSCGGGCS
T ss_pred             CccccCCCcCcccccCC
Confidence            44666666666666665

>1nc8_A Nucleocapsid protein; HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus 2} SCOP: g.40.1.1 PDB: 2di2_A

Probab=97.89  E-value=6.1e-06  Score=44.85  Aligned_cols=22  Identities=41%  Similarity=0.922  Sum_probs=19.3

Q ss_pred             CCCCccccCcCCeecccCCCCC
Q 030905          116 GSGACFNCGRTGHIARECYSRG  137 (169)
Q Consensus       116 ~~~~C~~Cg~~GH~a~~C~~~~  137 (169)
                      ....||+|++.||++++|+.+.
T Consensus         5 ~~~~C~nCgk~GH~ar~C~~pr   26 (29)
T 1nc8_A            5 KVIRCWNCGKEGHSARQCRAPR   26 (29)
T ss_dssp             CCCBCTTTSCBSSCGGGCCSSS
T ss_pred             CCCEEEECCccccCHhHCcccc
Confidence            4578999999999999999864

>1a6b_B Momulv, zinc finger protein NCP10; nucleocapsid protein, intercalation, nucleic acid, retrovirus, viral protein/DNA complex; HET: DNA; NMR {Synthetic} SCOP: g.40.1.1

Probab=97.83  E-value=1.1e-05  Score=47.11  Aligned_cols=25  Identities=28%  Similarity=0.656  Sum_probs=21.5

Q ss_pred             CCCCCCccccCcCCeecccCCCCCC
Q 030905          114 GAGSGACFNCGRTGHIARECYSRGR  138 (169)
Q Consensus       114 ~~~~~~C~~Cg~~GH~a~~C~~~~~  138 (169)
                      ......||+|++.||+|++||....
T Consensus         7 ~~~~~~C~~Cgk~GH~ardCP~~~~   31 (40)
T 1a6b_B            7 QLDRDQCAYCKEKGHWAKDCPKKPR   31 (40)
T ss_dssp             SCCSSSCSSSCCTTCCTTSCSSSCC
T ss_pred             CCCCCeeeECCCCCcchhhCcCCcc
Confidence            3466799999999999999998764

>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}

Probab=97.69  E-value=1.4e-05  Score=46.29  Aligned_cols=17  Identities=53%  Similarity=1.251  Sum_probs=16.1

Q ss_pred             cccccCCCCccCCCCCC
Q 030905          152 GCYNCGEEGHFARDCPN  168 (169)
Q Consensus       152 ~C~~Cg~~GH~ardCp~  168 (169)
                      .||+|+++||++++||+
T Consensus         2 ~C~~Cg~~GH~a~~C~~   18 (39)
T 2a51_A            2 TCFNCGKPGHTARMCRQ   18 (39)
T ss_dssp             BCTTTCCBSSCTTTCCS
T ss_pred             eeeccCCCCcccccCCC
Confidence            59999999999999996

>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1

Probab=97.68  E-value=1.9e-05  Score=47.94  Aligned_cols=20  Identities=50%  Similarity=1.008  Sum_probs=18.0

Q ss_pred             CCccccccCCCCccCCCCCC
Q 030905          149 GGGGCYNCGEEGHFARDCPN  168 (169)
Q Consensus       149 ~~~~C~~Cg~~GH~ardCp~  168 (169)
                      +...||+|+++||+++|||+
T Consensus         5 r~~~C~~Cg~~GH~a~~C~~   24 (49)
T 2ec7_A            5 KVIRCWNCGKEGHSARQCRA   24 (49)
T ss_dssp             CCCBCTTTCCBTCCTTTCCC
T ss_pred             CcCeeeecCCCCcChhhCcC
Confidence            36789999999999999986

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}

Probab=97.61  E-value=2e-05  Score=50.09  Aligned_cols=19  Identities=47%  Similarity=1.340  Sum_probs=17.7

Q ss_pred             CccccccCCCCccCCCCCC
Q 030905          150 GGGCYNCGEEGHFARDCPN  168 (169)
Q Consensus       150 ~~~C~~Cg~~GH~ardCp~  168 (169)
                      ...||+|+++||+|+|||+
T Consensus         4 ~~~C~~Cg~~GH~a~~C~~   22 (61)
T 2ihx_A            4 RGLCYTCGSPGHYQAQCPK   22 (61)
T ss_dssp             TTBCSSSCCBTCCGGGCTT
T ss_pred             CCcccccCCCCeehhhCcC
Confidence            5779999999999999997

>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}

Probab=97.59  E-value=2.3e-05  Score=44.78  Aligned_cols=17  Identities=47%  Similarity=1.322  Sum_probs=16.0

Q ss_pred             cccccCCCCccCCCCCC
Q 030905          152 GCYNCGEEGHFARDCPN  168 (169)
Q Consensus       152 ~C~~Cg~~GH~ardCp~  168 (169)
                      .||+|+++||++++||+
T Consensus         2 ~C~~Cg~~GH~~~~C~~   18 (37)
T 2bl6_A            2 TCYNCGKPGHLSSQCRA   18 (37)
T ss_dssp             CBSSSCCSSCCTTTSSC
T ss_pred             cccccCCCCcchhhCcC
Confidence            59999999999999986

>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A

Probab=97.58  E-value=1.4e-05  Score=49.56  Aligned_cols=20  Identities=45%  Similarity=1.130  Sum_probs=18.1

Q ss_pred             CCccccccCCCCccCCCCCC
Q 030905          149 GGGGCYNCGEEGHFARDCPN  168 (169)
Q Consensus       149 ~~~~C~~Cg~~GH~ardCp~  168 (169)
                      ....||+|+++||++++||+
T Consensus        11 ~~~~C~~Cg~~GH~a~~C~~   30 (55)
T 1a1t_A           11 KTVKCFNCGKEGHIAKNCRA   30 (55)
T ss_dssp             GTCBCTTTCCBSSCGGGCSS
T ss_pred             CCcceeeeCCCCcChhhcCC
Confidence            46789999999999999986

>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.57  E-value=3.8e-05  Score=49.12  Aligned_cols=20  Identities=45%  Similarity=1.089  Sum_probs=18.0

Q ss_pred             CCccccccCCCCccCCCCCC
Q 030905          149 GGGGCYNCGEEGHFARDCPN  168 (169)
Q Consensus       149 ~~~~C~~Cg~~GH~ardCp~  168 (169)
                      +...||+|+++||+++|||+
T Consensus         6 r~~~C~~Cg~~GH~a~~C~~   25 (63)
T 2cqf_A            6 SGDRCYNCGGLDHHAKECKL   25 (63)
T ss_dssp             SCCCCSSSCCSSSCTTTCCS
T ss_pred             CCCcccccCCCCcChhhCCC
Confidence            45789999999999999995

>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A

Probab=97.55  E-value=1.1e-05  Score=50.98  Aligned_cols=18  Identities=50%  Similarity=1.536  Sum_probs=0.0

Q ss_pred             ccccccCCCCccCCCCCC
Q 030905          151 GGCYNCGEEGHFARDCPN  168 (169)
Q Consensus       151 ~~C~~Cg~~GH~ardCp~  168 (169)
                      ..||+|+++||+|+|||+
T Consensus         2 ~~Cf~Cg~~GH~a~~C~~   19 (60)
T 1cl4_A            2 GSCFKCGKKGHFAKNCHE   19 (60)
T ss_dssp             ------------------
T ss_pred             CccccCCCCCcCHhhCcC
Confidence            359999999999999986

>1u6p_A GAG polyprotein; MLV, A-minor K-turn, stem loop, bulge, G-U mismatch, G-A MIS U mismatch, A-C mismatch, zinc finger, NC, viral protein-RN; HET: AP7; NMR {Moloney murine leukemia virus} SCOP: g.40.1.1 PDB: 1wwd_A 1wwe_A 1wwf_A 1wwg_A

Probab=97.55  E-value=4e-05  Score=47.97  Aligned_cols=24  Identities=29%  Similarity=0.697  Sum_probs=20.9

Q ss_pred             CCCCCccccCcCCeecccCCCCCC
Q 030905          115 AGSGACFNCGRTGHIARECYSRGR  138 (169)
Q Consensus       115 ~~~~~C~~Cg~~GH~a~~C~~~~~  138 (169)
                      .....||+|++.||++++||....
T Consensus        21 ~~~~~C~~Cge~GH~ardCp~~~~   44 (56)
T 1u6p_A           21 LDRDQCAYCKEKGHWAKDCPKKPR   44 (56)
T ss_dssp             CCTTBCSSSCCBSSCGGGCTTCCC
T ss_pred             CCCCcceeCCCCCcccccCcCCcc
Confidence            466789999999999999998654

>1a62_A RHO; transcription termination, termination, RNA binding domain, transcription regulation, OB fold, F1-ATPase; 1.55A {Escherichia coli BL21} SCOP: a.140.3.1 b.40.4.5 PDB: 1a63_A 2a8v_A 1a8v_A

Probab=97.31  E-value=0.00043  Score=50.40  Aligned_cols=68  Identities=25%  Similarity=0.502  Sum_probs=51.9

Q ss_pred             cceEEEEeeCCCCeeEEecCC-----CCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCC-ce-eEEEEEcCCCcccc
Q 030905            7 SSGTVKWFSAQKGFGFIAPED-----GGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDG-RT-KAVDVEAASRSRRF   79 (169)
Q Consensus         7 ~~G~Vk~~~~~kGfGFI~~~~-----~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kG-r~-~A~~V~~~~g~~~~   79 (169)
                      .+|++.--  ..||||+.+++     +.+||||..+.|...+   |..||.|+-.+.....+ |. .-+.|..+++.++.
T Consensus        51 ~~Gvlei~--~dG~GFlr~~~~~y~~~~~DiyVs~~~irrf~---lr~GD~V~g~vr~~~~~ek~~~l~~v~~vng~~pe  125 (130)
T 1a62_A           51 GDGVLEIL--QDGFGFLRSADSSYLAGPDDIYVSPSQIRRFN---LRTGDTISGKIRPPKEGERYFALLKVNEVNFDKPE  125 (130)
T ss_dssp             EEEEEEEC--TTSCEEEECGGGTTCCCTTCEEECHHHHHHTT---CCTTCEEEEEEECCCTTCCSEEEEEEEEETTBCCC
T ss_pred             EEEEEEEc--CCCeEEEecCCcCCCCCCCCEEECHHHHhHhC---CCCCCEEEEEEeCCCCCCcccceeEEEeECCCCHH
Confidence            56766643  46999999983     6789999999998754   88999999999876555 33 34678778876654

>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.25  E-value=0.00013  Score=45.42  Aligned_cols=21  Identities=33%  Similarity=0.983  Sum_probs=18.1

Q ss_pred             CCCCccccCcCCeecccCCCC
Q 030905          116 GSGACFNCGRTGHIARECYSR  136 (169)
Q Consensus       116 ~~~~C~~Cg~~GH~a~~C~~~  136 (169)
                      ....||+|++.||++++||..
T Consensus         6 ~~~~C~kCGk~GH~~k~Cp~~   26 (55)
T 2ysa_A            6 SGYTCFRCGKPGHYIKNCPTN   26 (55)
T ss_dssp             SSCCCTTTCCTTSCGGGCSGG
T ss_pred             CCCccccCCCcCcccccCCCC
Confidence            445799999999999999954

