Psyllid ID: psy547

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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-------200-------210-------220-------230-------240-------250-------260-------270-------280--
Protein Sequence
MQMCDSGTKAEATPSNPSANESPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQFAANKPKYNRRKAKANKRKRKSRRNNRLFGVKYQLEIPMEFSSKTMPFFMILFCCLQMCDSGTKAEATPSNPSASESPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLKNIVLYFSFVPQSV
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccEEEEEEEEEEEEEEccccEEEEEcccccccEEEEcEEEEEccccccccccccccEEEEEEEEcccccccEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccccccccccccccccccccccEEEEEEEEEccccEEEEEcccccccEEEEccccccccccccccccccccEEEEEEEEcccccccccccccccEEEEcccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccEEEEEEEEEEEEEEEEcccEEEEEcccccccEEEEHHHHHccccccEccccccccEEEEEEEEEccEEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccHHccccccHHHHcccccccccccccccccccccccccccccccEEEEEEEEEEEEEEEcccccEEEccccccccEEEEHHHHHcccccccEEEcccccEEEEEEccccccHHHHHHHHHEEEEEEEccccc
Coil and Loop (DISEMBL)
mqmcdsgtkaeatpsnpsanespkkepvVLATKVCGVVKWFsvksgygfiatpssnedvfvhskrikynnprkLYKTLaegetvefdimqgdkgheainvtgpdgrhvqgsqfaankpkynrrKAKANkrkrksrrnnrlfgvkyqleipmefssktmpFFMILFCCLQmcdsgtkaeatpsnpsasespkkepvVLATKVCGVVKWFsvksgygfiatpssnedvfvhskrikynnprkLYKTLaegetvefdimqgdkgnqfcFVLKNIVLYFSFVPQSV
Flexible Loop (DISEMBL)
mqmcdsgtkaeatpsnpsanespkkepVVLATKVCGVVKWFSVKSGYGFiatpssnedvfvhskrikynnprklYKTLAEGETVEFDIMQGDKGHEAINVTGPDGRHVQgsqfaankpkynrrkakankrkrksrrnnrlfgvkyqleiPMEFSSKTMPFFMILFCCLQMCDSGTKAEATpsnpsasespkkepvVLATKVCGVVKWFSVKSGYGFiatpssnedvfvhskrikynnprklYKTLAEGETVEFDIMQGDKGNQFCFVLKNIVLYFSFVPQSV
Low Complexity Region (SEG)
MQMCDSGTKAEATPSNPSANESPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQFaankpkynrrkakankrkrksrrnnrLFGVKYQLEIPMEFSSKTMPFFMILFCCLQMCDSGTKAEATPSNPSASESPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLKNIVLYFSFVPQSV
Disordered region (IsUnstruct)
***************************VVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ************************************************RLFGVKYQLEIPMEFSSKTMPFFMILFCCLQMCD**********************VVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLKNIVLYFSFV****
Disordered Region (DISOPRED)
*********************************VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQFAANKPKYNRRK**************************************************************************T*VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLKNIVLYF**V****
Disordered Region (DISEMBL)
**************************PVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQFAANKPK***************RRNNRLFGVKYQLEIPMEFSSKTMPFFMILFCCLQMCDSG********************VVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLKNIVLYFSFVPQSV
Disordered Region (DISPRO)
************************KEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGPDGR******************************************************FMILFC*************************KEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLKNIVLYFSFVPQ**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MQMCDSGTKAEATPSNPSANESPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQFAANKPKYNRRKAKANKRKRKSRRNNRLFGVKYQLEIPMEFSSKTMPFFMILFCCLQMCDSGTKAEATPSNPSASESPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLKNIVLYFSFVPQSV
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	282	2.2.26 [Sep-21-2011]
P41824	253	Y-box factor homolog OS=A	N/A	N/A	0.425	0.474	0.471	1e-27
Q62764	361	DNA-binding protein A OS=	yes	N/A	0.354	0.277	0.568	4e-27
Q9JKB3	361	DNA-binding protein A OS=	no	N/A	0.354	0.277	0.568	6e-27
P16989	372	DNA-binding protein A OS=	no	N/A	0.312	0.236	0.613	2e-26
P21573	303	Nuclease-sensitive elemen	N/A	N/A	0.312	0.290	0.602	2e-26
Q9Y2T7	364	Y-box-binding protein 2 O	no	N/A	0.397	0.307	0.504	4e-26
P62961	322	Nuclease-sensitive elemen	no	N/A	0.312	0.273	0.602	5e-26
P62960	322	Nuclease-sensitive elemen	no	N/A	0.312	0.273	0.602	5e-26
P67809	324	Nuclease-sensitive elemen	no	N/A	0.312	0.271	0.602	5e-26
P67808	324	Nuclease-sensitive elemen	no	N/A	0.312	0.271	0.602	5e-26

>sp|P41824|YBOXH_APLCA Y-box factor homolog OS=Aplysia californica PE=2 SV=1

 Score =  124 bits (310), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 57/121 (47%), Positives = 86/121 (71%), Gaps = 1/121 (0%)

Query: 3   MCDSGTKAEATPSNPSANESP-KKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFV 61
           M D+  + E   + P   ++  +KE  ++A++V G VKWF+VKSGYGFI    + EDVFV
Sbjct: 1   MADTEKQPEVEENQPDQEQNEEQKEKKIIASQVSGTVKWFNVKSGYGFINRDDTKEDVFV 60

Query: 62  HSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQFAANKPKYN 121
           H   I  NNPRK  +++ +GE VEFD+++G+KG+EA NVTGP+G +VQGS++AA++ ++ 
Sbjct: 61  HQTAIVKNNPRKYLRSVGDGEKVEFDVVEGEKGNEAANVTGPEGSNVQGSKYAADRRRFR 120

Query: 122 R 122
           R
Sbjct: 121 R 121

Binds RNA in vitro.
Aplysia californica (taxid: 6500)

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

 Score =  121 bits (304), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 58/102 (56%), Positives = 78/102 (76%), Gaps = 2/102 (1%)

Query: 15  SNPSANESPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKL 74
           S P+ +E  +K+  VLATKV G VKWF+V++GYGFI    + EDVFVH   IK NNPRK 
Sbjct: 66  SAPAGSEDAEKK--VLATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKY 123

Query: 75  YKTLAEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQFAAN 116
            +++ +GETVEFD+++G+KG EA NVTGPDG  V+GS++AA+
Sbjct: 124 LRSVGDGETVEFDVVEGEKGAEAANVTGPDGVPVEGSRYAAD 165

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)

>sp|Q9JKB3|DBPA_MOUSE DNA-binding protein A OS=Mus musculus GN=Csda PE=1 SV=2

 Score =  121 bits (304), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 58/102 (56%), Positives = 77/102 (75%), Gaps = 2/102 (1%)

Query: 15  SNPSANESPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKL 74
           S P+  E  +K+  VLATKV G VKWF+V++GYGFI    + EDVFVH   IK NNPRK 
Sbjct: 66  SAPAGGEDAEKK--VLATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKY 123

Query: 75  YKTLAEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQFAAN 116
            +++ +GETVEFD+++G+KG EA NVTGPDG  V+GS++AA+
Sbjct: 124 LRSVGDGETVEFDVVEGEKGAEAANVTGPDGVPVEGSRYAAD 165

Binds to the GM-CSF promoter. Seems to act as a repressor (By similarity). 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.

Mus musculus (taxid: 10090)

>sp|P16989|DBPA_HUMAN DNA-binding protein A OS=Homo sapiens GN=CSDA PE=1 SV=4

 Score =  119 bits (299), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 54/88 (61%), Positives = 70/88 (79%)

Query: 29  VLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDI 88
           VLATKV G VKWF+V++GYGFI    + EDVFVH   IK NNPRK  +++ +GETVEFD+
Sbjct: 86  VLATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDV 145

Query: 89  MQGDKGHEAINVTGPDGRHVQGSQFAAN 116
           ++G+KG EA NVTGPDG  V+GS++AA+
Sbjct: 146 VEGEKGAEAANVTGPDGVPVEGSRYAAD 173

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.

Homo sapiens (taxid: 9606)

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

 Score =  119 bits (299), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 53/88 (60%), Positives = 70/88 (79%)

Query: 29  VLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDI 88
           V+ATKV G VKWF+V++GYGFI    + EDVFVH   IK NNPRK  +++ +GETVEFD+
Sbjct: 32  VIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDV 91

Query: 89  MQGDKGHEAINVTGPDGRHVQGSQFAAN 116
           ++G+KG EA NVTGP+G  VQGS++AA+
Sbjct: 92  VEGEKGAEAANVTGPEGVPVQGSKYAAD 119

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|Q9Y2T7|YBOX2_HUMAN Y-box-binding protein 2 OS=Homo sapiens GN=YBX2 PE=1 SV=2

 Score =  118 bits (296), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 58/115 (50%), Positives = 80/115 (69%), Gaps = 3/115 (2%)

Query: 8   TKAEATPSNPSANESPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIK 67
           T    TP+ P+ +++ K    VLA +V G VKWF+V++GYGFI    + EDVFVH   IK
Sbjct: 71  TAVSGTPAPPARSQADKP---VLAIQVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIK 127

Query: 68  YNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQFAANKPKYNR 122
            NNPRK  +++ +GETVEFD+++G+KG EA NVTGP G  V+GS++A N+ K  R
Sbjct: 128 RNNPRKFLRSVGDGETVEFDVVEGEKGAEATNVTGPGGVPVKGSRYAPNRRKSRR 182

Major constituent of messenger ribonucleoprotein particles (mRNPs). Involved in the regulation of the stability and/or translation of germ cell mRNAs. Binds to Y-box consensus promoter element. Binds to full length mRNA with high affinity in a sequence-independent manner. Binds to short RNA sequences containing the consensus site 5'-UCCAUCA-3' with low affinity and limited sequence specificity. Its binding with maternal mRNAs is necessary for its cytoplasmic retention. May mark specific mRNAs (those transcribed from Y-box promoters) in the nucleus for cytoplasmic storage, thereby linking transcription and mRNA storage/translational delay.

Homo sapiens (taxid: 9606)

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

 Score =  118 bits (295), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 53/88 (60%), Positives = 69/88 (78%)

Query: 29  VLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDI 88
           V+ATKV G VKWF+V++GYGFI    + EDVFVH   IK NNPRK  +++ +GETVEFD+
Sbjct: 52  VIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDV 111

Query: 89  MQGDKGHEAINVTGPDGRHVQGSQFAAN 116
           ++G+KG EA NVTGP G  VQGS++AA+
Sbjct: 112 VEGEKGAEAANVTGPGGVPVQGSKYAAD 139

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 =  118 bits (295), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 53/88 (60%), Positives = 69/88 (78%)

Query: 29  VLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDI 88
           V+ATKV G VKWF+V++GYGFI    + EDVFVH   IK NNPRK  +++ +GETVEFD+
Sbjct: 52  VIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDV 111

Query: 89  MQGDKGHEAINVTGPDGRHVQGSQFAAN 116
           ++G+KG EA NVTGP G  VQGS++AA+
Sbjct: 112 VEGEKGAEAANVTGPGGVPVQGSKYAAD 139

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 =  118 bits (295), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 53/88 (60%), Positives = 69/88 (78%)

Query: 29  VLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDI 88
           V+ATKV G VKWF+V++GYGFI    + EDVFVH   IK NNPRK  +++ +GETVEFD+
Sbjct: 54  VIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDV 113

Query: 89  MQGDKGHEAINVTGPDGRHVQGSQFAAN 116
           ++G+KG EA NVTGP G  VQGS++AA+
Sbjct: 114 VEGEKGAEAANVTGPGGVPVQGSKYAAD 141

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 =  118 bits (295), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 53/88 (60%), Positives = 69/88 (78%)

Query: 29  VLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDI 88
           V+ATKV G VKWF+V++GYGFI    + EDVFVH   IK NNPRK  +++ +GETVEFD+
Sbjct: 54  VIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDV 113

Query: 89  MQGDKGHEAINVTGPDGRHVQGSQFAAN 116
           ++G+KG EA NVTGP G  VQGS++AA+
Sbjct: 114 VEGEKGAEAANVTGPGGVPVQGSKYAAD 141

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

Bos taurus (taxid: 9913)

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	282
194131839	181	Y-box protein Lyb2 [Lethenteron camtscha	0.351	0.546	0.585	6e-27
194131800	171	Y-box protein Lyb3 [Lethenteron camtscha	0.351	0.578	0.585	6e-27
291224890	283	PREDICTED: cold shock domain protein A s	0.351	0.349	0.563	4e-26
325297104	253	Y-box factor homolog [Aplysia californic	0.425	0.474	0.471	6e-26
195173115	335	GL15684 [Drosophila persimilis] gi|19846	0.436	0.367	0.496	7e-26
195327031	1378	GM24682 [Drosophila sechellia] gi|194119	0.379	0.077	0.568	1e-25
240849145	305	Y-box protein Ct-p40-like [Acyrthosiphon	0.368	0.340	0.537	2e-25
148235020	376	DNA-binding protein A [Bos taurus] gi|14	0.372	0.279	0.561	2e-25
395516174	255	PREDICTED: uncharacterized protein LOC10	0.354	0.392	0.57	2e-25
20806532	292	DNA-binding protein A short isoform [Mus	0.354	0.342	0.568	2e-25

>gi|194131839|gb|ACF33225.1| Y-box protein Lyb2 [Lethenteron camtschaticum]

 Score =  127 bits (319), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 58/99 (58%), Positives = 76/99 (76%)

Query: 24  KKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGET 83
           K E  V+ATKV G VKWF+VK+GYGFI    + EDVF+H   IK NNPRK  +++ +GET
Sbjct: 53  KPEKKVIATKVLGTVKWFNVKNGYGFINRNDTKEDVFIHQTAIKKNNPRKYLRSVGDGET 112

Query: 84  VEFDIMQGDKGHEAINVTGPDGRHVQGSQFAANKPKYNR 122
           VEFD+++G+KG EA NVTGPDG  VQGS++AA++ +Y R
Sbjct: 113 VEFDVVEGEKGAEAANVTGPDGAAVQGSRYAADRGRYRR 151

Source: Lethenteron camtschaticum

Species: Lethenteron camtschaticum

Genus: Lethenteron

Family: Petromyzontidae

Order: Petromyzontiformes

Phylum: Chordata

Superkingdom: Eukaryota

>gi|194131800|gb|ACF33224.1| Y-box protein Lyb3 [Lethenteron camtschaticum]

 Score =  127 bits (319), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 58/99 (58%), Positives = 76/99 (76%)

Query: 24  KKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGET 83
           K E  V+ATKV G VKWF+VK+GYGFI    + EDVF+H   IK NNPRK  +++ +GET
Sbjct: 53  KPEKKVIATKVLGTVKWFNVKNGYGFINRNDTKEDVFIHQTAIKKNNPRKYLRSVGDGET 112

Query: 84  VEFDIMQGDKGHEAINVTGPDGRHVQGSQFAANKPKYNR 122
           VEFD+++G+KG EA NVTGPDG  VQGS++AA++ +Y R
Sbjct: 113 VEFDVVEGEKGAEAANVTGPDGAAVQGSRYAADRGRYRR 151

Source: Lethenteron camtschaticum

Species: Lethenteron camtschaticum

Genus: Lethenteron

Family: Petromyzontidae

Order: Petromyzontiformes

Phylum: Chordata

Superkingdom: Eukaryota

>gi|291224890|ref|XP_002732435.1| PREDICTED: cold shock domain protein A short-like [Saccoglossus kowalevskii]

 Score =  124 bits (311), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 58/103 (56%), Positives = 78/103 (75%), Gaps = 4/103 (3%)

Query: 18  SANESPKK----EPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRK 73
           S+ + P+K    E  +LA KV G VKWF+VK+GYGFI    +NEDVFVH   IK NNPRK
Sbjct: 4   SSEQQPEKSVALEKKILAEKVSGTVKWFNVKNGYGFINRNDTNEDVFVHQTAIKKNNPRK 63

Query: 74  LYKTLAEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQFAAN 116
             +++ +GETVEFD+++G+KG+EA NVTGP+G  VQGS++AA+
Sbjct: 64  YLRSVGDGETVEFDVVEGEKGNEAANVTGPEGAPVQGSKYAAD 106

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

>gi|325297104|ref|NP_001191560.1| Y-box factor homolog [Aplysia californica] gi|1175568|sp|P41824.1|YBOXH_APLCA RecName: Full=Y-box factor homolog; AltName: Full=APY1 gi|409419|gb|AAA60373.1| Y-Box factor [Aplysia californica]

 Score =  124 bits (310), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 57/121 (47%), Positives = 86/121 (71%), Gaps = 1/121 (0%)

Query: 3   MCDSGTKAEATPSNPSANESP-KKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFV 61
           M D+  + E   + P   ++  +KE  ++A++V G VKWF+VKSGYGFI    + EDVFV
Sbjct: 1   MADTEKQPEVEENQPDQEQNEEQKEKKIIASQVSGTVKWFNVKSGYGFINRDDTKEDVFV 60

Query: 62  HSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQFAANKPKYN 121
           H   I  NNPRK  +++ +GE VEFD+++G+KG+EA NVTGP+G +VQGS++AA++ ++ 
Sbjct: 61  HQTAIVKNNPRKYLRSVGDGEKVEFDVVEGEKGNEAANVTGPEGSNVQGSKYAADRRRFR 120

Query: 122 R 122
           R
Sbjct: 121 R 121

Source: Aplysia californica

Species: Aplysia californica

Genus: Aplysia

Family: Aplysiidae

Class: Gastropoda

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|195173115|ref|XP_002027340.1| GL15684 [Drosophila persimilis] gi|198465413|ref|XP_002134972.1| GA23502 [Drosophila pseudoobscura pseudoobscura] gi|194113183|gb|EDW35226.1| GL15684 [Drosophila persimilis] gi|198150149|gb|EDY73599.1| GA23502 [Drosophila pseudoobscura pseudoobscura]

 Score =  123 bits (309), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 65/131 (49%), Positives = 86/131 (65%), Gaps = 8/131 (6%)

Query: 2   QMCDSGTKAEATPSNPSANESPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFV 61
           Q  D G + E  P+ P     PK+   ++ATKV G VKWF+VKSGYGFI    + EDVFV
Sbjct: 25  QQEDDGQQGEGKPAPP-----PKE---IIATKVTGTVKWFNVKSGYGFINRNDTKEDVFV 76

Query: 62  HSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQFAANKPKYN 121
           H   I  NNP+K  +++ +GE VEFD++ G+KG+EA NVTGP G  V+GSQFAA+K +  
Sbjct: 77  HQSAIARNNPKKAVRSVGDGEVVEFDVVIGEKGNEAANVTGPSGEPVRGSQFAADKRRNF 136

Query: 122 RRKAKANKRKR 132
           R   K N R++
Sbjct: 137 RPWMKKNTRRK 147

Source: Drosophila persimilis

Species: Drosophila persimilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195327031|ref|XP_002030225.1| GM24682 [Drosophila sechellia] gi|194119168|gb|EDW41211.1| GM24682 [Drosophila sechellia]

 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 62/109 (56%), Positives = 78/109 (71%), Gaps = 2/109 (1%)

Query: 23  PKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGE 82
           P KE  V+ATKV G VKWF+VKSGYGFI    + EDVFVH   I  NNP+K  +++ +GE
Sbjct: 53  PTKE--VIATKVTGTVKWFNVKSGYGFINRNDTREDVFVHQSAIARNNPKKAVRSVGDGE 110

Query: 83  TVEFDIMQGDKGHEAINVTGPDGRHVQGSQFAANKPKYNRRKAKANKRK 131
            VEFD++ G+KG+EA NVTGP G  V+GSQFAA+K +  R   K N+RK
Sbjct: 111 VVEFDVVIGEKGNEAANVTGPSGEPVRGSQFAADKRRNFRPWMKKNRRK 159

Source: Drosophila sechellia

Species: Drosophila sechellia

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|240849145|ref|NP_001155549.1| Y-box protein Ct-p40-like [Acyrthosiphon pisum] gi|239788387|dbj|BAH70879.1| ACYPI003867 [Acyrthosiphon pisum]

 Score =  122 bits (306), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 58/108 (53%), Positives = 80/108 (74%), Gaps = 4/108 (3%)

Query: 21  ESPKKEPV----VLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYK 76
           E P ++PV    V++ KV GVVKWF+VKSGYGFI    + ED+FVH   I  NNP+K+ +
Sbjct: 11  ERPPQKPVAQKPVISVKVTGVVKWFNVKSGYGFINRNDTKEDIFVHQSAIIKNNPKKIVR 70

Query: 77  TLAEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQFAANKPKYNRRK 124
           ++ +GETVEFD+++G+KGHEA NVTGPDG  V+GS +AA + + N R+
Sbjct: 71  SVGDGETVEFDVVEGEKGHEAANVTGPDGEAVKGSPYAAERRRNNYRQ 118

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|148235020|ref|NP_001091543.1| DNA-binding protein A [Bos taurus] gi|146186540|gb|AAI40645.1| CSDA protein [Bos taurus] gi|296487252|tpg|DAA29365.1| TPA: cold shock domain protein A [Bos taurus]

 Score =  122 bits (306), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 59/105 (56%), Positives = 78/105 (74%)

Query: 12  ATPSNPSANESPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNP 71
           A P++ +A  S   E  VLATKV G VKWF+V++GYGFI    + EDVFVH   IK NNP
Sbjct: 75  AAPASSAAVGSEDAEKKVLATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNP 134

Query: 72  RKLYKTLAEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQFAAN 116
           RK  +++ +GETVEFD+++G+KG EA NVTGPDG  V+GS++AA+
Sbjct: 135 RKYLRSVGDGETVEFDVVEGEKGAEAANVTGPDGVPVEGSRYAAD 179

Source: Bos taurus

Species: Bos taurus

Genus: Bos

Family: Bovidae

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|395516174|ref|XP_003762268.1| PREDICTED: uncharacterized protein LOC100914110 [Sarcophilus harrisii]

 Score =  122 bits (305), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 57/100 (57%), Positives = 74/100 (74%)

Query: 23  PKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGE 82
           P  E  VLATKV G VKWF+V++GYGFI    + EDVFVH   IK NNPRK  +++ +GE
Sbjct: 38  PSGEKKVLATKVWGTVKWFNVRNGYGFINRDDTKEDVFVHQTAIKKNNPRKYLRSVGDGE 97

Query: 83  TVEFDIMQGDKGHEAINVTGPDGRHVQGSQFAANKPKYNR 122
            VEFD+++G+KG EA NVTGP G  VQGS++AA++ +Y R
Sbjct: 98  PVEFDVVEGEKGVEAANVTGPGGAPVQGSKYAADRSEYRR 137

Source: Sarcophilus harrisii

Species: Sarcophilus harrisii

Genus: Sarcophilus

Family: Dasyuridae

Order: Dasyuromorphia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|20806532|ref|NP_035863.1| DNA-binding protein A short isoform [Mus musculus] gi|10185725|gb|AAG14419.1|AF248547_1 Y-box protein 3 short isoform [Mus musculus] gi|38382730|gb|AAH62377.1| Cold shock domain protein A [Mus musculus]

 Score =  122 bits (305), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 58/102 (56%), Positives = 77/102 (75%), Gaps = 2/102 (1%)

Query: 15  SNPSANESPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKL 74
           S P+  E  +K+  VLATKV G VKWF+V++GYGFI    + EDVFVH   IK NNPRK 
Sbjct: 66  SAPAGGEDAEKK--VLATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKY 123

Query: 75  YKTLAEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQFAAN 116
            +++ +GETVEFD+++G+KG EA NVTGPDG  V+GS++AA+
Sbjct: 124 LRSVGDGETVEFDVVEGEKGAEAANVTGPDGVPVEGSRYAAD 165

Source: Mus musculus

Species: Mus musculus

Genus: Mus

Family: Muridae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

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	282
UNIPROTKB|P21573	303	ybx1 "Nuclease-sensitive eleme	0.333	0.310	0.567	2e-28
UNIPROTKB|D4A0L4	306	Csda "DNA-binding protein A" [	0.343	0.316	0.565	2.5e-28
UNIPROTKB|P16989	372	CSDA "DNA-binding protein A" [	0.375	0.284	0.537	7.3e-27
UNIPROTKB|F1SQ46	312	CSDA "Uncharacterized protein"	0.361	0.326	0.558	1.2e-26
UNIPROTKB|I3LQF8	380	CSDA "Uncharacterized protein"	0.361	0.268	0.558	1.2e-26
UNIPROTKB|A5D7Q4	376	CSDA "Uncharacterized protein"	0.361	0.271	0.558	1.5e-26
RGD|621056	361	Ybx3 "Y box binding protein 3"	0.343	0.268	0.565	4e-26
UNIPROTKB|D4AAT9	308	Csda "DNA-binding protein A" [	0.343	0.314	0.565	4e-26
UNIPROTKB|F1MA18	361	Csda "DNA-binding protein A" [	0.343	0.268	0.565	4e-26
MGI|MGI:2137670	361	Ybx3 "Y box protein 3" [Mus mu	0.343	0.268	0.565	5.2e-26

UNIPROTKB|P21573 ybx1 "Nuclease-sensitive element-binding protein 1" [Xenopus laevis (taxid:8355)]

 Score = 287 (106.1 bits), Expect = 2.0e-28, Sum P(2) = 2.0e-28
 Identities = 55/97 (56%), Positives = 72/97 (74%)

Query:    17 PSANESPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYK 76
             P+A    KK   V+ATKV G VKWF+V++GYGFI    + EDVFVH   IK NNPRK  +
Sbjct:    23 PAATVGDKK---VIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLR 79

Query:    77 TLAEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQF 113
             ++ +GETVEFD+++G+KG EA NVTGP+G  VQGS++
Sbjct:    80 SVGDGETVEFDVVEGEKGAEAANVTGPEGVPVQGSKY 116

GO:0071204 "histone pre-mRNA 3'end processing complex" evidence=ISS

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

 Score = 295 (108.9 bits), Expect = 2.5e-28, Sum P(2) = 2.5e-28
 Identities = 56/99 (56%), Positives = 75/99 (75%)

Query:    15 SNPSANESPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKL 74
             S P+ +E  +K+  VLATKV G VKWF+V++GYGFI    + EDVFVH   IK NNPRK 
Sbjct:    66 SAPAGSEDAEKK--VLATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKY 123

Query:    75 YKTLAEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQF 113
              +++ +GETVEFD+++G+KG EA NVTGPDG  V+GS++
Sbjct:   124 LRSVGDGETVEFDVVEGEKGAEAANVTGPDGVPVEGSRY 162

GO:0003677 "DNA binding" evidence=IEA

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

UNIPROTKB|P16989 CSDA "DNA-binding protein A" [Homo sapiens (taxid:9606)]

 Score = 302 (111.4 bits), Expect = 7.3e-27, P = 7.3e-27
 Identities = 58/108 (53%), Positives = 80/108 (74%)

Query:     6 SGTKAEATPSNPSANESPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKR 65
             +GT A A+ +  + +E  +K+  VLATKV G VKWF+V++GYGFI    + EDVFVH   
Sbjct:    65 TGTAAAASLATAAGSEDAEKK--VLATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTA 122

Query:    66 IKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQF 113
             IK NNPRK  +++ +GETVEFD+++G+KG EA NVTGPDG  V+GS++
Sbjct:   123 IKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGPDGVPVEGSRY 170

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

GO:0001701 "in utero embryonic development" evidence=IEA

GO:0005844 "polysome" evidence=IEA

GO:0008584 "male gonad development" evidence=IEA

GO:0009566 "fertilization" evidence=IEA

GO:0043066 "negative regulation of apoptotic process" evidence=IEA

GO:0046622 "positive regulation of organ growth" evidence=IEA

GO:0048642 "negative regulation of skeletal muscle tissue development" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=TAS

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

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=NAS

GO:0003714 "transcription corepressor activity" evidence=TAS

GO:0009409 "response to cold" evidence=TAS

GO:0017048 "Rho GTPase binding" evidence=ISS

GO:0060547 "negative regulation of necrotic cell death" evidence=IMP

GO:0071474 "cellular hyperosmotic response" evidence=IMP

GO:0071356 "cellular response to tumor necrosis factor" evidence=IMP

GO:2000767 "positive regulation of cytoplasmic translation" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISS

GO:0005923 "tight junction" evidence=ISS

GO:0048471 "perinuclear region of cytoplasm" evidence=ISS

GO:0070935 "3'-UTR-mediated mRNA stabilization" evidence=IC

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|F1SQ46 CSDA "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 300 (110.7 bits), Expect = 1.2e-26, P = 1.2e-26
 Identities = 57/102 (55%), Positives = 75/102 (73%)

Query:    12 ATPSNPSANESPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNP 71
             A P++ +A  S   E  VLATKV G VKWF+V++GYGFI    + EDVFVH   IK NNP
Sbjct:    78 AAPASSAAAGSEDAEKKVLATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNP 137

Query:    72 RKLYKTLAEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQF 113
             RK  +++ +GETVEFD+++G+KG EA NVTGPDG  V+GS++
Sbjct:   138 RKYLRSVGDGETVEFDVVEGEKGAEAANVTGPDGVPVEGSRY 179

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|I3LQF8 CSDA "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 300 (110.7 bits), Expect = 1.2e-26, P = 1.2e-26
 Identities = 57/102 (55%), Positives = 75/102 (73%)

Query:    12 ATPSNPSANESPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNP 71
             A P++ +A  S   E  VLATKV G VKWF+V++GYGFI    + EDVFVH   IK NNP
Sbjct:    78 AAPASSAAAGSEDAEKKVLATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNP 137

Query:    72 RKLYKTLAEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQF 113
             RK  +++ +GETVEFD+++G+KG EA NVTGPDG  V+GS++
Sbjct:   138 RKYLRSVGDGETVEFDVVEGEKGAEAANVTGPDGVPVEGSRY 179

GO:0048642 "negative regulation of skeletal muscle tissue development" evidence=IEA

GO:0046622 "positive regulation of organ growth" evidence=IEA

GO:0043066 "negative regulation of apoptotic process" evidence=IEA

GO:0009566 "fertilization" evidence=IEA

GO:0008584 "male gonad development" evidence=IEA

GO:0005844 "polysome" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

GO:0001701 "in utero embryonic development" evidence=IEA

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

UNIPROTKB|A5D7Q4 CSDA "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 299 (110.3 bits), Expect = 1.5e-26, P = 1.5e-26
 Identities = 57/102 (55%), Positives = 75/102 (73%)

Query:    12 ATPSNPSANESPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNP 71
             A P++ +A  S   E  VLATKV G VKWF+V++GYGFI    + EDVFVH   IK NNP
Sbjct:    75 AAPASSAAVGSEDAEKKVLATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNP 134

Query:    72 RKLYKTLAEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQF 113
             RK  +++ +GETVEFD+++G+KG EA NVTGPDG  V+GS++
Sbjct:   135 RKYLRSVGDGETVEFDVVEGEKGAEAANVTGPDGVPVEGSRY 176

GO:0048642 "negative regulation of skeletal muscle tissue development" evidence=IEA

GO:0046622 "positive regulation of organ growth" evidence=IEA

GO:0043066 "negative regulation of apoptotic process" evidence=IEA

GO:0009566 "fertilization" evidence=IEA

GO:0008584 "male gonad development" evidence=IEA

GO:0005844 "polysome" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

GO:0001701 "in utero embryonic development" evidence=IEA

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

RGD|621056 Ybx3 "Y box binding protein 3" [Rattus norvegicus (taxid:10116)]

 Score = 295 (108.9 bits), Expect = 4.0e-26, P = 4.0e-26
 Identities = 56/99 (56%), Positives = 75/99 (75%)

Query:    15 SNPSANESPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKL 74
             S P+ +E  +K+  VLATKV G VKWF+V++GYGFI    + EDVFVH   IK NNPRK 
Sbjct:    66 SAPAGSEDAEKK--VLATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKY 123

Query:    75 YKTLAEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQF 113
              +++ +GETVEFD+++G+KG EA NVTGPDG  V+GS++
Sbjct:   124 LRSVGDGETVEFDVVEGEKGAEAANVTGPDGVPVEGSRY 162

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IMP

GO:0001701 "in utero embryonic development" evidence=ISO

GO:0003677 "DNA binding" evidence=ISO

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

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

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0005737 "cytoplasm" evidence=IEA;ISO

GO:0005921 "gap junction" evidence=IDA

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

GO:0007283 "spermatogenesis" evidence=IEP;ISO

GO:0008584 "male gonad development" evidence=ISO

GO:0009566 "fertilization" evidence=ISO

GO:0031100 "organ regeneration" evidence=IEP

GO:0043066 "negative regulation of apoptotic process" evidence=ISO

GO:0046622 "positive regulation of organ growth" evidence=ISO

GO:0048642 "negative regulation of skeletal muscle tissue development" evidence=ISO

GO:0060547 "negative regulation of necrotic cell death" evidence=ISO

GO:0071356 "cellular response to tumor necrosis factor" evidence=ISO

GO:0071474 "cellular hyperosmotic response" evidence=ISO

GO:0005844 "polysome" evidence=ISO

GO:0030529 "ribonucleoprotein complex" evidence=ISO

UNIPROTKB|D4AAT9 Csda "DNA-binding protein A" [Rattus norvegicus (taxid:10116)]

 Score = 295 (108.9 bits), Expect = 4.0e-26, P = 4.0e-26
 Identities = 56/99 (56%), Positives = 75/99 (75%)

Query:    15 SNPSANESPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKL 74
             S P+ +E  +K+  VLATKV G VKWF+V++GYGFI    + EDVFVH   IK NNPRK 
Sbjct:    66 SAPAGSEDAEKK--VLATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKY 123

