Psyllid ID: psy9900

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-
Protein Sequence
MTKFEIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNGIPVQGAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNGIPVQGAPKVP
Secondary Structure (PSIPRED)
cccccEEEEEEEEEEEEccccEEEEEcccccccEEEEcEEEEcccccccccccccccEEEEEEEEccccccEEEEccccccccccccccccccccccccccccccccccccEEEEEEEccccEEEEEcccccccEEEEcEEEEEccccccccccccccEEEEEEEEccccccEEEEEcccccccccccccc
Secondary Structure Prediction (SSPRO)
ccEEEEEEEEEEEEEEEccccEEEEEEccccccEEEEHHHEEccccccEEEEcccccEEEEEEEEcccccEEEEEccccccccccccccccccccccccccccccEEEEEEEEEEEEEccccEEEEEEccccccEEEEHHHEHHcccHHHHEEcccccEEEEEEEccccccEHEEEccccccccccccccc
Coil and Loop (DISEMBL)
mtkfeihtVRGIVkfydskrgfgfitrldnkedifvhkssivkmnpkkffqslglgeivdfnigvgkkdieainvtgpngipvqgapksssetvsgtyrndsffpavHTVRGIVkfydskrgfgfitrldnkedifvhkssivkmnpkkffqslglgeivdfnigvgkkdieainvtgpngipvqgapkvp
Flexible Loop (DISEMBL)
mtkfeihtvrgivkfydskrgfgFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTgpngipvqgapkssSETVSGTYRndsffpavhtvRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAInvtgpngipvqgapkvp
Low Complexity Region (SEG)
MTKFEIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNGIPVQGAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNGIPVQGAPKVP
Disordered region (IsUnstruct)
****************************************IVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPN*****************TYRNDSFFPAVHTVRGIVKFYDSKRGFGFI***************IVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG*************
Disordered Region (DISOPRED)
*********RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNGIPVQGAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNGIPVQ******
Disordered Region (DISEMBL)
MTKFEIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNGIPV************GTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNGIPVQGAPKVP
Disordered Region (DISPRO)
MTKFEIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPN***********************FFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNG**********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MTKFEIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNGIPVQGAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNGIPVQGAPKVP
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	191	2.2.26 [Sep-21-2011]
P45441	324	Y-box-binding protein 2-B	N/A	N/A	0.408	0.240	0.525	2e-19
P21574	336	Y-box-binding protein 2-A	N/A	N/A	0.408	0.232	0.525	2e-19
P21573	303	Nuclease-sensitive elemen	N/A	N/A	0.408	0.257	0.525	3e-19
Q28618	324	Nuclease-sensitive elemen	no	N/A	0.408	0.240	0.525	4e-19
P62961	322	Nuclease-sensitive elemen	yes	N/A	0.408	0.242	0.525	5e-19
P62960	322	Nuclease-sensitive elemen	yes	N/A	0.408	0.242	0.525	5e-19
P67809	324	Nuclease-sensitive elemen	yes	N/A	0.408	0.240	0.525	5e-19
P67808	324	Nuclease-sensitive elemen	yes	N/A	0.408	0.240	0.525	5e-19
Q06066	321	Nuclease-sensitive elemen	yes	N/A	0.408	0.242	0.525	6e-19
Q62764	361	DNA-binding protein A OS=	no	N/A	0.408	0.216	0.512	1e-18

>sp|P45441|YBX2B_XENLA Y-box-binding protein 2-B OS=Xenopus laevis GN=ybx2-b PE=1 SV=2

 Score = 95.1 bits (235), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 41/78 (52%), Positives = 62/78 (79%)

Query: 9   VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
           V+G VK+++ + G+GFI R D+KED+FVH+++I K NP+KF +S+G GE V+F++  G+K
Sbjct: 42  VQGTVKWFNVRNGYGFINRNDSKEDVFVHQTAIKKNNPRKFLRSVGDGETVEFDVVEGEK 101

Query: 69  DIEAINVTGPNGIPVQGA 86
             EA NVTGP G+PV+G+
Sbjct: 102 GAEAANVTGPGGVPVKGS 119

Putative translation regulator. May be involved in the developmental translational regulation of maternal mRNAs.
Xenopus laevis (taxid: 8355)

>sp|P21574|YBX2A_XENLA Y-box-binding protein 2-A OS=Xenopus laevis GN=ybx2-a PE=1 SV=3

 Score = 95.1 bits (235), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 41/78 (52%), Positives = 61/78 (78%)

Query: 9   VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
           V+G VK+++ + G+GFI R D KED+FVH+++I K NP+KF +S+G GE V+F++  G+K
Sbjct: 42  VQGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKFLRSVGDGETVEFDVVEGEK 101

Query: 69  DIEAINVTGPNGIPVQGA 86
             EA NVTGP G+PV+G+
Sbjct: 102 GAEAANVTGPGGVPVKGS 119

Has a dual function in oocytes: as a DNA-binding protein, binds to the Y-box sequence (CTGATTGGCCAA) in the promoters of target genes to stimulate transcription. May also function at CCAAT-containing promoters that lack the consensus Y-box sequence. Also binds mRNA to promote accumulation of the transcripts it contributes to produce.

Xenopus laevis (taxid: 8355)

>sp|P21573|YBOX1_XENLA Nuclease-sensitive element-binding protein 1 OS=Xenopus laevis GN=ybx1 PE=2 SV=1

 Score = 95.1 bits (235), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 41/78 (52%), Positives = 60/78 (76%)

Query: 9   VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
           V G VK+++ + G+GFI R D KED+FVH+++I K NP+K+ +S+G GE V+F++  G+K
Sbjct: 37  VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEK 96

Query: 69  DIEAINVTGPNGIPVQGA 86
             EA NVTGP G+PVQG+
Sbjct: 97  GAEAANVTGPEGVPVQGS 114

Mediates pre-mRNA alternative splicing regulation. Component of the coding region determinant (CRD)-mediated complex that promotes mRNA stability. Binds to splice sites in pre-mRNA and regulates splice site selection. Binds and stabilizes cytoplasmic mRNA. Binds to promoters that contain a Y-box (5'-CTGATTGGCCAA-3'), such as HSP70 genes. Regulates the transcription of numerous genes.

Xenopus laevis (taxid: 8355)

>sp|Q28618|YBOX1_RABIT Nuclease-sensitive element-binding protein 1 OS=Oryctolagus cuniculus GN=YBX1 PE=1 SV=3

 Score = 94.4 bits (233), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 41/78 (52%), Positives = 60/78 (76%)

Query: 9   VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
           V G VK+++ + G+GFI R D KED+FVH+++I K NP+K+ +S+G GE V+F++  G+K
Sbjct: 59  VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEK 118

Query: 69  DIEAINVTGPNGIPVQGA 86
             EA NVTGP G+PVQG+
Sbjct: 119 GAEAANVTGPGGVPVQGS 136

The secreted form acts as an extracellular mitogen and stimulates cell migration and proliferation.

Oryctolagus cuniculus (taxid: 9986)

>sp|P62961|YBOX1_RAT Nuclease-sensitive element-binding protein 1 OS=Rattus norvegicus GN=Ybx1 PE=1 SV=3

 Score = 94.0 bits (232), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 41/78 (52%), Positives = 60/78 (76%)

Query: 9   VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
           V G VK+++ + G+GFI R D KED+FVH+++I K NP+K+ +S+G GE V+F++  G+K
Sbjct: 57  VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEK 116

Query: 69  DIEAINVTGPNGIPVQGA 86
             EA NVTGP G+PVQG+
Sbjct: 117 GAEAANVTGPGGVPVQGS 134

The secreted form acts as an extracellular mitogen and stimulates cell migration and proliferation.

Rattus norvegicus (taxid: 10116)

>sp|P62960|YBOX1_MOUSE Nuclease-sensitive element-binding protein 1 OS=Mus musculus GN=Ybx1 PE=1 SV=3

 Score = 94.0 bits (232), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 41/78 (52%), Positives = 60/78 (76%)

Query: 9   VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
           V G VK+++ + G+GFI R D KED+FVH+++I K NP+K+ +S+G GE V+F++  G+K
Sbjct: 57  VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEK 116

Query: 69  DIEAINVTGPNGIPVQGA 86
             EA NVTGP G+PVQG+
Sbjct: 117 GAEAANVTGPGGVPVQGS 134

The secreted form acts as an extracellular mitogen and stimulates cell migration and proliferation.

Mus musculus (taxid: 10090)

>sp|P67809|YBOX1_HUMAN Nuclease-sensitive element-binding protein 1 OS=Homo sapiens GN=YBX1 PE=1 SV=3

 Score = 94.0 bits (232), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 41/78 (52%), Positives = 60/78 (76%)

Query: 9   VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
           V G VK+++ + G+GFI R D KED+FVH+++I K NP+K+ +S+G GE V+F++  G+K
Sbjct: 59  VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEK 118

Query: 69  DIEAINVTGPNGIPVQGA 86
             EA NVTGP G+PVQG+
Sbjct: 119 GAEAANVTGPGGVPVQGS 136

The secreted form acts as an extracellular mitogen and stimulates cell migration and proliferation.

Homo sapiens (taxid: 9606)

>sp|P67808|YBOX1_BOVIN Nuclease-sensitive element-binding protein 1 OS=Bos taurus GN=YBX1 PE=2 SV=3

 Score = 94.0 bits (232), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 41/78 (52%), Positives = 60/78 (76%)

Query: 9   VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
           V G VK+++ + G+GFI R D KED+FVH+++I K NP+K+ +S+G GE V+F++  G+K
Sbjct: 59  VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEK 118

Query: 69  DIEAINVTGPNGIPVQGA 86
             EA NVTGP G+PVQG+
Sbjct: 119 GAEAANVTGPGGVPVQGS 136

The secreted form acts as an extracellular mitogen and stimulates cell migration and proliferation.

Bos taurus (taxid: 9913)

>sp|Q06066|YBOX1_CHICK Nuclease-sensitive element-binding protein 1 OS=Gallus gallus GN=YBX1 PE=2 SV=1

 Score = 94.0 bits (232), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 41/78 (52%), Positives = 60/78 (76%)

Query: 9   VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
           V G VK+++ + G+GFI R D KED+FVH+++I K NP+K+ +S+G GE V+F++  G+K
Sbjct: 56  VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEK 115

Query: 69  DIEAINVTGPNGIPVQGA 86
             EA NVTGP G+PVQG+
Sbjct: 116 GAEAANVTGPGGVPVQGS 133

Mediates pre-mRNA alternative splicing regulation. Binds to splice sites in pre-mRNA and regulates splice site selection. Binds and stabilizes cytoplasmic mRNA. Binds to promoters that contain a Y-box (5'-CTGATTGGCCAA-3'). Regulates the transcription of numerous genes (By similarity). Component of the coding region determinant (CRD)-mediated complex that promotes mRNA stability.

Gallus gallus (taxid: 9031)

>sp|Q62764|DBPA_RAT DNA-binding protein A OS=Rattus norvegicus GN=Csda PE=2 SV=1

 Score = 93.2 bits (230), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 40/78 (51%), Positives = 61/78 (78%)

Query: 9   VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
           V G VK+++ + G+GFI R D KED+FVH+++I K NP+K+ +S+G GE V+F++  G+K
Sbjct: 83  VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEK 142

Query: 69  DIEAINVTGPNGIPVQGA 86
             EA NVTGP+G+PV+G+
Sbjct: 143 GAEAANVTGPDGVPVEGS 160

Binds to the GM-CSF promoter. Seems to act as a repressor. Binds also to full length mRNA and to short RNA sequences containing the consensus site 5'-UCCAUCA-3'. May have a role in translation repression.

Rattus norvegicus (taxid: 10116)

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	191
156385226	98	predicted protein [Nematostella vectensi	0.465	0.908	0.550	4e-20
91081961	297	PREDICTED: similar to Y-box binding prot	0.413	0.265	0.594	3e-19
91081963	286	PREDICTED: similar to Y-box binding prot	0.413	0.276	0.594	5e-19
391342360	309	PREDICTED: uncharacterized protein LOC10	0.434	0.268	0.554	7e-19
22901742	317	Y-box protein Ct-p50 [Chironomus tentans	0.413	0.249	0.569	1e-18
22901740	264	Y-box protein Ct-p40 [Chironomus tentans	0.413	0.299	0.569	1e-18
30089118	280	Y1 protein [Dugesia etrusca]	0.502	0.342	0.494	2e-18
342837647	378	TPA_inf: Y box protein 4-like protein [S	0.502	0.253	0.494	2e-18
242008099	288	Nuclease sensitive element-binding prote	0.429	0.284	0.560	2e-18
383849814	278	PREDICTED: uncharacterized protein LOC10	0.554	0.381	0.433	3e-18

>gi|156385226|ref|XP_001633532.1| predicted protein [Nematostella vectensis] gi|156220603|gb|EDO41469.1| predicted protein [Nematostella vectensis]

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 49/89 (55%), Positives = 65/89 (73%)

Query: 103 FFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDF 162
            F A   V G VK+++ K G+GFI R DNKEDIFVH+++I K NPKK+ +S+G GE+V+F
Sbjct: 1   MFIAATKVTGTVKWFNVKNGYGFINRDDNKEDIFVHQTAIAKNNPKKYLRSVGDGEVVEF 60

Query: 163 NIGVGKKDIEAINVTGPNGIPVQGAPKVP 191
           N+  G K +EA NVTGP+G PVQG+   P
Sbjct: 61  NVVSGTKGLEASNVTGPDGEPVQGSKYAP 89

Source: Nematostella vectensis

Species: Nematostella vectensis

Genus: Nematostella

Family: Edwardsiidae

Order: Actiniaria

Class: Anthozoa

Phylum: Cnidaria

Superkingdom: Eukaryota

>gi|91081961|ref|XP_966594.1| PREDICTED: similar to Y-box binding protein isoform 1 [Tribolium castaneum] gi|270007364|gb|EFA03812.1| hypothetical protein TcasGA2_TC013925 [Tribolium castaneum]

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 47/79 (59%), Positives = 63/79 (79%)

Query: 9   VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
           V G VK+++ K G+GFI R D KED+FVH+S+I+K NPKK  +S+G GEIV+F++ VG+K
Sbjct: 29  VTGTVKWFNVKSGYGFINRNDTKEDVFVHQSAIIKNNPKKAVRSVGDGEIVEFSVVVGEK 88

Query: 69  DIEAINVTGPNGIPVQGAP 87
             EA NVTGPNG PV+G+P
Sbjct: 89  GNEAANVTGPNGEPVRGSP 107

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91081963|ref|XP_975913.1| PREDICTED: similar to Y-box binding protein isoform 2 [Tribolium castaneum]

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 47/79 (59%), Positives = 63/79 (79%)

Query: 9   VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
           V G VK+++ K G+GFI R D KED+FVH+S+I+K NPKK  +S+G GEIV+F++ VG+K
Sbjct: 29  VTGTVKWFNVKSGYGFINRNDTKEDVFVHQSAIIKNNPKKAVRSVGDGEIVEFSVVVGEK 88

Query: 69  DIEAINVTGPNGIPVQGAP 87
             EA NVTGPNG PV+G+P
Sbjct: 89  GNEAANVTGPNGEPVRGSP 107

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|391342360|ref|XP_003745488.1| PREDICTED: uncharacterized protein LOC100904956 [Metaseiulus occidentalis]

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 46/83 (55%), Positives = 65/83 (78%)

Query: 9   VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
           VRG VK+++ K G+GFI R D KEDIFVH+++I+K NP+K  +S+G GE V+F++ VG+K
Sbjct: 33  VRGTVKWFNVKNGYGFINRNDTKEDIFVHQTAIMKNNPQKAVRSVGEGEEVEFDVVVGEK 92

Query: 69  DIEAINVTGPNGIPVQGAPKSSS 91
             EA NVTGP G PVQG+P +++
Sbjct: 93  GNEASNVTGPEGAPVQGSPYAAN 115

Source: Metaseiulus occidentalis

Species: Metaseiulus occidentalis

Genus: Metaseiulus

Family: Phytoseiidae

Order: Mesostigmata

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|22901742|gb|AAN10050.1| Y-box protein Ct-p50 [Chironomus tentans]

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 45/79 (56%), Positives = 62/79 (78%)

Query: 9   VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
           V G VK+++ K G+GFI R DNK+DIFVH+S+I+K NPKK  +S+G GE+V+F++  G+K
Sbjct: 30  VTGTVKWFNVKSGYGFINRNDNKQDIFVHQSAIIKNNPKKAVRSVGDGEVVEFDVVAGEK 89

Query: 69  DIEAINVTGPNGIPVQGAP 87
             EA NVTGP G PV+G+P
Sbjct: 90  GSEAANVTGPEGEPVKGSP 108

Source: Chironomus tentans

Species: Chironomus tentans

Genus: Chironomus

Family: Chironomidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|22901740|gb|AAN10049.1| Y-box protein Ct-p40 [Chironomus tentans]

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 45/79 (56%), Positives = 62/79 (78%)

Query: 9   VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
           V G VK+++ K G+GFI R DNK+DIFVH+S+I+K NPKK  +S+G GE+V+F++  G+K
Sbjct: 30  VTGTVKWFNVKSGYGFINRNDNKQDIFVHQSAIIKNNPKKAVRSVGDGEVVEFDVVAGEK 89

Query: 69  DIEAINVTGPNGIPVQGAP 87
             EA NVTGP G PV+G+P
Sbjct: 90  GSEAANVTGPEGEPVKGSP 108

Source: Chironomus tentans

Species: Chironomus tentans

Genus: Chironomus

Family: Chironomidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|30089118|emb|CAD27800.1| Y1 protein [Dugesia etrusca]

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 49/99 (49%), Positives = 74/99 (74%), Gaps = 3/99 (3%)

Query: 9   VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
           + G VK+++ K G+GFI R DN+EDIFVH+++I+K NP+K+ +S+G GE V+F++  G+K
Sbjct: 30  INGKVKWFNVKSGYGFINRNDNQEDIFVHQTAILKNNPRKWQRSVGDGEEVEFDVVEGEK 89

Query: 69  DIEAINVTGPNGIPVQGAPKSSSETVSGTYRNDSFFPAV 107
            +EA NVTGP+GIPVQG+  ++ +     YR+ SF  AV
Sbjct: 90  GLEAANVTGPDGIPVQGSKYAADKR---HYRSRSFGRAV 125

Source: Dugesia etrusca

Species: Dugesia etrusca

Genus: Dugesia

Family: Dugesiidae

Order: Tricladida

Phylum: Platyhelminthes

Superkingdom: Eukaryota

>gi|342837647|tpg|DAA34914.1| TPA_inf: Y box protein 4-like protein [Schmidtea mediterranea]

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 49/99 (49%), Positives = 74/99 (74%), Gaps = 3/99 (3%)

Query: 9   VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
           + G VK+++ K G+GFI R DN+EDIFVH+++I+K NP+K+ +S+G GE V+F++  G+K
Sbjct: 25  INGKVKWFNVKSGYGFINRNDNQEDIFVHQTAILKNNPRKWQRSVGDGEEVEFDVVEGEK 84

Query: 69  DIEAINVTGPNGIPVQGAPKSSSETVSGTYRNDSFFPAV 107
            +EA NVTGP+GIPVQG+  ++ +     YR+ SF  AV
Sbjct: 85  GLEAANVTGPDGIPVQGSKYAADKR---HYRSRSFGRAV 120

Source: Schmidtea mediterranea

Species: Schmidtea mediterranea

Genus: Schmidtea

Family: Dugesiidae

Order: Tricladida

Phylum: Platyhelminthes

Superkingdom: Eukaryota

>gi|242008099|ref|XP_002424850.1| Nuclease sensitive element-binding protein, putative [Pediculus humanus corporis] gi|212508400|gb|EEB12112.1| Nuclease sensitive element-binding protein, putative [Pediculus humanus corporis]

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 46/82 (56%), Positives = 64/82 (78%)

Query: 107 VHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGV 166
            + V G VK+++ K G+GFI R D KED+FVH+++IVK NPKKF +S+G GE+V+F++ V
Sbjct: 22  ANKVTGTVKWFNVKSGYGFINRDDTKEDVFVHQTAIVKNNPKKFVRSVGDGEVVEFDVVV 81

Query: 167 GKKDIEAINVTGPNGIPVQGAP 188
           G+K  EA NVTGPNG  V+G+P
Sbjct: 82  GEKGNEAANVTGPNGEAVKGSP 103

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383849814|ref|XP_003700531.1| PREDICTED: uncharacterized protein LOC100878915 [Megachile rotundata]

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 52/120 (43%), Positives = 75/120 (62%), Gaps = 14/120 (11%)

Query: 9   VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
           V G VK+++ K G+GFI R D KED+FVH+S+IVK NP+K  +S+G GE+V+F++ VG K
Sbjct: 24  VTGTVKWFNVKSGYGFINRNDTKEDVFVHQSAIVKNNPRKAVRSVGDGEVVEFDVVVGDK 83

Query: 69  DIEAINVTGPNGIPVQGAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITR 128
             EA NVTGP+G PV+G+P ++ +                  RG+  F + +RG G   R
Sbjct: 84  GHEAANVTGPSGEPVKGSPYAADKR--------------RGYRGVHWFNNQRRGNGRPQR 129

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

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	191
UNIPROTKB|F1PB10	370	CSDA "Uncharacterized protein"	0.429	0.221	0.506	5.8e-22
UNIPROTKB|A5D7M4	360	YBX2 "Uncharacterized protein"	0.670	0.355	0.4	2.1e-20
UNIPROTKB|I3LCJ2	360	YBX2 "Uncharacterized protein"	0.670	0.355	0.4	6.5e-20
UNIPROTKB|P21574	336	ybx2-a "Y-box-binding protein	0.591	0.336	0.413	7.2e-20
UNIPROTKB|F1SFU0	365	LOC100736899 "Uncharacterized	0.670	0.350	0.4	7.3e-20
UNIPROTKB|E2RMN5	367	YBX2 "Uncharacterized protein"	0.670	0.348	0.4	7.7e-20
UNIPROTKB|Q9Y2T7	364	YBX2 "Y-box-binding protein 2"	0.602	0.315	0.416	9.5e-20
UNIPROTKB|P45441	324	ybx2-b "Y-box-binding protein	0.429	0.253	0.512	1.2e-19
UNIPROTKB|F1M1Q9	277	F1M1Q9 "Uncharacterized protei	0.465	0.321	0.472	1.5e-19
UNIPROTKB|D4A0L4	306	Csda "DNA-binding protein A" [	0.591	0.369	0.418	1.5e-19

UNIPROTKB|F1PB10 CSDA "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 228 (85.3 bits), Expect = 5.8e-22, Sum P(2) = 5.8e-22
 Identities = 42/83 (50%), Positives = 63/83 (75%)

Query:   105 PAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI 164
             PA   V G VK+++ + G+GFI R D KED+FVH+++I K NP+K+ +S+G GE V+F++
Sbjct:    87 PATK-VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDV 145

Query:   165 GVGKKDIEAINVTGPNGIPVQGA 187
               G+K  EA NVTGP+G+PV+G+
Sbjct:   146 VEGEKGAEAANVTGPDGVPVEGS 168

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|A5D7M4 YBX2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 241 (89.9 bits), Expect = 2.1e-20, P = 2.1e-20
 Identities = 52/130 (40%), Positives = 79/130 (60%)

Query:    64 GVGKKDIEAINVTGPNGIPVQGAPKSS-SETVSGTYRNDSFFPAVHT-VRGIVKFYDSKR 121
             GVG     A+      G    G P ++ S T +   R+ +  P +   V G VK+++ + 
Sbjct:    48 GVGTASGPAVGTPSAPGPRTPGNPATAASGTPAPLARSQADKPVLAIQVLGTVKWFNVRN 107

Query:   122 GFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNG 181
             G+GFI R D KED+FVH+++I + NP+KF +S+G GE V+F++  G+K  EA NVTGP G
Sbjct:   108 GYGFINRNDTKEDVFVHQTAIKRNNPRKFLRSVGDGETVEFDVVEGEKGAEAANVTGPGG 167

Query:   182 IPVQGAPKVP 191
             +PV+G+   P
Sbjct:   168 VPVKGSRYAP 177

GO:0051100 "negative regulation of binding" evidence=IEA

GO:0048477 "oogenesis" evidence=IEA

GO:0048255 "mRNA stabilization" evidence=IEA

GO:0045182 "translation regulator activity" evidence=IEA

GO:0043021 "ribonucleoprotein complex binding" evidence=IEA

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

GO:0008289 "lipid binding" evidence=IEA

GO:0007286 "spermatid development" evidence=IEA

GO:0005844 "polysome" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0003730 "mRNA 3'-UTR binding" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|I3LCJ2 YBX2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 237 (88.5 bits), Expect = 6.5e-20, P = 6.5e-20
 Identities = 52/130 (40%), Positives = 78/130 (60%)

Query:    64 GVGKKDIEAINVTGPNGIPVQGAPKSS-SETVSGTYRNDSFFPAVHT-VRGIVKFYDSKR 121
             GVG     A       G    G P ++ S T +   R+ +  P +   V G VK+++ + 
Sbjct:    48 GVGAASGPAAGTPSAPGPRTPGNPATAASGTSAPPARSQADKPVLAIQVLGTVKWFNVRN 107

Query:   122 GFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNG 181
             G+GFI R D KED+FVH+++I + NP+KF +S+G GE V+F++  G+K  EA NVTGP G
Sbjct:   108 GYGFINRNDTKEDVFVHQTAIKRNNPRKFLRSVGDGETVEFDVVEGEKGAEAANVTGPGG 167

Query:   182 IPVQGAPKVP 191
             +PV+G+   P
Sbjct:   168 VPVKGSRYAP 177

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|P21574 ybx2-a "Y-box-binding protein 2-A" [Xenopus laevis (taxid:8355)]

 Score = 236 (88.1 bits), Expect = 7.2e-20, P = 7.2e-20
 Identities = 48/116 (41%), Positives = 75/116 (64%)

Query:    78 PNGIPV-QGAPKSSSETVSGTYRNDSFFPAVHT-VRGIVKFYDSKRGFGFITRLDNKEDI 135
             P  +P  +  P+     ++   RN +    + T V+G VK+++ + G+GFI R D KED+
Sbjct:     9 PEPVPQPESEPEIQKPGIAAA-RNQANKKVLATQVQGTVKWFNVRNGYGFINRNDTKEDV 67

Query:   136 FVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNGIPVQGAPKVP 191
             FVH+++I K NP+KF +S+G GE V+F++  G+K  EA NVTGP G+PV+G+   P
Sbjct:    68 FVHQTAIKKNNPRKFLRSVGDGETVEFDVVEGEKGAEAANVTGPGGVPVKGSRFAP 123

GO:0003723 "RNA binding" evidence=IDA

GO:0030529 "ribonucleoprotein complex" evidence=IPI

GO:0043565 "sequence-specific DNA binding" evidence=IDA

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

UNIPROTKB|F1SFU0 LOC100736899 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 237 (88.5 bits), Expect = 7.3e-20, P = 7.3e-20
 Identities = 52/130 (40%), Positives = 78/130 (60%)

Query:    64 GVGKKDIEAINVTGPNGIPVQGAPKSS-SETVSGTYRNDSFFPAVHT-VRGIVKFYDSKR 121
             GVG     A       G    G P ++ S T +   R+ +  P +   V G VK+++ + 
Sbjct:    48 GVGAASGPAAGTPSAPGPRTPGNPATAASGTSAPPARSQADKPVLAIQVLGTVKWFNVRN 107

Query:   122 GFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNG 181
             G+GFI R D KED+FVH+++I + NP+KF +S+G GE V+F++  G+K  EA NVTGP G
Sbjct:   108 GYGFINRNDTKEDVFVHQTAIKRNNPRKFLRSVGDGETVEFDVVEGEKGAEAANVTGPGG 167

Query:   182 IPVQGAPKVP 191
             +PV+G+   P
Sbjct:   168 VPVKGSRYAP 177

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|E2RMN5 YBX2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 237 (88.5 bits), Expect = 7.7e-20, P = 7.7e-20
 Identities = 52/130 (40%), Positives = 78/130 (60%)

Query:    64 GVGKKDIEAINVTGPNGIPVQGAPKSS-SETVSGTYRNDSFFPAVHT-VRGIVKFYDSKR 121
             GVG     A       G    G P ++ S T +   R+ +  P +   V G VK+++ + 
Sbjct:    48 GVGAASGPAAGTPSAPGPRTPGNPATAASGTPAPPARSQADKPVLAIQVLGTVKWFNVRN 107

Query:   122 GFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNG 181
             G+GFI R D KED+FVH+++I + NP+KF +S+G GE V+F++  G+K  EA NVTGP G
Sbjct:   108 GYGFINRNDTKEDVFVHQTAIKRNNPRKFLRSVGDGETVEFDVVEGEKGAEAANVTGPGG 167

Query:   182 IPVQGAPKVP 191
             +PV+G+   P
Sbjct:   168 VPVKGSRYAP 177

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|Q9Y2T7 YBX2 "Y-box-binding protein 2" [Homo sapiens (taxid:9606)]

 Score = 236 (88.1 bits), Expect = 9.5e-20, P = 9.5e-20
 Identities = 50/120 (41%), Positives = 75/120 (62%)

Query:    77 GPNGIPVQGAPKSSSETVSGT----YRNDSFFPAVHT-VRGIVKFYDSKRGFGFITRLDN 131
             G    P    P + +  VSGT     R+ +  P +   V G VK+++ + G+GFI R D 
Sbjct:    56 GTPSAPGSRTPGNPATAVSGTPAPPARSQADKPVLAIQVLGTVKWFNVRNGYGFINRNDT 115

Query:   132 KEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNGIPVQGAPKVP 191
             KED+FVH+++I + NP+KF +S+G GE V+F++  G+K  EA NVTGP G+PV+G+   P
Sbjct:   116 KEDVFVHQTAIKRNNPRKFLRSVGDGETVEFDVVEGEKGAEATNVTGPGGVPVKGSRYAP 175

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

GO:0003677 "DNA binding" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0003730 "mRNA 3'-UTR binding" evidence=IEA

GO:0005844 "polysome" evidence=IEA

GO:0007286 "spermatid development" evidence=IEA

GO:0008289 "lipid binding" evidence=IEA

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

GO:0043021 "ribonucleoprotein complex binding" evidence=IEA

GO:0045182 "translation regulator activity" evidence=IEA

GO:0048255 "mRNA stabilization" evidence=IEA

GO:0048599 "oocyte development" evidence=IEA

GO:0051100 "negative regulation of binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=TAS

GO:0007283 "spermatogenesis" evidence=TAS

GO:0009386 "translational attenuation" evidence=TAS

UNIPROTKB|P45441 ybx2-b "Y-box-binding protein 2-B" [Xenopus laevis (taxid:8355)]

 Score = 234 (87.4 bits), Expect = 1.2e-19, P = 1.2e-19
 Identities = 42/82 (51%), Positives = 63/82 (76%)

Query:   110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
             V+G VK+++ + G+GFI R D+KED+FVH+++I K NP+KF +S+G GE V+F++  G+K
Sbjct:    42 VQGTVKWFNVRNGYGFINRNDSKEDVFVHQTAIKKNNPRKFLRSVGDGETVEFDVVEGEK 101

Query:   170 DIEAINVTGPNGIPVQGAPKVP 191
               EA NVTGP G+PV+G+   P
Sbjct:   102 GAEAANVTGPGGVPVKGSRFAP 123

GO:0030529 "ribonucleoprotein complex" evidence=IPI

UNIPROTKB|F1M1Q9 F1M1Q9 "Uncharacterized protein" [Rattus norvegicus (taxid:10116)]

 Score = 233 (87.1 bits), Expect = 1.5e-19, P = 1.5e-19
 Identities = 43/91 (47%), Positives = 67/91 (73%)

Query:     9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
             V GIVK+++ +RG+GFI   D +ED+FVH+++I K  P+K+ +S+G GE V+F +  G+K
Sbjct:    40 VLGIVKWFNVRRGYGFINSNDTREDVFVHQTAIKKNKPRKYLRSVGDGETVEFEVVEGEK 99

Query:    69 DIEAINVTGPNGIPVQGAPKSSSETVSGTYR 99
              +EA NVTGP G+PVQG+  ++++  S  YR
Sbjct:   100 GVEAANVTGPGGVPVQGSKHAAAD--SNHYR 128

GO:0003677 "DNA binding" evidence=IEA

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

UNIPROTKB|D4A0L4 Csda "DNA-binding protein A" [Rattus norvegicus (taxid:10116)]

 Score = 233 (87.1 bits), Expect = 1.5e-19, P = 1.5e-19
 Identities = 49/117 (41%), Positives = 76/117 (64%)

Query:    72 AINVTGPNGIPVQGAPKSSSETVSGTYRNDSFFPAVHT-VRGIVKFYDSKRGFGFITRLD 130
             A+    P G    G P  +S   +G+   D+    + T V G VK+++ + G+GFI R D
Sbjct:    47 ALLAGSPGGDAAPG-PAPASSAPAGS--EDAEKKVLATKVLGTVKWFNVRNGYGFINRND 103

Query:   131 NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNGIPVQGA 187
              KED+FVH+++I K NP+K+ +S+G GE V+F++  G+K  EA NVTGP+G+PV+G+
Sbjct:   104 TKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGPDGVPVEGS 160

GO:0003677 "DNA binding" evidence=IEA

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q06066	YBOX1_CHICK	No assigned EC number	0.5256	0.4083	0.2429	yes	N/A
P67809	YBOX1_HUMAN	No assigned EC number	0.5256	0.4083	0.2407	yes	N/A
P67808	YBOX1_BOVIN	No assigned EC number	0.5256	0.4083	0.2407	yes	N/A
P62961	YBOX1_RAT	No assigned EC number	0.5256	0.4083	0.2422	yes	N/A
P62960	YBOX1_MOUSE	No assigned EC number	0.5256	0.4083	0.2422	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	191
pfam00313	66	pfam00313, CSD, 'Cold-shock' DNA-binding domain	8e-15
pfam00313	66	pfam00313, CSD, 'Cold-shock' DNA-binding domain	8e-15
cd04458	65	cd04458, CSP_CDS, Cold-Shock Protein (CSP) contain	9e-15
cd04458	65	cd04458, CSP_CDS, Cold-Shock Protein (CSP) contain	9e-15
COG1278	67	COG1278, CspC, Cold shock proteins [Transcription]	3e-10
COG1278	67	COG1278, CspC, Cold shock proteins [Transcription]	3e-10
PRK10943	69	PRK10943, PRK10943, cold shock-like protein CspC;	5e-08
PRK10943	69	PRK10943, PRK10943, cold shock-like protein CspC;	5e-08
PRK09507	69	PRK09507, cspE, cold shock protein CspE; Reviewed	9e-08
PRK09507	69	PRK09507, cspE, cold shock protein CspE; Reviewed	9e-08
PRK10354	70	PRK10354, PRK10354, RNA chaperone/anti-terminator;	1e-07
PRK10354	70	PRK10354, PRK10354, RNA chaperone/anti-terminator;	1e-07
smart00357	64	smart00357, CSP, Cold shock protein domain	2e-07
smart00357	64	smart00357, CSP, Cold shock protein domain	2e-07
PRK09890	70	PRK09890, PRK09890, cold shock protein CspG; Provi	5e-06
PRK09890	70	PRK09890, PRK09890, cold shock protein CspG; Provi	5e-06
TIGR02381	68	TIGR02381, cspD, cold shock domain protein CspD	1e-05
TIGR02381	68	TIGR02381, cspD, cold shock domain protein CspD	1e-05
PRK14998	73	PRK14998, PRK14998, cold shock-like protein CspD;	1e-04
PRK14998	73	PRK14998, PRK14998, cold shock-like protein CspD;	1e-04
PRK09937	74	PRK09937, PRK09937, stationary phase/starvation in	3e-04
PRK09937	74	PRK09937, PRK09937, stationary phase/starvation in	3e-04
PRK15463	70	PRK15463, PRK15463, cold shock-like protein CspF;	0.001
PRK15463	70	PRK15463, PRK15463, cold shock-like protein CspF;	0.001

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

 Score = 65.7 bits (161), Expect = 8e-15
 Identities = 30/70 (42%), Positives = 44/70 (62%), Gaps = 4/70 (5%)

Query: 9  VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
          + G VK++++K+GFGFIT  D  +D+FVH S+I        F+SL  G+ V+F+I  G K
Sbjct: 1  MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDG----FRSLQEGQRVEFDIVEGTK 56

Query: 69 DIEAINVTGP 78
            +A NVT  
Sbjct: 57 GPQAANVTLL 66

Length = 66

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

 Score = 65.7 bits (161), Expect = 8e-15
 Identities = 30/70 (42%), Positives = 44/70 (62%), Gaps = 4/70 (5%)

Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
           + G VK++++K+GFGFIT  D  +D+FVH S+I        F+SL  G+ V+F+I  G K
Sbjct: 1   MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDG----FRSLQEGQRVEFDIVEGTK 56

Query: 170 DIEAINVTGP 179
             +A NVT  
Sbjct: 57  GPQAANVTLL 66

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 = 65.3 bits (160), Expect = 9e-15
 Identities = 29/69 (42%), Positives = 42/69 (60%), Gaps = 4/69 (5%)

Query: 9  VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
          V G VK++D ++GFGFIT  D  ED+FVH S++        F+SL  G+ V+F +  G K
Sbjct: 1  VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDG----FRSLEEGDRVEFELEEGDK 56

Query: 69 DIEAINVTG 77
            +A+NV  
Sbjct: 57 GPQAVNVRL 65

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|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 = 65.3 bits (160), Expect = 9e-15
 Identities = 29/69 (42%), Positives = 42/69 (60%), Gaps = 4/69 (5%)

Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
           V G VK++D ++GFGFIT  D  ED+FVH S++        F+SL  G+ V+F +  G K
Sbjct: 1   VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDG----FRSLEEGDRVEFELEEGDK 56

Query: 170 DIEAINVTG 178
             +A+NV  
Sbjct: 57  GPQAVNVRL 65

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 = 53.7 bits (130), Expect = 3e-10
 Identities = 26/67 (38%), Positives = 41/67 (61%), Gaps = 4/67 (5%)

Query: 10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 69
           G VK++++ +GFGFIT  D  +D+FVH S+I +      F++L  G+ V+F +  G+K 
Sbjct: 3  TGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRAG----FRTLREGQKVEFEVEQGRKG 58

Query: 70 IEAINVT 76
            A NV 
Sbjct: 59 PSAANVR 65

Length = 67

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

 Score = 53.7 bits (130), Expect = 3e-10
 Identities = 26/67 (38%), Positives = 41/67 (61%), Gaps = 4/67 (5%)

Query: 111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 170
            G VK++++ +GFGFIT  D  +D+FVH S+I +      F++L  G+ V+F +  G+K 
Sbjct: 3   TGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRAG----FRTLREGQKVEFEVEQGRKG 58

Query: 171 IEAINVT 177
             A NV 
Sbjct: 59  PSAANVR 65

Length = 67

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

 Score = 47.8 bits (113), Expect = 5e-08
 Identities = 28/68 (41%), Positives = 43/68 (63%), Gaps = 4/68 (5%)

Query: 9  VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
          ++G VK+++  +GFGFIT  D  +D+FVH S+I        F++L  G+ V+F I  G+K
Sbjct: 4  IKGQVKWFNESKGFGFITPADGSKDVFVHFSAI----QGNGFKTLAEGQNVEFEIQDGQK 59

Query: 69 DIEAINVT 76
             A+NVT
Sbjct: 60 GPAAVNVT 67

Length = 69

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

 Score = 47.8 bits (113), Expect = 5e-08
 Identities = 28/68 (41%), Positives = 43/68 (63%), Gaps = 4/68 (5%)

Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
           ++G VK+++  +GFGFIT  D  +D+FVH S+I        F++L  G+ V+F I  G+K
Sbjct: 4   IKGQVKWFNESKGFGFITPADGSKDVFVHFSAI----QGNGFKTLAEGQNVEFEIQDGQK 59

Query: 170 DIEAINVT 177
              A+NVT
Sbjct: 60  GPAAVNVT 67

Length = 69

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

 Score = 47.0 bits (111), Expect = 9e-08
 Identities = 27/68 (39%), Positives = 40/68 (58%), Gaps = 4/68 (5%)

Query: 9  VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
          ++G VK+++  +GFGFIT  D  +D+FVH S+I        F++L  G+ V+F I  G K
Sbjct: 4  IKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNGAK 59

Query: 69 DIEAINVT 76
             A NV 
Sbjct: 60 GPSAANVI 67

Length = 69

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

 Score = 47.0 bits (111), Expect = 9e-08
 Identities = 27/68 (39%), Positives = 40/68 (58%), Gaps = 4/68 (5%)

Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
           ++G VK+++  +GFGFIT  D  +D+FVH S+I        F++L  G+ V+F I  G K
Sbjct: 4   IKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNGAK 59

Query: 170 DIEAINVT 177
              A NV 
Sbjct: 60  GPSAANVI 67

Length = 69

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

 Score = 46.9 bits (111), Expect = 1e-07
 Identities = 29/66 (43%), Positives = 40/66 (60%), Gaps = 4/66 (6%)

Query: 11 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI 70
          GIVK++++ +GFGFIT  D  +D+FVH S+I        ++SL  G+ V F I  G K  
Sbjct: 7  GIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIESGAKGP 62

Query: 71 EAINVT 76
           A NVT
Sbjct: 63 AAGNVT 68

Length = 70

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

 Score = 46.9 bits (111), Expect = 1e-07
 Identities = 29/66 (43%), Positives = 40/66 (60%), Gaps = 4/66 (6%)

Query: 112 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI 171
           GIVK++++ +GFGFIT  D  +D+FVH S+I        ++SL  G+ V F I  G K  
Sbjct: 7   GIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIESGAKGP 62

Query: 172 EAINVT 177
            A NVT
Sbjct: 63  AAGNVT 68

Length = 70

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

 Score = 45.7 bits (109), Expect = 2e-07
 Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 9/71 (12%)

Query: 10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI--GVGK 67
           G+VK+++  +GFGFI   D  +D+FVH S I     +   +SL  G+ V+F +    G 
Sbjct: 1  TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQI-----QGGLKSLREGDEVEFKVVSPEGG 53

Query: 68 KDIEAINVTGP 78
          +  EA NV   
Sbjct: 54 EKPEAENVVKL 64

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|214633 smart00357, CSP, Cold shock protein domain

 Score = 45.7 bits (109), Expect = 2e-07
 Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 9/71 (12%)

Query: 111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI--GVGK 168
            G+VK+++  +GFGFI   D  +D+FVH S I     +   +SL  G+ V+F +    G 
Sbjct: 1   TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQI-----QGGLKSLREGDEVEFKVVSPEGG 53

Query: 169 KDIEAINVTGP 179
           +  EA NV   
Sbjct: 54  EKPEAENVVKL 64

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|77467 PRK09890, PRK09890, cold shock protein CspG; Provisional

 Score = 42.4 bits (99), Expect = 5e-06
 Identities = 24/65 (36%), Positives = 41/65 (63%), Gaps = 4/65 (6%)

Query: 11 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI 70
          G+VK++++ +GFGFIT  D  +D+FVH ++I        F++L   + V+F+I  G++  
Sbjct: 7  GLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNE----FRTLNENQKVEFSIEQGQRGP 62

Query: 71 EAINV 75
           A NV
Sbjct: 63 AAANV 67

Length = 70

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

 Score = 42.4 bits (99), Expect = 5e-06
 Identities = 24/65 (36%), Positives = 41/65 (63%), Gaps = 4/65 (6%)

Query: 112 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI 171
           G+VK++++ +GFGFIT  D  +D+FVH ++I        F++L   + V+F+I  G++  
Sbjct: 7   GLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNE----FRTLNENQKVEFSIEQGQRGP 62

Query: 172 EAINV 176
            A NV
Sbjct: 63  AAANV 67

Length = 70

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

 Score = 41.4 bits (97), Expect = 1e-05
 Identities = 23/65 (35%), Positives = 38/65 (58%), Gaps = 4/65 (6%)

Query: 11 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI 70
          GIVK++++ +GFGFI       DIF H S+I +M+    +++L  G+ V F +  G K  
Sbjct: 4  GIVKWFNNAKGFGFICPEGVDGDIFAHYSTI-QMDG---YRTLKAGQKVQFEVVQGPKGA 59

Query: 71 EAINV 75
           A ++
Sbjct: 60 HATHI 64

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|131434 TIGR02381, cspD, cold shock domain protein CspD

 Score = 41.4 bits (97), Expect = 1e-05
 Identities = 23/65 (35%), Positives = 38/65 (58%), Gaps = 4/65 (6%)

Query: 112 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI 171
           GIVK++++ +GFGFI       DIF H S+I +M+    +++L  G+ V F +  G K  
Sbjct: 4   GIVKWFNNAKGFGFICPEGVDGDIFAHYSTI-QMDG---YRTLKAGQKVQFEVVQGPKGA 59

Query: 172 EAINV 176
            A ++
Sbjct: 60  HATHI 64

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

 Score = 38.5 bits (89), Expect = 1e-04
 Identities = 22/58 (37%), Positives = 36/58 (62%), Gaps = 4/58 (6%)

Query: 11 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
          G VK++++ +GFGFI      EDIF H S+I +M+    +++L  G+ V F++  G K
Sbjct: 4  GTVKWFNNAKGFGFICPEGGGEDIFAHYSTI-QMDG---YRTLKAGQSVRFDVHQGPK 57

Length = 73

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

 Score = 38.5 bits (89), Expect = 1e-04
 Identities = 22/58 (37%), Positives = 36/58 (62%), Gaps = 4/58 (6%)

Query: 112 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
           G VK++++ +GFGFI      EDIF H S+I +M+    +++L  G+ V F++  G K
Sbjct: 4   GTVKWFNNAKGFGFICPEGGGEDIFAHYSTI-QMDG---YRTLKAGQSVRFDVHQGPK 57

Length = 73

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

 Score = 37.8 bits (87), Expect = 3e-04
 Identities = 22/59 (37%), Positives = 37/59 (62%), Gaps = 4/59 (6%)

Query: 10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
          +G VK++++ +GFGFI      EDIF H S+I +M+    +++L  G+ V F++  G K
Sbjct: 3  KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTI-QMDG---YRTLKAGQSVQFDVHQGPK 57

Length = 74

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

 Score = 37.8 bits (87), Expect = 3e-04
 Identities = 22/59 (37%), Positives = 37/59 (62%), Gaps = 4/59 (6%)

Query: 111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
           +G VK++++ +GFGFI      EDIF H S+I +M+    +++L  G+ V F++  G K
Sbjct: 3   KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTI-QMDG---YRTLKAGQSVQFDVHQGPK 57

Length = 74

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

 Score = 36.0 bits (83), Expect = 0.001
 Identities = 15/31 (48%), Positives = 21/31 (67%)

Query: 11 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSI 41
          GIVK +D K G G IT  D ++D+ VH S++
Sbjct: 7  GIVKTFDGKSGKGLITPSDGRKDVQVHISAL 37

Length = 70

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

 Score = 36.0 bits (83), Expect = 0.001
 Identities = 15/31 (48%), Positives = 21/31 (67%)

Query: 112 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSI 142
           GIVK +D K G G IT  D ++D+ VH S++
Sbjct: 7   GIVKTFDGKSGKGLITPSDGRKDVQVHISAL 37

Length = 70

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	191
COG1278	67	CspC Cold shock proteins [Transcription]	99.91
COG1278	67	CspC Cold shock proteins [Transcription]	99.91
PRK15464	70	cold shock-like protein CspH; Provisional	99.9
PRK10943	69	cold shock-like protein CspC; Provisional	99.89
PRK15463	70	cold shock-like protein CspF; Provisional	99.89
PRK10354	70	RNA chaperone/anti-terminator; Provisional	99.89
PRK09890	70	cold shock protein CspG; Provisional	99.89
PRK09507	69	cspE cold shock protein CspE; Reviewed	99.89
PRK09937	74	stationary phase/starvation inducible regulatory p	99.89
PRK15464	70	cold shock-like protein CspH; Provisional	99.88
PRK10943	69	cold shock-like protein CspC; Provisional	99.88
PRK14998	73	cold shock-like protein CspD; Provisional	99.88
PRK15463	70	cold shock-like protein CspF; Provisional	99.88
TIGR02381	68	cspD cold shock domain protein CspD. This model re	99.88
PRK09890	70	cold shock protein CspG; Provisional	99.87
PRK10354	70	RNA chaperone/anti-terminator; Provisional	99.87
PRK09507	69	cspE cold shock protein CspE; Reviewed	99.87
PRK09937	74	stationary phase/starvation inducible regulatory p	99.87
TIGR02381	68	cspD cold shock domain protein CspD. This model re	99.86
PRK14998	73	cold shock-like protein CspD; Provisional	99.86
PF00313	66	CSD: 'Cold-shock' DNA-binding domain; InterPro: IP	99.82
PF00313	66	CSD: 'Cold-shock' DNA-binding domain; InterPro: IP	99.82
cd04458	65	CSP_CDS Cold-Shock Protein (CSP) contains an S1-li	99.81
cd04458	65	CSP_CDS Cold-Shock Protein (CSP) contains an S1-li	99.8
KOG3070|consensus	235		99.55
KOG3070|consensus	235		99.49
smart00357	64	CSP Cold shock protein domain. RNA-binding domain	99.0
smart00357	64	CSP Cold shock protein domain. RNA-binding domain	98.94
PRK11642	813	exoribonuclease R; Provisional	98.72
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	98.51
PRK05054	644	exoribonuclease II; Provisional	98.45
PF08206	58	OB_RNB: Ribonuclease B OB domain; InterPro: IPR013	98.37
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	98.27
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	98.22
PF08206	58	OB_RNB: Ribonuclease B OB domain; InterPro: IPR013	98.15
PF14444	58	S1-like: S1-like	97.35
PF14444	58	S1-like: S1-like	97.32
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	96.95
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	96.78
PF07497	78	Rho_RNA_bind: Rho termination factor, RNA-binding	96.66
COG0557	706	VacB Exoribonuclease R [Transcription]	96.59
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	96.56
PF07497	78	Rho_RNA_bind: Rho termination factor, RNA-binding	96.45
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	96.19
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	95.92
PRK11642	813	exoribonuclease R; Provisional	95.8
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	95.7
cd04459	68	Rho_CSD Rho_CSD: Rho protein cold-shock domain (CS	95.7
PRK07400	318	30S ribosomal protein S1; Reviewed	95.64
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	95.59
cd04459	68	Rho_CSD Rho_CSD: Rho protein cold-shock domain (CS	95.42
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	95.37
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	95.3
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	95.26
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	95.11
PRK05054	644	exoribonuclease II; Provisional	95.07
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	95.01
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	94.77
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	94.75
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	94.52
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	94.21
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	93.79
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	93.53
PRK09376	416	rho transcription termination factor Rho; Provisio	93.34
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	93.11
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	92.6
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	92.5
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	92.48
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	92.43
COG1158	422	Rho Transcription termination factor [Transcriptio	92.28
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	92.23
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	91.97
PRK07400	318	30S ribosomal protein S1; Reviewed	91.94
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	91.48
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	91.4
PRK12608	380	transcription termination factor Rho; Provisional	90.57
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	90.43
COG4776	645	Rnb Exoribonuclease II [Transcription]	90.4
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	90.33
PRK08582	139	hypothetical protein; Provisional	90.23
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	90.11
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	90.1
PRK08582	139	hypothetical protein; Provisional	90.0
PRK12608	380	transcription termination factor Rho; Provisional	89.63
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	89.63
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	89.23
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	89.2
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	89.15
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	89.13
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	89.08
PRK09376	416	rho transcription termination factor Rho; Provisio	88.88
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	88.86
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	88.7
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	88.56
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	88.36
PRK12678	672	transcription termination factor Rho; Provisional	88.21
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	88.07
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	87.88
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	86.93
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	86.86
COG1158	422	Rho Transcription termination factor [Transcriptio	86.85
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	86.58
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	86.57
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	86.16
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	85.08
PRK07252	120	hypothetical protein; Provisional	84.89
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	84.84
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	84.82
TIGR00767	415	rho transcription termination factor Rho. Members	84.62
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	84.41
PRK07252	120	hypothetical protein; Provisional	84.2
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	83.93
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	83.92
PRK05807	136	hypothetical protein; Provisional	83.83
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	83.68
PF11604	70	CusF_Ec: Copper binding periplasmic protein CusF;	83.67
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	82.78
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	82.64
PRK08059	123	general stress protein 13; Validated	82.62
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	82.58
TIGR00767	415	rho transcription termination factor Rho. Members	82.49
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	82.28
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	82.17
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	81.88
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	81.33
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	81.29
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	81.04
PRK05807	136	hypothetical protein; Provisional	81.03
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	80.42
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	80.4
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	80.27