>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A*

Probab=96.46  E-value=0.0021  Score=47.69  Aligned_cols=23  Identities=17%  Similarity=0.515  Sum_probs=20.0

Q ss_pred             CCCCccccCcCCeecccCCCCCC
Q 030905          116 GSGACFNCGRTGHIARECYSRGR  138 (169)
Q Consensus       116 ~~~~C~~Cg~~GH~a~~C~~~~~  138 (169)
                      ....||+|++.||++++||+...
T Consensus       118 ~~~~C~~Cg~~GH~~r~Cp~~~~  140 (148)
T 3ts2_A          118 QPKKCHFCQSINHMVASCPLKAQ  140 (148)
T ss_dssp             CCCCCTTTCCSSCCGGGCTTTTC
T ss_pred             CCCcccccCCcCCEeccCcCCCC
Confidence            35689999999999999998654

>2cqo_A Nucleolar protein of 40 kDa; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=94.79  E-value=0.071  Score=37.69  Aligned_cols=54  Identities=20%  Similarity=0.215  Sum_probs=40.0

Q ss_pred             ccccceEEEEeeCCCCee-EEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeC
Q 030905            4 VQRSSGTVKWFSAQKGFG-FIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVG   60 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfG-FI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~   60 (169)
                      ...+.|+|+...+   || ||..+....+-|+|+++|...-+    ..+++||.|...+..-
T Consensus        23 G~iv~G~V~~I~~---fGaFV~l~g~~~~Glvhisel~~~~~~~~~~~~~~Gd~V~VkV~~v   81 (119)
T 2cqo_A           23 YTIFQGEVAMVTD---YGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGR   81 (119)
T ss_dssp             TCEEEEEEEEEET---TEEEEECTTCSSCEEEEHHHHCSSCCSCHHHHCCTTCEEEEEEEEE
T ss_pred             CCEEEEEEEEEeC---ceEEEEECCCcEEEEEEHHHCCcccccChhhcCCCCCEEEEEEEEE
Confidence            4578999999965   67 56654434689999999975322    3589999999987753

>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii}

Probab=94.79  E-value=0.066  Score=34.91  Aligned_cols=53  Identities=15%  Similarity=0.166  Sum_probs=40.5

Q ss_pred             ccccceEEEEeeCCCCee-EEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeC
Q 030905            4 VQRSSGTVKWFSAQKGFG-FIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG   60 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfG-FI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~   60 (169)
                      ...+.|+|+...+   || ||..++ +.+-|+|+|++...-+..+++||.|...+..-
T Consensus         6 G~iv~G~V~~v~~---~G~fV~l~~-~~~Gllh~sel~~~~~~~~~~Gd~V~v~V~~v   59 (80)
T 2k52_A            6 GKFYKGVVTRIEK---YGAFINLNE-QVRGLLRPRDMISLRLENLNVGDEIIVQAIDV   59 (80)
T ss_dssp             TCEEEEEEEEEET---TEEEEEEET-TEEEEECGGGCSSCCGGGCCTTCEEEEEEEEE
T ss_pred             CCEEEEEEEEEeC---CEEEEEECC-CCEEEEEHHHCCcccceeeCCCCEEEEEEEEE
Confidence            4678999999864   67 455554 47899999999754334699999999988753

>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR family, hydrolase; 2.35A {Escherichia coli} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 PDB: 2ix0_A* 2ix1_A

Probab=94.66  E-value=0.052  Score=48.90  Aligned_cols=61  Identities=25%  Similarity=0.433  Sum_probs=46.7

Q ss_pred             cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcCC
Q 030905            5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAAS   74 (169)
Q Consensus         5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~~   74 (169)
                      ..++|+|+-  ..|||||+.+++ .+|||+.-.++..     .-.||+|...+... ++++.|.=|.++.
T Consensus        20 ~~~~G~~~~--~~~GfgF~~~d~-~~difi~~~~~~~-----a~~GD~V~v~i~~~-~~~~eg~v~~ile   80 (644)
T 2id0_A           20 PRAEGVVKA--TEKGFGFLEVDA-QKSYFIPPPQMKK-----VMHGDRIIAVIHSE-KERESAEPEELVE   80 (644)
T ss_dssp             CEEEEEEEC--CSSSCEEEECSS-SCEEEECHHHHTT-----SCTTCEEEEEEECC-SSSCEEEEEEEEE
T ss_pred             CeEEEEEEE--ecCCcEEEEECC-CCCEEECHHHHhc-----CCCCCEEEEEEecC-CCCeEEEEEEEEe
Confidence            457899886  468999999986 4899999888764     46999999998765 4556666555544

>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae}

Probab=93.97  E-value=0.25  Score=40.13  Aligned_cols=63  Identities=14%  Similarity=0.118  Sum_probs=46.0

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCC-CccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEE
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDG-GEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAV   68 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~-~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~   68 (169)
                      .....|+|++.+  +.||....-.. +.|+|+|+|++...--..+++||.|...+..++++|..|.
T Consensus        70 G~~~~g~V~~v~--~~~GaFVdiG~~~~d~lvp~sel~~~~~~~~~~Gd~v~v~l~iD~~~Ri~ls  133 (285)
T 3go5_A           70 DQFGWGRVTEVR--KDLGVFVDTGLPDKEIVVSLDILPELKELWPKKGDQLYIRLEVDKKDRIWGL  133 (285)
T ss_dssp             SSCEEEEEEEEE--TTTEEEEECSCTTCCEEEEGGGSCSSGGGSCCTTCEEEEEEEECTTSCEEEE
T ss_pred             CCEEEEEEEEEc--cCceEEEEECCCCcEEEEEHHHCCcccccccCCCCEEEEEEEECCCCcEEEE
Confidence            456789999876  34775554444 4799999999865322357999999888888887875554

>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae}

Probab=93.15  E-value=0.22  Score=40.49  Aligned_cols=55  Identities=11%  Similarity=0.033  Sum_probs=43.8

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEE
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAV   68 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~   68 (169)
                      ...++|+|+...+   ||++...+ +.++|+|.+.+..      ++||.|++-+-.++++++.|+
T Consensus         7 G~~v~g~V~~~~~---~G~fv~~~-g~egllp~se~~~------~vGdevev~v~~d~~~r~iat   61 (285)
T 3go5_A            7 ASFIVGLIIDEND---RFYFVQKD-GQTYALAKEEGQH------TVGDTVKGFAYTDMKQKLRLT   61 (285)
T ss_dssp             TEEEEEEEEEECS---SEEEEEET-TEEEEEEGGGCCC------CTTSEEEEEEEECTTSCEEEE
T ss_pred             CCEEEEEEEEEEC---CEEEEEcC-CeEEEEEHHHCcc------ccCCEEEEEEEECCCCCEEEe
Confidence            4578999998864   77666544 5799999999943      899999988888888877775

>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli}

Probab=92.88  E-value=0.56  Score=32.56  Aligned_cols=54  Identities=19%  Similarity=0.233  Sum_probs=39.4

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccC-----CcccCCCCCEEEEEEeeC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSE-----GFRTLSEGQTVEFSVDVG   60 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~-----~~~~l~~G~~V~F~~~~~   60 (169)
                      ...+.|+|+...+   ||+...-+.+.+-|+|+|+|...     .-..+++||.|...+..-
T Consensus        31 G~~~~G~V~~v~~---~G~FV~l~~~~~Glvhisel~~~~~~~~~~~~~~vGd~V~vkV~~v   89 (115)
T 2khi_A           31 GTKLTGRVTNLTD---YGCFVEIEEGVEGLVHVSEMDWTNKNIHPSKVVNVGDVVEVMVLDI   89 (115)
T ss_dssp             SCEEEEEEEEEET---TEEEEECSTTCEEEEETTSSSCSSTTCSSTTTCCTTCEEEEEEEEE
T ss_pred             CCEEEEEEEEEEC---CEEEEEECCCCEEEEEHHHCCccccccCcccEECCCCEEEEEEEEE
Confidence            4568999999865   77544434457999999999642     123689999999988754

>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis}

Probab=92.80  E-value=0.25  Score=35.25  Aligned_cols=64  Identities=22%  Similarity=0.259  Sum_probs=43.7

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC----cccCCCCCEEEEEEeeC-C-CCceeEEEEE
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDVG-E-DGRTKAVDVE   71 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~~-~-kGr~~A~~V~   71 (169)
                      ...+.|+|+...+   ||++..-+.+.+-|+|+|+|...-    -..|++||.|...+..- . +++ ..+.+.
T Consensus         8 G~iv~G~V~~i~~---~G~FV~l~~~~~Glihisel~~~~~~~~~~~~~vGd~V~vkV~~vd~~~~k-I~LSlk   77 (130)
T 2k4k_A            8 GSVYTGKVTGLQA---YGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQVKVLAVDEEKGK-ISLSIR   77 (130)
T ss_dssp             TCEEEEEEEEEET---TEEEEEEETTEEEEEEGGGTSSSCCSCGGGTCCTTCEEEEEEEEEETTTTE-EEEESH
T ss_pred             CCEEEEEEEEEeC---CeEEEEECCCcEEEEEHHHCCcccccCccccCCCCCEEEEEEEEEeCCCCE-EEEEEe
Confidence            4678999999854   675544333579999999997432    14689999999887753 3 553 333443

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=91.97  E-value=0.28  Score=42.05  Aligned_cols=68  Identities=18%  Similarity=0.397  Sum_probs=49.8

Q ss_pred             cceEEEEeeCCCCeeEEecC-----CCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCC-ce-eEEEEEcCCCcccc
Q 030905            7 SSGTVKWFSAQKGFGFIAPE-----DGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDG-RT-KAVDVEAASRSRRF   79 (169)
Q Consensus         7 ~~G~Vk~~~~~kGfGFI~~~-----~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kG-r~-~A~~V~~~~g~~~~   79 (169)
                      ..|++--.  ..|||||.+.     .+.+||||..+.|+..+   |+.||.|+=.+.....+ +. .-..|..+++.++.
T Consensus        58 ~~g~le~~--~~g~gflr~~~~~y~~~~~d~yvs~~~ir~~~---lr~gd~v~g~~r~~~~~e~~~~l~~v~~vng~~p~  132 (427)
T 3l0o_A           58 GEGVLEIH--PEGFGFLRRIEDNLLPSNDDIYISPSQIRKFN---LNTGDIISGVIRKPKEGEKYFAMIKIEAINYRPVE  132 (427)
T ss_dssp             EEEEEEEC--TTSCEEEECGGGTTCCCSSCEEECHHHHHHTT---CCTTCEEEEEEECCCSSSCSEEEEEEEEETTEEC-
T ss_pred             EEEEEEEc--CCCceEeeCCccCCCCCCCCeeeCHHHHHhcC---CCCCCEEEEEEeCCCCCcccccceEEEecCCCChH
Confidence            45555544  4699999987     46789999999999874   88999999998876555 32 33567777775543

>2eqs_A ATP-dependent RNA helicase DHX8; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=91.97  E-value=0.28  Score=33.51  Aligned_cols=57  Identities=26%  Similarity=0.309  Sum_probs=41.6