Query:    75 YKTLAEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQF 113
              +++ +GETVEFD+++G+KG EA NVTGPDG  V+GS++
Sbjct:   124 LRSVGDGETVEFDVVEGEKGAEAANVTGPDGVPVEGSRY 162

GO:0003677 "DNA binding" evidence=IEA

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

UNIPROTKB|F1MA18 Csda "DNA-binding protein A" [Rattus norvegicus (taxid:10116)]

 Score = 295 (108.9 bits), Expect = 4.0e-26, P = 4.0e-26
 Identities = 56/99 (56%), Positives = 75/99 (75%)

Query:    15 SNPSANESPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKL 74
             S P+ +E  +K+  VLATKV G VKWF+V++GYGFI    + EDVFVH   IK NNPRK 
Sbjct:    66 SAPAGSEDAEKK--VLATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKY 123

Query:    75 YKTLAEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQF 113
              +++ +GETVEFD+++G+KG EA NVTGPDG  V+GS++
Sbjct:   124 LRSVGDGETVEFDVVEGEKGAEAANVTGPDGVPVEGSRY 162

GO:0001701 "in utero embryonic development" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005844 "polysome" evidence=IEA

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

GO:0008584 "male gonad development" evidence=IEA

GO:0009566 "fertilization" evidence=IEA

GO:0043066 "negative regulation of apoptotic process" evidence=IEA

GO:0046622 "positive regulation of organ growth" evidence=IEA

GO:0048642 "negative regulation of skeletal muscle tissue development" evidence=IEA

MGI|MGI:2137670 Ybx3 "Y box protein 3" [Mus musculus (taxid:10090)]

 Score = 294 (108.6 bits), Expect = 5.2e-26, P = 5.2e-26
 Identities = 56/99 (56%), Positives = 74/99 (74%)

Query:    15 SNPSANESPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKL 74
             S P+  E  +K+  VLATKV G VKWF+V++GYGFI    + EDVFVH   IK NNPRK 
Sbjct:    66 SAPAGGEDAEKK--VLATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKY 123

Query:    75 YKTLAEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQF 113
              +++ +GETVEFD+++G+KG EA NVTGPDG  V+GS++
Sbjct:   124 LRSVGDGETVEFDVVEGEKGAEAANVTGPDGVPVEGSRY 162

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0001701 "in utero embryonic development" evidence=IGI

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IDA

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

GO:0003723 "RNA binding" evidence=IEA

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

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005844 "polysome" evidence=IDA

GO:0005921 "gap junction" evidence=ISO

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

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

GO:0007283 "spermatogenesis" evidence=IMP

GO:0008584 "male gonad development" evidence=IMP

GO:0009566 "fertilization" evidence=IMP

GO:0030529 "ribonucleoprotein complex" evidence=IDA

GO:0043066 "negative regulation of apoptotic process" evidence=IMP

GO:0046622 "positive regulation of organ growth" evidence=IMP

GO:0048642 "negative regulation of skeletal muscle tissue development" evidence=IDA

GO:0060547 "negative regulation of necrotic cell death" evidence=ISO

GO:0071356 "cellular response to tumor necrosis factor" evidence=ISO

GO:0071474 "cellular hyperosmotic response" evidence=ISO

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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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	282
pfam00313	66	pfam00313, CSD, 'Cold-shock' DNA-binding domain	1e-22
pfam00313	66	pfam00313, CSD, 'Cold-shock' DNA-binding domain	2e-19
cd04458	65	cd04458, CSP_CDS, Cold-Shock Protein (CSP) contain	2e-19
cd04458	65	cd04458, CSP_CDS, Cold-Shock Protein (CSP) contain	8e-17
COG1278	67	COG1278, CspC, Cold shock proteins [Transcription]	3e-15
COG1278	67	COG1278, CspC, Cold shock proteins [Transcription]	5e-14
PRK10943	69	PRK10943, PRK10943, cold shock-like protein CspC;	1e-13
PRK09507	69	PRK09507, cspE, cold shock protein CspE; Reviewed	3e-13
PRK10354	70	PRK10354, PRK10354, RNA chaperone/anti-terminator;	7e-13
smart00357	64	smart00357, CSP, Cold shock protein domain	1e-12
PRK09890	70	PRK09890, PRK09890, cold shock protein CspG; Provi	7e-12
TIGR02381	68	TIGR02381, cspD, cold shock domain protein CspD	1e-11
PRK09507	69	PRK09507, cspE, cold shock protein CspE; Reviewed	2e-11
PRK10943	69	PRK10943, PRK10943, cold shock-like protein CspC;	3e-11
TIGR02381	68	TIGR02381, cspD, cold shock domain protein CspD	3e-11
PRK10354	70	PRK10354, PRK10354, RNA chaperone/anti-terminator;	4e-11
PRK09937	74	PRK09937, PRK09937, stationary phase/starvation in	5e-11
PRK14998	73	PRK14998, PRK14998, cold shock-like protein CspD;	6e-11
PRK09937	74	PRK09937, PRK09937, stationary phase/starvation in	8e-11
PRK09890	70	PRK09890, PRK09890, cold shock protein CspG; Provi	1e-10
PRK14998	73	PRK14998, PRK14998, cold shock-like protein CspD;	1e-10
smart00357	64	smart00357, CSP, Cold shock protein domain	2e-10
PRK15463	70	PRK15463, PRK15463, cold shock-like protein CspF;	5e-05
PRK15463	70	PRK15463, PRK15463, cold shock-like protein CspF;	0.001

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

 Score = 88.4 bits (220), Expect = 1e-22
 Identities = 31/68 (45%), Positives = 44/68 (64%), Gaps = 4/68 (5%)

Query: 36  GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
           G VKWF+ K G+GFI     ++DVFVH   I+ +     +++L EG+ VEFDI++G KG 
Sbjct: 3   GTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDG----FRSLQEGQRVEFDIVEGTKGP 58

Query: 96  EAINVTGP 103
           +A NVT  
Sbjct: 59  QAANVTLL 66

Length = 66

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

 Score = 80.0 bits (198), Expect = 2e-19
 Identities = 28/61 (45%), Positives = 40/61 (65%), Gaps = 4/61 (6%)

Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
           G VKWF+ K G+GFI     ++DVFVH   I+ +     +++L EG+ VEFDI++G KG 
Sbjct: 3   GTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDG----FRSLQEGQRVEFDIVEGTKGP 58

Query: 263 Q 263
           Q
Sbjct: 59  Q 59

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 = 79.5 bits (197), Expect = 2e-19
 Identities = 28/67 (41%), Positives = 41/67 (61%), Gaps = 4/67 (5%)

Query: 36  GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
           G VKWF  + G+GFI      EDVFVH   ++       +++L EG+ VEF++ +GDKG 
Sbjct: 3   GTVKWFDDEKGFGFITPDDGGEDVFVHISALE----GDGFRSLEEGDRVEFELEEGDKGP 58

Query: 96  EAINVTG 102
           +A+NV  
Sbjct: 59  QAVNVRL 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 = 72.6 bits (179), Expect = 8e-17
 Identities = 26/61 (42%), Positives = 37/61 (60%), Gaps = 4/61 (6%)

Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
           G VKWF  + G+GFI      EDVFVH   ++       +++L EG+ VEF++ +GDKG 
Sbjct: 3   GTVKWFDDEKGFGFITPDDGGEDVFVHISALE----GDGFRSLEEGDRVEFELEEGDKGP 58

Query: 263 Q 263
           Q
Sbjct: 59  Q 59

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 = 68.3 bits (168), Expect = 3e-15
 Identities = 29/66 (43%), Positives = 38/66 (57%), Gaps = 4/66 (6%)

Query: 36  GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
           G VKWF+   G+GFI      +DVFVH   I+       ++TL EG+ VEF++ QG KG 
Sbjct: 4   GTVKWFNATKGFGFITPEDGGKDVFVHISAIQRAG----FRTLREGQKVEFEVEQGRKGP 59

Query: 96  EAINVT 101
            A NV 
Sbjct: 60  SAANVR 65

Length = 67

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

 Score = 64.9 bits (159), Expect = 5e-14
 Identities = 26/61 (42%), Positives = 35/61 (57%), Gaps = 4/61 (6%)

Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
           G VKWF+   G+GFI      +DVFVH   I+       ++TL EG+ VEF++ QG KG 
Sbjct: 4   GTVKWFNATKGFGFITPEDGGKDVFVHISAIQRAG----FRTLREGQKVEFEVEQGRKGP 59

Query: 263 Q 263
            
Sbjct: 60  S 60

Length = 67

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

 Score = 64.3 bits (156), Expect = 1e-13
 Identities = 34/69 (49%), Positives = 44/69 (63%), Gaps = 4/69 (5%)

Query: 33  KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 92
           K+ G VKWF+   G+GFI     ++DVFVH   I+ N     +KTLAEG+ VEF+I  G 
Sbjct: 3   KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNG----FKTLAEGQNVEFEIQDGQ 58

Query: 93  KGHEAINVT 101
           KG  A+NVT
Sbjct: 59  KGPAAVNVT 67

Length = 69

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

 Score = 63.5 bits (154), Expect = 3e-13
 Identities = 33/70 (47%), Positives = 43/70 (61%), Gaps = 4/70 (5%)

Query: 32  TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG 91
           +K+ G VKWF+   G+GFI     ++DVFVH   I+ N     +KTLAEG+ VEF+I  G
Sbjct: 2   SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNG 57

Query: 92  DKGHEAINVT 101
            KG  A NV 
Sbjct: 58  AKGPSAANVI 67

Length = 69

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

 Score = 62.3 bits (151), Expect = 7e-13
 Identities = 31/72 (43%), Positives = 43/72 (59%), Gaps = 4/72 (5%)

Query: 30  LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIM 89
           ++ K+ G+VKWF+   G+GFI     ++DVFVH   I+ +     YK+L EG+ V F I 
Sbjct: 1   MSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIE 56

Query: 90  QGDKGHEAINVT 101
            G KG  A NVT
Sbjct: 57  SGAKGPAAGNVT 68

Length = 70

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

 Score = 61.5 bits (150), Expect = 1e-12
 Identities = 28/70 (40%), Positives = 38/70 (54%), Gaps = 9/70 (12%)

Query: 36  GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDI--MQGDK 93
           GVVKWF+   G+GFI      +DVFVH  +I+        K+L EG+ VEF +   +G +
Sbjct: 2   GVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQGG-----LKSLREGDEVEFKVVSPEGGE 54

Query: 94  GHEAINVTGP 103
             EA NV   
Sbjct: 55  KPEAENVVKL 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 = 59.4 bits (143), Expect = 7e-12
 Identities = 30/71 (42%), Positives = 43/71 (60%), Gaps = 4/71 (5%)

Query: 30  LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIM 89
           ++ K+ G+VKWF+   G+GFI     ++DVFVH   I+ N     ++TL E + VEF I 
Sbjct: 1   MSNKMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNE----FRTLNENQKVEFSIE 56

Query: 90  QGDKGHEAINV 100
           QG +G  A NV
Sbjct: 57  QGQRGPAAANV 67

Length = 70

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

 Score = 58.3 bits (141), Expect = 1e-11
 Identities = 24/65 (36%), Positives = 39/65 (60%), Gaps = 4/65 (6%)

Query: 36  GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
           G+VKWF+   G+GFI     + D+F H   I+ +     Y+TL  G+ V+F+++QG KG 
Sbjct: 4   GIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDG----YRTLKAGQKVQFEVVQGPKGA 59

Query: 96  EAINV 100
            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|169931 PRK09507, cspE, cold shock protein CspE; Reviewed

 Score = 58.1 bits (140), Expect = 2e-11
 Identities = 30/63 (47%), Positives = 40/63 (63%), Gaps = 4/63 (6%)

Query: 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG 258
           +K+ G VKWF+   G+GFI     ++DVFVH   I+ N     +KTLAEG+ VEF+I  G
Sbjct: 2   SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNG 57

Query: 259 DKG 261
            KG
Sbjct: 58  AKG 60

Length = 69

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

 Score = 57.8 bits (139), Expect = 3e-11
 Identities = 30/62 (48%), Positives = 39/62 (62%), Gaps = 4/62 (6%)

Query: 200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 259
           K+ G VKWF+   G+GFI     ++DVFVH   I+ N     +KTLAEG+ VEF+I  G 
Sbjct: 3   KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNG----FKTLAEGQNVEFEIQDGQ 58

Query: 260 KG 261
           KG
Sbjct: 59  KG 60

Length = 69

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

 Score = 57.6 bits (139), Expect = 3e-11
 Identities = 23/60 (38%), Positives = 36/60 (60%), Gaps = 4/60 (6%)

Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
           G+VKWF+   G+GFI     + D+F H   I+ +     Y+TL  G+ V+F+++QG KG 
Sbjct: 4   GIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDG----YRTLKAGQKVQFEVVQGPKGA 59

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

 Score = 57.3 bits (138), Expect = 4e-11
 Identities = 27/65 (41%), Positives = 39/65 (60%), Gaps = 4/65 (6%)

Query: 197 LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIM 256
           ++ K+ G+VKWF+   G+GFI     ++DVFVH   I+ +     YK+L EG+ V F I 
Sbjct: 1   MSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIE 56

Query: 257 QGDKG 261
            G KG
Sbjct: 57  SGAKG 61

Length = 70

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

 Score = 57.4 bits (138), Expect = 5e-11
 Identities = 26/61 (42%), Positives = 36/61 (59%), Gaps = 4/61 (6%)

Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
           G VKWF+   G+GFI      ED+F H   I+ +     Y+TL  G++V+FD+ QG KGN
Sbjct: 4   GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG----YRTLKAGQSVQFDVHQGPKGN 59

Query: 263 Q 263
            
Sbjct: 60  H 60

Length = 74

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

 Score = 57.0 bits (137), Expect = 6e-11
 Identities = 26/61 (42%), Positives = 35/61 (57%), Gaps = 4/61 (6%)

Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
           G VKWF+   G+GFI      ED+F H   I+ +     Y+TL  G++V FD+ QG KGN
Sbjct: 4   GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG----YRTLKAGQSVRFDVHQGPKGN 59

Query: 263 Q 263
            
Sbjct: 60  H 60

Length = 73

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

 Score = 56.7 bits (136), Expect = 8e-11
 Identities = 26/62 (41%), Positives = 37/62 (59%), Gaps = 4/62 (6%)

Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
          G VKWF+   G+GFI      ED+F H   I+ +     Y+TL  G++V+FD+ QG KG+
Sbjct: 4  GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG----YRTLKAGQSVQFDVHQGPKGN 59

Query: 96 EA 97
           A
Sbjct: 60 HA 61

Length = 74

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

 Score = 55.9 bits (134), Expect = 1e-10
 Identities = 27/65 (41%), Positives = 40/65 (61%), Gaps = 4/65 (6%)

Query: 197 LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIM 256
           ++ K+ G+VKWF+   G+GFI     ++DVFVH   I+ N     ++TL E + VEF I 
Sbjct: 1   MSNKMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNE----FRTLNENQKVEFSIE 56

Query: 257 QGDKG 261
           QG +G
Sbjct: 57  QGQRG 61

Length = 70

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

 Score = 56.2 bits (135), Expect = 1e-10
 Identities = 26/62 (41%), Positives = 36/62 (58%), Gaps = 4/62 (6%)

Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
          G VKWF+   G+GFI      ED+F H   I+ +     Y+TL  G++V FD+ QG KG+
Sbjct: 4  GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG----YRTLKAGQSVRFDVHQGPKGN 59

Query: 96 EA 97
           A
Sbjct: 60 HA 61

Length = 73

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

 Score = 55.3 bits (134), Expect = 2e-10
 Identities = 24/63 (38%), Positives = 35/63 (55%), Gaps = 9/63 (14%)

Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDI--MQGDK 260
           GVVKWF+   G+GFI      +DVFVH  +I+        K+L EG+ VEF +   +G +
Sbjct: 2   GVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQGG-----LKSLREGDEVEFKVVSPEGGE 54

Query: 261 GNQ 263
             +
Sbjct: 55  KPE 57

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

 Score = 40.3 bits (94), Expect = 5e-05
 Identities = 24/71 (33%), Positives = 34/71 (47%), Gaps = 4/71 (5%)

Query: 30  LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIM 89
           ++ K+ G+VK F  KSG G I      +DV VH   +   +     + L  G  VEF  +
Sbjct: 1   MSRKMTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDA----EELTTGLRVEFCRI 56

Query: 90  QGDKGHEAINV 100
            G +G  A NV
Sbjct: 57  NGLRGPTAANV 67

Length = 70

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

 Score = 36.4 bits (84), Expect = 0.001
 Identities = 21/65 (32%), Positives = 31/65 (47%), Gaps = 4/65 (6%)

Query: 197 LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIM 256
           ++ K+ G+VK F  KSG G I      +DV VH   +   +     + L  G  VEF  +
Sbjct: 1   MSRKMTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDA----EELTTGLRVEFCRI 56

Query: 257 QGDKG 261
            G +G
Sbjct: 57  NGLRG 61

Length = 70

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	282
COG1278	67	CspC Cold shock proteins [Transcription]	99.9
COG1278	67	CspC Cold shock proteins [Transcription]	99.89
PRK10943	69	cold shock-like protein CspC; Provisional	99.88
PRK15464	70	cold shock-like protein CspH; Provisional	99.88
PRK09507	69	cspE cold shock protein CspE; Reviewed	99.87
PRK15463	70	cold shock-like protein CspF; Provisional	99.87
PRK10354	70	RNA chaperone/anti-terminator; Provisional	99.87
PRK09890	70	cold shock protein CspG; Provisional	99.87
PRK09937	74	stationary phase/starvation inducible regulatory p	99.87
PRK14998	73	cold shock-like protein CspD; Provisional	99.86
PRK15464	70	cold shock-like protein CspH; Provisional	99.86
TIGR02381	68	cspD cold shock domain protein CspD. This model re	99.86
PRK15463	70	cold shock-like protein CspF; Provisional	99.85
PRK10943	69	cold shock-like protein CspC; Provisional	99.85
PRK09507	69	cspE cold shock protein CspE; Reviewed	99.85
PRK09890	70	cold shock protein CspG; Provisional	99.85
PRK10354	70	RNA chaperone/anti-terminator; Provisional	99.84
PRK09937	74	stationary phase/starvation inducible regulatory p	99.84
TIGR02381	68	cspD cold shock domain protein CspD. This model re	99.84
PRK14998	73	cold shock-like protein CspD; Provisional	99.83
PF00313	66	CSD: 'Cold-shock' DNA-binding domain; InterPro: IP	99.8
cd04458	65	CSP_CDS Cold-Shock Protein (CSP) contains an S1-li	99.78
PF00313	66	CSD: 'Cold-shock' DNA-binding domain; InterPro: IP	99.77
cd04458	65	CSP_CDS Cold-Shock Protein (CSP) contains an S1-li	99.75
KOG3070|consensus	235		99.54
KOG3070|consensus	235		99.32
smart00357	64	CSP Cold shock protein domain. RNA-binding domain	98.9
smart00357	64	CSP Cold shock protein domain. RNA-binding domain	98.78
PF08206	58	OB_RNB: Ribonuclease B OB domain; InterPro: IPR013	97.65
PRK11642	813	exoribonuclease R; Provisional	97.64
PF08206	58	OB_RNB: Ribonuclease B OB domain; InterPro: IPR013	97.51
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	97.21
PRK05054	644	exoribonuclease II; Provisional	97.17
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	97.04
PF14444	58	S1-like: S1-like	96.94
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	96.71
PF14444	58	S1-like: S1-like	96.21
PF07497	78	Rho_RNA_bind: Rho termination factor, RNA-binding	94.45
PF07497	78	Rho_RNA_bind: Rho termination factor, RNA-binding	94.41
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	93.93
cd04459	68	Rho_CSD Rho_CSD: Rho protein cold-shock domain (CS	93.78
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	93.7
cd04459	68	Rho_CSD Rho_CSD: Rho protein cold-shock domain (CS	93.61
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	92.36
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	92.3
PRK11642	813	exoribonuclease R; Provisional	91.24
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	90.75
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	90.52
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	90.25
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	89.9
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	89.7
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	89.11
PRK05054	644	exoribonuclease II; Provisional	89.11
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	89.06
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	88.88
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	88.72
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	88.7
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	88.57
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	88.52
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	87.82
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	87.42
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	87.22
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	86.13
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	85.85
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	85.8
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	85.61
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	85.59
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	85.45
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	85.27
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	85.24
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	85.12
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	84.54
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	84.5
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	84.37
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	84.36
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	84.25
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	84.19
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	83.99
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	83.98
COG0557	706	VacB Exoribonuclease R [Transcription]	83.38
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	82.73
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	82.35
PRK08582	139	hypothetical protein; Provisional	81.33
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	81.24
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	81.19
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	81.12
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	80.98
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	80.74
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	80.52
PRK07400	318	30S ribosomal protein S1; Reviewed	80.48
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	80.45
TIGR01451	53	B_ant_repeat conserved repeat domain. This model r	80.33
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	80.08

>COG1278 CspC Cold shock proteins [Transcription]

Probab=99.90  E-value=4.6e-24  Score=154.86  Aligned_cols=66  Identities=44%  Similarity=0.795  Sum_probs=62.8

Q ss_pred             eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeC
Q psy547           33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTG  102 (282)
Q Consensus        33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~  102 (282)
                      +.+|+|||||..||||||+++++++|||+|+|+|+..    |+++|.+|++|+|+++.+.+|++|.+|+.
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            3589999999999999999999999999999999987    69999999999999999999999999975

>COG1278 CspC Cold shock proteins [Transcription]

Probab=99.89  E-value=2.9e-23  Score=150.70  Aligned_cols=65  Identities=43%  Similarity=0.781  Sum_probs=61.5

Q ss_pred             eeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547          201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK  269 (282)
Q Consensus       201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~  269 (282)
                      .+|+|||||..||||||+++++++|||||+|+|+    +.|+++|.+||+|+|++++++||++|++|+.
T Consensus         2 ~~GtVKwfn~~KGfGFI~p~~G~~DvFVH~Sai~----~~g~~~L~eGQ~V~f~~~~g~kgp~A~nv~~   66 (67)
T COG1278           2 ATGTVKWFNATKGFGFITPEDGGKDVFVHISAIQ----RAGFRTLREGQKVEFEVEQGRKGPSAANVRA   66 (67)
T ss_pred             CcceEEEeeCCCcceEcCCCCCCcCEEEEeeeec----cCCCcccCCCCEEEEEEecCCCCCceeEEEe
Confidence            4699999999999999999999999999999999    4579999999999999999999999999974

>PRK10943 cold shock-like protein CspC; Provisional

Probab=99.88  E-value=8.5e-23  Score=150.59  Aligned_cols=68  Identities=50%  Similarity=0.838  Sum_probs=63.9

Q ss_pred             eeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeCC
Q psy547           32 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGP  103 (282)
Q Consensus        32 ~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~~  103 (282)
                      ++++|+|||||.+||||||+++++++|||||+|+|...    |++.|.+|++|+|++..+++|++|.+|+.+
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            57899999999999999999999999999999999986    589999999999999999999999999853

>PRK15464 cold shock-like protein CspH; Provisional

Probab=99.88  E-value=1.2e-22  Score=150.02  Aligned_cols=66  Identities=36%  Similarity=0.437  Sum_probs=62.1

Q ss_pred             eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeC
Q psy547           33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTG  102 (282)
Q Consensus        33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~  102 (282)
                      +++|+|||||.+||||||+++++++|||||+|+|...    |++.|.+|++|+|+++.+++|++|.+|..
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            4689999999999999999999999999999999876    58899999999999999999999999974

>PRK09507 cspE cold shock protein CspE; Reviewed

Probab=99.87  E-value=2.8e-22  Score=147.83  Aligned_cols=68  Identities=49%  Similarity=0.806  Sum_probs=63.5

Q ss_pred             eeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeCC
Q psy547           32 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGP  103 (282)
Q Consensus        32 ~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~~  103 (282)
                      .+.+|+|||||.+||||||+++++++|||||+|+|...    |++.|.+|+.|+|+++.+++|++|.+|+.+
T Consensus         2 ~~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~~   69 (69)
T PRK09507          2 SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTN----GFKTLAEGQRVEFEITNGAKGPSAANVIAL   69 (69)
T ss_pred             CccceEEEEEeCCCCcEEEecCCCCeeEEEEeeccccc----CCCCCCCCCEEEEEEEECCCCcccEEEEeC
Confidence            46899999999999999999999999999999999986    589999999999999999999999999753

>PRK15463 cold shock-like protein CspF; Provisional

Probab=99.87  E-value=3.4e-22  Score=147.75  Aligned_cols=66  Identities=36%  Similarity=0.464  Sum_probs=62.1

Q ss_pred             eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeC
Q psy547           33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTG  102 (282)
Q Consensus        33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~  102 (282)
                      +++|+|||||.+||||||+++++++|||||+++|...    |++.|.+|++|+|++..+++|++|.+|..
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            4689999999999999999999999999999999876    58999999999999999999999999974

>PRK10354 RNA chaperone/anti-terminator; Provisional

Probab=99.87  E-value=4.5e-22  Score=147.16  Aligned_cols=66  Identities=47%  Similarity=0.822  Sum_probs=62.3

Q ss_pred             eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeC
Q psy547           33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTG  102 (282)
Q Consensus        33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~  102 (282)
                      +++|+|||||.+||||||+++++++|||||+|+|...    |++.|.+|++|+|++..+++|++|.+|+.
T Consensus         4 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~   69 (70)
T PRK10354          4 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQND----GYKSLDEGQKVSFTIESGAKGPAAGNVTS   69 (70)
T ss_pred             cceEEEEEEeCCCCcEEEecCCCCccEEEEEeecccc----CCCCCCCCCEEEEEEEECCCCceeEEEEe
Confidence            3589999999999999999999999999999999986    58999999999999999999999999985

>PRK09890 cold shock protein CspG; Provisional

Probab=99.87  E-value=5.2e-22  Score=146.80  Aligned_cols=66  Identities=45%  Similarity=0.821  Sum_probs=62.4

Q ss_pred             eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeC
Q psy547           33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTG  102 (282)
Q Consensus        33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~  102 (282)
                      +++|+|||||.+||||||+++++++|||||+|+|...    +++.|.+|++|+|+++.+++|++|.+|..
T Consensus         4 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~----~~~~l~~G~~V~f~~~~~~~G~~A~~V~~   69 (70)
T PRK09890          4 KMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSN----EFRTLNENQKVEFSIEQGQRGPAAANVVT   69 (70)
T ss_pred             cceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccC----CCCCCCCCCEEEEEEEECCCCceeEEEEe
Confidence            4689999999999999999999999999999999986    58999999999999999999999999975

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

Probab=99.87  E-value=5.8e-22  Score=147.94  Aligned_cols=68  Identities=38%  Similarity=0.720  Sum_probs=63.8

Q ss_pred             eeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeCCCC
Q psy547           34 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGPDG  105 (282)
Q Consensus        34 ~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~~~~  105 (282)
                      .+|+|||||.+||||||+++++++|||||+|+|...    |++.|.+|+.|+|++..+++|++|.+|..++.
T Consensus         2 ~~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~~~~   69 (74)
T PRK09937          2 EKGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMD----GYRTLKAGQSVQFDVHQGPKGNHASVIVPVEV   69 (74)
T ss_pred             CCeEEEEEeCCCCeEEEeeCCCCccEEEEEeecccc----CCCCCCCCCEEEEEEEECCCCceeeEEEECCc
Confidence            479999999999999999999999999999999986    58999999999999999999999999997643

>PRK14998 cold shock-like protein CspD; Provisional

Probab=99.86  E-value=8.5e-22  Score=146.70  Aligned_cols=68  Identities=38%  Similarity=0.739  Sum_probs=63.6

Q ss_pred             eeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeCCCC
Q psy547           34 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGPDG  105 (282)
Q Consensus        34 ~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~~~~  105 (282)
                      .+|+|||||.+||||||+++++++|||||+|+|+..    |++.|.+|++|+|++..+++|++|.+|..+..
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            479999999999999999999999999999999986    58999999999999999999999999987654

>PRK15464 cold shock-like protein CspH; Provisional

Probab=99.86  E-value=7.1e-22  Score=145.87  Aligned_cols=66  Identities=33%  Similarity=0.420  Sum_probs=61.2

Q ss_pred             eeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547          200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK  269 (282)
Q Consensus       200 ~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~  269 (282)
                      +++|+|||||.+||||||+++++++|||||+++|..    .+++.|.+||+|+|++.+++||++|++|..
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 KMTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTP----RDAEVLIPGLRVEFCRVNGLRGPTAANVYL   69 (70)
T ss_pred             cceEEEEEEECCCCeEEEccCCCCccEEEEehhehh----cCCCCCCCCCEEEEEEEECCCCceeEEEEc
Confidence            458999999999999999999999999999999984    357889999999999999999999999974

>TIGR02381 cspD cold shock domain protein CspD

Probab=99.86  E-value=7.4e-22  Score=145.19  Aligned_cols=66  Identities=36%  Similarity=0.765  Sum_probs=62.0

Q ss_pred             eeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeCC
Q psy547           34 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGP  103 (282)
Q Consensus        34 ~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~~  103 (282)
                      .+|+|||||.+||||||+++++++|||||+|+|...    |++.|.+|++|+|+++.+++|++|.+|..+
T Consensus         2 ~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~~   67 (68)
T TIGR02381         2 AIGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMD----GYRTLKAGQKVQFEVVQGPKGAHATHIVPI   67 (68)
T ss_pred             CCeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhc----CCCCCCCCCEEEEEEEECCCCceeEEEEEC
Confidence            479999999999999999999999999999999876    589999999999999999999999999753

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.

>PRK15463 cold shock-like protein CspF; Provisional

Probab=99.85  E-value=2e-21  Score=143.60  Aligned_cols=66  Identities=33%  Similarity=0.447  Sum_probs=61.1

Q ss_pred             eeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547          200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK  269 (282)
Q Consensus       200 ~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~  269 (282)
                      +++|+|||||.+||||||+++++++|||||+++|..    .|++.|.+|++|+|+++++++|++|.+|..
T Consensus         4 ~~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~----~g~~~l~~G~~V~f~v~~~~~G~~A~~V~~   69 (70)
T PRK15463          4 KMTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNL----RDAEELTTGLRVEFCRINGLRGPTAANVYL   69 (70)
T ss_pred             cceEEEEEEeCCCceEEEecCCCCccEEEEehhhhh----cCCCCCCCCCEEEEEEEECCCCceeEEEEc
Confidence            458999999999999999999999999999999994    357899999999999999999999999863

>PRK10943 cold shock-like protein CspC; Provisional

Probab=99.85  E-value=2.3e-21  Score=142.94  Aligned_cols=67  Identities=46%  Similarity=0.768  Sum_probs=62.0

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK  269 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~  269 (282)
                      ++++|+|||||..||||||+++++++|||||+++|...    +++.|.+|++|+|++.++++|++|.+|+.
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            36789999999999999999999999999999999943    57899999999999999999999999974

>PRK09507 cspE cold shock protein CspE; Reviewed

Probab=99.85  E-value=4.5e-21  Score=141.42  Aligned_cols=67  Identities=46%  Similarity=0.791  Sum_probs=61.9

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK  269 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~  269 (282)
                      .+.+|+|||||..||||||+++++++|||||+++|...    +++.|.+|++|+|++.++++|++|.+|+.
T Consensus         2 ~~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~   68 (69)
T PRK09507          2 SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTN----GFKTLAEGQRVEFEITNGAKGPSAANVIA   68 (69)
T ss_pred             CccceEEEEEeCCCCcEEEecCCCCeeEEEEeeccccc----CCCCCCCCCEEEEEEEECCCCcccEEEEe
Confidence            35789999999999999999999999999999999943    57899999999999999999999999974

>PRK09890 cold shock protein CspG; Provisional

Probab=99.85  E-value=5.1e-21  Score=141.49  Aligned_cols=66  Identities=42%  Similarity=0.784  Sum_probs=61.3

Q ss_pred             eeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547          200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK  269 (282)
Q Consensus       200 ~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~  269 (282)
                      +++|+|||||..||||||+++++++|||||+++|...    +++.|.+|++|+|++.++++|++|.+|..
T Consensus         4 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~----~~~~l~~G~~V~f~~~~~~~G~~A~~V~~   69 (70)
T PRK09890          4 KMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSN----EFRTLNENQKVEFSIEQGQRGPAAANVVT   69 (70)
T ss_pred             cceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccC----CCCCCCCCCEEEEEEEECCCCceeEEEEe
Confidence            4589999999999999999999999999999999954    57899999999999999999999999874

>PRK10354 RNA chaperone/anti-terminator; Provisional

Probab=99.84  E-value=7.2e-21  Score=140.72  Aligned_cols=66  Identities=42%  Similarity=0.756  Sum_probs=61.1

Q ss_pred             eeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547          200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK  269 (282)
Q Consensus       200 ~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~  269 (282)
                      +++|+|||||..||||||+++++++|||||+++|...    +++.|.+|++|+|++.++++|++|.+|+.
T Consensus         4 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~   69 (70)
T PRK10354          4 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQND----GYKSLDEGQKVSFTIESGAKGPAAGNVTS   69 (70)
T ss_pred             cceEEEEEEeCCCCcEEEecCCCCccEEEEEeecccc----CCCCCCCCCEEEEEEEECCCCceeEEEEe
Confidence            3579999999999999999999999999999999944    57899999999999999999999999974

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

Probab=99.84  E-value=9.2e-21  Score=141.45  Aligned_cols=65  Identities=40%  Similarity=0.784  Sum_probs=60.9

Q ss_pred             eeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEec
Q psy547          202 CGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLKN  270 (282)
Q Consensus       202 ~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~~  270 (282)
                      +|+|||||..||||||+++++++|||||+++|..    .|++.|.+|++|+|++.++++|++|.+|..-
T Consensus         3 ~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~----~g~~~l~~G~~V~f~~~~~~~G~~A~~V~~~   67 (74)
T PRK09937          3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQM----DGYRTLKAGQSVQFDVHQGPKGNHASVIVPV   67 (74)
T ss_pred             CeEEEEEeCCCCeEEEeeCCCCccEEEEEeeccc----cCCCCCCCCCEEEEEEEECCCCceeeEEEEC
Confidence            6999999999999999999999999999999994    3588999999999999999999999999854

>TIGR02381 cspD cold shock domain protein CspD

Probab=99.84  E-value=1e-20  Score=139.12  Aligned_cols=64  Identities=36%  Similarity=0.793  Sum_probs=60.3

Q ss_pred             eeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547          202 CGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK  269 (282)
Q Consensus       202 ~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~  269 (282)
                      +|+|||||.+||||||+++++++|||||+|+|...    |++.|.+|++|+|++.++++|++|.+|..
T Consensus         3 ~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~   66 (68)
T TIGR02381         3 IGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMD----GYRTLKAGQKVQFEVVQGPKGAHATHIVP   66 (68)
T ss_pred             CeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhc----CCCCCCCCCEEEEEEEECCCCceeEEEEE
Confidence            69999999999999999999999999999999843    57899999999999999999999999975

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=99.83  E-value=1.6e-20  Score=139.84  Aligned_cols=65  Identities=40%  Similarity=0.799  Sum_probs=60.7

Q ss_pred             eeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547          201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK  269 (282)
Q Consensus       201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~  269 (282)
                      .+|+|||||..||||||+++++++|||||+++|...    |++.|.+|++|+|+++++++|++|++|..
T Consensus         2 ~~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~   66 (73)
T PRK14998          2 ETGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMD----GYRTLKAGQSVRFDVHQGPKGNHASVIVP   66 (73)
T ss_pred             CCeEEEEEeCCCceEEEecCCCCccEEEEeeeeccc----CCCCCCCCCEEEEEEEECCCCceeEEEEE
Confidence            369999999999999999999999999999999854    57899999999999999999999999975

>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=99.80  E-value=2.7e-19  Score=130.31  Aligned_cols=66  Identities=41%  Similarity=0.814  Sum_probs=59.5

Q ss_pred             eeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeCC
Q psy547           34 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGP  103 (282)
Q Consensus        34 ~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~~  103 (282)
                      ++|+|||||..||||||+++++.+|||||+++|...    +++.|.+|++|+|++..+++|++|.+|+.+
T Consensus         1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~----~~~~l~~G~~V~F~~~~~~~g~~A~~V~~~   66 (66)
T PF00313_consen    1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGN----GFRSLKEGDRVEFEVEEGKKGPQAVNVRKI   66 (66)
T ss_dssp             EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSS----SSTS--TTSEEEEEEEECTTSEEEEEEEE-
T ss_pred             CeEEEEEEECCCCceEEEEcccceeEEecccccccc----ccccCCCCCEEEEEEEECCCCCEEEEEECc
Confidence            589999999999999999999999999999999987    378999999999999999999999999853

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=99.78  E-value=8e-19  Score=127.45  Aligned_cols=64  Identities=45%  Similarity=0.884  Sum_probs=60.4

Q ss_pred             eeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEe
Q psy547           34 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVT  101 (282)
Q Consensus        34 ~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~  101 (282)
                      ++|+|||||.+||||||+++++++|||||+++|...    ++..|.+|+.|+|++..+.+|++|.+|+
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            379999999999999999999999999999999986    4789999999999999999999999986

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.