>COG1278 CspC Cold shock proteins [Transcription]

Probab=99.91  E-value=2.1e-24  Score=142.62  Aligned_cols=66  Identities=39%  Similarity=0.693  Sum_probs=62.8

Q ss_pred             ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeec
Q psy9900           8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG   77 (191)
Q Consensus         8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~   77 (191)
                      +.+|+|||||..||||||.++++++|||||+|+++..    |++.|.+|++|+|++.++++|++|.+|..
T Consensus         1 ~~~GtVKwfn~~KGfGFI~p~~G~~DvFVH~Sai~~~----g~~~L~eGQ~V~f~~~~g~kgp~A~nv~~   66 (67)
T COG1278           1 MATGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRA----GFRTLREGQKVEFEVEQGRKGPSAANVRA   66 (67)
T ss_pred             CCcceEEEeeCCCcceEcCCCCCCcCEEEEeeeeccC----CCcccCCCCEEEEEEecCCCCCceeEEEe
Confidence            4689999999999999999999999999999999987    79999999999999999999999999974

>COG1278 CspC Cold shock proteins [Transcription]

Probab=99.91  E-value=2e-24  Score=142.70  Aligned_cols=66  Identities=39%  Similarity=0.684  Sum_probs=62.3

Q ss_pred             eeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecC
Q psy9900         110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGP  179 (191)
Q Consensus       110 ~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~  179 (191)
                      .+|+|||||..||||||+|+++++|||||+|++...    |+++|.+||+|+|++.+++||++|+||+.+
T Consensus         2 ~~GtVKwfn~~KGfGFI~p~~G~~DvFVH~Sai~~~----g~~~L~eGQ~V~f~~~~g~kgp~A~nv~~~   67 (67)
T COG1278           2 ATGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRA----GFRTLREGQKVEFEVEQGRKGPSAANVRAL   67 (67)
T ss_pred             CcceEEEeeCCCcceEcCCCCCCcCEEEEeeeeccC----CCcccCCCCEEEEEEecCCCCCceeEEEeC
Confidence            579999999999999999999999999999999974    699999999999999999999999999863

>PRK15464 cold shock-like protein CspH; Provisional

Probab=99.90  E-value=1.7e-23  Score=140.87  Aligned_cols=67  Identities=33%  Similarity=0.357  Sum_probs=62.4

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeec
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG   77 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~   77 (191)
                      .+++|+|||||..||||||.++++++|||||+++|...    +++.|.+|++|+|++.++++|++|.+|..
T Consensus         3 ~~~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~----g~~~l~~G~~V~f~v~~~~kG~~A~~v~~   69 (70)
T PRK15464          3 RKMTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPR----DAEVLIPGLRVEFCRVNGLRGPTAANVYL   69 (70)
T ss_pred             ccceEEEEEEECCCCeEEEccCCCCccEEEEehhehhc----CCCCCCCCCEEEEEEEECCCCceeEEEEc
Confidence            45689999999999999999999999999999999876    67899999999999999999999999874

>PRK10943 cold shock-like protein CspC; Provisional

Probab=99.89  E-value=3e-23  Score=139.67  Aligned_cols=67  Identities=42%  Similarity=0.708  Sum_probs=63.1

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeec
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG   77 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~   77 (191)
                      .+++|+|||||..||||||.++++++|||||+|+|...    +++.|.+|++|+|++.++++|++|.+|+.
T Consensus         2 ~~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~g~~A~~V~~   68 (69)
T PRK10943          2 AKIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGN----GFKTLAEGQNVEFEIQDGQKGPAAVNVTA   68 (69)
T ss_pred             CccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHcccc----CCCCCCCCCEEEEEEEECCCCceeEEEEc
Confidence            47899999999999999999999899999999999976    68999999999999999999999999975

>PRK15463 cold shock-like protein CspF; Provisional

Probab=99.89  E-value=4.9e-23  Score=138.84  Aligned_cols=68  Identities=34%  Similarity=0.359  Sum_probs=62.8

Q ss_pred             eeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeec
Q psy9900           6 IHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG   77 (191)
Q Consensus         6 ~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~   77 (191)
                      +.+++|+|||||..||||||.++++++|||||+++|...    |++.|.+|++|+|++.++++|++|.+|..
T Consensus         2 ~~~~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~----g~~~l~~G~~V~f~v~~~~~G~~A~~V~~   69 (70)
T PRK15463          2 SRKMTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLR----DAEELTTGLRVEFCRINGLRGPTAANVYL   69 (70)
T ss_pred             CccceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhc----CCCCCCCCCEEEEEEEECCCCceeEEEEc
Confidence            345689999999999999999999999999999999876    68999999999999999999999999864

>PRK10354 RNA chaperone/anti-terminator; Provisional

Probab=99.89  E-value=7.1e-23  Score=138.26  Aligned_cols=68  Identities=43%  Similarity=0.638  Sum_probs=62.8

Q ss_pred             eeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeec
Q psy9900           6 IHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG   77 (191)
Q Consensus         6 ~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~   77 (191)
                      +.+++|+|||||..||||||.++++++|||||+|+|...    +++.|.+|++|+|++.++++|++|.+|..
T Consensus         2 ~~~~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~   69 (70)
T PRK10354          2 SGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQND----GYKSLDEGQKVSFTIESGAKGPAAGNVTS   69 (70)
T ss_pred             CccceEEEEEEeCCCCcEEEecCCCCccEEEEEeecccc----CCCCCCCCCEEEEEEEECCCCceeEEEEe
Confidence            344589999999999999999999999999999999976    68999999999999999999999999975

>PRK09890 cold shock protein CspG; Provisional

Probab=99.89  E-value=8.5e-23  Score=137.83  Aligned_cols=67  Identities=36%  Similarity=0.659  Sum_probs=62.5

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeec
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG   77 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~   77 (191)
                      .+++|+|||||..||||||.++++++|||||+|+|...    +++.|.+|++|+|++.++++|++|.+|..
T Consensus         3 ~~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~----~~~~l~~G~~V~f~~~~~~~G~~A~~V~~   69 (70)
T PRK09890          3 NKMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSN----EFRTLNENQKVEFSIEQGQRGPAAANVVT   69 (70)
T ss_pred             ccceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccC----CCCCCCCCCEEEEEEEECCCCceeEEEEe
Confidence            34699999999999999999999889999999999976    68999999999999999999999999975

>PRK09507 cspE cold shock protein CspE; Reviewed

Probab=99.89  E-value=8.2e-23  Score=137.53  Aligned_cols=68  Identities=40%  Similarity=0.669  Sum_probs=63.1

Q ss_pred             eeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeec
Q psy9900           6 IHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG   77 (191)
Q Consensus         6 ~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~   77 (191)
                      |.+.+|+|||||..||||||.++++++|||||+|+|...    +++.|.+|++|+|++.++++|++|.+|..
T Consensus         1 ~~~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~   68 (69)
T PRK09507          1 MSKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTN----GFKTLAEGQRVEFEITNGAKGPSAANVIA   68 (69)
T ss_pred             CCccceEEEEEeCCCCcEEEecCCCCeeEEEEeeccccc----CCCCCCCCCEEEEEEEECCCCcccEEEEe
Confidence            346889999999999999999999999999999999976    68999999999999999999999999874

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

Probab=99.89  E-value=1.5e-22  Score=137.85  Aligned_cols=66  Identities=33%  Similarity=0.550  Sum_probs=62.6

Q ss_pred             cceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeecC
Q psy9900           9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGP   78 (191)
Q Consensus         9 ~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~~   78 (191)
                      .+|+|||||..||||||.++++++|||||+|+|...    |++.|.+|++|+|++.++++|++|.+|...
T Consensus         2 ~~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~~   67 (74)
T PRK09937          2 EKGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMD----GYRTLKAGQSVQFDVHQGPKGNHASVIVPV   67 (74)
T ss_pred             CCeEEEEEeCCCCeEEEeeCCCCccEEEEEeecccc----CCCCCCCCCEEEEEEEECCCCceeeEEEEC
Confidence            479999999999999999999999999999999976    689999999999999999999999999875

>PRK15464 cold shock-like protein CspH; Provisional

Probab=99.88  E-value=8.9e-23  Score=137.42  Aligned_cols=66  Identities=33%  Similarity=0.359  Sum_probs=61.6

Q ss_pred             eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeec
Q psy9900         109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG  178 (191)
Q Consensus       109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~  178 (191)
                      +++|+|||||..||||||+++++++|||||+++|...    +++.|.+|++|+|++.+++||++|++|..
T Consensus         4 ~~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~----g~~~l~~G~~V~f~v~~~~kG~~A~~v~~   69 (70)
T PRK15464          4 KMTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPR----DAEVLIPGLRVEFCRVNGLRGPTAANVYL   69 (70)
T ss_pred             cceEEEEEEECCCCeEEEccCCCCccEEEEehhehhc----CCCCCCCCCEEEEEEEECCCCceeEEEEc
Confidence            4689999999999999999999999999999999864    47899999999999999999999999974

>PRK10943 cold shock-like protein CspC; Provisional

Probab=99.88  E-value=9.5e-23  Score=137.21  Aligned_cols=68  Identities=41%  Similarity=0.685  Sum_probs=63.1

Q ss_pred             eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecC
Q psy9900         108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGP  179 (191)
Q Consensus       108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~  179 (191)
                      ++++|+|+|||..||||||+++++++|||||+|+|...    +++.|.+|++|+|++.++++|++|++|+.+
T Consensus         2 ~~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~g~~A~~V~~~   69 (69)
T PRK10943          2 AKIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGN----GFKTLAEGQNVEFEIQDGQKGPAAVNVTAI   69 (69)
T ss_pred             CccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHcccc----CCCCCCCCCEEEEEEEECCCCceeEEEEcC
Confidence            36789999999999999999999889999999999974    578999999999999999999999999864

>PRK14998 cold shock-like protein CspD; Provisional

Probab=99.88  E-value=1.6e-22  Score=137.44  Aligned_cols=67  Identities=33%  Similarity=0.522  Sum_probs=62.7

Q ss_pred             cceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeecCC
Q psy9900           9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPN   79 (191)
Q Consensus         9 ~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~~~   79 (191)
                      .+|+|||||..||||||.++++++|||||+|+|...    |++.|.+|++|+|++.++++|++|.+|....
T Consensus         2 ~~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~~~   68 (73)
T PRK14998          2 ETGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMD----GYRTLKAGQSVRFDVHQGPKGNHASVIVPIE   68 (73)
T ss_pred             CCeEEEEEeCCCceEEEecCCCCccEEEEeeeeccc----CCCCCCCCCEEEEEEEECCCCceeEEEEECc
Confidence            479999999999999999999999999999999876    6899999999999999999999999998643

>PRK15463 cold shock-like protein CspF; Provisional

Probab=99.88  E-value=1.8e-22  Score=136.13  Aligned_cols=66  Identities=35%  Similarity=0.376  Sum_probs=61.7

Q ss_pred             eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeec
Q psy9900         109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG  178 (191)
Q Consensus       109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~  178 (191)
                      +++|+|||||..||||||+++++++|||||+++|...    +++.|.+|++|+|++.++++|++|++|++
T Consensus         4 ~~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~----g~~~l~~G~~V~f~v~~~~~G~~A~~V~~   69 (70)
T PRK15463          4 KMTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLR----DAEELTTGLRVEFCRINGLRGPTAANVYL   69 (70)
T ss_pred             cceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhc----CCCCCCCCCEEEEEEEECCCCceeEEEEc
Confidence            4689999999999999999999999999999999864    47899999999999999999999999974

>TIGR02381 cspD cold shock domain protein CspD

Probab=99.88  E-value=1.6e-22  Score=135.83  Aligned_cols=65  Identities=34%  Similarity=0.564  Sum_probs=61.4

Q ss_pred             cceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeec
Q psy9900           9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG   77 (191)
Q Consensus         9 ~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~   77 (191)
                      .+|+|||||.+||||||.++++++|||||+|+|...    |++.|.+|++|+|++..+++|++|.+|..
T Consensus         2 ~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~   66 (68)
T TIGR02381         2 AIGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMD----GYRTLKAGQKVQFEVVQGPKGAHATHIVP   66 (68)
T ss_pred             CCeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhc----CCCCCCCCCEEEEEEEECCCCceeEEEEE
Confidence            479999999999999999999999999999999876    68999999999999999999999999975

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.

>PRK09890 cold shock protein CspG; Provisional

Probab=99.87  E-value=3.7e-22  Score=134.68  Aligned_cols=67  Identities=36%  Similarity=0.642  Sum_probs=62.4

Q ss_pred             eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecC
Q psy9900         109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGP  179 (191)
Q Consensus       109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~  179 (191)
                      +++|+|+|||..||||||+++++++|||||+++|...    +++.|.+|++|+|++.++++|++|.+|..+
T Consensus         4 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~----~~~~l~~G~~V~f~~~~~~~G~~A~~V~~~   70 (70)
T PRK09890          4 KMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSN----EFRTLNENQKVEFSIEQGQRGPAAANVVTL   70 (70)
T ss_pred             cceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccC----CCCCCCCCCEEEEEEEECCCCceeEEEEeC
Confidence            4689999999999999999999889999999999975    478999999999999999999999999864

>PRK10354 RNA chaperone/anti-terminator; Provisional

Probab=99.87  E-value=4.2e-22  Score=134.47  Aligned_cols=67  Identities=43%  Similarity=0.652  Sum_probs=62.2

Q ss_pred             eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecC
Q psy9900         109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGP  179 (191)
Q Consensus       109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~  179 (191)
                      +++|+|+|||..||||||+++++++|||||+++|...    +++.|.+|+.|+|++.++++|++|.+|+.+
T Consensus         4 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~~   70 (70)
T PRK10354          4 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQND----GYKSLDEGQKVSFTIESGAKGPAAGNVTSL   70 (70)
T ss_pred             cceEEEEEEeCCCCcEEEecCCCCccEEEEEeecccc----CCCCCCCCCEEEEEEEECCCCceeEEEEeC
Confidence            3589999999999999999999889999999999874    578999999999999999999999999863

>PRK09507 cspE cold shock protein CspE; Reviewed

Probab=99.87  E-value=4.8e-22  Score=133.77  Aligned_cols=66  Identities=41%  Similarity=0.678  Sum_probs=61.8

Q ss_pred             eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeec
Q psy9900         109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG  178 (191)
Q Consensus       109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~  178 (191)
                      +.+|+|+|||..||||||+++++++|||||+++|...    +++.|.+|+.|+|++.++++|++|++|+.
T Consensus         3 ~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~   68 (69)
T PRK09507          3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTN----GFKTLAEGQRVEFEITNGAKGPSAANVIA   68 (69)
T ss_pred             ccceEEEEEeCCCCcEEEecCCCCeeEEEEeeccccc----CCCCCCCCCEEEEEEEECCCCcccEEEEe
Confidence            4789999999999999999999899999999999864    57899999999999999999999999975

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

Probab=99.87  E-value=6.9e-22  Score=134.54  Aligned_cols=66  Identities=33%  Similarity=0.564  Sum_probs=62.5

Q ss_pred             eeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecCC
Q psy9900         111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPN  180 (191)
Q Consensus       111 ~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~~  180 (191)
                      +|+|+|||..||||||+++++++|||||+++|...    +++.|.+|+.|+|++.++++|++|++|..++
T Consensus         3 ~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~~~   68 (74)
T PRK09937          3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMD----GYRTLKAGQSVQFDVHQGPKGNHASVIVPVE   68 (74)
T ss_pred             CeEEEEEeCCCCeEEEeeCCCCccEEEEEeecccc----CCCCCCCCCEEEEEEEECCCCceeeEEEECC
Confidence            69999999999999999999999999999999864    5899999999999999999999999999884

>TIGR02381 cspD cold shock domain protein CspD

Probab=99.86  E-value=9.4e-22  Score=132.06  Aligned_cols=65  Identities=34%  Similarity=0.550  Sum_probs=61.1

Q ss_pred             eeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecC
Q psy9900         111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGP  179 (191)
Q Consensus       111 ~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~  179 (191)
                      +|+|||||..||||||+++++++|||||+|+|...    +++.|.+|++|+|++.++++|++|.+|+.+
T Consensus         3 ~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~~   67 (68)
T TIGR02381         3 IGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMD----GYRTLKAGQKVQFEVVQGPKGAHATHIVPI   67 (68)
T ss_pred             CeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhc----CCCCCCCCCEEEEEEEECCCCceeEEEEEC
Confidence            69999999999999999999899999999999864    578999999999999999999999999864

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=99.86  E-value=1.4e-21  Score=132.71  Aligned_cols=68  Identities=32%  Similarity=0.517  Sum_probs=63.0

Q ss_pred             eeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecCCC
Q psy9900         110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNG  181 (191)
Q Consensus       110 ~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~~~  181 (191)
                      .+|+|+|||..||||||+++++++|||||+|+|...    +++.|.+|++|+|++.++++|++|++|..++.
T Consensus         2 ~~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~~~~   69 (73)
T PRK14998          2 ETGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMD----GYRTLKAGQSVRFDVHQGPKGNHASVIVPIEA   69 (73)
T ss_pred             CCeEEEEEeCCCceEEEecCCCCccEEEEeeeeccc----CCCCCCCCCEEEEEEEECCCCceeEEEEECcc
Confidence            369999999999999999999999999999999864    57899999999999999999999999988753

>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=99.82  E-value=7e-20  Score=122.11  Aligned_cols=65  Identities=43%  Similarity=0.710  Sum_probs=59.0

Q ss_pred             cceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeec
Q psy9900           9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG   77 (191)
Q Consensus         9 ~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~   77 (191)
                      ++|+|+|||..||||||.++++++|||||++++...    +++.|..|++|+|++..+++|++|.+|..
T Consensus         1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~----~~~~l~~G~~V~F~~~~~~~g~~A~~V~~   65 (66)
T PF00313_consen    1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGN----GFRSLKEGDRVEFEVEEGKKGPQAVNVRK   65 (66)
T ss_dssp             EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSS----SSTS--TTSEEEEEEEECTTSEEEEEEEE
T ss_pred             CeEEEEEEECCCCceEEEEcccceeEEecccccccc----ccccCCCCCEEEEEEEECCCCCEEEEEEC
Confidence            589999999999999999999989999999999986    57899999999999999999999999974

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 ....

>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=99.82  E-value=8.2e-20  Score=121.77  Aligned_cols=65  Identities=43%  Similarity=0.710  Sum_probs=59.2

Q ss_pred             eeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeec
Q psy9900         110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG  178 (191)
Q Consensus       110 ~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~  178 (191)
                      ++|+|+||+..+|||||+++++++|||||++++...    +++.|+.|+.|+|.+..+++|++|++|+.
T Consensus         1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~----~~~~l~~G~~V~F~~~~~~~g~~A~~V~~   65 (66)
T PF00313_consen    1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGN----GFRSLKEGDRVEFEVEEGKKGPQAVNVRK   65 (66)
T ss_dssp             EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSS----SSTS--TTSEEEEEEEECTTSEEEEEEEE
T ss_pred             CeEEEEEEECCCCceEEEEcccceeEEecccccccc----ccccCCCCCEEEEEEEECCCCCEEEEEEC
Confidence            589999999999999999999889999999999985    36899999999999999999999999985

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=99.81  E-value=1.6e-19  Score=120.01  Aligned_cols=64  Identities=45%  Similarity=0.735  Sum_probs=60.2

Q ss_pred             cceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEee
Q psy9900           9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVT   76 (191)
Q Consensus         9 ~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~   76 (191)
                      ++|+|||||..||||||.++++++|||||+++|...    ++..|.+|++|+|++..+++|++|.+|.
T Consensus         1 ~~G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~----~~~~~~~G~~V~f~~~~~~~g~~A~~V~   64 (65)
T cd04458           1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGD----GFRSLEEGDRVEFELEEGDKGPQAVNVR   64 (65)
T ss_pred             CcEEEEEEECCCCeEEEecCCCCcCEEEEhhHhhcc----CCCcCCCCCEEEEEEEECCCCCeEEEeE
Confidence            479999999999999999999999999999999976    5799999999999999999999999986

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.

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

Probab=99.80  E-value=3e-19  Score=118.70  Aligned_cols=65  Identities=45%  Similarity=0.701  Sum_probs=60.4

Q ss_pred             eeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeec
Q psy9900         110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG  178 (191)
Q Consensus       110 ~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~  178 (191)
                      ++|+|+||+..+|||||+++++++|||||++++...    ++..|++|+.|+|++..+++|++|++|+.
T Consensus         1 ~~G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~----~~~~~~~G~~V~f~~~~~~~g~~A~~V~~   65 (65)
T cd04458           1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGD----GFRSLEEGDRVEFELEEGDKGPQAVNVRL   65 (65)
T ss_pred             CcEEEEEEECCCCeEEEecCCCCcCEEEEhhHhhcc----CCCcCCCCCEEEEEEEECCCCCeEEEeEC
Confidence            369999999999999999999999999999999974    36899999999999999999999999973

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

Probab=99.55  E-value=8.2e-15  Score=119.99  Aligned_cols=88  Identities=47%  Similarity=0.761  Sum_probs=80.2

Q ss_pred             ccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecCCCC
Q psy9900         103 FFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNGI  182 (191)
Q Consensus       103 ~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~~~~  182 (191)
                      ...+....+|+|||||..+|||||+++|+++|||||+++|....+..++++|.+++.|.|.++.+.+|.+|++|+.+++.
T Consensus        50 ~~~~~~~~~G~~k~fnv~~G~gFi~~~d~~~D~fvhQs~i~~~~~~~~~rs~~~~e~v~f~~~~~~~g~~a~~vt~p~g~  129 (235)
T KOG3070|consen   50 KKVQGARVKGTVKWFNVGKGYGFITRDDGPEDVFVHQSAITKYTPSEGFRSLKEGEAVPFDIQEGNKGTEAANVTGPDGV  129 (235)
T ss_pred             cccccccccCcceeEeccCCcceecccCCCCceeEEeeeecccccccchhhcccCCCccceecccCccceeeeecCCCCc
Confidence            34556678999999999999999999999999999999999966777899999999999999999999999999999999


Q ss_pred             CCCCCCCC
Q psy9900         183 PVQGAPKV  190 (191)
Q Consensus       183 ~~~~~~~~  190 (191)
                      ++..+++.
T Consensus       130 ~~~~s~~~  137 (235)
T KOG3070|consen  130 PVRGSKGA  137 (235)
T ss_pred             cccccccc
Confidence            99877653

>KOG3070|consensus

Probab=99.49  E-value=3.9e-14  Score=116.01  Aligned_cols=89  Identities=47%  Similarity=0.799  Sum_probs=79.3

Q ss_pred             eeceeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeecCCCCC
Q psy9900           3 KFEIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNGIP   82 (191)
Q Consensus         3 ~~~~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~~~~~~   82 (191)
                      +.+....+|+|||||..+|||||.++++.+|||||+++|....+.+++++|.+++.|.|.++...+|..|++|+.+++.+
T Consensus        51 ~~~~~~~~G~~k~fnv~~G~gFi~~~d~~~D~fvhQs~i~~~~~~~~~rs~~~~e~v~f~~~~~~~g~~a~~vt~p~g~~  130 (235)
T KOG3070|consen   51 KVQGARVKGTVKWFNVGKGYGFITRDDGPEDVFVHQSAITKYTPSEGFRSLKEGEAVPFDIQEGNKGTEAANVTGPDGVP  130 (235)
T ss_pred             ccccccccCcceeEeccCCcceecccCCCCceeEEeeeecccccccchhhcccCCCccceecccCccceeeeecCCCCcc
Confidence            35677889999999999999999999999999999999998656669999999999999999999999999999999988


Q ss_pred             ccCCCCCCC
Q psy9900          83 VQGAPKSSS   91 (191)
Q Consensus        83 ~~~~~~~~~   91 (191)
                      +..+.....
T Consensus       131 ~~~s~~~~~  139 (235)
T KOG3070|consen  131 VRGSKGAVK  139 (235)
T ss_pred             ccccccccc
Confidence            866554443

>smart00357 CSP Cold shock protein domain

Probab=99.00  E-value=2.7e-09  Score=69.41  Aligned_cols=62  Identities=40%  Similarity=0.643  Sum_probs=50.8

Q ss_pred             eeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEE--cCCCceeEEeecC
Q psy9900         111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGV--GKKDIEAINVTGP  179 (191)
Q Consensus       111 ~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~--~~kg~~A~~V~~~  179 (191)
                      +|+|.|++  +|||||.+++...++|||.+++...     ...+..||.|.|.+..  ..++++|..|+.+
T Consensus         1 ~G~i~~~~--~g~gfv~~~~~~~~i~v~~~~~~~~-----~~~~~~Gd~V~~~i~~~~~~~~~~a~~v~~~   64 (64)
T smart00357        1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQGG-----LKSLREGDEVEFKVVSPRGGGKPEAENVVKL   64 (64)
T ss_pred             CeEEEEEc--CCeeEEecCCCCccEEEEhHHhhcC-----CCcCCCCCEEEEEEEEccCCCCcEEEEEEeC
Confidence            48999996  7999999987657999999987541     4678899999999987  5566899988753

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.

>smart00357 CSP Cold shock protein domain

Probab=98.94  E-value=5.4e-09  Score=67.99  Aligned_cols=61  Identities=41%  Similarity=0.657  Sum_probs=48.4

Q ss_pred             ceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEE--cCCCceeeEeec
Q psy9900          10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGV--GKKDIEAINVTG   77 (191)
Q Consensus        10 ~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~--~~~g~~A~~v~~   77 (191)
                      +|+|+||+  +|||||.+++...|+|||.+++..     +...+..||.|.|.+..  ..++++|..+..
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            58999997  899999998765799999998764     24667899999999987  344567776643

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.

>PRK11642 exoribonuclease R; Provisional

Probab=98.72  E-value=1.9e-07  Score=88.91  Aligned_cols=125  Identities=22%  Similarity=0.252  Sum_probs=91.8

Q ss_pred             cceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEc-CCC-ceeeEeecCCCCCccCC
Q psy9900           9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG-KKD-IEAINVTGPNGIPVQGA   86 (191)
Q Consensus         9 ~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~-~~g-~~A~~v~~~~~~~~~~~   86 (191)
                      ..|+|+.  ..+||||+.++++++|||++...+..++         .||+|.+.+... .++ +.+.-+           
T Consensus        85 ~~G~v~~--~~~GfgFv~~e~~~~difI~~~~l~~A~---------~GD~V~v~i~~~~~~~r~eg~Vv-----------  142 (813)
T PRK11642         85 LKGTVIG--HRDGYGFLRVEGRKDDLYLSSEQMKTCI---------HGDQVLAQPLGADRKGRREARIV-----------  142 (813)
T ss_pred             EEEEEEE--CCCccEEEEECCCCCCEEEChHHHccCC---------CCCEEEEEEccCCCCCCcEEEEE-----------
Confidence            5688884  4899999999876789999999999886         899999997642 223 333333           


Q ss_pred             CCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCC--CcEEEeccchhccCcccccccCCCCCEEEEEE
Q psy9900          87 PKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNK--EDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI  164 (191)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~--~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i  164 (191)
                                       .++++..+-.|..|...++++|+.|+|..  .+||+...+..         .++.|+.|.++|
T Consensus       143 -----------------~IleR~~~~~vG~~~~~~~~~~v~P~d~r~~~~i~i~~~~~~---------~~~~gd~V~v~I  196 (813)
T PRK11642        143 -----------------RVLVPKTSQIVGRYFTDAGVGFVVPDDSRLSFDILIPPEQIM---------GARMGFVVVVEL  196 (813)
T ss_pred             -----------------EEEecCCCEEEEEEEEeCCeEEEEECCCCCCCcEEecccccc---------CCCCCCEEEEEE
Confidence                             34455556667777778899999999864  67888654443         557899999999


Q ss_pred             EEcCC---CceeEEeecCCC
Q psy9900         165 GVGKK---DIEAINVTGPNG  181 (191)
Q Consensus       165 ~~~~k---g~~A~~V~~~~~  181 (191)
                      ..-+.   -+.+.-|+.++.
T Consensus       197 ~~~p~~~~~~~g~iv~vLG~  216 (813)
T PRK11642        197 TQRPTRRTKAVGKIVEVLGD  216 (813)
T ss_pred             ecCCCcCCCCCEEEEEEecC
Confidence            97432   266777776664

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

Probab=98.51  E-value=2.1e-06  Score=80.25  Aligned_cols=127  Identities=24%  Similarity=0.311  Sum_probs=90.1

Q ss_pred             ccceEEEEeeCCCCeeEEEeCC-CCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEc-CCC-ceeeEeecCCCCCcc
Q psy9900           8 TVRGIVKFYDSKRGFGFITRLD-NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG-KKD-IEAINVTGPNGIPVQ   84 (191)
Q Consensus         8 ~~~G~vk~~~~~kGfGFI~~~~-~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~-~~g-~~A~~v~~~~~~~~~   84 (191)
                      ..+|+|+.  ..|||||+.+++ +++|||+.-..+..++         .||+|.+.+... .++ +.|.-+         
T Consensus        16 ~~~G~i~~--~~~gfgFv~~~~~~~~difI~~~~~~~a~---------~GD~V~v~i~~~~~~~~~~g~v~---------   75 (654)
T TIGR00358        16 LVKGVVKA--HNKGFGFLRPDDDDKKDYFIPPPQMKKVM---------HGDLVEACPLSQPQRGRFEAEVE---------   75 (654)
T ss_pred             eEEEEEEE--CCCccEEEEeCCCCCCcEEEchHHhCcCC---------CCCEEEEEEeecCCCCCceEEEE---------
Confidence            46799995  489999999986 3689999999999886         899999997543 233 234333         


Q ss_pred             CCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCC--CcEEEeccchhccCcccccccCCCCCEEEE
Q psy9900          85 GAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNK--EDIFVHKSSIVKMNPKKFFQSLGLGEIVDF  162 (191)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~--~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f  162 (191)
                                         .++++..+-.|+.|...++++|+.|++..  .+||+...+..        ..++.||.|..
T Consensus        76 -------------------~il~r~~~~~vG~~~~~~~~~~v~p~~~~~~~~i~i~~~~~~--------~~~~~g~~V~v  128 (654)
T TIGR00358        76 -------------------RILEPALTRFVGKFLGENDFGFVVPDDPRIYLDIIVPKASVK--------NELAEGDKVVV  128 (654)
T ss_pred             -------------------EEeccCCCEEEEEEEEeCCeEEEEECCCCCCCcEEEcCCccc--------cCCCCCCEEEE
Confidence                               23444455566667677889999998864  67888544222        25678999999


Q ss_pred             EEEEcC--CC-ceeEEeecCCC
Q psy9900         163 NIGVGK--KD-IEAINVTGPNG  181 (191)
Q Consensus       163 ~i~~~~--kg-~~A~~V~~~~~  181 (191)
                      +|..=+  .+ +.+.-++.++.
T Consensus       129 ~i~~~p~~~~~~~g~i~~~lG~  150 (654)
T TIGR00358       129 ELTEYPLRRNLFYGEITQILGN  150 (654)
T ss_pred             EEccCCCCCCCceEEEEEEEcC
Confidence            998733  22 66666666654

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.

>PRK05054 exoribonuclease II; Provisional

Probab=98.45  E-value=3.9e-06  Score=78.29  Aligned_cols=128  Identities=16%  Similarity=0.078  Sum_probs=86.4

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeecCCCCCccCC
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNGIPVQGA   86 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~~~~~~~~~~   86 (191)
                      ....|+|+.  ..|||||+.+++ .+||||+...+..++         .||+|.+.+....++.+|.-+.+         
T Consensus        20 ~~~~G~~~~--~~~gfgFv~~~~-~~difI~~~~l~~a~---------~GD~V~v~i~~~~~r~~g~v~~i---------   78 (644)
T PRK05054         20 PRVEGVVKA--TEKGFGFLEVDA-QKSYFIPPPQMKKVM---------HGDRIIAVIHTEKDREIAEPEEL---------   78 (644)
T ss_pred             CeEEEEEEE--CCCccEEEEECC-CCcEEEChHHHccCC---------CCCEEEEEEecCCCCcEEEEEEE---------
Confidence            356799984  489999998855 469999999999886         89999999764322333333222         


Q ss_pred             CCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCC--CcEEEeccchhccCcccccccCCCCCEEEEEE
Q psy9900          87 PKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNK--EDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI  164 (191)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~--~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i  164 (191)
                                         +.+...-.|+.|...++++|+.|++..  .+||+....-.       ...++.||.|.++|
T Consensus        79 -------------------l~r~~~~~vG~~~~~~~~~~~~p~d~~~~~~i~i~~~~~~-------~~~~~~gd~V~v~i  132 (644)
T PRK05054         79 -------------------IEPFLTRFVGRVQKKDDRLSIVPDHPLLKDAIPCRAAKGL-------NHEFKEGDWVVAEL  132 (644)
T ss_pred             -------------------EecCCCEEEEEEEEeCceEEEEECCCCCCccEEecccccc-------ccCCCCCCEEEEEE
Confidence                               222333445556667789999999864  67888532111       12467899999999


Q ss_pred             EEcC----CCceeEEeecCCC
Q psy9900         165 GVGK----KDIEAINVTGPNG  181 (191)
Q Consensus       165 ~~~~----kg~~A~~V~~~~~  181 (191)
                      ..-+    +.+++.-++.++.
T Consensus       133 ~~~p~~~~~~~~g~i~~~lG~  153 (644)
T PRK05054        133 RRHPLKGDRGFYAEITQFITD  153 (644)
T ss_pred             ecCCCCCCCCceEEEEEEECC
Confidence            8642    2266777776664

>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=98.37  E-value=1.2e-06  Score=56.80  Aligned_cols=45  Identities=27%  Similarity=0.389  Sum_probs=34.2

Q ss_pred             CCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCce
Q psy9900          18 SKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIE   71 (191)
Q Consensus        18 ~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~   71 (191)
                      +.+||||+.+++.++|||++..++..++         .||+|.+.+....++..
T Consensus         6 ~~~GfGFv~~~~~~~DifIp~~~l~~A~---------~gD~V~v~i~~~~~~~~   50 (58)
T PF08206_consen    6 HPKGFGFVIPDDGGEDIFIPPRNLNGAM---------DGDKVLVRITPPSRGKR   50 (58)
T ss_dssp             -SSS-EEEEECT-TEEEEE-HHHHTTS----------TT-EEEEEEEESSSEEE
T ss_pred             EcCCCEEEEECCCCCCEEECHHHHCCCC---------CCCEEEEEEecCCCCCC
Confidence            4899999999998899999999999986         99999999998444433

; PDB: 2ID0_D 2IX1_A 2IX0_A.

>TIGR02062 RNase_B exoribonuclease II

Probab=98.27  E-value=1.9e-05  Score=73.63  Aligned_cols=129  Identities=16%  Similarity=0.076  Sum_probs=85.1

Q ss_pred             eeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeecCCCCCccC
Q psy9900           6 IHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNGIPVQG   85 (191)
Q Consensus         6 ~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~~~~~~~~~   85 (191)
                      .....|+|+.  ..|||||+..++ .+|||++...+..++         .||+|.+.+....+..+|.-+.         
T Consensus        16 ~~~~~G~i~~--~~kGfgFv~~~~-~~difI~~~~l~~A~---------~GD~V~v~i~~~~~r~~~~v~~---------   74 (639)
T TIGR02062        16 TPRVEGVVKA--TEKGFGFLEVDA-QKSYFIPPPQMKKVM---------HGDKIIAVIHSEKERESAEPEE---------   74 (639)
T ss_pred             CceEEEEEEE--CCCccEEEEECC-CCcEEEChHHHccCC---------CCCEEEEEEecCCCCcEEEEEE---------
Confidence            3456799985  489999997655 569999999999886         8999999876533323332222         


Q ss_pred             CCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCC--CcEEEeccchhccCcccccccCCCCCEEEEE
Q psy9900          86 APKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNK--EDIFVHKSSIVKMNPKKFFQSLGLGEIVDFN  163 (191)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~--~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~  163 (191)
                                         ++++..+-.|..|...++++|+.|+|..  .+|++  ..-...     ...++.||.|.++
T Consensus        75 -------------------iver~~~~~vG~~~~~~~~~~v~p~d~~~~~~i~~--~~~~~~-----~~~~~~gd~V~v~  128 (639)
T TIGR02062        75 -------------------LIEPFLTRFVGKVQGKDDKLAIVPDHPLLKDAIPC--RAAKGL-----NHEFQEGDWAVAE  128 (639)
T ss_pred             -------------------EEccCCCEEEEEEEEeCCeEEEEECCCCCCccEEe--cCcccc-----ccCCCCCCEEEEE
Confidence                               2233444556666677889999999853  33333  111110     0245789999999


Q ss_pred             EEEcC-CC---ceeEEeecCCC
Q psy9900         164 IGVGK-KD---IEAINVTGPNG  181 (191)
Q Consensus       164 i~~~~-kg---~~A~~V~~~~~  181 (191)
                      |.+-+ ++   +++.-++.++.
T Consensus       129 I~~~p~~~~~~~~~~I~~vLG~  150 (639)
T TIGR02062       129 LRRHPLKGDRSFYAELTQYITF  150 (639)
T ss_pred             EeccCCCCCCCceEEEEEEeCC
Confidence            98632 22   67777777664

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.

>TIGR02063 RNase_R ribonuclease R

Probab=98.22  E-value=2.4e-05  Score=73.86  Aligned_cols=126  Identities=24%  Similarity=0.265  Sum_probs=87.6

Q ss_pred             ccceEEEEeeCCCCeeEEEeCC-CCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC--C-CceeeEeecCCCCCc
Q psy9900           8 TVRGIVKFYDSKRGFGFITRLD-NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK--K-DIEAINVTGPNGIPV   83 (191)
Q Consensus         8 ~~~G~vk~~~~~kGfGFI~~~~-~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~--~-g~~A~~v~~~~~~~~   83 (191)
                      ...|+++.  ..+||||+.+++ ...|+||....+..++         .||.|.+++....  + .+.|.-+.+      
T Consensus        68 ~~~G~i~~--~~~g~gFv~~~~~~~~di~I~~~~~~~a~---------~GD~Vlv~I~~~~~~~~~~eg~Vv~I------  130 (709)
T TIGR02063        68 LVKGTVIA--HRDGFGFLRPEDDDEDDIFIPPRQMNGAM---------HGDRVLVRITGKPDGGDRFEARVIKI------  130 (709)
T ss_pred             eEEEEEEE--CCCccEEEEECCCCCCcEEEChHHhCcCC---------CCCEEEEEEecccCCCCCceEEEEEE------
Confidence            35688875  589999999886 4579999998887764         8999999986532  2 234433322      


Q ss_pred             cCCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCC--CcEEEeccchhccCcccccccCCCCCEEE
Q psy9900          84 QGAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNK--EDIFVHKSSIVKMNPKKFFQSLGLGEIVD  161 (191)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~--~dvF~h~s~~~~~~~~~~~~~l~~G~~V~  161 (191)
                                            +.+...-.|+.|...++++|+.|+|..  .+||+..++.         ..+..|+.|.
T Consensus       131 ----------------------l~r~~~~~VG~~~~~~~~~~v~p~d~~~~~~I~i~~~~~---------~~~~~g~~v~  179 (709)
T TIGR02063       131 ----------------------LERANDQIVGTFYIENGIGFVIPDDKRIYLDIFIPPEQI---------LGAEEGDKVL  179 (709)
T ss_pred             ----------------------EeeCCCEEEEEEEEcCcEEEEEECCCCCCCCEEECCccc---------cCCCCCCEEE
Confidence                                  233334455556667789999999874  5788875543         3567899999


Q ss_pred             EEEEEcC---CCceeEEeecCCC
Q psy9900         162 FNIGVGK---KDIEAINVTGPNG  181 (191)
Q Consensus       162 f~i~~~~---kg~~A~~V~~~~~  181 (191)
                      ++|..-+   +-+.+.-++.++.
T Consensus       180 v~i~~~p~~~~~~~g~i~~~lg~  202 (709)
T TIGR02063       180 VEITKYPDRNRPAIGKVVEILGH  202 (709)
T ss_pred             EEEccCCCCCCCceEEEEEEeCC
Confidence            9998643   2266666666654

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.

>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=98.15  E-value=8.7e-06  Score=52.65  Aligned_cols=49  Identities=29%  Similarity=0.361  Sum_probs=35.9

Q ss_pred             CCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC--ceeEEee
Q psy9900         120 KRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD--IEAINVT  177 (191)
Q Consensus       120 ~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg--~~A~~V~  177 (191)
                      .+||||+.+++..+|||++..++..+         -.||+|.+.+...+++  +++.-|+
T Consensus         7 ~~GfGFv~~~~~~~DifIp~~~l~~A---------~~gD~V~v~i~~~~~~~~~eg~vv~   57 (58)
T PF08206_consen    7 PKGFGFVIPDDGGEDIFIPPRNLNGA---------MDGDKVLVRITPPSRGKRPEGEVVE   57 (58)
T ss_dssp             SSS-EEEEECT-TEEEEE-HHHHTTS----------TT-EEEEEEEESSSEEEEEEEEEE
T ss_pred             cCCCEEEEECCCCCCEEECHHHHCCC---------CCCCEEEEEEecCCCCCCCCEEEEe
Confidence            79999999999889999999999865         6899999999994443  5555443

; PDB: 2ID0_D 2IX1_A 2IX0_A.

>PF14444 S1-like: S1-like

Probab=97.35  E-value=0.00087  Score=43.07  Aligned_cols=48  Identities=21%  Similarity=0.324  Sum_probs=40.0

Q ss_pred             eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900         108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK  169 (191)
Q Consensus       108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k  169 (191)
                      +..+|.|..+.  ..||||     .++|||+.+.+.+.       .++.||+|.++...++.
T Consensus         2 r~~~GvVTkl~--~~yG~I-----De~vFF~~~vv~G~-------~P~vGdrV~v~A~~n~~   49 (58)
T PF14444_consen    2 RVFTGVVTKLC--DDYGFI-----DEDVFFQTDVVKGN-------VPKVGDRVLVEAIYNPN   49 (58)
T ss_pred             ceEEEEEEEEe--CCcceE-----cccEEEEcccEecC-------CCccCCEEEEEEEeCCC
Confidence            35789999994  679999     36899999998863       56999999999998876

>PF14444 S1-like: S1-like

Probab=97.32  E-value=0.00096  Score=42.86  Aligned_cols=47  Identities=21%  Similarity=0.327  Sum_probs=39.8

Q ss_pred             ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC
Q psy9900           8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK   68 (191)
Q Consensus         8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~   68 (191)
                      ..+|.|..+.  -.||||     .+||||+.+.+.+.       .|+.||+|.++...+++
T Consensus         3 ~~~GvVTkl~--~~yG~I-----De~vFF~~~vv~G~-------~P~vGdrV~v~A~~n~~   49 (58)
T PF14444_consen    3 VFTGVVTKLC--DDYGFI-----DEDVFFQTDVVKGN-------VPKVGDRVLVEAIYNPN   49 (58)
T ss_pred             eEEEEEEEEe--CCcceE-----cccEEEEcccEecC-------CCccCCEEEEEEEeCCC
Confidence            3589999995  789999     46899999998753       55899999999998877

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

Probab=96.95  E-value=0.038  Score=46.31  Aligned_cols=127  Identities=20%  Similarity=0.186  Sum_probs=84.3

Q ss_pred             CceeceeccceEEEEeeCCCCeeEEE-eCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCC-ceeeEeecC
Q psy9900           1 MTKFEIHTVRGIVKFYDSKRGFGFIT-RLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD-IEAINVTGP   78 (191)
Q Consensus         1 ~~~~~~~~~~G~vk~~~~~kGfGFI~-~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g-~~A~~v~~~   78 (191)
                      |........+..|..+.   .||... -.+.++.|+.|.+....       ..+.+||.|.+-+=.+.++ +.|.-... 
T Consensus         1 ~~~~iG~~~~l~V~~~~---~~g~fL~~~~~~~~ilL~k~~~~~-------~e~evGdev~vFiY~D~~~rl~aTt~~p-   69 (287)
T COG2996           1 MMIKIGQINSLEVVEFS---DFGYFLDAGEDGTTILLPKSEPEE-------DELEVGDEVTVFIYVDSEDRLIATTREP-   69 (287)
T ss_pred             CcccccceEEEEEEEee---ceeEEEecCCCceEEeccccCCcC-------CccccCcEEEEEEEECCCCceeheeecc-
Confidence            33445566778888774   556554 44444589999998854       5889999999988877665 44443322 


Q ss_pred             CCCCccCCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCccccccc--CCC
Q psy9900          79 NGIPVQGAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQS--LGL  156 (191)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~--l~~  156 (191)
                                                .+..-..|-.+--...+.-|-.....-.+|+++..+++...      .+  +++
T Consensus        70 --------------------------~~tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp~~------~~~wpq~  117 (287)
T COG2996          70 --------------------------KATVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDELPTL------KSLWPQK  117 (287)
T ss_pred             --------------------------eEeecceeEEEEEEEcCCcceEEecCCCcceeeehhhcccc------cccCCCC
Confidence                                      00111123333333444555544444459999999999853      45  899


Q ss_pred             CCEEEEEEEEcCCC
Q psy9900         157 GEIVDFNIGVGKKD  170 (191)
Q Consensus       157 G~~V~f~i~~~~kg  170 (191)
                      ||.+.+.+..+++|
T Consensus       118 Gd~l~v~l~~Dkk~  131 (287)
T COG2996         118 GDKLLVYLYVDKKG  131 (287)
T ss_pred             CCEEEEEEEEccCC
Confidence            99999999999998

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=96.78  E-value=0.032  Score=50.78  Aligned_cols=142  Identities=20%  Similarity=0.182  Sum_probs=87.0

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheec-CCCCCcccCCCCCEEEEEEEEcC--CCceeeEeecCCCCCc
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKM-NPKKFFQSLGLGEIVDFNIGVGK--KDIEAINVTGPNGIPV   83 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~-~~~~g~~~l~~Gd~V~f~~~~~~--~g~~A~~v~~~~~~~~   83 (191)
                      ....|+|+...   -||....-+.+-+.|+|.+++... ...+....++.||.|.+.+..-+  ++.....+......|-
T Consensus       294 ~~v~G~V~~v~---~~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~~~p~  370 (491)
T PRK13806        294 DKVTGKVVRLA---PFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPW  370 (491)
T ss_pred             CEEEEEEEEEe---CceEEEEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEeecccChh
Confidence            45678888774   488877665568899999998631 00011235789999999987532  2322333322111110


Q ss_pred             cCCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEE
Q psy9900          84 QGAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFN  163 (191)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~  163 (191)
                      ..  .            ...........|+|+...   .||.+..-+.+-+-|+|.+.+.......-...++.||.|.+.
T Consensus       371 ~~--~------------~~~~~vG~~v~G~V~~i~---~~G~FV~l~~gv~Gli~~se~s~~~~~~~~~~~~~Gd~v~~~  433 (491)
T PRK13806        371 AD--V------------AERFAPGTTVTGTVEKRA---QFGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGDSVTLV  433 (491)
T ss_pred             HH--h------------hhhCCCCCEEEEEEEEEe---cCceEEEcCCCcEEEEEHHHcCcccccchhhcCCCCCEEEEE
Confidence            00  0            001223457889998863   466654444489999999998753211224678999999998


Q ss_pred             EEEcC
Q psy9900         164 IGVGK  168 (191)
Q Consensus       164 i~~~~  168 (191)
                      |..-+
T Consensus       434 V~~id  438 (491)
T PRK13806        434 VEEID  438 (491)
T ss_pred             EEEEe
Confidence            77644

>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=96.66  E-value=0.0044  Score=42.43  Aligned_cols=62  Identities=23%  Similarity=0.498  Sum_probs=37.7

Q ss_pred             ceEEEEeeCCCCeeEEEeC-----CCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCC---ceeeEeecCCC
Q psy9900          10 RGIVKFYDSKRGFGFITRL-----DNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD---IEAINVTGPNG   80 (191)
Q Consensus        10 ~G~vk~~~~~kGfGFI~~~-----~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g---~~A~~v~~~~~   80 (191)
                      .|.+--  ...|||||...     -+..||||..+.++.       -.|+.||.|+-.+.....+   ..-..|..+++
T Consensus         4 ~GvLei--~~dGyGFLR~~~~~y~~~~~DvYVs~~qIrr-------f~LR~GD~V~G~vr~p~~~ek~~aL~~V~~VNg   73 (78)
T PF07497_consen    4 EGVLEI--LPDGYGFLRSPDNNYLPSPDDVYVSPSQIRR-------FGLRTGDLVEGQVRPPREGEKYFALLRVESVNG   73 (78)
T ss_dssp             EEEEEE---TTS-EEEE-GGGTTS-STTSEEE-CCCCCC-------TT--TTEEEEEEEE--STTSSSEEECEECEETT
T ss_pred             EEEEEE--CCCCcEEeECCCcCCCCCCCCEEECHHHHHH-------cCCCCCCEEEEEEeCCCCCCcceeeEEEEeECC
Confidence            455552  35799999987     245899999999986       4789999999998875544   23344444433

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 ....