Q ss_pred             ccccceEEEEeeCCCCee-EEecCC--CCccEEEEeeccccCC-----cccCCCCCEEEEEEeeCCCC
Q 030905            4 VQRSSGTVKWFSAQKGFG-FIAPED--GGEDLFVHQTSIKSEG-----FRTLSEGQTVEFSVDVGEDG   63 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfG-FI~~~~--~~~dvF~H~s~i~~~~-----~~~l~~G~~V~F~~~~~~kG   63 (169)
                      ...+.|+|+..-+   || ||..++  ...+-|+|+|+|....     -..+++||.|...+..-..+
T Consensus        13 G~i~~G~V~~v~~---fG~FV~l~~~~~~~~Glvhisel~~~~~~~~~~~~~~~Gd~V~VkV~~vd~~   77 (103)
T 2eqs_A           13 GDIYNGKVTSIMQ---FGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGT   77 (103)
T ss_dssp             TCEEEEEEEEECS---SCEEEEECSSSSCCEEEECGGGTSSSSCCCCHHHHCCTTCEEEEEEEEEETT
T ss_pred             CCEEEEEEEEEec---cEEEEEEcCCCCCeEEEEEHHHCCCCcccCCcccEeCCCCEEEEEEEEEECC
Confidence            4678999999843   77 666665  2578999999994221     14589999999988765444

>1y14_B B16, RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1 PDB: 1nt9_G 1wcm_G 1pqv_G 1y1v_G 1y1w_G 1y1y_G 1y77_G* 2b63_G* 2ja5_G* 2ja6_G* 2ja7_G* 2ja8_G* 2r7z_G 2r92_G 2r93_G 2vum_G* 3fki_G 3h3v_H 3hou_G* 3hov_G* ...

Probab=91.56  E-value=0.29  Score=36.43  Aligned_cols=53  Identities=15%  Similarity=0.177  Sum_probs=38.8

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccC------Cc--------ccCCCCCEEEEEEeeC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSE------GF--------RTLSEGQTVEFSVDVG   60 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~------~~--------~~l~~G~~V~F~~~~~   60 (169)
                      .+.+.|+|+.-.+   ||+...-.. .|.|+|+|.|...      ..        ..+++||.|.+.+..-
T Consensus        84 Gev~~G~V~~v~~---fG~FV~l~~-~dglvhis~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~v  150 (171)
T 1y14_B           84 GEVVDGTVVSCSQ---HGFEVQVGP-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGC  150 (171)
T ss_dssp             TCEEEEEEEEEET---TEEEEEETT-EEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEE
T ss_pred             CCEEEEEEEEEec---CEEEEEecC-eEEEEEHHHCCCCceECcccCceEEeccceEECCCCEEEEEEEEE
Confidence            4578999999875   887665544 8999999998532      00        3478899999887653

>2b8k_G B16, DNA-directed RNA polymerase II 19 kDa polypeptide; DNA-dependent RNA polymerase, cellular RNA polymerase; 4.15A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1

Probab=91.07  E-value=0.36  Score=37.65  Aligned_cols=53  Identities=15%  Similarity=0.177  Sum_probs=39.8

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccC------Cc--------ccCCCCCEEEEEEeeC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSE------GF--------RTLSEGQTVEFSVDVG   60 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~------~~--------~~l~~G~~V~F~~~~~   60 (169)
                      .+.+.|+|+.-.+   ||+...-.. .|.|||+|.|...      ..        ..+++||.|.+.+..-
T Consensus        84 Gev~~G~V~~vt~---fG~FVelg~-~dGlVhiS~l~d~~~~d~~~~~w~~~~~~~~~~~Gd~VrVkV~~v  150 (215)
T 2b8k_G           84 GEVVDGTVVSCSQ---HGFEVQVGP-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGC  150 (215)
T ss_dssp             TEEEEEEEEEEET---TEEEEECTT-SEEEEEGGGSCSSCCCBSSCSSCEEECSSCEEETTCEEEEEEEEE
T ss_pred             CCEEEEEEEEEec---ceEEEEecC-cEEEEEHHHCCccceeccccccceeeccccEECCCCEEEEEEEEE
Confidence            4568899999874   887766555 8999999999632      00        3478899999987753

>1kl9_A Eukaryotic translation initiation factor 2 subuni; OB fold, helical domain; 1.90A {Homo sapiens} SCOP: a.60.14.1 b.40.4.5

Probab=90.05  E-value=0.68  Score=35.08  Aligned_cols=54  Identities=7%  Similarity=0.016  Sum_probs=36.6

Q ss_pred             ccccceEEEEeeCCCCee-EEecC-CCCccEEEEeeccccCC----cccCCCCCEEEEEEeeC
Q 030905            4 VQRSSGTVKWFSAQKGFG-FIAPE-DGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDVG   60 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfG-FI~~~-~~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~~   60 (169)
                      ...+.|+|+...   -|| ||..+ ..+.+=|+|+|+|...-    -..+++||.|...+..-
T Consensus        16 G~iv~G~V~~I~---~fGaFV~L~e~~g~eGLvhiSels~~~v~~~~~~~~vGd~V~VkVl~v   75 (182)
T 1kl9_A           16 EDVVMVNVRSIA---EMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRV   75 (182)
T ss_dssp             TCEEEEEEEEEC---SSEEEEEETTTTTEEEEEEGGGC------------CTTCEEEEEEEEE
T ss_pred             CCEEEEEEEEEe---ccEEEEEEccCCCcEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEE
Confidence            567899999885   588 66664 34578999999996532    24588999999987753

>2qcp_X Cation efflux system protein CUSF; silver-binding, copper-binding, beta barrel, OB-fold, metall metal resistance, metal-binding; 1.00A {Escherichia coli str} PDB: 1zeq_X 3e6z_X

Probab=89.84  E-value=1.9  Score=28.22  Aligned_cols=61  Identities=15%  Similarity=0.157  Sum_probs=39.3

Q ss_pred             ccceEEEEeeCCCCeeEEecCCCC--------ccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEE
Q 030905            6 RSSGTVKWFSAQKGFGFIAPEDGG--------EDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVE   71 (169)
Q Consensus         6 ~~~G~Vk~~~~~kGfGFI~~~~~~--------~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~   71 (169)
                      ..+|+|+..+...+-  |+...+.        .-.-|.+.+  ...+..|++||.|.|+++....+ +.-+.|+
T Consensus         9 ~~~G~V~~id~~~~~--iTi~H~pI~~l~wpaMTM~F~v~~--~~~l~~lk~Gd~V~F~~~~~~~~-~~it~i~   77 (80)
T 2qcp_X            9 SATGVVKGIDLESKK--ITIHHDPIAAVNWPEMTMRFTITP--QTKMSEIKTGDKVAFNFVQQGNL-SLLQDIK   77 (80)
T ss_dssp             EEEEEEEEEETTTTE--EEEEECCBGGGTBCSEEEEEECCT--TCEECCCCTTCEEEEEEEEETTE-EEEEEEE
T ss_pred             EEEEEEEEEcCCCCE--EEEEcCCcccCCCCceEEEEEccC--hhhhhcCCCCCEEEEEEEEeCCE-EEEEEEE
Confidence            478999999987655  5544322        112233322  12256799999999999987655 5655554

>2l55_A SILB,silver efflux protein, MFP component of the components proton antiporter metal...; APO form, AG(I)-binding site; NMR {Cupriavidus metallidurans}

Probab=89.79  E-value=3  Score=27.39  Aligned_cols=61  Identities=15%  Similarity=0.208  Sum_probs=39.8

Q ss_pred             cceEEEEeeCCCCeeEEecCCCC-c-------cEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcC
Q 030905            7 SSGTVKWFSAQKGFGFIAPEDGG-E-------DLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAA   73 (169)
Q Consensus         7 ~~G~Vk~~~~~kGfGFI~~~~~~-~-------dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~   73 (169)
                      .+|+|+.++.+.    |+...+. .       -.-|.+.+  ...+..|++||+|.|+++....|.+.-+.|+..
T Consensus         6 ~~G~V~~vd~~~----iTi~H~pI~~l~wPaMTM~F~v~~--~~~l~~lk~Gd~V~F~~~~~~~g~~~it~i~~~   74 (82)
T 2l55_A            6 AVGRIQSIGERS----LIIAHEAIPSAQWGAMTMEFAAPP--AGLPQGLKAGDRVAFSFRLDPHGMATLVTVAPQ   74 (82)
T ss_dssp             EEEEEEECCSSE----EEEEECCCTTTTCCCEEEEEECCT--TCCCSSCSTTCEEEEEEEEETTTEEEEEEEEEC
T ss_pred             EeEEEEEEcccc----EEEecCCccccCCCceEEEEEcCC--hhHhhcCCCCCEEEEEEEECCCCeEEEEEEEec
Confidence            589999999875    5543221 1       12233322  123577999999999999987744666667654

>2vb2_X Copper protein, cation efflux system protein CUSF; cation PI, metal-binding, metal transport, copper tolerance, transport; 1.70A {Escherichia coli} PDB: 2vb3_X

Probab=89.67  E-value=1.7  Score=28.90  Aligned_cols=61  Identities=15%  Similarity=0.157  Sum_probs=39.2

Q ss_pred             ccceEEEEeeCCCCeeEEecCCCC--------ccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEE
Q 030905            6 RSSGTVKWFSAQKGFGFIAPEDGG--------EDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVE   71 (169)
Q Consensus         6 ~~~G~Vk~~~~~kGfGFI~~~~~~--------~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~   71 (169)
                      ..+|+|+..+...+-  |+...+.        .-.-|.+.+  ...+..|++|++|.|+++....+ +.-+.|+
T Consensus        17 ~~~G~V~~id~~~~~--iTi~H~pI~~l~wpaMTM~F~v~~--~~~l~~lk~Gd~V~F~~~~~~~~-~~it~i~   85 (88)
T 2vb2_X           17 SATGVVKGIDLESKK--ITIHHDPIAAVNWPEMTMRFTITP--QTKMSEIKTGDKVAFNFVQQGNL-SLLQDIK   85 (88)
T ss_dssp             EEEEEEEEEETTTTE--EEEEECCBGGGTBCSEEEEEECCT--TCEECCCCTTCEEEEEEEEETTE-EEEEEEE
T ss_pred             EEEEEEEEEcCCCCE--EEEecCCcccCCCCceEEEEEcCC--hhhhhcCCCCCEEEEEEEEeCCE-EEEEEEE
Confidence            478999999987654  5544321        112233322  12256799999999999987655 6655554

>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli}

Probab=88.84  E-value=0.56  Score=32.19  Aligned_cols=53  Identities=21%  Similarity=0.186  Sum_probs=38.7