>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=99.77  E-value=2.1e-18  Score=125.57  Aligned_cols=65  Identities=42%  Similarity=0.783  Sum_probs=58.7

Q ss_pred             eeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547          201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK  269 (282)
Q Consensus       201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~  269 (282)
                      ++|+|+|||..+|||||+++++.+|||||+++|...    +++.|..|++|+|++..+++|++|.+|++
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            579999999999999999999999999999999965    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=99.75  E-value=4.2e-18  Score=123.66  Aligned_cols=63  Identities=43%  Similarity=0.798  Sum_probs=59.1

Q ss_pred             eeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeE
Q psy547          202 CGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVL  268 (282)
Q Consensus       202 ~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~  268 (282)
                      +|+|||||..||||||+++++++|||||+++|...    ++..|.+|++|+|++..+++|++|.+|+
T Consensus         2 ~G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~----~~~~~~~G~~V~f~~~~~~~g~~A~~V~   64 (65)
T cd04458           2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGD----GFRSLEEGDRVEFELEEGDKGPQAVNVR   64 (65)
T ss_pred             cEEEEEEECCCCeEEEecCCCCcCEEEEhhHhhcc----CCCcCCCCCEEEEEEEECCCCCeEEEeE
Confidence            69999999999999999999999999999999954    4688999999999999999999999986

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=99.54  E-value=1.5e-14  Score=130.04  Aligned_cols=93  Identities=48%  Similarity=0.788  Sum_probs=83.9

Q ss_pred             CCceeeeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeCCCC
Q psy547           26 EPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGPDG  105 (282)
Q Consensus        26 ~~~~~~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~~~~  105 (282)
                      ..+++....+|+|||||..+|||||+++|+.+|||||+++|..+.++.++++|.+++.|+|+++.+.+|..|++|+.+++
T Consensus        49 ~~~~~~~~~~G~~k~fnv~~G~gFi~~~d~~~D~fvhQs~i~~~~~~~~~rs~~~~e~v~f~~~~~~~g~~a~~vt~p~g  128 (235)
T KOG3070|consen   49 AKKVQGARVKGTVKWFNVGKGYGFITRDDGPEDVFVHQSAITKYTPSEGFRSLKEGEAVPFDIQEGNKGTEAANVTGPDG  128 (235)
T ss_pred             ccccccccccCcceeEeccCCcceecccCCCCceeEEeeeecccccccchhhcccCCCccceecccCccceeeeecCCCC
Confidence            35677888999999999999999999999999999999999997777789999999999999999999999999999999


Q ss_pred             CccccccccCCCC
Q psy547          106 RHVQGSQFAANKP  118 (282)
Q Consensus       106 ~~~~~~~~~~~~~  118 (282)
                      .++..+.+.....
T Consensus       129 ~~~~~s~~~~~~~  141 (235)
T KOG3070|consen  129 VPVRGSKGAVKGN  141 (235)
T ss_pred             ccccccccccccc
Confidence            8887777665443

>KOG3070|consensus

Probab=99.32  E-value=2.1e-12  Score=116.10  Aligned_cols=72  Identities=44%  Similarity=0.786  Sum_probs=67.6

Q ss_pred             eeeeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeE
Q psy547          197 LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVL  268 (282)
Q Consensus       197 ~~~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~  268 (282)
                      +....+|+|||||..+|||||+++|+.+|||||+++|.++.++.+++.|.+++.|+|.++...+|.+|++|+
T Consensus        53 ~~~~~~G~~k~fnv~~G~gFi~~~d~~~D~fvhQs~i~~~~~~~~~rs~~~~e~v~f~~~~~~~g~~a~~vt  124 (235)
T KOG3070|consen   53 QGARVKGTVKWFNVGKGYGFITRDDGPEDVFVHQSAITKYTPSEGFRSLKEGEAVPFDIQEGNKGTEAANVT  124 (235)
T ss_pred             ccccccCcceeEeccCCcceecccCCCCceeEEeeeecccccccchhhcccCCCccceecccCccceeeeec
Confidence            346678999999999999999999999999999999998878889999999999999999999999999988

>smart00357 CSP Cold shock protein domain

Probab=98.90  E-value=8e-09  Score=73.28  Aligned_cols=61  Identities=46%  Similarity=0.822  Sum_probs=50.5

Q ss_pred             eeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEe--CCCCceEEEEeC
Q psy547           35 CGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ--GDKGHEAINVTG  102 (282)
Q Consensus        35 ~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~--~~kG~~A~~V~~  102 (282)
                      +|+|+|++  +|||||.+++...|+|||.+.+.. +    +..+..||.|.|.+..  ..++++|..|..
T Consensus         1 ~G~i~~~~--~g~gfv~~~~~~~~i~v~~~~~~~-~----~~~~~~Gd~V~~~i~~~~~~~~~~a~~v~~   63 (64)
T smart00357        1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQG-G----LKSLREGDEVEFKVVSPRGGGKPEAENVVK   63 (64)
T ss_pred             CeEEEEEc--CCeeEEecCCCCccEEEEhHHhhc-C----CCcCCCCCEEEEEEEEccCCCCcEEEEEEe
Confidence            58999997  899999998765799999998865 2    5678999999999987  455678877754

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=98.78  E-value=3.9e-08  Score=69.66  Aligned_cols=60  Identities=42%  Similarity=0.749  Sum_probs=48.5

Q ss_pred             eeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEE--cCCCceeeeeE
Q psy547          202 CGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ--GDKGNQFCFVL  268 (282)
Q Consensus       202 ~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~--~~kG~~A~~V~  268 (282)
                      +|+|+|++  +|||||.+++...+||||.+.++.     ++..+..||.|.|.+..  ..++++|..+.
T Consensus         1 ~G~i~~~~--~g~gfv~~~~~~~~i~v~~~~~~~-----~~~~~~~Gd~V~~~i~~~~~~~~~~a~~v~   62 (64)
T smart00357        1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQG-----GLKSLREGDEVEFKVVSPRGGGKPEAENVV   62 (64)
T ss_pred             CeEEEEEc--CCeeEEecCCCCccEEEEhHHhhc-----CCCcCCCCCEEEEEEEEccCCCCcEEEEEE
Confidence            48999996  799999998766799999998763     24678999999999987  45567776554

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.

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

Probab=97.65  E-value=0.00014  Score=51.50  Aligned_cols=42  Identities=24%  Similarity=0.589  Sum_probs=32.4

Q ss_pred             CCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCC
Q psy547           44 KSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG   94 (282)
Q Consensus        44 ~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG   94 (282)
                      .+||||+.+++...|||+...++...         ..||+|...+....++
T Consensus         7 ~~GfGFv~~~~~~~DifIp~~~l~~A---------~~gD~V~v~i~~~~~~   48 (58)
T PF08206_consen    7 PKGFGFVIPDDGGEDIFIPPRNLNGA---------MDGDKVLVRITPPSRG   48 (58)
T ss_dssp             SSS-EEEEECT-TEEEEE-HHHHTTS----------TT-EEEEEEEESSSE
T ss_pred             cCCCEEEEECCCCCCEEECHHHHCCC---------CCCCEEEEEEecCCCC
Confidence            89999999999899999999999776         7999999999884433

; PDB: 2ID0_D 2IX1_A 2IX0_A.

>PRK11642 exoribonuclease R; Provisional

Probab=97.64  E-value=0.0011  Score=69.70  Aligned_cols=47  Identities=23%  Similarity=0.460  Sum_probs=38.8

Q ss_pred             eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEe
Q psy547           33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ   90 (282)
Q Consensus        33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~   90 (282)
                      .+.|+|+.=  .+||||+.++++++||||+-..+...         ..||+|...+..
T Consensus        84 ~~~G~v~~~--~~GfgFv~~e~~~~difI~~~~l~~A---------~~GD~V~v~i~~  130 (813)
T PRK11642         84 LLKGTVIGH--RDGYGFLRVEGRKDDLYLSSEQMKTC---------IHGDQVLAQPLG  130 (813)
T ss_pred             eEEEEEEEC--CCccEEEEECCCCCCEEEChHHHccC---------CCCCEEEEEEcc
Confidence            477999954  89999999987678999988887664         689999988654

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

Probab=97.51  E-value=0.00038  Score=49.32  Aligned_cols=42  Identities=24%  Similarity=0.604  Sum_probs=32.1

Q ss_pred             CCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCC
Q psy547          211 KSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG  261 (282)
Q Consensus       211 ~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG  261 (282)
                      .+||||+.+++..+|||+...++.         ..-.||+|...+....++
T Consensus         7 ~~GfGFv~~~~~~~DifIp~~~l~---------~A~~gD~V~v~i~~~~~~   48 (58)
T PF08206_consen    7 PKGFGFVIPDDGGEDIFIPPRNLN---------GAMDGDKVLVRITPPSRG   48 (58)
T ss_dssp             SSS-EEEEECT-TEEEEE-HHHHT---------TS-TT-EEEEEEEESSSE
T ss_pred             cCCCEEEEECCCCCCEEECHHHHC---------CCCCCCEEEEEEecCCCC
Confidence            799999999999999999999988         357999999999984433

; PDB: 2ID0_D 2IX1_A 2IX0_A.

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

Probab=97.21  E-value=0.0098  Score=61.38  Aligned_cols=47  Identities=30%  Similarity=0.477  Sum_probs=38.4

Q ss_pred             eeeeEEEEeeCCCceEEEeCCC-CCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEe
Q psy547           33 KVCGVVKWFSVKSGYGFIATPS-SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ   90 (282)
Q Consensus        33 ~~~G~Vkwfn~~kGfGFI~~~d-~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~   90 (282)
                      .+.|+|+.=  .|||||+.+++ +++|+|+.-..+...         ..||+|...+..
T Consensus        16 ~~~G~i~~~--~~gfgFv~~~~~~~~difI~~~~~~~a---------~~GD~V~v~i~~   63 (654)
T TIGR00358        16 LVKGVVKAH--NKGFGFLRPDDDDKKDYFIPPPQMKKV---------MHGDLVEACPLS   63 (654)
T ss_pred             eEEEEEEEC--CCccEEEEeCCCCCCcEEEchHHhCcC---------CCCCEEEEEEee
Confidence            467999975  89999999986 368999998877654         689999998754

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=97.17  E-value=0.013  Score=60.30  Aligned_cols=47  Identities=26%  Similarity=0.451  Sum_probs=37.9

Q ss_pred             eeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEe
Q psy547           32 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ   90 (282)
Q Consensus        32 ~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~   90 (282)
                      ..+.|+|+.=  .|||||+.+++ .+|+|++-..+...         ..||+|...+..
T Consensus        20 ~~~~G~~~~~--~~gfgFv~~~~-~~difI~~~~l~~a---------~~GD~V~v~i~~   66 (644)
T PRK05054         20 PRVEGVVKAT--EKGFGFLEVDA-QKSYFIPPPQMKKV---------MHGDRIIAVIHT   66 (644)
T ss_pred             CeEEEEEEEC--CCccEEEEECC-CCcEEEChHHHccC---------CCCCEEEEEEec
Confidence            3467999964  89999998854 46999999988765         689999998754

>TIGR02063 RNase_R ribonuclease R

Probab=97.04  E-value=0.019  Score=59.71  Aligned_cols=47  Identities=23%  Similarity=0.475  Sum_probs=37.3

Q ss_pred             eeeeEEEEeeCCCceEEEeCCC-CCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEe
Q psy547           33 KVCGVVKWFSVKSGYGFIATPS-SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ   90 (282)
Q Consensus        33 ~~~G~Vkwfn~~kGfGFI~~~d-~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~   90 (282)
                      .+.|+++.  ..+||||+.+++ ...|+|+.-..+..         +..||.|...+..
T Consensus        68 ~~~G~i~~--~~~g~gFv~~~~~~~~di~I~~~~~~~---------a~~GD~Vlv~I~~  115 (709)
T TIGR02063        68 LVKGTVIA--HRDGFGFLRPEDDDEDDIFIPPRQMNG---------AMHGDRVLVRITG  115 (709)
T ss_pred             eEEEEEEE--CCCccEEEEECCCCCCcEEEChHHhCc---------CCCCCEEEEEEec
Confidence            46798886  489999999986 45799998776654         4789999998754

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.

>PF14444 S1-like: S1-like

Probab=96.94  E-value=0.0033  Score=44.50  Aligned_cols=49  Identities=31%  Similarity=0.453  Sum_probs=40.3

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCC
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG  261 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG  261 (282)
                      +..+|+|..+.  ..||||.     ++|||+.+.+...       .++.||+|..+...++.-
T Consensus         2 r~~~GvVTkl~--~~yG~ID-----e~vFF~~~vv~G~-------~P~vGdrV~v~A~~n~~~   50 (58)
T PF14444_consen    2 RVFTGVVTKLC--DDYGFID-----EDVFFQTDVVKGN-------VPKVGDRVLVEAIYNPNM   50 (58)
T ss_pred             ceEEEEEEEEe--CCcceEc-----ccEEEEcccEecC-------CCccCCEEEEEEEeCCCC
Confidence            34689999994  6799996     4899999998832       469999999999988754

>TIGR02062 RNase_B exoribonuclease II

Probab=96.71  E-value=0.051  Score=56.02  Aligned_cols=49  Identities=24%  Similarity=0.435  Sum_probs=38.8

Q ss_pred             eeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeC
Q psy547           31 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG   91 (282)
Q Consensus        31 ~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~   91 (282)
                      ...+.|+|+.=  .|||||+..++ .+|||++-..+...         ..||+|...+...
T Consensus        16 ~~~~~G~i~~~--~kGfgFv~~~~-~~difI~~~~l~~A---------~~GD~V~v~i~~~   64 (639)
T TIGR02062        16 TPRVEGVVKAT--EKGFGFLEVDA-QKSYFIPPPQMKKV---------MHGDKIIAVIHSE   64 (639)
T ss_pred             CceEEEEEEEC--CCccEEEEECC-CCcEEEChHHHccC---------CCCCEEEEEEecC
Confidence            34567999965  89999997654 56999999988765         6899999987543

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.

>PF14444 S1-like: S1-like

Probab=96.21  E-value=0.018  Score=40.76  Aligned_cols=48  Identities=31%  Similarity=0.444  Sum_probs=39.4

Q ss_pred             eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCC
Q psy547           33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG   94 (282)
Q Consensus        33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG   94 (282)
                      ..+|.|..+  ...||||.     +||||+.+.+.+.       .++.||+|..+...+++-
T Consensus         3 ~~~GvVTkl--~~~yG~ID-----e~vFF~~~vv~G~-------~P~vGdrV~v~A~~n~~~   50 (58)
T PF14444_consen    3 VFTGVVTKL--CDDYGFID-----EDVFFQTDVVKGN-------VPKVGDRVLVEAIYNPNM   50 (58)
T ss_pred             eEEEEEEEE--eCCcceEc-----ccEEEEcccEecC-------CCccCCEEEEEEEeCCCC
Confidence            358999999  47899997     4899999998763       448999999998877653

>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=94.45  E-value=0.081  Score=39.89  Aligned_cols=63  Identities=32%  Similarity=0.582  Sum_probs=39.6

Q ss_pred             eeeEEEEeeCCCceEEEeCC-----CCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCC---ceEEEEeCCCC
Q psy547           34 VCGVVKWFSVKSGYGFIATP-----SSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG---HEAINVTGPDG  105 (282)
Q Consensus        34 ~~G~Vkwfn~~kGfGFI~~~-----d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG---~~A~~V~~~~~  105 (282)
                      ..|.+---  .+|||||...     .+..||||..+.++..       .|+.||.|+=.+.....+   .....|..+++
T Consensus         3 ~~GvLei~--~dGyGFLR~~~~~y~~~~~DvYVs~~qIrrf-------~LR~GD~V~G~vr~p~~~ek~~aL~~V~~VNg   73 (78)
T PF07497_consen    3 VEGVLEIL--PDGYGFLRSPDNNYLPSPDDVYVSPSQIRRF-------GLRTGDLVEGQVRPPREGEKYFALLRVESVNG   73 (78)
T ss_dssp             EEEEEEE---TTS-EEEE-GGGTTS-STTSEEE-CCCCCCT-------T--TTEEEEEEEE--STTSSSEEECEECEETT
T ss_pred             EEEEEEEC--CCCcEEeECCCcCCCCCCCCEEECHHHHHHc-------CCCCCCEEEEEEeCCCCCCcceeeEEEEeECC
Confidence            34555522  5799999997     2678999999999875       579999999888775444   34455665554

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 ....

>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=94.41  E-value=0.17  Score=38.10  Aligned_cols=51  Identities=33%  Similarity=0.614  Sum_probs=33.4

Q ss_pred             eeEEEEEEcCCCeeEEecC-----CCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCC
Q psy547          202 CGVVKWFSVKSGYGFIATP-----SSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG  261 (282)
Q Consensus       202 ~G~Vk~fn~~kGfGFI~~~-----d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG  261 (282)
                      .|++--.  .+|||||...     -+..||||..+.++.       -.|..||.|+=.+.....+
T Consensus         4 ~GvLei~--~dGyGFLR~~~~~y~~~~~DvYVs~~qIrr-------f~LR~GD~V~G~vr~p~~~   59 (78)
T PF07497_consen    4 EGVLEIL--PDGYGFLRSPDNNYLPSPDDVYVSPSQIRR-------FGLRTGDLVEGQVRPPREG   59 (78)
T ss_dssp             EEEEEE---TTS-EEEE-GGGTTS-STTSEEE-CCCCCC-------TT--TTEEEEEEEE--STT
T ss_pred             EEEEEEC--CCCcEEeECCCcCCCCCCCCEEECHHHHHH-------cCCCCCCEEEEEEeCCCCC
Confidence            3555432  5799999987     257899999999994       3599999999988886665

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=93.93  E-value=1.1  Score=44.68  Aligned_cols=58  Identities=19%  Similarity=0.285  Sum_probs=40.9

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD  259 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~  259 (282)
                      ...+|+|+..   ..||....-+.+-+-|+|.+.+.......-...++.||.|.+.|..-+
T Consensus       381 ~~v~G~V~~i---~~~G~FV~l~~gv~Gli~~se~s~~~~~~~~~~~~~Gd~v~~~V~~id  438 (491)
T PRK13806        381 TTVTGTVEKR---AQFGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEID  438 (491)
T ss_pred             CEEEEEEEEE---ecCceEEEcCCCcEEEEEHHHcCcccccchhhcCCCCCEEEEEEEEEe
Confidence            3467999886   457765555558899999999975421122456899999999876643

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

Probab=93.78  E-value=0.2  Score=36.72  Aligned_cols=44  Identities=27%  Similarity=0.555  Sum_probs=35.1

Q ss_pred             CCCeeEEecCC-----CCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCC
Q psy547          211 KSGYGFIATPS-----SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG  261 (282)
Q Consensus       211 ~kGfGFI~~~d-----~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG  261 (282)
                      .+|||||...+     +..||||+.+-++.       ..|..||.|+=.+..-..+
T Consensus         9 ~~g~GFLR~~~~~y~~~~~DvyVs~~~Irr-------~~LR~GD~V~G~vr~p~~~   57 (68)
T cd04459           9 PDGFGFLRSSGYNYLPGPDDIYVSPSQIRR-------FNLRTGDTVVGQIRPPKEG   57 (68)
T ss_pred             CCCceEEecCCcCCCCCCCCEEECHHHHHH-------hCCCCCCEEEEEEeCCCCC
Confidence            34999999762     57899999999994       3589999999888764433

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.

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

Probab=93.70  E-value=0.42  Score=36.52  Aligned_cols=73  Identities=22%  Similarity=0.237  Sum_probs=48.5

Q ss_pred             eeeeeEEEEEEcCCC-eeEEecCCCCccEEEEeccccc---cCCcccccCCCCCCEEEEEEEEcCCCceeeeeEeccee
Q psy547          199 TKVCGVVKWFSVKSG-YGFIATPSSNEDVFVHSKRIKY---NNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLKNIVL  273 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kG-fGFI~~~d~~~dVF~H~s~l~~---~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~~~~~  273 (282)
                      ..+.|+|+..  .+. ||.+..-+.+.+-|+|++++..   .....-...++.||.|...+..-+.+-.+..++.++.+
T Consensus         9 ~iy~g~V~~i--~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~lt~~~~~   85 (88)
T cd04453           9 NIYLGRVKKI--VPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLTTNISL   85 (88)
T ss_pred             CEEEEEEEEe--ccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCceEEEEEEc
Confidence            5578999887  333 4665555557899999999853   00000123599999999999987666555556655543

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

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

Probab=93.61  E-value=0.13  Score=37.76  Aligned_cols=41  Identities=27%  Similarity=0.530  Sum_probs=34.1

Q ss_pred             CCceEEEeCC-----CCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeC
Q psy547           44 KSGYGFIATP-----SSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG   91 (282)
Q Consensus        44 ~kGfGFI~~~-----d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~   91 (282)
                      .+|||||...     .+..||||+.+.++..       .|+.||.|+=.+...
T Consensus         9 ~~g~GFLR~~~~~y~~~~~DvyVs~~~Irr~-------~LR~GD~V~G~vr~p   54 (68)
T cd04459           9 PDGFGFLRSSGYNYLPGPDDIYVSPSQIRRF-------NLRTGDTVVGQIRPP   54 (68)
T ss_pred             CCCceEEecCCcCCCCCCCCEEECHHHHHHh-------CCCCCCEEEEEEeCC
Confidence            3499999986     2678999999999875       579999999887753

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.

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=92.36  E-value=2.3  Score=42.59  Aligned_cols=58  Identities=16%  Similarity=0.168  Sum_probs=41.7

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD  259 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~  259 (282)
                      ..++|+|+..   ..||+....+.+-+-|+|++++.......--..++.||.|...|..-+
T Consensus       295 ~vv~G~V~~I---~~fGvFVeL~~gieGLvh~SeLs~~~v~~~~~~~kvGd~V~VkIi~ID  352 (486)
T PRK07899        295 QIVPGKVTKL---VPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDID  352 (486)
T ss_pred             CEEEEEEEEE---eccEEEEEeCCCcEEEEEHHHcCcccccCccceeCCCCEEEEEEEEEE
Confidence            3467899877   449988877667899999999975321111234799999999987643

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=92.30  E-value=2.2  Score=42.64  Aligned_cols=57  Identities=21%  Similarity=0.288  Sum_probs=40.0

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCC-cccccCCCCCCEEEEEEEEc
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNP-RKLYKTLAEGETVEFDIMQG  258 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~-r~g~~~l~~Gd~V~F~i~~~  258 (282)
                      ..+.|+|+..   ..||.+...+.+-+.|+|++++..... ..-...++.||.|.+.+..-
T Consensus       294 ~~v~G~V~~v---~~~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~i  351 (491)
T PRK13806        294 DKVTGKVVRL---APFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDI  351 (491)
T ss_pred             CEEEEEEEEE---eCceEEEEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEE
Confidence            4467899887   348988776667899999999874210 00013489999999988753

>PRK11642 exoribonuclease R; Provisional

Probab=91.24  E-value=0.51  Score=50.06  Aligned_cols=47  Identities=26%  Similarity=0.480  Sum_probs=38.1

Q ss_pred             eeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEE
Q psy547          200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ  257 (282)
Q Consensus       200 ~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~  257 (282)
                      .+.|+|+.  ..+||||+.++++++|||++-..+.         ..-.||+|...+..
T Consensus        84 ~~~G~v~~--~~~GfgFv~~e~~~~difI~~~~l~---------~A~~GD~V~v~i~~  130 (813)
T PRK11642         84 LLKGTVIG--HRDGYGFLRVEGRKDDLYLSSEQMK---------TCIHGDQVLAQPLG  130 (813)
T ss_pred             eEEEEEEE--CCCccEEEEECCCCCCEEEChHHHc---------cCCCCCEEEEEEcc
Confidence            35688874  3799999999876789999988777         35679999998765

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=90.75  E-value=5.4  Score=42.79  Aligned_cols=58  Identities=16%  Similarity=0.238  Sum_probs=40.9

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCC-cccccCCCCCCEEEEEEEEcC
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNP-RKLYKTLAEGETVEFDIMQGD  259 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~-r~g~~~l~~Gd~V~F~i~~~~  259 (282)
                      ...+|+|+..   ..||.+..-..+-+-|+|.+++..... ...-..+++||.|.+.|..-+
T Consensus       667 ~~v~G~V~~i---~~~G~fV~l~~gV~GlIh~sels~~~~~~~~~~~~kvGq~VkvkVl~ID  725 (863)
T PRK12269        667 ARFTRRIVKV---TNAGAFIEMEEGIDGFLHVDDLSWVKRTRPADHELEVGKEIECMVIECD  725 (863)
T ss_pred             CEEEEEEEEE---ecceEEEEeCCCcEEEEEhHHhhccccccchhhccCCCCEEEEEEEEEe
Confidence            4467999876   458887766668899999999863210 001125899999999887754

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=90.52  E-value=3.6  Score=44.13  Aligned_cols=58  Identities=19%  Similarity=0.222  Sum_probs=41.0

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEecccccc-CCcccccCCCCCCEEEEEEEEcC
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYN-NPRKLYKTLAEGETVEFDIMQGD  259 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~-~~r~g~~~l~~Gd~V~F~i~~~~  259 (282)
                      ...+|+|+...   .||.+..-..+-+-|+|++++... ....-...++.||.|.+.|..-+
T Consensus       580 ~iV~G~V~~I~---~fG~fVeL~~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD  638 (863)
T PRK12269        580 DVVKGRVTKIA---DFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYD  638 (863)
T ss_pred             CEEEEEEEEEe---CCeEEEEecCCceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEe
Confidence            44679998873   588777666678889999999741 10111234899999999887744

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

Probab=90.25  E-value=0.79  Score=47.47  Aligned_cols=47  Identities=30%  Similarity=0.521  Sum_probs=37.7

Q ss_pred             eeeeEEEEEEcCCCeeEEecCC-CCccEEEEeccccccCCcccccCCCCCCEEEEEEEE
Q psy547          200 KVCGVVKWFSVKSGYGFIATPS-SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ  257 (282)
Q Consensus       200 ~~~G~Vk~fn~~kGfGFI~~~d-~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~  257 (282)
                      ...|+|+.=  .+||||+.+++ +++|||+.-..+.         ..-.||+|.+.+..
T Consensus        16 ~~~G~i~~~--~~gfgFv~~~~~~~~difI~~~~~~---------~a~~GD~V~v~i~~   63 (654)
T TIGR00358        16 LVKGVVKAH--NKGFGFLRPDDDDKKDYFIPPPQMK---------KVMHGDLVEACPLS   63 (654)
T ss_pred             eEEEEEEEC--CCccEEEEeCCCCCCcEEEchHHhC---------cCCCCCEEEEEEee
Confidence            356999863  79999999886 3689999988776         35689999999865

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.

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

Probab=89.90  E-value=2.9  Score=42.37  Aligned_cols=142  Identities=19%  Similarity=0.304  Sum_probs=88.0

Q ss_pred             eeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC--CCceEEEEeCCCCCcc
Q psy547           31 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD--KGHEAINVTGPDGRHV  108 (282)
Q Consensus        31 ~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~--kG~~A~~V~~~~~~~~  108 (282)
                      ..-+.|+|+...+   ||-...-. +-|=++|+|.+..........-+++||.|...+-.-+  ++.....+..+...| 
T Consensus       193 G~vV~G~V~~It~---~GafVdig-GvdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~l~~dP-  267 (541)
T COG0539         193 GEVVEGVVKNITD---YGAFVDIG-GVDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQLEEDP-  267 (541)
T ss_pred             CceEEEEEEEeec---CcEEEEec-CeeeEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehhcccCc-
Confidence            3447899999865   66444443 4899999999977532222356899999999876543  344444443222100 


Q ss_pred             ccccccCCCCccccccccccccccCCCcCCccccccccccccccccCCCCcceeeeeeeeccCCCCCccccCCCCCCCCC
Q psy547          109 QGSQFAANKPKYNRRKAKANKRKRKSRRNNRLFGVKYQLEIPMEFSSKTMPFFMILFCCLQMCDSGTKAEATPSNPSASE  188 (282)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~g~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~  188 (282)
                                                          |     ....                                  
T Consensus       268 ------------------------------------w-----~~i~----------------------------------  272 (541)
T COG0539         268 ------------------------------------W-----EGIE----------------------------------  272 (541)
T ss_pred             ------------------------------------H-----HHHh----------------------------------
Confidence                                                0     0000                                  


Q ss_pred             CCCCCceeeeeeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547          189 SPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD  259 (282)
Q Consensus       189 ~~~~~~~~~~~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~  259 (282)
                          +......+..|+|..+   .-||.+..-..|-+=|+|+|++.-.....=-.-|+.||.|+..+..-+
T Consensus       273 ----~~~~~g~~v~G~Vt~i---~~~GafVei~~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id  336 (541)
T COG0539         273 ----KKYPVGDKVEGKVTNL---TDYGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDID  336 (541)
T ss_pred             ----hhcCCCCEEEEEEEEe---ecCcEEEEecCCccceeechhhcccccCCHHHhcccCCEEEEEEEeeC
Confidence                0000124567999887   458877777778899999998864321111133899999999877644

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

Probab=89.70  E-value=1.2  Score=32.01  Aligned_cols=60  Identities=17%  Similarity=0.211  Sum_probs=44.0

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCC
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG  261 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG  261 (282)
                      ..+.|+|...+.   +|++..-+.+-+.|+|.+++...........+..||.|.+.+..-+..
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            446799998865   776666567899999999998531111246799999999998875543

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 ....