>COG0557 VacB Exoribonuclease R [Transcription]

Probab=96.59  E-value=0.031  Score=53.01  Aligned_cols=124  Identities=23%  Similarity=0.215  Sum_probs=89.6

Q ss_pred             ceEEEEeeCCCCeeEEEeCC--CCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC-C--ceeeEeecCCCCCcc
Q psy9900          10 RGIVKFYDSKRGFGFITRLD--NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK-D--IEAINVTGPNGIPVQ   84 (191)
Q Consensus        10 ~G~vk~~~~~kGfGFI~~~~--~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~-g--~~A~~v~~~~~~~~~   84 (191)
                      .|++.+  ..+||||+.+++  ...|+|+....+..++         .||.|.+++....+ +  ..|.-+         
T Consensus        71 ~~~~~~--~~~gf~f~~~~~~~~~~d~~v~~~~~~~a~---------~gD~V~v~~~~~~~~~~~~~~~v~---------  130 (706)
T COG0557          71 EGIVEA--SAKGFGFLSPDDSKDADDIFVPKDPLNRAL---------HGDRVLVELLPSDKRGRFKEAAVV---------  130 (706)
T ss_pred             cceEEe--ccCCceeeccCccCCCCcEEeccccccccc---------cCCEEEEEECcccccCCCceEEEE---------
Confidence            344443  379999999998  6789999999988775         99999999865444 3  122222         


Q ss_pred             CCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCC--CcEEEeccchhccCcccccccCCCCCEEEE
Q psy9900          85 GAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNK--EDIFVHKSSIVKMNPKKFFQSLGLGEIVDF  162 (191)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~--~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f  162 (191)
                                         .++.+....+|+.|-...+.+++.+.|..  .++++--+...         .+..|+.|.+
T Consensus       131 -------------------~il~r~~~~~vG~~~~~~~~~~~~p~d~r~~~~i~i~~~~~~---------~~~~~~~v~~  182 (706)
T COG0557         131 -------------------RILERANSALVGELRPSQGIGRVLPDDKRLPFLIAIPPEQAP---------GAEEGHLVVV  182 (706)
T ss_pred             -------------------eeeccccceeEEEEEecCCeEEEEecCCCCccceeecccccc---------ccccCCEEEE
Confidence                               34556778888898888889999998854  25676554444         4578999999


Q ss_pred             EEEEcCCC---ceeEEeecCCC
Q psy9900         163 NIGVGKKD---IEAINVTGPNG  181 (191)
Q Consensus       163 ~i~~~~kg---~~A~~V~~~~~  181 (191)
                      +|..-...   +...-+..++.
T Consensus       183 ~i~~~~~~~~~~~g~v~~~lG~  204 (706)
T COG0557         183 EITRWPDTSRPPFGEVVEVLGD  204 (706)
T ss_pred             EecccCCcCCCCceeEEEeecC
Confidence            99995543   55555665554

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=96.56  E-value=0.063  Score=48.85  Aligned_cols=150  Identities=17%  Similarity=0.155  Sum_probs=89.0

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEE-cCC-CceeeEeecCCCCCcc
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGV-GKK-DIEAINVTGPNGIPVQ   84 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~-~~~-g~~A~~v~~~~~~~~~   84 (191)
                      ...+|+|+...   .||.+..-. +-+.|+|.++|......+....++.||.|++.+.. ++. +............|-.
T Consensus       210 ~iv~G~V~~i~---~~G~FVdlg-gv~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK~~~~dPw~  285 (486)
T PRK07899        210 QVRKGVVSSIV---NFGAFVDLG-GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKATQEDPWQ  285 (486)
T ss_pred             CEEEEEEEEEE---CCeEEEEEC-CEEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeeccccchh
Confidence            34679999874   466655444 58999999999753211112346899999999765 332 3222222221111110


Q ss_pred             CCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEE
Q psy9900          85 GAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI  164 (191)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i  164 (191)
                              ..      .........+.|+|...   ..||++..-+.+-+-++|++++.......--..++.||.|.+.|
T Consensus       286 --------~~------~~~~~vG~vv~G~V~~I---~~fGvFVeL~~gieGLvh~SeLs~~~v~~~~~~~kvGd~V~VkI  348 (486)
T PRK07899        286 --------QF------ARTHAIGQIVPGKVTKL---VPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKV  348 (486)
T ss_pred             --------hh------HHhcCCCCEEEEEEEEE---eccEEEEEeCCCcEEEEEHHHcCcccccCccceeCCCCEEEEEE
Confidence                    00      00022345688999887   34888777665789999999997531111113479999999998


Q ss_pred             EEcC--CCceeEEee
Q psy9900         165 GVGK--KDIEAINVT  177 (191)
Q Consensus       165 ~~~~--kg~~A~~V~  177 (191)
                      ..-+  ++.-...++
T Consensus       349 i~ID~e~rrI~LSlK  363 (486)
T PRK07899        349 IDIDLERRRISLSLK  363 (486)
T ss_pred             EEEECCCCEEEEEEE
Confidence            7744  343333444

>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=96.45  E-value=0.012  Score=40.38  Aligned_cols=64  Identities=25%  Similarity=0.549  Sum_probs=41.2

Q ss_pred             eeeEEEeecCCCceeEEeCC-----CCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC---ceeEEeecCCCC
Q psy9900         111 RGIVKFYDSKRGFGFITRLD-----NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD---IEAINVTGPNGI  182 (191)
Q Consensus       111 ~G~Vk~~~~~kgfGFI~~~d-----~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg---~~A~~V~~~~~~  182 (191)
                      .|++-..  .+||||+...+     +..||||..+.+..       -.|+.||.|+=.+.....+   ..-+.|.-++|.
T Consensus         4 ~GvLei~--~dGyGFLR~~~~~y~~~~~DvYVs~~qIrr-------f~LR~GD~V~G~vr~p~~~ek~~aL~~V~~VNg~   74 (78)
T PF07497_consen    4 EGVLEIL--PDGYGFLRSPDNNYLPSPDDVYVSPSQIRR-------FGLRTGDLVEGQVRPPREGEKYFALLRVESVNGR   74 (78)
T ss_dssp             EEEEEE---TTS-EEEE-GGGTTS-STTSEEE-CCCCCC-------TT--TTEEEEEEEE--STTSSSEEECEECEETTE
T ss_pred             EEEEEEC--CCCcEEeECCCcCCCCCCCCEEECHHHHHH-------cCCCCCCEEEEEEeCCCCCCcceeeEEEEeECCc
Confidence            4555533  57999999972     35899999999986       5899999999888886555   345566666654


Q ss_pred             C
Q psy9900         183 P  183 (191)
Q Consensus       183 ~  183 (191)
                      +
T Consensus        75 ~   75 (78)
T PF07497_consen   75 P   75 (78)
T ss_dssp             C
T ss_pred             C
Confidence            3

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 ....

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=96.19  E-value=0.15  Score=46.40  Aligned_cols=153  Identities=19%  Similarity=0.164  Sum_probs=88.9

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCC--c----eeeEeecCCC
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD--I----EAINVTGPNG   80 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g--~----~A~~v~~~~~   80 (191)
                      ...+|+|+...   .||.+..-..+-+.|+|.+++......+.-..+..||.|.+.+..-...  .    -.........
T Consensus       204 ~iv~G~V~~v~---~~G~fV~l~~gv~g~v~~sels~~~~~~~~~~~~vGd~i~vkVl~id~~~~~~~~ri~lS~K~~~~  280 (491)
T PRK13806        204 DVVEGTVTRLA---PFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQAGG  280 (491)
T ss_pred             CEEEEEEEEEe---CCeEEEEcCCCcEEEEEHHHCCCccccChhHhcCCCCEEEEEEEEEecccCCcceEEEEEehhhhc
Confidence            34579999874   3666655544689999999996431111123467999999998653321  1    1122221110


Q ss_pred             CCccCCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccC-cccccccCCCCCE
Q psy9900          81 IPVQGAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMN-PKKFFQSLGLGEI  159 (191)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~-~~~~~~~l~~G~~  159 (191)
                      .|-        ..      -.........+.|+|....   .||.+.....+-+.|+|.+++.... ...--..++.||.
T Consensus       281 ~p~--------~~------~~~~~~~G~~v~G~V~~v~---~~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~  343 (491)
T PRK13806        281 DPW--------DT------VGDRLKAGDKVTGKVVRLA---PFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDA  343 (491)
T ss_pred             ccc--------hh------hhccCCCCCEEEEEEEEEe---CceEEEEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCE
Confidence            000        00      0011233467889998873   4888776655789999999986310 0001135899999


Q ss_pred             EEEEEEEcC--CCceeEEeecC
Q psy9900         160 VDFNIGVGK--KDIEAINVTGP  179 (191)
Q Consensus       160 V~f~i~~~~--kg~~A~~V~~~  179 (191)
                      |.+.|..-+  ++.-...++.+
T Consensus       344 v~vkVl~iD~e~~ri~Ls~K~~  365 (491)
T PRK13806        344 VAVKIKDIDPAKRRISLSLRDA  365 (491)
T ss_pred             EEEEEEEEEccCCEEEEEEeec
Confidence            999998643  33333444433

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=95.92  E-value=0.23  Score=48.26  Aligned_cols=152  Identities=16%  Similarity=0.140  Sum_probs=90.6

Q ss_pred             ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC--CceeeEeecCCCCCccC
Q psy9900           8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK--DIEAINVTGPNGIPVQG   85 (191)
Q Consensus         8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~--g~~A~~v~~~~~~~~~~   85 (191)
                      ..+|+|+...   .||.+..-+ +-+-|+|.|.+....-.+....+..|+.|++.+..-++  +.-..........|   
T Consensus       496 ~V~G~Vk~i~---~~G~fVdl~-Gv~Gfvp~SeiS~~~v~~~~~~~kvGq~v~vkVi~iD~e~~rI~LSlK~l~~~p---  568 (863)
T PRK12269        496 SVSGVVKSFT---SFGAFIDLG-GFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSLKHFQPDP---  568 (863)
T ss_pred             EEEEEEEEEe---CCcEEEEEC-CEEEEEEchhccccccCCHHHhccCCCEEEEEEEEEecCCCeEEEEEeccccch---
Confidence            4689999885   467766554 56899999998643100012336789999999875443  32222222111100   


Q ss_pred             CCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhcc-CcccccccCCCCCEEEEEE
Q psy9900          86 APKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKM-NPKKFFQSLGLGEIVDFNI  164 (191)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~-~~~~~~~~l~~G~~V~f~i  164 (191)
                        ...         -.........++|+|+...   .||.+..-..+-+-++|++++... ....-...++.||.|.+.|
T Consensus       569 --~~~---------~~~~~~vG~iV~G~V~~I~---~fG~fVeL~~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkV  634 (863)
T PRK12269        569 --WLE---------FENKFGVNDVVKGRVTKIA---DFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMI  634 (863)
T ss_pred             --hhh---------hhccCCCCCEEEEEEEEEe---CCeEEEEecCCceeeeEHHHhcCccccCCHHHcCCCCCEEEEEE
Confidence              000         0011334467899999884   488766665578889999998641 1011124589999999998


Q ss_pred             EEcCC--CceeEEeecCC
Q psy9900         165 GVGKK--DIEAINVTGPN  180 (191)
Q Consensus       165 ~~~~k--g~~A~~V~~~~  180 (191)
                      ..-+.  +.-...++-+.
T Consensus       635 l~iD~e~~rIsLS~K~l~  652 (863)
T PRK12269        635 LGYDIQAGRVSLGLKQVT  652 (863)
T ss_pred             EEEecccCceEEEehhcc
Confidence            88543  34444554433

>PRK11642 exoribonuclease R; Provisional

Probab=95.80  E-value=0.027  Score=54.26  Aligned_cols=63  Identities=21%  Similarity=0.183  Sum_probs=49.4

Q ss_pred             eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEE-cCCC-ceeEEeecCCCC
Q psy9900         109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGV-GKKD-IEAINVTGPNGI  182 (191)
Q Consensus       109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~-~~kg-~~A~~V~~~~~~  182 (191)
                      .+.|+|..-  .+||||+.++++++|||++-..+..+         -.||.|.+.+.. +.+| ++|.-|.++..+
T Consensus        84 ~~~G~v~~~--~~GfgFv~~e~~~~difI~~~~l~~A---------~~GD~V~v~i~~~~~~~r~eg~Vv~IleR~  148 (813)
T PRK11642         84 LLKGTVIGH--RDGYGFLRVEGRKDDLYLSSEQMKTC---------IHGDQVLAQPLGADRKGRREARIVRVLVPK  148 (813)
T ss_pred             eEEEEEEEC--CCccEEEEECCCCCCEEEChHHHccC---------CCCCEEEEEEccCCCCCCcEEEEEEEEecC
Confidence            467888864  79999999987678999998887754         579999999876 3333 788888887764

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=95.70  E-value=0.22  Score=48.44  Aligned_cols=143  Identities=14%  Similarity=0.147  Sum_probs=89.2

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheec-CCCCCcccCCCCCEEEEEEEEcCC--CceeeEeecCCCCCc
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKM-NPKKFFQSLGLGEIVDFNIGVGKK--DIEAINVTGPNGIPV   83 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~-~~~~g~~~l~~Gd~V~f~~~~~~~--g~~A~~v~~~~~~~~   83 (191)
                      ...+|+|+...   -||.+..-..+-+-|+|.|++.-. ...+....++.||.|.+.+-.-+.  +.....+......|-
T Consensus       580 ~iV~G~V~~I~---~fG~fVeL~~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw  656 (863)
T PRK12269        580 DVVKGRVTKIA---DFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPW  656 (863)
T ss_pred             CEEEEEEEEEe---CCeEEEEecCCceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEecccCceEEEehhcccCch
Confidence            45689999885   488776665567889999998641 111123457999999999876432  333333322111110


Q ss_pred             cCCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCc-ccccccCCCCCEEEE
Q psy9900          84 QGAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNP-KKFFQSLGLGEIVDF  162 (191)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~-~~~~~~l~~G~~V~f  162 (191)
                      .        ..      ..........+|+|+..   ..||.+..-..+-+-|+|.+++.-... ...-..+++||.|.+
T Consensus       657 ~--------~~------~~~~~vG~~v~G~V~~i---~~~G~fV~l~~gV~GlIh~sels~~~~~~~~~~~~kvGq~Vkv  719 (863)
T PRK12269        657 E--------EI------EARYPVGARFTRRIVKV---TNAGAFIEMEEGIDGFLHVDDLSWVKRTRPADHELEVGKEIEC  719 (863)
T ss_pred             H--------HH------HHhCCCCCEEEEEEEEE---ecceEEEEeCCCcEEEEEhHHhhccccccchhhccCCCCEEEE
Confidence            0        00      01133456788999886   347777666568899999999864210 001135899999999


Q ss_pred             EEEEcCC
Q psy9900         163 NIGVGKK  169 (191)
Q Consensus       163 ~i~~~~k  169 (191)
                      .|..-+.
T Consensus       720 kVl~ID~  726 (863)
T PRK12269        720 MVIECDP  726 (863)
T ss_pred             EEEEEec
Confidence            9888654

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

Probab=95.70  E-value=0.025  Score=37.71  Aligned_cols=41  Identities=32%  Similarity=0.464  Sum_probs=33.7

Q ss_pred             CCCeeEEEeCC-----CCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEc
Q psy9900          19 KRGFGFITRLD-----NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG   66 (191)
Q Consensus        19 ~kGfGFI~~~~-----~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~   66 (191)
                      ..|||||...+     ...||||+.+-++.       -.|+.||.|+-.+...
T Consensus         9 ~~g~GFLR~~~~~y~~~~~DvyVs~~~Irr-------~~LR~GD~V~G~vr~p   54 (68)
T cd04459           9 PDGFGFLRSSGYNYLPGPDDIYVSPSQIRR-------FNLRTGDTVVGQIRPP   54 (68)
T ss_pred             CCCceEEecCCcCCCCCCCCEEECHHHHHH-------hCCCCCCEEEEEEeCC
Confidence            34999999762     45899999999996       4789999999988753

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.

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=95.64  E-value=0.52  Score=40.56  Aligned_cols=148  Identities=14%  Similarity=0.040  Sum_probs=91.2

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC-Cce-eeEeecCCCCCcc
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK-DIE-AINVTGPNGIPVQ   84 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~-g~~-A~~v~~~~~~~~~   84 (191)
                      ...+|+|+..+   .+|++..-+ +-+-|+|.|.+....    ......|+.|.+.+..-+. ..+ ...........  
T Consensus       120 ~~V~g~V~~~~---~~G~~V~l~-Gv~gfip~s~ls~~~----~~~~~vG~~i~~kVl~id~~~~~i~lS~K~~~~~~--  189 (318)
T PRK07400        120 ATVRSEVFATN---RGGALVRIE-GLRGFIPGSHISTRK----PKEELVGEELPLKFLEVDEERNRLVLSHRRALVER--  189 (318)
T ss_pred             CEEEEEEEEEE---CCeEEEEEC-CEEEEEEHHHcCccC----CccccCCCEEEEEEEEEEcccCEEEEEhhHhhhhh--
Confidence            44678888885   346666554 668899999997532    1233499999999865332 211 11111000000  


Q ss_pred             CCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEE
Q psy9900          85 GAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI  164 (191)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i  164 (191)
                               .      .........+.|+|+...   .||...... +-+-++|.+++.......-...++.||.|.+.+
T Consensus       190 ---------~------~~~~k~G~vv~G~V~~I~---~~G~fV~i~-gv~Gllhisels~~~~~~~~~~~~vGd~VkvkV  250 (318)
T PRK07400        190 ---------K------MNRLEVGEVVVGTVRGIK---PYGAFIDIG-GVSGLLHISEISHEHIETPHSVFNVNDEMKVMI  250 (318)
T ss_pred             ---------h------hccCCCCCEEEEEEEEEE---CCeEEEEEC-CEEEEEEHHHcccccccChhhccCCCCEEEEEE
Confidence                     0      001223456889998874   488877664 678999999997542112234579999999999


Q ss_pred             EEcC--CCceeEEeecCCCCC
Q psy9900         165 GVGK--KDIEAINVTGPNGIP  183 (191)
Q Consensus       165 ~~~~--kg~~A~~V~~~~~~~  183 (191)
                      ..-+  +|.-...++.+...|
T Consensus       251 l~iD~e~~rI~LS~K~l~~~P  271 (318)
T PRK07400        251 IDLDAERGRISLSTKQLEPEP  271 (318)
T ss_pred             EEEeCCCCEEEEEEeccccCh
Confidence            8865  456666666666544

>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

Probab=95.59  E-value=0.18  Score=46.28  Aligned_cols=140  Identities=16%  Similarity=0.195  Sum_probs=92.9

Q ss_pred             ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC--CceeeEeecCCCCCccC
Q psy9900           8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK--DIEAINVTGPNGIPVQG   85 (191)
Q Consensus         8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~--g~~A~~v~~~~~~~~~~   85 (191)
                      -..|+|+...+   ||-...-.+ -|=++|.+++.-....++..-+..||.|...+-.-+.  +.....+......|-. 
T Consensus       195 vV~G~V~~It~---~GafVdigG-vdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~l~~dPw~-  269 (541)
T COG0539         195 VVEGVVKNITD---YGAFVDIGG-VDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQLEEDPWE-  269 (541)
T ss_pred             eEEEEEEEeec---CcEEEEecC-eeeEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehhcccCcHH-
Confidence            45799998864   886666653 8999999999866544456667899999999987554  3334443332211100 


Q ss_pred             CCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEE
Q psy9900          86 APKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIG  165 (191)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~  165 (191)
                          .         -...........|+|..+.   .||.+..-..+-+=|+|+|.+.-.....--.-|+.||.|++.|-
T Consensus       270 ----~---------i~~~~~~g~~v~G~Vt~i~---~~GafVei~~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl  333 (541)
T COG0539         270 ----G---------IEKKYPVGDKVEGKVTNLT---DYGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVL  333 (541)
T ss_pred             ----H---------HhhhcCCCCEEEEEEEEee---cCcEEEEecCCccceeechhhcccccCCHHHhcccCCEEEEEEE
Confidence                0         0111444567889998873   47766666668889999998865432112244799999999987


Q ss_pred             EcC
Q psy9900         166 VGK  168 (191)
Q Consensus       166 ~~~  168 (191)
                      .=+
T Consensus       334 ~id  336 (541)
T COG0539         334 DID  336 (541)
T ss_pred             eeC
Confidence            744

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

Probab=95.42  E-value=0.049  Score=36.31  Aligned_cols=48  Identities=31%  Similarity=0.514  Sum_probs=37.3

Q ss_pred             eeEEEeecCCCceeEEeCC-----CCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcC
Q psy9900         112 GIVKFYDSKRGFGFITRLD-----NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK  168 (191)
Q Consensus       112 G~Vk~~~~~kgfGFI~~~d-----~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~  168 (191)
                      |++-..  ..||||+...+     +..||||+.+.+..       -.|+.||.|+=.+....
T Consensus         3 GiLdi~--~~g~GFLR~~~~~y~~~~~DvyVs~~~Irr-------~~LR~GD~V~G~vr~p~   55 (68)
T cd04459           3 GVLEIL--PDGFGFLRSSGYNYLPGPDDIYVSPSQIRR-------FNLRTGDTVVGQIRPPK   55 (68)
T ss_pred             EEEEEc--CCCceEEecCCcCCCCCCCCEEECHHHHHH-------hCCCCCCEEEEEEeCCC
Confidence            444433  34899999863     35899999999997       58999999998887643

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.

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=95.37  E-value=0.96  Score=39.70  Aligned_cols=156  Identities=19%  Similarity=0.196  Sum_probs=88.1

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEc-CC-CceeeEeecCCCCCcc
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG-KK-DIEAINVTGPNGIPVQ   84 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~-~~-g~~A~~v~~~~~~~~~   84 (191)
                      ....|+|+....   ||....-. +-+.|+|.+.+......+....++.||.|.+.+..- +. +.-..........|- 
T Consensus       194 ~~v~g~V~~v~~---~G~fV~l~-~v~g~v~~sels~~~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~~~~~~~-  268 (390)
T PRK06676        194 DVVEGTVARLTD---FGAFVDIG-GVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGPW-  268 (390)
T ss_pred             CEEEEEEEEEec---ceEEEEeC-CeEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEeecccCcc-
Confidence            456788988642   55444333 478999999986431100113468999999998653 32 322222221110000 


Q ss_pred             CCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEE
Q psy9900          85 GAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI  164 (191)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i  164 (191)
                             ...      .........+.|+|....   .||+...-+.+-+-++|.+++.......--..++.||.|...+
T Consensus       269 -------~~~------~~~~~~G~~v~g~V~~i~---~~G~fV~l~~gi~Glv~~se~~~~~~~~~~~~~~~Gd~v~v~V  332 (390)
T PRK06676        269 -------EGV------EEKLPEGDVIEGTVKRLT---DFGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKV  332 (390)
T ss_pred             -------ccc------hhhhcCCcEEEEEEEEEe---CceEEEEECCCCeEEEEhHHcCccccCChhhccCCCCEEEEEE
Confidence                   000      001223456889998864   3887666555678899999986421000113478999999998


Q ss_pred             EEcC--CCceeEEeecCCCCC
Q psy9900         165 GVGK--KDIEAINVTGPNGIP  183 (191)
Q Consensus       165 ~~~~--kg~~A~~V~~~~~~~  183 (191)
                      ..-+  ++.-...++.+...|
T Consensus       333 ~~id~e~~~i~ls~k~~~~~~  353 (390)
T PRK06676        333 LEVNEEEKRISLSIKALEEAP  353 (390)
T ss_pred             EEEECCCCEEEEEEEecccCh
Confidence            8865  344444455444433

>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed

Probab=95.30  E-value=0.64  Score=43.79  Aligned_cols=154  Identities=23%  Similarity=0.162  Sum_probs=89.6

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEc-CC-CceeeEeecCCCCCcc
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG-KK-DIEAINVTGPNGIPVQ   84 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~-~~-g~~A~~v~~~~~~~~~   84 (191)
                      ....|+|+...   .||++..- ++-+.|+|.+++...........++.||.|.+.+..- +. +.-..........|-.
T Consensus       479 ~iV~g~V~~v~---~~G~fV~l-~gv~Gll~~sels~~~~~~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~  554 (647)
T PRK00087        479 DVVEGEVKRLT---DFGAFVDI-GGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWE  554 (647)
T ss_pred             CEEEEEEEEEe---CCcEEEEE-CCEEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEeeccccChhh
Confidence            45688998874   35655444 4678999999986421111123578999999998653 22 3222222211111100


Q ss_pred             CCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEE
Q psy9900          85 GAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI  164 (191)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i  164 (191)
                              ..      .........+.|+|....   .||+...-+.+-+-++|.+++.......--..++.||.|...+
T Consensus       555 --------~~------~~~~~~G~~v~g~V~~i~---~~G~fV~l~~~i~Gli~~sel~~~~~~~~~~~~kvGd~V~vkV  617 (647)
T PRK00087        555 --------NV------EEKYPVGSIVLGKVVRIA---PFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKI  617 (647)
T ss_pred             --------hh------hhhccCCeEEEEEEEEEE---CCeEEEEECCCCEEEEEhhhcCccccCCHhhcCCCCCEEEEEE
Confidence                    00      000123456889998874   3777666555789999999987531111113579999999998


Q ss_pred             EEcC--CCceeEEeecCCC
Q psy9900         165 GVGK--KDIEAINVTGPNG  181 (191)
Q Consensus       165 ~~~~--kg~~A~~V~~~~~  181 (191)
                      ..-+  ++.-...++.+..
T Consensus       618 ~~id~e~~rI~lslk~~~~  636 (647)
T PRK00087        618 LEVDPEEKRIRLSIKEVEE  636 (647)
T ss_pred             EEEeCCCCEEEEEEeeccc
Confidence            8754  3444444554443

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

Probab=95.26  E-value=0.069  Score=50.31  Aligned_cols=63  Identities=27%  Similarity=0.372  Sum_probs=48.8

Q ss_pred             eeeeeEEEeecCCCceeEEeCCC-CCcEEEeccchhccCcccccccCCCCCEEEEEEEE-cCCC-ceeEEeecCCCC
Q psy9900         109 TVRGIVKFYDSKRGFGFITRLDN-KEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGV-GKKD-IEAINVTGPNGI  182 (191)
Q Consensus       109 ~~~G~Vk~~~~~kgfGFI~~~d~-~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~-~~kg-~~A~~V~~~~~~  182 (191)
                      ...|+|+.-  .+||||+.++++ ++|||+.-.++..+         -.||.|.+.+.. +++| ++|.-+.++..+
T Consensus        16 ~~~G~i~~~--~~gfgFv~~~~~~~~difI~~~~~~~a---------~~GD~V~v~i~~~~~~~~~~g~v~~il~r~   81 (654)
T TIGR00358        16 LVKGVVKAH--NKGFGFLRPDDDDKKDYFIPPPQMKKV---------MHGDLVEACPLSQPQRGRFEAEVERILEPA   81 (654)
T ss_pred             eEEEEEEEC--CCccEEEEeCCCCCCcEEEchHHhCcC---------CCCCEEEEEEeecCCCCCceEEEEEEeccC
Confidence            467999874  799999999863 68999998877654         579999999865 3344 588888877653

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.

>TIGR02062 RNase_B exoribonuclease II

Probab=95.11  E-value=0.092  Score=49.37  Aligned_cols=62  Identities=23%  Similarity=0.256  Sum_probs=46.9

Q ss_pred             eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecCCC
Q psy9900         108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNG  181 (191)
Q Consensus       108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~~~  181 (191)
                      ....|+|+.-  .+||||+.+++ .+|||++-..+..+         -.||.|.+.+....++.+|.-+.++..
T Consensus        17 ~~~~G~i~~~--~kGfgFv~~~~-~~difI~~~~l~~A---------~~GD~V~v~i~~~~~r~~~~v~~iver   78 (639)
T TIGR02062        17 PRVEGVVKAT--EKGFGFLEVDA-QKSYFIPPPQMKKV---------MHGDKIIAVIHSEKERESAEPEELIEP   78 (639)
T ss_pred             ceEEEEEEEC--CCccEEEEECC-CCcEEEChHHHccC---------CCCCEEEEEEecCCCCcEEEEEEEEcc
Confidence            4567999864  79999997654 57999999988754         579999999876444466666666644

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.

>PRK05054 exoribonuclease II; Provisional

Probab=95.07  E-value=0.084  Score=49.64  Aligned_cols=62  Identities=23%  Similarity=0.240  Sum_probs=46.8

Q ss_pred             eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecCCC
Q psy9900         108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNG  181 (191)
Q Consensus       108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~~~  181 (191)
                      ....|+|..-  .+||||+.+++ .+|||++-..+..+         -.||.|.+.+....++.+|.-+.++..
T Consensus        20 ~~~~G~~~~~--~~gfgFv~~~~-~~difI~~~~l~~a---------~~GD~V~v~i~~~~~r~~g~v~~il~r   81 (644)
T PRK05054         20 PRVEGVVKAT--EKGFGFLEVDA-QKSYFIPPPQMKKV---------MHGDRIIAVIHTEKDREIAEPEELIEP   81 (644)
T ss_pred             CeEEEEEEEC--CCccEEEEECC-CCcEEEChHHHccC---------CCCCEEEEEEecCCCCcEEEEEEEEec
Confidence            3467999864  79999998854 56999999988754         579999999876444467776666654

>TIGR00717 rpsA ribosomal protein S1

Probab=95.01  E-value=1.3  Score=40.32  Aligned_cols=142  Identities=16%  Similarity=0.169  Sum_probs=85.3

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCC-CCcccCCCCCEEEEEEEEcC-C-CceeeEeecCCCCCc
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPK-KFFQSLGLGEIVDFNIGVGK-K-DIEAINVTGPNGIPV   83 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~-~g~~~l~~Gd~V~f~~~~~~-~-g~~A~~v~~~~~~~~   83 (191)
                      ....|+|+.-   ..||+...-+.+-+.|+|.+++...... .....++.||.|.+.+..-+ . +.-..........|-
T Consensus       361 ~~v~g~V~~v---~~~G~fV~l~~~v~glv~~s~ls~~~~~~~~~~~~~~G~~V~~~Vl~vd~~~~~i~ls~K~~~~~p~  437 (516)
T TIGR00717       361 DRVTGKIKKI---TDFGAFVELEGGIDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQLTENPW  437 (516)
T ss_pred             CEEEEEEEEE---ecceEEEECCCCCEEEEEHHHCcCcccCCCHhHccCCCCEEEEEEEEEeCcCCEEEEeeccccCCch
Confidence            4567888875   4567776666678999999998632100 01246789999999865433 2 332222221111110


Q ss_pred             cCCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEE
Q psy9900          84 QGAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFN  163 (191)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~  163 (191)
                              ...      ...........|+|...   ..||+...-+.+-+-|+|.+++.......-...++.||.|.+.
T Consensus       438 --------~~~------~~~~~~G~~v~g~V~~v---~~~G~fV~l~~~~~Glv~~s~l~~~~~~~~~~~~~~Gd~v~~~  500 (516)
T TIGR00717       438 --------EKF------AAKYKVGSVVKGKVTEI---KDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAK  500 (516)
T ss_pred             --------hhh------hhccCcceEEEEEEEEE---ecceEEEEcCCCeEEEEEHHHcCccccccccccCCCCCEEEEE
Confidence                    000      00122345688999886   3478655555578999999998643111124578999999999


Q ss_pred             EEEcC
Q psy9900         164 IGVGK  168 (191)
Q Consensus       164 i~~~~  168 (191)
                      |..-+
T Consensus       501 V~~id  505 (516)
T TIGR00717       501 VVDID  505 (516)
T ss_pred             EEEEe
Confidence            87643

This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=94.77  E-value=1.4  Score=40.67  Aligned_cols=140  Identities=19%  Similarity=0.238  Sum_probs=83.6

Q ss_pred             ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEE-cC-CCceeeEeecCCCCCccC
Q psy9900           8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGV-GK-KDIEAINVTGPNGIPVQG   85 (191)
Q Consensus         8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~-~~-~g~~A~~v~~~~~~~~~~   85 (191)
                      ...|+|+...   -||....-+ +-+.|+|.+.+......+....++.||.|.+.+.. ++ ++.-..........|-..
T Consensus       204 iv~g~V~~v~---~~G~~V~i~-g~~glv~~se~s~~~~~~~~~~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~~~p~~~  279 (565)
T PRK06299        204 VVEGVVKNIT---DYGAFVDLG-GVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEA  279 (565)
T ss_pred             EEEEEEEEEe---CCeEEEEEC-CEEEEEEHHHhcccccCCHhhcCCCCCEEEEEEEEEeCCCCeEEEEEEecccChhHH
Confidence            3678888764   467666555 68999999998643110112336899999999764 33 343333332211111000


Q ss_pred             CCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccC-cccccccCCCCCEEEEEE
Q psy9900          86 APKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMN-PKKFFQSLGLGEIVDFNI  164 (191)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~-~~~~~~~l~~G~~V~f~i  164 (191)
                              .      .........+.|+|...   ..||+...-..+-+.|+|.+++.... .......++.|+.|.+.|
T Consensus       280 --------~------~~~~~~G~~v~g~V~~i---~~~G~fV~l~~~v~Glv~~sel~~~~~~~~~~~~~~~G~~v~v~V  342 (565)
T PRK06299        280 --------I------EKKYPVGSKVKGKVTNI---TDYGAFVELEEGIEGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMV  342 (565)
T ss_pred             --------H------HhhCCCCCEEEEEEEEE---eCCeEEEEeCCCCEEEEEHHHcCccccccCHHHhcCCCCEEEEEE
Confidence                    0      00123345788999886   34787766555789999999986321 000113478999999988


Q ss_pred             EEcC
Q psy9900         165 GVGK  168 (191)
Q Consensus       165 ~~~~  168 (191)
                      ..-+
T Consensus       343 ~~id  346 (565)
T PRK06299        343 LEID  346 (565)
T ss_pred             EEEc
Confidence            7643

>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

Probab=94.75  E-value=0.47  Score=43.66  Aligned_cols=144  Identities=19%  Similarity=0.171  Sum_probs=87.9

Q ss_pred             eeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC--CceeeEeecCCCCCc
Q psy9900           6 IHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK--DIEAINVTGPNGIPV   83 (191)
Q Consensus         6 ~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~--g~~A~~v~~~~~~~~   83 (191)
                      .....|+|..+-   -||.+..-..+-+-|+|.|.+.-..-..+-..|+.||.|++.+-.-+.  ..--.++.-....|-
T Consensus       278 g~~v~G~Vt~i~---~~GafVei~~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw  354 (541)
T COG0539         278 GDKVEGKVTNLT---DYGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPW  354 (541)
T ss_pred             CCEEEEEEEEee---cCcEEEEecCCccceeechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEeeehhhhcChh
Confidence            345779998874   577776666688999999977544211123457999999999865332  221222222111111


Q ss_pred             cCCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEE
Q psy9900          84 QGAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFN  163 (191)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~  163 (191)
                      ..              -....+.....+|.|+...   .||-+.-.+++-|=|+|.+++.-..+..-...++.|+.|+..
T Consensus       355 ~~--------------~~~~~~~g~~v~g~v~~~t---~~g~fv~le~gidG~vh~~d~sw~~~~~~~~~~k~Gd~v~~~  417 (541)
T COG0539         355 EE--------------FADKHPVGDVVEGKVKSIT---DFGAFVELEGGIDGLVHLSDLSWDRPGEEAEKYKKGDEVEAK  417 (541)
T ss_pred             hh--------------hhhhcCCCCeEEEEEeeec---ccceEEccCCCccceEEHHhcCccccCcHHHhhccCcEEEEE
Confidence            00              0011344567899998873   366444444579999999999743221212266899999998


Q ss_pred             EEEcCC
Q psy9900         164 IGVGKK  169 (191)
Q Consensus       164 i~~~~k  169 (191)
                      +..-+.
T Consensus       418 vl~vd~  423 (541)
T COG0539         418 VLAVDK  423 (541)
T ss_pred             EEEEec
Confidence            877544

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=94.52  E-value=1.2  Score=41.06  Aligned_cols=150  Identities=16%  Similarity=0.143  Sum_probs=88.5

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCC-CCCcccCCCCCEEEEEEEEc-CC-CceeeEeecCCCCCc
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNP-KKFFQSLGLGEIVDFNIGVG-KK-DIEAINVTGPNGIPV   83 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~-~~g~~~l~~Gd~V~f~~~~~-~~-g~~A~~v~~~~~~~~   83 (191)
                      ....|+|+...   .||+...-+.+-+.|+|.+++..... ......++.||.|.+.+..- +. +.-..........|.
T Consensus       375 ~~v~g~V~~v~---~~G~fV~l~~~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~k~~~~~p~  451 (565)
T PRK06299        375 DVVEGKVKNIT---DFGAFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQLEEDPF  451 (565)
T ss_pred             CEEEEEEEEEe---cceEEEECCCCCEEEEEHHHcCccccccChHhhCCCCCEEEEEEEEEeCCCCEEEEEEehhhcCch
Confidence            45678888864   56777666556899999999974210 11235678999999987643 22 332333322111110


Q ss_pred             cCCCCCCCccccccccCCcccccceeeeeeEEEeecCCCce-eEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEE
Q psy9900          84 QGAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFG-FITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDF  162 (191)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfG-FI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f  162 (191)
                      .        ..      ...........|+|.....   || |+... .+-.-|+|.+.+.......-...++.||.|..
T Consensus       452 ~--------~~------~~~~~~G~vV~G~V~~v~~---~G~fV~l~-~gi~g~i~~se~s~~~~~~~~~~~~~Gd~v~~  513 (565)
T PRK06299        452 E--------EF------AKKHKKGSIVTGTVTEVKD---KGAFVELE-DGVEGLIRASELSRDRVEDATEVLKVGDEVEA  513 (565)
T ss_pred             h--------HH------HhhcCCCCEEEEEEEEEec---CceEEecC-CCcEEEEEHHHhcchhccCccccCCCCCEEEE
Confidence            0        00      0001234568899988753   46 45554 37889999999854311122456799999999


Q ss_pred             EEEEcC--CCceeEEee
Q psy9900         163 NIGVGK--KDIEAINVT  177 (191)
Q Consensus       163 ~i~~~~--kg~~A~~V~  177 (191)
                      .+..-+  ++.-...++
T Consensus       514 ~V~~vd~~~~~i~LS~k  530 (565)
T PRK06299        514 KVINIDRKNRRISLSIK  530 (565)
T ss_pred             EEEEEccccCEEEEEee
Confidence            988744  343333333

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=94.21  E-value=0.15  Score=33.03  Aligned_cols=52  Identities=19%  Similarity=0.292  Sum_probs=33.2

Q ss_pred             eeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC-ceeE
Q psy9900         112 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD-IEAI  174 (191)
Q Consensus       112 G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg-~~A~  174 (191)
                      -+|...+   .+|+....+.+.+|++|.+.+.        ..++.||.|++-+-.+.++ +.|+
T Consensus         7 L~V~~~~---~~g~fL~~~~~~~vlLp~~e~~--------~~~~~Gd~v~VFvY~D~~~rl~AT   59 (61)
T PF13509_consen    7 LKVVDKN---EFGYFLDDGEGKEVLLPKSEVP--------EPLKVGDEVEVFVYLDKEGRLVAT   59 (61)
T ss_dssp             --EEEE----SSEEEEEETT-EEEEEEGGG--------------TTSEEEEEEEE-TTS-EEEE
T ss_pred             eEEEEEe---CCEEEEECCCCCEEEechHHcC--------CCCCCCCEEEEEEEECCCCCEEEe
Confidence            3454443   5777777666799999999987        3689999999999999988 5553

>TIGR02063 RNase_R ribonuclease R

Probab=93.79  E-value=0.19  Score=47.74  Aligned_cols=63  Identities=25%  Similarity=0.323  Sum_probs=47.3

Q ss_pred             eeeeeEEEeecCCCceeEEeCC-CCCcEEEeccchhccCcccccccCCCCCEEEEEEEEc---CCCceeEEeecCCCC
Q psy9900         109 TVRGIVKFYDSKRGFGFITRLD-NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG---KKDIEAINVTGPNGI  182 (191)
Q Consensus       109 ~~~G~Vk~~~~~kgfGFI~~~d-~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~---~kg~~A~~V~~~~~~  182 (191)
                      .+.|+++.  ..+||||+.+++ ...|+|+...++..         +..||.|.+.+...   .+.++|.-|++++.+
T Consensus        68 ~~~G~i~~--~~~g~gFv~~~~~~~~di~I~~~~~~~---------a~~GD~Vlv~I~~~~~~~~~~eg~Vv~Il~r~  134 (709)
T TIGR02063        68 LVKGTVIA--HRDGFGFLRPEDDDEDDIFIPPRQMNG---------AMHGDRVLVRITGKPDGGDRFEARVIKILERA  134 (709)
T ss_pred             eEEEEEEE--CCCccEEEEECCCCCCcEEEChHHhCc---------CCCCCEEEEEEecccCCCCCceEEEEEEEeeC
Confidence            46787765  378999999986 35799998776654         46899999998764   234788877777654

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.

>TIGR00717 rpsA ribosomal protein S1

Probab=93.53  E-value=2.2  Score=38.86  Aligned_cols=142  Identities=16%  Similarity=0.167  Sum_probs=83.1

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecC-CCCCcccCCCCCEEEEEEEE-cCC-CceeeEeecCCCCCc
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMN-PKKFFQSLGLGEIVDFNIGV-GKK-DIEAINVTGPNGIPV   83 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~-~~~g~~~l~~Gd~V~f~~~~-~~~-g~~A~~v~~~~~~~~   83 (191)
                      ...+|+|+...   .||.+..-..+-+.|+|.+++.... ..+....+..||.|.+.+.. ++. +.-..........|-
T Consensus       274 ~i~~g~V~~v~---~~G~fV~l~~~v~g~v~~sels~~~~~~~~~~~~~vG~~v~v~V~~id~~~~~i~lS~k~~~~~p~  350 (516)
T TIGR00717       274 DKITGRVTNLT---DYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANPW  350 (516)
T ss_pred             CEEEEEEEEee---CCcEEEEeCCCCEEEEEHHHcCCccccCCHHHhccCCCEEEEEEEEEcCCCCEEEEEehhcccCcH
Confidence            34578898864   5675544334678999999886320 00011247899999999764 443 333333222111110


Q ss_pred             cCCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcc-cccccCCCCCEEEE
Q psy9900          84 QGAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPK-KFFQSLGLGEIVDF  162 (191)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~-~~~~~l~~G~~V~f  162 (191)
                              ...      ...........|+|+..   ..||....-+.+.+.|+|.+++....+. .-...++.|+.|.+
T Consensus       351 --------~~~------~~~~~~G~~v~g~V~~v---~~~G~fV~l~~~v~glv~~s~ls~~~~~~~~~~~~~~G~~V~~  413 (516)
T TIGR00717       351 --------EQF------EEKHPVGDRVTGKIKKI---TDFGAFVELEGGIDGLIHLSDISWDKDGREADHLYKKGDEIEA  413 (516)
T ss_pred             --------HHH------HHhCCCCCEEEEEEEEE---ecceEEEECCCCCEEEEEHHHCcCcccCCCHhHccCCCCEEEE
Confidence                    000      00122345688999875   4567766666689999999998632100 01246789999999


Q ss_pred             EEEEcC
Q psy9900         163 NIGVGK  168 (191)
Q Consensus       163 ~i~~~~  168 (191)
                      .+..-+
T Consensus       414 ~Vl~vd  419 (516)
T TIGR00717       414 VVLAVD  419 (516)
T ss_pred             EEEEEe
Confidence            876643

This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=93.34  E-value=0.22  Score=44.30  Aligned_cols=70  Identities=29%  Similarity=0.430  Sum_probs=52.3

Q ss_pred             eeeeeEEEeecCCCceeEEeCCC-----CCcEEEeccchhccCcccccccCCCCCEEEEEEEEcC---CCceeEEeecCC
Q psy9900         109 TVRGIVKFYDSKRGFGFITRLDN-----KEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK---KDIEAINVTGPN  180 (191)
Q Consensus       109 ~~~G~Vk~~~~~kgfGFI~~~d~-----~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~---kg~~A~~V~~~~  180 (191)
                      ...|++...  ..||||+...+.     ..||||..+.+..       -.|+.||.|+=.+..-+   |.+.-..|..++
T Consensus        50 ~~~g~le~~--~~g~gflr~~~~~y~~~~~d~yvs~~~ir~-------~~lr~gd~v~g~~r~~~~~e~~~~l~~v~~vn  120 (416)
T PRK09376         50 FGEGVLEIL--PDGFGFLRSPDANYLPGPDDIYVSPSQIRR-------FNLRTGDTVEGKIRPPKEGERYFALLKVETVN  120 (416)
T ss_pred             EEEEEEEEc--CCCCeEEeCCCcCCCCCCCCeeeCHHHHHh-------cCCCCCCEEEEEeeCCCCCCCccceEEEeeeC
Confidence            356777665  349999998643     3899999999997       58999999998887643   335667888888


Q ss_pred             CCCCCCC
Q psy9900         181 GIPVQGA  187 (191)
Q Consensus       181 ~~~~~~~  187 (191)
                      |.+....
T Consensus       121 g~~~~~~  127 (416)
T PRK09376        121 GEDPEKA  127 (416)
T ss_pred             CCCHHHh
Confidence            7664433

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

Probab=93.11  E-value=0.82  Score=31.72  Aligned_cols=62  Identities=18%  Similarity=0.086  Sum_probs=40.8

Q ss_pred             cceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhcc---CcccccccCCCCCEEEEEEEEcC
Q psy9900         106 AVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKM---NPKKFFQSLGLGEIVDFNIGVGK  168 (191)
Q Consensus       106 ~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~---~~~~~~~~l~~G~~V~f~i~~~~  168 (191)
                      ....+.|+|+...+.- +|.+..-+.+.+-|+|++++...   ....--..++.||.|.+.+..-.
T Consensus         7 ~G~iy~g~V~~i~~~~-~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~   71 (88)
T cd04453           7 VGNIYLGRVKKIVPGL-QAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEP   71 (88)
T ss_pred             CCCEEEEEEEEeccCC-cEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEec
Confidence            3456889999884322 45555544478999999998430   00001246899999999998843

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=92.60  E-value=1  Score=29.17  Aligned_cols=59  Identities=17%  Similarity=0.181  Sum_probs=41.0

Q ss_pred             eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC
Q psy9900         109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD  170 (191)
Q Consensus       109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg  170 (191)
                      .+.|+|....   .||.+..-..+-+-|+|.+++.......-...++.||.|++.+..-++.
T Consensus         3 ~~~g~V~~v~---~~G~~V~l~~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~   61 (70)
T cd05698           3 KTHGTIVKVK---PNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPE   61 (70)
T ss_pred             EEEEEEEEEe---cCcEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCC
Confidence            4678888873   3666665555689999999997432111123488999999999886654

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.

>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=92.50  E-value=1.1  Score=30.31  Aligned_cols=60  Identities=15%  Similarity=0.051  Sum_probs=43.6

Q ss_pred             ceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900         107 VHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK  169 (191)
Q Consensus       107 ~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k  169 (191)
                      ...+.|+|+...   .||.+..-..+-+.|+|.+++.......-...++.||.|++.+..-+.
T Consensus        15 G~i~~g~V~~v~---~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~   74 (83)
T cd04461          15 GMVVHGYVRNIT---PYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDE   74 (83)
T ss_pred             CCEEEEEEEEEe---eceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcC
Confidence            356789998874   388877766678999999999654211112457889999999988654

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.

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=92.48  E-value=2.8  Score=38.30  Aligned_cols=140  Identities=16%  Similarity=0.102  Sum_probs=79.2

Q ss_pred             ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCccc--CCCCCEEEEEEEEcCCCceeeEeecCCCCCccC
Q psy9900           8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQS--LGLGEIVDFNIGVGKKDIEAINVTGPNGIPVQG   85 (191)
Q Consensus         8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~--l~~Gd~V~f~~~~~~~g~~A~~v~~~~~~~~~~   85 (191)
                      ..+|+|+...  + +|++..-  +-.-|+|.|.+....    ...  ...|+.|.|.+..-++...-..+........  
T Consensus       125 ~V~G~V~~v~--k-~G~~Vdl--Gi~gflP~Sel~~~~----~~~~~~~vGq~V~vkVleid~~~~~ivLSrr~~l~~--  193 (486)
T PRK07899        125 VVTGTVIEVV--K-GGLILDI--GLRGFLPASLVEMRR----VRDLQPYIGQEIEAKIIELDKNRNNVVLSRRAWLEQ--  193 (486)
T ss_pred             EEEEEEEEEE--C-CeEEEEE--CCEEEEEhhHhcccc----cCChhhcCCCEEEEEEEEEECCCCEEEEEhHHHHHh--
Confidence            5689999985  2 4666655  357999999876431    112  2489999999987544322111111000000  


Q ss_pred             CCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEE
Q psy9900          86 APKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIG  165 (191)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~  165 (191)
                       ..  .... .  .-.........+.|+|+...   .||.+..-. +-+.|+|.+++.......--..++.||.|++.|.
T Consensus       194 -~~--~~~~-~--~~~~~lk~G~iv~G~V~~i~---~~G~FVdlg-gv~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl  263 (486)
T PRK07899        194 -TQ--SEVR-S--EFLNQLQKGQVRKGVVSSIV---NFGAFVDLG-GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVL  263 (486)
T ss_pred             -hh--HHHH-H--HHHHhccCCCEEEEEEEEEE---CCeEEEEEC-CEEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEE
Confidence             00  0000 0  00001223456889999873   366655544 6899999999975311011134689999999977


Q ss_pred             EcC
Q psy9900         166 VGK  168 (191)
Q Consensus       166 ~~~  168 (191)
                      .-+
T Consensus       264 ~iD  266 (486)
T PRK07899        264 DVD  266 (486)
T ss_pred             EEE
Confidence            633

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=92.43  E-value=2.7  Score=36.86  Aligned_cols=141  Identities=12%  Similarity=0.036  Sum_probs=79.3

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC--CceeeEeecCCCCCcc
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK--DIEAINVTGPNGIPVQ   84 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~--g~~A~~v~~~~~~~~~   84 (191)
                      ...+|+|+..+.  .+=||..+..+-+.|+|.+++......+....+..||.|++.+.....  +.-...........  
T Consensus        19 ~iv~G~V~~i~~--~g~~V~i~~~~~~g~lp~~e~~~~~~~~~~~~~~vGd~v~~~V~~v~~~~~~i~lS~k~~~~~~--   94 (390)
T PRK06676         19 DVVTGEVLKVED--KQVFVNIEGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRLEAEK--   94 (390)
T ss_pred             CEEEEEEEEEEC--CeEEEEEecCCcEEEEEHHHhccccccCcccccCCCCEEEEEEEEEECCCCCEEEEHHHhhhhh--
Confidence            446799999963  334454434467899999999653222233457899999999876543  21111111110000  


Q ss_pred             CCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEE
Q psy9900          85 GAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI  164 (191)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i  164 (191)
                         ..  ...      ....-......|+|....  + +|++..-+ +-..|+|.+++..... ..... ..|+.|.|.|
T Consensus        95 ---~~--~~~------~~~~~~G~~v~g~V~~v~--~-~G~~V~~~-G~~gflp~~el~~~~~-~~~~~-~vG~~v~~~V  157 (390)
T PRK06676         95 ---AW--DKL------EEKFEEGEVVEVKVTEVV--K-GGLVVDVE-GVRGFIPASLISTRFV-EDFSD-FKGKTLEVKI  157 (390)
T ss_pred             ---hH--HHH------HHhccCCCEEEEEEEEEE--C-CeEEEEEC-CEEEEEEHHHcCCccC-CChHH-cCCCEEEEEE
Confidence               00  000      000122345789998874  3 45555554 4488999998864310 00112 2799999999


Q ss_pred             EEcC
Q psy9900         165 GVGK  168 (191)
Q Consensus       165 ~~~~  168 (191)
                      ..-+
T Consensus       158 l~~d  161 (390)
T PRK06676        158 IELD  161 (390)
T ss_pred             EEEE
Confidence            7533

>COG1158 Rho Transcription termination factor [Transcription]

Probab=92.28  E-value=0.29  Score=42.67  Aligned_cols=72  Identities=26%  Similarity=0.422  Sum_probs=54.2

Q ss_pred             eeeeEEEeecCCCceeEEeCC-----CCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC--c-eeEEeecCCC
Q psy9900         110 VRGIVKFYDSKRGFGFITRLD-----NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD--I-EAINVTGPNG  181 (191)
Q Consensus       110 ~~G~Vk~~~~~kgfGFI~~~d-----~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg--~-~A~~V~~~~~  181 (191)
                      ..|+....  ..||||+.+.+     +..|||+.-|.+..       -.|+.||.|+=.+..-+.|  + .-+.|..+++
T Consensus        54 ~~GvLeil--~dGfGFLR~~~~~yl~~~~DiYvSpSQIRr-------f~LrtGD~v~G~vR~Pke~Ery~aLl~ve~vN~  124 (422)
T COG1158          54 GDGVLEIL--PDGFGFLRSADSSYLPGPDDIYVSPSQIRR-------FNLRTGDTVEGKVRPPKEGERYFALLKVEAVNG  124 (422)
T ss_pred             eeeEEEec--cCCcceeecCccccCCCCCceEECHHHHhh-------ccCccCCEEeeeecCCCcccceeeeEEEeecCC
Confidence            34676665  48999999876     24899999999997       5899999999998887666  3 3457777777


Q ss_pred             CCCCCCCCC
Q psy9900         182 IPVQGAPKV  190 (191)
Q Consensus       182 ~~~~~~~~~  190 (191)
                      .+...++.+
T Consensus       125 ~~pe~~~~R  133 (422)
T COG1158         125 DDPEKAKNR  133 (422)
T ss_pred             CCHHHhhcc
Confidence            765554443

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

Probab=92.23  E-value=1.2  Score=29.07  Aligned_cols=60  Identities=20%  Similarity=0.237  Sum_probs=44.8

Q ss_pred             eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC
Q psy9900         108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD  170 (191)
Q Consensus       108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg  170 (191)
                      ..+.|+|...+.   +|++..-..+-+.|+|.+++...........+..||.|.+.+..-+..
T Consensus         6 ~iv~g~V~~v~~---~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~   65 (74)
T PF00575_consen    6 DIVEGKVTSVED---FGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKE   65 (74)
T ss_dssp             SEEEEEEEEEET---TEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETT
T ss_pred             CEEEEEEEEEEC---CEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECC
Confidence            467899998865   777666556899999999998521112347889999999999886554

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 ....