Q ss_pred             ccccceEEEEeeCCCCee-EEecCCCCccEEEEeeccccCC----cccCCCCCEEEEEEeeC
Q 030905            4 VQRSSGTVKWFSAQKGFG-FIAPEDGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDVG   60 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfG-FI~~~~~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~~   60 (169)
                      ...++|+|+...+   || ||..++ +.+-|+|+++|...-    -..+++||.|...+..-
T Consensus        32 G~iv~G~V~~v~~---~G~fV~l~~-~~~Gll~~sel~~~~~~~~~~~~~vGd~V~v~V~~v   89 (109)
T 2khj_A           32 GAIVTGKVTAVDA---KGATVELAD-GVEGYLRASEASRDRVEDATLVLSVGDEVEAKFTGV   89 (109)
T ss_dssp             SSEEEEEEEEECS---SCEEEECST-TCBCCBCTTCCCSSSSSSGGGSCCTTCEEEEEEEEE
T ss_pred             CCEEEEEEEEEEC---CeEEEEECC-CCEEEEEHHHcCcccccChhhccCCCCEEEEEEEEE
Confidence            4578999999854   45 455544 478999999996432    13589999999888754

>3ice_A Transcription termination factor RHO; transcription, ATPase, hexamer, helicase, RNA, RECA, OB fold ATP-binding, hydrolase; HET: MSE ADP SPD; 2.80A {Escherichia coli k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A* 1xpr_A* 1xpu_A* 2ht1_A

Probab=87.36  E-value=0.65  Score=39.79  Aligned_cols=65  Identities=25%  Similarity=0.510  Sum_probs=46.4

Q ss_pred             cceEEEEeeCCCCeeEEecC-----CCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCC-ce-eEEEEEcCCCc
Q 030905            7 SSGTVKWFSAQKGFGFIAPE-----DGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDG-RT-KAVDVEAASRS   76 (169)
Q Consensus         7 ~~G~Vk~~~~~kGfGFI~~~-----~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kG-r~-~A~~V~~~~g~   76 (169)
                      ..|++--.  ..||||+.+.     .+.+||||..+.|+..+   |+.||.|+=.+.....+ |. .-.+|..+++.
T Consensus        54 ~~g~le~~--~~g~gflr~~~~~~~~~~~d~yvs~~~ir~~~---lr~gd~v~g~~r~~~~~ER~faLl~v~~vn~~  125 (422)
T 3ice_A           54 GDGVLEIL--QDGFGFLRSADSSYLAGPDDIYVSPSQIRRFN---LRTGDTISGKIRPPKEGERYFALLKVNEVNFD  125 (422)
T ss_dssp             EEEEEEEC--TTSCEEEECGGGTTCCCTTCEEBCHHHHHHHT---CCTTCEEEEEEECCCSSCCSEEEEEEEEESSS
T ss_pred             EEEEEEEc--CCCceEeeCCCcCCCCCCCCeeeCHHHHHhcC---CCCCCEEEEEEeCCCccchHHHHhccCcccCC
Confidence            45666544  4699999984     35689999999999864   89999999988876554 22 23455555543

>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB: 1yz6_A

Probab=87.11  E-value=1.6  Score=35.13  Aligned_cols=54  Identities=28%  Similarity=0.338  Sum_probs=40.7

Q ss_pred             ccccceEEEEeeCCCCee-EEecCC-CCccEEEEeeccccCC----cccCCCCCEEEEEEeeC
Q 030905            4 VQRSSGTVKWFSAQKGFG-FIAPED-GGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDVG   60 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfG-FI~~~~-~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~~   60 (169)
                      ...+.|+|+...+   || ||..++ .+.+-|+|+|+|...-    -..+++||.|...+..-
T Consensus        12 Gdiv~G~V~~I~~---fGaFV~L~e~~gieGlIhiSels~~~v~~~~~~~kvGd~V~vkVi~v   71 (275)
T 3aev_A           12 GEFVVATVKRIHN---YGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRV   71 (275)
T ss_dssp             TCEEEEEEEEEET---TEEEEEETTSTTCEEEEEGGGSCSSCCSCGGGTCCTTCEEEEEEEEE
T ss_pred             CCEEEEEEEEEEC---cEEEEEECCCCCeEEEEEHHHcCcccccCHHhccCCCCEEEEEEEEE
Confidence            4678999999854   66 666653 4579999999996432    14689999999988754

>2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonu nuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A

Probab=84.52  E-value=3  Score=36.57  Aligned_cols=69  Identities=20%  Similarity=0.222  Sum_probs=50.7

Q ss_pred             cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC------------c-ccCCCCCEEEEEEeeCC---CCceeEE
Q 030905            5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG------------F-RTLSEGQTVEFSVDVGE---DGRTKAV   68 (169)
Q Consensus         5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~------------~-~~l~~G~~V~F~~~~~~---kGr~~A~   68 (169)
                      ..+.|+|+..-+--.=-||....+ .+-|+|++++...-            . ..|++||.|..++...+   ||..-..
T Consensus        47 nIY~GkV~rv~p~~~aAFVdiG~g-k~gfLhisei~~~~~~~~~~~~~~~~i~d~lk~Gq~VlVQV~Ke~~g~KGa~lTt  125 (517)
T 2bx2_L           47 NIYKGKITRIEPSLEAAFVDYGAE-RHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTT  125 (517)
T ss_dssp             CEEEEEEEEEETTTTEEEEESSSS-SCEEEEGGGSCGGGCC-------CCCGGGTCCTTCEEEEEEEECCCTTCCCEEES
T ss_pred             CEEEEEEEEeccCCceEEEEeCCC-cEEEEEHHHcChhhhccccccccccchhhhccCCCEEEEEEEeeccccCCceEEe
Confidence            468999999999888999998765 79999999985321            1 24889999999999865   5532333


Q ss_pred             EEEcCC
Q 030905           69 DVEAAS   74 (169)
Q Consensus        69 ~V~~~~   74 (169)
                      +|++++
T Consensus       126 ~isl~G  131 (517)
T 2bx2_L          126 FISLAG  131 (517)
T ss_dssp             SCCEEC
T ss_pred             eEEecc
Confidence            444444

>2c35_B Human RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transcription, nucleotidyltransferase; 2.70A {Homo sapiens} SCOP: b.40.4.5 d.230.1.1

Probab=83.90  E-value=1.2  Score=32.88  Aligned_cols=52  Identities=13%  Similarity=0.151  Sum_probs=36.8

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccC-C---------------cccCCCCCEEEEEEee
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSE-G---------------FRTLSEGQTVEFSVDV   59 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~-~---------------~~~l~~G~~V~F~~~~   59 (169)
                      .+.+.|+|+.-.+   ||+...-.. -+.|+|+|.|... -               -..+++||.|.+.+..
T Consensus        82 Gev~~G~V~~v~~---fG~fV~l~~-~~glvhis~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~  149 (172)
T 2c35_B           82 GEVVDAVVTQVNK---VGLFTEIGP-MSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVG  149 (172)
T ss_dssp             TCEEEEEEEEEET---TEEEEEETT-EEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEE
T ss_pred             CCEEEEEEEEEeC---CEEEEEECC-EEEEEEHHHCCCCcEECCCCCccEEEeCCCCEEECCCCEEEEEEEE
Confidence            4568899999874   777655544 4599999988532 0               1147789999988765

>4ayb_E DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_E 4b1o_E 4b1p_T 2waq_E 2wb1_E 2pmz_E 3hkz_E

Probab=82.94  E-value=3.3  Score=30.71  Aligned_cols=53  Identities=19%  Similarity=0.249  Sum_probs=40.3

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc---------------ccCCCCCEEEEEEeeC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF---------------RTLSEGQTVEFSVDVG   60 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~---------------~~l~~G~~V~F~~~~~   60 (169)
                      .+.+.|+|+.-+.   ||+..... ..|-++|++.|....+               ..+++||.|.+.+..-
T Consensus        82 Gev~~G~V~~v~~---~G~fv~l~-~~~glvh~s~l~~d~~~~d~~~~~~~g~~~~~~~~~Gd~VrvkV~~v  149 (180)
T 4ayb_E           82 QEVVEGEVLQVDN---YGVFVNLG-PMDGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISV  149 (180)
T ss_dssp             TCEEEEEEEEEET---TEEEEECS-SSEEEEEGGGSCSSCEEECSSSCCEEETTTCCCCCTTCEEEEEEEEE
T ss_pred             CCEEEEEEeeecc---ceEEEEEC-CccceEEeeecCCCccccchhcceEEEeccCeEECCCCEEEEEEEEE
Confidence            4568899999874   67666554 4789999999976532               2589999999998753

>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: b.40.4.5 d.230.1.1

Probab=82.49  E-value=3  Score=31.08  Aligned_cols=53  Identities=19%  Similarity=0.115  Sum_probs=38.4

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC---------------cccCCCCCEEEEEEeeC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG---------------FRTLSEGQTVEFSVDVG   60 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~---------------~~~l~~G~~V~F~~~~~   60 (169)
                      ...+.|+|+.-.+   ||+...-.. .+-|+|+|.+....               -..+++||.|.+.+..-
T Consensus        82 Gev~~G~V~~v~~---~G~fV~l~~-~eglvhis~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~v  149 (187)
T 1go3_E           82 YELIEGEVVDVVE---FGSFVRLGP-LDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAI  149 (187)
T ss_dssp             TCEEEEEEEEEET---TEEEEECSS-SEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEE
T ss_pred             CCEEEEEEEEEeC---cEEEEEEcC-ccEEEEhHHhCCCcceECCccceEEecCCCeEEcCCCEEEEEEEEE
Confidence            4568899999874   665554443 79999999986321               14588999999988753

>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=81.93  E-value=0.95  Score=33.71  Aligned_cols=53  Identities=17%  Similarity=0.271  Sum_probs=37.9

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC-c-------------ccCCCCCEEEEEEeeC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG-F-------------RTLSEGQTVEFSVDVG   60 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~-~-------------~~l~~G~~V~F~~~~~   60 (169)
                      .+.+.|+|+.-.+   |||...-+. -+.|+|+|.|...- |             ..+++||.|.+.+..-
T Consensus        85 Gev~~G~V~~v~~---fG~FV~l~~-~~glVh~s~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~v  151 (172)
T 3h0g_G           85 GEVVDAIVTTVNK---MGFFANIGP-LNVFVSSHLVPPDMKFDPTANPPNYSGEDQVIEKGSNVRLKIVGT  151 (172)
T ss_dssp             TCEEECCCCEEET---TEEECCBTT-BCCEEEGGGSCTTCCCBSSSSSCBEESSSCEECSSCCEEEEEEEE
T ss_pred             CCEEEEEEEEEEc---ceEEEEeCC-eEEEEEHHHCCCccccCcccccceEecCCcEECCCCEEEEEEEEE
Confidence            3567888888874   887766554 56999999995320 1             3578999999888753

>1q8k_A Eukaryotic translation initiation factor 2 subunit 1; NMR {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 d.58.51.1

Probab=81.67  E-value=3.2  Score=33.98  Aligned_cols=54  Identities=9%  Similarity=0.105  Sum_probs=40.8