>TIGR02062 RNase_B exoribonuclease II

Probab=89.11  E-value=1.1  Score=46.40  Aligned_cols=53  Identities=23%  Similarity=0.449  Sum_probs=39.2

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCce
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQ  263 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~  263 (282)
                      ....|+|+.  ..+||||+..++ .+|||++-..+..         .-.||+|.+.+....+..+
T Consensus        17 ~~~~G~i~~--~~kGfgFv~~~~-~~difI~~~~l~~---------A~~GD~V~v~i~~~~~r~~   69 (639)
T TIGR02062        17 PRVEGVVKA--TEKGFGFLEVDA-QKSYFIPPPQMKK---------VMHGDKIIAVIHSEKERES   69 (639)
T ss_pred             ceEEEEEEE--CCCccEEEEECC-CCcEEEChHHHcc---------CCCCCEEEEEEecCCCCcE
Confidence            445699975  379999997654 5699999988873         4579999998865433333

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=89.11  E-value=1.1  Score=46.49  Aligned_cols=52  Identities=23%  Similarity=0.436  Sum_probs=38.7

Q ss_pred             eeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCce
Q psy547          200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQ  263 (282)
Q Consensus       200 ~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~  263 (282)
                      ...|+|+.  ..+||||+.+++ .+|||++-..+..         .-.||+|.+.+....++.+
T Consensus        21 ~~~G~~~~--~~~gfgFv~~~~-~~difI~~~~l~~---------a~~GD~V~v~i~~~~~r~~   72 (644)
T PRK05054         21 RVEGVVKA--TEKGFGFLEVDA-QKSYFIPPPQMKK---------VMHGDRIIAVIHTEKDREI   72 (644)
T ss_pred             eEEEEEEE--CCCccEEEEECC-CCcEEEChHHHcc---------CCCCCEEEEEEecCCCCcE
Confidence            45699975  379999998754 5699999888873         4579999999865433333

>TIGR00717 rpsA ribosomal protein S1

Probab=89.06  E-value=9  Score=38.20  Aligned_cols=57  Identities=14%  Similarity=0.215  Sum_probs=40.3

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEc
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG  258 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~  258 (282)
                      ...+|+|+..   ..||+...-+.+-+-|+|.+++..+....-...++.||.|.+.+..-
T Consensus       448 ~~v~g~V~~v---~~~G~fV~l~~~~~Glv~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~i  504 (516)
T TIGR00717       448 SVVKGKVTEI---KDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDI  504 (516)
T ss_pred             eEEEEEEEEE---ecceEEEEcCCCeEEEEEHHHcCccccccccccCCCCCEEEEEEEEE
Confidence            4467888875   34886655555789999999986542112245689999999988664

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.

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

Probab=88.88  E-value=1.5  Score=29.65  Aligned_cols=56  Identities=16%  Similarity=0.267  Sum_probs=38.3

Q ss_pred             eeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC
Q psy547          202 CGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK  260 (282)
Q Consensus       202 ~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k  260 (282)
                      .|+|+..+   .+|+....+.+.+.|+|.+++...........++.||.|.+.+..-+.
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            47888875   355555445578999999999743111112458999999999887543

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.

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=88.72  E-value=1  Score=31.93  Aligned_cols=49  Identities=16%  Similarity=0.287  Sum_probs=31.3

Q ss_pred             eEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCc
Q psy547          203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN  262 (282)
Q Consensus       203 G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~  262 (282)
                      -+|+..+   .+|+.-..+.+.+||+|.+++.        ..+++||.|+.=+-.+.++.
T Consensus         7 L~V~~~~---~~g~fL~~~~~~~vlLp~~e~~--------~~~~~Gd~v~VFvY~D~~~r   55 (61)
T PF13509_consen    7 LKVVDKN---EFGYFLDDGEGKEVLLPKSEVP--------EPLKVGDEVEVFVYLDKEGR   55 (61)
T ss_dssp             --EEEE----SSEEEEEETT-EEEEEEGGG--------------TTSEEEEEEEE-TTS-
T ss_pred             eEEEEEe---CCEEEEECCCCCEEEechHHcC--------CCCCCCCEEEEEEEECCCCC
Confidence            4565554   4777776776799999999997        35999999999999998883

>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=88.70  E-value=2.5  Score=29.95  Aligned_cols=59  Identities=15%  Similarity=0.179  Sum_probs=41.3

Q ss_pred             eeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCC
Q psy547          200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG  261 (282)
Q Consensus       200 ~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG  261 (282)
                      .+.|+|+...   .||.+..-.++-+-|+|.+++..+....-...++.||.|++.+..-++.
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            3568888874   3777666655789999999997432111123489999999999886543

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.

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

Probab=88.57  E-value=1.5  Score=29.63  Aligned_cols=56  Identities=18%  Similarity=0.209  Sum_probs=37.3

Q ss_pred             eeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC
Q psy547           34 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD   92 (282)
Q Consensus        34 ~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~   92 (282)
                      +.|+|+..+  +..-|+..+ .+.+.|+|.+.+...........++.||.|.+.+..-+
T Consensus         1 v~g~V~~v~--~~g~~v~l~-~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d   56 (65)
T cd00164           1 VTGKVVSIT--KFGVFVELE-DGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVD   56 (65)
T ss_pred             CEEEEEEEE--eeeEEEEec-CCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEc
Confidence            368888886  222345544 46899999999875310001246899999999987643

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.

>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=88.52  E-value=2.3  Score=31.47  Aligned_cols=59  Identities=15%  Similarity=0.120  Sum_probs=42.9

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK  260 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k  260 (282)
                      ..+.|+|+...   .||++..-..+-+.|+|.+++....-..-...++.||.|++.+..-+.
T Consensus        16 ~i~~g~V~~v~---~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~   74 (83)
T cd04461          16 MVVHGYVRNIT---PYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDE   74 (83)
T ss_pred             CEEEEEEEEEe---eceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcC
Confidence            44678998874   488888776678999999999754211112448899999999887553

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

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

Probab=87.82  E-value=2.1  Score=30.99  Aligned_cols=55  Identities=15%  Similarity=0.048  Sum_probs=37.9

Q ss_pred             eEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547          203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD  259 (282)
Q Consensus       203 G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~  259 (282)
                      |+|+...  ..||.+..-..+-+-|+|++.+..+....-...++.||.|++.+..-+
T Consensus         7 g~V~~v~--~~~G~~V~l~~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id   61 (71)
T cd05696           7 VKVTKVE--PDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYS   61 (71)
T ss_pred             eEEEEEc--cCceEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEe
Confidence            7787763  447776655447899999999964321112345999999999987544

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.

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=87.42  E-value=11  Score=38.13  Aligned_cols=57  Identities=21%  Similarity=0.299  Sum_probs=39.8

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCC-cccccCCCCCCEEEEEEEEc
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNP-RKLYKTLAEGETVEFDIMQG  258 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~-r~g~~~l~~Gd~V~F~i~~~  258 (282)
                      ..+.|+|+...   .||....-+.+-+.|+|++++..... ..-...++.||.|.+.+..-
T Consensus       375 ~~v~g~V~~v~---~~G~fV~l~~~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~Il~v  432 (565)
T PRK06299        375 DVVEGKVKNIT---DFGAFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKV  432 (565)
T ss_pred             CEEEEEEEEEe---cceEEEECCCCCEEEEEHHHcCccccccChHhhCCCCCEEEEEEEEE
Confidence            34678998863   57877766657899999999974310 11124578999999976554

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

Probab=87.22  E-value=3  Score=31.79  Aligned_cols=62  Identities=19%  Similarity=0.221  Sum_probs=40.6

Q ss_pred             eeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccC---CCcccccCCCCCCEEEEEEEeCCC
Q psy547           31 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYN---NPRKLYKTLAEGETVEFDIMQGDK   93 (282)
Q Consensus        31 ~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~---~~~~g~~~l~~Gd~V~f~v~~~~k   93 (282)
                      ...+.|+|+-...--.=-||+-.+ +.+-|+|++++...   ....--..+++||.|...+..-+.
T Consensus         8 G~iy~g~V~~i~~~~~GaFV~l~~-g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~   72 (88)
T cd04453           8 GNIYLGRVKKIVPGLQAAFVDIGL-GKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPI   72 (88)
T ss_pred             CCEEEEEEEEeccCCcEEEEEeCC-CCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecC
Confidence            456789999985432225666554 68999999998431   000002458999999999877443

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

>TIGR00717 rpsA ribosomal protein S1

Probab=86.13  E-value=14  Score=36.77  Aligned_cols=57  Identities=16%  Similarity=0.317  Sum_probs=39.3

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcc-cccCCCCCCEEEEEEEEc
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRK-LYKTLAEGETVEFDIMQG  258 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~-g~~~l~~Gd~V~F~i~~~  258 (282)
                      ....|+|+..   ..||+...-+.+-+.|+|.+++....... -...++.||.|...+..-
T Consensus       361 ~~v~g~V~~v---~~~G~fV~l~~~v~glv~~s~ls~~~~~~~~~~~~~~G~~V~~~Vl~v  418 (516)
T TIGR00717       361 DRVTGKIKKI---TDFGAFVELEGGIDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAV  418 (516)
T ss_pred             CEEEEEEEEE---ecceEEEECCCCCEEEEEHHHCcCcccCCCHhHccCCCCEEEEEEEEE
Confidence            3456899875   45777776666899999999987431100 124588999999976554

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.

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

Probab=85.85  E-value=2.2  Score=30.53  Aligned_cols=58  Identities=16%  Similarity=0.205  Sum_probs=41.7

Q ss_pred             eeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC
Q psy547           32 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD   92 (282)
Q Consensus        32 ~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~   92 (282)
                      ..+.|+|...+.   +|++..-..+-+.|+|.+++...........+..|++|.+.+..-+
T Consensus         6 ~iv~g~V~~v~~---~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd   63 (74)
T PF00575_consen    6 DIVEGKVTSVED---FGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVD   63 (74)
T ss_dssp             SEEEEEEEEEET---TEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEE
T ss_pred             CEEEEEEEEEEC---CEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEE
Confidence            457899998876   5555554468899999999985300012468999999999986543

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 ....

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=85.80  E-value=24  Score=33.82  Aligned_cols=58  Identities=19%  Similarity=0.317  Sum_probs=39.6

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD  259 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~  259 (282)
                      ..++|+|+...   .||+...-+.+-+-++|++++.......-...++.||.|...+..-+
T Consensus       279 ~~v~g~V~~i~---~~G~fV~l~~gi~Glv~~se~~~~~~~~~~~~~~~Gd~v~v~V~~id  336 (390)
T PRK06676        279 DVIEGTVKRLT---DFGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVN  336 (390)
T ss_pred             cEEEEEEEEEe---CceEEEEECCCCeEEEEhHHcCccccCChhhccCCCCEEEEEEEEEE
Confidence            44678998864   48887765556788999999864311001134799999999877654

>TIGR02063 RNase_R ribonuclease R

Probab=85.61  E-value=2.4  Score=44.31  Aligned_cols=48  Identities=23%  Similarity=0.477  Sum_probs=37.9

Q ss_pred             eeeeEEEEEEcCCCeeEEecCC-CCccEEEEeccccccCCcccccCCCCCCEEEEEEEEc
Q psy547          200 KVCGVVKWFSVKSGYGFIATPS-SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG  258 (282)
Q Consensus       200 ~~~G~Vk~fn~~kGfGFI~~~d-~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~  258 (282)
                      .+.|+++.  ..+||||+.+++ ...|||+....+.         ....||+|.+.+...
T Consensus        68 ~~~G~i~~--~~~g~gFv~~~~~~~~di~I~~~~~~---------~a~~GD~Vlv~I~~~  116 (709)
T TIGR02063        68 LVKGTVIA--HRDGFGFLRPEDDDEDDIFIPPRQMN---------GAMHGDRVLVRITGK  116 (709)
T ss_pred             eEEEEEEE--CCCccEEEEECCCCCCcEEEChHHhC---------cCCCCCEEEEEEecc
Confidence            35688875  478999999876 4679999877665         367899999998764

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.

>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=85.59  E-value=4.6  Score=29.85  Aligned_cols=58  Identities=16%  Similarity=0.115  Sum_probs=41.2

Q ss_pred             eeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC
Q psy547           32 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD   92 (282)
Q Consensus        32 ~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~   92 (282)
                      ..+.|+|+-..   -||++..-.++-+.|+|.+.+....-..-...++.||.|++.+..-+
T Consensus        16 ~i~~g~V~~v~---~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id   73 (83)
T cd04461          16 MVVHGYVRNIT---PYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVD   73 (83)
T ss_pred             CEEEEEEEEEe---eceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEc
Confidence            45788988775   37777665557899999999965421111245889999999987654

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.

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

Probab=85.45  E-value=20  Score=33.31  Aligned_cols=49  Identities=14%  Similarity=0.201  Sum_probs=35.9

Q ss_pred             CCCeeEEecCCCCccEEEEeccccccCCcccccC--CCCCCEEEEEEEEcCCCceee
Q psy547          211 KSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKT--LAEGETVEFDIMQGDKGNQFC  265 (282)
Q Consensus       211 ~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~--l~~Gd~V~F~i~~~~kG~~A~  265 (282)
                      .+.-|--...+-.+|++|..+++..      +.+  ++.||++.+.+..+.+|.-..
T Consensus        85 ~~~lGaFlD~Gl~KDl~vp~~elp~------~~~~wpq~Gd~l~v~l~~Dkk~Ri~g  135 (287)
T COG2996          85 NKDLGAFLDWGLPKDLLVPLDELPT------LKSLWPQKGDKLLVYLYVDKKGRIWG  135 (287)
T ss_pred             cCCcceEEecCCCcceeeehhhccc------ccccCCCCCCEEEEEEEEccCCcEEE
Confidence            3444443434446899999999984      234  899999999999999994443

>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=85.27  E-value=4.3  Score=28.73  Aligned_cols=58  Identities=16%  Similarity=0.185  Sum_probs=38.8

Q ss_pred             eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCC
Q psy547           33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK   93 (282)
Q Consensus        33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~k   93 (282)
                      .+.|+|+-...   ||.+..-.++-+-|+|.+.|..+.-..-...++.||.|++.+..-+.
T Consensus         3 ~~~g~V~~v~~---~G~~V~l~~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~   60 (70)
T cd05698           3 KTHGTIVKVKP---NGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDP   60 (70)
T ss_pred             EEEEEEEEEec---CcEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcC
Confidence            46788888843   45554444468999999999643100012348999999999877544

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.

>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=85.24  E-value=6.3  Score=28.14  Aligned_cols=59  Identities=8%  Similarity=-0.048  Sum_probs=40.7

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK  260 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k  260 (282)
                      ....|+|+...   .+|.+..-+.+-+-|+|.+++..+....-...+..||.|.+.+..-+.
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            34568888863   366666555578999999999754211112347999999999877553

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.

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

Probab=85.12  E-value=4  Score=28.22  Aligned_cols=56  Identities=21%  Similarity=0.338  Sum_probs=39.2

Q ss_pred             eeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547          201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD  259 (282)
Q Consensus       201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~  259 (282)
                      +.|+|....   .||+...-+.+.+.|+|.+++.......-...++.||.|...+..-+
T Consensus         4 ~~g~V~~i~---~~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~   59 (69)
T cd05692           4 VEGTVTRLK---PFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID   59 (69)
T ss_pred             EEEEEEEEE---eeeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEEC
Confidence            568887764   37877776667899999999974321000134799999999886644

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.

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

Probab=84.54  E-value=18  Score=37.42  Aligned_cols=58  Identities=28%  Similarity=0.365  Sum_probs=40.9

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD  259 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~  259 (282)
                      ..++|+|+...   .||+...-+.+-+-|+|.+++.......--..++.||.|...+..-+
T Consensus       564 ~~v~g~V~~i~---~~G~fV~l~~~i~Gli~~sel~~~~~~~~~~~~kvGd~V~vkV~~id  621 (647)
T PRK00087        564 SIVLGKVVRIA---PFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVD  621 (647)
T ss_pred             eEEEEEEEEEE---CCeEEEEECCCCEEEEEhhhcCccccCCHhhcCCCCCEEEEEEEEEe
Confidence            34678998874   37877765667899999999975321111235799999999887654

>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=84.50  E-value=5.4  Score=28.87  Aligned_cols=61  Identities=13%  Similarity=0.132  Sum_probs=42.5

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCC
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG  261 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG  261 (282)
                      ..+.|+|+...  .-||.+..-..+.+-++|++++.+.....-...++.||.|...+..-.+|
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            34578888863  23676666666899999999997542111123478899999998887654

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.

>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=84.37  E-value=5.6  Score=28.18  Aligned_cols=57  Identities=14%  Similarity=0.160  Sum_probs=41.1

Q ss_pred             eeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC
Q psy547          201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK  260 (282)
Q Consensus       201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k  260 (282)
                      +.|+|+..+   .||.+..-+.+-+-|+|++++.......-...++.||.|.+.+..-+.
T Consensus         4 v~g~V~~v~---~~Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~   60 (69)
T cd05697           4 VKGTIRKLR---PSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEP   60 (69)
T ss_pred             EEEEEEEEe---ccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEEC
Confidence            568888874   478777666678999999999754211112358999999999887654

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.

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

Probab=84.36  E-value=6.8  Score=27.16  Aligned_cols=57  Identities=19%  Similarity=0.261  Sum_probs=40.5

Q ss_pred             eeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC
Q psy547          201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK  260 (282)
Q Consensus       201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k  260 (282)
                      +.|+|.....   ||+...-..+.+-|+|.+++.......-...++.||.|...+..-+.
T Consensus         4 ~~g~V~~v~~---~G~~v~l~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d~   60 (68)
T cd04472           4 YEGKVVKIKD---FGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD   60 (68)
T ss_pred             EEEEEEEEEE---eEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECC
Confidence            5688877753   89888766678999999999743211011347999999999877553

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.

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

Probab=84.25  E-value=5.6  Score=27.27  Aligned_cols=58  Identities=14%  Similarity=0.225  Sum_probs=40.7

Q ss_pred             eeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC
Q psy547          200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK  260 (282)
Q Consensus       200 ~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k  260 (282)
                      .+.|+|...+.   +|++...+.+-..|+|.+++...........++.||.|.+.+..-+.
T Consensus         5 ~v~g~V~~v~~---~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~   62 (72)
T smart00316        5 VVEGTVTEITP---FGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDE   62 (72)
T ss_pred             EEEEEEEEEEc---cEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeC
Confidence            45689988864   56666555578899999999853111112348999999999887654

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

Probab=84.19  E-value=5.1  Score=28.34  Aligned_cols=58  Identities=17%  Similarity=0.224  Sum_probs=40.8

Q ss_pred             eeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCC
Q psy547          201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG  261 (282)
Q Consensus       201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG  261 (282)
                      +.|+|+...   .+|.+..-..+-+-|+|.+++..+....-...++.||.|++.+..-+..
T Consensus         4 v~g~V~~v~---~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~   61 (73)
T cd05691           4 VTGKVTEVD---AKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRK   61 (73)
T ss_pred             EEEEEEEEE---CCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCC
Confidence            468888873   4777776655789999999997542111123479999999998886543

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.

>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=83.99  E-value=4  Score=29.50  Aligned_cols=53  Identities=15%  Similarity=0.069  Sum_probs=34.8

Q ss_pred             eEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEe
Q psy547           36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ   90 (282)
Q Consensus        36 G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~   90 (282)
                      |+|+.-...+| -|++..+ +-+-|+|+|.|....-..-...++.|+.|++.+..
T Consensus         7 g~V~~v~~~~G-~~V~l~~-gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~   59 (71)
T cd05696           7 VKVTKVEPDLG-AVFELKD-GLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIG   59 (71)
T ss_pred             eEEEEEccCce-EEEEeCC-CCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEE
Confidence            78888643333 3455545 58999999999643100113459999999999754

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.

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=83.98  E-value=18  Score=36.55  Aligned_cols=58  Identities=16%  Similarity=0.207  Sum_probs=39.1

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD  259 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~  259 (282)
                      ....|+|+....   ||.....+.+-.-|+|.+++.......-...+..||.|...+..-+
T Consensus       462 ~vV~G~V~~v~~---~G~fV~l~~gi~g~i~~se~s~~~~~~~~~~~~~Gd~v~~~V~~vd  519 (565)
T PRK06299        462 SIVTGTVTEVKD---KGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINID  519 (565)
T ss_pred             CEEEEEEEEEec---CceEEecCCCcEEEEEHHHhcchhccCccccCCCCCEEEEEEEEEc
Confidence            345689988753   4644433447789999999964422223456899999999877643

>COG0557 VacB Exoribonuclease R [Transcription]

Probab=83.38  E-value=16  Score=38.26  Aligned_cols=47  Identities=23%  Similarity=0.521  Sum_probs=37.4

Q ss_pred             eeeeEEEEeeCCCceEEEeCCC--CCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEe
Q psy547           33 KVCGVVKWFSVKSGYGFIATPS--SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ   90 (282)
Q Consensus        33 ~~~G~Vkwfn~~kGfGFI~~~d--~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~   90 (282)
                      .+.|++.+=  .+||||+.+++  ...|+|+-...+...         ..||.|..++..
T Consensus        69 ~~~~~~~~~--~~gf~f~~~~~~~~~~d~~v~~~~~~~a---------~~gD~V~v~~~~  117 (706)
T COG0557          69 LVEGIVEAS--AKGFGFLSPDDSKDADDIFVPKDPLNRA---------LHGDRVLVELLP  117 (706)
T ss_pred             cccceEEec--cCCceeeccCccCCCCcEEecccccccc---------ccCCEEEEEECc
Confidence            356777665  89999999998  678999998886554         689999998633

>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=82.73  E-value=8.5  Score=27.81  Aligned_cols=61  Identities=13%  Similarity=0.131  Sum_probs=40.8

Q ss_pred             eeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCC
Q psy547           32 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG   94 (282)
Q Consensus        32 ~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG   94 (282)
                      +.+.|+|+--...  ||.+..-..+.+-|+|+|.+...--..-...+++||.|...+..-+++
T Consensus         5 ~iv~G~V~~i~~~--~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~~   65 (72)
T cd05704           5 AVTLGMVTKVIPH--SGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKDG   65 (72)
T ss_pred             CEEEEEEEEeeCC--cEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecCC
Confidence            4468899886433  455555555789999999996641100013468899999998776654

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.

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

Probab=82.35  E-value=9  Score=27.21  Aligned_cols=57  Identities=19%  Similarity=0.345  Sum_probs=40.6

Q ss_pred             eeeeEEEEEEcCCCeeEEecCCCCccEEEEecccccc-CCcccccCCCCCCEEEEEEEEcC
Q psy547          200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYN-NPRKLYKTLAEGETVEFDIMQGD  259 (282)
Q Consensus       200 ~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~-~~r~g~~~l~~Gd~V~F~i~~~~  259 (282)
                      .+.|+|+..   +.||+...-+.+.+-|+|++++... ........++.||.|...+..-+
T Consensus         6 ~~~g~V~~i---~~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id   63 (72)
T cd05689           6 RLFGKVTNL---TDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDID   63 (72)
T ss_pred             EEEEEEEEE---EeeEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEee
Confidence            467888886   4489888766678999999999632 10111244789999999887754

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.

>PRK08582 hypothetical protein; Provisional

Probab=81.33  E-value=5.9  Score=32.89  Aligned_cols=58  Identities=19%  Similarity=0.337  Sum_probs=42.0

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD  259 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~  259 (282)
                      ..+.|+|+..   ..||+....+.+.+-++|++++....-..-...+..||.|...|..-.
T Consensus         7 ~iv~G~V~~I---~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id   64 (139)
T PRK08582          7 SKLQGKVTGI---TNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVE   64 (139)
T ss_pred             CEEEEEEEEE---ECCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEEC
Confidence            3467888875   448888777768899999999975421111245899999999887754

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

Probab=81.24  E-value=6.3  Score=28.46  Aligned_cols=59  Identities=15%  Similarity=0.184  Sum_probs=39.8

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCC-CccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSS-NEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK  260 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~-~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k  260 (282)
                      ..+.|+|+...   .||....-++ ..+-|+|++++.......-...++.||+|...+..-+.
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            34678888874   4887776543 36899999999754211111226889999998877543

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.

>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=81.19  E-value=8.1  Score=27.55  Aligned_cols=58  Identities=9%  Similarity=-0.056  Sum_probs=38.3

Q ss_pred             eeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC
Q psy547           32 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD   92 (282)
Q Consensus        32 ~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~   92 (282)
                      ..+.|+|+-...   ||.+..-+.+-+.|+|.++|..+....-...++.||.|++.+..-+
T Consensus         5 ~iv~g~V~~v~~---~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d   62 (73)
T cd05706           5 DILPGRVTKVND---RYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVD   62 (73)
T ss_pred             CEEEEEEEEEeC---CeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEe
Confidence            346888888633   4444444446899999999975421101244799999999987644

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.

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

Probab=81.12  E-value=5.6  Score=27.92  Aligned_cols=56  Identities=23%  Similarity=0.360  Sum_probs=39.5

Q ss_pred             eeeEEEEEEcCCCeeEEecCCCCccEEEEecccccc-CCcccccCCCCCCEEEEEEEEcC
Q psy547          201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYN-NPRKLYKTLAEGETVEFDIMQGD  259 (282)
Q Consensus       201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~-~~r~g~~~l~~Gd~V~F~i~~~~  259 (282)
                      +.|+|+..   +.||+...-+.+.+-++|++++... ..+.-...++.||.|...+..-+
T Consensus         4 ~~g~V~~i---~~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id   60 (69)
T cd05690           4 VSGKIKSI---TDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNID   60 (69)
T ss_pred             EEEEEEEE---EeeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEE
Confidence            56888876   3588887766678999999999731 10111234799999999887644

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.

>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=80.98  E-value=9.4  Score=26.97  Aligned_cols=58  Identities=14%  Similarity=0.147  Sum_probs=39.8

Q ss_pred             eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCC
Q psy547           33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK   93 (282)
Q Consensus        33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~k   93 (282)
                      .+.|+|+-.+   .||.+..-+.+-+-|+|.+.+.......-...++.||.|.+.+..-+.
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            3678888874   356665555568999999999654111012458999999999876543

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.

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

Probab=80.74  E-value=7.1  Score=28.58  Aligned_cols=49  Identities=14%  Similarity=0.222  Sum_probs=39.4

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEc
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG  258 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~  258 (282)
                      ..+.|+|...   ..||+...-+.+.+-|+|.+++.        ..++.||.|...+..-
T Consensus        18 ~~~~g~V~~i---~~~G~fV~l~~~~~Glv~~se~~--------~~~~iGd~v~v~I~~i   66 (77)
T cd04473          18 KLYKGKVNGV---AKYGVFVDLNDHVRGLIHRSNLL--------RDYEVGDEVIVQVTDI   66 (77)
T ss_pred             CEEEEEEEeE---ecceEEEEECCCcEEEEEchhcc--------CcCCCCCEEEEEEEEE
Confidence            4567888876   45888887776789999999986        3589999999887664

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.

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

Probab=80.52  E-value=7.2  Score=26.84  Aligned_cols=57  Identities=21%  Similarity=0.321  Sum_probs=38.1

Q ss_pred             eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC
Q psy547           33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD   92 (282)
Q Consensus        33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~   92 (282)
                      .+.|+|+-...   ||+...-+.+.+.|+|.+.+.......-...++.||.|...+..-+
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            35788887653   6666655556899999999965310000145799999999875543

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.

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=80.48  E-value=25  Score=33.24  Aligned_cols=57  Identities=16%  Similarity=0.187  Sum_probs=41.1

Q ss_pred             eeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC
Q psy547          200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK  260 (282)
Q Consensus       200 ~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k  260 (282)
                      .+.|+|+..   +.||...... +-+-|+|++++.......-...++.||.|.+.+..-+.
T Consensus       199 vv~G~V~~I---~~~G~fV~i~-gv~Gllhisels~~~~~~~~~~~~vGd~VkvkVl~iD~  255 (318)
T PRK07400        199 VVVGTVRGI---KPYGAFIDIG-GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDA  255 (318)
T ss_pred             EEEEEEEEE---ECCeEEEEEC-CEEEEEEHHHcccccccChhhccCCCCEEEEEEEEEeC
Confidence            456899887   4588877654 67899999999854322223458999999999877553

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

Probab=80.45  E-value=5.9  Score=27.17  Aligned_cols=58  Identities=14%  Similarity=0.219  Sum_probs=39.3

Q ss_pred             eeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC
Q psy547           32 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD   92 (282)
Q Consensus        32 ~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~   92 (282)
                      ..+.|+|+-.+.   +|++..-+.+-..|+|.+.+...........++.||.|.+.+..-.
T Consensus         4 ~~v~g~V~~v~~---~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~   61 (72)
T smart00316        4 DVVEGTVTEITP---FGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVD   61 (72)
T ss_pred             CEEEEEEEEEEc---cEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEe
Confidence            346889998865   4444444446789999999976411111245899999999987644

>TIGR01451 B_ant_repeat conserved repeat domain

Probab=80.33  E-value=3.3  Score=28.53  Aligned_cols=40  Identities=25%  Similarity=0.331  Sum_probs=30.6

Q ss_pred             cCCCCCCEEEEEEEEcCCCc-ee--eeeEecceeeeeeeecCC
Q psy547          243 KTLAEGETVEFDIMQGDKGN-QF--CFVLKNIVLYFSFVPQSV  282 (282)
Q Consensus       243 ~~l~~Gd~V~F~i~~~~kG~-~A--~~V~~~~~~~~~~~~~~~  282 (282)
                      ..+.+||.|+|.|.-...|. .|  +.|.-.+.--+.|+|.|+
T Consensus         6 ~~~~~Gd~v~Yti~v~N~g~~~a~~v~v~D~lP~g~~~v~~S~   48 (53)
T TIGR01451         6 TVATIGDTITYTITVTNNGNVPATNVVVTDILPSGTTFVSNSV   48 (53)
T ss_pred             cccCCCCEEEEEEEEEECCCCceEeEEEEEcCCCCCEEEeCcE
Confidence            46899999999999988883 33  345567777888888763

This model represents the conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis, and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydial outer membrane proteins.