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

Probab=91.97  E-value=0.65  Score=28.81  Aligned_cols=55  Identities=20%  Similarity=0.222  Sum_probs=38.0

Q ss_pred             ceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC
Q psy9900          10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK   67 (191)
Q Consensus        10 ~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~   67 (191)
                      .|+|+..+   .+|+....+.+.+.|+|.+.+......+....++.||.|.+.+..-.
T Consensus         2 ~g~V~~v~---~~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d   56 (65)
T cd00164           2 TGKVVSIT---KFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVD   56 (65)
T ss_pred             EEEEEEEE---eeeEEEEecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEc
Confidence            68888886   45554444446899999999875311112356899999999987643

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.

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=91.94  E-value=2.7  Score=36.22  Aligned_cols=137  Identities=17%  Similarity=0.082  Sum_probs=78.7

Q ss_pred             ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC--CceeeEeecCCCCCccC
Q psy9900           8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK--DIEAINVTGPNGIPVQG   85 (191)
Q Consensus         8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~--g~~A~~v~~~~~~~~~~   85 (191)
                      ...|+|....  +. |.+..-...-+-|+|.+++......+....+..||.|+|.+..-..  +.-.........     
T Consensus        34 iv~G~V~~i~--~~-g~~Vdig~k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i~lS~k~~~~-----  105 (318)
T PRK07400         34 IVNGTVFSLE--PR-GALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQLTLSIRRIEY-----  105 (318)
T ss_pred             EEEEEEEEEE--CC-EEEEEECCCeEEEEEHHHhccccccCHHHccCCCCEEEEEEEEEeCCCCeEEEehhhhhh-----
Confidence            3579999975  33 4444444456889999999754211122347899999999875332  321111111000     


Q ss_pred             CCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEE
Q psy9900          86 APKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIG  165 (191)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~  165 (191)
                        ..+=.+.      ..........+|+|+..+   .+|++..-+ +-.-|+|.+.+....    ......|+.|.+.|.
T Consensus       106 --~~~w~~l------~~~~~~~~~V~g~V~~~~---~~G~~V~l~-Gv~gfip~s~ls~~~----~~~~~vG~~i~~kVl  169 (318)
T PRK07400        106 --MRAWERV------RQLQKEDATVRSEVFATN---RGGALVRIE-GLRGFIPGSHISTRK----PKEELVGEELPLKFL  169 (318)
T ss_pred             --hhHHHHH------HHhccCCCEEEEEEEEEE---CCeEEEEEC-CEEEEEEHHHcCccC----CccccCCCEEEEEEE
Confidence              0000000      001112345788888874   356766664 678899999997532    123358999999987


Q ss_pred             EcC
Q psy9900         166 VGK  168 (191)
Q Consensus       166 ~~~  168 (191)
                      +-+
T Consensus       170 ~id  172 (318)
T PRK07400        170 EVD  172 (318)
T ss_pred             EEE
Confidence            644

>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=91.48  E-value=2  Score=28.31  Aligned_cols=56  Identities=16%  Similarity=-0.009  Sum_probs=37.6

Q ss_pred             eeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900         112 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK  169 (191)
Q Consensus       112 G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k  169 (191)
                      |+|....  ..||.+..-..+-+-|+|.|++.......-...++.||.|++.+..-++
T Consensus         7 g~V~~v~--~~~G~~V~l~~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~   62 (71)
T cd05696           7 VKVTKVE--PDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSP   62 (71)
T ss_pred             eEEEEEc--cCceEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeC
Confidence            7787763  3476655544468999999998643211123459999999999876443

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.

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

Probab=91.40  E-value=0.62  Score=30.56  Aligned_cols=59  Identities=20%  Similarity=0.226  Sum_probs=43.6

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK   68 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~   68 (191)
                      ....|+|..-+.   +|++..-..+-+.|+|.+++...........+..||.|.+.+..-+.
T Consensus         6 ~iv~g~V~~v~~---~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~   64 (74)
T PF00575_consen    6 DIVEGKVTSVED---FGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDK   64 (74)
T ss_dssp             SEEEEEEEEEET---TEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEET
T ss_pred             CEEEEEEEEEEC---CEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEEC
Confidence            456899998875   66666555678999999999853212235788999999999876444

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 ....

>PRK12608 transcription termination factor Rho; Provisional

Probab=90.57  E-value=0.67  Score=40.89  Aligned_cols=68  Identities=24%  Similarity=0.419  Sum_probs=47.9

Q ss_pred             eeccceEEEEeeCCCCeeEEEeC-----CCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCc-eeeEeecCC
Q psy9900           6 IHTVRGIVKFYDSKRGFGFITRL-----DNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI-EAINVTGPN   79 (191)
Q Consensus         6 ~~~~~G~vk~~~~~kGfGFI~~~-----~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~-~A~~v~~~~   79 (191)
                      .....|++.-..  .||||+...     .+..||||..+.++.       ..|+.||.|.-.... +-+. ---.|..+.
T Consensus        16 ~~~~~g~l~~~~--~g~gflr~~~~~~~~~~~d~yv~~~~i~~-------~~l~~Gd~V~~~~r~-~~~~~~LgrV~~~~   85 (380)
T PRK12608         16 TEEVLGVLEILG--DGFGFLRSARRNYLPSPDDVFVPPALIRR-------FNLRTGDVVEGVARP-RERYRVLVRVDSVN   85 (380)
T ss_pred             CCcceEEEEEcC--CCceEeecCccCCCCCCCCeeeCHHHHHH-------hCCCCCCEEEeccCC-CCChhheEEEeccC
Confidence            445678887653  599999985     335899999999986       478999999988766 3332 233455555


Q ss_pred             CCCc
Q psy9900          80 GIPV   83 (191)
Q Consensus        80 ~~~~   83 (191)
                      +.|.
T Consensus        86 G~p~   89 (380)
T PRK12608         86 GTDP   89 (380)
T ss_pred             CcCc
Confidence            5553

>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=90.43  E-value=2.4  Score=27.95  Aligned_cols=61  Identities=16%  Similarity=0.089  Sum_probs=42.9

Q ss_pred             eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC
Q psy9900         108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD  170 (191)
Q Consensus       108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg  170 (191)
                      ..+.|+|....  ..||.+..-..+.+-++|++++.......-...++.||.|...+..-++|
T Consensus         5 ~iv~G~V~~i~--~~~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~~   65 (72)
T cd05704           5 AVTLGMVTKVI--PHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKDG   65 (72)
T ss_pred             CEEEEEEEEee--CCcEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecCC
Confidence            45788888863  23666666666899999999996542111123468899999999887655

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.

>COG4776 Rnb Exoribonuclease II [Transcription]

Probab=90.40  E-value=0.33  Score=43.78  Aligned_cols=51  Identities=25%  Similarity=0.411  Sum_probs=42.3

Q ss_pred             eeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC
Q psy9900           6 IHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK   68 (191)
Q Consensus         6 ~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~   68 (191)
                      .++..|+||.=  +|||||+..|. .+..|+.--..+..|         .||++.-.+.....
T Consensus        19 ~prvEGvVK~t--ekgfGFLEvD~-qkSYFIpPp~MKkvM---------HGDkIiA~i~te~e   69 (645)
T COG4776          19 TPRVEGVVKAT--EKGFGFLEVDA-QKSYFIPPPQMKKVM---------HGDKIIAVIHTEKE   69 (645)
T ss_pred             Ccccceeeeec--cccceeEEEcC-ccccccCCHHHhhhc---------ccCeEEEEEEecCc
Confidence            45788999975  89999999997 678999998888877         89999888765433

>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=90.33  E-value=1  Score=30.48  Aligned_cols=58  Identities=16%  Similarity=0.079  Sum_probs=41.6

Q ss_pred             ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC
Q psy9900           8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK   68 (191)
Q Consensus         8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~   68 (191)
                      ...|+|+...   -||++..-.++-+.|+|.+++......+-...++.||.|++.+..-..
T Consensus        17 i~~g~V~~v~---~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~   74 (83)
T cd04461          17 VVHGYVRNIT---PYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDE   74 (83)
T ss_pred             EEEEEEEEEe---eceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcC
Confidence            4578888775   488887766678999999999654211122447889999999876543

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.

>PRK08582 hypothetical protein; Provisional

Probab=90.23  E-value=4.5  Score=30.57  Aligned_cols=74  Identities=18%  Similarity=0.219  Sum_probs=49.7

Q ss_pred             ceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcC-CCceeEEeecCCCCC
Q psy9900         107 VHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK-KDIEAINVTGPNGIP  183 (191)
Q Consensus       107 ~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~-kg~~A~~V~~~~~~~  183 (191)
                      ...+.|+|...   ..||+....+.+.+-++|++++.......-...++.||.|.+.|..-+ .|.-...++.+...|
T Consensus         6 G~iv~G~V~~I---~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~~gkI~LSlk~~~~~~   80 (139)
T PRK08582          6 GSKLQGKVTGI---TNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIKKAKDRP   80 (139)
T ss_pred             CCEEEEEEEEE---ECCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECCCCcEEEEEEecccCc
Confidence            34578999886   347877666667899999999974321111246899999999988855 365455555544433

>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=90.11  E-value=2.7  Score=27.13  Aligned_cols=59  Identities=14%  Similarity=0.149  Sum_probs=41.6

Q ss_pred             eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC
Q psy9900         109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD  170 (191)
Q Consensus       109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg  170 (191)
                      .+.|+|....   .||.+..-+.+-+-|+|.+++.......-...++.||.+.+.+..-+..
T Consensus         3 ~v~g~V~~v~---~~Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~~   61 (69)
T cd05697           3 VVKGTIRKLR---PSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPE   61 (69)
T ss_pred             EEEEEEEEEe---ccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECC
Confidence            4678888874   4777766655789999999986532111124589999999999886553

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.

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

Probab=90.10  E-value=1.8  Score=26.67  Aligned_cols=56  Identities=20%  Similarity=0.215  Sum_probs=37.8

Q ss_pred             eeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900         111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK  169 (191)
Q Consensus       111 ~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k  169 (191)
                      .|+|...+   .+|.+...+.+.+.|+|.+++...........++.||.|.+.+..-+.
T Consensus         2 ~g~V~~v~---~~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~   57 (65)
T cd00164           2 TGKVVSIT---KFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDP   57 (65)
T ss_pred             EEEEEEEE---eeeEEEEecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcC
Confidence            57888875   345444444568999999998753110112468999999999987553

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.

>PRK08582 hypothetical protein; Provisional

Probab=90.00  E-value=3.9  Score=30.89  Aligned_cols=73  Identities=18%  Similarity=0.184  Sum_probs=48.1

Q ss_pred             CceeceeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC-CCceeeEee
Q psy9900           1 MTKFEIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK-KDIEAINVT   76 (191)
Q Consensus         1 ~~~~~~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~-~g~~A~~v~   76 (191)
                      |.--.-....|+|+.-.   .||+...-+.+.+-++|.+.+.......-...+..||.|.+.+..-. .|.....+.
T Consensus         1 m~~kvG~iv~G~V~~I~---~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~~gkI~LSlk   74 (139)
T PRK08582          1 MSIEVGSKLQGKVTGIT---NFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIK   74 (139)
T ss_pred             CCCcCCCEEEEEEEEEE---CCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECCCCcEEEEEE
Confidence            33334456788998864   47877666657899999999975421111245789999999987644 354333443

>PRK12608 transcription termination factor Rho; Provisional

Probab=89.63  E-value=1  Score=39.72  Aligned_cols=65  Identities=25%  Similarity=0.442  Sum_probs=46.4

Q ss_pred             eeeeeEEEeecCCCceeEEeCC-----CCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC-ceeEEeecCCCC
Q psy9900         109 TVRGIVKFYDSKRGFGFITRLD-----NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD-IEAINVTGPNGI  182 (191)
Q Consensus       109 ~~~G~Vk~~~~~kgfGFI~~~d-----~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg-~~A~~V~~~~~~  182 (191)
                      ...|+.....  .||||+...+     +..||||..+.+..       ..|+.|+.|.-.... .-| .--..|--+.|.
T Consensus        18 ~~~g~l~~~~--~g~gflr~~~~~~~~~~~d~yv~~~~i~~-------~~l~~Gd~V~~~~r~-~~~~~~LgrV~~~~G~   87 (380)
T PRK12608         18 EVLGVLEILG--DGFGFLRSARRNYLPSPDDVFVPPALIRR-------FNLRTGDVVEGVARP-RERYRVLVRVDSVNGT   87 (380)
T ss_pred             cceEEEEEcC--CCceEeecCccCCCCCCCCeeeCHHHHHH-------hCCCCCCEEEeccCC-CCChhheEEEeccCCc
Confidence            3568887663  5999999853     34899999999997       589999999988766 333 223344444454


Q ss_pred             C
Q psy9900         183 P  183 (191)
Q Consensus       183 ~  183 (191)
                      |
T Consensus        88 p   88 (380)
T PRK12608         88 D   88 (380)
T ss_pred             C
Confidence            4

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

Probab=89.63  E-value=3.1  Score=26.36  Aligned_cols=58  Identities=21%  Similarity=0.199  Sum_probs=40.7

Q ss_pred             eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900         109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK  169 (191)
Q Consensus       109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k  169 (191)
                      .+.|+|....+   ||+...-..+.+-|+|.+++.......-...++.||.|.+.+..-+.
T Consensus         3 ~~~g~V~~v~~---~G~~v~l~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d~   60 (68)
T cd04472           3 IYEGKVVKIKD---FGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD   60 (68)
T ss_pred             EEEEEEEEEEE---eEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECC
Confidence            45788877753   88877765568999999998653110111346899999999888654

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.

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

Probab=89.23  E-value=2  Score=29.80  Aligned_cols=61  Identities=18%  Similarity=0.081  Sum_probs=39.4

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheec---CCCCCcccCCCCCEEEEEEEEcCC
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKM---NPKKFFQSLGLGEIVDFNIGVGKK   68 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~---~~~~g~~~l~~Gd~V~f~~~~~~~   68 (191)
                      ....|+|+.... .-||.+..-+.+.+-|+|.+++...   ...+-...++.||.|.+++..-+.
T Consensus         9 ~iy~g~V~~i~~-~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~   72 (88)
T cd04453           9 NIYLGRVKKIVP-GLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPI   72 (88)
T ss_pred             CEEEEEEEEecc-CCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecC
Confidence            346789998842 2245555444468999999998430   000012458999999999987544

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

>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=89.20  E-value=1.8  Score=28.54  Aligned_cols=53  Identities=17%  Similarity=0.019  Sum_probs=35.7

Q ss_pred             eEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEE
Q psy9900          11 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGV   65 (191)
Q Consensus        11 G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~   65 (191)
                      |+|+.-.  ..||.+..-..+-+-|+|.|.+...........++.||.|++.+..
T Consensus         7 g~V~~v~--~~~G~~V~l~~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~   59 (71)
T cd05696           7 VKVTKVE--PDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIG   59 (71)
T ss_pred             eEEEEEc--cCceEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEE
Confidence            7888864  3466655444368999999998543111123458999999999764

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.

>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=89.15  E-value=2.2  Score=27.56  Aligned_cols=58  Identities=17%  Similarity=0.169  Sum_probs=39.7

Q ss_pred             ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC
Q psy9900           8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK   68 (191)
Q Consensus         8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~   68 (191)
                      ...|+|+...   -||.+..-.++-+-|+|.+++....-.+....++.||.|++.+..-..
T Consensus         3 ~~~g~V~~v~---~~G~~V~l~~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~   60 (70)
T cd05698           3 KTHGTIVKVK---PNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDP   60 (70)
T ss_pred             EEEEEEEEEe---cCcEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcC
Confidence            3578888885   366666555468999999999743211122347899999999876444

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.

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

Probab=89.13  E-value=3.2  Score=26.02  Aligned_cols=59  Identities=20%  Similarity=0.212  Sum_probs=41.1

Q ss_pred             eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900         108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK  169 (191)
Q Consensus       108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k  169 (191)
                      ..+.|+|...+.   +|++..-+.+...|+|.+++...........++.||.|.+.+..-+.
T Consensus         4 ~~v~g~V~~v~~---~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~   62 (72)
T smart00316        4 DVVEGTVTEITP---FGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDE   62 (72)
T ss_pred             CEEEEEEEEEEc---cEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeC
Confidence            357789988855   56655555568899999998753100111348999999999988654

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

Probab=89.08  E-value=3.7  Score=25.85  Aligned_cols=58  Identities=24%  Similarity=0.218  Sum_probs=39.7

Q ss_pred             eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900         109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK  169 (191)
Q Consensus       109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k  169 (191)
                      .+.|+|....   .||+...-+.+.+.|+|.+++.......-...++.||.|...+..-+.
T Consensus         3 ~~~g~V~~i~---~~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~~   60 (69)
T cd05692           3 VVEGTVTRLK---PFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA   60 (69)
T ss_pred             EEEEEEEEEE---eeeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECC
Confidence            4578887764   377776666678999999998743100011347899999999877553

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.

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=88.88  E-value=1.4  Score=39.28  Aligned_cols=64  Identities=30%  Similarity=0.486  Sum_probs=45.2

Q ss_pred             cceEEEEeeCCCCeeEEEeCCC-----CccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCC---ceeeEeecCCC
Q psy9900           9 VRGIVKFYDSKRGFGFITRLDN-----KEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD---IEAINVTGPNG   80 (191)
Q Consensus         9 ~~G~vk~~~~~kGfGFI~~~~~-----~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g---~~A~~v~~~~~   80 (191)
                      ..|.+--.  ..||||+...+.     ..||||..+.++.       -.|+.||.|.-.+.....+   ..-..|..+++
T Consensus        51 ~~g~le~~--~~g~gflr~~~~~y~~~~~d~yvs~~~ir~-------~~lr~gd~v~g~~r~~~~~e~~~~l~~v~~vng  121 (416)
T PRK09376         51 GEGVLEIL--PDGFGFLRSPDANYLPGPDDIYVSPSQIRR-------FNLRTGDTVEGKIRPPKEGERYFALLKVETVNG  121 (416)
T ss_pred             EEEEEEEc--CCCCeEEeCCCcCCCCCCCCeeeCHHHHHh-------cCCCCCCEEEEEeeCCCCCCCccceEEEeeeCC
Confidence            45666644  349999998532     4899999999996       4789999999988764333   34455655554


Q ss_pred             C
Q psy9900          81 I   81 (191)
Q Consensus        81 ~   81 (191)
                      .
T Consensus       122 ~  122 (416)
T PRK09376        122 E  122 (416)
T ss_pred             C
Confidence            3

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

Probab=88.86  E-value=2  Score=27.18  Aligned_cols=57  Identities=25%  Similarity=0.236  Sum_probs=39.3

Q ss_pred             ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC
Q psy9900           8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK   67 (191)
Q Consensus         8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~   67 (191)
                      ...|+|.....   ||+...-+.+.+.|+|.+++......+....++.||.|.+.+..-.
T Consensus         3 ~~~g~V~~i~~---~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~   59 (69)
T cd05692           3 VVEGTVTRLKP---FGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID   59 (69)
T ss_pred             EEEEEEEEEEe---eeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEEC
Confidence            35688888653   7777766657899999999975421111134789999999986544

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.

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

Probab=88.70  E-value=2.2  Score=27.03  Aligned_cols=57  Identities=21%  Similarity=0.200  Sum_probs=40.1

Q ss_pred             ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC
Q psy9900           8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK   67 (191)
Q Consensus         8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~   67 (191)
                      ...|+|.....   ||+...-....+-|+|.+++......+-...++.||.|.+.+...+
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            35678887764   8888876556899999999975421111134689999999987654

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.

>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=88.56  E-value=5  Score=26.08  Aligned_cols=59  Identities=12%  Similarity=-0.019  Sum_probs=40.3

Q ss_pred             eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900         108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK  169 (191)
Q Consensus       108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k  169 (191)
                      ....|+|+...   .+|.+..-+.+-+-|+|.+++.......--..++.||.|++.+..-+.
T Consensus         5 ~iv~g~V~~v~---~~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~   63 (73)
T cd05706           5 DILPGRVTKVN---DRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDV   63 (73)
T ss_pred             CEEEEEEEEEe---CCeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeC
Confidence            35678888863   356555544468999999999753211112347899999999988654

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.

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=88.36  E-value=1.3  Score=28.58  Aligned_cols=52  Identities=19%  Similarity=0.291  Sum_probs=31.9

Q ss_pred             ceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCC-cee
Q psy9900          10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD-IEA   72 (191)
Q Consensus        10 ~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g-~~A   72 (191)
                      +-+|+.-+   .+|+....+..++||+|.+.+..        .+..||.|++-+=.+.++ +.|
T Consensus         6 ~L~V~~~~---~~g~fL~~~~~~~vlLp~~e~~~--------~~~~Gd~v~VFvY~D~~~rl~A   58 (61)
T PF13509_consen    6 TLKVVDKN---EFGYFLDDGEGKEVLLPKSEVPE--------PLKVGDEVEVFVYLDKEGRLVA   58 (61)
T ss_dssp             ---EEEE----SSEEEEEETT-EEEEEEGGG--------------TTSEEEEEEEE-TTS-EEE
T ss_pred             ceEEEEEe---CCEEEEECCCCCEEEechHHcCC--------CCCCCCEEEEEEEECCCCCEEE
Confidence            44566665   56777766667999999998863        578999999999888776 444

>PRK12678 transcription termination factor Rho; Provisional

Probab=88.21  E-value=1.2  Score=41.71  Aligned_cols=70  Identities=20%  Similarity=0.381  Sum_probs=48.9

Q ss_pred             eeeeEEEeecCCCceeEEeCC---CCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC---------ceeEEee
Q psy9900         110 VRGIVKFYDSKRGFGFITRLD---NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD---------IEAINVT  177 (191)
Q Consensus       110 ~~G~Vk~~~~~kgfGFI~~~d---~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg---------~~A~~V~  177 (191)
                      ..|++-..   .|||||...+   +..||||..+.+..       ..|+.||.|.=.+..-..|         ..-+.|.
T Consensus       296 ~~GiLdi~---dg~gFlR~~~y~~~~~Dvyvs~~qirr-------~~Lr~Gd~v~G~vr~p~~~e~~~~r~k~~~l~~v~  365 (672)
T PRK12678        296 VAGILDVL---DNYAFVRTSGYLPGPNDVYVSMNQVRK-------NGLRKGDAVTGAVRAPREGEQGNQRQKFNPLVRLD  365 (672)
T ss_pred             eeEEEEec---CCeeEeeCCCCCCCCCCeeeCHHHHHH-------cCCCCCCEEEEeecCCCCCccccccceeeeeeeEe
Confidence            44555444   5999999863   35899999999997       5899999999777653332         2345677


Q ss_pred             cCCCCCCCCCCC
Q psy9900         178 GPNGIPVQGAPK  189 (191)
Q Consensus       178 ~~~~~~~~~~~~  189 (191)
                      -+++.+....+.
T Consensus       366 ~vNg~~~e~~~~  377 (672)
T PRK12678        366 SVNGMSPEEAKK  377 (672)
T ss_pred             eeCCCChHHhcc
Confidence            777766444433

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

Probab=88.07  E-value=4.3  Score=26.18  Aligned_cols=59  Identities=17%  Similarity=0.224  Sum_probs=40.9

Q ss_pred             eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC
Q psy9900         109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD  170 (191)
Q Consensus       109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg  170 (191)
                      .+.|+|+...   .+|.+..-..+-+-|+|.+++.....+.-...++.||.|++.+..-+..
T Consensus         3 ~v~g~V~~v~---~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~   61 (73)
T cd05691           3 IVTGKVTEVD---AKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRK   61 (73)
T ss_pred             EEEEEEEEEE---CCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCC
Confidence            3578888773   4677666555688999999987542111123468999999999886653

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.

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

Probab=87.88  E-value=1.8  Score=27.31  Aligned_cols=59  Identities=20%  Similarity=0.212  Sum_probs=40.6

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK   68 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~   68 (191)
                      ....|+|...+.   +|++..-+.+-+.|+|.+++......+....++.||.|.+.+..-..
T Consensus         4 ~~v~g~V~~v~~---~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~   62 (72)
T smart00316        4 DVVEGTVTEITP---FGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDE   62 (72)
T ss_pred             CEEEEEEEEEEc---cEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeC
Confidence            346789998875   56655555468899999999754111112347999999999876543

>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=86.93  E-value=2.4  Score=27.39  Aligned_cols=58  Identities=14%  Similarity=0.136  Sum_probs=40.7

Q ss_pred             ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC
Q psy9900           8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK   68 (191)
Q Consensus         8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~   68 (191)
                      ...|+|+.-+   .||.+..-+.+-+-|+|.+++......+....++.||.+.+.+..-+.
T Consensus         3 ~v~g~V~~v~---~~Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~   60 (69)
T cd05697           3 VVKGTIRKLR---PSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEP   60 (69)
T ss_pred             EEEEEEEEEe---ccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEEC
Confidence            3578888875   478777665568999999999653211112458899999999876443

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.

>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=86.86  E-value=5.1  Score=26.67  Aligned_cols=54  Identities=19%  Similarity=0.279  Sum_probs=41.1

Q ss_pred             eeeeeeEEEeecCCCceeEEeCC-CCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC
Q psy9900         108 HTVRGIVKFYDSKRGFGFITRLD-NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD  170 (191)
Q Consensus       108 ~~~~G~Vk~~~~~kgfGFI~~~d-~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg  170 (191)
                      ....|+|+...   .||++..-. .+-+-|+|.+++...      ..+++||.|.+.+..-++.
T Consensus         6 ~~v~g~V~si~---d~G~~v~~g~~gv~Gfl~~~~~~~~------~~~~~Gq~v~~~V~~vd~~   60 (74)
T cd05694           6 MVLSGCVSSVE---DHGYILDIGIPGTTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKDD   60 (74)
T ss_pred             CEEEEEEEEEe---CCEEEEEeCCCCcEEEEEHHHCCcc------cccCCCCEEEEEEEEEECC
Confidence            34789998863   588866653 357899999999852      5789999999998865543

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.

>COG1158 Rho Transcription termination factor [Transcription]

Probab=86.85  E-value=0.91  Score=39.64  Aligned_cols=63  Identities=30%  Similarity=0.525  Sum_probs=44.5

Q ss_pred             eEEEEeeCCCCeeEEEeCC-----CCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCC--cee-eEeecCCCCC
Q psy9900          11 GIVKFYDSKRGFGFITRLD-----NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD--IEA-INVTGPNGIP   82 (191)
Q Consensus        11 G~vk~~~~~kGfGFI~~~~-----~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g--~~A-~~v~~~~~~~   82 (191)
                      |++.--  .-||||+...+     +..||||.-|.+...       .|+.||.|+-.+.....|  .-| ..|..+++.+
T Consensus        56 GvLeil--~dGfGFLR~~~~~yl~~~~DiYvSpSQIRrf-------~LrtGD~v~G~vR~Pke~Ery~aLl~ve~vN~~~  126 (422)
T COG1158          56 GVLEIL--PDGFGFLRSADSSYLPGPDDIYVSPSQIRRF-------NLRTGDTVEGKVRPPKEGERYFALLKVEAVNGDD  126 (422)
T ss_pred             eEEEec--cCCcceeecCccccCCCCCceEECHHHHhhc-------cCccCCEEeeeecCCCcccceeeeEEEeecCCCC
Confidence            444444  48999999765     348999999999863       789999999998765555  223 4455444433

>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=86.58  E-value=5.9  Score=26.18  Aligned_cols=59  Identities=8%  Similarity=-0.045  Sum_probs=39.4

Q ss_pred             eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccC--cccccccCCCCCEEEEEEEEcCCC
Q psy9900         109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMN--PKKFFQSLGLGEIVDFNIGVGKKD  170 (191)
Q Consensus       109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~--~~~~~~~l~~G~~V~f~i~~~~kg  170 (191)
                      ...|+|+...   .+|....-..+-+-|+|.+++....  ...-...++.||.|++.|..=++.
T Consensus         3 ~V~g~V~~i~---~~g~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~   63 (73)
T cd05703           3 EVTGFVNNVS---KEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKE   63 (73)
T ss_pred             EEEEEEEEEe---CCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCC
Confidence            3578888873   3455443333689999999996320  112235689999999998875543

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.

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

Probab=86.57  E-value=6.7  Score=25.38  Aligned_cols=59  Identities=19%  Similarity=0.175  Sum_probs=41.0

Q ss_pred             eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccC-cccccccCCCCCEEEEEEEEcCC
Q psy9900         108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMN-PKKFFQSLGLGEIVDFNIGVGKK  169 (191)
Q Consensus       108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~-~~~~~~~l~~G~~V~f~i~~~~k  169 (191)
                      ..+.|+|...   +.||+...-+.+.+-++|.+++.... .......++.||.|.+.+..-+.
T Consensus         5 ~~~~g~V~~i---~~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~   64 (72)
T cd05689           5 TRLFGKVTNL---TDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDE   64 (72)
T ss_pred             CEEEEEEEEE---EeeEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeC
Confidence            3578888886   34888776655789999999996321 00112356899999999877554

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.

>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=86.16  E-value=4.3  Score=26.38  Aligned_cols=57  Identities=12%  Similarity=-0.012  Sum_probs=38.9

Q ss_pred             ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC
Q psy9900           8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK   67 (191)
Q Consensus         8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~   67 (191)
                      ...|+|+.-.   .||.+..-+.+-+-|+|.+++......+....++.||.|++.+..-.
T Consensus         6 iv~g~V~~v~---~~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d   62 (73)
T cd05706           6 ILPGRVTKVN---DRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVD   62 (73)
T ss_pred             EEEEEEEEEe---CCeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEe
Confidence            4578888864   35666555546899999999975421111234789999999987644

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.

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

Probab=85.08  E-value=4.6  Score=26.00  Aligned_cols=57  Identities=18%  Similarity=0.233  Sum_probs=39.8

Q ss_pred             cceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC
Q psy9900           9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK   68 (191)
Q Consensus         9 ~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~   68 (191)
                      ..|+|+...   .+|.+..-..+-+-|+|.+++......+-...++.||.|++.+..-..
T Consensus         4 v~g~V~~v~---~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~   60 (73)
T cd05691           4 VTGKVTEVD---AKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDR   60 (73)
T ss_pred             EEEEEEEEE---CCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeC
Confidence            568888874   467776655567899999998764211112346899999999876544

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.

>PRK07252 hypothetical protein; Provisional

Probab=84.89  E-value=12  Score=27.44  Aligned_cols=59  Identities=20%  Similarity=0.200  Sum_probs=42.3

Q ss_pred             eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900         108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK  169 (191)
Q Consensus       108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k  169 (191)
                      ..+.|+|....   .||++..-+.+.+-|+|.+++.......-...++.||.|.+.|..-+.
T Consensus         5 ~iv~G~V~~V~---~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~   63 (120)
T PRK07252          5 DKLKGTITGIK---PYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDE   63 (120)
T ss_pred             CEEEEEEEEEe---CcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeC
Confidence            35788888874   488877766678999999998643110111347899999999998654

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

Probab=84.84  E-value=9.2  Score=25.41  Aligned_cols=50  Identities=16%  Similarity=0.263  Sum_probs=39.8

Q ss_pred             ceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEc
Q psy9900         107 VHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG  167 (191)
Q Consensus       107 ~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~  167 (191)
                      ...+.|+|...   ..||+...-+.+.+-++|.+++.        ..++.||.|...+..-
T Consensus        17 G~~~~g~V~~i---~~~G~fV~l~~~~~Glv~~se~~--------~~~~iGd~v~v~I~~i   66 (77)
T cd04473          17 GKLYKGKVNGV---AKYGVFVDLNDHVRGLIHRSNLL--------RDYEVGDEVIVQVTDI   66 (77)
T ss_pred             CCEEEEEEEeE---ecceEEEEECCCcEEEEEchhcc--------CcCCCCCEEEEEEEEE
Confidence            35678888876   34888777666789999999985        4689999999998775

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.

>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed

Probab=84.82  E-value=25  Score=33.21  Aligned_cols=136  Identities=13%  Similarity=0.130  Sum_probs=76.4

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEE--cCCCceeeEeecCCCCCcc
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGV--GKKDIEAINVTGPNGIPVQ   84 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~--~~~g~~A~~v~~~~~~~~~   84 (191)
                      ....|+|...+. .  |.+..-...-+-|++.+++...........+..||.|++.+..  .+++.-......+....  
T Consensus       304 ~iV~G~V~~v~~-~--gv~Vdig~~~~G~lp~~els~~~~~~~~~~~~vGd~V~v~V~~vd~~~g~i~LS~k~~~~~~--  378 (647)
T PRK00087        304 DIVKGTVVSVNE-N--EVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSKKEADREK--  378 (647)
T ss_pred             CEEEEEEEEEEC-C--EEEEEECCCeEEEEEHHHhcccccCChhhccCCCCEEEEEEEEEECCCCcEEEEeehhcchh--
Confidence            346799999964 2  3333333345789999988743222233567899999999876  33342111111110000  


Q ss_pred             CCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccC--CCCCEEEE
Q psy9900          85 GAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSL--GLGEIVDF  162 (191)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l--~~G~~V~f  162 (191)
                           +-...      ....-......|+|....   .+|++..-+ +-+.|+|.+++....    ...+  ..|+.|.|
T Consensus       379 -----~~~~l------~~~~~~G~iv~g~V~~v~---~~G~~V~lg-gi~gfiP~sel~~~~----~~d~~~~vG~~v~v  439 (647)
T PRK00087        379 -----AWKEL------EEAFENGEPVKGKVKEVV---KGGLLVDYG-GVRAFLPASHVELGY----VEDLSEYKGQELEV  439 (647)
T ss_pred             -----HHHHH------HHHhhCCCEEEEEEEEEE---CCeEEEEEC-CEEEEEEHHHhCccc----cCCHHHhCCCEEEE
Confidence                 00000      000122345788888763   246665554 489999999876431    1222  28999999


Q ss_pred             EEEE
Q psy9900         163 NIGV  166 (191)
Q Consensus       163 ~i~~  166 (191)
                      .+..
T Consensus       440 ~Vl~  443 (647)
T PRK00087        440 KIIE  443 (647)
T ss_pred             EEEE
Confidence            9844

>TIGR00767 rho transcription termination factor Rho

Probab=84.62  E-value=1.8  Score=38.62  Aligned_cols=51  Identities=29%  Similarity=0.519  Sum_probs=39.8

Q ss_pred             eeeeeEEEeecCCCceeEEeCC-----CCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcC
Q psy9900         109 TVRGIVKFYDSKRGFGFITRLD-----NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK  168 (191)
Q Consensus       109 ~~~G~Vk~~~~~kgfGFI~~~d-----~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~  168 (191)
                      ...|++...  ..||||+...+     +..||||..+.+..       -.|+.||.|+=.+..-.
T Consensus        50 ~~~g~le~~--~~g~gflr~~~~~~~~~~~d~yvs~~~i~~-------~~lr~gd~v~g~~R~~~  105 (415)
T TIGR00767        50 FGEGVLEIL--PDGFGFLRSPDSSYLPGPDDIYVSPSQIRR-------FNLRTGDTIEGQIRSPK  105 (415)
T ss_pred             EEEEEEEEc--CCCCeEEeCCCcCCCCCCCCeeeCHHHHHh-------cCCCCCCEEEEEEeccc
Confidence            356777655  35999999863     35899999999997       58999999998776543

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

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

Probab=84.41  E-value=4.4  Score=26.09  Aligned_cols=56  Identities=14%  Similarity=0.056  Sum_probs=38.1

Q ss_pred             ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEc
Q psy9900           8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG   66 (191)
Q Consensus         8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~   66 (191)
                      ..+|+|...+.  ..-||.. ....+-|+|.+++......+....++.||.|++.+..-
T Consensus         3 iv~g~V~~i~~--~~~~v~l-~~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~   58 (70)
T cd05687           3 IVKGTVVSVDD--DEVLVDI-GYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRV   58 (70)
T ss_pred             EEEEEEEEEeC--CEEEEEe-CCCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEE
Confidence            35799999863  2345554 43578999999997532111234579999999998763

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.

>PRK07252 hypothetical protein; Provisional

Probab=84.20  E-value=9.3  Score=28.10  Aligned_cols=59  Identities=20%  Similarity=0.200  Sum_probs=41.8

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK   68 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~   68 (191)
                      ....|+|....   .||++..-+.+.+-|+|.++|....-..-...++.||.|.+.+..-..
T Consensus         5 ~iv~G~V~~V~---~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~   63 (120)
T PRK07252          5 DKLKGTITGIK---PYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDE   63 (120)
T ss_pred             CEEEEEEEEEe---CcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeC
Confidence            34678888885   488887766668999999999653211112457899999999987543

>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=83.93  E-value=7.8  Score=25.43  Aligned_cols=60  Identities=17%  Similarity=0.113  Sum_probs=40.9

Q ss_pred             ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCC
Q psy9900           8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD   69 (191)
Q Consensus         8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g   69 (191)
                      ...|+|+.-...  ||.+..-..+.+-++|.+++......+....++.||.|...+..-.++
T Consensus         6 iv~G~V~~i~~~--~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~~   65 (72)
T cd05704           6 VTLGMVTKVIPH--SGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKDG   65 (72)
T ss_pred             EEEEEEEEeeCC--cEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecCC
Confidence            457888886422  666666666789999999997643211223468899999998776543

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.

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

Probab=83.92  E-value=7.6  Score=24.73  Aligned_cols=57  Identities=25%  Similarity=0.194  Sum_probs=39.4

Q ss_pred             eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhc-cCcccccccCCCCCEEEEEEEEcC
Q psy9900         109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVK-MNPKKFFQSLGLGEIVDFNIGVGK  168 (191)
Q Consensus       109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~-~~~~~~~~~l~~G~~V~f~i~~~~  168 (191)
                      .+.|+|....   .||+...-+.+.+-++|.+++.. ...+.-...++.||.|...+..-+
T Consensus         3 ~~~g~V~~i~---~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id   60 (69)
T cd05690           3 VVSGKIKSIT---DFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNID   60 (69)
T ss_pred             EEEEEEEEEE---eeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEE
Confidence            3678887763   48877766667899999999862 110111234689999999987754

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.

>PRK05807 hypothetical protein; Provisional

Probab=83.83  E-value=4.7  Score=30.30  Aligned_cols=72  Identities=17%  Similarity=0.151  Sum_probs=47.4

Q ss_pred             CceeceeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC-CCceeeEee
Q psy9900           1 MTKFEIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK-KDIEAINVT   76 (191)
Q Consensus         1 ~~~~~~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~-~g~~A~~v~   76 (191)
                      |.-.......|+|....   .||+...-+ +..-++|.+.+......+-...++.||.|.+.+..-. .|.....+.
T Consensus         1 m~~~vG~vv~G~Vt~i~---~~GafV~L~-~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~~gkI~LSlk   73 (136)
T PRK05807          1 MTLKAGSILEGTVVNIT---NFGAFVEVE-GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKISLSIK   73 (136)
T ss_pred             CCccCCCEEEEEEEEEE---CCeEEEEEC-CEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECCCCcEEEEEE
Confidence            44445567889999874   477766554 5689999999975432222355799999999987643 454333443

>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=83.68  E-value=7.4  Score=25.83  Aligned_cols=59  Identities=19%  Similarity=0.148  Sum_probs=40.5

Q ss_pred             eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccC---cccccccCCCCCEEEEEEEEcCC
Q psy9900         108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMN---PKKFFQSLGLGEIVDFNIGVGKK  169 (191)
Q Consensus       108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~---~~~~~~~l~~G~~V~f~i~~~~k  169 (191)
                      ....|+|+...   .||....-..+-+-|+|++++....   +..-...++.||.|.+.+..-+.
T Consensus         5 ~~V~g~V~~i~---~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~   66 (74)
T cd05705           5 QLLRGYVSSVT---KQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNS   66 (74)
T ss_pred             CEEEEEEEEEe---CCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEEC
Confidence            35789999874   4555444445789999999987642   10012457999999999987654

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.

>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=83.67  E-value=2  Score=28.52  Aligned_cols=28  Identities=14%  Similarity=0.191  Sum_probs=22.2

Q ss_pred             cccCCCCCEEEEEEEEcCCC-ceeEEeec
Q psy9900         151 FQSLGLGEIVDFNIGVGKKD-IEAINVTG  178 (191)
Q Consensus       151 ~~~l~~G~~V~f~i~~~~kg-~~A~~V~~  178 (191)
                      +..|++||.|.|.+..++.| +.-+.++.
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            57899999999999999998 87777653

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.

>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=82.78  E-value=7.2  Score=25.00  Aligned_cols=58  Identities=24%  Similarity=0.236  Sum_probs=39.6

Q ss_pred             eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900         109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK  169 (191)
Q Consensus       109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k  169 (191)
                      .+.|+|+...   .+|.+..-..+-+-|+|.+++.......-...++.||.|++.+..-+.
T Consensus         3 ~v~g~V~~v~---~~Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~   60 (68)
T cd05707           3 VVRGFVKNIA---NNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDP   60 (68)
T ss_pred             EEEEEEEEEE---CccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeC
Confidence            3678888863   466655554568999999998643111112348999999999887554

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.

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=82.64  E-value=7  Score=34.96  Aligned_cols=74  Identities=16%  Similarity=0.089  Sum_probs=51.1

Q ss_pred             ceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccC------------cccccccCCCCCEEEEEEEEcC---CCc
Q psy9900         107 VHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMN------------PKKFFQSLGLGEIVDFNIGVGK---KDI  171 (191)
Q Consensus       107 ~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~------------~~~~~~~l~~G~~V~f~i~~~~---kg~  171 (191)
                      ...+.|+|+...+.-.--||.-.+ ++.-|+|++++....            ...-...|++||.|.++|...+   ||+
T Consensus        26 GnIY~GrV~~i~p~l~aAFVdiG~-~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke~~~~Kgp  104 (414)
T TIGR00757        26 GNIYKGRVTRILPSLQAAFVDIGL-EKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVKEPRGNKGA  104 (414)
T ss_pred             CCEEEEEEeeecCCCceEEEEcCC-CceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEeeCCcCCCCC
Confidence            346789999987766688888765 678999999985310            0000114899999999999954   664


Q ss_pred             e-eEEeecCCC
Q psy9900         172 E-AINVTGPNG  181 (191)
Q Consensus       172 ~-A~~V~~~~~  181 (191)
                      . ..++++++.
T Consensus       105 ~lT~~Isl~Gr  115 (414)
T TIGR00757       105 RLTTDISLPGR  115 (414)
T ss_pred             eEEEEEEeccc
Confidence            4 336666554

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.

>PRK08059 general stress protein 13; Validated

Probab=82.62  E-value=11  Score=27.69  Aligned_cols=71  Identities=20%  Similarity=0.243  Sum_probs=47.1

Q ss_pred             eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC--CceeEEeecCCC
Q psy9900         108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK--DIEAINVTGPNG  181 (191)
Q Consensus       108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k--g~~A~~V~~~~~  181 (191)
                      ..+.|+|.....   ||+...-+.+.+-++|.+++.......-...++.||.|.+.|..-+.  |.-...++.+..
T Consensus         9 ~iv~G~V~~i~~---~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk~~~~   81 (123)
T PRK08059          9 SVVTGKVTGIQP---YGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEE   81 (123)
T ss_pred             CEEEEEEEEEec---ceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEEccc
Confidence            467888887643   78777766678999999998543111112356899999999988543  544444554444

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

Probab=82.58  E-value=29  Score=29.41  Aligned_cols=117  Identities=15%  Similarity=0.035  Sum_probs=69.6

Q ss_pred             CeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCc-eeeEeecCCCCCccCCCCCCCcccccccc
Q psy9900          21 GFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI-EAINVTGPNGIPVQGAPKSSSETVSGTYR   99 (191)
Q Consensus        21 GfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~-~A~~v~~~~~~~~~~~~~~~~~~~~~~~~   99 (191)
                      .-|--....-..|++|..+++..-    --..|+.||.+.+.+..+.++. .|.-...  . ....-+.++..       
T Consensus        87 ~lGaFlD~Gl~KDl~vp~~elp~~----~~~wpq~Gd~l~v~l~~Dkk~Ri~g~~a~~--~-~l~~l~~~~~~-------  152 (287)
T COG2996          87 DLGAFLDWGLPKDLLVPLDELPTL----KSLWPQKGDKLLVYLYVDKKGRIWGTLAIE--K-ILENLATPAYN-------  152 (287)
T ss_pred             CcceEEecCCCcceeeehhhcccc----cccCCCCCCEEEEEEEEccCCcEEEEecch--h-HHHhcCCccch-------
Confidence            334333334458999999999853    1235899999999999999883 2221111  0 00000000000       


Q ss_pred             CCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEE
Q psy9900         100 NDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGV  166 (191)
Q Consensus       100 ~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~  166 (191)
                          -.......|+|-.+...   |++...+.+--.|+|.|+..        ..++.|++|.-.+..
T Consensus       153 ----~l~nq~v~~tVYr~~~~---G~fv~~e~~~~GfIh~sEr~--------~~prlG~~l~~rVi~  204 (287)
T COG2996         153 ----NLKNQEVDATVYRLLES---GTFVITENGYLGFIHKSERF--------AEPRLGERLTARVIG  204 (287)
T ss_pred             ----hhhcCeeeeEEEEEecc---ceEEEEcCCeEEEEcchhhc--------ccccCCceEEEEEEE
Confidence                01123467888777332   33222245788999999886        467899999887765

>TIGR00767 rho transcription termination factor Rho

Probab=82.49  E-value=1.4  Score=39.40  Aligned_cols=50  Identities=28%  Similarity=0.508  Sum_probs=38.6

Q ss_pred             cceEEEEeeCCCCeeEEEeC-----CCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC
Q psy9900           9 VRGIVKFYDSKRGFGFITRL-----DNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK   67 (191)
Q Consensus         9 ~~G~vk~~~~~kGfGFI~~~-----~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~   67 (191)
                      ..|.+--.  ..||||+...     .+..||||..+.++.       -.|+.||.|.-.+....
T Consensus        51 ~~g~le~~--~~g~gflr~~~~~~~~~~~d~yvs~~~i~~-------~~lr~gd~v~g~~R~~~  105 (415)
T TIGR00767        51 GEGVLEIL--PDGFGFLRSPDSSYLPGPDDIYVSPSQIRR-------FNLRTGDTIEGQIRSPK  105 (415)
T ss_pred             EEEEEEEc--CCCCeEEeCCCcCCCCCCCCeeeCHHHHHh-------cCCCCCCEEEEEEeccc
Confidence            45666644  3599999985     345899999999996       37899999999876543

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

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

Probab=82.28  E-value=6.8  Score=25.70  Aligned_cols=58  Identities=17%  Similarity=0.225  Sum_probs=38.1

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCC-CccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDN-KEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK   67 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~-~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~   67 (191)
                      ....|+|+...   -||....-++ ..+-|+|.+.+.......-...++.||+|.+.+..-.
T Consensus         5 ~~~~g~V~~i~---~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd   63 (73)
T cd05686           5 QIFKGEVASVT---EYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGRE   63 (73)
T ss_pred             CEEEEEEEEEE---eeeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEEC
Confidence            34678888875   4787765543 3689999999965421001122578999999987643

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.

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

Probab=82.17  E-value=11  Score=24.31  Aligned_cols=57  Identities=18%  Similarity=0.160  Sum_probs=38.9

Q ss_pred             ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheec-CCCCCcccCCCCCEEEEEEEEcC
Q psy9900           8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKM-NPKKFFQSLGLGEIVDFNIGVGK   67 (191)
Q Consensus         8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~-~~~~g~~~l~~Gd~V~f~~~~~~   67 (191)
                      ...|+|+.-.   -||+...-+.+.+-|+|.+++... ........++.||.|.+.+..-+
T Consensus         6 ~~~g~V~~i~---~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id   63 (72)
T cd05689           6 RLFGKVTNLT---DYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDID   63 (72)
T ss_pred             EEEEEEEEEE---eeEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEee
Confidence            4678888764   488887665568999999999631 10012234688999999886643

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.

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

Probab=81.88  E-value=6.2  Score=25.17  Aligned_cols=55  Identities=25%  Similarity=0.198  Sum_probs=38.1

Q ss_pred             cceEEEEeeCCCCeeEEEeCCCCccEEEEeeehee-cCCCCCcccCCCCCEEEEEEEEc
Q psy9900           9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVK-MNPKKFFQSLGLGEIVDFNIGVG   66 (191)
Q Consensus         9 ~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~-~~~~~g~~~l~~Gd~V~f~~~~~   66 (191)
                      ..|+|+...   .||+...-+.+.+-++|.+++.. .........++.||.|.+.+..-
T Consensus         4 ~~g~V~~i~---~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~i   59 (69)
T cd05690           4 VSGKIKSIT---DFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNI   59 (69)
T ss_pred             EEEEEEEEE---eeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEE
Confidence            567787764   58888766667899999999962 11111123468999999987654

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.