Q ss_pred             ccccceEEEEeeCCCCee-EEecCC-CCccEEEEeeccccCC----cccCCCCCEEEEEEeeC
Q 030905            4 VQRSSGTVKWFSAQKGFG-FIAPED-GGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDVG   60 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfG-FI~~~~-~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~~   60 (169)
                      ...+.|+|+...+   || ||..++ .+.+-|+|+|+|...-    -..+++||.|...+..-
T Consensus        14 G~iv~G~V~~I~~---fGaFV~L~ey~gveGLvhiSels~~~i~~~~~~~kvGd~V~VkVl~v   73 (308)
T 1q8k_A           14 EDVVMVNVRSIQE---MGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNECVKVIRV   73 (308)
T ss_dssp             CCEEEEEEEEEET---TEEEEESCTTTSCCEEECGGGTSCSSCSCCTTTCSSSCEEEEEEEEE
T ss_pred             CCEEEEEEEEEeC---cEEEEEECCCCCeEEEEEhHHcCcccccCHHHhcCCCCEEEEEEEEE
Confidence            4578999999975   77 666553 4579999999996432    24588999999988754

>2a19_A EIF-2- alpha, eukaryotic translation initiation factor 2 alpha; transferase, protein biosynthesis, protein synthesis transferase complex; HET: TPO ANP; 2.50A {Saccharomyces cerevisiae} PDB: 2a1a_A* 1q46_A

Probab=80.47  E-value=2.8  Score=31.39  Aligned_cols=54  Identities=7%  Similarity=-0.015  Sum_probs=36.4

Q ss_pred             ccccceEEEEeeCCCCee-EEecC-CCCccEEEEeeccccCC----cccCCCCCEEEEEEeeC
Q 030905            4 VQRSSGTVKWFSAQKGFG-FIAPE-DGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDVG   60 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfG-FI~~~-~~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~~   60 (169)
                      ...+.|+|+...   -|| ||..+ ..+.+-|+|+|+|...-    -..+++||.|...+..-
T Consensus        16 G~iv~G~V~~i~---~fGaFV~L~e~~gveGLvhiSels~~~v~~~~~~~~vGd~V~vkVl~v   75 (175)
T 2a19_A           16 DDIVMVNVQQIA---EMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRV   75 (175)
T ss_dssp             TCEEEEEEEEEE---TTEEEEEETTTTTCEEEEECC--------CCCCCCCTTSEEEEEEEEE
T ss_pred             CCEEEEEEEEEe---cceEEEEEcCCCCcEEEEEHHHcCCcccCCHHHcCCCCCEEEEEEEEE
Confidence            467899999884   577 66664 24578999999996432    24588999999987754

---

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	169
d1mjca_	69	b.40.4.5 (A:) Major cold shock protein {Escherichi	1e-21
d1h95a_	79	b.40.4.5 (A:) Y-box protein 1 cold shock domain (Y	1e-19
d1c9oa_	66	b.40.4.5 (A:) Major cold shock protein {Bacillus c	3e-18
d1g6pa_	66	b.40.4.5 (A:) Major cold shock protein {Thermotoga	5e-18
d1wfqa_	89	b.40.4.5 (A:) Cold shock domain protein E1 (UNR) {	2e-09
d2exfa1	42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	3e-09

>d1mjca_ b.40.4.5 (A:) Major cold shock protein {Escherichia coli [TaxId: 562]} Length = 69

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Major cold shock protein
species: Escherichia coli [TaxId: 562]

 Score = 80.9 bits (200), Expect = 1e-21
 Identities = 31/65 (47%), Positives = 49/65 (75%), Gaps = 1/65 (1%)

Query: 6  RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRT 65
          + +G VKWF+A KGFGFI P+DG +D+FVH ++I+++G+++L EGQ V F+++ G  G  
Sbjct: 3  KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGP- 61

Query: 66 KAVDV 70
           A +V
Sbjct: 62 AAGNV 66

>d1h95a_ b.40.4.5 (A:) Y-box protein 1 cold shock domain (YB1-CSD) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Y-box protein 1 cold shock domain (YB1-CSD)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 76.4 bits (188), Expect = 1e-19
 Identities = 32/70 (45%), Positives = 44/70 (62%), Gaps = 5/70 (7%)

Query: 5  QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDVG 60
           +  GTVKWF+ + G+GFI   D  ED+FVHQT+IK        R++ +G+TVEF V  G
Sbjct: 7  TKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEG 66

Query: 61 EDGRTKAVDV 70
          E G  +A +V
Sbjct: 67 EKGA-EAANV 75

>d1c9oa_ b.40.4.5 (A:) Major cold shock protein {Bacillus caldolyticus [TaxId: 1394]} Length = 66

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Major cold shock protein
species: Bacillus caldolyticus [TaxId: 1394]

 Score = 72.1 bits (177), Expect = 3e-18
 Identities = 32/62 (51%), Positives = 43/62 (69%), Gaps = 2/62 (3%)

Query: 9  GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAV 68
          G VKWF+ +KG+GFI   +GG D+FVH T+I+ EGF+TL EGQ V F +  G  G  +A 
Sbjct: 4  GKVKWFNNEKGYGFIEV-EGGSDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGNRGP-QAA 61

Query: 69 DV 70
          +V
Sbjct: 62 NV 63

>d1g6pa_ b.40.4.5 (A:) Major cold shock protein {Thermotoga maritima [TaxId: 2336]} Length = 66

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Major cold shock protein
species: Thermotoga maritima [TaxId: 2336]

 Score = 71.7 bits (176), Expect = 5e-18
 Identities = 31/64 (48%), Positives = 45/64 (70%), Gaps = 2/64 (3%)

Query: 9  GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAV 68
          G VKWF ++KG+GFI  ++G  D+FVH ++I+ EGF+TL EGQ VEF +  G+ G  +A 
Sbjct: 3  GKVKWFDSKKGYGFITKDEG-GDVFVHWSAIEMEGFKTLKEGQVVEFEIQEGKKGP-QAA 60

Query: 69 DVEA 72
           V+ 
Sbjct: 61 HVKV 64

>d1wfqa_ b.40.4.5 (A:) Cold shock domain protein E1 (UNR) {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Cold shock domain protein E1 (UNR)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.9 bits (119), Expect = 2e-09
 Identities = 18/71 (25%), Positives = 27/71 (38%), Gaps = 4/71 (5%)

Query: 5  QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGE-DG 63
           R +G ++       +GFI   +    LF H +       + L  G  VEF V      G
Sbjct: 17 LRETGVIEKLL--TSYGFIQCSERQARLFFHCSQYN-GNLQDLKVGDDVEFEVSSDRRTG 73

Query: 64 RTKAVDVEAAS 74
          +  AV +   S
Sbjct: 74 KPIAVKLVKIS 84

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Length = 42

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

 Score = 48.3 bits (115), Expect = 3e-09
 Identities = 19/49 (38%), Positives = 25/49 (51%), Gaps = 12/49 (24%)

Query: 120 CFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPN 168
           CFNCG+ GH AR C +  +             GC+ CG+EGH  +DC  
Sbjct: 4   CFNCGKEGHTARNCRAPRK------------KGCWKCGKEGHQMKDCTE 40

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	169
d1mjca_	69	Major cold shock protein {Escherichia coli [TaxId:	99.94
d1h95a_	79	Y-box protein 1 cold shock domain (YB1-CSD) {Human	99.93
d1g6pa_	66	Major cold shock protein {Thermotoga maritima [Tax	99.92
d1c9oa_	66	Major cold shock protein {Bacillus caldolyticus [T	99.92
d1wfqa_	89	Cold shock domain protein E1 (UNR) {Human (Homo sa	99.8
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	99.51
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	98.18
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	98.15
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	97.72
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	97.61
d2ix0a2	79	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	97.61
d1a62a2	78	Rho termination factor, RNA-binding domain {Escher	97.4
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	97.23
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	96.35
d1cl4a_	32	Nucleocapsid protein from mason-pfizer monkey viru	95.97
d1dsva_	31	Nucleic acid binding protein p14 {Mouse mammary tu	95.78
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	95.35
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	94.18
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	93.68
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	93.65
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	93.54
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	92.22
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	91.84
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	91.48
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	90.77
d1u0la1	66	Probable GTPase EngC (YjeQ), N-terminal domain {Th	90.59
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	89.94
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	89.58
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	89.33
d2ix0a1	90	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	85.99
d1j6qa_	100	Heme chaperone CcmE {Shewanella putrefaciens [TaxI	84.27

>d1mjca_ b.40.4.5 (A:) Major cold shock protein {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Major cold shock protein
species: Escherichia coli [TaxId: 562]

Probab=99.94  E-value=1.2e-26  Score=152.26  Aligned_cols=68  Identities=46%  Similarity=0.971  Sum_probs=64.5

Q ss_pred             cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcC
Q 030905            5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAA   73 (169)
Q Consensus         5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~   73 (169)
                      .+++|+|||||.+||||||+++++++|||||+|+|+..+++.|.+||+|+|++.++++| ++|+||+.+
T Consensus         2 ~r~~G~Vk~f~~~kGfGFI~~d~g~~diFvH~s~l~~~~~~~L~~G~~V~f~~~~~~~G-~~A~~V~~l   69 (69)
T d1mjca_           2 GKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKG-PAAGNVTSL   69 (69)
T ss_dssp             CCEEEEEEEEETTTTEEEEEETTSCCCEEEEGGGBCCTTTCCCCTTCEEEEEEECCSSS-CEEEEEEEC
T ss_pred             CCEEEEEEEEeCCCCEEEEEEcCCCccEEEEhHHhcccCCCcCCCCCEEEEEEEeCCCC-cEEEEEEeC
Confidence            57999999999999999999999889999999999998999999999999999999999 799999864

>d1h95a_ b.40.4.5 (A:) Y-box protein 1 cold shock domain (YB1-CSD) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Y-box protein 1 cold shock domain (YB1-CSD)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.93  E-value=1e-26  Score=156.31  Aligned_cols=69  Identities=46%  Similarity=0.860  Sum_probs=63.9

Q ss_pred             cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC----cccCCCCCEEEEEEeeCCCCceeEEEEEcCC
Q 030905            5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDVGEDGRTKAVDVEAAS   74 (169)
Q Consensus         5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~~   74 (169)
                      .+++|+|||||.+||||||+++++++|||||+|+|...+    ++.|.+||.|+|++.++++| ++|++|+.|+
T Consensus         7 ~r~~G~VKwfn~~KGfGFI~~ddg~~DvFvH~s~i~~~g~~~~~~~L~~G~~V~f~~~~~~~G-~~A~~Vtgpg   79 (79)
T d1h95a_           7 TKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKG-AEAANVTGPG   79 (79)
T ss_dssp             EEEEEEEEEEETTTTEEEEEEGGGTEEEEEEGGGBCSCCCSCCSCSCCSSCEEEEEEEECSSS-EEEESBCCCC
T ss_pred             CcccEEEEEEcCCCCeEEEEECCCCccEEEEhhHcccCCCcceeeecCCCCEEEEEEEeCCCC-CeeEEEeCCC
Confidence            678899999999999999999998899999999998876    67899999999999999999 6999998663

>d1g6pa_ b.40.4.5 (A:) Major cold shock protein {Thermotoga maritima [TaxId: 2336]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Major cold shock protein
species: Thermotoga maritima [TaxId: 2336]

Probab=99.92  E-value=1.6e-25  Score=145.64  Aligned_cols=66  Identities=47%  Similarity=0.941  Sum_probs=61.9