>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=80.08  E-value=6.1  Score=27.87  Aligned_cols=57  Identities=23%  Similarity=0.215  Sum_probs=39.6

Q ss_pred             eeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC
Q psy547          201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK  260 (282)
Q Consensus       201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k  260 (282)
                      +.|+|+...   .||.+..-..+-+-|+|++++....-..-...+..||.|++.+..-+.
T Consensus         4 v~g~V~~v~---~~Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~   60 (68)
T cd05707           4 VRGFVKNIA---NNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDP   60 (68)
T ss_pred             EEEEEEEEE---CccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeC
Confidence            568888863   477666555578999999999643211112348999999999876553

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	282
1h95_A	79	Solution Structure Of The Single-Stranded Dna-Bindi		8e-23
1h95_A	79	Solution Structure Of The Single-Stranded Dna-Bindi		7e-19
3i2z_B	71	Structure Of Cold Shock Protein E From Salmonella T		7e-11
3i2z_B	71	Structure Of Cold Shock Protein E From Salmonella T		2e-09
2l15_A	70	Solution Structure Of Cold Shock Protein Cspa Using		2e-09
2l15_A	70	Solution Structure Of Cold Shock Protein Cspa Using		5e-08
1mjc_A	69	Crystal Structure Of Cspa, The Major Cold Shock Pro		4e-09
1mjc_A	69	Crystal Structure Of Cspa, The Major Cold Shock Pro		1e-07
3mef_A	69	Major Cold-Shock Protein From Escherichia Coli Solu		5e-09
3mef_A	69	Major Cold-Shock Protein From Escherichia Coli Solu		1e-07
3trz_A	148	Mouse Lin28a In Complex With Let-7d Microrna Pre-El		6e-09
3trz_A	148	Mouse Lin28a In Complex With Let-7d Microrna Pre-El		9e-05
3ts0_A	146	Mouse Lin28a In Complex With Let-7f-1 Microrna Pre-		6e-09
3ts0_A	146	Mouse Lin28a In Complex With Let-7f-1 Microrna Pre-		9e-05
1hza_A	67	Bacillus Caldolyticus Cold-Shock Protein Mutants To		2e-08
1hza_A	67	Bacillus Caldolyticus Cold-Shock Protein Mutants To		4e-07
1g6p_A	66	Solution Nmr Structure Of The Cold Shock Protein Fr		2e-08
1g6p_A	66	Solution Nmr Structure Of The Cold Shock Protein Fr		3e-08
3ulj_A	90	Crystal Structure Of Apo Lin28b Cold Shock Domain L		2e-08
3ulj_A	90	Crystal Structure Of Apo Lin28b Cold Shock Domain L		2e-04
3cam_A	67	Crystal Structure Of The Cold Shock Domain Protein		3e-08
3cam_A	67	Crystal Structure Of The Cold Shock Domain Protein		2e-07
2es2_A	67	Crystal Structure Analysis Of The Bacillus Subtilis		4e-08
2es2_A	67	Crystal Structure Analysis Of The Bacillus Subtilis		1e-06
2i5m_X	67	Crystal Structure Of Bacillus Subtilis Cold Shock P		4e-08
2i5m_X	67	Crystal Structure Of Bacillus Subtilis Cold Shock P		1e-06
2i5l_X	67	Crystal Structure Of Bacillus Subtilis Cold Shock P		4e-08
2i5l_X	67	Crystal Structure Of Bacillus Subtilis Cold Shock P		2e-06
1hz9_A	66	Bacillus Caldolyticus Cold-Shock Protein Mutants To		4e-08
1hz9_A	66	Bacillus Caldolyticus Cold-Shock Protein Mutants To		2e-07
1hzc_A	66	Bacillus Caldolyticus Cold-Shock Protein Mutants To		5e-08
1hzc_A	66	Bacillus Caldolyticus Cold-Shock Protein Mutants To		2e-07
4a4i_A	90	Crystal Structure Of The Human Lin28b Cold Shock Do		5e-08
1i5f_A	66	Bacillus Caldolyticus Cold-Shock Protein Mutants To		6e-08
1i5f_A	66	Bacillus Caldolyticus Cold-Shock Protein Mutants To		2e-07
1c9o_A	66	Crystal Structure Analysis Of The Bacillus Caldolyt		6e-08
1c9o_A	66	Crystal Structure Analysis Of The Bacillus Caldolyt		3e-07
1hzb_A	66	Bacillus Caldolyticus Cold-Shock Protein Mutants To		6e-08
1hzb_A	66	Bacillus Caldolyticus Cold-Shock Protein Mutants To		2e-07
3a0j_A	73	Crystal Structure Of Cold Shock Protein 1 From Ther		5e-07
3a0j_A	73	Crystal Structure Of Cold Shock Protein 1 From Ther		2e-05
2lss_A	70	Solution Structure Of The R. Rickettsii Cold Shock-		2e-04
2lss_A	70	Solution Structure Of The R. Rickettsii Cold Shock-		7e-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 =  103 bits (258), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 46/75 (61%), Positives = 59/75 (78%)
Query: 29  VLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDI 88
           V+ATKV G VKWF+V++GYGFI    + EDVFVH   IK NNPRK  +++ +GETVEFD+
Sbjct: 4   VIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDV 63
Query: 89  MQGDKGHEAINVTGP 103
           ++G+KG EA NVTGP
Sbjct: 64  VEGEKGAEAANVTGP 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 = 90.9 bits (224), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 40/72 (55%), Positives = 54/72 (75%)
Query: 196 VLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDI 255
           V+ATKV G VKWF+V++GYGFI    + EDVFVH   IK NNPRK  +++ +GETVEFD+
Sbjct: 4   VIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDV 63
Query: 256 MQGDKGNQFCFV 267
           ++G+KG +   V
Sbjct: 64  VEGEKGAEAANV 75

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 34/70 (48%), Positives = 44/70 (62%), Gaps = 4/70 (5%)
Query: 32  TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG 91
           +K+ G VKWF+   G+GFI     ++DVFVH   I+ N     +KTLAEG+ VEF+I  G
Sbjct: 4   SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNG 59
Query: 92  DKGHEAINVT 101
            KG  A NVT
Sbjct: 60  AKGPSAANVT 69

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

Iteration: 1
 Score = 59.3 bits (142), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 30/63 (47%), Positives = 40/63 (63%), Gaps = 4/63 (6%)
Query: 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG 258
           +K+ G VKWF+   G+GFI     ++DVFVH   I+ N     +KTLAEG+ VEF+I  G
Sbjct: 4   SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNG 59
Query: 259 DKG 261
            KG
Sbjct: 60  AKG 62

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

Iteration: 1
 Score = 59.3 bits (142), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 31/72 (43%), Positives = 43/72 (59%), Gaps = 4/72 (5%)
Query: 30  LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIM 89
           ++ K+ G+VKWF+   G+GFI     ++DVFVH   I+ +     YK+L EG+ V F I 
Sbjct: 1   MSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIE 56
Query: 90  QGDKGHEAINVT 101
            G KG  A NVT
Sbjct: 57  SGAKGPAAGNVT 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 = 54.7 bits (130), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 27/65 (41%), Positives = 39/65 (60%), Gaps = 4/65 (6%)
Query: 197 LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIM 256
           ++ K+ G+VKWF+   G+GFI     ++DVFVH   I+ +     YK+L EG+ V F I 
Sbjct: 1   MSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIE 56
Query: 257 QGDKG 261
            G KG
Sbjct: 57  SGAKG 61

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 31/69 (44%), Positives = 41/69 (59%), Gaps = 4/69 (5%)
Query: 33  KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 92
           K+ G+VKWF+   G+GFI     ++DVFVH   I+ +     YK+L EG+ V F I  G 
Sbjct: 3   KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIESGA 58
Query: 93  KGHEAINVT 101
           KG  A NVT
Sbjct: 59  KGPAAGNVT 67

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 27/62 (43%), Positives = 37/62 (59%), Gaps = 4/62 (6%)
Query: 200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 259
           K+ G+VKWF+   G+GFI     ++DVFVH   I+ +     YK+L EG+ V F I  G 
Sbjct: 3   KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIESGA 58
Query: 260 KG 261
           KG
Sbjct: 59  KG 60

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

Iteration: 1
 Score = 58.2 bits (139), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 31/69 (44%), Positives = 41/69 (59%), Gaps = 4/69 (5%)
Query: 33  KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 92
           K+ G+VKWF+   G+GFI     ++DVFVH   I+ +     YK+L EG+ V F I  G 
Sbjct: 3   KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIESGA 58
Query: 93  KGHEAINVT 101
           KG  A NVT
Sbjct: 59  KGPAAGNVT 67

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 27/62 (43%), Positives = 37/62 (59%), Gaps = 4/62 (6%)
Query: 200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 259
           K+ G+VKWF+   G+GFI     ++DVFVH   I+ +     YK+L EG+ V F I  G 
Sbjct: 3   KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIESGA 58
Query: 260 KG 261
           KG
Sbjct: 59  KG 60

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

Iteration: 1
 Score = 57.8 bits (138), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 34/94 (36%), Positives = 50/94 (53%), Gaps = 13/94 (13%)
Query: 26  EPVVLATKVCGVVKWFSVKSGYGFIATPSSNE-------DVFVHSKRIKYNNPRKLYKTL 78
           EP +L     G+ KWF+V+ G+GF++  +          DVFVH  ++        +++L
Sbjct: 4   EPQLLHGA--GICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEG----FRSL 57
Query: 79  AEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQ 112
            EGE VEF   +  KG E+I VTGP G    GS+
Sbjct: 58  KEGEAVEFTFKKSAKGLESIRVTGPGGVFCIGSE 91

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 13/76 (17%)
Query: 193 EPVVLATKVCGVVKWFSVKSGYGFIATPSSNE-------DVFVHSKRIKYNNPRKLYKTL 245
           EP +L     G+ KWF+V+ G+GF++  +          DVFVH  ++        +++L
Sbjct: 4   EPQLLHGA--GICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEG----FRSL 57
Query: 246 AEGETVEFDIMQGDKG 261
            EGE VEF   +  KG
Sbjct: 58  KEGEAVEFTFKKSAKG 73

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

Iteration: 1
 Score = 57.8 bits (138), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 34/94 (36%), Positives = 50/94 (53%), Gaps = 13/94 (13%)
Query: 26  EPVVLATKVCGVVKWFSVKSGYGFIATPSSNE-------DVFVHSKRIKYNNPRKLYKTL 78
           EP +L     G+ KWF+V+ G+GF++  +          DVFVH  ++        +++L
Sbjct: 2   EPQLLHGA--GICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEG----FRSL 55
Query: 79  AEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQ 112
            EGE VEF   +  KG E+I VTGP G    GS+
Sbjct: 56  KEGEAVEFTFKKSAKGLESIRVTGPGGVFCIGSE 89

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 13/76 (17%)
Query: 193 EPVVLATKVCGVVKWFSVKSGYGFIATPSSNE-------DVFVHSKRIKYNNPRKLYKTL 245
           EP +L     G+ KWF+V+ G+GF++  +          DVFVH  ++        +++L
Sbjct: 2   EPQLLHGA--GICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEG----FRSL 55
Query: 246 AEGETVEFDIMQGDKG 261
            EGE VEF   +  KG
Sbjct: 56  KEGEAVEFTFKKSAKG 71

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 31/66 (46%), Positives = 42/66 (63%), Gaps = 5/66 (7%)
Query: 36  GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
           G VKWF+ + GYGFI     + DVFVH   I+       +KTL EG+ V F+I+QG++G 
Sbjct: 4   GKVKWFNNEKGYGFIEVEGGS-DVFVHFTAIQGEG----FKTLEEGQEVSFEIVQGNRGP 58
Query: 96  EAINVT 101
           +A NVT
Sbjct: 59  QAANVT 64

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 30/67 (44%), Positives = 40/67 (59%), Gaps = 5/67 (7%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
           G VKWF+ + GYGFI     + DVFVH   I+       +KTL EG+ V F+I+QG++G 
Sbjct: 4   GKVKWFNNEKGYGFIEVEGGS-DVFVHFTAIQGEG----FKTLEEGQEVSFEIVQGNRGP 58
Query: 263 QFCFVLK 269
           Q   V K
Sbjct: 59  QAANVTK 65

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

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 32/65 (49%), Positives = 39/65 (60%), Gaps = 5/65 (7%)
Query: 36  GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
           G VKWF  K GYGFI T     DVFVH   I+       +KTL EG+ VEF+I +G KG 
Sbjct: 3   GKVKWFDSKKGYGFI-TKDEGGDVFVHWSAIEMEG----FKTLKEGQVVEFEIQEGKKGP 57
Query: 96  EAINV 100
           +A +V
Sbjct: 58  QAAHV 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 = 55.5 bits (132), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 32/65 (49%), Positives = 37/65 (56%), Gaps = 5/65 (7%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
           G VKWF  K GYGFI T     DVFVH   I+       +KTL EG+ VEF+I +G KG 
Sbjct: 3   GKVKWFDSKKGYGFI-TKDEGGDVFVHWSAIEMEG----FKTLKEGQVVEFEIQEGKKGP 57
Query: 263 QFCFV 267
           Q   V
Sbjct: 58  QAAHV 62

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

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 34/94 (36%), Positives = 50/94 (53%), Gaps = 13/94 (13%)
Query: 26  EPVVLATKVCGVVKWFSVKSGYGFIATPSSNE-------DVFVHSKRIKYNNPRKLYKTL 78
           +P VL  +  G  KWF+V+ G+GFI+  S          DVFVH  ++        +++L
Sbjct: 3   DPQVL--RGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEG----FRSL 56
Query: 79  AEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQ 112
            EGE VEF   +  KG E++ VTGP G    G++
Sbjct: 57  KEGEPVEFTFKKSSKGFESLRVTGPGGNPCLGNE 90

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/76 (35%), Positives = 39/76 (51%), Gaps = 13/76 (17%)
Query: 193 EPVVLATKVCGVVKWFSVKSGYGFIATPSSNE-------DVFVHSKRIKYNNPRKLYKTL 245
           +P VL  +  G  KWF+V+ G+GFI+  S          DVFVH  ++        +++L
Sbjct: 3   DPQVL--RGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEG----FRSL 56
Query: 246 AEGETVEFDIMQGDKG 261
            EGE VEF   +  KG
Sbjct: 57  KEGEPVEFTFKKSSKG 72

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

Iteration: 1
 Score = 55.5 bits (132), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 27/65 (41%), Positives = 36/65 (55%), Gaps = 4/65 (6%)
Query: 36  GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
           G+VKWF+   G+GFI      ED+F H   I        +KTL EG+ V FD+  G KG 
Sbjct: 4   GIVKWFNDAKGFGFITPDEGGEDLFAHFSAINXEG----FKTLKEGQRVSFDVTTGPKGK 59
Query: 96  EAINV 100
           +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 = 52.8 bits (125), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 26/61 (42%), Positives = 33/61 (54%), Gaps = 4/61 (6%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
           G+VKWF+   G+GFI      ED+F H   I        +KTL EG+ V FD+  G KG 
Sbjct: 4   GIVKWFNDAKGFGFITPDEGGEDLFAHFSAINXEG----FKTLKEGQRVSFDVTTGPKGK 59
Query: 263 Q 263
           Q
Sbjct: 60  Q 60

>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 = 55.1 bits (131), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 29/66 (43%), Positives = 42/66 (63%), Gaps = 5/66 (7%)
Query: 36  GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
           G VKWF+ + G+GFI     + DVFVH   I+       +KTL EG+ V F+I++G++G 
Sbjct: 4   GKVKWFNSEKGFGFIEVEGQD-DVFVHFSAIQGEG----FKTLEEGQAVSFEIVEGNRGP 58
Query: 96  EAINVT 101
           +A NVT
Sbjct: 59  QAANVT 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 = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/67 (41%), Positives = 40/67 (59%), Gaps = 5/67 (7%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
           G VKWF+ + G+GFI     + DVFVH   I+       +KTL EG+ V F+I++G++G 
Sbjct: 4   GKVKWFNSEKGFGFIEVEGQD-DVFVHFSAIQGEG----FKTLEEGQAVSFEIVEGNRGP 58
Query: 263 QFCFVLK 269
           Q   V K
Sbjct: 59  QAANVTK 65

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 29/66 (43%), Positives = 42/66 (63%), Gaps = 5/66 (7%)
Query: 36  GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
           G VKWF+ + G+GFI     + DVFVH   I+       +KTL EG+ V F+I++G++G 
Sbjct: 4   GKVKWFNSEKGFGFIEVEGQD-DVFVHFSAIQGEG----FKTLEEGQKVRFEIVEGNRGP 58
Query: 96  EAINVT 101
           +A NVT
Sbjct: 59  QAANVT 64

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

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/67 (41%), Positives = 40/67 (59%), Gaps = 5/67 (7%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
           G VKWF+ + G+GFI     + DVFVH   I+       +KTL EG+ V F+I++G++G 
Sbjct: 4   GKVKWFNSEKGFGFIEVEGQD-DVFVHFSAIQGEG----FKTLEEGQKVRFEIVEGNRGP 58
Query: 263 QFCFVLK 269
           Q   V K
Sbjct: 59  QAANVTK 65

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 29/66 (43%), Positives = 42/66 (63%), Gaps = 5/66 (7%)
Query: 36  GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
           G VKWF+ + G+GFI      +DVFVH   I+       +KTL EG+ V F+I++G++G 
Sbjct: 4   GKVKWFNSEKGFGFIEV-EGQDDVFVHFSAIQGEG----FKTLEEGQAVSFEIVEGNRGP 58
Query: 96  EAINVT 101
           +A NVT
Sbjct: 59  QAANVT 64

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 26/61 (42%), Positives = 38/61 (62%), Gaps = 5/61 (8%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
           G VKWF+ + G+GFI      +DVFVH   I+       +KTL EG+ V F+I++G++G 
Sbjct: 4   GKVKWFNSEKGFGFIEV-EGQDDVFVHFSAIQGEG----FKTLEEGQAVSFEIVEGNRGP 58
Query: 263 Q 263
           Q
Sbjct: 59  Q 59

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 30/66 (45%), Positives = 41/66 (62%), Gaps = 5/66 (7%)
Query: 36  GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
           G VKWF+ + GYGFI     + DVFVH   I+       +KTL EG+ V F+I+QG++G 
Sbjct: 4   GKVKWFNNEKGYGFIEVEGGS-DVFVHFTAIQGEG----FKTLEEGQAVSFEIVQGNRGP 58
Query: 96  EAINVT 101
           +A NV 
Sbjct: 59  QAANVV 64

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 30/67 (44%), Positives = 41/67 (61%), Gaps = 5/67 (7%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
           G VKWF+ + GYGFI     + DVFVH   I+       +KTL EG+ V F+I+QG++G 
Sbjct: 4   GKVKWFNNEKGYGFIEVEGGS-DVFVHFTAIQGEG----FKTLEEGQAVSFEIVQGNRGP 58
Query: 263 QFCFVLK 269
           Q   V+K
Sbjct: 59  QAANVVK 65

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 30/66 (45%), Positives = 41/66 (62%), Gaps = 5/66 (7%)
Query: 36  GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
           G VKWF+ + GYGFI     + DVFVH   I+       +KTL EG+ V F+I+QG++G 
Sbjct: 4   GKVKWFNNEKGYGFIEVEGGS-DVFVHFTAIQGEG----FKTLEEGQAVSFEIVQGNRGP 58
Query: 96  EAINVT 101
           +A NV 
Sbjct: 59  QAANVV 64

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 30/67 (44%), Positives = 41/67 (61%), Gaps = 5/67 (7%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
           G VKWF+ + GYGFI     + DVFVH   I+       +KTL EG+ V F+I+QG++G 
Sbjct: 4   GKVKWFNNEKGYGFIEVEGGS-DVFVHFTAIQGEG----FKTLEEGQAVSFEIVQGNRGP 58
Query: 263 QFCFVLK 269
           Q   V+K
Sbjct: 59  QAANVVK 65

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

Iteration: 1
 Score = 54.7 bits (130), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 32/84 (38%), Positives = 45/84 (53%), Gaps = 11/84 (13%)
Query: 36  GVVKWFSVKSGYGFIATPSSNE-------DVFVHSKRIKYNNPRKLYKTLAEGETVEFDI 88
           G  KWF+V+ G+GFI+  +          DVFVH  ++        +++L EGE VEF  
Sbjct: 11  GHCKWFNVRMGFGFISMINREGSPLDIPVDVFVHQSKLFMEG----FRSLKEGEPVEFTF 66
Query: 89  MQGDKGHEAINVTGPDGRHVQGSQ 112
            +  KG E+I VTGP G    GS+
Sbjct: 67  KKSSKGLESIRVTGPGGSPCLGSE 90

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

Iteration: 1
 Score = 54.7 bits (130), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 30/66 (45%), Positives = 41/66 (62%), Gaps = 5/66 (7%)
Query: 36  GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
           G VKWF+ + GYGFI     + DVFVH   I+       +KTL EG+ V F+I+QG++G 
Sbjct: 4   GKVKWFNNEKGYGFIEVEGGS-DVFVHFTAIQGEG----FKTLEEGQEVSFEIVQGNRGP 58
Query: 96  EAINVT 101
           +A NV 
Sbjct: 59  QAANVV 64

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 30/67 (44%), Positives = 41/67 (61%), Gaps = 5/67 (7%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
           G VKWF+ + GYGFI     + DVFVH   I+       +KTL EG+ V F+I+QG++G 
Sbjct: 4   GKVKWFNNEKGYGFIEVEGGS-DVFVHFTAIQGEG----FKTLEEGQEVSFEIVQGNRGP 58
Query: 263 QFCFVLK 269
           Q   V+K
Sbjct: 59  QAANVVK 65

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

Iteration: 1
 Score = 54.7 bits (130), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 30/66 (45%), Positives = 41/66 (62%), Gaps = 5/66 (7%)
Query: 36  GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
           G VKWF+ + GYGFI     + DVFVH   I+       +KTL EG+ V F+I+QG++G 
Sbjct: 4   GKVKWFNNEKGYGFIEVEGGS-DVFVHFTAIQGEG----FKTLEEGQEVSFEIVQGNRGP 58
Query: 96  EAINVT 101
           +A NV 
Sbjct: 59  QAANVV 64

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 30/67 (44%), Positives = 41/67 (61%), Gaps = 5/67 (7%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
           G VKWF+ + GYGFI     + DVFVH   I+       +KTL EG+ V F+I+QG++G 
Sbjct: 4   GKVKWFNNEKGYGFIEVEGGS-DVFVHFTAIQGEG----FKTLEEGQEVSFEIVQGNRGP 58
Query: 263 QFCFVLK 269
           Q   V+K
Sbjct: 59  QAANVVK 65

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

Iteration: 1
 Score = 54.7 bits (130), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 30/66 (45%), Positives = 41/66 (62%), Gaps = 5/66 (7%)
Query: 36  GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
           G VKWF+ + GYGFI     + DVFVH   I+       +KTL EG+ V F+I+QG++G 
Sbjct: 4   GKVKWFNNEKGYGFIEVEGGS-DVFVHFTAIQGEG----FKTLEEGQEVSFEIVQGNRGP 58
Query: 96  EAINVT 101
           +A NV 
Sbjct: 59  QAANVV 64

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 30/67 (44%), Positives = 41/67 (61%), Gaps = 5/67 (7%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
           G VKWF+ + GYGFI     + DVFVH   I+       +KTL EG+ V F+I+QG++G 
Sbjct: 4   GKVKWFNNEKGYGFIEVEGGS-DVFVHFTAIQGEG----FKTLEEGQEVSFEIVQGNRGP 58
Query: 263 QFCFVLK 269
           Q   V+K
Sbjct: 59  QAANVVK 65

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 31/68 (45%), Positives = 40/68 (58%), Gaps = 7/68 (10%)
Query: 36  GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG--DK 93
           G VKWF+ + GYGFI     + DVFVH   I      K ++TL EG+ V FD+  G   K
Sbjct: 4   GRVKWFNAEKGYGFIER-EGDTDVFVHYTAIN----AKGFRTLNEGDIVTFDVEPGRNGK 58
Query: 94  GHEAINVT 101
           G +A+NVT
Sbjct: 59  GPQAVNVT 66

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/59 (44%), Positives = 33/59 (55%), Gaps = 5/59 (8%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG 261
           G VKWF+ + GYGFI     + DVFVH   I      K ++TL EG+ V FD+  G  G
Sbjct: 4   GRVKWFNAEKGYGFIER-EGDTDVFVHYTAIN----AKGFRTLNEGDIVTFDVEPGRNG 57

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 30  LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIM 89
           +AT + G VKW++    +GFI   +  +DVFVH   +          +L EG+ V FD+ 
Sbjct: 1   MATNIVGKVKWYNSTKNFGFIEQDNGGKDVFVHKSAVDAAG----LHSLEEGQDVIFDLE 56
Query: 90  QGDKGHEAINV 100
           +      A+N+
Sbjct: 57  EKQGKAYAVNL 67

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

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 4/59 (6%)
Query: 197 LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDI 255
           +AT + G VKW++    +GFI   +  +DVFVH   +          +L EG+ V FD+
Sbjct: 1   MATNIVGKVKWYNSTKNFGFIEQDNGGKDVFVHKSAVDAAG----LHSLEEGQDVIFDL 55

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	282
1h95_A	79	CSD, Y-box binding protein; translation factor, tr	6e-31
1h95_A	79	CSD, Y-box binding protein; translation factor, tr	3e-26
3ulj_A	90	LIN28B, DNA-binding protein; beta barrel, cold sho	9e-28
3ulj_A	90	LIN28B, DNA-binding protein; beta barrel, cold sho	4e-18
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	3e-25
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	2e-16
2kcm_A	74	Cold shock domain family protein; nucleic acid bin	1e-20
2kcm_A	74	Cold shock domain family protein; nucleic acid bin	2e-17
3i2z_B	71	RNA chaperone, negative regulator of CSPA transcri	1e-19
3i2z_B	71	RNA chaperone, negative regulator of CSPA transcri	7e-18
1g6p_A	66	Cold shock protein TMCSP; greek-KEY, beta barrel,	2e-19
1g6p_A	66	Cold shock protein TMCSP; greek-KEY, beta barrel,	2e-17
1c9o_A	66	CSPB, cold-shock protein; beta barrel, homodimer,	3e-19
1c9o_A	66	CSPB, cold-shock protein; beta barrel, homodimer,	2e-17
3cam_A	67	Cold-shock domain family protein; cold shock prote	5e-19
3cam_A	67	Cold-shock domain family protein; cold shock prote	1e-17
2lss_A	70	Cold shock-like protein; CSD, CSP, oligonucleotide	2e-18
2lss_A	70	Cold shock-like protein; CSD, CSP, oligonucleotide	2e-16
2k5n_A	74	Putative cold-shock protein; GFT protein structure	7e-17
2k5n_A	74	Putative cold-shock protein; GFT protein structure	1e-14
3a0j_A	73	Cold shock protein; OB-fold, cytoplasm, transcript	7e-17
3a0j_A	73	Cold shock protein; OB-fold, cytoplasm, transcript	6e-15
2ytx_A	97	Cold shock domain-containing protein E1; cell-free	8e-14
2ytx_A	97	Cold shock domain-containing protein E1; cell-free	2e-11
3aqq_A	147	Calcium-regulated heat stable protein 1; compact b	3e-13
3aqq_A	147	Calcium-regulated heat stable protein 1; compact b	1e-11
2bh8_A	101	1B11; transcription, molecular evolution, unique a	2e-12
2bh8_A	101	1B11; transcription, molecular evolution, unique a	5e-11
2yty_A	88	Cold shock domain-containing protein E1; cell-free	3e-10
2yty_A	88	Cold shock domain-containing protein E1; cell-free	7e-09
1wfq_A	89	UNR protein; beta-barrel, translational regulation	2e-07
1wfq_A	89	UNR protein; beta-barrel, translational regulation	2e-07
1x65_A	89	UNR protein; cell-free protein synthesis, beta-bar	9e-06
1x65_A	89	UNR protein; cell-free protein synthesis, beta-bar	2e-05

>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 =  109 bits (275), Expect = 6e-31
 Identities = 46/75 (61%), Positives = 59/75 (78%)

Query: 29  VLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDI 88
           V+ATKV G VKWF+V++GYGFI    + EDVFVH   IK NNPRK  +++ +GETVEFD+
Sbjct: 4   VIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDV 63

Query: 89  MQGDKGHEAINVTGP 103
           ++G+KG EA NVTGP
Sbjct: 64  VEGEKGAEAANVTGP 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 = 97.4 bits (243), Expect = 3e-26
 Identities = 39/68 (57%), Positives = 53/68 (77%)

Query: 196 VLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDI 255
           V+ATKV G VKWF+V++GYGFI    + EDVFVH   IK NNPRK  +++ +GETVEFD+
Sbjct: 4   VIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDV 63

Query: 256 MQGDKGNQ 263
           ++G+KG +
Sbjct: 64  VEGEKGAE 71

>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 =  101 bits (254), Expect = 9e-28
 Identities = 31/89 (34%), Positives = 46/89 (51%), Gaps = 11/89 (12%)

Query: 31  ATKVCGVVKWFSVKSGYGFIATPSSN-------EDVFVHSKRIKYNNPRKLYKTLAEGET 83
             +  G  KWF+V+ G+GFI+  S          DVFVH  ++        +++L EGE 
Sbjct: 6   VLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEG----FRSLKEGEP 61

Query: 84  VEFDIMQGDKGHEAINVTGPDGRHVQGSQ 112
           VEF   +  KG E++ VTGP G    G++
Sbjct: 62  VEFTFKKSSKGFESLRVTGPGGNPCLGNE 90

>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 = 76.4 bits (188), Expect = 4e-18
 Identities = 24/73 (32%), Positives = 36/73 (49%), Gaps = 11/73 (15%)

Query: 198 ATKVCGVVKWFSVKSGYGFIATPSSN-------EDVFVHSKRIKYNNPRKLYKTLAEGET 250
             +  G  KWF+V+ G+GFI+  S          DVFVH  ++        +++L EGE 
Sbjct: 6   VLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEG----FRSLKEGEP 61

Query: 251 VEFDIMQGDKGNQ 263
           VEF   +  KG +
Sbjct: 62  VEFTFKKSSKGFE 74

>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 = 97.0 bits (241), Expect = 3e-25
 Identities = 31/94 (32%), Positives = 46/94 (48%), Gaps = 11/94 (11%)

Query: 31  ATKVCGVVKWFSVKSGYGFIATPSSN-------EDVFVHSKRIKYNNPRKLYKTLAEGET 83
                G+ KWF+V+ G+GF++  +          DVFVH  ++        +++L EGE 
Sbjct: 7   LLHGAGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEG----FRSLKEGEA 62

Query: 84  VEFDIMQGDKGHEAINVTGPDGRHVQGSQFAANK 117
           VEF   +  KG E+I VTGP G    GS+     
Sbjct: 63  VEFTFKKSAKGLESIRVTGPGGVFCIGSERRPKG 96

>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 = 73.5 bits (180), Expect = 2e-16
 Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 11/73 (15%)

Query: 198 ATKVCGVVKWFSVKSGYGFIATPSSN-------EDVFVHSKRIKYNNPRKLYKTLAEGET 250
                G+ KWF+V+ G+GF++  +          DVFVH  ++        +++L EGE 
Sbjct: 7   LLHGAGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEG----FRSLKEGEA 62

Query: 251 VEFDIMQGDKGNQ 263
           VEF   +  KG +
Sbjct: 63  VEFTFKKSAKGLE 75

>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 = 82.7 bits (205), Expect = 1e-20
 Identities = 19/72 (26%), Positives = 25/72 (34%), Gaps = 4/72 (5%)

Query: 36  GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
           G V  +     YGFI      E  F+H   +           L +G  V FD     KG 
Sbjct: 3   GKVVSYLAAKKYGFI-QGDDGESYFLHFSELLDKKD---EGKLVKGSMVHFDPTPTPKGL 58

Query: 96  EAINVTGPDGRH 107
            A  ++ P   H
Sbjct: 59  AAKAISLPLEHH 70

>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 = 73.9 bits (182), Expect = 2e-17
 Identities = 16/61 (26%), Positives = 20/61 (32%), Gaps = 4/61 (6%)

Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
           G V  +     YGFI      E  F+H   +           L +G  V FD     KG 
Sbjct: 3   GKVVSYLAAKKYGFI-QGDDGESYFLHFSELLDKKD---EGKLVKGSMVHFDPTPTPKGL 58

Query: 263 Q 263
            
Sbjct: 59  A 59

>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 = 80.0 bits (198), Expect = 1e-19
 Identities = 34/70 (48%), Positives = 44/70 (62%), Gaps = 4/70 (5%)

Query: 32  TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG 91
           +K+ G VKWF+   G+GFI     ++DVFVH   I+ N     +KTLAEG+ VEF+I  G
Sbjct: 4   SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNG 59

Query: 92  DKGHEAINVT 101
            KG  A NVT
Sbjct: 60  AKGPSAANVT 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 = 75.0 bits (185), Expect = 7e-18
 Identities = 30/65 (46%), Positives = 40/65 (61%), Gaps = 4/65 (6%)

Query: 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG 258
           +K+ G VKWF+   G+GFI     ++DVFVH   I+ N     +KTLAEG+ VEF+I  G
Sbjct: 4   SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNG 59

Query: 259 DKGNQ 263
            KG  
Sbjct: 60  AKGPS 64

>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 = 79.2 bits (196), Expect = 2e-19
 Identities = 32/66 (48%), Positives = 39/66 (59%), Gaps = 5/66 (7%)

Query: 36  GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
           G VKWF  K GYGFI T     DVFVH   I+       +KTL EG+ VEF+I +G KG 
Sbjct: 3   GKVKWFDSKKGYGFI-TKDEGGDVFVHWSAIEMEG----FKTLKEGQVVEFEIQEGKKGP 57

Query: 96  EAINVT 101
           +A +V 
Sbjct: 58  QAAHVK 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 = 74.2 bits (183), Expect = 2e-17
 Identities = 31/61 (50%), Positives = 36/61 (59%), Gaps = 5/61 (8%)

Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
           G VKWF  K GYGFI T     DVFVH   I+       +KTL EG+ VEF+I +G KG 
Sbjct: 3   GKVKWFDSKKGYGFI-TKDEGGDVFVHWSAIEMEG----FKTLKEGQVVEFEIQEGKKGP 57

Query: 263 Q 263
           Q
Sbjct: 58  Q 58

>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 = 78.4 bits (194), Expect = 3e-19
 Identities = 30/66 (45%), Positives = 40/66 (60%), Gaps = 5/66 (7%)

Query: 36  GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
           G VKWF+ + GYGFI       DVFVH   I+       +KTL EG+ V F+I+QG++G 
Sbjct: 4   GKVKWFNNEKGYGFI-EVEGGSDVFVHFTAIQGEG----FKTLEEGQEVSFEIVQGNRGP 58

Query: 96  EAINVT 101
           +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 = 73.4 bits (181), Expect = 2e-17
 Identities = 28/61 (45%), Positives = 37/61 (60%), Gaps = 5/61 (8%)

Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
           G VKWF+ + GYGFI       DVFVH   I+       +KTL EG+ V F+I+QG++G 
Sbjct: 4   GKVKWFNNEKGYGFI-EVEGGSDVFVHFTAIQGEG----FKTLEEGQEVSFEIVQGNRGP 58

Query: 263 Q 263
           Q
Sbjct: 59  Q 59

>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 = 78.0 bits (193), Expect = 5e-19
 Identities = 27/66 (40%), Positives = 36/66 (54%), Gaps = 4/66 (6%)

Query: 36  GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
           G+VKWF+   G+GFI      ED+F H   I        +KTL EG+ V FD+  G KG 
Sbjct: 4   GIVKWFNDAKGFGFITPDEGGEDLFAHFSAINMEG----FKTLKEGQRVSFDVTTGPKGK 59

Query: 96  EAINVT 101
           +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 = 74.2 bits (183), Expect = 1e-17
 Identities = 26/61 (42%), Positives = 33/61 (54%), Gaps = 4/61 (6%)

Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
           G+VKWF+   G+GFI      ED+F H   I        +KTL EG+ V FD+  G KG 
Sbjct: 4   GIVKWFNDAKGFGFITPDEGGEDLFAHFSAINMEG----FKTLKEGQRVSFDVTTGPKGK 59

Query: 263 Q 263
           Q
Sbjct: 60  Q 60

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

 Score = 76.5 bits (189), Expect = 2e-18
 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 4/72 (5%)

Query: 30  LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIM 89
           +AT + G VKW++    +GFI   +  +DVFVH   +          +L EG+ V FD+ 
Sbjct: 1   MATNIVGKVKWYNSTKNFGFIEQDNGGKDVFVHKSAVDAAG----LHSLEEGQDVIFDLE 56

Query: 90  QGDKGHEAINVT 101
           +      A+N+ 
Sbjct: 57  EKQGKAYAVNLR 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 = 71.1 bits (175), Expect = 2e-16
 Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 4/67 (5%)

Query: 197 LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIM 256
           +AT + G VKW++    +GFI   +  +DVFVH   +          +L EG+ V FD+ 
Sbjct: 1   MATNIVGKVKWYNSTKNFGFIEQDNGGKDVFVHKSAVDAAG----LHSLEEGQDVIFDLE 56

Query: 257 QGDKGNQ 263
           +      
Sbjct: 57  EKQGKAY 63

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

 Score = 72.4 bits (178), Expect = 7e-17
 Identities = 12/66 (18%), Positives = 25/66 (37%), Gaps = 7/66 (10%)

Query: 36  GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
           G +  +    G+GFI    + ++ + H  ++           + +   V F+    +KG 
Sbjct: 5   GTITTWFKDKGFGFI-KDENGDNRYFHVIKVAN------PDLIKKDAAVTFEPTTNNKGL 57

Query: 96  EAINVT 101
            A  V 
Sbjct: 58  SAYAVK 63

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

 Score = 66.6 bits (163), Expect = 1e-14
 Identities = 10/61 (16%), Positives = 23/61 (37%), Gaps = 7/61 (11%)

Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
           G +  +    G+GFI    + ++ + H  ++           + +   V F+    +KG 
Sbjct: 5   GTITTWFKDKGFGFI-KDENGDNRYFHVIKVAN------PDLIKKDAAVTFEPTTNNKGL 57

Query: 263 Q 263
            
Sbjct: 58  S 58

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

 Score = 72.4 bits (178), Expect = 7e-17
 Identities = 30/68 (44%), Positives = 39/68 (57%), Gaps = 7/68 (10%)

Query: 36  GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG--DK 93
           G VKWF+ + GYGFI     + DVFVH   I        ++TL EG+ V FD+  G   K
Sbjct: 4   GRVKWFNAEKGYGFI-EREGDTDVFVHYTAINAKG----FRTLNEGDIVTFDVEPGRNGK 58

Query: 94  GHEAINVT 101
           G +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 = 67.3 bits (165), Expect = 6e-15
 Identities = 27/63 (42%), Positives = 34/63 (53%), Gaps = 7/63 (11%)

Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG--DK 260
           G VKWF+ + GYGFI     + DVFVH   I        ++TL EG+ V FD+  G   K
Sbjct: 4   GRVKWFNAEKGYGFI-EREGDTDVFVHYTAINAKG----FRTLNEGDIVTFDVEPGRNGK 58

Query: 261 GNQ 263
           G Q
Sbjct: 59  GPQ 61

>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 = 64.9 bits (158), Expect = 8e-14
 Identities = 19/66 (28%), Positives = 28/66 (42%), Gaps = 7/66 (10%)

Query: 36  GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
           GVV     K  +GFI      +++F H    K +      +TL  G+ VEF I   +   
Sbjct: 21  GVVCAM--KEAFGFIERGDVVKEIFFHYSEFKGD-----LETLQPGDDVEFTIKDRNGKE 73

Query: 96  EAINVT 101
            A +V 
Sbjct: 74  VATDVR 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 = 58.7 bits (142), Expect = 2e-11
 Identities = 17/61 (27%), Positives = 25/61 (40%), Gaps = 7/61 (11%)

Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
           GVV     K  +GFI      +++F H    K +      +TL  G+ VEF I   +   
Sbjct: 21  GVVCAM--KEAFGFIERGDVVKEIFFHYSEFKGD-----LETLQPGDDVEFTIKDRNGKE 73

Query: 263 Q 263
            
Sbjct: 74  V 74

>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 = 65.0 bits (158), Expect = 3e-13
 Identities = 18/79 (22%), Positives = 31/79 (39%), Gaps = 13/79 (16%)

Query: 36  GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG---D 92
           GV K F    G+GFI       D+F+H   ++            EG+ V + +      +
Sbjct: 65  GVCKCFCRSKGHGFITPADGGPDIFLHISDVEG------EYVPVEGDEVTYKMCSIPPKN 118

Query: 93  KGHEAINVT----GPDGRH 107
           +  +A+ V      P  +H
Sbjct: 119 EKLQAVEVVITHLAPGTKH 137

>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 = 60.4 bits (146), Expect = 1e-11
 Identities = 15/60 (25%), Positives = 23/60 (38%), Gaps = 6/60 (10%)

Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
           GV K F    G+GFI       D+F+H   ++            EG+ V + +      N
Sbjct: 65  GVCKCFCRSKGHGFITPADGGPDIFLHISDVEG------EYVPVEGDEVTYKMCSIPPKN 118

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

 Score = 61.3 bits (149), Expect = 2e-12
 Identities = 23/76 (30%), Positives = 33/76 (43%), Gaps = 3/76 (3%)

Query: 31  ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ 90
           + K+ G+VKWF+   G+GFI     ++DVFVH                 +G+ VE  I  
Sbjct: 14  SGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAGSSGAAV--RGNPQQGDRVEGKIKS 71

Query: 91  GDKGHEAINV-TGPDG 105
                  I +  G DG
Sbjct: 72  ITDFGIFIGLDGGIDG 87

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

 Score = 57.5 bits (139), Expect = 5e-11
 Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 2/67 (2%)

Query: 198 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ 257
           + K+ G+VKWF+   G+GFI     ++DVFVH                 +G+ VE  I  
Sbjct: 14  SGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAGSSGAAV--RGNPQQGDRVEGKIKS 71

Query: 258 GDKGNQF 264
                 F
Sbjct: 72  ITDFGIF 78

>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 = 54.8 bits (132), Expect = 3e-10
 Identities = 17/71 (23%), Positives = 29/71 (40%), Gaps = 8/71 (11%)

Query: 36  GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG-DKG 94
           G V     K  +GFI T + ++++F H      +       +L  G+ VE+ + +G    
Sbjct: 21  GYVATL--KDNFGFIETANHDKEIFFHYSEFSGD-----VDSLELGDMVEYSLSKGKGNK 73

Query: 95  HEAINVTGPDG 105
             A  V    G
Sbjct: 74  VSAEKVNKTSG 84

>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 = 51.0 bits (122), Expect = 7e-09
 Identities = 14/59 (23%), Positives = 26/59 (44%), Gaps = 7/59 (11%)

Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG 261
           G V     K  +GFI T + ++++F H      +       +L  G+ VE+ + +G   
Sbjct: 21  GYVATL--KDNFGFIETANHDKEIFFHYSEFSGD-----VDSLELGDMVEYSLSKGKGN 72

>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 = 47.2 bits (112), Expect = 2e-07
 Identities = 17/79 (21%), Positives = 30/79 (37%), Gaps = 7/79 (8%)

Query: 185 SASESPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKT 244
           S S          A +  GV++   + + YGFI        +F H  +   N      + 
Sbjct: 3   SGSSGGYPNGTSAALRETGVIE--KLLTSYGFIQCSERQARLFFHCSQYNGN-----LQD 55

Query: 245 LAEGETVEFDIMQGDKGNQ 263
           L  G+ VEF++    +  +
Sbjct: 56  LKVGDDVEFEVSSDRRTGK 74

>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 = 46.9 bits (111), Expect = 2e-07
 Identities = 17/86 (19%), Positives = 33/86 (38%), Gaps = 9/86 (10%)

Query: 18  SANESPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKT 77
           S +          A +  GV++   + + YGFI        +F H  +   N      + 
Sbjct: 3   SGSSGGYPNGTSAALRETGVIE--KLLTSYGFIQCSERQARLFFHCSQYNGN-----LQD 55

Query: 78  LAEGETVEFDIMQGDKGHE--AINVT 101
           L  G+ VEF++    +  +  A+ + 
Sbjct: 56  LKVGDDVEFEVSSDRRTGKPIAVKLV 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 = 42.6 bits (100), Expect = 9e-06
 Identities = 15/61 (24%), Positives = 25/61 (40%), Gaps = 8/61 (13%)

Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
           GV+   +++ G+GFI     +  +F H   I   N       L   + VEF ++      
Sbjct: 11  GVIA--AMRDGFGFIKCVDRDVRMFFHFSEILDGN------QLHIADEVEFTVVPDMLSA 62

Query: 263 Q 263
           Q
Sbjct: 63  Q 63

>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 = 41.4 bits (97), Expect = 2e-05
 Identities = 16/69 (23%), Positives = 28/69 (40%), Gaps = 11/69 (15%)

Query: 36  GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
           GV+   +++ G+GFI     +  +F H   I   N       L   + VEF ++      
Sbjct: 11  GVIA--AMRDGFGFIKCVDRDVRMFFHFSEILDGN------QLHIADEVEFTVVPDMLSA 62

Query: 96  E---AINVT 101
           +   AI + 
Sbjct: 63  QRNHAIRIK 71

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	282
1h95_A	79	CSD, Y-box binding protein; translation factor, tr	99.9
3ulj_A	90	LIN28B, DNA-binding protein; beta barrel, cold sho	99.9
3i2z_B	71	RNA chaperone, negative regulator of CSPA transcri	99.88
3cam_A	67	Cold-shock domain family protein; cold shock prote	99.88
1h95_A	79	CSD, Y-box binding protein; translation factor, tr	99.87
3a0j_A	73	Cold shock protein; OB-fold, cytoplasm, transcript	99.87
1c9o_A	66	CSPB, cold-shock protein; beta barrel, homodimer,	99.87
3cam_A	67	Cold-shock domain family protein; cold shock prote	99.86
2kcm_A	74	Cold shock domain family protein; nucleic acid bin	99.86
2k5n_A	74	Putative cold-shock protein; GFT protein structure	99.85
1g6p_A	66	Cold shock protein TMCSP; greek-KEY, beta barrel,	99.85
3i2z_B	71	RNA chaperone, negative regulator of CSPA transcri	99.85
2lss_A	70	Cold shock-like protein; CSD, CSP, oligonucleotide	99.76
1c9o_A	66	CSPB, cold-shock protein; beta barrel, homodimer,	99.84
3ulj_A	90	LIN28B, DNA-binding protein; beta barrel, cold sho	99.84
3a0j_A	73	Cold shock protein; OB-fold, cytoplasm, transcript	99.83
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	99.83
1wfq_A	89	UNR protein; beta-barrel, translational regulation	99.83
1g6p_A	66	Cold shock protein TMCSP; greek-KEY, beta barrel,	99.82
2lss_A	70	Cold shock-like protein; CSD, CSP, oligonucleotide	99.71
2kcm_A	74	Cold shock domain family protein; nucleic acid bin	99.82
2k5n_A	74	Putative cold-shock protein; GFT protein structure	99.81
3aqq_A	147	Calcium-regulated heat stable protein 1; compact b	99.78
2yty_A	88	Cold shock domain-containing protein E1; cell-free	99.78
2ytx_A	97	Cold shock domain-containing protein E1; cell-free	99.78
1wfq_A	89	UNR protein; beta-barrel, translational regulation	99.77
1x65_A	89	UNR protein; cell-free protein synthesis, beta-bar	99.75
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	99.75
2yty_A	88	Cold shock domain-containing protein E1; cell-free	99.73
3aqq_A	147	Calcium-regulated heat stable protein 1; compact b	99.73
2ytx_A	97	Cold shock domain-containing protein E1; cell-free	99.71
1x65_A	89	UNR protein; cell-free protein synthesis, beta-bar	99.71
2ytv_A	79	Cold shock domain-containing protein E1; cell-free	99.7
2ytv_A	79	Cold shock domain-containing protein E1; cell-free	99.66
2bh8_A	101	1B11; transcription, molecular evolution, unique a	99.56
2bh8_A	101	1B11; transcription, molecular evolution, unique a	99.48
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	97.37
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	97.03
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	96.28
1a62_A	130	RHO; transcription termination, termination, RNA b	95.97
1a62_A	130	RHO; transcription termination, termination, RNA b	95.9
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	91.54
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	91.4
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	90.39
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	88.66
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	86.95
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	85.76
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	85.42
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	84.84
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	83.54
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	81.65
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	81.44

>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=99.90  E-value=4.6e-24  Score=160.31  Aligned_cols=76  Identities=61%  Similarity=1.054  Sum_probs=70.5

Q ss_pred             ceeeeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeCC
Q psy547           28 VVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGP  103 (282)
Q Consensus        28 ~~~~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~~  103 (282)
                      +++.++.+|+|||||..||||||+++++++|||||+|+|...++++|+++|.+|++|+|++..+++|++|++|+.+
T Consensus         3 ~~~~~~~~G~Vkwfn~~kGfGFI~~~~gg~DvFvH~s~i~~~~~~~g~~~l~~G~~V~f~~~~~~kG~~A~~V~~p   78 (79)
T 1h95_A            3 KVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGP   78 (79)
T ss_dssp             SCCEEEEEEEEEEEETTTTEEEEEEGGGTEEEEEEGGGBCSCCCSCCSCSCCSSCEEEEEEEECSSSEEEESBCCC
T ss_pred             cccccccceEEEEEECCCCcEEEecCCCCccEEEEhHHccccccccccccCCCCCEEEEEEEECCCCceeEEEECc
Confidence            4567788999999999999999999998999999999999887777899999999999999999999999999865

>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=99.90  E-value=4.4e-24  Score=163.88  Aligned_cols=77  Identities=39%  Similarity=0.762  Sum_probs=70.2

Q ss_pred             eeeeeeEEEEeeCCCceEEEe-------CCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeCC
Q psy547           31 ATKVCGVVKWFSVKSGYGFIA-------TPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGP  103 (282)
Q Consensus        31 ~~~~~G~Vkwfn~~kGfGFI~-------~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~~  103 (282)
                      .++.+|+|||||..||||||+       ++++++|||||+|+|...    |+++|.+|+.|+|++..+++|++|++|+.+
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            467899999999999999997       456778999999999987    699999999999999999999999999999


Q ss_pred             CCCccccc
Q psy547          104 DGRHVQGS  111 (282)
Q Consensus       104 ~~~~~~~~  111 (282)
                      ++.|+.++
T Consensus        82 ~G~p~~gs   89 (90)
T 3ulj_A           82 GGNPCLGN   89 (90)
T ss_dssp             GGCCCCCC
T ss_pred             CCccccCC
Confidence            98887665

>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=7.3e-23  Score=150.71  Aligned_cols=69  Identities=49%  Similarity=0.806  Sum_probs=63.3

Q ss_pred             eeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeCC
Q psy547           31 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGP  103 (282)
Q Consensus        31 ~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~~  103 (282)
                      +++.+|+|||||..||||||+++++++|||||+|+|...    |++.|.+|++|+|++..+++|++|.+|+.+
T Consensus         3 m~~~~G~Vk~fn~~kGfGFI~~~~g~~dvFvH~s~i~~~----g~~~l~~G~~V~f~~~~~~kG~~A~~V~~~   71 (71)
T 3i2z_B            3 MSKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTN----GFKTLAEGQRVEFEITNGAKGPSAANVTAL   71 (71)
T ss_dssp             --CEEEEEEEEETTTTEEEEEETTCCCCEEEEGGGBCCS----SCCCCCTTCEEEEEEEEETTEEEEEEEEEC
T ss_pred             cccccEEEEEEECCCCcEEEecCCCCccEEEEhHHcccc----cCcCCCCCCEEEEEEEECCCCCEeEEEEeC
Confidence            457899999999999999999999889999999999976    588999999999999999999999999853

>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=99.88  E-value=7.2e-23  Score=149.10  Aligned_cols=65  Identities=42%  Similarity=0.805  Sum_probs=61.7

Q ss_pred             eeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeC
Q psy547           34 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTG  102 (282)
Q Consensus        34 ~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~  102 (282)
                      .+|+|||||.+||||||+++++++|||||+|+|...    |+++|.+|++|+|++..+++|++|.+|+.
T Consensus         2 ~~G~Vk~fn~~kGfGFI~~~~gg~dvFvH~s~i~~~----g~~~l~~G~~V~f~~~~~~kG~~A~~V~~   66 (67)
T 3cam_A            2 ATGIVKWFNDAKGFGFITPDEGGEDLFAHFSAINME----GFKTLKEGQRVSFDVTTGPKGKQAANIQA   66 (67)
T ss_dssp             EEEEEEEEETTTTEEEEEETTSCCCEEEEGGGBCGG----GGSSCCTTCEEEEEEEEETTEEEEEEEEE
T ss_pred             CCEEEEEEECCCCeEEEecCCCCccEEEEHHHcccc----CCCCCCCCCEEEEEEEECCCCccceEEEe
Confidence            589999999999999999999899999999999876    68999999999999999999999999974

>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=99.87  E-value=1.8e-22  Score=151.60  Aligned_cols=73  Identities=55%  Similarity=0.970  Sum_probs=67.3

Q ss_pred             eeeeeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeE
Q psy547          196 VLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVL  268 (282)
Q Consensus       196 ~~~~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~  268 (282)
                      ++..+.+|+|||||..||||||+++++++|||||+|+|...+++.|++.|.+||+|+|++.++++|++|++|+
T Consensus         4 ~~~~~~~G~Vkwfn~~kGfGFI~~~~gg~DvFvH~s~i~~~~~~~g~~~l~~G~~V~f~~~~~~kG~~A~~V~   76 (79)
T 1h95_A            4 VIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVT   76 (79)
T ss_dssp             CCEEEEEEEEEEEETTTTEEEEEEGGGTEEEEEEGGGBCSCCCSCCSCSCCSSCEEEEEEEECSSSEEEESBC
T ss_pred             ccccccceEEEEEECCCCcEEEecCCCCccEEEEhHHccccccccccccCCCCCEEEEEEEECCCCceeEEEE
Confidence            3467789999999999999999999989999999999997766678999999999999999999999999886

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

Probab=99.87  E-value=3.9e-22  Score=147.60  Aligned_cols=67  Identities=45%  Similarity=0.765  Sum_probs=62.4

Q ss_pred             eeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC--CCceEEEEeCCCC
Q psy547           34 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD--KGHEAINVTGPDG  105 (282)
Q Consensus        34 ~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~--kG~~A~~V~~~~~  105 (282)
                      .+|+|||||..||||||+++++ +|||||+|+|...    |+++|.+|++|+|++..++  +|++|.+|+.++.
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            5899999999999999999987 9999999999986    6899999999999999999  9999999997653

>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=2.4e-22  Score=145.95  Aligned_cols=64  Identities=47%  Similarity=0.809  Sum_probs=60.7

Q ss_pred             eeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeC
Q psy547           34 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTG  102 (282)
Q Consensus        34 ~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~  102 (282)
                      .+|+|||||..||||||+++++ +|||||+|+|...    |+++|.+|++|+|++..+++|++|.+|+.
T Consensus         2 ~~G~Vk~fn~~kGfGFI~~~~g-~dvFvH~s~i~~~----g~~~l~~G~~V~f~~~~~~kG~~A~~V~~   65 (66)
T 1c9o_A            2 QRGKVKWFNNEKGYGFIEVEGG-SDVFVHFTAIQGE----GFKTLEEGQEVSFEIVQGNRGPQAANVVK   65 (66)
T ss_dssp             EEEEEEEEETTTTEEEEEETTE-EEEEEEGGGBCSS----SCCCCCTTCEEEEEEEEETTEEEEEEEEE
T ss_pred             CceEEEEEECCCCeEEEecCCC-ccEEEEHHHcccc----CCCCCCCCCEEEEEEEECCCCcEeEEEEe
Confidence            5899999999999999999997 9999999999986    68999999999999999999999999975

>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=99.86  E-value=8.7e-22  Score=143.35  Aligned_cols=65  Identities=40%  Similarity=0.747  Sum_probs=60.7

Q ss_pred             eeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547          201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK  269 (282)
Q Consensus       201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~  269 (282)
                      .+|+|||||.+||||||+++++++|||||+|+|..    .|++.|.+||+|+|++.++++|++|.+|+.
T Consensus         2 ~~G~Vk~fn~~kGfGFI~~~~gg~dvFvH~s~i~~----~g~~~l~~G~~V~f~~~~~~kG~~A~~V~~   66 (67)
T 3cam_A            2 ATGIVKWFNDAKGFGFITPDEGGEDLFAHFSAINM----EGFKTLKEGQRVSFDVTTGPKGKQAANIQA   66 (67)
T ss_dssp             EEEEEEEEETTTTEEEEEETTSCCCEEEEGGGBCG----GGGSSCCTTCEEEEEEEEETTEEEEEEEEE
T ss_pred             CCEEEEEEECCCCeEEEecCCCCccEEEEHHHccc----cCCCCCCCCCEEEEEEEECCCCccceEEEe
Confidence            47999999999999999999999999999999984    367899999999999999999999999974

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

Probab=99.86  E-value=4.8e-22  Score=147.35  Aligned_cols=67  Identities=27%  Similarity=0.340  Sum_probs=62.6

Q ss_pred             eeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccc-cCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeCCCC
Q psy547           34 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIK-YNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGPDG  105 (282)
Q Consensus        34 ~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~-~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~~~~  105 (282)
                      ++|+|||||..||||||+++++ +|||||+|+|. ..    |+++|.+|++|+|++..+++|++|++|+.++.
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 99999999999 65    68999999999999999999999999997764

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

Probab=99.85  E-value=1.4e-21  Score=144.86  Aligned_cols=67  Identities=18%  Similarity=0.313  Sum_probs=61.8

Q ss_pred             eeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeCCCC
Q psy547           32 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGPDG  105 (282)
Q Consensus        32 ~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~~~~  105 (282)
                      |+.+|+|||||..||||||+++++++| |||+|+|...    |  .|.+|++|+|++..+++|++|++|+.+..
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            467999999999999999999998777 9999999986    4  89999999999999999999999997764

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

Probab=99.85  E-value=6.3e-22  Score=143.70  Aligned_cols=65  Identities=48%  Similarity=0.796  Sum_probs=60.6

Q ss_pred             eeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeCC
Q psy547           34 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGP  103 (282)
Q Consensus        34 ~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~~  103 (282)
                      ++|+|||||..||||||+++++ +|||||+|+|...    |++.|.+|++|+|++..+++|++|.+|+.+
T Consensus         1 m~G~Vk~fn~~kGfGFI~~~~g-~dvFvH~s~i~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~~   65 (66)
T 1g6p_A            1 MRGKVKWFDSKKGYGFITKDEG-GDVFVHWSAIEME----GFKTLKEGQVVEFEIQEGKKGPQAAHVKVV   65 (66)
T ss_dssp             CCEEEEEEETTTTEEEEEETTS-CBCBBCSSSSCCS----SCCCCCSSSEEEEEEECSSSCCEEEEEEEE
T ss_pred             CcEEEEEEECCCCEEEEecCCC-ceEEEEhHHcccc----CCCCCCCCCEEEEEEEECCCCCEEEEEEEC
Confidence            4799999999999999999974 9999999999986    589999999999999999999999999854

>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=99.85  E-value=2.4e-21  Score=142.63  Aligned_cols=67  Identities=46%  Similarity=0.771  Sum_probs=61.8

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK  269 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~  269 (282)
                      .+.+|+|||||..||||||+++++++|||||+++|..+    |++.|.+||+|+|++.++++|++|++|+.
T Consensus         4 ~~~~G~Vk~fn~~kGfGFI~~~~g~~dvFvH~s~i~~~----g~~~l~~G~~V~f~~~~~~kG~~A~~V~~   70 (71)
T 3i2z_B            4 SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTN----GFKTLAEGQRVEFEITNGAKGPSAANVTA   70 (71)
T ss_dssp             -CEEEEEEEEETTTTEEEEEETTCCCCEEEEGGGBCCS----SCCCCCTTCEEEEEEEEETTEEEEEEEEE
T ss_pred             ccccEEEEEEECCCCcEEEecCCCCccEEEEhHHcccc----cCcCCCCCCEEEEEEEECCCCCEeEEEEe
Confidence            46789999999999999999999889999999999954    57899999999999999999999999975

>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=4e-23  Score=151.71  Aligned_cols=69  Identities=32%  Similarity=0.590  Sum_probs=64.1

Q ss_pred             eeeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeC
Q psy547           30 LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTG  102 (282)
Q Consensus        30 ~~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~  102 (282)
                      |+++++|+|||||.+||||||+++++++|||||+|+|...    |+++|.+|++|+|++..+++|++|.+|+.
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            4567899999999999999999999889999999999986    58999999999999999999999999873

>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=99.84  E-value=4.5e-21  Score=139.18  Aligned_cols=64  Identities=47%  Similarity=0.793  Sum_probs=59.3

Q ss_pred             eeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547          201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK  269 (282)
Q Consensus       201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~  269 (282)
                      .+|+|||||.+||||||+++++ +|||||+|+|...    |++.|.+||+|+|++.++++|++|.+|+.
T Consensus         2 ~~G~Vk~fn~~kGfGFI~~~~g-~dvFvH~s~i~~~----g~~~l~~G~~V~f~~~~~~kG~~A~~V~~   65 (66)
T 1c9o_A            2 QRGKVKWFNNEKGYGFIEVEGG-SDVFVHFTAIQGE----GFKTLEEGQEVSFEIVQGNRGPQAANVVK   65 (66)
T ss_dssp             EEEEEEEEETTTTEEEEEETTE-EEEEEEGGGBCSS----SCCCCCTTCEEEEEEEEETTEEEEEEEEE
T ss_pred             CceEEEEEECCCCeEEEecCCC-ccEEEEHHHcccc----CCCCCCCCCEEEEEEEECCCCcEeEEEEe
Confidence            4799999999999999999987 9999999999953    57899999999999999999999999874

>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=99.84  E-value=2.8e-21  Score=148.20  Aligned_cols=66  Identities=36%  Similarity=0.656  Sum_probs=60.6

Q ss_pred             eeeeeEEEEEEcCCCeeEEe-------cCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeE
Q psy547          199 TKVCGVVKWFSVKSGYGFIA-------TPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVL  268 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~-------~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~  268 (282)
                      .|.+|+|||||..||||||+       ++++++|||||+|+|..    .|++.|.+||+|+|++.+++||++|++|+
T Consensus         7 ~r~tG~VKWFn~~KGfGFI~~~~~~~~p~dgg~DvFVH~s~i~~----~g~~~L~eG~~V~f~v~~g~kG~~A~~Vt   79 (90)
T 3ulj_A            7 LRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYM----EGFRSLKEGEPVEFTFKKSSKGFESLRVT   79 (90)
T ss_dssp             EEEEEEEEEEETTTTEEEEEEEEETTEEEEEEEEEEEEGGGBCC----SSSCCCCTTCEEEEEEEEETTEEEEEEEE
T ss_pred             cccceEEEEeeCCCCeEEeEecCcCcCCCCCCccEEEEeehhcc----cCCCccCCCCEEEEEEEECCCCcEEEEEE
Confidence            56789999999999999998       45678999999999984    46899999999999999999999999997

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

Probab=99.83  E-value=1.6e-20  Score=138.83  Aligned_cols=64  Identities=45%  Similarity=0.735  Sum_probs=59.2

Q ss_pred             eeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC--CCceeeeeEe
Q psy547          201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD--KGNQFCFVLK  269 (282)
Q Consensus       201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~--kG~~A~~V~~  269 (282)
                      .+|+|||||..||||||+++++ +|||||+|+|..    .|++.|.+||+|+|++..++  +|++|.+|+.
T Consensus         2 ~~G~Vk~fn~~kGfGFI~~~~g-~dvFvH~s~i~~----~g~~~l~~G~~V~f~~~~~~~~kG~~A~~V~~   67 (73)
T 3a0j_A            2 QKGRVKWFNAEKGYGFIEREGD-TDVFVHYTAINA----KGFRTLNEGDIVTFDVEPGRNGKGPQAVNVTV   67 (73)
T ss_dssp             EEEEEEEEETTTTEEEEECTTS-CCEEEEGGGBCS----SSCSSCCTTCEEEEEEECCSCCSSSEEEEEEE
T ss_pred             CCEEEEEEECCCCEEEEecCCC-CcEEEEhhhccc----cCCCCCCCCCEEEEEEEECCCCCCCEEEEEEe
Confidence            4799999999999999999986 999999999994    35789999999999999999  9999999974

>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=99.83  E-value=7.9e-21  Score=158.66  Aligned_cols=80  Identities=39%  Similarity=0.741  Sum_probs=72.4

Q ss_pred             eeeeeeEEEEeeCCCceEEEeCC-------CCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeCC
Q psy547           31 ATKVCGVVKWFSVKSGYGFIATP-------SSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGP  103 (282)
Q Consensus        31 ~~~~~G~Vkwfn~~kGfGFI~~~-------d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~~  103 (282)
                      .++.+|+|||||..||||||+++       ++++|||||+|+|...    |+++|.+|++|+|+++.+++|++|++|+.+
T Consensus         7 l~~~~G~Vkwfn~~kGfGFI~~~~~~g~p~~~g~DvFvH~s~i~~~----g~~~l~eG~~V~f~~~~g~kG~~A~~V~~p   82 (148)
T 3ts2_A            7 LLHGAGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHME----GFRSLKEGEAVEFTFKKSAKGLESIRVTGP   82 (148)
T ss_dssp             CEEEEEEEEEEETTTTEEEEEEEEETTEEEEEEEEEEEEGGGBCSS----SSCCCCTTCEEEEEEEEETTEEEEEEEESG
T ss_pred             cccceeEEEEEECCCCeeEEeeCccccccCCCCccEEEEhHHhccc----CCccCCCCCEEEEEEEEccccchhhccccc
Confidence            46689999999999999999987       4678999999999886    699999999999999999999999999999


Q ss_pred             CCCcccccccc
Q psy547          104 DGRHVQGSQFA  114 (282)
Q Consensus       104 ~~~~~~~~~~~  114 (282)
                      +..++.++...
T Consensus        83 gg~pv~GS~rr   93 (148)
T 3ts2_A           83 GGVFCIGSERR   93 (148)
T ss_dssp             GGCCCCCCTTS
T ss_pred             CCccccccccc
Confidence            98888777633

>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=1.5e-20  Score=144.10  Aligned_cols=69  Identities=26%  Similarity=0.497  Sum_probs=62.9

Q ss_pred             eeeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCC-C-ceEEEEeCCCC
Q psy547           30 LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK-G-HEAINVTGPDG  105 (282)
Q Consensus        30 ~~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~k-G-~~A~~V~~~~~  105 (282)
                      +.++.+|+|||||  ||||||+++++++|||||+++|...     ++.|.+|++|+|++..+++ | ++|.+|+.++.
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            3567899999997  9999999999889999999999875     6899999999999999998 7 89999998754

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

Probab=99.82  E-value=1.3e-20  Score=136.78  Aligned_cols=64  Identities=48%  Similarity=0.797  Sum_probs=58.9

Q ss_pred             eeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547          201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK  269 (282)
Q Consensus       201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~  269 (282)
                      ++|+|||||..||||||++++ ++|||||+|+|...    |++.|.+||+|+|++..+++|++|.+|+.
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            469999999999999999997 59999999999953    57899999999999999999999999874

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

Probab=99.71  E-value=6.9e-22  Score=145.09  Aligned_cols=68  Identities=29%  Similarity=0.522  Sum_probs=62.3

Q ss_pred             eeeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547          198 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK  269 (282)
Q Consensus       198 ~~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~  269 (282)
                      ..+++|+|||||.+||||||+++++++|||||+|+|...    |++.|.+||+|+|++..+++|++|.+|+.
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            356789999999999999999999899999999999943    57889999999999999999999999874

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

Probab=99.82  E-value=1.6e-20  Score=139.11  Aligned_cols=64  Identities=25%  Similarity=0.289  Sum_probs=59.3

Q ss_pred             eeeEEEEEEcCCCeeEEecCCCCccEEEEecccc-ccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547          201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIK-YNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK  269 (282)
Q Consensus       201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~-~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~  269 (282)
                      ++|+|||||..||||||+++++ +|||||+|+|. ..    |++.|.+||+|+|++.+++||++|++|+.
T Consensus         1 ~~G~Vkwfn~~KGfGFI~~~dG-~DvFvH~s~i~~~~----g~~~l~~G~~V~F~~~~g~kG~~A~~V~~   65 (74)
T 2kcm_A            1 MKGKVVSYLAAKKYGFIQGDDG-ESYFLHFSELLDKK----DEGKLVKGSMVHFDPTPTPKGLAAKAISL   65 (74)
T ss_dssp             CEEEEEEEETTTTEEEEEETTS-CEECCCGGGSSCSG----GGTTCCTTSEEEEEEECTTTSCEEEEEEC
T ss_pred             CCEEEEEEECCCCEEEEecCCC-ceEEEEhhhcccCC----CCCCCCCCCEEEEEEEECCCCceeEEEEE
Confidence            3699999999999999999997 99999999998 54    57899999999999999999999999984

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

Probab=99.81  E-value=6.4e-20  Score=135.91  Aligned_cols=63  Identities=17%  Similarity=0.329  Sum_probs=57.8

Q ss_pred             eeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547          200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK  269 (282)
Q Consensus       200 ~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~  269 (282)
                      +.+|+|||||..||||||+++++++| |||+|+|...    +  .|.+||+|+|++..++||++|++|+.
T Consensus         2 ~~~G~Vkwfn~~KGfGFI~~~dg~~d-FvH~s~i~~~----g--~l~~G~~V~F~~~~g~kG~~A~~V~~   64 (74)
T 2k5n_A            2 AMNGTITTWFKDKGFGFIKDENGDNR-YFHVIKVANP----D--LIKKDAAVTFEPTTNNKGLSAYAVKV   64 (74)
T ss_dssp             CEEEEEEEEETTTTEEEEEESSSCEE-EEEGGGBSSG----G--GCCTTCEEEEEEEECSSSEEEEEEEE
T ss_pred             CcceEEEEEECCCCeEEEecCCCCce-EEEHhHcccC----C--CCCCCCEEEEEEEeCCCCceeEEEEe
Confidence            46899999999999999999998888 9999999943    3  79999999999999999999999984

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

Probab=99.78  E-value=2.7e-19  Score=148.63  Aligned_cols=69  Identities=23%  Similarity=0.386  Sum_probs=61.7

Q ss_pred             eeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEe---CCCCceEEEEeCCCC
Q psy547           31 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ---GDKGHEAINVTGPDG  105 (282)
Q Consensus        31 ~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~---~~kG~~A~~V~~~~~  105 (282)
                      .++.+|+|||||..||||||+++++++|||||+++|...      ..|.+|++|+|++..   +.+|++|++|+.++.
T Consensus        60 g~m~~GtVKwFn~~KGfGFI~~ddGg~DVFVH~Sai~~~------~~L~eGq~V~Fev~~~~~~~~g~qA~nV~~~~~  131 (147)
T 3aqq_A           60 GPVYKGVCKCFCRSKGHGFITPADGGPDIFLHISDVEGE------YVPVEGDEVTYKMCSIPPKNEKLQAVEVVITHL  131 (147)
T ss_dssp             SCCEEEEEEEEETTTTEEEEEESSSCSCEEEEGGGEESS------BCCCTTCEEEEEEEEC--CCSCEEEEEEEEEEC
T ss_pred             CCccceEEEEEeCCCCeEEeccCCCCccEEEEeeeecCC------CcCCCCCEEEEEEEeccCCCCCceEEEEEeCCC
Confidence            357899999999999999999999989999999999853      489999999999987   457799999998764