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

Probab=81.33  E-value=8.9  Score=25.13  Aligned_cols=59  Identities=17%  Similarity=0.213  Sum_probs=39.2

Q ss_pred             eeeeeeEEEeecCCCceeEEeCCC-CCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900         108 HTVRGIVKFYDSKRGFGFITRLDN-KEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK  169 (191)
Q Consensus       108 ~~~~G~Vk~~~~~kgfGFI~~~d~-~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k  169 (191)
                      ..+.|+|....   .||....-++ ..+-++|.+++.......-..-++.||.|.+.+..-+.
T Consensus         5 ~~~~g~V~~i~---~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~   64 (73)
T cd05686           5 QIFKGEVASVT---EYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREM   64 (73)
T ss_pred             CEEEEEEEEEE---eeeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECC
Confidence            35778888874   3787666543 36899999999653210111225889999999877544

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.

>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=81.29  E-value=13  Score=24.57  Aligned_cols=68  Identities=15%  Similarity=0.166  Sum_probs=43.2

Q ss_pred             eeeeeEEEeecCCCceeEEeCC---CCCcEEEeccchhccCc-ccccccCCCCCEEEEEEEEcCCCceeEEeecC
Q psy9900         109 TVRGIVKFYDSKRGFGFITRLD---NKEDIFVHKSSIVKMNP-KKFFQSLGLGEIVDFNIGVGKKDIEAINVTGP  179 (191)
Q Consensus       109 ~~~G~Vk~~~~~kgfGFI~~~d---~~~dvF~h~s~~~~~~~-~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~  179 (191)
                      .+.|+|....   .||+...-+   .+.+-|+|.+++..... ..-...++.||.|...+..-+++.-...++.+
T Consensus         3 ~~~g~V~~v~---~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd~~~i~~s~k~~   74 (79)
T cd05684           3 IYKGKVTSIM---DFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQNGKISLSMKDV   74 (79)
T ss_pred             EEEEEEEEEE---eeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEeCCEEEEEEEec
Confidence            3567777763   367766544   25789999999964310 01113468999999999886655444444433

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.

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

Probab=81.04  E-value=11  Score=24.23  Aligned_cols=57  Identities=14%  Similarity=0.088  Sum_probs=38.0

Q ss_pred             eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcC
Q psy9900         109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK  168 (191)
Q Consensus       109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~  168 (191)
                      .+.|+|.....   +|.+..-..+.+-|+|.+++...........+++||.|++.+..-+
T Consensus         3 iv~g~V~~i~~---~~~~v~l~~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~   59 (70)
T cd05687           3 IVKGTVVSVDD---DEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVE   59 (70)
T ss_pred             EEEEEEEEEeC---CEEEEEeCCCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEE
Confidence            46788888743   3444444446789999999975321111245899999999988744

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.

>PRK05807 hypothetical protein; Provisional

Probab=81.03  E-value=19  Score=26.99  Aligned_cols=70  Identities=14%  Similarity=0.141  Sum_probs=46.7

Q ss_pred             ceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcC-CCceeEEeecCC
Q psy9900         107 VHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK-KDIEAINVTGPN  180 (191)
Q Consensus       107 ~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~-kg~~A~~V~~~~  180 (191)
                      ...+.|+|....   .||.+...+ +..-++|++++.......-...++.||.|.+.|..-+ .|.-...++.+.
T Consensus         6 G~vv~G~Vt~i~---~~GafV~L~-~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~~gkI~LSlk~~~   76 (136)
T PRK05807          6 GSILEGTVVNIT---NFGAFVEVE-GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKISLSIKQAM   76 (136)
T ss_pred             CCEEEEEEEEEE---CCeEEEEEC-CEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECCCCcEEEEEEecc
Confidence            356789998863   477766664 5789999999964321111245799999999987754 454445555443

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

Probab=80.42  E-value=13  Score=24.08  Aligned_cols=59  Identities=14%  Similarity=0.032  Sum_probs=39.7

Q ss_pred             eeeeeeEEEeecCCCceeEEeCC--CCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900         108 HTVRGIVKFYDSKRGFGFITRLD--NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK  169 (191)
Q Consensus       108 ~~~~G~Vk~~~~~kgfGFI~~~d--~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k  169 (191)
                      ..+.|+|....   .||.+..-.  .+.+-++|.+++.......-...++.||.|+..+..-+.
T Consensus         5 ~~~~g~V~~v~---~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~   65 (76)
T cd04452           5 ELVVVTVKSIA---DMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDK   65 (76)
T ss_pred             CEEEEEEEEEE---ccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEEC
Confidence            35778888763   477766543  247899999998753211111347899999999887554

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

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

Probab=80.40  E-value=9.3  Score=25.40  Aligned_cols=49  Identities=16%  Similarity=0.293  Sum_probs=38.1

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEc
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG   66 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~   66 (191)
                      ...+|+|....   .||+...-+.+.+-|+|.+++.        ..++.||.|...+..-
T Consensus        18 ~~~~g~V~~i~---~~G~fV~l~~~~~Glv~~se~~--------~~~~iGd~v~v~I~~i   66 (77)
T cd04473          18 KLYKGKVNGVA---KYGVFVDLNDHVRGLIHRSNLL--------RDYEVGDEVIVQVTDI   66 (77)
T ss_pred             CEEEEEEEeEe---cceEEEEECCCcEEEEEchhcc--------CcCCCCCEEEEEEEEE
Confidence            45678888753   5888877666689999999975        4588999999988664

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.

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

Probab=80.27  E-value=11  Score=24.26  Aligned_cols=51  Identities=24%  Similarity=0.215  Sum_probs=37.1

Q ss_pred             eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcC
Q psy9900         108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK  168 (191)
Q Consensus       108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~  168 (191)
                      ....|+|...+.   +|.+...+ +-+-|++.+.+...      ..++.||.|.+.+..-+
T Consensus         5 ~iV~G~V~~~~~---~~~~vdig-~~eg~lp~~e~~~~------~~~~~Gd~v~v~v~~v~   55 (67)
T cd04455           5 EIVTGIVKRVDR---GNVIVDLG-KVEAILPKKEQIPG------ESYRPGDRIKAYVLEVR   55 (67)
T ss_pred             CEEEEEEEEEcC---CCEEEEcC-CeEEEeeHHHCCCC------CcCCCCCEEEEEEEEEe
Confidence            356899988854   24444443 37889999999743      46799999999998754

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	191
1h95_A	79	Solution Structure Of The Single-Stranded Dna-Bindi		6e-16
1h95_A	79	Solution Structure Of The Single-Stranded Dna-Bindi		9e-16
1g6p_A	66	Solution Nmr Structure Of The Cold Shock Protein Fr		1e-07
1g6p_A	66	Solution Nmr Structure Of The Cold Shock Protein Fr		1e-07
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-		3e-07
3ulj_A	90	Crystal Structure Of Apo Lin28b Cold Shock Domain L		4e-07
4a4i_A	90	Crystal Structure Of The Human Lin28b Cold Shock Do		9e-07
4a4i_A	90	Crystal Structure Of The Human Lin28b Cold Shock Do		1e-06
3i2z_B	71	Structure Of Cold Shock Protein E From Salmonella T		1e-06
3i2z_B	71	Structure Of Cold Shock Protein E From Salmonella T		1e-06
1mjc_A	69	Crystal Structure Of Cspa, The Major Cold Shock Pro		3e-06
1mjc_A	69	Crystal Structure Of Cspa, The Major Cold Shock Pro		3e-06
2l15_A	70	Solution Structure Of Cold Shock Protein Cspa Using		4e-06
2l15_A	70	Solution Structure Of Cold Shock Protein Cspa Using		4e-06
3mef_A	69	Major Cold-Shock Protein From Escherichia Coli Solu		4e-06
3mef_A	69	Major Cold-Shock Protein From Escherichia Coli Solu		4e-06
3cam_A	67	Crystal Structure Of The Cold Shock Domain Protein		2e-05
3cam_A	67	Crystal Structure Of The Cold Shock Domain Protein		2e-05
2i5l_X	67	Crystal Structure Of Bacillus Subtilis Cold Shock P		4e-05
2i5l_X	67	Crystal Structure Of Bacillus Subtilis Cold Shock P		4e-05
2es2_A	67	Crystal Structure Analysis Of The Bacillus Subtilis		5e-05
2es2_A	67	Crystal Structure Analysis Of The Bacillus Subtilis		5e-05
3a0j_A	73	Crystal Structure Of Cold Shock Protein 1 From Ther		7e-05
3a0j_A	73	Crystal Structure Of Cold Shock Protein 1 From Ther		7e-05
2i5m_X	67	Crystal Structure Of Bacillus Subtilis Cold Shock P		2e-04
2i5m_X	67	Crystal Structure Of Bacillus Subtilis Cold Shock P		2e-04
2bh8_A	101	Combinatorial Protein 1b11 Length = 101		4e-04
2bh8_A	101	Combinatorial Protein 1b11 Length = 101		6e-04
1hza_A	67	Bacillus Caldolyticus Cold-Shock Protein Mutants To		8e-04
1hza_A	67	Bacillus Caldolyticus Cold-Shock Protein Mutants To		8e-04

>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 = 80.1 bits (196), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 38/78 (48%), Positives = 55/78 (70%)
Query: 1  MTKFEIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVD 60
          M K     V G VK+++ + G+GFI R D KED+FVH+++I K NP+K+ +S+G GE V+
Sbjct: 1  MKKVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVE 60
Query: 61 FNIGVGKKDIEAINVTGP 78
          F++  G+K  EA NVTGP
Sbjct: 61 FDVVEGEKGAEAANVTGP 78

>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 = 79.7 bits (195), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 36/70 (51%), Positives = 53/70 (75%)
Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
           V G VK+++ + G+GFI R D KED+FVH+++I K NP+K+ +S+G GE V+F++  G+K
Sbjct: 9   VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEK 68
Query: 170 DIEAINVTGP 179
             EA NVTGP
Sbjct: 69  GAEAANVTGP 78

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 30/67 (44%), Positives = 46/67 (68%), Gaps = 5/67 (7%)
Query: 9  VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
          +RG VK++DSK+G+GFIT+ D   D+FVH S+I      + F++L  G++V+F I  GKK
Sbjct: 1  MRGKVKWFDSKKGYGFITK-DEGGDVFVHWSAI----EMEGFKTLKEGQVVEFEIQEGKK 55
Query: 69 DIEAINV 75
            +A +V
Sbjct: 56 GPQAAHV 62

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 30/67 (44%), Positives = 46/67 (68%), Gaps = 5/67 (7%)
Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
           +RG VK++DSK+G+GFIT+ D   D+FVH S+I      + F++L  G++V+F I  GKK
Sbjct: 1   MRGKVKWFDSKKGYGFITK-DEGGDVFVHWSAI----EMEGFKTLKEGQVVEFEIQEGKK 55
Query: 170 DIEAINV 176
             +A +V
Sbjct: 56  GPQAAHV 62

>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 = 31/87 (35%), Positives = 47/87 (54%), Gaps = 11/87 (12%)
Query: 112 GIVKFYDSKRGFGFIT-------RLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI 164
           GI K+++ + GFGF++        LD   D+FVH+S +        F+SL  GE V+F  
Sbjct: 12  GICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEG----FRSLKEGEAVEFTF 67
Query: 165 GVGKKDIEAINVTGPNGIPVQGAPKVP 191
               K +E+I VTGP G+   G+ + P
Sbjct: 68  KKSAKGLESIRVTGPGGVFCIGSERRP 94

>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 = 3e-07,   Method: Compositional matrix adjust.
 Identities = 31/87 (35%), Positives = 47/87 (54%), Gaps = 11/87 (12%)
Query: 112 GIVKFYDSKRGFGFIT-------RLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI 164
           GI K+++ + GFGF++        LD   D+FVH+S +        F+SL  GE V+F  
Sbjct: 10  GICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEG----FRSLKEGEAVEFTF 65
Query: 165 GVGKKDIEAINVTGPNGIPVQGAPKVP 191
               K +E+I VTGP G+   G+ + P
Sbjct: 66  KKSAKGLESIRVTGPGGVFCIGSERRP 92

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 32/89 (35%), Positives = 45/89 (50%), Gaps = 11/89 (12%)
Query: 105 PAVHTVRGIVKFYDSKRGFGFITR-------LDNKEDIFVHKSSIVKMNPKKFFQSLGLG 157
           P V    G  K+++ + GFGFI+        L+N  D+FVH+S +        F+SL  G
Sbjct: 4   PQVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEG----FRSLKEG 59
Query: 158 EIVDFNIGVGKKDIEAINVTGPNGIPVQG 186
           E V+F      K  E++ VTGP G P  G
Sbjct: 60  EPVEFTFKKSSKGFESLRVTGPGGNPCLG 88

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 33/91 (36%), Positives = 47/91 (51%), Gaps = 13/91 (14%)
Query: 5  EIHTVRGI--VKFYDSKRGFGFITR-------LDNKEDIFVHKSSIVKMNPKKFFQSLGL 55
          E   +RG    K+++ + GFGFI+        LD   D+FVH+S +        F+SL  
Sbjct: 3  ESQVLRGTGHCKWFNVRMGFGFISMINREGSPLDIPVDVFVHQSKLFMEG----FRSLKE 58
Query: 56 GEIVDFNIGVGKKDIEAINVTGPNGIPVQGA 86
          GE V+F      K +E+I VTGP G P  G+
Sbjct: 59 GEPVEFTFKKSSKGLESIRVTGPGGSPCLGS 89

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 31/83 (37%), Positives = 44/83 (53%), Gaps = 11/83 (13%)
Query: 112 GIVKFYDSKRGFGFITR-------LDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI 164
           G  K+++ + GFGFI+        LD   D+FVH+S +        F+SL  GE V+F  
Sbjct: 11  GHCKWFNVRMGFGFISMINREGSPLDIPVDVFVHQSKLFMEG----FRSLKEGEPVEFTF 66
Query: 165 GVGKKDIEAINVTGPNGIPVQGA 187
               K +E+I VTGP G P  G+
Sbjct: 67  KKSSKGLESIRVTGPGGSPCLGS 89

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/69 (40%), Positives = 41/69 (59%), Gaps = 4/69 (5%)
Query: 9  VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
          ++G VK+++  +GFGFIT  D  +D+FVH S+I        F++L  G+ V+F I  G K
Sbjct: 6  IKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNGAK 61
Query: 69 DIEAINVTG 77
             A NVT 
Sbjct: 62 GPSAANVTA 70

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/69 (40%), Positives = 41/69 (59%), Gaps = 4/69 (5%)
Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
           ++G VK+++  +GFGFIT  D  +D+FVH S+I        F++L  G+ V+F I  G K
Sbjct: 6   IKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNGAK 61
Query: 170 DIEAINVTG 178
              A NVT 
Sbjct: 62  GPSAANVTA 70

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 29/68 (42%), Positives = 41/68 (60%), Gaps = 4/68 (5%)
Query: 9  VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
          + GIVK++++ +GFGFIT  D  +D+FVH S+I        ++SL  G+ V F I  G K
Sbjct: 4  MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAI----QNDGYKSLDEGQKVSFTIESGAK 59
Query: 69 DIEAINVT 76
             A NVT
Sbjct: 60 GPAAGNVT 67

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 29/68 (42%), Positives = 41/68 (60%), Gaps = 4/68 (5%)
Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
           + GIVK++++ +GFGFIT  D  +D+FVH S+I        ++SL  G+ V F I  G K
Sbjct: 4   MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAI----QNDGYKSLDEGQKVSFTIESGAK 59
Query: 170 DIEAINVT 177
              A NVT
Sbjct: 60  GPAAGNVT 67

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 29/68 (42%), Positives = 41/68 (60%), Gaps = 4/68 (5%)
Query: 9  VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
          + GIVK++++ +GFGFIT  D  +D+FVH S+I        ++SL  G+ V F I  G K
Sbjct: 5  MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAI----QNDGYKSLDEGQKVSFTIESGAK 60
Query: 69 DIEAINVT 76
             A NVT
Sbjct: 61 GPAAGNVT 68

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 29/68 (42%), Positives = 41/68 (60%), Gaps = 4/68 (5%)
Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
           + GIVK++++ +GFGFIT  D  +D+FVH S+I        ++SL  G+ V F I  G K
Sbjct: 5   MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAI----QNDGYKSLDEGQKVSFTIESGAK 60
Query: 170 DIEAINVT 177
              A NVT
Sbjct: 61  GPAAGNVT 68

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 29/68 (42%), Positives = 41/68 (60%), Gaps = 4/68 (5%)
Query: 9  VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
          + GIVK++++ +GFGFIT  D  +D+FVH S+I        ++SL  G+ V F I  G K
Sbjct: 4  MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAI----QNDGYKSLDEGQKVSFTIESGAK 59
Query: 69 DIEAINVT 76
             A NVT
Sbjct: 60 GPAAGNVT 67

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 29/68 (42%), Positives = 41/68 (60%), Gaps = 4/68 (5%)
Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
           + GIVK++++ +GFGFIT  D  +D+FVH S+I        ++SL  G+ V F I  G K
Sbjct: 4   MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAI----QNDGYKSLDEGQKVSFTIESGAK 59
Query: 170 DIEAINVT 177
              A NVT
Sbjct: 60  GPAAGNVT 67

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/65 (38%), Positives = 39/65 (60%), Gaps = 4/65 (6%)
Query: 11 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI 70
          GIVK+++  +GFGFIT  +  ED+F H S+I        F++L  G+ V F++  G K  
Sbjct: 4  GIVKWFNDAKGFGFITPDEGGEDLFAHFSAINXEG----FKTLKEGQRVSFDVTTGPKGK 59
Query: 71 EAINV 75
          +A N+
Sbjct: 60 QAANI 64

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/65 (38%), Positives = 39/65 (60%), Gaps = 4/65 (6%)
Query: 112 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI 171
           GIVK+++  +GFGFIT  +  ED+F H S+I        F++L  G+ V F++  G K  
Sbjct: 4   GIVKWFNDAKGFGFITPDEGGEDLFAHFSAINXEG----FKTLKEGQRVSFDVTTGPKGK 59
Query: 172 EAINV 176
           +A N+
Sbjct: 60  QAANI 64

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 26/68 (38%), Positives = 45/68 (66%), Gaps = 5/68 (7%)
Query: 9  VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
          ++G VK+++S++GFGFI  ++ ++D+FVH S+I      + F++L  G+ V F I  G +
Sbjct: 2  LKGKVKWFNSEKGFGFI-EVEGQDDVFVHFSAI----QGEGFKTLEEGQAVSFEIVEGNR 56
Query: 69 DIEAINVT 76
            +A NVT
Sbjct: 57 GPQAANVT 64

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 26/68 (38%), Positives = 45/68 (66%), Gaps = 5/68 (7%)
Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
           ++G VK+++S++GFGFI  ++ ++D+FVH S+I      + F++L  G+ V F I  G +
Sbjct: 2   LKGKVKWFNSEKGFGFI-EVEGQDDVFVHFSAI----QGEGFKTLEEGQAVSFEIVEGNR 56
Query: 170 DIEAINVT 177
             +A NVT
Sbjct: 57  GPQAANVT 64

>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 = 43.9 bits (102), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 26/68 (38%), Positives = 44/68 (64%), Gaps = 5/68 (7%)
Query: 9  VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
          + G VK+++S++GFGFI  ++ ++D+FVH S+I      + F++L  G+ V F I  G +
Sbjct: 2  LEGKVKWFNSEKGFGFI-EVEGQDDVFVHFSAI----QGEGFKTLEEGQAVSFEIVEGNR 56
Query: 69 DIEAINVT 76
            +A NVT
Sbjct: 57 GPQAANVT 64

>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 = 43.9 bits (102), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 26/68 (38%), Positives = 44/68 (64%), Gaps = 5/68 (7%)
Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
           + G VK+++S++GFGFI  ++ ++D+FVH S+I      + F++L  G+ V F I  G +
Sbjct: 2   LEGKVKWFNSEKGFGFI-EVEGQDDVFVHFSAI----QGEGFKTLEEGQAVSFEIVEGNR 56
Query: 170 DIEAINVT 177
             +A NVT
Sbjct: 57  GPQAANVT 64

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 26/69 (37%), Positives = 46/69 (66%), Gaps = 7/69 (10%)
Query: 10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK-- 67
          +G VK++++++G+GFI R +   D+FVH ++I      K F++L  G+IV F++  G+  
Sbjct: 3  KGRVKWFNAEKGYGFIER-EGDTDVFVHYTAI----NAKGFRTLNEGDIVTFDVEPGRNG 57
Query: 68 KDIEAINVT 76
          K  +A+NVT
Sbjct: 58 KGPQAVNVT 66

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 26/69 (37%), Positives = 46/69 (66%), Gaps = 7/69 (10%)
Query: 111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK-- 168
           +G VK++++++G+GFI R +   D+FVH ++I      K F++L  G+IV F++  G+  
Sbjct: 3   KGRVKWFNAEKGYGFIER-EGDTDVFVHYTAI----NAKGFRTLNEGDIVTFDVEPGRNG 57
Query: 169 KDIEAINVT 177
           K  +A+NVT
Sbjct: 58  KGPQAVNVT 66

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/68 (38%), Positives = 44/68 (64%), Gaps = 5/68 (7%)
Query: 9  VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
          + G VK+++S++GFGFI  ++ ++D+FVH S+I      + F++L  G+ V F I  G +
Sbjct: 2  LEGKVKWFNSEKGFGFI-EVEGQDDVFVHFSAI----QGEGFKTLEEGQKVRFEIVEGNR 56
Query: 69 DIEAINVT 76
            +A NVT
Sbjct: 57 GPQAANVT 64

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/68 (38%), Positives = 44/68 (64%), Gaps = 5/68 (7%)
Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
           + G VK+++S++GFGFI  ++ ++D+FVH S+I      + F++L  G+ V F I  G +
Sbjct: 2   LEGKVKWFNSEKGFGFI-EVEGQDDVFVHFSAI----QGEGFKTLEEGQKVRFEIVEGNR 56
Query: 170 DIEAINVT 177
             +A NVT
Sbjct: 57  GPQAANVT 64

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

Iteration: 1
 Score = 40.8 bits (94), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 25/71 (35%), Positives = 43/71 (60%), Gaps = 6/71 (8%)
Query: 2  TKFEIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKS-----SIVKMNPKKFFQSLG-L 55
          ++ +   + GIVK++++ +GFGFIT  D  +D+FVH S     + V+ NP++  +  G +
Sbjct: 10 SRLQSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAGSSGAAVRGNPQQGDRVEGKI 69
Query: 56 GEIVDFNIGVG 66
            I DF I +G
Sbjct: 70 KSITDFGIFIG 80

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

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 25/64 (39%), Positives = 40/64 (62%), Gaps = 6/64 (9%)
Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKS-----SIVKMNPKKFFQSLG-LGEIVDFN 163
           + GIVK++++ +GFGFIT  D  +D+FVH S     + V+ NP++  +  G +  I DF 
Sbjct: 17  MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAGSSGAAVRGNPQQGDRVEGKIKSITDFG 76
Query: 164 IGVG 167
           I +G
Sbjct: 77  IFIG 80

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

Iteration: 1
 Score = 40.0 bits (92), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 24/67 (35%), Positives = 42/67 (62%), Gaps = 5/67 (7%)
Query: 10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 69
          RG VK++++++G+GFI  ++   D+FVH ++I      + F++L  G+ V F I  G + 
Sbjct: 3  RGKVKWFNNEKGYGFI-EVEGGSDVFVHFTAI----QGEGFKTLEEGQEVSFEIVQGNRG 57
Query: 70 IEAINVT 76
           +A NVT
Sbjct: 58 PQAANVT 64

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

Iteration: 1
 Score = 40.0 bits (92), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 24/67 (35%), Positives = 42/67 (62%), Gaps = 5/67 (7%)
Query: 111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 170
           RG VK++++++G+GFI  ++   D+FVH ++I      + F++L  G+ V F I  G + 
Sbjct: 3   RGKVKWFNNEKGYGFI-EVEGGSDVFVHFTAI----QGEGFKTLEEGQEVSFEIVQGNRG 57
Query: 171 IEAINVT 177
            +A NVT
Sbjct: 58  PQAANVT 64

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	191
1h95_A	79	CSD, Y-box binding protein; translation factor, tr	3e-21
1h95_A	79	CSD, Y-box binding protein; translation factor, tr	3e-21
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	1e-19
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	3e-19
3ulj_A	90	LIN28B, DNA-binding protein; beta barrel, cold sho	2e-18
3ulj_A	90	LIN28B, DNA-binding protein; beta barrel, cold sho	2e-18
2kcm_A	74	Cold shock domain family protein; nucleic acid bin	1e-13
2kcm_A	74	Cold shock domain family protein; nucleic acid bin	1e-13
2k5n_A	74	Putative cold-shock protein; GFT protein structure	7e-12
2k5n_A	74	Putative cold-shock protein; GFT protein structure	7e-12
3i2z_B	71	RNA chaperone, negative regulator of CSPA transcri	2e-11
3i2z_B	71	RNA chaperone, negative regulator of CSPA transcri	2e-11
1g6p_A	66	Cold shock protein TMCSP; greek-KEY, beta barrel,	1e-10
1g6p_A	66	Cold shock protein TMCSP; greek-KEY, beta barrel,	1e-10
3cam_A	67	Cold-shock domain family protein; cold shock prote	1e-10
3cam_A	67	Cold-shock domain family protein; cold shock prote	1e-10
2lss_A	70	Cold shock-like protein; CSD, CSP, oligonucleotide	2e-10
2lss_A	70	Cold shock-like protein; CSD, CSP, oligonucleotide	2e-10
1c9o_A	66	CSPB, cold-shock protein; beta barrel, homodimer,	5e-10
1c9o_A	66	CSPB, cold-shock protein; beta barrel, homodimer,	5e-10
2ytx_A	97	Cold shock domain-containing protein E1; cell-free	7e-10
2ytx_A	97	Cold shock domain-containing protein E1; cell-free	7e-10
3aqq_A	147	Calcium-regulated heat stable protein 1; compact b	1e-09
3aqq_A	147	Calcium-regulated heat stable protein 1; compact b	1e-08
3a0j_A	73	Cold shock protein; OB-fold, cytoplasm, transcript	9e-09
3a0j_A	73	Cold shock protein; OB-fold, cytoplasm, transcript	9e-09
2yty_A	88	Cold shock domain-containing protein E1; cell-free	4e-08
2yty_A	88	Cold shock domain-containing protein E1; cell-free	4e-08
2bh8_A	101	1B11; transcription, molecular evolution, unique a	5e-08
2bh8_A	101	1B11; transcription, molecular evolution, unique a	9e-08
1wfq_A	89	UNR protein; beta-barrel, translational regulation	5e-05
1wfq_A	89	UNR protein; beta-barrel, translational regulation	5e-05
1x65_A	89	UNR protein; cell-free protein synthesis, beta-bar	4e-04

>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 Length = 79

 Score = 82.0 bits (203), Expect = 3e-21
 Identities = 36/70 (51%), Positives = 53/70 (75%)

Query: 9  VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
          V G VK+++ + G+GFI R D KED+FVH+++I K NP+K+ +S+G GE V+F++  G+K
Sbjct: 9  VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEK 68

Query: 69 DIEAINVTGP 78
            EA NVTGP
Sbjct: 69 GAEAANVTGP 78

>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 Length = 79

 Score = 82.0 bits (203), Expect = 3e-21
 Identities = 36/70 (51%), Positives = 53/70 (75%)

Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
           V G VK+++ + G+GFI R D KED+FVH+++I K NP+K+ +S+G GE V+F++  G+K
Sbjct: 9   VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEK 68

Query: 170 DIEAINVTGP 179
             EA NVTGP
Sbjct: 69  GAEAANVTGP 78

>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* Length = 148

 Score = 80.1 bits (197), Expect = 1e-19
 Identities = 32/94 (34%), Positives = 49/94 (52%), Gaps = 11/94 (11%)

Query: 105 PAVHTVRGIVKFYDSKRGFGFITR-------LDNKEDIFVHKSSIVKMNPKKFFQSLGLG 157
           P +    GI K+++ + GFGF++        LD   D+FVH+S +        F+SL  G
Sbjct: 5   PQLLHGAGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEG----FRSLKEG 60

Query: 158 EIVDFNIGVGKKDIEAINVTGPNGIPVQGAPKVP 191
           E V+F      K +E+I VTGP G+   G+ + P
Sbjct: 61  EAVEFTFKKSAKGLESIRVTGPGGVFCIGSERRP 94

>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* Length = 148

 Score = 78.9 bits (194), Expect = 3e-19
 Identities = 30/89 (33%), Positives = 46/89 (51%), Gaps = 11/89 (12%)

Query: 9  VRGIVKFYDSKRGFGFITR-------LDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDF 61
            GI K+++ + GFGF++        LD   D+FVH+S +        F+SL  GE V+F
Sbjct: 10 GAGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEG----FRSLKEGEAVEF 65

Query: 62 NIGVGKKDIEAINVTGPNGIPVQGAPKSS 90
                K +E+I VTGP G+   G+ +  
Sbjct: 66 TFKKSAKGLESIRVTGPGGVFCIGSERRP 94

>3ulj_A LIN28B, DNA-binding protein; beta barrel, cold shock domain fold, nucleic acid binding, D binding protein; 1.06A {Silurana} PDB: 4a4i_A Length = 90

 Score = 75.2 bits (185), Expect = 2e-18
 Identities = 32/90 (35%), Positives = 45/90 (50%), Gaps = 11/90 (12%)

Query: 105 PAVHTVRGIVKFYDSKRGFGFITR-------LDNKEDIFVHKSSIVKMNPKKFFQSLGLG 157
           P V    G  K+++ + GFGFI+        L+N  D+FVH+S +        F+SL  G
Sbjct: 4   PQVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEG----FRSLKEG 59

Query: 158 EIVDFNIGVGKKDIEAINVTGPNGIPVQGA 187
           E V+F      K  E++ VTGP G P  G 
Sbjct: 60  EPVEFTFKKSSKGFESLRVTGPGGNPCLGN 89

>3ulj_A LIN28B, DNA-binding protein; beta barrel, cold shock domain fold, nucleic acid binding, D binding protein; 1.06A {Silurana} PDB: 4a4i_A Length = 90

 Score = 75.2 bits (185), Expect = 2e-18
 Identities = 30/85 (35%), Positives = 43/85 (50%), Gaps = 11/85 (12%)

Query: 9  VRGIVKFYDSKRGFGFITR-------LDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDF 61
            G  K+++ + GFGFI+        L+N  D+FVH+S +        F+SL  GE V+F
Sbjct: 9  GSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEG----FRSLKEGEPVEF 64

Query: 62 NIGVGKKDIEAINVTGPNGIPVQGA 86
                K  E++ VTGP G P  G 
Sbjct: 65 TFKKSSKGFESLRVTGPGGNPCLGN 89

>2kcm_A Cold shock domain family protein; nucleic acid binding protein, beta barrel, structural genomi 2, protein structure initiative; NMR {Shewanella oneidensis} Length = 74

 Score = 62.3 bits (152), Expect = 1e-13
 Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 4/70 (5%)

Query: 9  VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
          ++G V  Y + + +GFI   D+ E  F+H S ++          L  G +V F+     K
Sbjct: 1  MKGKVVSYLAAKKYGFIQG-DDGESYFLHFSELLDKKD---EGKLVKGSMVHFDPTPTPK 56

Query: 69 DIEAINVTGP 78
           + A  ++ P
Sbjct: 57 GLAAKAISLP 66

>2kcm_A Cold shock domain family protein; nucleic acid binding protein, beta barrel, structural genomi 2, protein structure initiative; NMR {Shewanella oneidensis} Length = 74

 Score = 62.3 bits (152), Expect = 1e-13
 Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 4/70 (5%)

Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
           ++G V  Y + + +GFI   D+ E  F+H S ++          L  G +V F+     K
Sbjct: 1   MKGKVVSYLAAKKYGFIQG-DDGESYFLHFSELLDKKD---EGKLVKGSMVHFDPTPTPK 56

Query: 170 DIEAINVTGP 179
            + A  ++ P
Sbjct: 57  GLAAKAISLP 66

>2k5n_A Putative cold-shock protein; GFT protein structure, PSI, nesgc, OB fold, cold shock structural genomics; NMR {Pectobacterium atrosepticum} Length = 74

 Score = 57.7 bits (140), Expect = 7e-12
 Identities = 13/69 (18%), Positives = 24/69 (34%), Gaps = 7/69 (10%)

Query: 8  TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 67
           + G +  +   +GFGFI   +N ++ + H   +           +     V F      
Sbjct: 2  AMNGTITTWFKDKGFGFIKD-ENGDNRYFHVIKVAN------PDLIKKDAAVTFEPTTNN 54

Query: 68 KDIEAINVT 76
          K + A  V 
Sbjct: 55 KGLSAYAVK 63

>2k5n_A Putative cold-shock protein; GFT protein structure, PSI, nesgc, OB fold, cold shock structural genomics; NMR {Pectobacterium atrosepticum} Length = 74

 Score = 57.7 bits (140), Expect = 7e-12
 Identities = 13/69 (18%), Positives = 24/69 (34%), Gaps = 7/69 (10%)

Query: 109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 168
            + G +  +   +GFGFI   +N ++ + H   +           +     V F      
Sbjct: 2   AMNGTITTWFKDKGFGFIKD-ENGDNRYFHVIKVAN------PDLIKKDAAVTFEPTTNN 54

Query: 169 KDIEAINVT 177
           K + A  V 
Sbjct: 55  KGLSAYAVK 63

>3i2z_B RNA chaperone, negative regulator of CSPA transcription; beta barrel, DNA binding protein/transcription, cytoplasm, gene regulation; 1.10A {Salmonella typhimurium} PDB: 2l15_A 1mjc_A 3mef_A Length = 71

 Score = 56.1 bits (136), Expect = 2e-11
 Identities = 28/69 (40%), Positives = 41/69 (59%), Gaps = 4/69 (5%)

Query: 8  TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 67
           ++G VK+++  +GFGFIT  D  +D+FVH S+I        F++L  G+ V+F I  G 
Sbjct: 5  KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNGA 60

Query: 68 KDIEAINVT 76
          K   A NVT
Sbjct: 61 KGPSAANVT 69

>3i2z_B RNA chaperone, negative regulator of CSPA transcription; beta barrel, DNA binding protein/transcription, cytoplasm, gene regulation; 1.10A {Salmonella typhimurium} PDB: 2l15_A 1mjc_A 3mef_A Length = 71

 Score = 56.1 bits (136), Expect = 2e-11
 Identities = 28/69 (40%), Positives = 41/69 (59%), Gaps = 4/69 (5%)

Query: 109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 168
            ++G VK+++  +GFGFIT  D  +D+FVH S+I        F++L  G+ V+F I  G 
Sbjct: 5   KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNGA 60

Query: 169 KDIEAINVT 177
           K   A NVT
Sbjct: 61  KGPSAANVT 69

>1g6p_A Cold shock protein TMCSP; greek-KEY, beta barrel, OB-fold, structural genomics; NMR {Thermotoga maritima} SCOP: b.40.4.5 Length = 66

 Score = 54.1 bits (131), Expect = 1e-10
 Identities = 30/68 (44%), Positives = 45/68 (66%), Gaps = 5/68 (7%)

Query: 9  VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
          +RG VK++DSK+G+GFIT+ D   D+FVH S+I        F++L  G++V+F I  GKK
Sbjct: 1  MRGKVKWFDSKKGYGFITK-DEGGDVFVHWSAIEMEG----FKTLKEGQVVEFEIQEGKK 55

Query: 69 DIEAINVT 76
            +A +V 
Sbjct: 56 GPQAAHVK 63

>1g6p_A Cold shock protein TMCSP; greek-KEY, beta barrel, OB-fold, structural genomics; NMR {Thermotoga maritima} SCOP: b.40.4.5 Length = 66

 Score = 54.1 bits (131), Expect = 1e-10
 Identities = 30/68 (44%), Positives = 45/68 (66%), Gaps = 5/68 (7%)

Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
           +RG VK++DSK+G+GFIT+ D   D+FVH S+I        F++L  G++V+F I  GKK
Sbjct: 1   MRGKVKWFDSKKGYGFITK-DEGGDVFVHWSAIEMEG----FKTLKEGQVVEFEIQEGKK 55

Query: 170 DIEAINVT 177
             +A +V 
Sbjct: 56  GPQAAHVK 63

>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} Length = 67

 Score = 54.1 bits (131), Expect = 1e-10
 Identities = 25/66 (37%), Positives = 39/66 (59%), Gaps = 4/66 (6%)

Query: 11 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI 70
          GIVK+++  +GFGFIT  +  ED+F H S+I        F++L  G+ V F++  G K  
Sbjct: 4  GIVKWFNDAKGFGFITPDEGGEDLFAHFSAINMEG----FKTLKEGQRVSFDVTTGPKGK 59

Query: 71 EAINVT 76
          +A N+ 
Sbjct: 60 QAANIQ 65

>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} Length = 67

 Score = 54.1 bits (131), Expect = 1e-10
 Identities = 25/66 (37%), Positives = 39/66 (59%), Gaps = 4/66 (6%)

Query: 112 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI 171
           GIVK+++  +GFGFIT  +  ED+F H S+I        F++L  G+ V F++  G K  
Sbjct: 4   GIVKWFNDAKGFGFITPDEGGEDLFAHFSAINMEG----FKTLKEGQRVSFDVTTGPKGK 59

Query: 172 EAINVT 177
           +A N+ 
Sbjct: 60  QAANIQ 65

>2lss_A Cold shock-like protein; CSD, CSP, oligonucleotide binding F fold, RNA binding protein, DNA binding protein; NMR {Rickettsia rickettsii} Length = 70

 Score = 53.8 bits (130), Expect = 2e-10
 Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 4/69 (5%)

Query: 8  TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 67
           + G VK+Y+S + FGFI + +  +D+FVHKS++          SL  G+ V F++   +
Sbjct: 4  NIVGKVKWYNSTKNFGFIEQDNGGKDVFVHKSAVDAAG----LHSLEEGQDVIFDLEEKQ 59

Query: 68 KDIEAINVT 76
              A+N+ 
Sbjct: 60 GKAYAVNLR 68

>2lss_A Cold shock-like protein; CSD, CSP, oligonucleotide binding F fold, RNA binding protein, DNA binding protein; NMR {Rickettsia rickettsii} Length = 70

 Score = 53.8 bits (130), Expect = 2e-10
 Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 4/69 (5%)

Query: 109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 168
            + G VK+Y+S + FGFI + +  +D+FVHKS++          SL  G+ V F++   +
Sbjct: 4   NIVGKVKWYNSTKNFGFIEQDNGGKDVFVHKSAVDAAG----LHSLEEGQDVIFDLEEKQ 59

Query: 169 KDIEAINVT 177
               A+N+ 
Sbjct: 60  GKAYAVNLR 68

>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 Length = 66

 Score = 52.2 bits (126), Expect = 5e-10
 Identities = 22/66 (33%), Positives = 38/66 (57%), Gaps = 5/66 (7%)

Query: 11 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI 70
          G VK++++++G+GFI   +   D+FVH ++I        F++L  G+ V F I  G +  
Sbjct: 4  GKVKWFNNEKGYGFIEV-EGGSDVFVHFTAIQGEG----FKTLEEGQEVSFEIVQGNRGP 58

Query: 71 EAINVT 76
          +A NV 
Sbjct: 59 QAANVV 64

>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 Length = 66

 Score = 52.2 bits (126), Expect = 5e-10
 Identities = 22/66 (33%), Positives = 38/66 (57%), Gaps = 5/66 (7%)

Query: 112 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI 171
           G VK++++++G+GFI   +   D+FVH ++I        F++L  G+ V F I  G +  
Sbjct: 4   GKVKWFNNEKGYGFIEV-EGGSDVFVHFTAIQGEG----FKTLEEGQEVSFEIVQGNRGP 58

Query: 172 EAINVT 177
           +A NV 
Sbjct: 59  QAANVV 64

>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} Length = 97

 Score = 52.9 bits (127), Expect = 7e-10
 Identities = 21/67 (31%), Positives = 30/67 (44%), Gaps = 7/67 (10%)

Query: 10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 69
          +G+V     K  FGFI R D  ++IF H S       K   ++L  G+ V+F I      
Sbjct: 20 QGVVCAM--KEAFGFIERGDVVKEIFFHYSEF-----KGDLETLQPGDDVEFTIKDRNGK 72

Query: 70 IEAINVT 76
            A +V 
Sbjct: 73 EVATDVR 79

>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} Length = 97

 Score = 52.9 bits (127), Expect = 7e-10
 Identities = 21/67 (31%), Positives = 30/67 (44%), Gaps = 7/67 (10%)

Query: 111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 170
           +G+V     K  FGFI R D  ++IF H S       K   ++L  G+ V+F I      
Sbjct: 20  QGVVCAM--KEAFGFIERGDVVKEIFFHYSEF-----KGDLETLQPGDDVEFTIKDRNGK 72

Query: 171 IEAINVT 177
             A +V 
Sbjct: 73  EVATDVR 79

>3aqq_A Calcium-regulated heat stable protein 1; compact beta-barrel, cold shock domain, ssDNA binding, DNA B protein; 2.80A {Homo sapiens} Length = 147

 Score = 53.5 bits (128), Expect = 1e-09
 Identities = 20/89 (22%), Positives = 36/89 (40%), Gaps = 9/89 (10%)

Query: 10  RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK-- 67
           +G+ K +   +G GFIT  D   DIF+H S +      +       G+ V + +      
Sbjct: 64  KGVCKCFCRSKGHGFITPADGGPDIFLHISDV------EGEYVPVEGDEVTYKMCSIPPK 117

Query: 68  -KDIEAINVTGPNGIPVQGAPKSSSETVS 95
            + ++A+ V   +  P       S   +S
Sbjct: 118 NEKLQAVEVVITHLAPGTKHETWSGHVIS 146

>3aqq_A Calcium-regulated heat stable protein 1; compact beta-barrel, cold shock domain, ssDNA binding, DNA B protein; 2.80A {Homo sapiens} Length = 147

 Score = 50.8 bits (121), Expect = 1e-08
 Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 9/76 (11%)

Query: 111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK-- 168
           +G+ K +   +G GFIT  D   DIF+H S +      +       G+ V + +      
Sbjct: 64  KGVCKCFCRSKGHGFITPADGGPDIFLHISDV------EGEYVPVEGDEVTYKMCSIPPK 117

Query: 169 -KDIEAINVTGPNGIP 183
            + ++A+ V   +  P
Sbjct: 118 NEKLQAVEVVITHLAP 133

>3a0j_A Cold shock protein; OB-fold, cytoplasm, transcription, structural genomics, NPPSFA; 1.65A {Thermus thermophilus} Length = 73

 Score = 49.2 bits (118), Expect = 9e-09
 Identities = 25/68 (36%), Positives = 43/68 (63%), Gaps = 7/68 (10%)

Query: 11 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI--GVGKK 68
          G VK++++++G+GFI R +   D+FVH ++I        F++L  G+IV F++  G   K
Sbjct: 4  GRVKWFNAEKGYGFIER-EGDTDVFVHYTAINAKG----FRTLNEGDIVTFDVEPGRNGK 58

Query: 69 DIEAINVT 76
            +A+NVT
Sbjct: 59 GPQAVNVT 66

>3a0j_A Cold shock protein; OB-fold, cytoplasm, transcription, structural genomics, NPPSFA; 1.65A {Thermus thermophilus} Length = 73

 Score = 49.2 bits (118), Expect = 9e-09
 Identities = 25/68 (36%), Positives = 43/68 (63%), Gaps = 7/68 (10%)

Query: 112 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI--GVGKK 169
           G VK++++++G+GFI R +   D+FVH ++I        F++L  G+IV F++  G   K
Sbjct: 4   GRVKWFNAEKGYGFIER-EGDTDVFVHYTAINAKG----FRTLNEGDIVTFDVEPGRNGK 58

Query: 170 DIEAINVT 177
             +A+NVT
Sbjct: 59  GPQAVNVT 66

>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} Length = 88

 Score = 47.9 bits (114), Expect = 4e-08
 Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 7/68 (10%)

Query: 19 KRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK-KDIEAINVTG 77
          K  FGFI   ++ ++IF H S            SL LG++V++++  GK   + A  V  
Sbjct: 27 KDNFGFIETANHDKEIFFHYSEF-----SGDVDSLELGDMVEYSLSKGKGNKVSAEKVNK 81

Query: 78 PNGIPVQG 85
           +G P  G
Sbjct: 82 TSG-PSSG 88

>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} Length = 88

 Score = 47.9 bits (114), Expect = 4e-08
 Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 7/68 (10%)

Query: 120 KRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK-KDIEAINVTG 178
           K  FGFI   ++ ++IF H S            SL LG++V++++  GK   + A  V  
Sbjct: 27  KDNFGFIETANHDKEIFFHYSEF-----SGDVDSLELGDMVEYSLSKGKGNKVSAEKVNK 81

Query: 179 PNGIPVQG 186
            +G P  G
Sbjct: 82  TSG-PSSG 88

>2bh8_A 1B11; transcription, molecular evolution, unique architecture, transcription regulation, phosphorylation; 1.9A {Escherichia coli} Length = 101

 Score = 47.8 bits (114), Expect = 5e-08
 Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 2/85 (2%)

Query: 94  VSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQS 153
           + G++ +         + GIVK++++ +GFGFIT  D  +D+FVH S+    +      +
Sbjct: 1   MRGSHHHHGSRLQSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAG--SSGAAVRGN 58

Query: 154 LGLGEIVDFNIGVGKKDIEAINVTG 178
              G+ V+  I         I + G
Sbjct: 59  PQQGDRVEGKIKSITDFGIFIGLDG 83

>2bh8_A 1B11; transcription, molecular evolution, unique architecture, transcription regulation, phosphorylation; 1.9A {Escherichia coli} Length = 101

 Score = 47.5 bits (113), Expect = 9e-08
 Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 2/69 (2%)

Query: 9  VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
          + GIVK++++ +GFGFIT  D  +D+FVH S+    +      +   G+ V+  I     
Sbjct: 17 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAG--SSGAAVRGNPQQGDRVEGKIKSITD 74

Query: 69 DIEAINVTG 77
              I + G
Sbjct: 75 FGIFIGLDG 83

>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 Length = 89

 Score = 39.5 bits (92), Expect = 5e-05
 Identities = 12/60 (20%), Positives = 24/60 (40%), Gaps = 7/60 (11%)

Query: 19 KRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK--DIEAINVT 76
             +GFI   + +  +F H S           Q L +G+ V+F +   ++     A+ + 
Sbjct: 27 LTSYGFIQCSERQARLFFHCSQY-----NGNLQDLKVGDDVEFEVSSDRRTGKPIAVKLV 81

>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 Length = 89

 Score = 39.5 bits (92), Expect = 5e-05
 Identities = 12/60 (20%), Positives = 24/60 (40%), Gaps = 7/60 (11%)

Query: 120 KRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK--DIEAINVT 177
              +GFI   + +  +F H S           Q L +G+ V+F +   ++     A+ + 
Sbjct: 27  LTSYGFIQCSERQARLFFHCSQY-----NGNLQDLKVGDDVEFEVSSDRRTGKPIAVKLV 81

>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} Length = 89

 Score = 36.8 bits (85), Expect = 4e-04
 Identities = 18/80 (22%), Positives = 32/80 (40%), Gaps = 13/80 (16%)

Query: 19 KRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGP 78
          + GFGFI  +D    +F H S I+          L + + V+F +          +    
Sbjct: 17 RDGFGFIKCVDRDVRMFFHFSEILD------GNQLHIADEVEFTVVPDML-----SAQRN 65

Query: 79 NGIPVQGAPKSS--SETVSG 96
          + I ++  PK +    + SG
Sbjct: 66 HAIRIKKLPKGTVSFHSHSG 85

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	191
3ulj_A	90	LIN28B, DNA-binding protein; beta barrel, cold sho	99.93
1h95_A	79	CSD, Y-box binding protein; translation factor, tr	99.92
3ulj_A	90	LIN28B, DNA-binding protein; beta barrel, cold sho	99.91
1h95_A	79	CSD, Y-box binding protein; translation factor, tr	99.91
3i2z_B	71	RNA chaperone, negative regulator of CSPA transcri	99.9
3cam_A	67	Cold-shock domain family protein; cold shock prote	99.9
3cam_A	67	Cold-shock domain family protein; cold shock prote	99.89
3i2z_B	71	RNA chaperone, negative regulator of CSPA transcri	99.88
1c9o_A	66	CSPB, cold-shock protein; beta barrel, homodimer,	99.88
3a0j_A	73	Cold shock protein; OB-fold, cytoplasm, transcript	99.88
1c9o_A	66	CSPB, cold-shock protein; beta barrel, homodimer,	99.87
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	99.87
2kcm_A	74	Cold shock domain family protein; nucleic acid bin	99.87
3a0j_A	73	Cold shock protein; OB-fold, cytoplasm, transcript	99.87
2kcm_A	74	Cold shock domain family protein; nucleic acid bin	99.87
1g6p_A	66	Cold shock protein TMCSP; greek-KEY, beta barrel,	99.87
2lss_A	70	Cold shock-like protein; CSD, CSP, oligonucleotide	99.78
1g6p_A	66	Cold shock protein TMCSP; greek-KEY, beta barrel,	99.87
2k5n_A	74	Putative cold-shock protein; GFT protein structure	99.86
2k5n_A	74	Putative cold-shock protein; GFT protein structure	99.86
2lss_A	70	Cold shock-like protein; CSD, CSP, oligonucleotide	99.76
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	99.85
1wfq_A	89	UNR protein; beta-barrel, translational regulation	99.84
1wfq_A	89	UNR protein; beta-barrel, translational regulation	99.83
2yty_A	88	Cold shock domain-containing protein E1; cell-free	99.82
3aqq_A	147	Calcium-regulated heat stable protein 1; compact b	99.82
3aqq_A	147	Calcium-regulated heat stable protein 1; compact b	99.8
2ytx_A	97	Cold shock domain-containing protein E1; cell-free	99.8
2yty_A	88	Cold shock domain-containing protein E1; cell-free	99.8
1x65_A	89	UNR protein; cell-free protein synthesis, beta-bar	99.79
2ytx_A	97	Cold shock domain-containing protein E1; cell-free	99.77
1x65_A	89	UNR protein; cell-free protein synthesis, beta-bar	99.75
2ytv_A	79	Cold shock domain-containing protein E1; cell-free	99.73
2ytv_A	79	Cold shock domain-containing protein E1; cell-free	99.73
2bh8_A	101	1B11; transcription, molecular evolution, unique a	99.62
2bh8_A	101	1B11; transcription, molecular evolution, unique a	99.52
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	98.43
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	97.85
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	97.63
1a62_A	130	RHO; transcription termination, termination, RNA b	97.45
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	97.38
1a62_A	130	RHO; transcription termination, termination, RNA b	97.05
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	96.76
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	95.79
3l0o_A	427	Transcription termination factor RHO; helicase, RH	93.52
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	92.11
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	91.7
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	91.5
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	90.27
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	89.61
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	89.31
3l0o_A	427	Transcription termination factor RHO; helicase, RH	89.06
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	87.94
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	87.49
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	87.4
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	87.08
3ice_A	422	Transcription termination factor RHO; transcriptio	86.13
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	85.83
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	85.62
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	85.25
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	84.0
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	83.71
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	83.59
3ice_A	422	Transcription termination factor RHO; transcriptio	83.01
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	82.76
2qcp_X	80	Cation efflux system protein CUSF; silver-binding,	82.36
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	81.99
2vb2_X	88	Copper protein, cation efflux system protein CUSF;	81.97
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	81.8
2l55_A	82	SILB,silver efflux protein, MFP component of the c	81.75
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	80.96
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	80.23
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	80.01