Q ss_pred             cceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcCC
Q 030905            7 SSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAAS   74 (169)
Q Consensus         7 ~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~~   74 (169)
                      ++|+|||||++||||||+++++ +|||||+|+|...+++.|.+|++|+|++.++++| ++|.+|++++
T Consensus         1 l~G~Vk~f~~~kGfGFI~~~~g-~diFvH~s~l~~~g~~~l~~G~~V~f~~~~~~~G-~~A~~V~~id   66 (66)
T d1g6pa_           1 MRGKVKWFDSKKGYGFITKDEG-GDVFVHWSAIEMEGFKTLKEGQVVEFEIQEGKKG-PQAAHVKVVE   66 (66)
T ss_dssp             CCEEEEEEETTTTEEEEEETTS-CBCBBCSSSSCCSSCCCCCSSSEEEEEEECSSSC-CEEEEEEEEC
T ss_pred             CeEEEEEEeCCCCeeEEEecCC-ceEEEEhHHhcccCCCcCCCCCEEEEEEEECCCC-CEEEEEEecC
Confidence            5799999999999999999876 6999999999999999999999999999999999 7999999864

>d1c9oa_ b.40.4.5 (A:) Major cold shock protein {Bacillus caldolyticus [TaxId: 1394]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Major cold shock protein
species: Bacillus caldolyticus [TaxId: 1394]

Probab=99.92  E-value=2.7e-25  Score=144.55  Aligned_cols=66  Identities=48%  Similarity=0.883  Sum_probs=61.0

Q ss_pred             ccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcC
Q 030905            6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAA   73 (169)
Q Consensus         6 ~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~   73 (169)
                      |.+|+|||||++||||||++++ ++|||||+|+|+..+++.|.+|++|+|++.++++| ++|++|+.+
T Consensus         1 M~~G~Vk~fn~~kGfGFI~~d~-g~DiF~H~s~l~~~~~~~L~~G~~V~f~~~~~~~G-~~A~~V~~l   66 (66)
T d1c9oa_           1 MQRGKVKWFNNEKGYGFIEVEG-GSDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGNRG-PQAANVVKL   66 (66)
T ss_dssp             CEEEEEEEEETTTTEEEEEETT-EEEEEEEGGGBCSSSCCCCCTTCEEEEEEEEETTE-EEEEEEEEC
T ss_pred             CCCeEEEEEECCCCEEEEEecC-CceEEEEehhcccccCCcCCCCCEEEEEEEECCCC-CEEEEEEEC
Confidence            4589999999999999999986 47999999999999999999999999999999999 799999864

>d1wfqa_ b.40.4.5 (A:) Cold shock domain protein E1 (UNR) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Cold shock domain protein E1 (UNR)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=9.7e-20  Score=124.47  Aligned_cols=69  Identities=26%  Similarity=0.455  Sum_probs=61.7

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCC-CceeEEEEEcCCC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGED-GRTKAVDVEAASR   75 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~k-Gr~~A~~V~~~~g   75 (169)
                      .++.+|+|+||+  ++||||+++++.+|||||+++|.. +++.|++||+|+|++.++++ ++++|++|..+.+
T Consensus        16 ~~r~~G~I~~~~--~gfGFI~~~~~~~dvF~H~s~~~~-~~~~l~~G~~VeF~v~~~~kg~k~~Av~V~~~~~   85 (89)
T d1wfqa_          16 ALRETGVIEKLL--TSYGFIQCSERQARLFFHCSQYNG-NLQDLKVGDDVEFEVSSDRRTGKPIAVKLVKISG   85 (89)
T ss_dssp             CCEEEEEEEEEC--SSEEEEEETTTTEEEEEETTTCSS-CTTTCCTTCCEEEEEEECSSSCCEEEEEEEESSC
T ss_pred             cceEEEEEEEec--CccceEEeCCCCceEEEEeehhhc-cCCcccCCCEEEEEEEECCCCCceEEEEEEECCC
Confidence            478999999995  599999999998999999999974 57889999999999999976 6889999987764

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

Probab=99.51  E-value=4.4e-15  Score=87.35  Aligned_cols=41  Identities=46%  Similarity=1.139  Sum_probs=36.5

Q ss_pred             CCCccccCcCCeecccCCCCCCCCCCCCCCCCCCccccccCCCCccCCCCCCC
Q 030905          117 SGACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPNY  169 (169)
Q Consensus       117 ~~~C~~Cg~~GH~a~~C~~~~~~~~~~~~g~~~~~~C~~Cg~~GH~ardCp~~  169 (169)
                      ++.||+|++.||++++||.+.            ...||+|++.||+++|||+.
T Consensus         1 ni~C~~Cg~~GH~~~~Cp~~~------------~~~C~~Cg~~GH~~~~Cp~r   41 (42)
T d2exfa1           1 NVKCFNCGKEGHTARNCRAPR------------KKGCWKCGKEGHQMKDCTER   41 (42)
T ss_dssp             CCCCTTTCCSSSCTTTCSSCC------------CSSCSSSCCSSSCTTTCCSS
T ss_pred             CCccccCCCcCcCcccCcCCC------------cCccccCCCCCeecccCCCC
Confidence            468999999999999999853            45799999999999999973

>d1nc8a_ g.40.1.1 (A:) HIV nucleocapsid {Human immunodeficiency virus type 2 [TaxId: 11709]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 2 [TaxId: 11709]

Probab=98.18  E-value=2.7e-07  Score=47.87  Aligned_cols=19  Identities=53%  Similarity=1.066  Sum_probs=16.6

Q ss_pred             CCccccccCCCCccCCCCC
Q 030905          149 GGGGCYNCGEEGHFARDCP  167 (169)
Q Consensus       149 ~~~~C~~Cg~~GH~ardCp  167 (169)
                      ...+||+|+++||+|++|.
T Consensus         5 ~~ikCfNCGkeGH~ar~Cr   23 (29)
T d1nc8a_           5 KVIRCWNCGKEGHSARQCR   23 (29)
T ss_dssp             CCCBCTTTSCBSSCGGGCC
T ss_pred             ceeEeecCCccchhhhhcc
Confidence            3678999999999999995

>d1nc8a_ g.40.1.1 (A:) HIV nucleocapsid {Human immunodeficiency virus type 2 [TaxId: 11709]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 2 [TaxId: 11709]

Probab=98.15  E-value=5.6e-07  Score=46.63  Aligned_cols=23  Identities=39%  Similarity=0.874  Sum_probs=20.4

Q ss_pred             CCCCCccccCcCCeecccCCCCC
Q 030905          115 AGSGACFNCGRTGHIARECYSRG  137 (169)
Q Consensus       115 ~~~~~C~~Cg~~GH~a~~C~~~~  137 (169)
                      ...+.|||||+.||+|++|..+.
T Consensus         4 r~~ikCfNCGkeGH~ar~CrAPR   26 (29)
T d1nc8a_           4 RKVIRCWNCGKEGHSARQCRAPR   26 (29)
T ss_dssp             CCCCBCTTTSCBSSCGGGCCSSS
T ss_pred             cceeEeecCCccchhhhhccCcc
Confidence            46789999999999999999864

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

Probab=97.72  E-value=5.4e-06  Score=47.58  Aligned_cols=18  Identities=56%  Similarity=1.274  Sum_probs=16.8

Q ss_pred             ccccccCCCCccCCCCCC
Q 030905          151 GGCYNCGEEGHFARDCPN  168 (169)
Q Consensus       151 ~~C~~Cg~~GH~ardCp~  168 (169)
                      .+||+|++.||+++|||+
T Consensus         2 i~C~~Cg~~GH~~~~Cp~   19 (42)
T d2exfa1           2 VKCFNCGKEGHTARNCRA   19 (42)
T ss_dssp             CCCTTTCCSSSCTTTCSS
T ss_pred             CccccCCCcCcCcccCcC
Confidence            579999999999999996

>d1dsqa_ g.40.1.1 (A:) Nucleic acid binding protein p14 {Mouse mammary tumor virus [TaxId: 11757]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Nucleic acid binding protein p14
species: Mouse mammary tumor virus [TaxId: 11757]

Probab=97.61  E-value=1.2e-05  Score=39.83  Aligned_cols=18  Identities=44%  Similarity=1.224  Sum_probs=15.4

Q ss_pred             ccccccCCCCccCCCCCC
Q 030905          151 GGCYNCGEEGHFARDCPN  168 (169)
Q Consensus       151 ~~C~~Cg~~GH~ardCp~  168 (169)
                      ..||.|++.||+.+||.+
T Consensus         3 pvcfscgktghikkdck~   20 (26)
T d1dsqa_           3 PVCFSCGKTGHIKRDCKE   20 (26)
T ss_dssp             CBCTTTCCBSSCTTTTTC
T ss_pred             CEEEecCCcccchhhhhh
Confidence            469999999999999965

>d2ix0a2 b.40.4.5 (A:4-82) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exoribonuclease 2, RNB
species: Escherichia coli [TaxId: 562]

Probab=97.61  E-value=3.6e-05  Score=49.87  Aligned_cols=61  Identities=26%  Similarity=0.436  Sum_probs=44.1

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAA   73 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~   73 (169)
                      ...++|+|.-  ..+||||+.+++ .+|||+...++...     -.||.|...+.. .++|+.|.=|.++
T Consensus        16 ~~~~~G~i~~--~~~G~GFv~~d~-~~DifI~~~~~~~A-----~~GD~V~v~i~~-~~~r~eg~I~~il   76 (79)
T d2ix0a2          16 TPRAEGVVKA--TEKGFGFLEVDA-QKSYFIPPPQMKKV-----MHGDRIIAVIHS-EKERESAEPEELV   76 (79)
T ss_dssp             SCEEEEEEEC--CC--CEEEEEET-TEEEEECHHHHTTC-----CTTCEEEEEEEC-C--CCEEEEEEEE
T ss_pred             CCEEEEEEEE--eCCCcEEEEECC-CCcEEECHHHHcCC-----CCCCEEEEEEEe-CCCcEEEEEEEEe
Confidence            4567788875  368999999987 58999999999753     699999999864 4566777655543

>d1a62a2 b.40.4.5 (A:48-125) Rho termination factor, RNA-binding domain {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Rho termination factor, RNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=97.40  E-value=0.0002  Score=46.08  Aligned_cols=58  Identities=24%  Similarity=0.499  Sum_probs=46.4

Q ss_pred             CCCeeEEecC-----CCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCc--eeEEEEEcCCCcc
Q 030905           17 QKGFGFIAPE-----DGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGR--TKAVDVEAASRSR   77 (169)
Q Consensus        17 ~kGfGFI~~~-----~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr--~~A~~V~~~~g~~   77 (169)
                      ..|||||...     .+.+||||..+.|+..+   |+.|+.|+=.+.....+.  +..+.|..+++.+
T Consensus        12 ~dGyGFLR~~~~~y~~~~~DiyVs~s~Irrfg---LR~GD~V~G~vr~p~~~ek~~~L~~V~~VNG~~   76 (78)
T d1a62a2          12 QDGFGFLRSADSSYLAGPDDIYVSPSQIRRFN---LRTGDTISGKIRPPKEGERYFALLKVNEVNFDK   76 (78)
T ss_dssp             TTSCEEEECGGGTTCCCTTCEEECHHHHHHTT---CCTTCEEEEEEECCCTTCCSEEEEEEEEETTBC
T ss_pred             CCCcEEeECCccCCCCCCcceEECHHHHHHhC---CCcCcEEEEEEECCCCCCCceeeEEEeeeCCcC
Confidence            4799999973     35679999999999875   889999999998775552  5567888887654