>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=99.78  E-value=9.2e-20  Score=139.44  Aligned_cols=68  Identities=24%  Similarity=0.491  Sum_probs=62.2

Q ss_pred             eeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCC-ceEEEEeCCCC
Q psy547           31 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG-HEAINVTGPDG  105 (282)
Q Consensus        31 ~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG-~~A~~V~~~~~  105 (282)
                      .++.+|+|||||  ||||||+++++++|||||+|+|...     ++.|.+|++|+|++..+.+| ++|.+|+.++.
T Consensus        16 ~~~~~G~Vk~f~--kGfGFI~~ddgg~DvFvH~S~i~~~-----~~~L~~G~~V~F~~~~g~~Gk~~A~~V~~~~~   84 (88)
T 2yty_A           16 SKRLLGYVATLK--DNFGFIETANHDKEIFFHYSEFSGD-----VDSLELGDMVEYSLSKGKGNKVSAEKVNKTSG   84 (88)
T ss_dssp             CCCEEEEEEEEC--SSEEEEECSSSSCEEEEETTTCCSC-----TTTCCTTCEEEECCCCCSCSCCBCCSCEECCC
T ss_pred             CCceeEEEEEEE--CCccEEecCCCCceEEEEEhhhccc-----cCcCCCCCEEEEEEEECCCCCeEeEEEEECCC
Confidence            466899999997  9999999999899999999999975     68999999999999999999 89999997653

>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=99.78  E-value=1e-18  Score=135.89  Aligned_cols=70  Identities=27%  Similarity=0.388  Sum_probs=63.5

Q ss_pred             eeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeCCCCCc
Q psy547           31 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGPDGRH  107 (282)
Q Consensus        31 ~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~~~~~~  107 (282)
                      .++.+|+||||  .||||||+++++++|||||+|+|...     ++.|.+|++|+|++..+.+|++|.+|+.+....
T Consensus        16 ~~~~~G~Vkwf--~KGfGFI~~ddg~~DvFvH~s~i~~~-----~~~L~~G~~V~F~v~~~~~g~~A~~V~~~~~~~   85 (97)
T 2ytx_A           16 QARCQGVVCAM--KEAFGFIERGDVVKEIFFHYSEFKGD-----LETLQPGDDVEFTIKDRNGKEVATDVRLLPQGT   85 (97)
T ss_dssp             CCCEEEEECCC--CSSEEEEECSSSCCCEEEETTTCCSC-----TTSCCSCCEEEEEECCCSSSCBEEEEEECCCSS
T ss_pred             CcceeEEEEEE--eCCceEEecCCCCceEEEEehHhccc-----cCCCCCCCEEEEEEEcCCCCcEEEEEEECCCCc
Confidence            46689999999  99999999999889999999999975     689999999999999888889999999887643

>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=99.77  E-value=6.4e-19  Score=134.99  Aligned_cols=64  Identities=25%  Similarity=0.481  Sum_probs=58.4

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC-C-ceeeeeEe
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK-G-NQFCFVLK  269 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k-G-~~A~~V~~  269 (282)
                      .+.+|+|||||  ||||||+++++++|||||+++|...     ++.|.+||+|+|++.++++ | ++|++|+.
T Consensus        17 ~~~~G~Vkwf~--KGfGFI~~ddgg~DVFvH~s~i~~~-----~~~L~~G~~V~F~v~~~~k~Gk~~A~~V~~   82 (89)
T 1wfq_A           17 LRETGVIEKLL--TSYGFIQCSERQARLFFHCSQYNGN-----LQDLKVGDDVEFEVSSDRRTGKPIAVKLVK   82 (89)
T ss_dssp             CEEEEEEEEEC--SSEEEEEETTTTEEEEEETTTCSSC-----TTTCCTTCCEEEEEEECSSSCCEEEEEEEE
T ss_pred             cccceEEEEEe--CCeeEEecCCCCccEEEEhHHhhCc-----cCCCCCCCEEEEEEEECCCCCCcEEEEEEE
Confidence            56789999996  9999999999889999999999943     5789999999999999998 7 89999985

>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=2.9e-19  Score=136.80  Aligned_cols=68  Identities=22%  Similarity=0.330  Sum_probs=60.5

Q ss_pred             eeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCC---CceEEEEeCCCCC
Q psy547           31 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK---GHEAINVTGPDGR  106 (282)
Q Consensus        31 ~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~k---G~~A~~V~~~~~~  106 (282)
                      .++.+|+|||||  ||||||+++++++|||||+|+|..     + +.|.+|++|+|++..+++   +++|.+|+.+...
T Consensus         6 ~~r~~G~Vk~f~--KGfGFI~~~~gg~DvFvH~s~i~~-----~-~~L~~G~~V~F~v~~g~kg~G~~~A~~V~~~~~~   76 (89)
T 1x65_A            6 SGREMGVIAAMR--DGFGFIKCVDRDVRMFFHFSEILD-----G-NQLHIADEVEFTVVPDMLSAQRNHAIRIKKLPKG   76 (89)
T ss_dssp             CCCEEEEEEECC--TTBCEEEESSSSSCCCCBTTGGGG-----S-CCCCTTCCEEECCBCCSSSCCCCBCCSCEECCBT
T ss_pred             CcceeEEEEEEe--CCcceeecCCCCccEEEEhhhccC-----C-CCCCCCCEEEEEEEeCCCcCCCceeeEEEECCCC
Confidence            357899999996  999999999989999999999986     2 689999999999999987   4899999987653

>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=99.75  E-value=1.6e-18  Score=144.68  Aligned_cols=67  Identities=34%  Similarity=0.674  Sum_probs=61.3

Q ss_pred             eeeeeEEEEEEcCCCeeEEecC-------CCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547          199 TKVCGVVKWFSVKSGYGFIATP-------SSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK  269 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~-------d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~  269 (282)
                      .+.+|+|||||..||||||+++       ++++|||||+++|..    .|++.|.+|++|+|++..+++|++|++|+.
T Consensus         8 ~~~~G~Vkwfn~~kGfGFI~~~~~~g~p~~~g~DvFvH~s~i~~----~g~~~l~eG~~V~f~~~~g~kG~~A~~V~~   81 (148)
T 3ts2_A            8 LHGAGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHM----EGFRSLKEGEAVEFTFKKSAKGLESIRVTG   81 (148)
T ss_dssp             EEEEEEEEEEETTTTEEEEEEEEETTEEEEEEEEEEEEGGGBCS----SSSCCCCTTCEEEEEEEEETTEEEEEEEES
T ss_pred             ccceeEEEEEECCCCeeEEeeCccccccCCCCccEEEEhHHhcc----cCCccCCCCCEEEEEEEEccccchhhcccc
Confidence            4578999999999999999987       468999999999984    468999999999999999999999999985

>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=99.73  E-value=2.2e-18  Score=131.75  Aligned_cols=64  Identities=23%  Similarity=0.434  Sum_probs=58.5

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCC-ceeeeeEe
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG-NQFCFVLK  269 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG-~~A~~V~~  269 (282)
                      .+.+|+|||||  ||||||+++++++|||||+++|...     ++.|.+||+|+|++.++++| ++|.+|+.
T Consensus        17 ~~~~G~Vk~f~--kGfGFI~~ddgg~DvFvH~S~i~~~-----~~~L~~G~~V~F~~~~g~~Gk~~A~~V~~   81 (88)
T 2yty_A           17 KRLLGYVATLK--DNFGFIETANHDKEIFFHYSEFSGD-----VDSLELGDMVEYSLSKGKGNKVSAEKVNK   81 (88)
T ss_dssp             CCEEEEEEEEC--SSEEEEECSSSSCEEEEETTTCCSC-----TTTCCTTCEEEECCCCCSCSCCBCCSCEE
T ss_pred             CceeEEEEEEE--CCccEEecCCCCceEEEEEhhhccc-----cCcCCCCCEEEEEEEECCCCCeEeEEEEE
Confidence            45689999997  8999999999999999999999943     57899999999999999999 79999985

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

Probab=99.73  E-value=7.3e-18  Score=140.02  Aligned_cols=65  Identities=25%  Similarity=0.384  Sum_probs=58.3

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEE---cCCCceeeeeEe
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ---GDKGNQFCFVLK  269 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~---~~kG~~A~~V~~  269 (282)
                      .+.+|+|||||.+||||||+++++++|||||+++|...      ..|.+||+|+|++..   +.+|++|.+|+.
T Consensus        61 ~m~~GtVKwFn~~KGfGFI~~ddGg~DVFVH~Sai~~~------~~L~eGq~V~Fev~~~~~~~~g~qA~nV~~  128 (147)
T 3aqq_A           61 PVYKGVCKCFCRSKGHGFITPADGGPDIFLHISDVEGE------YVPVEGDEVTYKMCSIPPKNEKLQAVEVVI  128 (147)
T ss_dssp             CCEEEEEEEEETTTTEEEEEESSSCSCEEEEGGGEESS------BCCCTTCEEEEEEEEC--CCSCEEEEEEEE
T ss_pred             CccceEEEEEeCCCCeEEeccCCCCccEEEEeeeecCC------CcCCCCCEEEEEEEeccCCCCCceEEEEEe
Confidence            46789999999999999999999899999999999832      489999999999987   457799999984

>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=99.71  E-value=1.2e-17  Score=129.97  Aligned_cols=65  Identities=28%  Similarity=0.379  Sum_probs=58.8

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEec
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLKN  270 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~~  270 (282)
                      .+.+|+||||  .||||||+++++++|||||+++|...     ++.|.+||+|+|++..+++|++|.+|+..
T Consensus        17 ~~~~G~Vkwf--~KGfGFI~~ddg~~DvFvH~s~i~~~-----~~~L~~G~~V~F~v~~~~~g~~A~~V~~~   81 (97)
T 2ytx_A           17 ARCQGVVCAM--KEAFGFIERGDVVKEIFFHYSEFKGD-----LETLQPGDDVEFTIKDRNGKEVATDVRLL   81 (97)
T ss_dssp             CCEEEEECCC--CSSEEEEECSSSCCCEEEETTTCCSC-----TTSCCSCCEEEEEECCCSSSCBEEEEEEC
T ss_pred             cceeEEEEEE--eCCceEEecCCCCceEEEEehHhccc-----cCCCCCCCEEEEEEEcCCCCcEEEEEEEC
Confidence            5578999999  89999999999889999999999943     57899999999999998888999999843

>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=99.71  E-value=2.7e-18  Score=131.43  Aligned_cols=68  Identities=22%  Similarity=0.245  Sum_probs=58.8

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC---CceeeeeEecceee
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK---GNQFCFVLKNIVLY  274 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k---G~~A~~V~~~~~~~  274 (282)
                      .+.+|+||||+  ||||||+++++++|||||+++|..     + +.|.+||+|+|++..+++   +++|++|+..-..+
T Consensus         7 ~r~~G~Vk~f~--KGfGFI~~~~gg~DvFvH~s~i~~-----~-~~L~~G~~V~F~v~~g~kg~G~~~A~~V~~~~~~s   77 (89)
T 1x65_A            7 GREMGVIAAMR--DGFGFIKCVDRDVRMFFHFSEILD-----G-NQLHIADEVEFTVVPDMLSAQRNHAIRIKKLPKGT   77 (89)
T ss_dssp             CCEEEEEEECC--TTBCEEEESSSSSCCCCBTTGGGG-----S-CCCCTTCCEEECCBCCSSSCCCCBCCSCEECCBTT
T ss_pred             cceeEEEEEEe--CCcceeecCCCCccEEEEhhhccC-----C-CCCCCCCEEEEEEEeCCCcCCCceeeEEEECCCCc
Confidence            46789999995  999999999989999999999993     2 689999999999999997   48999998543333

>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=99.70  E-value=7.5e-18  Score=126.32  Aligned_cols=66  Identities=26%  Similarity=0.435  Sum_probs=59.7

Q ss_pred             eeeeeeEEEEeeCCCceEEEeCCCC-CCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCC-Cc-eEEEEeCCC
Q psy547           31 ATKVCGVVKWFSVKSGYGFIATPSS-NEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK-GH-EAINVTGPD  104 (282)
Q Consensus        31 ~~~~~G~Vkwfn~~kGfGFI~~~d~-~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~k-G~-~A~~V~~~~  104 (282)
                      .++.+|+|+||  .||||||+++++ ++|||||+++|. .    + +.|.+|++|+|+++.+++ |+ +|++|+.+.
T Consensus         6 ~~~~~G~V~~~--~KGfGFI~~ddg~g~DvFvH~s~i~-~----g-~~l~~G~~V~F~v~~~~k~G~~~A~~V~~~~   74 (79)
T 2ytv_A            6 SGLRRATVECV--KDQFGFINYEVGDSKKLFFHVKEVQ-D----G-IELQAGDEVEFSVILNQRTGKCSACNVWRVS   74 (79)
T ss_dssp             CSBCCEEEEEC--CSSEEEESCCCSSSSSEEEETTTCC-S----S-CCCCTTCEEECBCEECSSSCCEECCSCEECS
T ss_pred             CCcccEEEEEe--cccceeEeCCCCCCCcEEEEhHHcC-C----C-CcCCCCCEEEEEEEECCCCCCceeEEEEECC
Confidence            46689999999  699999999987 699999999998 4    5 799999999999999988 88 999999765

>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=99.66  E-value=9.5e-17  Score=120.28  Aligned_cols=64  Identities=25%  Similarity=0.478  Sum_probs=56.8

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCC-CccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC-Cc-eeeeeEec
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSS-NEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK-GN-QFCFVLKN  270 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~-~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k-G~-~A~~V~~~  270 (282)
                      ++.+|+|+||  .||||||+++++ ++|||||+++|. .    + +.|.+||+|+|++..+++ |+ +|++|+..
T Consensus         7 ~~~~G~V~~~--~KGfGFI~~ddg~g~DvFvH~s~i~-~----g-~~l~~G~~V~F~v~~~~k~G~~~A~~V~~~   73 (79)
T 2ytv_A            7 GLRRATVECV--KDQFGFINYEVGDSKKLFFHVKEVQ-D----G-IELQAGDEVEFSVILNQRTGKCSACNVWRV   73 (79)
T ss_dssp             SBCCEEEEEC--CSSEEEESCCCSSSSSEEEETTTCC-S----S-CCCCTTCEEECBCEECSSSCCEECCSCEEC
T ss_pred             CcccEEEEEe--cccceeEeCCCCCCCcEEEEhHHcC-C----C-CcCCCCCEEEEEEEECCCCCCceeEEEEEC
Confidence            4467999999  699999999987 699999999999 3    3 689999999999999998 88 99999854

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

Probab=99.56  E-value=4.8e-15  Score=115.94  Aligned_cols=58  Identities=33%  Similarity=0.552  Sum_probs=51.8

Q ss_pred             eeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccc--cCCCCCCEEEEEEEeCC
Q psy547           31 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLY--KTLAEGETVEFDIMQGD   92 (282)
Q Consensus        31 ~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~--~~l~~Gd~V~f~v~~~~   92 (282)
                      ..+.+|+|||||..||||||+++++++|+|||+|+|...    ++  +.|.+|+.|+|++....
T Consensus        14 ~~~~~G~Vk~fn~~kGfGFI~~~~gg~dvfvH~s~l~~~----~~~~~~l~~Ge~V~g~V~~i~   73 (101)
T 2bh8_A           14 SGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAGSSG----AAVRGNPQQGDRVEGKIKSIT   73 (101)
T ss_dssp             --CEEEEEEEEEGGGTEEEEEESSSSCEEEEECCCSCSS----SCCCCCCCTTCEEEEEEEECC
T ss_pred             cccceeEEEEEECCCCCEEEEeCCCCcEEEEEEEEEecC----CccccCCCCCCEEEEEEEEeC
Confidence            456799999999999999999999999999999999976    47  89999999999998755

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

Probab=99.48  E-value=6e-14  Score=109.69  Aligned_cols=60  Identities=33%  Similarity=0.552  Sum_probs=52.4

Q ss_pred             eeeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccc--cCCCCCCEEEEEEEEcC-CC
Q psy547          198 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLY--KTLAEGETVEFDIMQGD-KG  261 (282)
Q Consensus       198 ~~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~--~~l~~Gd~V~F~i~~~~-kG  261 (282)
                      ..+.+|+|||||..||||||+++++++|+|||+++|...    ++  +.|.+|+.|+|++.... .|
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            356789999999999999999999999999999999954    46  78999999999999865 46

>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=97.37  E-value=0.0022  Score=64.54  Aligned_cols=47  Identities=23%  Similarity=0.423  Sum_probs=39.6

Q ss_pred             eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeC
Q psy547           33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG   91 (282)
Q Consensus        33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~   91 (282)
                      .+.|+|+-=  .|||||+.+++ ++|||+.-..+...         ..||+|...+...
T Consensus        21 ~~~G~~~~~--~~GfgF~~~d~-~~difi~~~~~~~a---------~~GD~V~v~i~~~   67 (644)
T 2id0_A           21 RAEGVVKAT--EKGFGFLEVDA-QKSYFIPPPQMKKV---------MHGDRIIAVIHSE   67 (644)
T ss_dssp             EEEEEEECC--SSSCEEEECSS-SCEEEECHHHHTTS---------CTTCEEEEEEECC
T ss_pred             eEEEEEEEe--cCCcEEEEECC-CCCEEECHHHHhcC---------CCCCEEEEEEecC
Confidence            578999864  79999999986 68999999888665         7999999998754

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

Probab=97.03  E-value=0.0075  Score=54.81  Aligned_cols=62  Identities=13%  Similarity=0.047  Sum_probs=42.5

Q ss_pred             eeeeeeEEEEeeCCCceE-EEeCCCC-CCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEE
Q psy547           31 ATKVCGVVKWFSVKSGYG-FIATPSS-NEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAIN   99 (282)
Q Consensus        31 ~~~~~G~Vkwfn~~kGfG-FI~~~d~-~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~   99 (282)
                      .....|+|++-+  +.|| |+.- .. +.|+|+|+|++....    -..+..||.|...+..+.++..+..
T Consensus        70 G~~~~g~V~~v~--~~~GaFVdi-G~~~~d~lvp~sel~~~~----~~~~~~Gd~v~v~l~iD~~~Ri~ls  133 (285)
T 3go5_A           70 DQFGWGRVTEVR--KDLGVFVDT-GLPDKEIVVSLDILPELK----ELWPKKGDQLYIRLEVDKKDRIWGL  133 (285)
T ss_dssp             SSCEEEEEEEEE--TTTEEEEEC-SCTTCCEEEEGGGSCSSG----GGSCCTTCEEEEEEEECTTSCEEEE
T ss_pred             CCEEEEEEEEEc--cCceEEEEE-CCCCcEEEEEHHHCCccc----ccccCCCCEEEEEEEECCCCcEEEE
Confidence            445789999874  3456 5554 44 479999999985431    2467999999888877765544333

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

Probab=96.28  E-value=0.13  Score=46.58  Aligned_cols=56  Identities=11%  Similarity=0.088  Sum_probs=39.7

Q ss_pred             eeeEEEEEEcCCCeeEEecCCC-CccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCc
Q psy547          201 VCGVVKWFSVKSGYGFIATPSS-NEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN  262 (282)
Q Consensus       201 ~~G~Vk~fn~~kGfGFI~~~d~-~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~  262 (282)
                      ..|+|++.+  +.||....-+. +.|+|+|++++....    ...++.||.|...+..++++.
T Consensus        73 ~~g~V~~v~--~~~GaFVdiG~~~~d~lvp~sel~~~~----~~~~~~Gd~v~v~l~iD~~~R  129 (285)
T 3go5_A           73 GWGRVTEVR--KDLGVFVDTGLPDKEIVVSLDILPELK----ELWPKKGDQLYIRLEVDKKDR  129 (285)
T ss_dssp             EEEEEEEEE--TTTEEEEECSCTTCCEEEEGGGSCSSG----GGSCCTTCEEEEEEEECTTSC
T ss_pred             EEEEEEEEc--cCceEEEEECCCCcEEEEEHHHCCccc----ccccCCCCEEEEEEEECCCCc
Confidence            458998873  45775554454 589999999986321    135799999988887776653

>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=95.97  E-value=0.014  Score=46.95  Aligned_cols=52  Identities=25%  Similarity=0.535  Sum_probs=42.4

Q ss_pred             eeeEEEEEEcCCCeeEEecCC-----CCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCC
Q psy547          201 VCGVVKWFSVKSGYGFIATPS-----SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG  261 (282)
Q Consensus       201 ~~G~Vk~fn~~kGfGFI~~~d-----~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG  261 (282)
                      ..|++.--  .+||||+.+++     +..||||+.+.++.       ..|..||.|+-.+.....|
T Consensus        51 ~~Gvlei~--~dG~GFlr~~~~~y~~~~~DiyVs~~~irr-------f~lr~GD~V~g~vr~~~~~  107 (130)
T 1a62_A           51 GDGVLEIL--QDGFGFLRSADSSYLAGPDDIYVSPSQIRR-------FNLRTGDTISGKIRPPKEG  107 (130)
T ss_dssp             EEEEEEEC--TTSCEEEECGGGTTCCCTTCEEECHHHHHH-------TTCCTTCEEEEEEECCCTT
T ss_pred             EEEEEEEc--CCCeEEEecCCcCCCCCCCCEEECHHHHhH-------hCCCCCCEEEEEEeCCCCC
Confidence            46777543  57999999873     67899999999994       3589999999999877666

>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=95.90  E-value=0.019  Score=46.24  Aligned_cols=64  Identities=22%  Similarity=0.422  Sum_probs=48.9

Q ss_pred             eeeeEEEEeeCCCceEEEeCCC-----CCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCC---ceEEEEeCCC
Q psy547           33 KVCGVVKWFSVKSGYGFIATPS-----SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG---HEAINVTGPD  104 (282)
Q Consensus        33 ~~~G~Vkwfn~~kGfGFI~~~d-----~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG---~~A~~V~~~~  104 (282)
                      ...|++.--  .+||||+.+++     +..||||+.+.++..       .|..||.|+-.+.....+   ..-..|..++
T Consensus        50 ~~~Gvlei~--~dG~GFlr~~~~~y~~~~~DiyVs~~~irrf-------~lr~GD~V~g~vr~~~~~ek~~~l~~v~~vn  120 (130)
T 1a62_A           50 FGDGVLEIL--QDGFGFLRSADSSYLAGPDDIYVSPSQIRRF-------NLRTGDTISGKIRPPKEGERYFALLKVNEVN  120 (130)
T ss_dssp             EEEEEEEEC--TTSCEEEECGGGTTCCCTTCEEECHHHHHHT-------TCCTTCEEEEEEECCCTTCCSEEEEEEEEET
T ss_pred             EEEEEEEEc--CCCeEEEecCCcCCCCCCCCEEECHHHHhHh-------CCCCCCEEEEEEeCCCCCCcccceeEEEeEC
Confidence            367877654  57999999983     678999999999753       579999999998876554   3446676666


Q ss_pred             C
Q psy547          105 G  105 (282)
Q Consensus       105 ~  105 (282)
                      +
T Consensus       121 g  121 (130)
T 1a62_A          121 F  121 (130)
T ss_dssp             T
T ss_pred             C
Confidence            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=91.54  E-value=0.24  Score=49.63  Aligned_cols=47  Identities=23%  Similarity=0.482  Sum_probs=38.8

Q ss_pred             eeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEc
Q psy547          200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG  258 (282)
Q Consensus       200 ~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~  258 (282)
                      ...|+|+.  ..+||||+.+++ ++|||+.-..+.         ..-.||+|...+...
T Consensus        21 ~~~G~~~~--~~~GfgF~~~d~-~~difi~~~~~~---------~a~~GD~V~v~i~~~   67 (644)
T 2id0_A           21 RAEGVVKA--TEKGFGFLEVDA-QKSYFIPPPQMK---------KVMHGDRIIAVIHSE   67 (644)
T ss_dssp             EEEEEEEC--CSSSCEEEECSS-SCEEEECHHHHT---------TSCTTCEEEEEEECC
T ss_pred             eEEEEEEE--ecCCcEEEEECC-CCCEEECHHHHh---------cCCCCCEEEEEEecC
Confidence            45788875  479999999986 689999988777         357999999999865

>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=91.40  E-value=0.86  Score=35.56  Aligned_cols=60  Identities=23%  Similarity=0.321  Sum_probs=40.6

Q ss_pred             eeeeeeeeEEEEeeCCCceE-EEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeC
Q psy547           29 VLATKVCGVVKWFSVKSGYG-FIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG   91 (282)
Q Consensus        29 ~~~~~~~G~Vkwfn~~kGfG-FI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~   91 (282)
                      ..-..+.|+|+....   || ||..+....+-|+|+++|....-..-...++.||.|...+..-
T Consensus        21 ~vG~iv~G~V~~I~~---fGaFV~l~g~~~~Glvhisel~~~~~~~~~~~~~~Gd~V~VkV~~v   81 (119)
T 2cqo_A           21 ALYTIFQGEVAMVTD---YGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGR   81 (119)
T ss_dssp             CTTCEEEEEEEEEET---TEEEEECTTCSSCEEEEHHHHCSSCCSCHHHHCCTTCEEEEEEEEE
T ss_pred             CCCCEEEEEEEEEeC---ceEEEEECCCcEEEEEEHHHCCcccccChhhcCCCCCEEEEEEEEE
Confidence            345668999999854   56 6666433469999999996531000013589999999987653

>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=90.39  E-value=0.49  Score=36.99  Aligned_cols=57  Identities=23%  Similarity=0.327  Sum_probs=38.9

Q ss_pred             eeeeeEEEEEEcCCCee-EEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEc
Q psy547          199 TKVCGVVKWFSVKSGYG-FIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG  258 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfG-FI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~  258 (282)
                      ..+.|+|+....   || ||..++.+.+-|+|++++.......-...++.||.|...|..-
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            557899998743   77 5555333579999999997431111113489999999988764

>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=88.66  E-value=2  Score=41.94  Aligned_cols=81  Identities=20%  Similarity=0.228  Sum_probs=57.9

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCC--------cccc-cCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNP--------RKLY-KTLAEGETVEFDIMQGDKGNQFCFVLK  269 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~--------r~g~-~~l~~Gd~V~F~i~~~~kG~~A~~V~~  269 (282)
                      +-+.|+|+..-+--+--||.-.. +++-|+|++++.....        ...+ ..|++||.|...|...+.|-....++.
T Consensus        47 nIY~GkV~rv~p~~~aAFVdiG~-gk~gfLhisei~~~~~~~~~~~~~~~~i~d~lk~Gq~VlVQV~Ke~~g~KGa~lTt  125 (517)
T 2bx2_L           47 NIYKGKITRIEPSLEAAFVDYGA-ERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTT  125 (517)
T ss_dssp             CEEEEEEEEEETTTTEEEEESSS-SSCEEEEGGGSCGGGCC-------CCCGGGTCCTTCEEEEEEEECCCTTCCCEEES
T ss_pred             CEEEEEEEEeccCCceEEEEeCC-CcEEEEEHHHcChhhhccccccccccchhhhccCCCEEEEEEEeeccccCCceEEe
Confidence            56889999886655588998765 8899999999852210        0001 238999999999999887766666776


Q ss_pred             cc---eeeeeeeec
Q psy547          270 NI---VLYFSFVPQ  280 (282)
Q Consensus       270 ~~---~~~~~~~~~  280 (282)
                      +|   .-|+-|+|.
T Consensus       126 ~isl~GRylVl~P~  139 (517)
T 2bx2_L          126 FISLAGSYLVLMPN  139 (517)
T ss_dssp             SCCEECSSEEEETT
T ss_pred             eEEeccceEEEeCC
Confidence            65   345566664

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

Probab=86.95  E-value=1.3  Score=31.71  Aligned_cols=53  Identities=13%  Similarity=0.179  Sum_probs=38.7

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEc
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG  258 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~  258 (282)
                      ..+.|+|+...   .||+...-+.+.+-|+|++++....    ...++.||.|...+..-
T Consensus         7 ~iv~G~V~~v~---~~G~fV~l~~~~~Gllh~sel~~~~----~~~~~~Gd~V~v~V~~v   59 (80)
T 2k52_A            7 KFYKGVVTRIE---KYGAFINLNEQVRGLLRPRDMISLR----LENLNVGDEIIVQAIDV   59 (80)
T ss_dssp             CEEEEEEEEEE---TTEEEEEEETTEEEEECGGGCSSCC----GGGCCTTCEEEEEEEEE
T ss_pred             CEEEEEEEEEe---CCEEEEEECCCCEEEEEHHHCCccc----ceeeCCCCEEEEEEEEE
Confidence            44679998874   3775544444789999999997431    24699999999988764

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

Probab=85.76  E-value=1.6  Score=34.47  Aligned_cols=57  Identities=16%  Similarity=0.285  Sum_probs=40.4

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEc
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG  258 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~  258 (282)
                      ..+.|+|+...   .||+...-+.+.+-|+|++++.......-...++.||.|...|..-
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            44679998873   4776665555789999999997432111124699999999988764

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

Probab=85.42  E-value=3.4  Score=31.69  Aligned_cols=58  Identities=22%  Similarity=0.352  Sum_probs=40.8

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEecccccc-CCcccccCCCCCCEEEEEEEEcC
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYN-NPRKLYKTLAEGETVEFDIMQGD  259 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~-~~r~g~~~l~~Gd~V~F~i~~~~  259 (282)
                      ..+.|+|+...   .||+...-+.+-+-|+|++++..+ ..+.-...+..||.|...|..-+
T Consensus        32 ~~~~G~V~~v~---~~G~FV~l~~~~~Glvhisel~~~~~~~~~~~~~~vGd~V~vkV~~vd   90 (115)
T 2khi_A           32 TKLTGRVTNLT---DYGCFVEIEEGVEGLVHVSEMDWTNKNIHPSKVVNVGDVVEVMVLDID   90 (115)
T ss_dssp             CEEEEEEEEEE---TTEEEEECSTTCEEEEETTSSSCSSTTCSSTTTCCTTCEEEEEEEEEE
T ss_pred             CEEEEEEEEEE---CCEEEEEECCCCEEEEEHHHCCccccccCcccEECCCCEEEEEEEEEE
Confidence            45779998874   378666555578999999999642 00111246999999999987644

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

Probab=84.84  E-value=1.7  Score=31.17  Aligned_cols=51  Identities=18%  Similarity=0.278  Sum_probs=38.1

Q ss_pred             eeeeeEEEEeeCCCceE-EEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEe
Q psy547           32 TKVCGVVKWFSVKSGYG-FIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ   90 (282)
Q Consensus        32 ~~~~G~Vkwfn~~kGfG-FI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~   90 (282)
                      ..+.|+|+...+   || ||+.++ +-+-|+|+|++....    ...++.||.|...+..
T Consensus         7 ~iv~G~V~~v~~---~G~fV~l~~-~~~Gllh~sel~~~~----~~~~~~Gd~V~v~V~~   58 (80)
T 2k52_A            7 KFYKGVVTRIEK---YGAFINLNE-QVRGLLRPRDMISLR----LENLNVGDEIIVQAID   58 (80)
T ss_dssp             CEEEEEEEEEET---TEEEEEEET-TEEEEECGGGCSSCC----GGGCCTTCEEEEEEEE
T ss_pred             CEEEEEEEEEeC---CEEEEEECC-CCEEEEEHHHCCccc----ceeeCCCCEEEEEEEE
Confidence            347899988753   56 555544 678999999996531    2579999999998865

>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=83.54  E-value=2.1  Score=32.27  Aligned_cols=60  Identities=13%  Similarity=0.252  Sum_probs=40.5

Q ss_pred             eeeeeEEEEEEcCCCee-EEecCC--CCccEEEEeccccccCC-cccccCCCCCCEEEEEEEEcCCC
Q psy547          199 TKVCGVVKWFSVKSGYG-FIATPS--SNEDVFVHSKRIKYNNP-RKLYKTLAEGETVEFDIMQGDKG  261 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfG-FI~~~d--~~~dVF~H~s~l~~~~~-r~g~~~l~~Gd~V~F~i~~~~kG  261 (282)
                      ..+.|+|+..   ..|| ||...+  .+.+-|+|++++..... ..-...++.||.|...+..-+.+
T Consensus        14 ~i~~G~V~~v---~~fG~FV~l~~~~~~~~Glvhisel~~~~~~~~~~~~~~~Gd~V~VkV~~vd~~   77 (103)
T 2eqs_A           14 DIYNGKVTSI---MQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGT   77 (103)
T ss_dssp             CEEEEEEEEE---CSSCEEEEECSSSSCCEEEECGGGTSSSSCCCCHHHHCCTTCEEEEEEEEEETT
T ss_pred             CEEEEEEEEE---eccEEEEEEcCCCCCeEEEEEHHHCCCCcccCCcccEeCCCCEEEEEEEEEECC
Confidence            5578999887   3488 555544  27899999999942210 00113489999999998876543

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

Probab=81.65  E-value=3  Score=32.88  Aligned_cols=58  Identities=16%  Similarity=0.281  Sum_probs=39.0

Q ss_pred             eeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeC
Q psy547           31 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG   91 (282)
Q Consensus        31 ~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~   91 (282)
                      ...+.|+|+....   ||+...-+.+-+-|+|+|.+...--..-...++.||.|...|..-
T Consensus         8 G~iv~G~V~~i~~---~G~FV~l~~~~~Glihisel~~~~~~~~~~~~~vGd~V~vkV~~v   65 (130)
T 2k4k_A            8 GSVYTGKVTGLQA---YGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQVKVLAV   65 (130)
T ss_dssp             TCEEEEEEEEEET---TEEEEEEETTEEEEEEGGGTSSSCCSCGGGTCCTTCEEEEEEEEE
T ss_pred             CCEEEEEEEEEeC---CeEEEEECCCcEEEEEHHHCCcccccCccccCCCCCEEEEEEEEE
Confidence            3457899998843   564444444689999999996431000125689999999988653