>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=99.93  E-value=6.6e-26  Score=158.68  Aligned_cols=78  Identities=40%  Similarity=0.667  Sum_probs=71.7

Q ss_pred             ceeeeeeEEEeecCCCceeEE-------eCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecC
Q psy9900         107 VHTVRGIVKFYDSKRGFGFIT-------RLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGP  179 (191)
Q Consensus       107 ~~~~~G~Vk~~~~~kgfGFI~-------~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~  179 (191)
                      ..+.+|+|||||..||||||+       ++++++|||||+|+|...    +++.|.+|++|+|++.+++||++|++|+.+
T Consensus         6 ~~r~tG~VKWFn~~KGfGFI~~~~~~~~p~dgg~DvFVH~s~i~~~----g~~~L~eG~~V~f~v~~g~kG~~A~~Vtg~   81 (90)
T 3ulj_A            6 VLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYME----GFRSLKEGEPVEFTFKKSSKGFESLRVTGP   81 (90)
T ss_dssp             CEEEEEEEEEEETTTTEEEEEEEEETTEEEEEEEEEEEEGGGBCCS----SSCCCCTTCEEEEEEEEETTEEEEEEEECG
T ss_pred             ccccceEEEEeeCCCCeEEeEecCcCcCCCCCCccEEEEeehhccc----CCCccCCCCEEEEEEEECCCCcEEEEEECC
Confidence            457899999999999999998       456678999999999874    689999999999999999999999999999


Q ss_pred             CCCCCCCCC
Q psy9900         180 NGIPVQGAP  188 (191)
Q Consensus       180 ~~~~~~~~~  188 (191)
                      +|+|+++++
T Consensus        82 ~G~p~~gse   90 (90)
T 3ulj_A           82 GGNPCLGNE   90 (90)
T ss_dssp             GGCCCCCCC
T ss_pred             CCccccCCC
Confidence            999999985

>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=99.92  E-value=1.5e-25  Score=153.77  Aligned_cols=78  Identities=49%  Similarity=0.856  Sum_probs=72.0

Q ss_pred             CceeceeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeecC
Q psy9900           1 MTKFEIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGP   78 (191)
Q Consensus         1 ~~~~~~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~~   78 (191)
                      |+++++.+.+|+|||||..||||||.++++++|||||+|+|....++.|++.|.+|++|+|++..+++|++|.+|+.+
T Consensus         1 ~~~~~~~~~~G~Vkwfn~~kGfGFI~~~~gg~DvFvH~s~i~~~~~~~g~~~l~~G~~V~f~~~~~~kG~~A~~V~~p   78 (79)
T 1h95_A            1 MKKVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGP   78 (79)
T ss_dssp             CCSCCEEEEEEEEEEEETTTTEEEEEEGGGTEEEEEEGGGBCSCCCSCCSCSCCSSCEEEEEEEECSSSEEEESBCCC
T ss_pred             CccccccccceEEEEEECCCCcEEEecCCCCccEEEEhHHccccccccccccCCCCCEEEEEEEECCCCceeEEEECc
Confidence            889999999999999999999999999998899999999998754344789999999999999999999999999875

>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=99.91  E-value=1.1e-24  Score=152.40  Aligned_cols=77  Identities=39%  Similarity=0.677  Sum_probs=70.0

Q ss_pred             eeccceEEEEeeCCCCeeEEE-------eCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeecC
Q psy9900           6 IHTVRGIVKFYDSKRGFGFIT-------RLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGP   78 (191)
Q Consensus         6 ~~~~~G~vk~~~~~kGfGFI~-------~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~~   78 (191)
                      ..|.+|+|||||..||||||.       ++++++|||||+|+|...    |++.|.+|++|+|++..+++|++|++|+.+
T Consensus         6 ~~r~tG~VKWFn~~KGfGFI~~~~~~~~p~dgg~DvFVH~s~i~~~----g~~~L~eG~~V~f~v~~g~kG~~A~~Vtg~   81 (90)
T 3ulj_A            6 VLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYME----GFRSLKEGEPVEFTFKKSSKGFESLRVTGP   81 (90)
T ss_dssp             CEEEEEEEEEEETTTTEEEEEEEEETTEEEEEEEEEEEEGGGBCCS----SSCCCCTTCEEEEEEEEETTEEEEEEEECG
T ss_pred             ccccceEEEEeeCCCCeEEeEecCcCcCCCCCCccEEEEeehhccc----CCCccCCCCEEEEEEEECCCCcEEEEEECC
Confidence            357899999999999999997       456678999999999876    799999999999999999999999999999


Q ss_pred             CCCCccCC
Q psy9900          79 NGIPVQGA   86 (191)
Q Consensus        79 ~~~~~~~~   86 (191)
                      ++.|+.++
T Consensus        82 ~G~p~~gs   89 (90)
T 3ulj_A           82 GGNPCLGN   89 (90)
T ss_dssp             GGCCCCCC
T ss_pred             CCccccCC
Confidence            99888764

>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=99.91  E-value=2.3e-24  Score=147.80  Aligned_cols=76  Identities=47%  Similarity=0.851  Sum_probs=69.5

Q ss_pred             ccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecCC
Q psy9900         105 PAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPN  180 (191)
Q Consensus       105 ~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~~  180 (191)
                      .+..+.+|+|||||..||||||+++++++|||||+|+|...+++.+++.|.+|+.|+|++.++++|++|++|++++
T Consensus         4 ~~~~~~~G~Vkwfn~~kGfGFI~~~~gg~DvFvH~s~i~~~~~~~g~~~l~~G~~V~f~~~~~~kG~~A~~V~~p~   79 (79)
T 1h95_A            4 VIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGPG   79 (79)
T ss_dssp             CCEEEEEEEEEEEETTTTEEEEEEGGGTEEEEEEGGGBCSCCCSCCSCSCCSSCEEEEEEEECSSSEEEESBCCCC
T ss_pred             ccccccceEEEEEECCCCcEEEecCCCCccEEEEhHHccccccccccccCCCCCEEEEEEEECCCCceeEEEECcC
Confidence            4566789999999999999999999988999999999998655567899999999999999999999999999875

>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=99.90  E-value=1.3e-23  Score=141.28  Aligned_cols=69  Identities=41%  Similarity=0.676  Sum_probs=62.8

Q ss_pred             ceeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeec
Q psy9900           5 EIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG   77 (191)
Q Consensus         5 ~~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~   77 (191)
                      +|.+.+|+|||||..||||||.++++++|||||+|+|...    |++.|.+|++|+|++..+++|++|.+|+.
T Consensus         2 ~m~~~~G~Vk~fn~~kGfGFI~~~~g~~dvFvH~s~i~~~----g~~~l~~G~~V~f~~~~~~kG~~A~~V~~   70 (71)
T 3i2z_B            2 HMSKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTN----GFKTLAEGQRVEFEITNGAKGPSAANVTA   70 (71)
T ss_dssp             ---CEEEEEEEEETTTTEEEEEETTCCCCEEEEGGGBCCS----SCCCCCTTCEEEEEEEEETTEEEEEEEEE
T ss_pred             ccccccEEEEEEECCCCcEEEecCCCCccEEEEhHHcccc----cCcCCCCCCEEEEEEEECCCCCEeEEEEe
Confidence            3568999999999999999999999889999999999976    68899999999999999999999999975

>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=99.90  E-value=1.5e-23  Score=139.37  Aligned_cols=66  Identities=38%  Similarity=0.644  Sum_probs=61.8

Q ss_pred             ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeec
Q psy9900           8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG   77 (191)
Q Consensus         8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~   77 (191)
                      |.+|+|||||..||||||.++++++|||||+|+|...    |++.|.+|++|+|++..+++|++|.+|..
T Consensus         1 m~~G~Vk~fn~~kGfGFI~~~~gg~dvFvH~s~i~~~----g~~~l~~G~~V~f~~~~~~kG~~A~~V~~   66 (67)
T 3cam_A            1 MATGIVKWFNDAKGFGFITPDEGGEDLFAHFSAINME----GFKTLKEGQRVSFDVTTGPKGKQAANIQA   66 (67)
T ss_dssp             CEEEEEEEEETTTTEEEEEETTSCCCEEEEGGGBCGG----GGSSCCTTCEEEEEEEEETTEEEEEEEEE
T ss_pred             CCCEEEEEEECCCCeEEEecCCCCccEEEEHHHcccc----CCCCCCCCCEEEEEEEECCCCccceEEEe
Confidence            3589999999999999999999889999999999976    78999999999999999999999999974

>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=99.89  E-value=4e-23  Score=137.36  Aligned_cols=66  Identities=38%  Similarity=0.648  Sum_probs=61.7

Q ss_pred             eeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecC
Q psy9900         110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGP  179 (191)
Q Consensus       110 ~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~  179 (191)
                      .+|+|||||..||||||+++++++|||||+|+|...    +++.|.+|++|+|++.++++|++|++|+.+
T Consensus         2 ~~G~Vk~fn~~kGfGFI~~~~gg~dvFvH~s~i~~~----g~~~l~~G~~V~f~~~~~~kG~~A~~V~~~   67 (67)
T 3cam_A            2 ATGIVKWFNDAKGFGFITPDEGGEDLFAHFSAINME----GFKTLKEGQRVSFDVTTGPKGKQAANIQAA   67 (67)
T ss_dssp             EEEEEEEEETTTTEEEEEETTSCCCEEEEGGGBCGG----GGSSCCTTCEEEEEEEEETTEEEEEEEEEC
T ss_pred             CCEEEEEEECCCCeEEEecCCCCccEEEEHHHcccc----CCCCCCCCCEEEEEEEECCCCccceEEEeC
Confidence            479999999999999999999889999999999874    588999999999999999999999999863

>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=99.88  E-value=9.8e-23  Score=136.97  Aligned_cols=67  Identities=42%  Similarity=0.671  Sum_probs=62.7

Q ss_pred             eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecC
Q psy9900         109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGP  179 (191)
Q Consensus       109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~  179 (191)
                      +.+|+|||||..||||||+++++++|||||+++|...    +++.|.+||+|+|++.++++|++|++|+++
T Consensus         5 ~~~G~Vk~fn~~kGfGFI~~~~g~~dvFvH~s~i~~~----g~~~l~~G~~V~f~~~~~~kG~~A~~V~~~   71 (71)
T 3i2z_B            5 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTN----GFKTLAEGQRVEFEITNGAKGPSAANVTAL   71 (71)
T ss_dssp             CEEEEEEEEETTTTEEEEEETTCCCCEEEEGGGBCCS----SCCCCCTTCEEEEEEEEETTEEEEEEEEEC
T ss_pred             cccEEEEEEECCCCcEEEecCCCCccEEEEhHHcccc----cCcCCCCCCEEEEEEEECCCCCEeEEEEeC
Confidence            5789999999999999999999889999999999864    578999999999999999999999999863

>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=99.88  E-value=6.3e-23  Score=136.08  Aligned_cols=65  Identities=35%  Similarity=0.596  Sum_probs=60.8

Q ss_pred             ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeec
Q psy9900           8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG   77 (191)
Q Consensus         8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~   77 (191)
                      |.+|+|||||..||||||.++++ +|||||+|+|...    |++.|.+|++|+|++..+++|++|.+|..
T Consensus         1 m~~G~Vk~fn~~kGfGFI~~~~g-~dvFvH~s~i~~~----g~~~l~~G~~V~f~~~~~~kG~~A~~V~~   65 (66)
T 1c9o_A            1 MQRGKVKWFNNEKGYGFIEVEGG-SDVFVHFTAIQGE----GFKTLEEGQEVSFEIVQGNRGPQAANVVK   65 (66)
T ss_dssp             CEEEEEEEEETTTTEEEEEETTE-EEEEEEGGGBCSS----SCCCCCTTCEEEEEEEEETTEEEEEEEEE
T ss_pred             CCceEEEEEECCCCeEEEecCCC-ccEEEEHHHcccc----CCCCCCCCCEEEEEEEECCCCcEeEEEEe
Confidence            35899999999999999999997 9999999999976    78999999999999999999999999974

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

Probab=99.88  E-value=1e-22  Score=137.62  Aligned_cols=66  Identities=38%  Similarity=0.707  Sum_probs=61.4

Q ss_pred             ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC--CCceeeEeecC
Q psy9900           8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK--KDIEAINVTGP   78 (191)
Q Consensus         8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~--~g~~A~~v~~~   78 (191)
                      |.+|+|||||..||||||.++++ +|||||+|+|...    |++.|.+|++|+|++..++  +|++|.+|..+
T Consensus         1 m~~G~Vk~fn~~kGfGFI~~~~g-~dvFvH~s~i~~~----g~~~l~~G~~V~f~~~~~~~~kG~~A~~V~~~   68 (73)
T 3a0j_A            1 MQKGRVKWFNAEKGYGFIEREGD-TDVFVHYTAINAK----GFRTLNEGDIVTFDVEPGRNGKGPQAVNVTVV   68 (73)
T ss_dssp             CEEEEEEEEETTTTEEEEECTTS-CCEEEEGGGBCSS----SCSSCCTTCEEEEEEECCSCCSSSEEEEEEEE
T ss_pred             CCCEEEEEEECCCCEEEEecCCC-CcEEEEhhhcccc----CCCCCCCCCEEEEEEEECCCCCCCEEEEEEeC
Confidence            35899999999999999999986 9999999999976    7899999999999999999  89999999875

>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=99.87  E-value=1.5e-22  Score=134.21  Aligned_cols=65  Identities=35%  Similarity=0.588  Sum_probs=60.7

Q ss_pred             eeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecC
Q psy9900         110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGP  179 (191)
Q Consensus       110 ~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~  179 (191)
                      .+|+|||||..||||||+++++ +|||||+|+|...    +++.|.+|++|+|++.++++|++|++|+++
T Consensus         2 ~~G~Vk~fn~~kGfGFI~~~~g-~dvFvH~s~i~~~----g~~~l~~G~~V~f~~~~~~kG~~A~~V~~~   66 (66)
T 1c9o_A            2 QRGKVKWFNNEKGYGFIEVEGG-SDVFVHFTAIQGE----GFKTLEEGQEVSFEIVQGNRGPQAANVVKL   66 (66)
T ss_dssp             EEEEEEEEETTTTEEEEEETTE-EEEEEEGGGBCSS----SCCCCCTTCEEEEEEEEETTEEEEEEEEEC
T ss_pred             CceEEEEEECCCCeEEEecCCC-ccEEEEHHHcccc----CCCCCCCCCEEEEEEEECCCCcEeEEEEeC
Confidence            5799999999999999999997 9999999999974    578999999999999999999999999864

>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=99.87  E-value=1.1e-22  Score=155.08  Aligned_cols=80  Identities=38%  Similarity=0.649  Sum_probs=74.1

Q ss_pred             eeeeeeEEEeecCCCceeEEeC-------CCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecCC
Q psy9900         108 HTVRGIVKFYDSKRGFGFITRL-------DNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPN  180 (191)
Q Consensus       108 ~~~~G~Vk~~~~~kgfGFI~~~-------d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~~  180 (191)
                      .+.+|+|||||..||||||+++       ++++|||||+++|...    +++.|.+|+.|+|++.++++|++|++|+.++
T Consensus         8 ~~~~G~Vkwfn~~kGfGFI~~~~~~g~p~~~g~DvFvH~s~i~~~----g~~~l~eG~~V~f~~~~g~kG~~A~~V~~pg   83 (148)
T 3ts2_A            8 LHGAGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHME----GFRSLKEGEAVEFTFKKSAKGLESIRVTGPG   83 (148)
T ss_dssp             EEEEEEEEEEETTTTEEEEEEEEETTEEEEEEEEEEEEGGGBCSS----SSCCCCTTCEEEEEEEEETTEEEEEEEESGG
T ss_pred             ccceeEEEEEECCCCeeEEeeCccccccCCCCccEEEEhHHhccc----CCccCCCCCEEEEEEEEccccchhhcccccC
Confidence            5679999999999999999987       4679999999999864    6899999999999999999999999999999


Q ss_pred             CCCCCCCCCCC
Q psy9900         181 GIPVQGAPKVP  191 (191)
Q Consensus       181 ~~~~~~~~~~p  191 (191)
                      ++++++++++|
T Consensus        84 g~pv~GS~rrp   94 (148)
T 3ts2_A           84 GVFCIGSERRP   94 (148)
T ss_dssp             GCCCCCCTTSC
T ss_pred             Ccccccccccc
Confidence            99999998776

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

Probab=99.87  E-value=1.5e-22  Score=136.82  Aligned_cols=67  Identities=28%  Similarity=0.373  Sum_probs=62.2

Q ss_pred             eeeeEEEeecCCCceeEEeCCCCCcEEEeccchh-ccCcccccccCCCCCEEEEEEEEcCCCceeEEeecCCC
Q psy9900         110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIV-KMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNG  181 (191)
Q Consensus       110 ~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~-~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~~~  181 (191)
                      ++|+|||||..||||||+++++ +|||||+|+|. ..    +++.|.+|++|+|++.++++|++|++|+.++-
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-ESYFLHFSELLDKK----DEGKLVKGSMVHFDPTPTPKGLAAKAISLPLE   68 (74)
T ss_dssp             CEEEEEEEETTTTEEEEEETTS-CEECCCGGGSSCSG----GGTTCCTTSEEEEEEECTTTSCEEEEEECCSC
T ss_pred             CCEEEEEEECCCCEEEEecCCC-ceEEEEhhhcccCC----CCCCCCCCCEEEEEEEECCCCceeEEEEEcCc
Confidence            4799999999999999999997 99999999998 53    68999999999999999999999999998763

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

Probab=99.87  E-value=3.1e-22  Score=135.21  Aligned_cols=67  Identities=37%  Similarity=0.696  Sum_probs=62.1

Q ss_pred             eeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcC--CCceeEEeecCCC
Q psy9900         110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK--KDIEAINVTGPNG  181 (191)
Q Consensus       110 ~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~--kg~~A~~V~~~~~  181 (191)
                      .+|+|||||..||||||+++++ +|||||+|+|...    +++.|.+|+.|+|++.+++  +|++|++|++++.
T Consensus         2 ~~G~Vk~fn~~kGfGFI~~~~g-~dvFvH~s~i~~~----g~~~l~~G~~V~f~~~~~~~~kG~~A~~V~~~~~   70 (73)
T 3a0j_A            2 QKGRVKWFNAEKGYGFIEREGD-TDVFVHYTAINAK----GFRTLNEGDIVTFDVEPGRNGKGPQAVNVTVVEP   70 (73)
T ss_dssp             EEEEEEEEETTTTEEEEECTTS-CCEEEEGGGBCSS----SCSSCCTTCEEEEEEECCSCCSSSEEEEEEEEEC
T ss_pred             CCEEEEEEECCCCEEEEecCCC-CcEEEEhhhcccc----CCCCCCCCCEEEEEEEECCCCCCCEEEEEEeCCC
Confidence            5799999999999999999986 9999999999974    5889999999999999999  9999999998753

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

Probab=99.87  E-value=1.7e-22  Score=136.62  Aligned_cols=65  Identities=29%  Similarity=0.404  Sum_probs=61.0

Q ss_pred             cceEEEEeeCCCCeeEEEeCCCCccEEEEeeehe-ecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeecC
Q psy9900           9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIV-KMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGP   78 (191)
Q Consensus         9 ~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~-~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~~   78 (191)
                      ++|+|||||..||||||.++++ +|||||+|+|. ..    |++.|.+|++|+|++..+++|++|.+|..+
T Consensus         1 ~~G~Vkwfn~~KGfGFI~~~dG-~DvFvH~s~i~~~~----g~~~l~~G~~V~F~~~~g~kG~~A~~V~~~   66 (74)
T 2kcm_A            1 MKGKVVSYLAAKKYGFIQGDDG-ESYFLHFSELLDKK----DEGKLVKGSMVHFDPTPTPKGLAAKAISLP   66 (74)
T ss_dssp             CEEEEEEEETTTTEEEEEETTS-CEECCCGGGSSCSG----GGTTCCTTSEEEEEEECTTTSCEEEEEECC
T ss_pred             CCEEEEEEECCCCEEEEecCCC-ceEEEEhhhcccCC----CCCCCCCCCEEEEEEEECCCCceeEEEEEc
Confidence            4799999999999999999997 99999999999 65    789999999999999999999999999874

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

Probab=99.87  E-value=2.1e-22  Score=133.52  Aligned_cols=64  Identities=45%  Similarity=0.727  Sum_probs=60.0

Q ss_pred             cceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeec
Q psy9900           9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG   77 (191)
Q Consensus         9 ~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~   77 (191)
                      ++|+|||||..||||||.+++ ++|||||+|+|...    |++.|.+|++|+|++..+++|++|.+|..
T Consensus         1 m~G~Vk~fn~~kGfGFI~~~~-g~dvFvH~s~i~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~   64 (66)
T 1g6p_A            1 MRGKVKWFDSKKGYGFITKDE-GGDVFVHWSAIEME----GFKTLKEGQVVEFEIQEGKKGPQAAHVKV   64 (66)
T ss_dssp             CCEEEEEEETTTTEEEEEETT-SCBCBBCSSSSCCS----SCCCCCSSSEEEEEEECSSSCCEEEEEEE
T ss_pred             CcEEEEEEECCCCEEEEecCC-CceEEEEhHHcccc----CCCCCCCCCEEEEEEEECCCCCEEEEEEE
Confidence            579999999999999999997 49999999999976    78999999999999999999999999975

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

Probab=99.78  E-value=8.4e-24  Score=141.84  Aligned_cols=69  Identities=32%  Similarity=0.483  Sum_probs=64.0

Q ss_pred             ceeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeec
Q psy9900           5 EIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG   77 (191)
Q Consensus         5 ~~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~   77 (191)
                      |+.+++|+|||||..||||||.++++++|||||+|+|...    |++.|.+|++|+|++..+++|++|.+|..
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 MATNIVGKVKWYNSTKNFGFIEQDNGGKDVFVHKSAVDAA----GLHSLEEGQDVIFDLEEKQGKAYAVNLRI   69 (70)
Confidence            4567899999999999999999999889999999999976    68899999999999999999999999864

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

Probab=99.87  E-value=2.1e-22  Score=133.48  Aligned_cols=66  Identities=44%  Similarity=0.700  Sum_probs=60.9

Q ss_pred             eeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecCC
Q psy9900         110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPN  180 (191)
Q Consensus       110 ~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~~  180 (191)
                      ++|+|||||..||||||++++ ++|||||+|+|...    +++.|.+|++|+|++.++++|++|++|++++
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 MRGKVKWFDSKKGYGFITKDE-GGDVFVHWSAIEME----GFKTLKEGQVVEFEIQEGKKGPQAAHVKVVE   66 (66)
T ss_dssp             CCEEEEEEETTTTEEEEEETT-SCBCBBCSSSSCCS----SCCCCCSSSEEEEEEECSSSCCEEEEEEEEC
T ss_pred             CcEEEEEEECCCCEEEEecCC-CceEEEEhHHcccc----CCCCCCCCCEEEEEEEECCCCCEEEEEEECC
Confidence            479999999999999999997 59999999999974    5889999999999999999999999999753

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

Probab=99.86  E-value=9.9e-22  Score=132.90  Aligned_cols=67  Identities=18%  Similarity=0.272  Sum_probs=61.4

Q ss_pred             eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecCCC
Q psy9900         108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNG  181 (191)
Q Consensus       108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~~~  181 (191)
                      ++.+|+|||||..||||||+++++++| |||+|+|...    +  .|.+|++|+|++.++++|++|++|+.++.
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-YFHVIKVANP----D--LIKKDAAVTFEPTTNNKGLSAYAVKVVPL   67 (74)
T ss_dssp             CCEEEEEEEEETTTTEEEEEESSSCEE-EEEGGGBSSG----G--GCCTTCEEEEEEEECSSSEEEEEEEECCS
T ss_pred             CCcceEEEEEECCCCeEEEecCCCCce-EEEHhHcccC----C--CCCCCCEEEEEEEeCCCCceeEEEEeCCC
Confidence            357899999999999999999998788 9999999974    3  89999999999999999999999998764

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

Probab=99.86  E-value=1.1e-21  Score=132.62  Aligned_cols=65  Identities=18%  Similarity=0.309  Sum_probs=59.8

Q ss_pred             ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeecCC
Q psy9900           8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPN   79 (191)
Q Consensus         8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~~~   79 (191)
                      |.+|+|||||..||||||.++++++| |||+|+|...    +  .|.+|++|+|++..+++|++|.+|..+.
T Consensus         2 ~~~G~Vkwfn~~KGfGFI~~~dg~~d-FvH~s~i~~~----g--~l~~G~~V~F~~~~g~kG~~A~~V~~~~   66 (74)
T 2k5n_A            2 AMNGTITTWFKDKGFGFIKDENGDNR-YFHVIKVANP----D--LIKKDAAVTFEPTTNNKGLSAYAVKVVP   66 (74)
T ss_dssp             CEEEEEEEEETTTTEEEEEESSSCEE-EEEGGGBSSG----G--GCCTTCEEEEEEEECSSSEEEEEEEECC
T ss_pred             CcceEEEEEECCCCeEEEecCCCCce-EEEHhHcccC----C--CCCCCCEEEEEEEeCCCCceeEEEEeCC
Confidence            46899999999999999999998777 9999999975    4  8999999999999999999999998753

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

Probab=99.76  E-value=3.7e-23  Score=138.71  Aligned_cols=68  Identities=32%  Similarity=0.504  Sum_probs=62.8

Q ss_pred             ceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeec
Q psy9900         107 VHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG  178 (191)
Q Consensus       107 ~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~  178 (191)
                      .++++|+|||||..||||||+++++++|||||+|+|...    +++.|.+|+.|+|++.++++|++|++|++
T Consensus         2 ~~~~~G~Vk~fn~~kGfGFI~~~~gg~dvFvH~s~i~~~----g~~~l~~G~~V~f~~~~~~~g~~A~~V~~   69 (70)
T 2lss_A            2 ATNIVGKVKWYNSTKNFGFIEQDNGGKDVFVHKSAVDAA----GLHSLEEGQDVIFDLEEKQGKAYAVNLRI   69 (70)
Confidence            346889999999999999999999889999999999974    57899999999999999999999999974

>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=99.85  E-value=1.5e-21  Score=148.82  Aligned_cols=79  Identities=37%  Similarity=0.633  Sum_probs=71.6

Q ss_pred             eccceEEEEeeCCCCeeEEEeC-------CCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeecCC
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRL-------DNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPN   79 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~-------~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~~~   79 (191)
                      .+.+|+|||||..||||||.++       ++++|||||+|+|...    |++.|.+|++|+|++..+++|++|++|+.++
T Consensus         8 ~~~~G~Vkwfn~~kGfGFI~~~~~~g~p~~~g~DvFvH~s~i~~~----g~~~l~eG~~V~f~~~~g~kG~~A~~V~~pg   83 (148)
T 3ts2_A            8 LHGAGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHME----GFRSLKEGEAVEFTFKKSAKGLESIRVTGPG   83 (148)
T ss_dssp             EEEEEEEEEEETTTTEEEEEEEEETTEEEEEEEEEEEEGGGBCSS----SSCCCCTTCEEEEEEEEETTEEEEEEEESGG
T ss_pred             ccceeEEEEEECCCCeeEEeeCccccccCCCCccEEEEhHHhccc----CCccCCCCCEEEEEEEEccccchhhcccccC
Confidence            5678999999999999999987       4678999999999876    7899999999999999999999999999999


Q ss_pred             CCCccCCCCC
Q psy9900          80 GIPVQGAPKS   89 (191)
Q Consensus        80 ~~~~~~~~~~   89 (191)
                      +.+++++.+.
T Consensus        84 g~pv~GS~rr   93 (148)
T 3ts2_A           84 GVFCIGSERR   93 (148)
T ss_dssp             GCCCCCCTTS
T ss_pred             Cccccccccc
Confidence            9888776643

>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=99.84  E-value=8.6e-21  Score=132.63  Aligned_cols=69  Identities=22%  Similarity=0.393  Sum_probs=62.5

Q ss_pred             cceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC-C-ceeEEeecCCC
Q psy9900         106 AVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK-D-IEAINVTGPNG  181 (191)
Q Consensus       106 ~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k-g-~~A~~V~~~~~  181 (191)
                      ++++.+|+|||||  ||||||+++++++|||||+++|...     ++.|.+||+|+|++.++++ | ++|++|++++.
T Consensus        15 ~~~~~~G~Vkwf~--KGfGFI~~ddgg~DVFvH~s~i~~~-----~~~L~~G~~V~F~v~~~~k~Gk~~A~~V~~~~~   85 (89)
T 1wfq_A           15 AALRETGVIEKLL--TSYGFIQCSERQARLFFHCSQYNGN-----LQDLKVGDDVEFEVSSDRRTGKPIAVKLVKISG   85 (89)
T ss_dssp             CCCEEEEEEEEEC--SSEEEEEETTTTEEEEEETTTCSSC-----TTTCCTTCCEEEEEEECSSSCCEEEEEEEESSC
T ss_pred             cccccceEEEEEe--CCeeEEecCCCCccEEEEhHHhhCc-----cCCCCCCCEEEEEEEECCCCCCcEEEEEEECCc
Confidence            3467899999996  9999999999889999999999863     5899999999999999998 7 89999998864

>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=99.83  E-value=7.9e-21  Score=132.83  Aligned_cols=68  Identities=19%  Similarity=0.351  Sum_probs=61.4

Q ss_pred             ceeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC-C-ceeeEeecCC
Q psy9900           5 EIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK-D-IEAINVTGPN   79 (191)
Q Consensus         5 ~~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~-g-~~A~~v~~~~   79 (191)
                      +..+.+|+|||||  ||||||.++++++|||||+++|...     ++.|.+||+|+|++..+++ | ++|.+|+.++
T Consensus        15 ~~~~~~G~Vkwf~--KGfGFI~~ddgg~DVFvH~s~i~~~-----~~~L~~G~~V~F~v~~~~k~Gk~~A~~V~~~~   84 (89)
T 1wfq_A           15 AALRETGVIEKLL--TSYGFIQCSERQARLFFHCSQYNGN-----LQDLKVGDDVEFEVSSDRRTGKPIAVKLVKIS   84 (89)
T ss_dssp             CCCEEEEEEEEEC--SSEEEEEETTTTEEEEEETTTCSSC-----TTTCCTTCCEEEEEEECSSSCCEEEEEEEESS
T ss_pred             cccccceEEEEEe--CCeeEEecCCCCccEEEEhHHhhCc-----cCCCCCCCEEEEEEEECCCCCCcEEEEEEECC
Confidence            3467899999996  9999999999889999999999863     5899999999999999998 7 8999999864

>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=99.82  E-value=1.1e-20  Score=131.87  Aligned_cols=67  Identities=30%  Similarity=0.560  Sum_probs=61.7

Q ss_pred             eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC-ceeEEeecCCC
Q psy9900         108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD-IEAINVTGPNG  181 (191)
Q Consensus       108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg-~~A~~V~~~~~  181 (191)
                      ++.+|+|+||+  ||||||+++++++|||||+++|...     ++.|.+||+|+|++.++++| ++|++|+.++.
T Consensus        17 ~~~~G~Vk~f~--kGfGFI~~ddgg~DvFvH~S~i~~~-----~~~L~~G~~V~F~~~~g~~Gk~~A~~V~~~~~   84 (88)
T 2yty_A           17 KRLLGYVATLK--DNFGFIETANHDKEIFFHYSEFSGD-----VDSLELGDMVEYSLSKGKGNKVSAEKVNKTSG   84 (88)
T ss_dssp             CCEEEEEEEEC--SSEEEEECSSSSCEEEEETTTCCSC-----TTTCCTTCEEEECCCCCSCSCCBCCSCEECCC
T ss_pred             CceeEEEEEEE--CCccEEecCCCCceEEEEEhhhccc-----cCcCCCCCEEEEEEEECCCCCeEeEEEEECCC
Confidence            56789999997  8999999999889999999999964     68999999999999999999 89999998864

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

Probab=99.82  E-value=5.1e-20  Score=139.43  Aligned_cols=72  Identities=25%  Similarity=0.371  Sum_probs=63.9

Q ss_pred             ceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEE---cCCCceeEEeecCCCCC
Q psy9900         107 VHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGV---GKKDIEAINVTGPNGIP  183 (191)
Q Consensus       107 ~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~---~~kg~~A~~V~~~~~~~  183 (191)
                      .++.+|+|||||..||||||+++++++|||||+++|...      ..|.+||+|+|++..   +.+|++|++|++++.++
T Consensus        60 g~m~~GtVKwFn~~KGfGFI~~ddGg~DVFVH~Sai~~~------~~L~eGq~V~Fev~~~~~~~~g~qA~nV~~~~~~p  133 (147)
T 3aqq_A           60 GPVYKGVCKCFCRSKGHGFITPADGGPDIFLHISDVEGE------YVPVEGDEVTYKMCSIPPKNEKLQAVEVVITHLAP  133 (147)
T ss_dssp             SCCEEEEEEEEETTTTEEEEEESSSCSCEEEEGGGEESS------BCCCTTCEEEEEEEEC--CCSCEEEEEEEEEECCS
T ss_pred             CCccceEEEEEeCCCCeEEeccCCCCccEEEEeeeecCC------CcCCCCCEEEEEEEeccCCCCCceEEEEEeCCCCC
Confidence            356899999999999999999999889999999999853      599999999999997   45679999999998766


Q ss_pred             C
Q psy9900         184 V  184 (191)
Q Consensus       184 ~  184 (191)
                      -
T Consensus       134 ~  134 (147)
T 3aqq_A          134 G  134 (147)
T ss_dssp             S
T ss_pred             C
Confidence            3

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

Probab=99.80  E-value=9.5e-20  Score=137.93  Aligned_cols=70  Identities=26%  Similarity=0.397  Sum_probs=61.5

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEc---CCCceeeEeecCCCCC
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG---KKDIEAINVTGPNGIP   82 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~---~~g~~A~~v~~~~~~~   82 (191)
                      .+.+|+|||||..||||||.++++++|||||+++|...      ..|.+||+|+|++..+   .+|++|.+|+.++..|
T Consensus        61 ~m~~GtVKwFn~~KGfGFI~~ddGg~DVFVH~Sai~~~------~~L~eGq~V~Fev~~~~~~~~g~qA~nV~~~~~~p  133 (147)
T 3aqq_A           61 PVYKGVCKCFCRSKGHGFITPADGGPDIFLHISDVEGE------YVPVEGDEVTYKMCSIPPKNEKLQAVEVVITHLAP  133 (147)
T ss_dssp             CCEEEEEEEEETTTTEEEEEESSSCSCEEEEGGGEESS------BCCCTTCEEEEEEEEC--CCSCEEEEEEEEEECCS
T ss_pred             CccceEEEEEeCCCCeEEeccCCCCccEEEEeeeecCC------CcCCCCCEEEEEEEeccCCCCCceEEEEEeCCCCC
Confidence            46789999999999999999999889999999999843      5999999999999874   4579999999876544

>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=99.80  E-value=9.4e-20  Score=129.37  Aligned_cols=69  Identities=29%  Similarity=0.331  Sum_probs=62.9

Q ss_pred             eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecCCCCC
Q psy9900         108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNGIP  183 (191)
Q Consensus       108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~~~~~  183 (191)
                      .+.+|+||||  .||||||+++++++|||||+++|...     ++.|.+||+|+|++..+++|++|++|++++...
T Consensus        17 ~~~~G~Vkwf--~KGfGFI~~ddg~~DvFvH~s~i~~~-----~~~L~~G~~V~F~v~~~~~g~~A~~V~~~~~~~   85 (97)
T 2ytx_A           17 ARCQGVVCAM--KEAFGFIERGDVVKEIFFHYSEFKGD-----LETLQPGDDVEFTIKDRNGKEVATDVRLLPQGT   85 (97)
T ss_dssp             CCEEEEECCC--CSSEEEEECSSSCCCEEEETTTCCSC-----TTSCCSCCEEEEEECCCSSSCBEEEEEECCCSS
T ss_pred             cceeEEEEEE--eCCceEEecCCCCceEEEEehHhccc-----cCCCCCCCEEEEEEEcCCCCcEEEEEEECCCCc
Confidence            4678999999  89999999999889999999999964     589999999999999888889999999987654

>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=99.80  E-value=4.9e-20  Score=128.60  Aligned_cols=67  Identities=28%  Similarity=0.518  Sum_probs=60.9

Q ss_pred             eeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCC-ceeeEeecCC
Q psy9900           6 IHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD-IEAINVTGPN   79 (191)
Q Consensus         6 ~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g-~~A~~v~~~~   79 (191)
                      ..+.+|+|||||  ||||||.++++++|||||+|+|...     ++.|.+||+|+|++..+++| ++|.+|..+.
T Consensus        16 ~~~~~G~Vk~f~--kGfGFI~~ddgg~DvFvH~S~i~~~-----~~~L~~G~~V~F~~~~g~~Gk~~A~~V~~~~   83 (88)
T 2yty_A           16 SKRLLGYVATLK--DNFGFIETANHDKEIFFHYSEFSGD-----VDSLELGDMVEYSLSKGKGNKVSAEKVNKTS   83 (88)
T ss_dssp             CCCEEEEEEEEC--SSEEEEECSSSSCEEEEETTTCCSC-----TTTCCTTCEEEECCCCCSCSCCBCCSCEECC
T ss_pred             CCceeEEEEEEE--CCccEEecCCCCceEEEEEhhhccc-----cCcCCCCCEEEEEEEECCCCCeEeEEEEECC
Confidence            467899999997  9999999999889999999999864     58999999999999999999 7999998753

>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=99.79  E-value=4.7e-20  Score=128.79  Aligned_cols=67  Identities=24%  Similarity=0.340  Sum_probs=60.4

Q ss_pred             eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC---CceeEEeecCCCC
Q psy9900         108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK---DIEAINVTGPNGI  182 (191)
Q Consensus       108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k---g~~A~~V~~~~~~  182 (191)
                      ++.+|+|+||+  ||||||+++++++|||||+++|...      ..|++||+|+|++.++++   +++|++|++++..
T Consensus         7 ~r~~G~Vk~f~--KGfGFI~~~~gg~DvFvH~s~i~~~------~~L~~G~~V~F~v~~g~kg~G~~~A~~V~~~~~~   76 (89)
T 1x65_A            7 GREMGVIAAMR--DGFGFIKCVDRDVRMFFHFSEILDG------NQLHIADEVEFTVVPDMLSAQRNHAIRIKKLPKG   76 (89)
T ss_dssp             CCEEEEEEECC--TTBCEEEESSSSSCCCCBTTGGGGS------CCCCTTCCEEECCBCCSSSCCCCBCCSCEECCBT
T ss_pred             cceeEEEEEEe--CCcceeecCCCCccEEEEhhhccCC------CCCCCCCEEEEEEEeCCCcCCCceeeEEEECCCC
Confidence            46899999995  9999999999889999999999862      699999999999999987   3999999998753

>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=99.77  E-value=6.3e-19  Score=125.11  Aligned_cols=68  Identities=29%  Similarity=0.348  Sum_probs=61.3

Q ss_pred             eeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeecCCC
Q psy9900           6 IHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNG   80 (191)
Q Consensus         6 ~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~~~~   80 (191)
                      ..+.+|+||||  .||||||.++++++|||||+++|...     ++.|.+||+|+|++..+++|++|.+|..++.
T Consensus        16 ~~~~~G~Vkwf--~KGfGFI~~ddg~~DvFvH~s~i~~~-----~~~L~~G~~V~F~v~~~~~g~~A~~V~~~~~   83 (97)
T 2ytx_A           16 QARCQGVVCAM--KEAFGFIERGDVVKEIFFHYSEFKGD-----LETLQPGDDVEFTIKDRNGKEVATDVRLLPQ   83 (97)
T ss_dssp             CCCEEEEECCC--CSSEEEEECSSSCCCEEEETTTCCSC-----TTSCCSCCEEEEEECCCSSSCBEEEEEECCC
T ss_pred             CcceeEEEEEE--eCCceEEecCCCCceEEEEehHhccc-----cCCCCCCCEEEEEEEcCCCCcEEEEEEECCC
Confidence            46789999999  99999999999889999999999864     5899999999999988877899999998654

>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=99.75  E-value=2.4e-19  Score=125.18  Aligned_cols=66  Identities=24%  Similarity=0.356  Sum_probs=58.9

Q ss_pred             eeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC---CceeeEeecCC
Q psy9900           6 IHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK---DIEAINVTGPN   79 (191)
Q Consensus         6 ~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~---g~~A~~v~~~~   79 (191)
                      ..|.+|+||||+  ||||||.++++++|||||+|+|..     + ..|.+||+|+|++..+++   +++|.+|..+.
T Consensus         6 ~~r~~G~Vk~f~--KGfGFI~~~~gg~DvFvH~s~i~~-----~-~~L~~G~~V~F~v~~g~kg~G~~~A~~V~~~~   74 (89)
T 1x65_A            6 SGREMGVIAAMR--DGFGFIKCVDRDVRMFFHFSEILD-----G-NQLHIADEVEFTVVPDMLSAQRNHAIRIKKLP   74 (89)
T ss_dssp             CCCEEEEEEECC--TTBCEEEESSSSSCCCCBTTGGGG-----S-CCCCTTCCEEECCBCCSSSCCCCBCCSCEECC
T ss_pred             CcceeEEEEEEe--CCcceeecCCCCccEEEEhhhccC-----C-CCCCCCCEEEEEEEeCCCcCCCceeeEEEECC
Confidence            457899999996  999999999988999999999985     3 799999999999999987   38999998754

>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=99.73  E-value=2.4e-18  Score=117.69  Aligned_cols=65  Identities=25%  Similarity=0.305  Sum_probs=59.1

Q ss_pred             eeeeeeEEEeecCCCceeEEeCCC-CCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC-Cc-eeEEeecCC
Q psy9900         108 HTVRGIVKFYDSKRGFGFITRLDN-KEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK-DI-EAINVTGPN  180 (191)
Q Consensus       108 ~~~~G~Vk~~~~~kgfGFI~~~d~-~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k-g~-~A~~V~~~~  180 (191)
                      ++.+|+|+||  .||||||+++++ ++|||||+++|. .    + ..|.+||+|+|++.++++ |+ +|++|+.++
T Consensus         7 ~~~~G~V~~~--~KGfGFI~~ddg~g~DvFvH~s~i~-~----g-~~l~~G~~V~F~v~~~~k~G~~~A~~V~~~~   74 (79)
T 2ytv_A            7 GLRRATVECV--KDQFGFINYEVGDSKKLFFHVKEVQ-D----G-IELQAGDEVEFSVILNQRTGKCSACNVWRVS   74 (79)
T ss_dssp             SBCCEEEEEC--CSSEEEESCCCSSSSSEEEETTTCC-S----S-CCCCTTCEEECBCEECSSSCCEECCSCEECS
T ss_pred             CcccEEEEEe--cccceeEeCCCCCCCcEEEEhHHcC-C----C-CcCCCCCEEEEEEEECCCCCCceeEEEEECC
Confidence            5678999999  699999999987 699999999999 3    3 799999999999999998 88 999999885

>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=99.73  E-value=3.5e-18  Score=116.84  Aligned_cols=65  Identities=25%  Similarity=0.305  Sum_probs=58.8

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCC-CccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC-Cc-eeeEeecCC
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDN-KEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK-DI-EAINVTGPN   79 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~-~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~-g~-~A~~v~~~~   79 (191)
                      .+.+|+|+||  .||||||.++++ ++|||||+++|. .    + ..|.+||+|+|++..+++ |+ +|++|..+.
T Consensus         7 ~~~~G~V~~~--~KGfGFI~~ddg~g~DvFvH~s~i~-~----g-~~l~~G~~V~F~v~~~~k~G~~~A~~V~~~~   74 (79)
T 2ytv_A            7 GLRRATVECV--KDQFGFINYEVGDSKKLFFHVKEVQ-D----G-IELQAGDEVEFSVILNQRTGKCSACNVWRVS   74 (79)
T ss_dssp             SBCCEEEEEC--CSSEEEESCCCSSSSSEEEETTTCC-S----S-CCCCTTCEEECBCEECSSSCCEECCSCEECS
T ss_pred             CcccEEEEEe--cccceeEeCCCCCCCcEEEEhHHcC-C----C-CcCCCCCEEEEEEEECCCCCCceeEEEEECC
Confidence            5689999999  699999999987 599999999999 4    6 899999999999999988 88 999998753

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

Probab=99.62  E-value=8.7e-16  Score=109.72  Aligned_cols=64  Identities=31%  Similarity=0.463  Sum_probs=53.5

Q ss_pred             eeceeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCc--ccCCCCCEEEEEEEEcCC-Cc
Q psy9900           3 KFEIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFF--QSLGLGEIVDFNIGVGKK-DI   70 (191)
Q Consensus         3 ~~~~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~--~~l~~Gd~V~f~~~~~~~-g~   70 (191)
                      +.+..+.+|+|||||..||||||.++++++|+|||+|+|...    ++  ..|.+|+.|+|++..... |+
T Consensus        11 ~~~~~~~~G~Vk~fn~~kGfGFI~~~~gg~dvfvH~s~l~~~----~~~~~~l~~Ge~V~g~V~~i~~fG~   77 (101)
T 2bh8_A           11 RLQSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAGSSG----AAVRGNPQQGDRVEGKIKSITDFGI   77 (101)
T ss_dssp             -----CEEEEEEEEEGGGTEEEEEESSSSCEEEEECCCSCSS----SCCCCCCCTTCEEEEEEEECCSEEE
T ss_pred             ccccccceeEEEEEECCCCCEEEEeCCCCcEEEEEEEEEecC----CccccCCCCCCEEEEEEEEeCCcEE
Confidence            345677899999999999999999999889999999999976    67  899999999999987654 54

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

Probab=99.52  E-value=2.7e-14  Score=101.94  Aligned_cols=60  Identities=32%  Similarity=0.440  Sum_probs=52.7

Q ss_pred             ceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCccccc--ccCCCCCEEEEEEEEcCC-C
Q psy9900         107 VHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFF--QSLGLGEIVDFNIGVGKK-D  170 (191)
Q Consensus       107 ~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~--~~l~~G~~V~f~i~~~~k-g  170 (191)
                      ..+.+|+|||||..||||||+++++++|+|||+++|...    ++  ..|.+|+.|+|.+..... |
T Consensus        14 ~~~~~G~Vk~fn~~kGfGFI~~~~gg~dvfvH~s~l~~~----~~~~~~l~~Ge~V~g~V~~i~~fG   76 (101)
T 2bh8_A           14 SGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAGSSG----AAVRGNPQQGDRVEGKIKSITDFG   76 (101)
T ss_dssp             --CEEEEEEEEEGGGTEEEEEESSSSCEEEEECCCSCSS----SCCCCCCCTTCEEEEEEEECCSEE
T ss_pred             cccceeEEEEEECCCCCEEEEeCCCCcEEEEEEEEEecC----CccccCCCCCCEEEEEEEEeCCcE
Confidence            356789999999999999999999889999999999864    46  799999999999998664 5

>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=98.43  E-value=1.2e-06  Score=80.49  Aligned_cols=128  Identities=15%  Similarity=0.052  Sum_probs=88.5

Q ss_pred             ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeecCCCCCccCCC
Q psy9900           8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNGIPVQGAP   87 (191)
Q Consensus         8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~~~~~~~~~~~   87 (191)
                      ...|+|+.  +.|||||+.+++ ++|||++...+..++         .||+|.+.+......+++.-+.           
T Consensus        21 ~~~G~~~~--~~~GfgF~~~d~-~~difi~~~~~~~a~---------~GD~V~v~i~~~~~~~eg~v~~-----------   77 (644)
T 2id0_A           21 RAEGVVKA--TEKGFGFLEVDA-QKSYFIPPPQMKKVM---------HGDRIIAVIHSEKERESAEPEE-----------   77 (644)
T ss_dssp             EEEEEEEC--CSSSCEEEECSS-SCEEEECHHHHTTSC---------TTCEEEEEEECCSSSCEEEEEE-----------
T ss_pred             eEEEEEEE--ecCCcEEEEECC-CCCEEECHHHHhcCC---------CCCEEEEEEecCCCCeEEEEEE-----------
Confidence            46788885  489999999986 689999999999886         9999999997642224443333           


Q ss_pred             CCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCC-CcEEEeccchhccCcccccccCCCCCEEEEEEEE
Q psy9900          88 KSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNK-EDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGV  166 (191)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~-~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~  166 (191)
                                       ++++..+-.|..|...++++|+.|+|.. .. ++...+....     ...++.|+.|..+|..
T Consensus        78 -----------------iler~~~~~vg~~~~~~~~~~v~pdd~~~~~-~i~~~~~~~~-----~~~~~~g~~v~v~i~~  134 (644)
T 2id0_A           78 -----------------LVEPFLTRFVGKVQGKNDRLAIVPDHPLLKD-AIPCRAARGL-----NHEFKEGDWAVAEMRR  134 (644)
T ss_dssp             -----------------EEECSCSEEEEEEEEETTEEEEEESSTTCCS-CEECCBCSSC-----CCCCCSSCEEEEEEEE
T ss_pred             -----------------EEecCCCEEEEEEEEeCCEEEEEECCCCccc-cccccccccc-----cccCCCCCEEEEEEec
Confidence                             2333344455555567889999998854 23 6655544322     1355899999999998


Q ss_pred             cCC---Cc-eeEEeecCCC
Q psy9900         167 GKK---DI-EAINVTGPNG  181 (191)
Q Consensus       167 ~~k---g~-~A~~V~~~~~  181 (191)
                      -+.   .+ .+.-|+.++.
T Consensus       135 ~p~~~~~p~~g~i~~~LG~  153 (644)
T 2id0_A          135 HPLKGDRSFYAELTQYITF  153 (644)
T ss_dssp             CGGGTCSSCEEEEEEEEEC
T ss_pred             CcCCCCCCceEEEEEEeCC
Confidence            542   25 6776666654

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

Probab=97.85  E-value=0.00084  Score=55.69  Aligned_cols=126  Identities=13%  Similarity=0.054  Sum_probs=87.6