>d1a6bb_ g.40.1.1 (B:) Zinc finger protein ncp10 {Moloney murine leukemia virus, MoMLV [TaxId: 11801]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Zinc finger protein ncp10
species: Moloney murine leukemia virus, MoMLV [TaxId: 11801]

Probab=97.23  E-value=6.2e-05  Score=41.59  Aligned_cols=20  Identities=45%  Similarity=1.082  Sum_probs=17.1

Q ss_pred             CccccccCCCCccCCCCCCC
Q 030905          150 GGGCYNCGEEGHFARDCPNY  169 (169)
Q Consensus       150 ~~~C~~Cg~~GH~ardCp~~  169 (169)
                      ...|-.|.+.|||++|||..
T Consensus        10 kDQCAyCke~GHW~~dCPkk   29 (40)
T d1a6bb_          10 RDQCAYCKEKGHWAKDCPKK   29 (40)
T ss_dssp             SSSCSSSCCTTCCTTSCSSS
T ss_pred             chhhHHHhhcCchhhhCccC
Confidence            46799999999999999863

>d1cl4a_ g.40.1.1 (A:) Nucleocapsid protein from mason-pfizer monkey virus (MPMV) {Mason-pfizer monkey virus [TaxId: 11855]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Nucleocapsid protein from mason-pfizer monkey virus (MPMV)
species: Mason-pfizer monkey virus [TaxId: 11855]

Probab=95.97  E-value=0.0018  Score=34.05  Aligned_cols=20  Identities=30%  Similarity=0.715  Sum_probs=16.8

Q ss_pred             CccccccCCCCccCCCCCCC
Q 030905          150 GGGCYNCGEEGHFARDCPNY  169 (169)
Q Consensus       150 ~~~C~~Cg~~GH~ardCp~~  169 (169)
                      +..|.+|.+--|||+||.++
T Consensus         2 P~lCPrC~kG~HWa~~Crsk   21 (32)
T d1cl4a_           2 PGLCPRCKRGKHWANECKSK   21 (32)
T ss_dssp             CCSCSSCSSCSSCSTTCCCT
T ss_pred             CccCccccCcchHHHHhhhh
Confidence            35799999999999999763

>d1dsva_ g.40.1.1 (A:) Nucleic acid binding protein p14 {Mouse mammary tumor virus [TaxId: 11757]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Nucleic acid binding protein p14
species: Mouse mammary tumor virus [TaxId: 11757]

Probab=95.78  E-value=0.0024  Score=33.34  Aligned_cols=20  Identities=25%  Similarity=0.625  Sum_probs=16.9

Q ss_pred             CccccccCCCCccCCCCCCC
Q 030905          150 GGGCYNCGEEGHFARDCPNY  169 (169)
Q Consensus       150 ~~~C~~Cg~~GH~ardCp~~  169 (169)
                      ...|.+|.+--|||+||-++
T Consensus         2 p~lCPrC~kG~HWa~~Crsk   21 (31)
T d1dsva_           2 PGLCPRCKKGYHWKSECKSK   21 (31)
T ss_dssp             CCBCTTTCSSBSCTTTCCCS
T ss_pred             CccCccccCcchHHHHhhhh
Confidence            35799999999999999764

>d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase
species: Escherichia coli [TaxId: 562]

Probab=95.35  E-value=0.03  Score=34.82  Aligned_cols=58  Identities=28%  Similarity=0.375  Sum_probs=44.7

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEee-CCCCc
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDV-GEDGR   64 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~-~~kGr   64 (169)
                      .+.++|+|+...+   ||.+..-....+-|+|+++|...-.    ..+++||.|++.+.. ++++|
T Consensus         6 G~iv~G~V~~v~~---~G~fV~l~~~~~Glv~~sels~~~~~~~~~~~~~G~~v~v~Vi~id~~~r   68 (76)
T d1sroa_           6 GRVYTGKVTRIVD---FGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDRQGR   68 (76)
T ss_dssp             TSEEEEEEEEEET---TEEEEECSSSCCCBCCTTSSCSSCCSCHHHHCCTTCEEEEEEEECCTTCC
T ss_pred             CCEEEEEEEEEeC---cEEEEEeCCCCEEEEEhHHhCccccCCHHHccCCCCEEEEEEEEECCCCC
Confidence            5678999999985   7766665555789999999976532    348999999998887 45564

>d2ba0a1 b.40.4.5 (A:53-135) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=94.18  E-value=0.15  Score=31.82  Aligned_cols=58  Identities=12%  Similarity=0.022  Sum_probs=41.9

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC-----cccCCCCCEEEEEEee-CCCCc
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG-----FRTLSEGQTVEFSVDV-GEDGR   64 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~-----~~~l~~G~~V~F~~~~-~~kGr   64 (169)
                      .+.+.|+|+.-.+   ||.+..-...-+-|+|++++....     ...+++||.|...+.. +++++
T Consensus         6 Gd~V~G~V~~v~~---~g~~V~i~~~~~g~l~~se~s~~~~~~~~~~~~~vGd~V~~kV~~vd~~~~   69 (83)
T d2ba0a1           6 GDVVIGIIREVAA---NGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDPKMK   69 (83)
T ss_dssp             TCEEEEEEEEECS---SEEEEECSSSSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECTTCC
T ss_pred             CCEEEEEEEEEEC---CEEEEecCCCeeEEEecccccccccccChhhhcccccEEEEEEEEECCCCC
Confidence            4678999999865   455555444579999999997532     2348999999998876 34553

>d1smxa_ b.40.4.5 (A:) S1-domain of Ribonuclease E {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of Ribonuclease E
species: Escherichia coli [TaxId: 562]

Probab=93.68  E-value=0.11  Score=33.27  Aligned_cols=57  Identities=21%  Similarity=0.207  Sum_probs=46.3

Q ss_pred             cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC-------------cccCCCCCEEEEEEeeCCC
Q 030905            5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG-------------FRTLSEGQTVEFSVDVGED   62 (169)
Q Consensus         5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~-------------~~~l~~G~~V~F~~~~~~k   62 (169)
                      ..+.|+|+...+.-.=-||..... ++-|+|++++....             -..|++||.|.-++..++.
T Consensus         2 NIY~G~V~~V~pgl~AAFVDiG~~-k~gFL~~~di~~~~~~~~~~~~~~~~i~~~l~~G~~ilVQV~Ke~~   71 (87)
T d1smxa_           2 NIYKGKITRIEPSLEAAFVDYGAE-RHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEER   71 (87)
T ss_dssp             CCEEEEEEEEEGGGTEEEEESSSS-SCEEEEGGGSCGGGCSSCCCSSSCCCGGGTCCTTCEEEEEEEECCB
T ss_pred             CcEEEEEEEecCCceEEEEEeCCC-ccceeEecccceeeeccccccccccchhhhccCCCeEEEEEeeccc
Confidence            468899999999999999998765 78999999875432             1358999999999998753

>d1kl9a2 b.40.4.5 (A:3-88) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.65  E-value=0.092  Score=33.11  Aligned_cols=53  Identities=8%  Similarity=0.072  Sum_probs=36.3

Q ss_pred             ccccceEEEEeeCCCCee-EEecCC-CCccEEEEeeccccCC----cccCCCCCEEEEEEee
Q 030905            4 VQRSSGTVKWFSAQKGFG-FIAPED-GGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDV   59 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfG-FI~~~~-~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~   59 (169)
                      .+.++|+|+...   -|| ||.-+. .+-+-|+|+++|...-    ...+++||.|...+..
T Consensus        14 G~iv~G~V~~i~---~~G~fV~l~~~~~i~G~i~~sels~~~~~~~~~~~~~Gd~v~~kV~~   72 (86)
T d1kl9a2          14 EDVVMVNVRSIA---EMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIR   72 (86)
T ss_dssp             TCEEEEEEEEEC---SSEEEEEETTTTTEEEEEEGGGC------------CTTCEEEEEEEE
T ss_pred             CCEEEEEEEEEe---CCeEEEEEecCCCEEEEEEeeeccccccccceEEeecccEEEEEEEE
Confidence            467899999985   488 666654 3468999999996542    2447899999998876

>d1a6bb_ g.40.1.1 (B:) Zinc finger protein ncp10 {Moloney murine leukemia virus, MoMLV [TaxId: 11801]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Zinc finger protein ncp10
species: Moloney murine leukemia virus, MoMLV [TaxId: 11801]

Probab=93.54  E-value=0.023  Score=30.97  Aligned_cols=23  Identities=30%  Similarity=0.745  Sum_probs=19.4

Q ss_pred             CCCCccccCcCCeecccCCCCCC
Q 030905          116 GSGACFNCGRTGHIARECYSRGR  138 (169)
Q Consensus       116 ~~~~C~~Cg~~GH~a~~C~~~~~  138 (169)
                      ....|--|-+.||++++||....
T Consensus         9 ~kDQCAyCke~GHW~~dCPkkpr   31 (40)
T d1a6bb_           9 DRDQCAYCKEKGHWAKDCPKKPR   31 (40)
T ss_dssp             CSSSCSSSCCTTCCTTSCSSSCC
T ss_pred             cchhhHHHhhcCchhhhCccCCC
Confidence            44579999999999999998653

>d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=92.22  E-value=0.13  Score=32.07  Aligned_cols=54  Identities=22%  Similarity=0.254  Sum_probs=39.1

Q ss_pred             ccccceEEEEeeCCCCee-EEecCC-CCccEEEEeeccccCC----cccCCCCCEEEEEEeeC
Q 030905            4 VQRSSGTVKWFSAQKGFG-FIAPED-GGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDVG   60 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfG-FI~~~~-~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~~   60 (169)
                      .+.++|+|+...+   || ||+.+. .+-+-|+|+++|...-    ...+++||.|.+.+..-
T Consensus        12 G~iv~G~V~~v~~---~G~fV~l~~~~gi~Gli~~sels~~~~~~~~~~~~~G~~v~~kV~~v   71 (84)
T d2ahob2          12 GEILIATVKQVFD---YGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRV   71 (84)
T ss_dssp             TCCCEEEEEEEET---TEEEEEETTTTTEEEEECGGGCC-----CHHHHTCSSCEEECEEEEE
T ss_pred             CCEEEEEEEEEEC---CEEEEEECCcCCEEEEEEccccccccccccceEeecccEEEEEEEEE
Confidence            4678999999964   67 455553 3468999999998642    23489999999988763

>d1go3e1 b.40.4.5 (E:79-184) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=91.84  E-value=0.21  Score=32.80  Aligned_cols=52  Identities=19%  Similarity=0.180  Sum_probs=40.0