Q ss_pred             CceeceeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCC-ceeeEeecCC
Q psy9900           1 MTKFEIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD-IEAINVTGPN   79 (191)
Q Consensus         1 ~~~~~~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g-~~A~~v~~~~   79 (191)
                      |........+|+|+...   -||+....+ +.++|+|.+.+..          ..||.|++.+-.+..+ +.|.. ..  
T Consensus         2 ~~~~~G~~v~g~V~~~~---~~G~fv~~~-g~egllp~se~~~----------~vGdevev~v~~d~~~r~iat~-~~--   64 (285)
T 3go5_A            2 MNTNLASFIVGLIIDEN---DRFYFVQKD-GQTYALAKEEGQH----------TVGDTVKGFAYTDMKQKLRLTT-LE--   64 (285)
T ss_dssp             CCTTTTEEEEEEEEEEC---SSEEEEEET-TEEEEEEGGGCCC----------CTTSEEEEEEEECTTSCEEEEC-SC--
T ss_pred             ccccCCCEEEEEEEEEE---CCEEEEEcC-CeEEEEEHHHCcc----------ccCCEEEEEEEECCCCCEEEec-cc--
Confidence            45556677899999885   367666544 6899999999842          6999999998776655 33321 00  


Q ss_pred             CCCccCCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCC-CCcEEEeccchhccCcccccccCCCCC
Q psy9900          80 GIPVQGAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDN-KEDIFVHKSSIVKMNPKKFFQSLGLGE  158 (191)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~-~~dvF~h~s~~~~~~~~~~~~~l~~G~  158 (191)
                        |                    .........|+|+..  .+.||....-.. +.|.|+|+|++...    ....++.||
T Consensus        65 --p--------------------~~~~G~~~~g~V~~v--~~~~GaFVdiG~~~~d~lvp~sel~~~----~~~~~~~Gd  116 (285)
T 3go5_A           65 --V--------------------TATQDQFGWGRVTEV--RKDLGVFVDTGLPDKEIVVSLDILPEL----KELWPKKGD  116 (285)
T ss_dssp             --C--------------------CSCSSSCEEEEEEEE--ETTTEEEEECSCTTCCEEEEGGGSCSS----GGGSCCTTC
T ss_pred             --c--------------------cccCCCEEEEEEEEE--ccCceEEEEECCCCcEEEEEHHHCCcc----cccccCCCC
Confidence              0                    022345678999887  345786655554 58999999998542    124679999


Q ss_pred             EEEEEEEEcCCCc
Q psy9900         159 IVDFNIGVGKKDI  171 (191)
Q Consensus       159 ~V~f~i~~~~kg~  171 (191)
                      .|.+.+..++++.
T Consensus       117 ~v~v~l~iD~~~R  129 (285)
T 3go5_A          117 QLYIRLEVDKKDR  129 (285)
T ss_dssp             EEEEEEEECTTSC
T ss_pred             EEEEEEEECCCCc
Confidence            9998888777663

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

Probab=97.63  E-value=0.0012  Score=54.70  Aligned_cols=143  Identities=14%  Similarity=0.022  Sum_probs=91.6

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCC-CccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeecC-CCCCcc
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDN-KEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGP-NGIPVQ   84 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~-~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~~-~~~~~~   84 (191)
                      ....|+|++-+  +.||....-+. +.|.|+|+|++....    ...+..||.|.+.+..++++.-+...... ...|..
T Consensus        71 ~~~~g~V~~v~--~~~GaFVdiG~~~~d~lvp~sel~~~~----~~~~~~Gd~v~v~l~iD~~~Ri~ls~k~~~~~~~~~  144 (285)
T 3go5_A           71 QFGWGRVTEVR--KDLGVFVDTGLPDKEIVVSLDILPELK----ELWPKKGDQLYIRLEVDKKDRIWGLLAYQEDFQRLA  144 (285)
T ss_dssp             SCEEEEEEEEE--TTTEEEEECSCTTCCEEEEGGGSCSSG----GGSCCTTCEEEEEEEECTTSCEEEEECCHHHHHHHC
T ss_pred             CEEEEEEEEEc--cCceEEEEECCCCcEEEEEHHHCCccc----ccccCCCCEEEEEEEECCCCcEEEEehhhhhcchhh
Confidence            44678898874  45776555554 579999999986431    24679999999888777655323222100 000000


Q ss_pred             CCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEE-eCCCCCcEEEeccchhccCcccccccCCCCCEEEEE
Q psy9900          85 GAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFIT-RLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFN  163 (191)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~-~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~  163 (191)
                        .            ............|+|....+   ||+.. ..+.+-+-|+|.|++.        ..|+.||.|+..
T Consensus       145 --~------------~~~~~~~G~~V~g~V~~i~~---~G~fV~~i~~g~~Glih~SEl~--------~~l~~Gd~v~~~  199 (285)
T 3go5_A          145 --R------------PAYNNMQNQNWPAIVYRLKL---SGTFVYLPENNMLGFIHPSERY--------AEPRLGQVLDAR  199 (285)
T ss_dssp             --C------------CCCSCCTTCEEEEEEEEEET---TEEEEEETTTTEEEEECGGGCS--------SCCCTTCEEEEE
T ss_pred             --h------------hhhhCCCCCEEEEEEEEEeC---CcEEEEEeCCCeEEEEEHHHcc--------ccCCCCCEEEEE
Confidence              0            00112334578999988743   67655 6666889999999997        478999999999


Q ss_pred             EEEc-C-CCceeEEeecCC
Q psy9900         164 IGVG-K-KDIEAINVTGPN  180 (191)
Q Consensus       164 i~~~-~-kg~~A~~V~~~~  180 (191)
                      |..- + +|.-...++.+.
T Consensus       200 V~~id~~d~kI~LSlk~~~  218 (285)
T 3go5_A          200 VIGFREVDRTLNLSLKPRS  218 (285)
T ss_dssp             EEEEETTTTEEEEECSCCC
T ss_pred             EEEEECCCCeEEEEeChhh
Confidence            8873 3 454445554443

>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=97.45  E-value=0.00036  Score=51.39  Aligned_cols=69  Identities=26%  Similarity=0.407  Sum_probs=52.3

Q ss_pred             eeeeEEEeecCCCceeEEeCC-----CCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC---ceeEEeecCCC
Q psy9900         110 VRGIVKFYDSKRGFGFITRLD-----NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD---IEAINVTGPNG  181 (191)
Q Consensus       110 ~~G~Vk~~~~~kgfGFI~~~d-----~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg---~~A~~V~~~~~  181 (191)
                      ..|++..-  .+||||+.+++     +..||||+.+.+..       -.|..||.|+-.+...+.|   ..-+.|.-++|
T Consensus        51 ~~Gvlei~--~dG~GFlr~~~~~y~~~~~DiyVs~~~irr-------f~lr~GD~V~g~vr~~~~~ek~~~l~~v~~vng  121 (130)
T 1a62_A           51 GDGVLEIL--QDGFGFLRSADSSYLAGPDDIYVSPSQIRR-------FNLRTGDTISGKIRPPKEGERYFALLKVNEVNF  121 (130)
T ss_dssp             EEEEEEEC--TTSCEEEECGGGTTCCCTTCEEECHHHHHH-------TTCCTTCEEEEEEECCCTTCCSEEEEEEEEETT
T ss_pred             EEEEEEEc--CCCeEEEecCCcCCCCCCCCEEECHHHHhH-------hCCCCCCEEEEEEeCCCCCCcccceeEEEeECC
Confidence            56777654  57999999984     56899999999985       4789999999999876665   34457777777


Q ss_pred             CCCCCC
Q psy9900         182 IPVQGA  187 (191)
Q Consensus       182 ~~~~~~  187 (191)
                      .+...+
T Consensus       122 ~~pe~~  127 (130)
T 1a62_A          122 DKPENA  127 (130)
T ss_dssp             BCCC--
T ss_pred             CCHHHh
Confidence            665443

>2vnu_D Exosome complex exonuclease RRP44; hydrolase-RNA complex, RNA degradation, RNA-binding, RNA Pro; HET: 1PE; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16

Probab=97.38  E-value=0.0011  Score=61.79  Aligned_cols=152  Identities=11%  Similarity=0.039  Sum_probs=87.7

Q ss_pred             ccceEEEEeeCCCCe--eEEEeCCCCccEEEEe-eeheecCCCCCcccCCCCCEEEEEEEEcCCCce-eeEeec------
Q psy9900           8 TVRGIVKFYDSKRGF--GFITRLDNKEDIFVHK-SSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIE-AINVTG------   77 (191)
Q Consensus         8 ~~~G~vk~~~~~kGf--GFI~~~~~~~dvFvh~-s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~-A~~v~~------   77 (191)
                      ..+|++.-  +.+||  ||+..++.++|||+.. .++..++         +||.|.+++........ ...+..      
T Consensus        32 l~~G~l~~--~~~~~~~gfv~~~~~~~di~I~~~~~~n~A~---------~GD~V~V~i~~~~~~~~~~~~~~~~~~~~~  100 (760)
T 2vnu_D           32 LYQGNIQI--SEYNFLEGSVSLPRFSKPVLIVGQKNLNRAF---------NGDQVIVELLPQSEWKAPSSIVLDSEHFDV  100 (760)
T ss_dssp             EEEEEEEE--CSSBTTEEEECCSSSSSCEEEESHHHHTTCC---------TTCEEEEEECCGGGCBCCCSSCBCTTTCC-
T ss_pred             EEEEEEEE--ecCCCccEEEEcCCCCCCEEEcChhhhcccc---------CCCEEEEEEecccccccccccccccccccc
Confidence            35787775  47899  9999998789999998 8898886         99999999964321000 000000      


Q ss_pred             ---CCC-----------------CCccCCCCCCCc------cccccccCCcccccceeeeeeEEEeecCC--------Cc
Q psy9900          78 ---PNG-----------------IPVQGAPKSSSE------TVSGTYRNDSFFPAVHTVRGIVKFYDSKR--------GF  123 (191)
Q Consensus        78 ---~~~-----------------~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~G~Vk~~~~~k--------gf  123 (191)
                         ..+                 .+.........+      .....+......++++..+-.|..+....        .+
T Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eG~Vv~IleR~~~~~vG~l~~~~~~~~~~~~~~  180 (760)
T 2vnu_D          101 NDNPDIEAGDDDDNNESSSNTTVISDKQRRLLAKDAMIAQRSKKIQPTAKVVYIQRRSWRQYVGQLAPSSVDPQSSSTQN  180 (760)
T ss_dssp             --------------------------------------------CBCBEEEEEEEECCCCEEEEEECGGGCCTTCCSCEE
T ss_pred             cccccccccccccccccccccccccchhhhhhhhhhhhccccCCCCceEEEEEEEEECCceEEEEEEEccCccccCccce
Confidence               000                 000000000000      00011223334455555555677775443        26


Q ss_pred             eeEEeCCCC-CcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC---ceeEEeecCC
Q psy9900         124 GFITRLDNK-EDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD---IEAINVTGPN  180 (191)
Q Consensus       124 GFI~~~d~~-~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg---~~A~~V~~~~  180 (191)
                      +|+.|+|.. ..|++.......          ..|+.|.++|..=+.+   +.+.-|+.++
T Consensus       181 ~~~~P~d~ri~~i~i~~~~~~~----------~~g~~vvv~i~~~p~~~~~p~G~i~~~LG  231 (760)
T 2vnu_D          181 VFVILMDKCLPKVRIRTRRAAE----------LLDKRIVISIDSWPTTHKYPLGHFVRDLG  231 (760)
T ss_dssp             EEEEESSTTSCCEEEEETTGGG----------GTTEEEEEEEEECCTTCSSCEEEEEEEEE
T ss_pred             EEEEECCCCCccEEEecccccc----------cCCCEEEEEEeeccCCCCCCcEEEEEEeC
Confidence            899999865 578887665432          3599999999885533   6666666654

>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=97.05  E-value=0.00079  Score=49.53  Aligned_cols=64  Identities=27%  Similarity=0.419  Sum_probs=46.4

Q ss_pred             cceEEEEeeCCCCeeEEEeCC-----CCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCC--c-eeeEeecCCC
Q psy9900           9 VRGIVKFYDSKRGFGFITRLD-----NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD--I-EAINVTGPNG   80 (191)
Q Consensus         9 ~~G~vk~~~~~kGfGFI~~~~-----~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g--~-~A~~v~~~~~   80 (191)
                      ..|++.--  .+||||+.+++     +..||||+.+.+..       -.|..||.|...+.....+  . .-..|..+++
T Consensus        51 ~~Gvlei~--~dG~GFlr~~~~~y~~~~~DiyVs~~~irr-------f~lr~GD~V~g~vr~~~~~ek~~~l~~v~~vng  121 (130)
T 1a62_A           51 GDGVLEIL--QDGFGFLRSADSSYLAGPDDIYVSPSQIRR-------FNLRTGDTISGKIRPPKEGERYFALLKVNEVNF  121 (130)
T ss_dssp             EEEEEEEC--TTSCEEEECGGGTTCCCTTCEEECHHHHHH-------TTCCTTCEEEEEEECCCTTCCSEEEEEEEEETT
T ss_pred             EEEEEEEc--CCCeEEEecCCcCCCCCCCCEEECHHHHhH-------hCCCCCCEEEEEEeCCCCCCcccceeEEEeECC
Confidence            46666643  67999999883     57899999999985       3678999999999765544  2 2345555544


Q ss_pred             C
Q psy9900          81 I   81 (191)
Q Consensus        81 ~   81 (191)
                      .
T Consensus       122 ~  122 (130)
T 1a62_A          122 D  122 (130)
T ss_dssp             B
T ss_pred             C
Confidence            4

>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae}

Probab=96.76  E-value=0.0082  Score=57.50  Aligned_cols=152  Identities=11%  Similarity=0.032  Sum_probs=86.6

Q ss_pred             ccceEEEEeeCCCCe--eEEEeCCCCccEEEEe-eeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeecC------
Q psy9900           8 TVRGIVKFYDSKRGF--GFITRLDNKEDIFVHK-SSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGP------   78 (191)
Q Consensus         8 ~~~G~vk~~~~~kGf--GFI~~~~~~~dvFvh~-s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~~------   78 (191)
                      -.+|++.-  +.+||  ||+.+++.++|||+.. .++..++         +||.|.+++...............      
T Consensus       249 l~~G~l~v--~~~~~~egfV~~~~~~~DI~I~~~~~~n~A~---------~GD~V~V~i~~~~~~~~~~~~~~~~~~~~~  317 (977)
T 2wp8_J          249 LYQGNIQI--SEYNFLEGSVSLPRFSKPVLIVGQKNLNRAF---------NGDQVIVELLPQSEWKAPSSIVLDSEHFDV  317 (977)
T ss_dssp             SEEEEEEE--CSSBTTEEEECCTTCSSCEEEESHHHHTTCC---------TTCEEEEEECCGGGCBCCCSCCBCGGGSST
T ss_pred             EEEEEEEE--ccCCCccEEEEcCCCCCCEEEcChHHhhhCc---------CCCEEEEEEecccccccccccccccccccc
Confidence            35677765  58999  9999998789999998 8888886         999999999643221000000000      


Q ss_pred             CCCCccCC---------C---CCCCcc---------------ccccccCCcccccceeeeeeEEEeecCC--------Cc
Q psy9900          79 NGIPVQGA---------P---KSSSET---------------VSGTYRNDSFFPAVHTVRGIVKFYDSKR--------GF  123 (191)
Q Consensus        79 ~~~~~~~~---------~---~~~~~~---------------~~~~~~~~~~~~~~~~~~G~Vk~~~~~k--------gf  123 (191)
                      ...+....         .   ...+..               ....+......++++..+-.|..+....        .+
T Consensus       318 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eG~Vv~IleR~~~~~vG~l~~~~~~~~g~~~~~  397 (977)
T 2wp8_J          318 NDNPDIEAGDDDDNNESSSNTTVISDKQRRLLAKDAMIAQRSKKIQPTAKVVYIQRRSWRQYVGQLAPSSVDPQSSSTQN  397 (977)
T ss_dssp             TCCCCCC------------CCCCCCHHHHHHHHHHHHHHHHCSCCBCBEEEEEEEECCCCEEEEEECGGGCCTTCCSCEE
T ss_pred             ccccccccccccccccccccccccchhhhhhhhhhhhhccccCCCCceEEEEEEEEECCCeEEEEEEEecCcccCCccce
Confidence            00000000         0   000000               0001222333445555455667775443        23


Q ss_pred             eeEEeCCCC-CcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC---CceeEEeecCC
Q psy9900         124 GFITRLDNK-EDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK---DIEAINVTGPN  180 (191)
Q Consensus       124 GFI~~~d~~-~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k---g~~A~~V~~~~  180 (191)
                      .|+.|+|.. ..|++.......          ..|+.|.++|..=+.   -+.+.-|+.++
T Consensus       398 ~~~~P~D~ri~~i~I~~~~~~~----------~~g~~vvv~I~~wp~~~~~p~G~iv~~LG  448 (977)
T 2wp8_J          398 VFVILMDKCLPKVRIRTRRAAE----------LLDKRIVISIDSWPTTHKYPLGHFVRDLG  448 (977)
T ss_dssp             EEEEESSTTSCCEEEEETTTTG----------GGGEEEEEEEEECCTTCSSCEEEEEEEEE
T ss_pred             EEEEECCCCCccEEeccccccc----------cCCCEEEEEEeeccCCCCCccEEEEEEeC
Confidence            589998865 578887654321          358999999988543   26666666654

>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=95.79  E-value=0.013  Score=53.68  Aligned_cols=62  Identities=21%  Similarity=0.252  Sum_probs=49.2

Q ss_pred             eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecCCCC
Q psy9900         109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNGI  182 (191)
Q Consensus       109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~~~~  182 (191)
                      ...|+|..-  .+||||+.+++ ++|||++-.++..+         -.||+|.+.+......++|.-++++..+
T Consensus        21 ~~~G~~~~~--~~GfgF~~~d~-~~difi~~~~~~~a---------~~GD~V~v~i~~~~~~~eg~v~~iler~   82 (644)
T 2id0_A           21 RAEGVVKAT--EKGFGFLEVDA-QKSYFIPPPQMKKV---------MHGDRIIAVIHSEKERESAEPEELVEPF   82 (644)
T ss_dssp             EEEEEEECC--SSSCEEEECSS-SCEEEECHHHHTTS---------CTTCEEEEEEECCSSSCEEEEEEEEECS
T ss_pred             eEEEEEEEe--cCCcEEEEECC-CCCEEECHHHHhcC---------CCCCEEEEEEecCCCCeEEEEEEEEecC
Confidence            578888764  78999999986 68999999888754         5899999999875333788777776653

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

Probab=93.52  E-value=0.19  Score=43.64  Aligned_cols=69  Identities=29%  Similarity=0.524  Sum_probs=50.7

Q ss_pred             eeeeEEEeecCCCceeEEeCC-----CCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC---ceeEEeecCCC
Q psy9900         110 VRGIVKFYDSKRGFGFITRLD-----NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD---IEAINVTGPNG  181 (191)
Q Consensus       110 ~~G~Vk~~~~~kgfGFI~~~d-----~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg---~~A~~V~~~~~  181 (191)
                      ..|+....  ..||||+.+.+     +..||||..+.+..       -.|+.||.|+=.+..-+.|   ..-..|.-++|
T Consensus        58 ~~g~le~~--~~g~gflr~~~~~y~~~~~d~yvs~~~ir~-------~~lr~gd~v~g~~r~~~~~e~~~~l~~v~~vng  128 (427)
T 3l0o_A           58 GEGVLEIH--PEGFGFLRRIEDNLLPSNDDIYISPSQIRK-------FNLNTGDIISGVIRKPKEGEKYFAMIKIEAINY  128 (427)
T ss_dssp             EEEEEEEC--TTSCEEEECGGGTTCCCSSCEEECHHHHHH-------TTCCTTCEEEEEEECCCSSSCSEEEEEEEEETT
T ss_pred             EEEEEEEc--CCCceEeeCCccCCCCCCCCeeeCHHHHHh-------cCCCCCCEEEEEEeCCCCCcccccceEEEecCC
Confidence            56777665  57999999873     45899999999997       5899999999998875554   34456777777


Q ss_pred             CCCCCC
Q psy9900         182 IPVQGA  187 (191)
Q Consensus       182 ~~~~~~  187 (191)
                      .+....
T Consensus       129 ~~p~~~  134 (427)
T 3l0o_A          129 RPVEAV  134 (427)
T ss_dssp             EEC---
T ss_pred             CChHHh
Confidence            554433

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

Probab=92.11  E-value=0.29  Score=32.12  Aligned_cols=56  Identities=11%  Similarity=0.160  Sum_probs=40.6

Q ss_pred             eeceeccceEEEEeeCCCCeeE-EEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEc
Q psy9900           3 KFEIHTVRGIVKFYDSKRGFGF-ITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG   66 (191)
Q Consensus         3 ~~~~~~~~G~vk~~~~~kGfGF-I~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~   66 (191)
                      -..-....|+|+.-..   ||+ +..++ +-+-|+|.|++....    ...++.||.|.+.+..-
T Consensus         3 ~~~G~iv~G~V~~v~~---~G~fV~l~~-~~~Gllh~sel~~~~----~~~~~~Gd~V~v~V~~v   59 (80)
T 2k52_A            3 VEPGKFYKGVVTRIEK---YGAFINLNE-QVRGLLRPRDMISLR----LENLNVGDEIIVQAIDV   59 (80)
T ss_dssp             CCTTCEEEEEEEEEET---TEEEEEEET-TEEEEECGGGCSSCC----GGGCCTTCEEEEEEEEE
T ss_pred             CCCCCEEEEEEEEEeC---CEEEEEECC-CCEEEEEHHHCCccc----ceeeCCCCEEEEEEEEE
Confidence            3344567899998753   674 44444 688999999997531    24789999999998753

>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=91.70  E-value=0.31  Score=34.75  Aligned_cols=57  Identities=18%  Similarity=0.241  Sum_probs=38.7

Q ss_pred             eccceEEEEeeCCCCee-EEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEc
Q psy9900           7 HTVRGIVKFYDSKRGFG-FITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG   66 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfG-FI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~   66 (191)
                      ....|+|+....   || ||..++.+.+-|+|.+++......+-...++.||.|.+.+..-
T Consensus        24 ~iv~G~V~~I~~---fGaFV~l~g~~~~Glvhisel~~~~~~~~~~~~~~Gd~V~VkV~~v   81 (119)
T 2cqo_A           24 TIFQGEVAMVTD---YGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGR   81 (119)
T ss_dssp             CEEEEEEEEEET---TEEEEECTTCSSCEEEEHHHHCSSCCSCHHHHCCTTCEEEEEEEEE
T ss_pred             CEEEEEEEEEeC---ceEEEEECCCcEEEEEEHHHCCcccccChhhcCCCCCEEEEEEEEE
Confidence            457899998853   67 5555343469999999996531000113588999999998753

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

Probab=91.50  E-value=1.4  Score=28.67  Aligned_cols=54  Identities=11%  Similarity=0.262  Sum_probs=39.7

Q ss_pred             eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcC
Q psy9900         108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK  168 (191)
Q Consensus       108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~  168 (191)
                      ..+.|+|....+   ||+...-+.+.+-++|.|++...    ....++.||.|.+.+..-+
T Consensus         7 ~iv~G~V~~v~~---~G~fV~l~~~~~Gllh~sel~~~----~~~~~~~Gd~V~v~V~~vd   60 (80)
T 2k52_A            7 KFYKGVVTRIEK---YGAFINLNEQVRGLLRPRDMISL----RLENLNVGDEIIVQAIDVR   60 (80)
T ss_dssp             CEEEEEEEEEET---TEEEEEEETTEEEEECGGGCSSC----CGGGCCTTCEEEEEEEEEE
T ss_pred             CEEEEEEEEEeC---CEEEEEECCCCEEEEEHHHCCcc----cceeeCCCCEEEEEEEEEE
Confidence            458899988743   77544433378999999998743    1247999999999998744

>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=90.27  E-value=3.2  Score=28.42  Aligned_cols=63  Identities=16%  Similarity=0.129  Sum_probs=42.8

Q ss_pred             ccceeeeeeEEEeecCCCce-eEEeCC--CCCcEEEeccchhccC-cccccccCCCCCEEEEEEEEcCCC
Q psy9900         105 PAVHTVRGIVKFYDSKRGFG-FITRLD--NKEDIFVHKSSIVKMN-PKKFFQSLGLGEIVDFNIGVGKKD  170 (191)
Q Consensus       105 ~~~~~~~G~Vk~~~~~kgfG-FI~~~d--~~~dvF~h~s~~~~~~-~~~~~~~l~~G~~V~f~i~~~~kg  170 (191)
                      .....+.|+|+...   .|| ||.-.+  .+.+-|+|++++.... ...--..++.||.|.+.+..-+.+
T Consensus        11 ~vG~i~~G~V~~v~---~fG~FV~l~~~~~~~~Glvhisel~~~~~~~~~~~~~~~Gd~V~VkV~~vd~~   77 (103)
T 2eqs_A           11 TIGDIYNGKVTSIM---QFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGT   77 (103)
T ss_dssp             CTTCEEEEEEEEEC---SSCEEEEECSSSSCCEEEECGGGTSSSSCCCCHHHHCCTTCEEEEEEEEEETT
T ss_pred             CCCCEEEEEEEEEe---ccEEEEEEcCCCCCeEEEEEHHHCCCCcccCCcccEeCCCCEEEEEEEEEECC
Confidence            34467899998873   377 555554  2789999999994210 000114589999999999886655

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

Probab=89.61  E-value=3.9  Score=28.51  Aligned_cols=75  Identities=12%  Similarity=0.156  Sum_probs=48.0

Q ss_pred             cceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhcc-CcccccccCCCCCEEEEEEEEcC--CCceeEEeecCCCC
Q psy9900         106 AVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKM-NPKKFFQSLGLGEIVDFNIGVGK--KDIEAINVTGPNGI  182 (191)
Q Consensus       106 ~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~-~~~~~~~~l~~G~~V~f~i~~~~--kg~~A~~V~~~~~~  182 (191)
                      ....+.|+|....+   ||+...-+.+.+-|+|++++... ..+.--..++.||.|.+.|..-+  +|.-...++.+...
T Consensus        30 ~G~~~~G~V~~v~~---~G~FV~l~~~~~Glvhisel~~~~~~~~~~~~~~vGd~V~vkV~~vd~~~~rI~lslk~~~~~  106 (115)
T 2khi_A           30 EGTKLTGRVTNLTD---YGCFVEIEEGVEGLVHVSEMDWTNKNIHPSKVVNVGDVVEVMVLDIDEERRRISLGLKQCKAN  106 (115)
T ss_dssp             SSCEEEEEEEEEET---TEEEEECSTTCEEEEETTSSSCSSTTCSSTTTCCTTCEEEEEEEEEETTTTEEEECCCCCCSS
T ss_pred             CCCEEEEEEEEEEC---CEEEEEECCCCEEEEEHHHCCccccccCcccEECCCCEEEEEEEEEECCCCEEEEEEEecCcC
Confidence            34568999988743   78665555578999999998541 00011246899999999998754  34333334433333


Q ss_pred             C
Q psy9900         183 P  183 (191)
Q Consensus       183 ~  183 (191)
                      |
T Consensus       107 p  107 (115)
T 2khi_A          107 P  107 (115)
T ss_dssp             C
T ss_pred             H
Confidence            3

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

Probab=89.31  E-value=1.4  Score=31.61  Aligned_cols=59  Identities=20%  Similarity=0.230  Sum_probs=41.3

Q ss_pred             ceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcC
Q psy9900         107 VHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK  168 (191)
Q Consensus       107 ~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~  168 (191)
                      ...+.|+|....   .||+...-+.+.+-++|++++.......--..++.||.|.+.|..-+
T Consensus         8 G~iv~G~V~~i~---~~G~FV~l~~~~~Glihisel~~~~~~~~~~~~~vGd~V~vkV~~vd   66 (130)
T 2k4k_A            8 GSVYTGKVTGLQ---AYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQVKVLAVD   66 (130)
T ss_dssp             TCEEEEEEEEEE---TTEEEEEEETTEEEEEEGGGTSSSCCSCGGGTCCTTCEEEEEEEEEE
T ss_pred             CCEEEEEEEEEe---CCeEEEEECCCcEEEEEHHHCCcccccCccccCCCCCEEEEEEEEEe
Confidence            346789998873   36765555457899999999964310011256899999999988743

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

Probab=89.06  E-value=0.73  Score=39.97  Aligned_cols=64  Identities=28%  Similarity=0.500  Sum_probs=45.5

Q ss_pred             cceEEEEeeCCCCeeEEEeC-----CCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCC---ceeeEeecCCC
Q psy9900           9 VRGIVKFYDSKRGFGFITRL-----DNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD---IEAINVTGPNG   80 (191)
Q Consensus         9 ~~G~vk~~~~~kGfGFI~~~-----~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g---~~A~~v~~~~~   80 (191)
                      ..|++.--  ..||||+.+.     .+..||||..+.++..       .|+.||.|.-.+.....+   ..-..|..+++
T Consensus        58 ~~g~le~~--~~g~gflr~~~~~y~~~~~d~yvs~~~ir~~-------~lr~gd~v~g~~r~~~~~e~~~~l~~v~~vng  128 (427)
T 3l0o_A           58 GEGVLEIH--PEGFGFLRRIEDNLLPSNDDIYISPSQIRKF-------NLNTGDIISGVIRKPKEGEKYFAMIKIEAINY  128 (427)
T ss_dssp             EEEEEEEC--TTSCEEEECGGGTTCCCSSCEEECHHHHHHT-------TCCTTCEEEEEEECCCSSSCSEEEEEEEEETT
T ss_pred             EEEEEEEc--CCCceEeeCCccCCCCCCCCeeeCHHHHHhc-------CCCCCCEEEEEEeCCCCCcccccceEEEecCC
Confidence            34655544  5799999976     3468999999999974       789999999998765444   22344555554


Q ss_pred             C
Q psy9900          81 I   81 (191)
Q Consensus        81 ~   81 (191)
                      .
T Consensus       129 ~  129 (427)
T 3l0o_A          129 R  129 (427)
T ss_dssp             E
T ss_pred             C
Confidence            3

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

Probab=87.94  E-value=4.5  Score=28.19  Aligned_cols=58  Identities=14%  Similarity=0.189  Sum_probs=40.1

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheec-CCCCCcccCCCCCEEEEEEEEcC
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKM-NPKKFFQSLGLGEIVDFNIGVGK   67 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~-~~~~g~~~l~~Gd~V~f~~~~~~   67 (191)
                      ....|+|+.-..   ||+...-+.+-+-|+|.|++... ........++.||.|.+.+..-.
T Consensus        32 ~~~~G~V~~v~~---~G~FV~l~~~~~Glvhisel~~~~~~~~~~~~~~vGd~V~vkV~~vd   90 (115)
T 2khi_A           32 TKLTGRVTNLTD---YGCFVEIEEGVEGLVHVSEMDWTNKNIHPSKVVNVGDVVEVMVLDID   90 (115)
T ss_dssp             CEEEEEEEEEET---TEEEEECSTTCEEEEETTSSSCSSTTCSSTTTCCTTCEEEEEEEEEE
T ss_pred             CEEEEEEEEEEC---CEEEEEECCCCEEEEEHHHCCccccccCcccEECCCCEEEEEEEEEE
Confidence            456788888753   77655555568999999998541 11112346899999999997643

>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=87.49  E-value=3.4  Score=36.75  Aligned_cols=63  Identities=13%  Similarity=0.123  Sum_probs=46.4

Q ss_pred             ceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCc--------cccc-ccCCCCCEEEEEEEEcCCC
Q psy9900         107 VHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNP--------KKFF-QSLGLGEIVDFNIGVGKKD  170 (191)
Q Consensus       107 ~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~--------~~~~-~~l~~G~~V~f~i~~~~kg  170 (191)
                      ...+.|+|+...+.-+--||.-.. +++-|+|++++.....        .... .-|++||.|.+.|...+.|
T Consensus        46 GnIY~GkV~rv~p~~~aAFVdiG~-gk~gfLhisei~~~~~~~~~~~~~~~~i~d~lk~Gq~VlVQV~Ke~~g  117 (517)
T 2bx2_L           46 ANIYKGKITRIEPSLEAAFVDYGA-ERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERG  117 (517)
T ss_dssp             TCEEEEEEEEEETTTTEEEEESSS-SSCEEEEGGGSCGGGCC-------CCCGGGTCCTTCEEEEEEEECCCT
T ss_pred             CCEEEEEEEEeccCCceEEEEeCC-CcEEEEEHHHcChhhhccccccccccchhhhccCCCEEEEEEEeeccc
Confidence            346899999997777788998775 7899999999853200        0001 2489999999999996644

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

Probab=87.40  E-value=1  Score=32.41  Aligned_cols=57  Identities=21%  Similarity=0.254  Sum_probs=39.6

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEc
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG   66 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~   66 (191)
                      ....|+|+.-.   -||+...-+.+-+-|+|.|++...........++.||.|.+.+..-
T Consensus         9 ~iv~G~V~~i~---~~G~FV~l~~~~~Glihisel~~~~~~~~~~~~~vGd~V~vkV~~v   65 (130)
T 2k4k_A            9 SVYTGKVTGLQ---AYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQVKVLAV   65 (130)
T ss_dssp             CEEEEEEEEEE---TTEEEEEEETTEEEEEEGGGTSSSCCSCGGGTCCTTCEEEEEEEEE
T ss_pred             CEEEEEEEEEe---CCeEEEEECCCcEEEEEHHHCCcccccCccccCCCCCEEEEEEEEE
Confidence            34679999884   3676554444689999999997432111225689999999998753

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

Probab=87.08  E-value=2.6  Score=29.04  Aligned_cols=61  Identities=16%  Similarity=0.134  Sum_probs=41.9

Q ss_pred             cceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900         106 AVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK  169 (191)
Q Consensus       106 ~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k  169 (191)
                      ....+.|+|....   .||....-+.+.+-|+|.+++.......--..++.||.|.+.|..-+.
T Consensus        31 ~G~iv~G~V~~v~---~~G~fV~l~~~~~Gll~~sel~~~~~~~~~~~~~vGd~V~v~V~~vd~   91 (109)
T 2khj_A           31 KGAIVTGKVTAVD---AKGATVELADGVEGYLRASEASRDRVEDATLVLSVGDEVEAKFTGVDR   91 (109)
T ss_dssp             SSSEEEEEEEEEC---SSCEEEECSTTCBCCBCTTCCCSSSSSSGGGSCCTTCEEEEEEEEEET
T ss_pred             CCCEEEEEEEEEE---CCeEEEEECCCCEEEEEHHHcCcccccChhhccCCCCEEEEEEEEEEC
Confidence            3456899999874   366655555578999999998642100112468999999999987543

>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=86.13  E-value=0.64  Score=40.29  Aligned_cols=63  Identities=27%  Similarity=0.454  Sum_probs=46.4

Q ss_pred             eeeeEEEeecCCCceeEEeCC-----CCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC---ceeEEeecCCC
Q psy9900         110 VRGIVKFYDSKRGFGFITRLD-----NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD---IEAINVTGPNG  181 (191)
Q Consensus       110 ~~G~Vk~~~~~kgfGFI~~~d-----~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg---~~A~~V~~~~~  181 (191)
                      ..|+....  ..||||+.+.+     +..||||..+.+..       -.|+.||.|.=.+..-+.+   ..-.+|..+++
T Consensus        54 ~~g~le~~--~~g~gflr~~~~~~~~~~~d~yvs~~~ir~-------~~lr~gd~v~g~~r~~~~~ER~faLl~v~~vn~  124 (422)
T 3ice_A           54 GDGVLEIL--QDGFGFLRSADSSYLAGPDDIYVSPSQIRR-------FNLRTGDTISGKIRPPKEGERYFALLKVNEVNF  124 (422)
T ss_dssp             EEEEEEEC--TTSCEEEECGGGTTCCCTTCEEBCHHHHHH-------HTCCTTCEEEEEEECCCSSCCSEEEEEEEEESS
T ss_pred             EEEEEEEc--CCCceEeeCCCcCCCCCCCCeeeCHHHHHh-------cCCCCCCEEEEEEeCCCccchHHHHhccCcccC
Confidence            56777665  57999999853     34899999999997       5899999999888765554   23335544443

>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=85.83  E-value=1.7  Score=34.12  Aligned_cols=58  Identities=17%  Similarity=0.163  Sum_probs=40.0

Q ss_pred             eceeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCc----------ccCCCCCEEEEEEEE
Q psy9900           4 FEIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFF----------QSLGLGEIVDFNIGV   65 (191)
Q Consensus         4 ~~~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~----------~~l~~Gd~V~f~~~~   65 (191)
                      ...+...|+|+.-.   -||+...-.. .|.|||.|.|....-.+..          ..++.||.|.+.+..
T Consensus        82 ~vGev~~G~V~~vt---~fG~FVelg~-~dGlVhiS~l~d~~~~d~~~~~w~~~~~~~~~~~Gd~VrVkV~~  149 (215)
T 2b8k_G           82 FKGEVVDGTVVSCS---QHGFEVQVGP-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEG  149 (215)
T ss_dssp             CTTEEEEEEEEEEE---TTEEEEECTT-SEEEEEGGGSCSSCCCBSSCSSCEEECSSCEEETTCEEEEEEEE
T ss_pred             CCCCEEEEEEEEEe---cceEEEEecC-cEEEEEHHHCCccceeccccccceeeccccEECCCCEEEEEEEE
Confidence            34455778888876   4888776665 8999999998632100000          347899999999865

>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=85.62  E-value=3.3  Score=28.33  Aligned_cols=61  Identities=16%  Similarity=0.129  Sum_probs=40.7

Q ss_pred             eeccceEEEEeeCCCCee-EEEeCC--CCccEEEEeeeheec-CCCCCcccCCCCCEEEEEEEEcCCC
Q psy9900           6 IHTVRGIVKFYDSKRGFG-FITRLD--NKEDIFVHKSSIVKM-NPKKFFQSLGLGEIVDFNIGVGKKD   69 (191)
Q Consensus         6 ~~~~~G~vk~~~~~kGfG-FI~~~~--~~~dvFvh~s~l~~~-~~~~g~~~l~~Gd~V~f~~~~~~~g   69 (191)
                      -....|+|+.--   -|| ||...+  .+-+-|+|.|++... ...+....++.||.|.+.+..-..+
T Consensus        13 G~i~~G~V~~v~---~fG~FV~l~~~~~~~~Glvhisel~~~~~~~~~~~~~~~Gd~V~VkV~~vd~~   77 (103)
T 2eqs_A           13 GDIYNGKVTSIM---QFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGT   77 (103)
T ss_dssp             TCEEEEEEEEEC---SSCEEEEECSSSSCCEEEECGGGTSSSSCCCCHHHHCCTTCEEEEEEEEEETT
T ss_pred             CCEEEEEEEEEe---ccEEEEEEcCCCCCeEEEEEHHHCCCCcccCCcccEeCCCCEEEEEEEEEECC
Confidence            345789999873   377 566654  267899999999421 0000124589999999999865443

>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=85.25  E-value=7.8  Score=27.22  Aligned_cols=60  Identities=13%  Similarity=0.215  Sum_probs=40.7

Q ss_pred             cceeeeeeEEEeecCCCceeEEeCCC-CCcEEEeccchhccCcccccccCCCCCEEEEEEEEcC
Q psy9900         106 AVHTVRGIVKFYDSKRGFGFITRLDN-KEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK  168 (191)
Q Consensus       106 ~~~~~~G~Vk~~~~~kgfGFI~~~d~-~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~  168 (191)
                      ....+.|+|+...+   ||....-++ +.+-|+|++++.......--..++.||.|.+.|..-+
T Consensus        22 vG~iv~G~V~~I~~---fGaFV~l~g~~~~Glvhisel~~~~~~~~~~~~~~Gd~V~VkV~~vd   82 (119)
T 2cqo_A           22 LYTIFQGEVAMVTD---YGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGRE   82 (119)
T ss_dssp             TTCEEEEEEEEEET---TEEEEECTTCSSCEEEEHHHHCSSCCSCHHHHCCTTCEEEEEEEEEE
T ss_pred             CCCEEEEEEEEEeC---ceEEEEECCCcEEEEEEHHHCCcccccChhhcCCCCCEEEEEEEEEe
Confidence            34668999998843   775444443 4799999999964210001135899999999987643

>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=84.00  E-value=1.4  Score=33.10  Aligned_cols=57  Identities=16%  Similarity=0.137  Sum_probs=38.3

Q ss_pred             ceeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCC---CCC-------cccCCCCCEEEEEEEE
Q psy9900           5 EIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNP---KKF-------FQSLGLGEIVDFNIGV   65 (191)
Q Consensus         5 ~~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~---~~g-------~~~l~~Gd~V~f~~~~   65 (191)
                      ......|+|+.-.   -||+...-.. .|.|+|.|.+....-   ...       ...++.||.|.+.+..
T Consensus        83 ~Gev~~G~V~~v~---~fG~FV~l~~-~dglvhis~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~  149 (171)
T 1y14_B           83 KGEVVDGTVVSCS---QHGFEVQVGP-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEG  149 (171)
T ss_dssp             TTCEEEEEEEEEE---TTEEEEEETT-EEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEE
T ss_pred             CCCEEEEEEEEEe---cCEEEEEecC-eEEEEEHHHCCCCceECcccCceEEeccceEECCCCEEEEEEEE
Confidence            3455778888876   3787666555 899999999853100   000       0347889999998865

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

Probab=83.71  E-value=1.7  Score=30.05  Aligned_cols=58  Identities=17%  Similarity=0.147  Sum_probs=39.4

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK   67 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~   67 (191)
                      ....|+|+.-.   .||+...-+.+-+-|+|.+++...........++.||.|.+.+..-.
T Consensus        33 ~iv~G~V~~v~---~~G~fV~l~~~~~Gll~~sel~~~~~~~~~~~~~vGd~V~v~V~~vd   90 (109)
T 2khj_A           33 AIVTGKVTAVD---AKGATVELADGVEGYLRASEASRDRVEDATLVLSVGDEVEAKFTGVD   90 (109)
T ss_dssp             SEEEEEEEEEC---SSCEEEECSTTCBCCBCTTCCCSSSSSSGGGSCCTTCEEEEEEEEEE
T ss_pred             CEEEEEEEEEE---CCeEEEEECCCCEEEEEHHHcCcccccChhhccCCCCEEEEEEEEEE
Confidence            44779999884   35655544446789999999864311112246899999999987643

>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=83.59  E-value=2.1  Score=38.16  Aligned_cols=64  Identities=13%  Similarity=0.095  Sum_probs=46.1

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCC--------CCc-ccCCCCCEEEEEEEEcCCCce
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPK--------KFF-QSLGLGEIVDFNIGVGKKDIE   71 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~--------~g~-~~l~~Gd~V~f~~~~~~~g~~   71 (191)
                      .-..|+|+.-.+--+=-||.... +.+-|+|++++......        ... ..|++||.|.+.+...+.|-+
T Consensus        47 nIY~GkV~rv~p~~~aAFVdiG~-gk~gfLhisei~~~~~~~~~~~~~~~~i~d~lk~Gq~VlVQV~Ke~~g~K  119 (517)
T 2bx2_L           47 NIYKGKITRIEPSLEAAFVDYGA-ERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNK  119 (517)
T ss_dssp             CEEEEEEEEEETTTTEEEEESSS-SSCEEEEGGGSCGGGCC-------CCCGGGTCCTTCEEEEEEEECCCTTC
T ss_pred             CEEEEEEEEeccCCceEEEEeCC-CcEEEEEHHHcChhhhccccccccccchhhhccCCCEEEEEEEeeccccC
Confidence            34679999988777788998766 68999999998532100        001 238899999999998776533

>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=83.01  E-value=0.71  Score=40.02  Aligned_cols=52  Identities=27%  Similarity=0.524  Sum_probs=39.9

Q ss_pred             cceEEEEeeCCCCeeEEEeC-----CCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCC
Q psy9900           9 VRGIVKFYDSKRGFGFITRL-----DNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD   69 (191)
Q Consensus         9 ~~G~vk~~~~~kGfGFI~~~-----~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g   69 (191)
                      ..|++.--  ..||||+.+.     .+..||||..+.++..       .|+.||.|.-.+.....+
T Consensus        54 ~~g~le~~--~~g~gflr~~~~~~~~~~~d~yvs~~~ir~~-------~lr~gd~v~g~~r~~~~~  110 (422)
T 3ice_A           54 GDGVLEIL--QDGFGFLRSADSSYLAGPDDIYVSPSQIRRF-------NLRTGDTISGKIRPPKEG  110 (422)
T ss_dssp             EEEEEEEC--TTSCEEEECGGGTTCCCTTCEEBCHHHHHHH-------TCCTTCEEEEEEECCCSS
T ss_pred             EEEEEEEc--CCCceEeeCCCcCCCCCCCCeeeCHHHHHhc-------CCCCCCEEEEEEeCCCcc
Confidence            34666544  5799999974     3458999999999974       789999999988755443

>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=82.76  E-value=7.5  Score=32.16  Aligned_cols=61  Identities=15%  Similarity=0.091  Sum_probs=42.7

Q ss_pred             cceeeeeeEEEeecCCCceeEEeCC--CCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900         106 AVHTVRGIVKFYDSKRGFGFITRLD--NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK  169 (191)
Q Consensus       106 ~~~~~~G~Vk~~~~~kgfGFI~~~d--~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k  169 (191)
                      ....+.|+|+...+   ||....-+  .+.+-|+|+|++.....+.--..++.||.|.+.|..-+.
T Consensus        13 vG~iv~G~V~~I~~---fGaFV~L~ey~gveGLvhiSels~~~i~~~~~~~kvGd~V~VkVl~vD~   75 (308)
T 1q8k_A           13 VEDVVMVNVRSIQE---MGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNECVKVIRVDK   75 (308)
T ss_dssp             SCCEEEEEEEEEET---TEEEEESCTTTSCCEEECGGGTSCSSCSCCTTTCSSSCEEEEEEEEEET
T ss_pred             CCCEEEEEEEEEeC---cEEEEEECCCCCeEEEEEhHHcCcccccCHHHhcCCCCEEEEEEEEEeC
Confidence            34568999998854   78544443  578999999999642111112458899999999987553

>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=82.36  E-value=1.4  Score=29.08  Aligned_cols=61  Identities=16%  Similarity=0.116  Sum_probs=39.4

Q ss_pred             eeeeeEEEeecCCCceeEEeCCC--------CCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEee
Q psy9900         109 TVRGIVKFYDSKRGFGFITRLDN--------KEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVT  177 (191)
Q Consensus       109 ~~~G~Vk~~~~~kgfGFI~~~d~--------~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~  177 (191)
                      ..+|+|+..+...+-  |+-.-+        ..-.-|...+-.      -+..|++||.|.|.+...+.++.-+.++
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--ITIHHDPIAAVNWPEMTMRFTITPQT------KMSEIKTGDKVAFNFVQQGNLSLLQDIK   77 (80)
T ss_dssp             EEEEEEEEEETTTTE--EEEEECCBGGGTBCSEEEEEECCTTC------EECCCCTTCEEEEEEEEETTEEEEEEEE
T ss_pred             EEEEEEEEEcCCCCE--EEEEcCCcccCCCCceEEEEEccChh------hhhcCCCCCEEEEEEEEeCCEEEEEEEE
Confidence            478999999766543  443211        122233333222      2579999999999999988777766665

>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=81.99  E-value=3.4  Score=30.92  Aligned_cols=58  Identities=17%  Similarity=0.151  Sum_probs=40.0

Q ss_pred             ceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhcc---Ccccc-------cccCCCCCEEEEEEEEcC
Q psy9900         107 VHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKM---NPKKF-------FQSLGLGEIVDFNIGVGK  168 (191)
Q Consensus       107 ~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~---~~~~~-------~~~l~~G~~V~f~i~~~~  168 (191)
                      .+.+.|+|+...   .||+...-.. .|.|+|.|.+...   ++...       -..++.||.|.+.+..-+
T Consensus        84 Gev~~G~V~~v~---~fG~FV~l~~-~dglvhis~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd  151 (171)
T 1y14_B           84 GEVVDGTVVSCS---QHGFEVQVGP-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCI  151 (171)
T ss_dssp             TCEEEEEEEEEE---TTEEEEEETT-EEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEE
T ss_pred             CCEEEEEEEEEe---cCEEEEEecC-eEEEEEHHHCCCCceECcccCceEEeccceEECCCCEEEEEEEEEE
Confidence            456899999875   3887666554 8999999998532   00000       044889999999987743

>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=81.97  E-value=1.5  Score=29.60  Aligned_cols=61  Identities=16%  Similarity=0.116  Sum_probs=39.5

Q ss_pred             eeeeeEEEeecCCCceeEEeCCC--------CCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEee
Q psy9900         109 TVRGIVKFYDSKRGFGFITRLDN--------KEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVT  177 (191)
Q Consensus       109 ~~~G~Vk~~~~~kgfGFI~~~d~--------~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~  177 (191)
                      ..+|+|+..+...+-  |+-.-+        ..-.-|...+-.      -+..|++||.|.|.+...+.++.-+.|+
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--ITIHHDPIAAVNWPEMTMRFTITPQT------KMSEIKTGDKVAFNFVQQGNLSLLQDIK   85 (88)
T ss_dssp             EEEEEEEEEETTTTE--EEEEECCBGGGTBCSEEEEEECCTTC------EECCCCTTCEEEEEEEEETTEEEEEEEE
T ss_pred             EEEEEEEEEcCCCCE--EEEecCCcccCCCCceEEEEEcCChh------hhhcCCCCCEEEEEEEEeCCEEEEEEEE
Confidence            478999999866543  443211        122223333222      2579999999999999988777766665

>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=81.80  E-value=4.9  Score=31.51  Aligned_cols=59  Identities=15%  Similarity=0.108  Sum_probs=41.2

Q ss_pred             cceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccC---cccc-------cccCCCCCEEEEEEEEcC
Q psy9900         106 AVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMN---PKKF-------FQSLGLGEIVDFNIGVGK  168 (191)
Q Consensus       106 ~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~---~~~~-------~~~l~~G~~V~f~i~~~~  168 (191)
                      ..+.+.|+|....   .||+...-.. .|.++|++.+....   +...       -..++.||.|.+.|..-+
T Consensus        83 vGev~~G~V~~vt---~fG~FVelg~-~dGlVhiS~l~d~~~~d~~~~~w~~~~~~~~~~~Gd~VrVkV~~vd  151 (215)
T 2b8k_G           83 KGEVVDGTVVSCS---QHGFEVQVGP-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCI  151 (215)
T ss_dssp             TTEEEEEEEEEEE---TTEEEEECTT-SEEEEEGGGSCSSCCCBSSCSSCEEECSSCEEETTCEEEEEEEEEE
T ss_pred             CCCEEEEEEEEEe---cceEEEEecC-cEEEEEHHHCCccceeccccccceeeccccEECCCCEEEEEEEEEE
Confidence            3466899998875   3888776654 89999999985320   0000       034889999999987743

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

Probab=81.75  E-value=2.1  Score=28.45  Aligned_cols=61  Identities=11%  Similarity=0.107  Sum_probs=39.5