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc---------------ccCCCCCEEEEEEee
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF---------------RTLSEGQTVEFSVDV   59 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~---------------~~l~~G~~V~F~~~~   59 (169)
                      ...+.|+|+..+.   |||...-+ +-+-|+|+++|...-+               ..+++||.|...|..
T Consensus         4 gei~~g~V~~v~~---~G~FVel~-~ieGlv~~s~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkV~~   70 (106)
T d1go3e1           4 YELIEGEVVDVVE---FGSFVRLG-PLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVA   70 (106)
T ss_dssp             TCEEEEEEEEEET---TEEEEECS-SSEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEE
T ss_pred             CCEEEEEEEEEee---eEEEEEee-CeEEEEEeecccCceeeeccceeEEeecccccceeecceEEEEEEE
Confidence            4568899999874   56655554 3799999999986433               568999999988875

>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Tex S1-domain
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=91.48  E-value=0.49  Score=30.07  Aligned_cols=65  Identities=17%  Similarity=0.198  Sum_probs=47.6

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC----cccCCCCCEEEEEEeeC--CCCceeEEEEEc
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDVG--EDGRTKAVDVEA   72 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~~--~kGr~~A~~V~~   72 (169)
                      .+.++|+|+....   ||.+..-..+-+-|+|++++...-    -..+++||.|...+..-  .+++ ..+.+..
T Consensus        19 G~iv~g~V~~v~~---~G~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~vGq~v~~~V~~id~~~~~-i~LS~K~   89 (94)
T d3bzka4          19 GMVLEGVVTNVTN---FGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNR-VGLSMRM   89 (94)
T ss_dssp             TCEEEEEEEEEET---TEEEEECSSSSCEEEEGGGGCSSCCSCHHHHCCTTCEEEEEEEEEETTTTE-EEEESCT
T ss_pred             CCEEEEEEEEEEC---cEEEEEeCCCceEEeehhhhhcccccChhhhhccCcEEEEEEEEEECCCCE-EEEEEec
Confidence            5678999999974   677777666689999999997542    14578999999997763  4553 4555443

>d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of RRP5 protein homolog (PDCD11, KIAA0185)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.77  E-value=0.51  Score=31.37  Aligned_cols=56  Identities=18%  Similarity=0.158  Sum_probs=41.9

Q ss_pred             ccccceEEEEeeCCCCeeEEecC-CCCccEEEEeeccccC-----CcccCCCCCEEEEEEeeCCC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPE-DGGEDLFVHQTSIKSE-----GFRTLSEGQTVEFSVDVGED   62 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~-~~~~dvF~H~s~i~~~-----~~~~l~~G~~V~F~~~~~~k   62 (169)
                      .+.++|+|+...   -||++..- ...-+=|+|+++|...     ....|++||.|.+.+..-..
T Consensus        22 G~iv~G~V~~i~---~~G~~V~lg~~~~~G~l~~~els~~~~~~~~~~~~~vGq~v~~~V~~vd~   83 (119)
T d1wi5a_          22 GMLLTGTVSSLE---DHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKG   83 (119)
T ss_dssp             TCEEEEEEEEEC---SSEEEEECCCSSCEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCT
T ss_pred             CCEEEEEEEEEe---ccEEEEEEeccccceEEeHHHhccccccCCHHHhcccceEEEEEEEEEeC
Confidence            678999999995   45766665 3446899999998642     23478999999999877543

>d1u0la1 b.40.4.5 (A:3-68) Probable GTPase EngC (YjeQ), N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Probable GTPase EngC (YjeQ), N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=90.59  E-value=0.89  Score=27.14  Aligned_cols=56  Identities=21%  Similarity=0.357  Sum_probs=37.7

Q ss_pred             cccceEEEEeeCCCCeeEEecCCCCccEEEEeec-cccCCcccCCCCCEEEEEEeeCCCC
Q 030905            5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTS-IKSEGFRTLSEGQTVEFSVDVGEDG   63 (169)
Q Consensus         5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~-i~~~~~~~l~~G~~V~F~~~~~~kG   63 (169)
                      |+.+|+|....  .+|=.|..++.++.+-.++.. |.... ..|.+||.|.|+......|
T Consensus         1 m~~~G~Vi~~~--~~~y~V~~~e~g~~~~c~~rG~lr~~~-~~~~VGD~V~~~~~~~~~g   57 (66)
T d1u0la1           1 LRRRGIVVSFH--SNMVTVEDEETGERILCKLRGKFRLQN-LKIYVGDRVEYTPDETGSG   57 (66)
T ss_dssp             CCEEEEEEEEE--TTEEEEEETTTCCEEEEEECGGGTTTT-CCCCTTCEEEEECCCSSSE
T ss_pred             CCeeEEEEEEE--CCEEEEEECCCCcEEEEEeeccccccC-CccccCCEEEEEECCCCeE
Confidence            45889988875  467777776555555577765 33333 3588999999987765444

>d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=89.94  E-value=0.48  Score=29.58  Aligned_cols=54  Identities=13%  Similarity=0.145  Sum_probs=40.2

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC-------cccCCCCCEEEEEEeeC
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG-------FRTLSEGQTVEFSVDVG   60 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~-------~~~l~~G~~V~F~~~~~   60 (169)
                      .+.+.|+|+....   ||++..-...-+-|+|+++|...-       ...+++||.|...+..-
T Consensus         8 Gdiv~G~V~~i~~---~g~fV~i~~~~~gll~~s~~~~~~~~~~~~~~~~~~~Gd~v~~kV~~v   68 (87)
T d2je6i1           8 NDIVIGLVEDVEI---YGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENF   68 (87)
T ss_dssp             TCEEEEEEEEECS---SEEEEECSSSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEE
T ss_pred             CCEEEEEEEEEEC---CEEEEEeCCCEEEEEehHHhCCceeccccccchhhcccceEEEEEEEE
Confidence            4678999999864   565555555579999999996531       13589999999998753

>d1y14b1 b.40.4.5 (B:81-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.58  E-value=0.41  Score=30.14  Aligned_cols=52  Identities=15%  Similarity=0.177  Sum_probs=37.0

Q ss_pred             cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC--------------cccCCCCCEEEEEEeeC
Q 030905            5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG--------------FRTLSEGQTVEFSVDVG   60 (169)
Q Consensus         5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~--------------~~~l~~G~~V~F~~~~~   60 (169)
                      +.+.|+|+.-++ .|+ |++..  .-|.|+|++.|...-              -..++.|+.|.+.+..-
T Consensus         5 ev~~g~I~~v~~-~G~-fv~lg--~~eg~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~v   70 (91)
T d1y14b1           5 EVVDGTVVSCSQ-HGF-EVQVG--PMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGC   70 (91)
T ss_dssp             CEEEEEEEEEET-TEE-EEEET--TEEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEE
T ss_pred             CEEEEEEEEEEe-eEE-EEEEc--CeEEEEEhhhcCcceEEccccceeEecccCeEEeCCCEEEEEEEEE
Confidence            457899999874 455 55553  358999999996431              12578899998887743

>d2z0sa1 b.40.4.5 (A:60-147) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

Probab=89.33  E-value=0.81  Score=28.46  Aligned_cols=58  Identities=9%  Similarity=0.047  Sum_probs=42.0

Q ss_pred             ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc--------ccCCCCCEEEEEEee-CCCCc
Q 030905            4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF--------RTLSEGQTVEFSVDV-GEDGR   64 (169)
Q Consensus         4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~--------~~l~~G~~V~F~~~~-~~kGr   64 (169)
                      .+.+.|+|+.-.   .||++..-....+-|+|++++.....        ..+++||.|...+.. +++++
T Consensus         8 GdvV~G~V~~v~---~~g~fV~i~~~~~g~l~~se~~~~~~~~~~~~~~~~~~vGd~V~~kV~~vd~~~~   74 (88)
T d2z0sa1           8 GDVVIGLIQSVG---IMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDKTRS   74 (88)
T ss_dssp             TCCEEEEEEEEC---SSEEEEECSSSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECTTSC
T ss_pred             CCEEEEEEEEEE---CCeEEEEeCCCeEEEEehHHhCcccccccccchhhhcccCcEEEEEEEEECCCCC
Confidence            467889999976   35655555556799999999965421        347899999998886 45553

>d2ix0a1 b.40.4.5 (A:83-172) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exoribonuclease 2, RNB
species: Escherichia coli [TaxId: 562]

Probab=85.99  E-value=1.7  Score=27.32  Aligned_cols=63  Identities=14%  Similarity=0.060  Sum_probs=43.1

Q ss_pred             ccceEEEEeeCCCCeeEEecCCCC--ccEEEEeeccccCCcccCCCCCEEEEEEeeCC-C-Cc-eeEEEEEcCC
Q 030905            6 RSSGTVKWFSAQKGFGFIAPEDGG--EDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGE-D-GR-TKAVDVEAAS   74 (169)
Q Consensus         6 ~~~G~Vk~~~~~kGfGFI~~~~~~--~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~-k-Gr-~~A~~V~~~~   74 (169)
                      +..|++   -..++|.||.+|+..  .+||+-......   ..+++||.|.-+|.+-+ + .+ ++|.=+..++
T Consensus         3 rfVGr~---~~~~~~~fVvPd~~ri~~~I~I~~~~~~~---~~ak~Gd~Vvvei~~~P~~~~~~~~g~I~evlG   70 (90)
T d2ix0a1           3 RFVGKV---QGKNDRLAIVPDHPLLKDAIPCRAARGLN---HEFKEGDWAVAEMRRHPLKGDRSFYAELTQYIT   70 (90)
T ss_dssp             EEEEEE---ESCSSSEEEEESCTTCCSCEEEEECTTCC---CCCCTTCEEEEEEEECGGGTCSSCEEEEEEECC
T ss_pred             cEEEEE---EEeCCEEEEEeCCCccccccccccccccc---ccCCCCCEEEEEEEeCCCCCCCCceEEEEEEEe
Confidence            355665   467899999999864  578876555432   34789999999998764 2 32 3565555554

>d1j6qa_ b.40.9.1 (A:) Heme chaperone CcmE {Shewanella putrefaciens [TaxId: 24]}

class: All beta proteins
fold: OB-fold
superfamily: Heme chaperone CcmE
family: Heme chaperone CcmE
domain: Heme chaperone CcmE
species: Shewanella putrefaciens [TaxId: 24]

Probab=84.27  E-value=2.5  Score=27.26  Aligned_cols=60  Identities=22%  Similarity=0.313  Sum_probs=44.7

Q ss_pred             eEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEE
Q 030905            9 GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVE   71 (169)
Q Consensus         9 G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~   71 (169)
                      |.|+|-.....+=|+..|....+|-|+++-+...   .+++|+.|.-+=.-.++|...|.+|.
T Consensus        38 gSi~~~~~~~~~~F~itD~~~~~i~V~Y~G~lPd---lF~eg~gVVveG~~~~~g~F~A~~vl   97 (100)
T d1j6qa_          38 GSMVRDPNSLHVQFAVHDSLGGEILVTYDDLLPD---LFREGQGIVAQGVLGEDGKLAATEVL   97 (100)
T ss_dssp             TCCEECTTSSCEEEEEECTTCCCEEEEECSCCTT---SCCSSSEEEEEEEECSTTSEEEEEEE
T ss_pred             eEEEecCCccEEEEEEcCCceeEEEEEeCCCCCc---hhcCCCeEEEEEEECCCCEEEEEEEE
Confidence            4455433333588999886557899999998764   47899999887777777878998875