Q ss_pred             eeeeEEEeecCCCceeEEeCCC--------CCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC-CceeEEeecCC
Q psy9900         110 VRGIVKFYDSKRGFGFITRLDN--------KEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK-DIEAINVTGPN  180 (191)
Q Consensus       110 ~~G~Vk~~~~~kgfGFI~~~d~--------~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k-g~~A~~V~~~~  180 (191)
                      .+|+|+..+...    |+-.-+        ..-.-|...+-.      -+..|++||.|.|++...+. ++.-+.|+..+
T Consensus         6 ~~G~V~~vd~~~----iTi~H~pI~~l~wPaMTM~F~v~~~~------~l~~lk~Gd~V~F~~~~~~~g~~~it~i~~~~   75 (82)
T 2l55_A            6 AVGRIQSIGERS----LIIAHEAIPSAQWGAMTMEFAAPPAG------LPQGLKAGDRVAFSFRLDPHGMATLVTVAPQV   75 (82)
T ss_dssp             EEEEEEECCSSE----EEEEECCCTTTTCCCEEEEEECCTTC------CCSSCSTTCEEEEEEEEETTTEEEEEEEEECC
T ss_pred             EeEEEEEEcccc----EEEecCCccccCCCceEEEEEcCChh------HhhcCCCCCEEEEEEEECCCCeEEEEEEEecC
Confidence            578888887664    443211        122333333222      25789999999999999988 47777777543

>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=80.96  E-value=3.6  Score=31.14  Aligned_cols=58  Identities=10%  Similarity=0.012  Sum_probs=36.9

Q ss_pred             eeccceEEEEeeCCCCee-EEEeC-CCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEc
Q psy9900           6 IHTVRGIVKFYDSKRGFG-FITRL-DNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG   66 (191)
Q Consensus         6 ~~~~~G~vk~~~~~kGfG-FI~~~-~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~   66 (191)
                      .....|+|+.-   .-|| ||..+ ..+-+-++|.|.+......+....++.||.|.+.+..-
T Consensus        16 G~iv~G~V~~i---~~fGaFV~L~e~~gveGLvhiSels~~~v~~~~~~~~vGd~V~vkVl~v   75 (175)
T 2a19_A           16 DDIVMVNVQQI---AEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRV   75 (175)
T ss_dssp             TCEEEEEEEEE---ETTEEEEEETTTTTCEEEEECC--------CCCCCCCTTSEEEEEEEEE
T ss_pred             CCEEEEEEEEE---ecceEEEEEcCCCCcEEEEEHHHcCCcccCCHHHcCCCCCEEEEEEEEE
Confidence            45578999987   3577 56664 24678999999996532112235688999999998764

>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=80.23  E-value=7.5  Score=29.34  Aligned_cols=60  Identities=10%  Similarity=0.015  Sum_probs=38.0

Q ss_pred             cceeeeeeEEEeecCCCce-eEEeC-CCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcC
Q psy9900         106 AVHTVRGIVKFYDSKRGFG-FITRL-DNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK  168 (191)
Q Consensus       106 ~~~~~~G~Vk~~~~~kgfG-FI~~~-d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~  168 (191)
                      ....+.|+|...   ..|| ||.-+ ..+-+-++|+|++.....+.--..++.||.|.+.|..-+
T Consensus        15 ~G~iv~G~V~~i---~~fGaFV~L~e~~gveGLvhiSels~~~v~~~~~~~~vGd~V~vkVl~vd   76 (175)
T 2a19_A           15 IDDIVMVNVQQI---AEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVD   76 (175)
T ss_dssp             TTCEEEEEEEEE---ETTEEEEEETTTTTCEEEEECC--------CCCCCCCTTSEEEEEEEEEE
T ss_pred             CCCEEEEEEEEE---ecceEEEEEcCCCCcEEEEEHHHcCCcccCCHHHcCCCCCEEEEEEEEEE
Confidence            456789999887   3478 45554 246899999999964311111246889999999988754

>2vnu_D Exosome complex exonuclease RRP44; hydrolase-RNA complex, RNA degradation, RNA-binding, RNA Pro; HET: 1PE; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16

Probab=80.01  E-value=2.4  Score=39.39  Aligned_cols=49  Identities=10%  Similarity=0.115  Sum_probs=38.6

Q ss_pred             eeeeeeEEEeecCCCc--eeEEeCCCCCcEEEec-cchhccCcccccccCCCCCEEEEEEEEc
Q psy9900         108 HTVRGIVKFYDSKRGF--GFITRLDNKEDIFVHK-SSIVKMNPKKFFQSLGLGEIVDFNIGVG  167 (191)
Q Consensus       108 ~~~~G~Vk~~~~~kgf--GFI~~~d~~~dvF~h~-s~~~~~~~~~~~~~l~~G~~V~f~i~~~  167 (191)
                      ..++|++.--  .+||  ||+.+++..+|||++- .++..+         -.||.|.+++...
T Consensus        31 ~l~~G~l~~~--~~~~~~gfv~~~~~~~di~I~~~~~~n~A---------~~GD~V~V~i~~~   82 (760)
T 2vnu_D           31 VLYQGNIQIS--EYNFLEGSVSLPRFSKPVLIVGQKNLNRA---------FNGDQVIVELLPQ   82 (760)
T ss_dssp             SEEEEEEEEC--SSBTTEEEECCSSSSSCEEEESHHHHTTC---------CTTCEEEEEECCG
T ss_pred             CEEEEEEEEe--cCCCccEEEEcCCCCCCEEEcChhhhccc---------cCCCEEEEEEecc
Confidence            3578887653  6789  9999998789999997 666643         5899999999743

---

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	191
d1h95a_	79	b.40.4.5 (A:) Y-box protein 1 cold shock domain (Y	4e-20
d1h95a_	79	b.40.4.5 (A:) Y-box protein 1 cold shock domain (Y	6e-20
d1mjca_	69	b.40.4.5 (A:) Major cold shock protein {Escherichi	2e-14
d1mjca_	69	b.40.4.5 (A:) Major cold shock protein {Escherichi	2e-14
d1c9oa_	66	b.40.4.5 (A:) Major cold shock protein {Bacillus c	1e-11
d1c9oa_	66	b.40.4.5 (A:) Major cold shock protein {Bacillus c	1e-11
d1g6pa_	66	b.40.4.5 (A:) Major cold shock protein {Thermotoga	1e-11
d1g6pa_	66	b.40.4.5 (A:) Major cold shock protein {Thermotoga	1e-11
d1wfqa_	89	b.40.4.5 (A:) Cold shock domain protein E1 (UNR) {	8e-08
d1wfqa_	89	b.40.4.5 (A:) Cold shock domain protein E1 (UNR) {	8e-08

>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 = 77.9 bits (192), Expect = 4e-20
 Identities = 38/78 (48%), Positives = 55/78 (70%)

Query: 1  MTKFEIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVD 60
          M K     V G VK+++ + G+GFI R D KED+FVH+++I K NP+K+ +S+G GE V+
Sbjct: 1  MKKVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVE 60

Query: 61 FNIGVGKKDIEAINVTGP 78
          F++  G+K  EA NVTGP
Sbjct: 61 FDVVEGEKGAEAANVTGP 78

>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 = 77.6 bits (191), Expect = 6e-20
 Identities = 36/70 (51%), Positives = 53/70 (75%)

Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
           V G VK+++ + G+GFI R D KED+FVH+++I K NP+K+ +S+G GE V+F++  G+K
Sbjct: 9   VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEK 68

Query: 170 DIEAINVTGP 179
             EA NVTGP
Sbjct: 69  GAEAANVTGP 78

>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 = 62.8 bits (153), Expect = 2e-14
 Identities = 29/68 (42%), Positives = 41/68 (60%), Gaps = 4/68 (5%)

Query: 9  VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
          + GIVK++++ +GFGFIT  D  +D+FVH S+I        ++SL  G+ V F I  G K
Sbjct: 4  MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIESGAK 59

Query: 69 DIEAINVT 76
             A NVT
Sbjct: 60 GPAAGNVT 67

>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 = 62.8 bits (153), Expect = 2e-14
 Identities = 29/68 (42%), Positives = 41/68 (60%), Gaps = 4/68 (5%)

Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
           + GIVK++++ +GFGFIT  D  +D+FVH S+I        ++SL  G+ V F I  G K
Sbjct: 4   MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIESGAK 59

Query: 170 DIEAINVT 177
              A NVT
Sbjct: 60  GPAAGNVT 67

>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 = 55.6 bits (134), Expect = 1e-11
 Identities = 23/67 (34%), Positives = 39/67 (58%), Gaps = 5/67 (7%)

Query: 10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 69
          RG VK++++++G+GFI   +   D+FVH ++I        F++L  G+ V F I  G + 
Sbjct: 3  RGKVKWFNNEKGYGFIEV-EGGSDVFVHFTAIQGEG----FKTLEEGQEVSFEIVQGNRG 57

Query: 70 IEAINVT 76
           +A NV 
Sbjct: 58 PQAANVV 64

>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 = 55.6 bits (134), Expect = 1e-11
 Identities = 23/67 (34%), Positives = 39/67 (58%), Gaps = 5/67 (7%)

Query: 111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 170
           RG VK++++++G+GFI   +   D+FVH ++I        F++L  G+ V F I  G + 
Sbjct: 3   RGKVKWFNNEKGYGFIEV-EGGSDVFVHFTAIQGEG----FKTLEEGQEVSFEIVQGNRG 57

Query: 171 IEAINVT 177
            +A NV 
Sbjct: 58  PQAANVV 64

>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 = 55.5 bits (134), Expect = 1e-11
 Identities = 30/67 (44%), Positives = 44/67 (65%), Gaps = 5/67 (7%)

Query: 10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 69
          RG VK++DSK+G+GFIT+ D   D+FVH S+I        F++L  G++V+F I  GKK 
Sbjct: 2  RGKVKWFDSKKGYGFITK-DEGGDVFVHWSAIEMEG----FKTLKEGQVVEFEIQEGKKG 56

Query: 70 IEAINVT 76
           +A +V 
Sbjct: 57 PQAAHVK 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 = 55.5 bits (134), Expect = 1e-11
 Identities = 30/67 (44%), Positives = 44/67 (65%), Gaps = 5/67 (7%)

Query: 111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 170
           RG VK++DSK+G+GFIT+ D   D+FVH S+I        F++L  G++V+F I  GKK 
Sbjct: 2   RGKVKWFDSKKGYGFITK-DEGGDVFVHWSAIEMEG----FKTLKEGQVVEFEIQEGKKG 56

Query: 171 IEAINVT 177
            +A +V 
Sbjct: 57  PQAAHVK 63

>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 = 46.1 bits (109), Expect = 8e-08
 Identities = 14/73 (19%), Positives = 30/73 (41%), Gaps = 9/73 (12%)

Query: 10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 69
           G+++       +GFI   + +  +F H S           Q L +G+ V+F +   ++ 
Sbjct: 20 TGVIEKL--LTSYGFIQCSERQARLFFHCSQYNGN-----LQDLKVGDDVEFEVSSDRRT 72

Query: 70 --IEAINVTGPNG 80
              A+ +   +G
Sbjct: 73 GKPIAVKLVKISG 85

>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 = 46.1 bits (109), Expect = 8e-08
 Identities = 14/73 (19%), Positives = 30/73 (41%), Gaps = 9/73 (12%)

Query: 111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 170
            G+++       +GFI   + +  +F H S           Q L +G+ V+F +   ++ 
Sbjct: 20  TGVIEKL--LTSYGFIQCSERQARLFFHCSQYNGN-----LQDLKVGDDVEFEVSSDRRT 72

Query: 171 --IEAINVTGPNG 181
               A+ +   +G
Sbjct: 73  GKPIAVKLVKISG 85

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	191
d1h95a_	79	Y-box protein 1 cold shock domain (YB1-CSD) {Human	99.92
d1h95a_	79	Y-box protein 1 cold shock domain (YB1-CSD) {Human	99.91
d1mjca_	69	Major cold shock protein {Escherichia coli [TaxId:	99.9
d1mjca_	69	Major cold shock protein {Escherichia coli [TaxId:	99.9
d1c9oa_	66	Major cold shock protein {Bacillus caldolyticus [T	99.87
d1g6pa_	66	Major cold shock protein {Thermotoga maritima [Tax	99.87
d1g6pa_	66	Major cold shock protein {Thermotoga maritima [Tax	99.86
d1c9oa_	66	Major cold shock protein {Bacillus caldolyticus [T	99.86
d1wfqa_	89	Cold shock domain protein E1 (UNR) {Human (Homo sa	99.68
d1wfqa_	89	Cold shock domain protein E1 (UNR) {Human (Homo sa	99.67
d2ix0a2	79	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	98.14
d2ix0a2	79	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	98.03
d1a62a2	78	Rho termination factor, RNA-binding domain {Escher	97.0
d1a62a2	78	Rho termination factor, RNA-binding domain {Escher	96.75
d2ix0a1	90	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	96.55
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	92.62
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	92.15
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	91.67
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	91.55
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	90.83
d2ix0a1	90	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	90.29
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	89.61
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	88.87
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	88.47
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	86.34
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	85.23
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	84.15
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	83.84
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	83.44
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	82.05
d1u0la1	66	Probable GTPase EngC (YjeQ), N-terminal domain {Th	81.71
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	80.1
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	80.09

>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=99.92  E-value=5.4e-26  Score=154.13  Aligned_cols=78  Identities=49%  Similarity=0.856  Sum_probs=71.5

Q ss_pred             CceeceeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeecC
Q psy9900           1 MTKFEIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGP   78 (191)
Q Consensus         1 ~~~~~~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~~   78 (191)
                      |.++|+.+.+|+|||||..||||||.++++++|||||+|+|........++.|.+|++|+|++..+++|++|.+|+.|
T Consensus         1 ~~k~~~~r~~G~VKwfn~~KGfGFI~~ddg~~DvFvH~s~i~~~g~~~~~~~L~~G~~V~f~~~~~~~G~~A~~Vtgp   78 (79)
T d1h95a_           1 MKKVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGP   78 (79)
T ss_dssp             CCSCCEEEEEEEEEEEETTTTEEEEEEGGGTEEEEEEGGGBCSCCCSCCSCSCCSSCEEEEEEEECSSSEEEESBCCC
T ss_pred             CchHhcCcccEEEEEEcCCCCeEEEEECCCCccEEEEhhHcccCCCcceeeecCCCCEEEEEEEeCCCCCeeEEEeCC
Confidence            899999999999999999999999999998899999999998763333478899999999999999999999999875

>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=99.91  E-value=6e-25  Score=148.90  Aligned_cols=77  Identities=47%  Similarity=0.826  Sum_probs=69.9

Q ss_pred             cccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecCC
Q psy9900         104 FPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPN  180 (191)
Q Consensus       104 ~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~~  180 (191)
                      .+++.++.|+|||||..||||||+++++++|||||+++|...+.+..++.|.+|+.|+|++.++++|++|++|++|+
T Consensus         3 k~~~~r~~G~VKwfn~~KGfGFI~~ddg~~DvFvH~s~i~~~g~~~~~~~L~~G~~V~f~~~~~~~G~~A~~Vtgpg   79 (79)
T d1h95a_           3 KVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGPG   79 (79)
T ss_dssp             SCCEEEEEEEEEEEETTTTEEEEEEGGGTEEEEEEGGGBCSCCCSCCSCSCCSSCEEEEEEEECSSSEEEESBCCCC
T ss_pred             hHhcCcccEEEEEEcCCCCeEEEEECCCCccEEEEhhHcccCCCcceeeecCCCCEEEEEEEeCCCCCeeEEEeCCC
Confidence            45677899999999999999999999989999999999988654455789999999999999999999999999875

>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=99.90  E-value=4.8e-24  Score=140.92  Aligned_cols=67  Identities=43%  Similarity=0.656  Sum_probs=63.3

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeec
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG   77 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~   77 (191)
                      .+++|+|||||..||||||.++++++|||||+|+|...    +++.|.+|++|+|++..+++|++|++|+.
T Consensus         2 ~r~~G~Vk~f~~~kGfGFI~~d~g~~diFvH~s~l~~~----~~~~L~~G~~V~f~~~~~~~G~~A~~V~~   68 (69)
T d1mjca_           2 GKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQND----GYKSLDEGQKVSFTIESGAKGPAAGNVTS   68 (69)
T ss_dssp             CCEEEEEEEEETTTTEEEEEETTSCCCEEEEGGGBCCT----TTCCCCTTCEEEEEEECCSSSCEEEEEEE
T ss_pred             CCEEEEEEEEeCCCCEEEEEEcCCCccEEEEhHHhccc----CCCcCCCCCEEEEEEEeCCCCcEEEEEEe
Confidence            57899999999999999999999889999999999876    68999999999999999999999999975

>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=99.90  E-value=6.4e-24  Score=140.32  Aligned_cols=68  Identities=43%  Similarity=0.635  Sum_probs=63.4

Q ss_pred             eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecC
Q psy9900         108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGP  179 (191)
Q Consensus       108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~  179 (191)
                      .+++|+|||||..||||||+++++++|||||+++|...    +++.|.+|+.|+|++.++++|++|++|+.+
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 GKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQND----GYKSLDEGQKVSFTIESGAKGPAAGNVTSL   69 (69)
T ss_dssp             CCEEEEEEEEETTTTEEEEEETTSCCCEEEEGGGBCCT----TTCCCCTTCEEEEEEECCSSSCEEEEEEEC
T ss_pred             CCEEEEEEEEeCCCCEEEEEEcCCCccEEEEhHHhccc----CCCcCCCCCEEEEEEEeCCCCcEEEEEEeC
Confidence            36899999999999999999999889999999999864    588999999999999999999999999864

>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=99.87  E-value=9.6e-23  Score=133.50  Aligned_cols=65  Identities=35%  Similarity=0.589  Sum_probs=59.9

Q ss_pred             ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeec
Q psy9900           8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG   77 (191)
Q Consensus         8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~   77 (191)
                      |.+|+|||||..||||||.+++ ++|||||+|+|...    +++.|.+|++|+|.+..+++|++|.+|+.
T Consensus         1 M~~G~Vk~fn~~kGfGFI~~d~-g~DiF~H~s~l~~~----~~~~L~~G~~V~f~~~~~~~G~~A~~V~~   65 (66)
T d1c9oa_           1 MQRGKVKWFNNEKGYGFIEVEG-GSDVFVHFTAIQGE----GFKTLEEGQEVSFEIVQGNRGPQAANVVK   65 (66)
T ss_dssp             CEEEEEEEEETTTTEEEEEETT-EEEEEEEGGGBCSS----SCCCCCTTCEEEEEEEEETTEEEEEEEEE
T ss_pred             CCCeEEEEEECCCCEEEEEecC-CceEEEEehhcccc----cCCcCCCCCEEEEEEEECCCCCEEEEEEE
Confidence            4589999999999999999975 68999999999876    68999999999999999999999999974

>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=99.87  E-value=6.1e-23  Score=134.41  Aligned_cols=66  Identities=44%  Similarity=0.700  Sum_probs=60.8

Q ss_pred             eeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecCC
Q psy9900         110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPN  180 (191)
Q Consensus       110 ~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~~  180 (191)
                      ++|+|||||..||||||++++ ++|||||+|+|...    +++.|.+|+.|+|++.++++|++|.+|++++
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 MRGKVKWFDSKKGYGFITKDE-GGDVFVHWSAIEME----GFKTLKEGQVVEFEIQEGKKGPQAAHVKVVE   66 (66)
T ss_dssp             CCEEEEEEETTTTEEEEEETT-SCBCBBCSSSSCCS----SCCCCCSSSEEEEEEECSSSCCEEEEEEEEC
T ss_pred             CeEEEEEEeCCCCeeEEEecC-CceEEEEhHHhccc----CCCcCCCCCEEEEEEEECCCCCEEEEEEecC
Confidence            479999999999999999987 56999999999864    5889999999999999999999999999864

>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=99.86  E-value=1.5e-22  Score=132.57  Aligned_cols=65  Identities=45%  Similarity=0.706  Sum_probs=60.1

Q ss_pred             cceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeecC
Q psy9900           9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGP   78 (191)
Q Consensus         9 ~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~~   78 (191)
                      ++|+|||||..||||||.+++ ++|||||.|+|...    +++.|.+|++|+|++..+++|++|.+|..+
T Consensus         1 l~G~Vk~f~~~kGfGFI~~~~-g~diFvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~i   65 (66)
T d1g6pa_           1 MRGKVKWFDSKKGYGFITKDE-GGDVFVHWSAIEME----GFKTLKEGQVVEFEIQEGKKGPQAAHVKVV   65 (66)
T ss_dssp             CCEEEEEEETTTTEEEEEETT-SCBCBBCSSSSCCS----SCCCCCSSSEEEEEEECSSSCCEEEEEEEE
T ss_pred             CeEEEEEEeCCCCeeEEEecC-CceEEEEhHHhccc----CCCcCCCCCEEEEEEEECCCCCEEEEEEec
Confidence            579999999999999999987 56999999999876    689999999999999999999999999864

>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=99.86  E-value=2.6e-22  Score=131.41  Aligned_cols=65  Identities=35%  Similarity=0.580  Sum_probs=59.8

Q ss_pred             eeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecC
Q psy9900         110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGP  179 (191)
Q Consensus       110 ~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~  179 (191)
                      .+|+|||||..||||||++++ ++|||||+|+|...    +++.|.+|++|+|.+.++++|++|++|+.+
T Consensus         2 ~~G~Vk~fn~~kGfGFI~~d~-g~DiF~H~s~l~~~----~~~~L~~G~~V~f~~~~~~~G~~A~~V~~l   66 (66)
T d1c9oa_           2 QRGKVKWFNNEKGYGFIEVEG-GSDVFVHFTAIQGE----GFKTLEEGQEVSFEIVQGNRGPQAANVVKL   66 (66)
T ss_dssp             EEEEEEEEETTTTEEEEEETT-EEEEEEEGGGBCSS----SCCCCCTTCEEEEEEEEETTEEEEEEEEEC
T ss_pred             CCeEEEEEECCCCEEEEEecC-CceEEEEehhcccc----cCCcCCCCCEEEEEEEECCCCCEEEEEEEC
Confidence            479999999999999999975 78999999999864    578999999999999999999999999864

>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=99.68  E-value=8.7e-17  Score=110.62  Aligned_cols=71  Identities=21%  Similarity=0.374  Sum_probs=61.8

Q ss_pred             cccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC--ceeEEeecCCC
Q psy9900         104 FPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD--IEAINVTGPNG  181 (191)
Q Consensus       104 ~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg--~~A~~V~~~~~  181 (191)
                      .....+.+|+|+||+  +|||||+++++.+|||||++++...     ++.|++||.|+|++.+++|+  ++|++|..+.+
T Consensus        13 ~~~~~r~~G~I~~~~--~gfGFI~~~~~~~dvF~H~s~~~~~-----~~~l~~G~~VeF~v~~~~kg~k~~Av~V~~~~~   85 (89)
T d1wfqa_          13 TSAALRETGVIEKLL--TSYGFIQCSERQARLFFHCSQYNGN-----LQDLKVGDDVEFEVSSDRRTGKPIAVKLVKISG   85 (89)
T ss_dssp             SSCCCEEEEEEEEEC--SSEEEEEETTTTEEEEEETTTCSSC-----TTTCCTTCCEEEEEEECSSSCCEEEEEEEESSC
T ss_pred             CCccceEEEEEEEec--CccceEEeCCCCceEEEEeehhhcc-----CCcccCCCEEEEEEEECCCCCceEEEEEEECCC
Confidence            345567899999994  6999999999889999999999743     68899999999999999987  78999987764

>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=99.67  E-value=8.7e-17  Score=110.62  Aligned_cols=70  Identities=20%  Similarity=0.354  Sum_probs=61.2

Q ss_pred             eceeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCC--ceeeEeecCCC
Q psy9900           4 FEIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD--IEAINVTGPNG   80 (191)
Q Consensus         4 ~~~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g--~~A~~v~~~~~   80 (191)
                      .+..|.+|+|+||+  +|||||.++++++|||||++++..     +++.|.+||+|+|++..++++  ++|++|..+.+
T Consensus        14 ~~~~r~~G~I~~~~--~gfGFI~~~~~~~dvF~H~s~~~~-----~~~~l~~G~~VeF~v~~~~kg~k~~Av~V~~~~~   85 (89)
T d1wfqa_          14 SAALRETGVIEKLL--TSYGFIQCSERQARLFFHCSQYNG-----NLQDLKVGDDVEFEVSSDRRTGKPIAVKLVKISG   85 (89)
T ss_dssp             SCCCEEEEEEEEEC--SSEEEEEETTTTEEEEEETTTCSS-----CTTTCCTTCCEEEEEEECSSSCCEEEEEEEESSC
T ss_pred             CccceEEEEEEEec--CccceEEeCCCCceEEEEeehhhc-----cCCcccCCCEEEEEEEECCCCCceEEEEEEECCC
Confidence            46778999999995  699999999998999999999975     468999999999999999986  67888876543

>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=98.14  E-value=8.5e-07  Score=58.42  Aligned_cols=57  Identities=23%  Similarity=0.330  Sum_probs=42.2

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEe
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINV   75 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v   75 (191)
                      ....|+|.-  ..+||||+.+++ ++|||++...+..++         .||+|.+.+....+.+++.-+
T Consensus        17 ~~~~G~i~~--~~~G~GFv~~d~-~~DifI~~~~~~~A~---------~GD~V~v~i~~~~~r~eg~I~   73 (79)
T d2ix0a2          17 PRAEGVVKA--TEKGFGFLEVDA-QKSYFIPPPQMKKVM---------HGDRIIAVIHSEKERESAEPE   73 (79)
T ss_dssp             CEEEEEEEC--CC--CEEEEEET-TEEEEECHHHHTTCC---------TTCEEEEEEECC--CCEEEEE
T ss_pred             CEEEEEEEE--eCCCcEEEEECC-CCcEEECHHHHcCCC---------CCCEEEEEEEeCCCcEEEEEE
Confidence            345687765  479999999987 789999999999986         999999998754444555443

>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=98.03  E-value=3.1e-06  Score=55.63  Aligned_cols=61  Identities=21%  Similarity=0.254  Sum_probs=45.9

Q ss_pred             eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecCC
Q psy9900         108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPN  180 (191)
Q Consensus       108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~~  180 (191)
                      ..+.|+|..-  .+||||+.+++ ++|||++..++..+         -.||+|++.+...++.++|.-+++++
T Consensus        17 ~~~~G~i~~~--~~G~GFv~~d~-~~DifI~~~~~~~A---------~~GD~V~v~i~~~~~r~eg~I~~ilE   77 (79)
T d2ix0a2          17 PRAEGVVKAT--EKGFGFLEVDA-QKSYFIPPPQMKKV---------MHGDRIIAVIHSEKERESAEPEELVE   77 (79)
T ss_dssp             CEEEEEEECC--C--CEEEEEET-TEEEEECHHHHTTC---------CTTCEEEEEEECC--CCEEEEEEEEE
T ss_pred             CEEEEEEEEe--CCCcEEEEECC-CCcEEECHHHHcCC---------CCCCEEEEEEEeCCCcEEEEEEEEec
Confidence            3567888653  78999999987 78999999999865         57999999998665558887776653

>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=97.00  E-value=0.00054  Score=44.34  Aligned_cols=64  Identities=27%  Similarity=0.442  Sum_probs=49.2

Q ss_pred             eeeEEEeecCCCceeEEeCC-----CCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC---ceeEEeecCCCC
Q psy9900         111 RGIVKFYDSKRGFGFITRLD-----NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD---IEAINVTGPNGI  182 (191)
Q Consensus       111 ~G~Vk~~~~~kgfGFI~~~d-----~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg---~~A~~V~~~~~~  182 (191)
                      .|++-..  ..|||||...+     +..||||+.+.+..       -.|+.||.|+=.+.....|   +.-+.|..++|.
T Consensus         5 ~GiLei~--~dGyGFLR~~~~~y~~~~~DiyVs~s~Irr-------fgLR~GD~V~G~vr~p~~~ek~~~L~~V~~VNG~   75 (78)
T d1a62a2           5 DGVLEIL--QDGFGFLRSADSSYLAGPDDIYVSPSQIRR-------FNLRTGDTISGKIRPPKEGERYFALLKVNEVNFD   75 (78)
T ss_dssp             EEEEEEC--TTSCEEEECGGGTTCCCTTCEEECHHHHHH-------TTCCTTCEEEEEEECCCTTCCSEEEEEEEEETTB
T ss_pred             EEEEEEc--CCCcEEeECCccCCCCCCcceEECHHHHHH-------hCCCcCcEEEEEEECCCCCCCceeeEEEeeeCCc
Confidence            3555443  58999999843     34899999999997       5899999999999886665   557788877764


Q ss_pred             C
Q psy9900         183 P  183 (191)
Q Consensus       183 ~  183 (191)
                      +
T Consensus        76 ~   76 (78)
T d1a62a2          76 K   76 (78)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=96.75  E-value=0.0013  Score=42.42  Aligned_cols=62  Identities=26%  Similarity=0.475  Sum_probs=44.3

Q ss_pred             ceEEEEeeCCCCeeEEEeC-----CCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCC---ceeeEeecCCC
Q psy9900          10 RGIVKFYDSKRGFGFITRL-----DNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD---IEAINVTGPNG   80 (191)
Q Consensus        10 ~G~vk~~~~~kGfGFI~~~-----~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g---~~A~~v~~~~~   80 (191)
                      .|.+---  ..|||||...     ...+||||+.+.++..       .|+.||.|+-.+.....+   +....|..+++
T Consensus         5 ~GiLei~--~dGyGFLR~~~~~y~~~~~DiyVs~s~Irrf-------gLR~GD~V~G~vr~p~~~ek~~~L~~V~~VNG   74 (78)
T d1a62a2           5 DGVLEIL--QDGFGFLRSADSSYLAGPDDIYVSPSQIRRF-------NLRTGDTISGKIRPPKEGERYFALLKVNEVNF   74 (78)
T ss_dssp             EEEEEEC--TTSCEEEECGGGTTCCCTTCEEECHHHHHHT-------TCCTTCEEEEEEECCCTTCCSEEEEEEEEETT
T ss_pred             EEEEEEc--CCCcEEeECCccCCCCCCcceEECHHHHHHh-------CCCcCcEEEEEEECCCCCCCceeeEEEeeeCC
Confidence            3554332  5899999973     2357999999999973       789999999998876554   33455555443

>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=96.55  E-value=0.012  Score=38.66  Aligned_cols=63  Identities=10%  Similarity=-0.130  Sum_probs=48.3

Q ss_pred             eEEEeecCCCceeEEeCCCC--CcEEEeccchhccCcccccccCCCCCEEEEEEEEcC----CCceeEEeecCCCC
Q psy9900         113 IVKFYDSKRGFGFITRLDNK--EDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK----KDIEAINVTGPNGI  182 (191)
Q Consensus       113 ~Vk~~~~~kgfGFI~~~d~~--~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~----kg~~A~~V~~~~~~  182 (191)
                      .|+.|...++++|+.|++..  .+||+-......       ..++.||.|..+|.+=+    +.++|.-++.++.+
T Consensus         4 fVGr~~~~~~~~fVvPd~~ri~~~I~I~~~~~~~-------~~ak~Gd~Vvvei~~~P~~~~~~~~g~I~evlG~~   72 (90)
T d2ix0a1           4 FVGKVQGKNDRLAIVPDHPLLKDAIPCRAARGLN-------HEFKEGDWAVAEMRRHPLKGDRSFYAELTQYITFG   72 (90)
T ss_dssp             EEEEEESCSSSEEEEESCTTCCSCEEEEECTTCC-------CCCCTTCEEEEEEEECGGGTCSSCEEEEEEECCCT
T ss_pred             EEEEEEEeCCEEEEEeCCCccccccccccccccc-------ccCCCCCEEEEEEEeCCCCCCCCceEEEEEEEecC
Confidence            56777789999999999976  789997655432       35689999999999843    23678888877753

>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=92.62  E-value=0.21  Score=31.05  Aligned_cols=61  Identities=20%  Similarity=0.212  Sum_probs=44.2

Q ss_pred             ceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEc-CCC
Q psy9900         107 VHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG-KKD  170 (191)
Q Consensus       107 ~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~-~kg  170 (191)
                      ...+.|+|+...+   ||.+..-+.+.+-|+|.+++.......--.-+++||.|.+.+..- +++
T Consensus         6 G~iv~G~V~~v~~---~G~fV~l~~~~~Glv~~sels~~~~~~~~~~~~~G~~v~v~Vi~id~~~   67 (76)
T d1sroa_           6 GRVYTGKVTRIVD---FGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDRQG   67 (76)
T ss_dssp             TSEEEEEEEEEET---TEEEEECSSSCCCBCCTTSSCSSCCSCHHHHCCTTCEEEEEEEECCTTC
T ss_pred             CCEEEEEEEEEeC---cEEEEEeCCCCEEEEEhHHhCccccCCHHHccCCCCEEEEEEEEECCCC
Confidence            3568899999853   787777666789999999997542111123489999999999884 444

>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=92.15  E-value=0.4  Score=30.27  Aligned_cols=59  Identities=12%  Similarity=0.099  Sum_probs=36.8

Q ss_pred             ceeeeeeEEEeecCCCce-eEEeCC-CCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcC
Q psy9900         107 VHTVRGIVKFYDSKRGFG-FITRLD-NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK  168 (191)
Q Consensus       107 ~~~~~G~Vk~~~~~kgfG-FI~~~d-~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~  168 (191)
                      ...+.|+|....   .|| ||.-.+ .+-+-|+|.+++.......-...++.||.|.+.|..-+
T Consensus        14 G~iv~G~V~~i~---~~G~fV~l~~~~~i~G~i~~sels~~~~~~~~~~~~~Gd~v~~kV~~vd   74 (86)
T d1kl9a2          14 EDVVMVNVRSIA---EMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVD   74 (86)
T ss_dssp             TCEEEEEEEEEC---SSEEEEEETTTTTEEEEEEGGGC------------CTTCEEEEEEEEEE
T ss_pred             CCEEEEEEEEEe---CCeEEEEEecCCCEEEEEEeeeccccccccceEEeecccEEEEEEEEEE
Confidence            456889998873   478 566554 36789999999965422222355789999999998843

>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=91.67  E-value=0.52  Score=30.20  Aligned_cols=62  Identities=13%  Similarity=0.091  Sum_probs=46.8

Q ss_pred             eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcc---------cccccCCCCCEEEEEEEEcCCCc
Q psy9900         109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPK---------KFFQSLGLGEIVDFNIGVGKKDI  171 (191)
Q Consensus       109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~---------~~~~~l~~G~~V~f~i~~~~kg~  171 (191)
                      -+.|+|....+.-.--||.-.. +++-|+|++++......         .--..|++||.|.+++...+.|-
T Consensus         3 IY~G~V~~V~pgl~AAFVDiG~-~k~gFL~~~di~~~~~~~~~~~~~~~~i~~~l~~G~~ilVQV~Ke~~~~   73 (87)
T d1smxa_           3 IYKGKITRIEPSLEAAFVDYGA-ERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGN   73 (87)
T ss_dssp             CEEEEEEEEEGGGTEEEEESSS-SSCEEEEGGGSCGGGCSSCCCSSSCCCGGGTCCTTCEEEEEEEECCBTT
T ss_pred             cEEEEEEEecCCceEEEEEeCC-CccceeEecccceeeeccccccccccchhhhccCCCeEEEEEeecccCC
Confidence            4789999998888889997766 78899999987543100         01235899999999999977553

>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=91.55  E-value=0.22  Score=31.56  Aligned_cols=58  Identities=12%  Similarity=0.094  Sum_probs=36.0

Q ss_pred             eeccceEEEEeeCCCCee-EEEeCC-CCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEc
Q psy9900           6 IHTVRGIVKFYDSKRGFG-FITRLD-NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG   66 (191)
Q Consensus         6 ~~~~~G~vk~~~~~kGfG-FI~~~~-~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~   66 (191)
                      ..-..|+|+...   -|| ||...+ ++-+-|+|.+++......+....++.||.|.+.+..-
T Consensus        14 G~iv~G~V~~i~---~~G~fV~l~~~~~i~G~i~~sels~~~~~~~~~~~~~Gd~v~~kV~~v   73 (86)
T d1kl9a2          14 EDVVMVNVRSIA---EMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRV   73 (86)
T ss_dssp             TCEEEEEEEEEC---SSEEEEEETTTTTEEEEEEGGGC------------CTTCEEEEEEEEE
T ss_pred             CCEEEEEEEEEe---CCeEEEEEecCCCEEEEEEeeeccccccccceEEeecccEEEEEEEEE
Confidence            345789999884   478 666654 3578999999996543222345578999999998763

>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=90.83  E-value=0.12  Score=32.26  Aligned_cols=57  Identities=21%  Similarity=0.221  Sum_probs=42.1

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEc
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG   66 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~   66 (191)
                      ....|+|+....   ||....-+.+-+-|+|.+++......+....++.||.|.+.+..-
T Consensus         7 ~iv~G~V~~v~~---~G~fV~l~~~~~Glv~~sels~~~~~~~~~~~~~G~~v~v~Vi~i   63 (76)
T d1sroa_           7 RVYTGKVTRIVD---FGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEV   63 (76)
T ss_dssp             SEEEEEEEEEET---TEEEEECSSSCCCBCCTTSSCSSCCSCHHHHCCTTCEEEEEEEEC
T ss_pred             CEEEEEEEEEeC---cEEEEEeCCCCEEEEEhHHhCccccCCHHHccCCCCEEEEEEEEE
Confidence            346799999974   787776666789999999997542111223479999999998873

>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=90.29  E-value=1.4  Score=28.09  Aligned_cols=62  Identities=13%  Similarity=-0.042  Sum_probs=42.8

Q ss_pred             ccceEEEEeeCCCCeeEEEeCCCC--ccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC-CC---ceeeEeecCC
Q psy9900           8 TVRGIVKFYDSKRGFGFITRLDNK--EDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK-KD---IEAINVTGPN   79 (191)
Q Consensus         8 ~~~G~vk~~~~~kGfGFI~~~~~~--~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~-~g---~~A~~v~~~~   79 (191)
                      +..|++   -..++++|+.+++..  .+||+.-.....       ...++||.|..++.+-+ ++   +.|.-+..++
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            344555   368899999999875  689987665421       34679999999999865 22   4555444443

>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=89.61  E-value=1.4  Score=27.23  Aligned_cols=58  Identities=19%  Similarity=0.185  Sum_probs=42.2

Q ss_pred             eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccC-cccccccCCCCCEEEEEEEEcC
Q psy9900         108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMN-PKKFFQSLGLGEIVDFNIGVGK  168 (191)
Q Consensus       108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~-~~~~~~~l~~G~~V~f~i~~~~  168 (191)
                      +.+.|+|....   .+|....-+.+-+-|+|.+++.... .......++.||.|...|..-+
T Consensus         7 d~V~G~V~~v~---~~g~~V~i~~~~~g~l~~se~s~~~~~~~~~~~~~vGd~V~~kV~~vd   65 (83)
T d2ba0a1           7 DVVIGIIREVA---ANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNID   65 (83)
T ss_dssp             CEEEEEEEEEC---SSEEEEECSSSSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEEC
T ss_pred             CEEEEEEEEEE---CCEEEEecCCCeeEEEecccccccccccChhhhcccccEEEEEEEEEC
Confidence            46789998864   3677777666889999999997532 1122345899999999998743

>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=88.87  E-value=1.7  Score=27.71  Aligned_cols=69  Identities=17%  Similarity=0.249  Sum_probs=48.6

Q ss_pred             ceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEc--CCCceeEEeec
Q psy9900         107 VHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG--KKDIEAINVTG  178 (191)
Q Consensus       107 ~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~--~kg~~A~~V~~  178 (191)
                      ...+.|+|....   .||.+..-+.+-+-|+|.+++.......--..++.||.|.+.|..-  +++.-...++.
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 GMVLEGVVTNVT---NFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGLSMRM   89 (94)
T ss_dssp             TCEEEEEEEEEE---TTEEEEECSSSSCEEEEGGGGCSSCCSCHHHHCCTTCEEEEEEEEEETTTTEEEEESCT
T ss_pred             CCEEEEEEEEEE---CcEEEEEeCCCceEEeehhhhhcccccChhhhhccCcEEEEEEEEEECCCCEEEEEEec
Confidence            456889999985   3787777766889999999996432112224678999999998884  34544444443

>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=88.47  E-value=0.26  Score=31.05  Aligned_cols=57  Identities=14%  Similarity=0.054  Sum_probs=38.6

Q ss_pred             eccceEEEEeeCCCCee-EEEeCC-CCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEc
Q psy9900           7 HTVRGIVKFYDSKRGFG-FITRLD-NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG   66 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfG-FI~~~~-~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~   66 (191)
                      ...+|+|+...+   || ||..++ ++-+-|+|.+++......+....++.||.|.+.+..-
T Consensus        13 ~iv~G~V~~v~~---~G~fV~l~~~~gi~Gli~~sels~~~~~~~~~~~~~G~~v~~kV~~v   71 (84)
T d2ahob2          13 EILIATVKQVFD---YGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRV   71 (84)
T ss_dssp             CCCEEEEEEEET---TEEEEEETTTTTEEEEECGGGCC-----CHHHHTCSSCEEECEEEEE
T ss_pred             CEEEEEEEEEEC---CEEEEEECCcCCEEEEEEccccccccccccceEeecccEEEEEEEEE
Confidence            457899999863   66 555554 3568999999998653222234479999999998763

>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=86.34  E-value=1.6  Score=29.06  Aligned_cols=69  Identities=12%  Similarity=0.138  Sum_probs=47.6

Q ss_pred             cceeeeeeEEEeecCCCceeEEeC-CCCCcEEEeccchhccC-cccccccCCCCCEEEEEEEEcCCCceeEEee
Q psy9900         106 AVHTVRGIVKFYDSKRGFGFITRL-DNKEDIFVHKSSIVKMN-PKKFFQSLGLGEIVDFNIGVGKKDIEAINVT  177 (191)
Q Consensus       106 ~~~~~~G~Vk~~~~~kgfGFI~~~-d~~~dvF~h~s~~~~~~-~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~  177 (191)
                      ..+.++|+|+..   ..||++..- ..+-+-|+|.+++.... .......+++||.|.+.|..-+..-.-+.++
T Consensus        21 ~G~iv~G~V~~i---~~~G~~V~lg~~~~~G~l~~~els~~~~~~~~~~~~~vGq~v~~~V~~vd~~~~~i~LS   91 (119)
T d1wi5a_          21 PGMLLTGTVSSL---EDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLS   91 (119)
T ss_dssp             TTCEEEEEEEEE---CSSEEEEECCCSSCEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCTTSCEEEEE
T ss_pred             CCCEEEEEEEEE---eccEEEEEEeccccceEEeHHHhccccccCCHHHhcccceEEEEEEEEEeCCCCEEEEE
Confidence            346789999987   346777766 35678999999986420 0011357899999999999977654444444

>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=85.23  E-value=1.2  Score=28.50  Aligned_cols=57  Identities=21%  Similarity=0.308  Sum_probs=42.2

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEc
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG   66 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~   66 (191)
                      ....|+|+...   -||.+..-..+-+-|+|.+++......+-...++.||.|.+.+..-
T Consensus        20 ~iv~g~V~~v~---~~G~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~vGq~v~~~V~~i   76 (94)
T d3bzka4          20 MVLEGVVTNVT---NFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEV   76 (94)
T ss_dssp             CEEEEEEEEEE---TTEEEEECSSSSCEEEEGGGGCSSCCSCHHHHCCTTCEEEEEEEEE
T ss_pred             CEEEEEEEEEE---CcEEEEEeCCCceEEeehhhhhcccccChhhhhccCcEEEEEEEEE
Confidence            34679999997   3788877776889999999997542222234568999999998763

>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=84.15  E-value=1.6  Score=28.58  Aligned_cols=56  Identities=27%  Similarity=0.225  Sum_probs=40.5

Q ss_pred             eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCc-----------ccccccCCCCCEEEEEEEEc
Q psy9900         108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNP-----------KKFFQSLGLGEIVDFNIGVG  167 (191)
Q Consensus       108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~-----------~~~~~~l~~G~~V~f~i~~~  167 (191)
                      ..+.|+|...+   .||+...-+ +-+-|+|.++|....-           +.--..++.||.|...|..-
T Consensus         5 ei~~g~V~~v~---~~G~FVel~-~ieGlv~~s~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkV~~v   71 (106)
T d1go3e1           5 ELIEGEVVDVV---EFGSFVRLG-PLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAI   71 (106)
T ss_dssp             CEEEEEEEEEE---TTEEEEECS-SSEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEE
T ss_pred             CEEEEEEEEEe---eeEEEEEee-CeEEEEEeecccCceeeeccceeEEeecccccceeecceEEEEEEEE
Confidence            45778988863   478777765 5899999999975310           00115789999999999874

>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=83.84  E-value=2.6  Score=26.64  Aligned_cols=67  Identities=13%  Similarity=0.112  Sum_probs=47.9

Q ss_pred             cceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCC---------CCcccCCCCCEEEEEEEEcCCCceeeEee
Q psy9900           9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPK---------KFFQSLGLGEIVDFNIGVGKKDIEAINVT   76 (191)
Q Consensus         9 ~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~---------~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~   76 (191)
                      ..|+|+...+--.=-||.... +.+-|+|++++......         .-...|++||.|.+++...+.+-+...++
T Consensus         4 Y~G~V~~V~pgl~AAFVDiG~-~k~gFL~~~di~~~~~~~~~~~~~~~~i~~~l~~G~~ilVQV~Ke~~~~KGprlT   79 (87)
T d1smxa_           4 YKGKITRIEPSLEAAFVDYGA-ERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALT   79 (87)
T ss_dssp             EEEEEEEEEGGGTEEEEESSS-SSCEEEEGGGSCGGGCSSCCCSSSCCCGGGTCCTTCEEEEEEEECCBTTBCCEEE
T ss_pred             EEEEEEEecCCceEEEEEeCC-CccceeEecccceeeeccccccccccchhhhccCCCeEEEEEeecccCCCCceEE
Confidence            468899988888888998776 67899999987543100         00135799999999999887764443343

>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=83.44  E-value=2.3  Score=26.16  Aligned_cols=57  Identities=19%  Similarity=0.188  Sum_probs=40.4

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecC-CCCCcccCCCCCEEEEEEEEc
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMN-PKKFFQSLGLGEIVDFNIGVG   66 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~-~~~g~~~l~~Gd~V~f~~~~~   66 (191)
                      ....|+|+.-..   ||+...-+++-+-|+|.+++.... ..+....+..||.|.+.+..-
T Consensus         7 d~V~G~V~~v~~---~g~~V~i~~~~~g~l~~se~s~~~~~~~~~~~~~vGd~V~~kV~~v   64 (83)
T d2ba0a1           7 DVVIGIIREVAA---NGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNI   64 (83)
T ss_dssp             CEEEEEEEEECS---SEEEEECSSSSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEE
T ss_pred             CEEEEEEEEEEC---CEEEEecCCCeeEEEecccccccccccChhhhcccccEEEEEEEEE
Confidence            456799998753   566666565789999999986431 112334589999999999764

>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=82.05  E-value=4  Score=25.25  Aligned_cols=59  Identities=15%  Similarity=0.254  Sum_probs=42.4

Q ss_pred             eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCc---ccccccCCCCCEEEEEEEEcCC
Q psy9900         108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNP---KKFFQSLGLGEIVDFNIGVGKK  169 (191)
Q Consensus       108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~---~~~~~~l~~G~~V~f~i~~~~k  169 (191)
                      ....|+|+...   .||.+..-+.+-+-|+|.+++.....   ..-..-+++||.|...|..-++
T Consensus         9 div~G~V~~i~---~~g~fV~i~~~~~gll~~s~~~~~~~~~~~~~~~~~~~Gd~v~~kV~~vd~   70 (87)
T d2je6i1           9 DIVIGLVEDVE---IYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDR   70 (87)
T ss_dssp             CEEEEEEEEEC---SSEEEEECSSSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEET
T ss_pred             CEEEEEEEEEE---CCEEEEEeCCCEEEEEehHHhCCceeccccccchhhcccceEEEEEEEECC
Confidence            46789998863   47887777668899999999975310   0012358999999999987443

>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=81.71  E-value=3  Score=24.84  Aligned_cols=56  Identities=14%  Similarity=0.219  Sum_probs=35.5

Q ss_pred             eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC
Q psy9900         109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD  170 (191)
Q Consensus       109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg  170 (191)
                      +.+|+|...  ..+|=.+..++.++.+=.+..-.....    -..+..||.|+|+......|
T Consensus         2 ~~~G~Vi~~--~~~~y~V~~~e~g~~~~c~~rG~lr~~----~~~~~VGD~V~~~~~~~~~g   57 (66)
T d1u0la1           2 RRRGIVVSF--HSNMVTVEDEETGERILCKLRGKFRLQ----NLKIYVGDRVEYTPDETGSG   57 (66)
T ss_dssp             CEEEEEEEE--ETTEEEEEETTTCCEEEEEECGGGTTT----TCCCCTTCEEEEECCCSSSE
T ss_pred             CeeEEEEEE--ECCEEEEEECCCCcEEEEEeecccccc----CCccccCCEEEEEECCCCeE
Confidence            467877665  566777777655555546655433221    13578999999987765544

>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=80.10  E-value=2  Score=26.57  Aligned_cols=59  Identities=14%  Similarity=-0.008  Sum_probs=39.4

Q ss_pred             ceeeeeeEEEeecCCCcee-EEeCC-CCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcC
Q psy9900         107 VHTVRGIVKFYDSKRGFGF-ITRLD-NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK  168 (191)
Q Consensus       107 ~~~~~G~Vk~~~~~kgfGF-I~~~d-~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~  168 (191)
                      ...+.|+|+...+   ||. |.-.+ .+-+-|+|.+++.......-...++.||.|.+.+..-+
T Consensus        12 G~iv~G~V~~v~~---~G~fV~l~~~~gi~Gli~~sels~~~~~~~~~~~~~G~~v~~kV~~vd   72 (84)
T d2ahob2          12 GEILIATVKQVFD---YGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVD   72 (84)
T ss_dssp             TCCCEEEEEEEET---TEEEEEETTTTTEEEEECGGGCC-----CHHHHTCSSCEEECEEEEEE
T ss_pred             CCEEEEEEEEEEC---CEEEEEECCcCCEEEEEEccccccccccccceEeecccEEEEEEEEEE
Confidence            3567899988743   664 55553 35789999999976422122345899999999998743

>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=80.09  E-value=2.2  Score=27.82  Aligned_cols=55  Identities=27%  Similarity=0.256  Sum_probs=38.5

Q ss_pred             eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCC-----------CCCcccCCCCCEEEEEEEE
Q psy9900           7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNP-----------KKFFQSLGLGEIVDFNIGV   65 (191)
Q Consensus         7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~-----------~~g~~~l~~Gd~V~f~~~~   65 (191)
                      +-..|+|+.-+   .|||...-+ +-+-|+|.+.|....-           ...-..++.||.|.+.+..
T Consensus         5 ei~~g~V~~v~---~~G~FVel~-~ieGlv~~s~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkV~~   70 (106)
T d1go3e1           5 ELIEGEVVDVV---EFGSFVRLG-PLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVA   70 (106)
T ss_dssp             CEEEEEEEEEE---TTEEEEECS-SSEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEE
T ss_pred             CEEEEEEEEEe---eeEEEEEee-CeEEEEEeecccCceeeeccceeEEeecccccceeecceEEEEEEE
Confidence            44678888875   456666555 5899999999975310           0012568999999999875