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

Probab=81.44  E-value=2.9  Score=31.70  Aligned_cols=58  Identities=16%  Similarity=0.160  Sum_probs=40.3

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD  259 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~  259 (282)
                      ..+.|+|+...   .||+...-+.+-+-|+|++++.......-...+..||.|.+.|..-+
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            45779998873   36665555557899999999964311111235899999999887644

---

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	282
d1h95a_	79	b.40.4.5 (A:) Y-box protein 1 cold shock domain (Y	4e-27
d1h95a_	79	b.40.4.5 (A:) Y-box protein 1 cold shock domain (Y	8e-22
d1mjca_	69	b.40.4.5 (A:) Major cold shock protein {Escherichi	4e-20
d1mjca_	69	b.40.4.5 (A:) Major cold shock protein {Escherichi	2e-17
d1g6pa_	66	b.40.4.5 (A:) Major cold shock protein {Thermotoga	9e-18
d1g6pa_	66	b.40.4.5 (A:) Major cold shock protein {Thermotoga	7e-15
d1c9oa_	66	b.40.4.5 (A:) Major cold shock protein {Bacillus c	5e-17
d1c9oa_	66	b.40.4.5 (A:) Major cold shock protein {Bacillus c	2e-14
d1wfqa_	89	b.40.4.5 (A:) Cold shock domain protein E1 (UNR) {	9e-14
d1wfqa_	89	b.40.4.5 (A:) Cold shock domain protein E1 (UNR) {	4e-12

>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 = 98.7 bits (246), Expect = 4e-27
 Identities = 46/75 (61%), Positives = 59/75 (78%)

Query: 29  VLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDI 88
           V+ATKV G VKWF+V++GYGFI    + EDVFVH   IK NNPRK  +++ +GETVEFD+
Sbjct: 4   VIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDV 63

Query: 89  MQGDKGHEAINVTGP 103
           ++G+KG EA NVTGP
Sbjct: 64  VEGEKGAEAANVTGP 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 = 84.9 bits (210), Expect = 8e-22
 Identities = 39/68 (57%), Positives = 53/68 (77%)

Query: 196 VLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDI 255
           V+ATKV G VKWF+V++GYGFI    + EDVFVH   IK NNPRK  +++ +GETVEFD+
Sbjct: 4   VIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDV 63

Query: 256 MQGDKGNQ 263
           ++G+KG +
Sbjct: 64  VEGEKGAE 71

>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 = 79.8 bits (197), Expect = 4e-20
 Identities = 31/71 (43%), Positives = 42/71 (59%), Gaps = 4/71 (5%)

Query: 31  ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ 90
           + K+ G+VKWF+   G+GFI     ++DVFVH   I+ +     YK+L EG+ V F I  
Sbjct: 1   SGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIES 56

Query: 91  GDKGHEAINVT 101
           G KG  A NVT
Sbjct: 57  GAKGPAAGNVT 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 = 72.5 bits (178), Expect = 2e-17
 Identities = 27/66 (40%), Positives = 38/66 (57%), Gaps = 4/66 (6%)

Query: 198 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ 257
           + K+ G+VKWF+   G+GFI     ++DVFVH   I+ +     YK+L EG+ V F I  
Sbjct: 1   SGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIES 56

Query: 258 GDKGNQ 263
           G KG  
Sbjct: 57  GAKGPA 62

>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 = 73.3 bits (180), Expect = 9e-18
 Identities = 32/69 (46%), Positives = 40/69 (57%), Gaps = 5/69 (7%)

Query: 36  GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
           G VKWF  K GYGFI T     DVFVH   I+       +KTL EG+ VEF+I +G KG 
Sbjct: 3   GKVKWFDSKKGYGFI-TKDEGGDVFVHWSAIEMEG----FKTLKEGQVVEFEIQEGKKGP 57

Query: 96  EAINVTGPD 104
           +A +V   +
Sbjct: 58  QAAHVKVVE 66

>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 = 65.5 bits (160), Expect = 7e-15
 Identities = 31/61 (50%), Positives = 36/61 (59%), Gaps = 5/61 (8%)

Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
           G VKWF  K GYGFI T     DVFVH   I+       +KTL EG+ VEF+I +G KG 
Sbjct: 3   GKVKWFDSKKGYGFI-TKDEGGDVFVHWSAIEMEG----FKTLKEGQVVEFEIQEGKKGP 57

Query: 263 Q 263
           Q
Sbjct: 58  Q 58

>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 = 71.4 bits (175), Expect = 5e-17
 Identities = 30/66 (45%), Positives = 40/66 (60%), Gaps = 5/66 (7%)

Query: 36  GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
           G VKWF+ + GYGFI       DVFVH   I+       +KTL EG+ V F+I+QG++G 
Sbjct: 4   GKVKWFNNEKGYGFI-EVEGGSDVFVHFTAIQGEG----FKTLEEGQEVSFEIVQGNRGP 58

Query: 96  EAINVT 101
           +A NV 
Sbjct: 59  QAANVV 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 = 64.8 bits (158), Expect = 2e-14
 Identities = 28/61 (45%), Positives = 37/61 (60%), Gaps = 5/61 (8%)

Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
           G VKWF+ + GYGFI       DVFVH   I+       +KTL EG+ V F+I+QG++G 
Sbjct: 4   GKVKWFNNEKGYGFI-EVEGGSDVFVHFTAIQGEG----FKTLEEGQEVSFEIVQGNRGP 58

Query: 263 Q 263
           Q
Sbjct: 59  Q 59

>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 = 63.4 bits (154), Expect = 9e-14
 Identities = 17/77 (22%), Positives = 31/77 (40%), Gaps = 9/77 (11%)

Query: 31  ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ 90
           A +  GV++     + YGFI        +F H  +   N      + L  G+ VEF++  
Sbjct: 16  ALRETGVIEKL--LTSYGFIQCSERQARLFFHCSQYNGN-----LQDLKVGDDVEFEVSS 68

Query: 91  GDKGHE--AINVTGPDG 105
             +  +  A+ +    G
Sbjct: 69  DRRTGKPIAVKLVKISG 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 = 58.8 bits (142), Expect = 4e-12
 Identities = 18/82 (21%), Positives = 32/82 (39%), Gaps = 9/82 (10%)

Query: 182 SNPSASESPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKL 241
           S+ S+   P       A +  GV++     + YGFI        +F H  +   N     
Sbjct: 2   SSGSSGGYPNGTSA--ALRETGVIEKL--LTSYGFIQCSERQARLFFHCSQYNGN----- 52

Query: 242 YKTLAEGETVEFDIMQGDKGNQ 263
            + L  G+ VEF++    +  +
Sbjct: 53  LQDLKVGDDVEFEVSSDRRTGK 74

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	282
d1h95a_	79	Y-box protein 1 cold shock domain (YB1-CSD) {Human	99.9
d1mjca_	69	Major cold shock protein {Escherichia coli [TaxId:	99.89
d1h95a_	79	Y-box protein 1 cold shock domain (YB1-CSD) {Human	99.87
d1mjca_	69	Major cold shock protein {Escherichia coli [TaxId:	99.86
d1c9oa_	66	Major cold shock protein {Bacillus caldolyticus [T	99.85
d1g6pa_	66	Major cold shock protein {Thermotoga maritima [Tax	99.85
d1c9oa_	66	Major cold shock protein {Bacillus caldolyticus [T	99.83
d1g6pa_	66	Major cold shock protein {Thermotoga maritima [Tax	99.81
d1wfqa_	89	Cold shock domain protein E1 (UNR) {Human (Homo sa	99.62
d1wfqa_	89	Cold shock domain protein E1 (UNR) {Human (Homo sa	99.58
d2ix0a2	79	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	97.67
d2ix0a2	79	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	97.23
d1a62a2	78	Rho termination factor, RNA-binding domain {Escher	95.45
d1a62a2	78	Rho termination factor, RNA-binding domain {Escher	94.85
d2ix0a1	90	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	92.02
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	90.42
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	90.18
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	89.85
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	88.36
d2ix0a1	90	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	87.56
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	87.12
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	83.57
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	83.38
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	81.91
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	81.28
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	80.98
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	80.83

>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=99.90  E-value=4.6e-24  Score=158.41  Aligned_cols=77  Identities=60%  Similarity=1.038  Sum_probs=70.4

Q ss_pred             CceeeeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeCC
Q psy547           27 PVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGP  103 (282)
Q Consensus        27 ~~~~~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~~  103 (282)
                      ...++.++.|+|||||..||||||+++++++|||||+|+|...+.++.+++|.+|+.|+|++..+++|++|.+|+.|
T Consensus         2 ~k~~~~r~~G~VKwfn~~KGfGFI~~ddg~~DvFvH~s~i~~~g~~~~~~~L~~G~~V~f~~~~~~~G~~A~~Vtgp   78 (79)
T d1h95a_           2 KKVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGP   78 (79)
T ss_dssp             CSCCEEEEEEEEEEEETTTTEEEEEEGGGTEEEEEEGGGBCSCCCSCCSCSCCSSCEEEEEEEECSSSEEEESBCCC
T ss_pred             chHhcCcccEEEEEEcCCCCeEEEEECCCCccEEEEhhHcccCCCcceeeecCCCCEEEEEEEeCCCCCeeEEEeCC
Confidence            35678889999999999999999999999999999999999886666689999999999999999999999999865

>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=99.89  E-value=2.9e-23  Score=150.29  Aligned_cols=68  Identities=46%  Similarity=0.781  Sum_probs=63.7

Q ss_pred             eeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeCC
Q psy547           32 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGP  103 (282)
Q Consensus        32 ~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~~  103 (282)
                      .+++|+|||||..||||||+++++++|||||+|+|...    +++.|.+|++|+|++..+++|++|.+|+.+
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            46899999999999999999999999999999999876    589999999999999999999999999864

>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=99.87  E-value=1.2e-22  Score=150.57  Aligned_cols=73  Identities=55%  Similarity=0.970  Sum_probs=67.1

Q ss_pred             eeeeeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeE
Q psy547          196 VLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVL  268 (282)
Q Consensus       196 ~~~~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~  268 (282)
                      ++..++.|+|||||..||||||+++++++|||||+++|..++++..++.|.+||.|+|++..+++|++|.+|+
T Consensus         4 ~~~~r~~G~VKwfn~~KGfGFI~~ddg~~DvFvH~s~i~~~g~~~~~~~L~~G~~V~f~~~~~~~G~~A~~Vt   76 (79)
T d1h95a_           4 VIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVT   76 (79)
T ss_dssp             CCEEEEEEEEEEEETTTTEEEEEEGGGTEEEEEEGGGBCSCCCSCCSCSCCSSCEEEEEEEECSSSEEEESBC
T ss_pred             HhcCcccEEEEEEcCCCCeEEEEECCCCccEEEEhhHcccCCCcceeeecCCCCEEEEEEEeCCCCCeeEEEe
Confidence            4568899999999999999999999999999999999997765556889999999999999999999999986

>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=99.86  E-value=4.1e-22  Score=144.10  Aligned_cols=67  Identities=42%  Similarity=0.739  Sum_probs=62.3

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK  269 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~  269 (282)
                      .+++|+|||||..||||||+++++++|||||+++|...    +++.|.+||+|+|++.++++|++|++|+.
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            46889999999999999999999999999999999844    57899999999999999999999999975

>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=99.85  E-value=5.5e-22  Score=142.26  Aligned_cols=66  Identities=45%  Similarity=0.766  Sum_probs=60.4

Q ss_pred             eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeCC
Q psy547           33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGP  103 (282)
Q Consensus        33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~~  103 (282)
                      |.+|+|||||..||||||++++ ++|||||+|+|...    +++.|.+|++|+|++..+++|++|.+|+.+
T Consensus         1 M~~G~Vk~fn~~kGfGFI~~d~-g~DiF~H~s~l~~~----~~~~L~~G~~V~f~~~~~~~G~~A~~V~~l   66 (66)
T d1c9oa_           1 MQRGKVKWFNNEKGYGFIEVEG-GSDVFVHFTAIQGE----GFKTLEEGQEVSFEIVQGNRGPQAANVVKL   66 (66)
T ss_dssp             CEEEEEEEEETTTTEEEEEETT-EEEEEEEGGGBCSS----SCCCCCTTCEEEEEEEEETTEEEEEEEEEC
T ss_pred             CCCeEEEEEECCCCEEEEEecC-CceEEEEehhcccc----cCCcCCCCCEEEEEEEECCCCCEEEEEEEC
Confidence            3589999999999999999975 67999999999876    589999999999999999999999999853

>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=99.85  E-value=4.4e-22  Score=142.74  Aligned_cols=66  Identities=47%  Similarity=0.798  Sum_probs=60.8

Q ss_pred             eeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeCCC
Q psy547           34 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGPD  104 (282)
Q Consensus        34 ~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~~~  104 (282)
                      ++|+|||||..||||||++++ ++|||||+|+|...    |++.|.+|+.|+|++..+++|++|.+|+.++
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 56999999999876    5899999999999999999999999998753

>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=99.83  E-value=5.3e-21  Score=137.06  Aligned_cols=64  Identities=47%  Similarity=0.793  Sum_probs=58.7

Q ss_pred             eeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547          201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK  269 (282)
Q Consensus       201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~  269 (282)
                      .+|+|||||..||||||++++ ++|||||+++|...    +++.|.+|++|+|.+.++++|++|++|++
T Consensus         2 ~~G~Vk~fn~~kGfGFI~~d~-g~DiF~H~s~l~~~----~~~~L~~G~~V~f~~~~~~~G~~A~~V~~   65 (66)
T d1c9oa_           2 QRGKVKWFNNEKGYGFIEVEG-GSDVFVHFTAIQGE----GFKTLEEGQEVSFEIVQGNRGPQAANVVK   65 (66)
T ss_dssp             EEEEEEEEETTTTEEEEEETT-EEEEEEEGGGBCSS----SCCCCCTTCEEEEEEEEETTEEEEEEEEE
T ss_pred             CCeEEEEEECCCCEEEEEecC-CceEEEEehhcccc----cCCcCCCCCEEEEEEEECCCCCEEEEEEE
Confidence            479999999999999999875 78999999999854    57899999999999999999999999985

>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=99.81  E-value=1.5e-20  Score=134.71  Aligned_cols=64  Identities=48%  Similarity=0.797  Sum_probs=58.4

Q ss_pred             eeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547          201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK  269 (282)
Q Consensus       201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~  269 (282)
                      ++|+|||||..||||||++++ ++|||||+++|...    +++.|.+|++|+|++.++++|++|.+|+.
T Consensus         1 l~G~Vk~f~~~kGfGFI~~~~-g~diFvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~   64 (66)
T d1g6pa_           1 MRGKVKWFDSKKGYGFITKDE-GGDVFVHWSAIEME----GFKTLKEGQVVEFEIQEGKKGPQAAHVKV   64 (66)
T ss_dssp             CCEEEEEEETTTTEEEEEETT-SCBCBBCSSSSCCS----SCCCCCSSSEEEEEEECSSSCCEEEEEEE
T ss_pred             CeEEEEEEeCCCCeeEEEecC-CceEEEEhHHhccc----CCCcCCCCCEEEEEEEECCCCCEEEEEEe
Confidence            469999999999999999977 56999999999844    57899999999999999999999999874

>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=99.62  E-value=5.5e-16  Score=116.85  Aligned_cols=69  Identities=23%  Similarity=0.427  Sum_probs=61.2

Q ss_pred             eeeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCC--ceEEEEeCCCC
Q psy547           30 LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG--HEAINVTGPDG  105 (282)
Q Consensus        30 ~~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG--~~A~~V~~~~~  105 (282)
                      .+++.+|+|+||+  +|||||+++++++|||||+++|..     +++.|.+||+|+|++..++++  ++|++|..+..
T Consensus        15 ~~~r~~G~I~~~~--~gfGFI~~~~~~~dvF~H~s~~~~-----~~~~l~~G~~VeF~v~~~~kg~k~~Av~V~~~~~   85 (89)
T d1wfqa_          15 AALRETGVIEKLL--TSYGFIQCSERQARLFFHCSQYNG-----NLQDLKVGDDVEFEVSSDRRTGKPIAVKLVKISG   85 (89)
T ss_dssp             CCCEEEEEEEEEC--SSEEEEEETTTTEEEEEETTTCSS-----CTTTCCTTCCEEEEEEECSSSCCEEEEEEEESSC
T ss_pred             ccceEEEEEEEec--CccceEEeCCCCceEEEEeehhhc-----cCCcccCCCEEEEEEEECCCCCceEEEEEEECCC
Confidence            5677899999994  699999999999999999999975     378999999999999999987  78889987664

>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=99.58  E-value=2.3e-15  Score=113.40  Aligned_cols=65  Identities=23%  Similarity=0.412  Sum_probs=56.9

Q ss_pred             eeeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCC--ceeeeeEe
Q psy547          198 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG--NQFCFVLK  269 (282)
Q Consensus       198 ~~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG--~~A~~V~~  269 (282)
                      ..|.+|+|+||+  +|||||+++++.+|||||++++..     +++.|++||+|+|++.+++|+  ++|++|++
T Consensus        16 ~~r~~G~I~~~~--~gfGFI~~~~~~~dvF~H~s~~~~-----~~~~l~~G~~VeF~v~~~~kg~k~~Av~V~~   82 (89)
T d1wfqa_          16 ALRETGVIEKLL--TSYGFIQCSERQARLFFHCSQYNG-----NLQDLKVGDDVEFEVSSDRRTGKPIAVKLVK   82 (89)
T ss_dssp             CCEEEEEEEEEC--SSEEEEEETTTTEEEEEETTTCSS-----CTTTCCTTCCEEEEEEECSSSCCEEEEEEEE
T ss_pred             cceEEEEEEEec--CccceEEeCCCCceEEEEeehhhc-----cCCcccCCCEEEEEEEECCCCCceEEEEEEE
Confidence            466789999994  699999999999999999999973     367899999999999999988  67777764

>d2ix0a2 b.40.4.5 (A:4-82) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exoribonuclease 2, RNB
species: Escherichia coli [TaxId: 562]

Probab=97.67  E-value=1.9e-05  Score=56.82  Aligned_cols=61  Identities=20%  Similarity=0.298  Sum_probs=45.4

Q ss_pred             eeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeCCC
Q psy547           32 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGPD  104 (282)
Q Consensus        32 ~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~~~  104 (282)
                      ..+.|+|.-=  .+||||+.+++ ++|||++..++...         ..||+|+..+....+.+++.-+.+++
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            3567887754  79999999987 68999999999776         69999999998665557776665543

>d2ix0a2 b.40.4.5 (A:4-82) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exoribonuclease 2, RNB
species: Escherichia coli [TaxId: 562]

Probab=97.23  E-value=0.0002  Score=51.31  Aligned_cols=58  Identities=19%  Similarity=0.335  Sum_probs=41.4

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK  269 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~  269 (282)
                      ..+.|+|..  ..+||||+.+++ ++|||++..++..         .-.||+|++.+....+.++| +|++
T Consensus        17 ~~~~G~i~~--~~~G~GFv~~d~-~~DifI~~~~~~~---------A~~GD~V~v~i~~~~~r~eg-~I~~   74 (79)
T d2ix0a2          17 PRAEGVVKA--TEKGFGFLEVDA-QKSYFIPPPQMKK---------VMHGDRIIAVIHSEKERESA-EPEE   74 (79)
T ss_dssp             CEEEEEEEC--CC--CEEEEEET-TEEEEECHHHHTT---------CCTTCEEEEEEECC--CCEE-EEEE
T ss_pred             CEEEEEEEE--eCCCcEEEEECC-CCcEEECHHHHcC---------CCCCCEEEEEEEeCCCcEEE-EEEE
Confidence            345788865  378999999987 7899999999983         56899999998755444554 4544

>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=95.45  E-value=0.012  Score=41.43  Aligned_cols=62  Identities=23%  Similarity=0.475  Sum_probs=46.8

Q ss_pred             eeEEEEeeCCCceEEEeCC-----CCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCC---ceEEEEeCCCC
Q psy547           35 CGVVKWFSVKSGYGFIATP-----SSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG---HEAINVTGPDG  105 (282)
Q Consensus        35 ~G~Vkwfn~~kGfGFI~~~-----d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG---~~A~~V~~~~~  105 (282)
                      .|.+---  ..|||||...     .+..||||+.+.++..       .|+.||.|+=.+.....|   +...+|..+++
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            4555333  5899999983     2568999999999875       579999999988876555   55677776664

>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=94.85  E-value=0.019  Score=40.41  Aligned_cols=51  Identities=25%  Similarity=0.594  Sum_probs=40.1

Q ss_pred             eEEEEEEcCCCeeEEecCC-----CCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCc
Q psy547          203 GVVKWFSVKSGYGFIATPS-----SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN  262 (282)
Q Consensus       203 G~Vk~fn~~kGfGFI~~~d-----~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~  262 (282)
                      |++--.  .+|||||...+     +..||||+.+.++.       -.|+.||.|+=.+.....|.
T Consensus         6 GiLei~--~dGyGFLR~~~~~y~~~~~DiyVs~s~Irr-------fgLR~GD~V~G~vr~p~~~e   61 (78)
T d1a62a2           6 GVLEIL--QDGFGFLRSADSSYLAGPDDIYVSPSQIRR-------FNLRTGDTISGKIRPPKEGE   61 (78)
T ss_dssp             EEEEEC--TTSCEEEECGGGTTCCCTTCEEECHHHHHH-------TTCCTTCEEEEEEECCCTTC
T ss_pred             EEEEEc--CCCcEEeECCccCCCCCCcceEECHHHHHH-------hCCCcCcEEEEEEECCCCCC
Confidence            555333  58999999742     46799999999994       35999999999998877663

>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=92.02  E-value=0.41  Score=33.88  Aligned_cols=60  Identities=15%  Similarity=0.138  Sum_probs=42.6

Q ss_pred             EEEEEcCCCeeEEecCCC--CccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC-CCc-e-eeeeEecc
Q psy547          205 VKWFSVKSGYGFIATPSS--NEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD-KGN-Q-FCFVLKNI  271 (282)
Q Consensus       205 Vk~fn~~kGfGFI~~~d~--~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~-kG~-~-A~~V~~~~  271 (282)
                      |-.+-..++++|+.+++.  ..+||+--....       ...++.||.|..+|...+ ++. . ..+|+.-|
T Consensus         5 VGr~~~~~~~~fVvPd~~ri~~~I~I~~~~~~-------~~~ak~Gd~Vvvei~~~P~~~~~~~~g~I~evl   69 (90)
T d2ix0a1           5 VGKVQGKNDRLAIVPDHPLLKDAIPCRAARGL-------NHEFKEGDWAVAEMRRHPLKGDRSFYAELTQYI   69 (90)
T ss_dssp             EEEEESCSSSEEEEESCTTCCSCEEEEECTTC-------CCCCCTTCEEEEEEEECGGGTCSSCEEEEEEEC
T ss_pred             EEEEEEeCCEEEEEeCCCcccccccccccccc-------cccCCCCCEEEEEEEeCCCCCCCCceEEEEEEE
Confidence            334456889999999986  468888765543       245899999999999987 442 2 24666544

>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=90.42  E-value=0.9  Score=31.93  Aligned_cols=72  Identities=18%  Similarity=0.180  Sum_probs=53.9

Q ss_pred             eeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCC---------cccccCCCCCCEEEEEEEEcCCCceeeeeEec
Q psy547          200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNP---------RKLYKTLAEGETVEFDIMQGDKGNQFCFVLKN  270 (282)
Q Consensus       200 ~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~---------r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~~  270 (282)
                      -+.|+|+...+.=.=-||.-.. +++-|+|++++.....         ..--..|++||.|..++...+.|-....++.+
T Consensus         3 IY~G~V~~V~pgl~AAFVDiG~-~k~gFL~~~di~~~~~~~~~~~~~~~~i~~~l~~G~~ilVQV~Ke~~~~KGprlT~~   81 (87)
T d1smxa_           3 IYKGKITRIEPSLEAAFVDYGA-ERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTTF   81 (87)
T ss_dssp             CEEEEEEEEEGGGTEEEEESSS-SSCEEEEGGGSCGGGCSSCCCSSSCCCGGGTCCTTCEEEEEEEECCBTTBCCEEESC
T ss_pred             cEEEEEEEecCCceEEEEEeCC-CccceeEecccceeeeccccccccccchhhhccCCCeEEEEEeecccCCCCceEEEE
Confidence            4679999987777778888765 7889999998753210         00123589999999999999988777788776


Q ss_pred             ce
Q psy547          271 IV  272 (282)
Q Consensus       271 ~~  272 (282)
                      |-
T Consensus        82 Is   83 (87)
T d1smxa_          82 IS   83 (87)
T ss_dssp             CC
T ss_pred             EE
Confidence            64

>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=90.18  E-value=0.25  Score=33.74  Aligned_cols=58  Identities=19%  Similarity=0.270  Sum_probs=42.5

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD  259 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~  259 (282)
                      ..+.|+|+....   ||....-+.+-+-|+|.+++....-..-...+++||.|.+.+..-+
T Consensus         7 ~iv~G~V~~v~~---~G~fV~l~~~~~Glv~~sels~~~~~~~~~~~~~G~~v~v~Vi~id   64 (76)
T d1sroa_           7 RVYTGKVTRIVD---FGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVD   64 (76)
T ss_dssp             SEEEEEEEEEET---TEEEEECSSSCCCBCCTTSSCSSCCSCHHHHCCTTCEEEEEEEECC
T ss_pred             CEEEEEEEEEeC---cEEEEEeCCCCEEEEEhHHhCccccCCHHHccCCCCEEEEEEEEEC
Confidence            456799999853   7877766667899999999975421111233899999999998843

>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=89.85  E-value=0.47  Score=32.93  Aligned_cols=57  Identities=12%  Similarity=0.146  Sum_probs=35.6

Q ss_pred             eeeeeEEEEEEcCCCee-EEecCC-CCccEEEEeccccccCCcccccCCCCCCEEEEEEEEc
Q psy547          199 TKVCGVVKWFSVKSGYG-FIATPS-SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG  258 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfG-FI~~~d-~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~  258 (282)
                      ..++|+|...   ..|| ||.-.+ .+-+-|+|.+++.......-...+.+||.|...|..-
T Consensus        15 ~iv~G~V~~i---~~~G~fV~l~~~~~i~G~i~~sels~~~~~~~~~~~~~Gd~v~~kV~~v   73 (86)
T d1kl9a2          15 DVVMVNVRSI---AEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRV   73 (86)
T ss_dssp             CEEEEEEEEE---CSSEEEEEETTTTTEEEEEEGGGC------------CTTCEEEEEEEEE
T ss_pred             CEEEEEEEEE---eCCeEEEEEecCCCEEEEEEeeeccccccccceEEeecccEEEEEEEEE
Confidence            4567999887   3588 566554 4678999999997543222234588999999998773

>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=88.36  E-value=0.44  Score=32.37  Aligned_cols=60  Identities=18%  Similarity=0.297  Sum_probs=41.9

Q ss_pred             eeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEe-CCCC
Q psy547           32 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ-GDKG   94 (282)
Q Consensus        32 ~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~-~~kG   94 (282)
                      +.+.|+|+....   ||....-..+-+-|+|.+++....-..--..+++||+|++.+.. ++++
T Consensus         7 ~iv~G~V~~v~~---~G~fV~l~~~~~Glv~~sels~~~~~~~~~~~~~G~~v~v~Vi~id~~~   67 (76)
T d1sroa_           7 RVYTGKVTRIVD---FGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDRQG   67 (76)
T ss_dssp             SEEEEEEEEEET---TEEEEECSSSCCCBCCTTSSCSSCCSCHHHHCCTTCEEEEEEEECCTTC
T ss_pred             CEEEEEEEEEeC---cEEEEEeCCCCEEEEEhHHhCccccCCHHHccCCCCEEEEEEEEECCCC
Confidence            457899999974   56555555577899999999764211112348999999999876 3444

>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=87.56  E-value=2.1  Score=29.86  Aligned_cols=63  Identities=13%  Similarity=0.007  Sum_probs=44.6

Q ss_pred             eeeeEEEEeeCCCceEEEeCCCCC--CcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC----CCceEEEEeCCCC
Q psy547           33 KVCGVVKWFSVKSGYGFIATPSSN--EDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD----KGHEAINVTGPDG  105 (282)
Q Consensus        33 ~~~G~Vkwfn~~kGfGFI~~~d~~--~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~----kG~~A~~V~~~~~  105 (282)
                      +.-|++.   ..++|+||.+++..  .+||+--....       ...++.||.|..++..-+    +.++|.-+..++.
T Consensus         3 rfVGr~~---~~~~~~fVvPd~~ri~~~I~I~~~~~~-------~~~ak~Gd~Vvvei~~~P~~~~~~~~g~I~evlG~   71 (90)
T d2ix0a1           3 RFVGKVQ---GKNDRLAIVPDHPLLKDAIPCRAARGL-------NHEFKEGDWAVAEMRRHPLKGDRSFYAELTQYITF   71 (90)
T ss_dssp             EEEEEEE---SCSSSEEEEESCTTCCSCEEEEECTTC-------CCCCCTTCEEEEEEEECGGGTCSSCEEEEEEECCC
T ss_pred             cEEEEEE---EeCCEEEEEeCCCcccccccccccccc-------cccCCCCCEEEEEEEeCCCCCCCCceEEEEEEEec
Confidence            4557664   68899999999854  67887654432       235689999999998753    2356776766654

>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=87.12  E-value=0.65  Score=32.12  Aligned_cols=57  Identities=12%  Similarity=0.165  Sum_probs=35.4

Q ss_pred             eeeeeeEEEEeeCCCceE-EEeCCC-CCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEe
Q psy547           31 ATKVCGVVKWFSVKSGYG-FIATPS-SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ   90 (282)
Q Consensus        31 ~~~~~G~Vkwfn~~kGfG-FI~~~d-~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~   90 (282)
                      ...+.|+|+-..   -|| ||.-.+ ++-+-|+|.++|.......-...+++||.|.+.+..
T Consensus        14 G~iv~G~V~~i~---~~G~fV~l~~~~~i~G~i~~sels~~~~~~~~~~~~~Gd~v~~kV~~   72 (86)
T d1kl9a2          14 EDVVMVNVRSIA---EMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIR   72 (86)
T ss_dssp             TCEEEEEEEEEC---SSEEEEEETTTTTEEEEEEGGGC------------CTTCEEEEEEEE
T ss_pred             CCEEEEEEEEEe---CCeEEEEEecCCCEEEEEEeeeccccccccceEEeecccEEEEEEEE
Confidence            445789999884   367 666654 457899999999654211113458899999999865

>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=83.57  E-value=2.8  Score=28.32  Aligned_cols=58  Identities=17%  Similarity=0.253  Sum_probs=41.6

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCC-cccccCCCCCCEEEEEEEEcC
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNP-RKLYKTLAEGETVEFDIMQGD  259 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~-r~g~~~l~~Gd~V~F~i~~~~  259 (282)
                      ..+.|+|+...   .||+...-+.+-+-|+|.+++..... ..-...+++||.|...+..-+
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            45679998863   36777766668899999999974321 112345899999999988743

>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=83.38  E-value=2.5  Score=29.49  Aligned_cols=68  Identities=18%  Similarity=0.226  Sum_probs=50.9

Q ss_pred             eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCC---------cccccCCCCCCEEEEEEEeCCCCceEEEEe
Q psy547           33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNP---------RKLYKTLAEGETVEFDIMQGDKGHEAINVT  101 (282)
Q Consensus        33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~---------~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~  101 (282)
                      -..|+|+...+.-.=-||.-.. +.+-|+|++++.....         ..--..|++|+.|..++...+.|-....++
T Consensus         3 IY~G~V~~V~pgl~AAFVDiG~-~k~gFL~~~di~~~~~~~~~~~~~~~~i~~~l~~G~~ilVQV~Ke~~~~KGprlT   79 (87)
T d1smxa_           3 IYKGKITRIEPSLEAAFVDYGA-ERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALT   79 (87)
T ss_dssp             CEEEEEEEEEGGGTEEEEESSS-SSCEEEEGGGSCGGGCSSCCCSSSCCCGGGTCCTTCEEEEEEEECCBTTBCCEEE
T ss_pred             cEEEEEEEecCCceEEEEEeCC-CccceeEecccceeeeccccccccccchhhhccCCCeEEEEEeecccCCCCceEE
Confidence            3679999999998889998866 6789999998754310         000135899999999999988776555555

>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=81.91  E-value=1.8  Score=30.29  Aligned_cols=57  Identities=19%  Similarity=0.315  Sum_probs=42.5

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEc
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG  258 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~  258 (282)
                      ..+.|+|+....   ||.+..-+.+-+-|+|.+++.......-...++.||.|.+.|..-
T Consensus        20 ~iv~g~V~~v~~---~G~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~vGq~v~~~V~~i   76 (94)
T d3bzka4          20 MVLEGVVTNVTN---FGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEV   76 (94)
T ss_dssp             CEEEEEEEEEET---TEEEEECSSSSCEEEEGGGGCSSCCSCHHHHCCTTCEEEEEEEEE
T ss_pred             CEEEEEEEEEEC---cEEEEEeCCCceEEeehhhhhcccccChhhhhccCcEEEEEEEEE
Confidence            456799999863   788777777889999999997542111223488999999998774

>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=81.28  E-value=3.2  Score=27.99  Aligned_cols=57  Identities=14%  Similarity=0.207  Sum_probs=38.6

Q ss_pred             eeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCC-CcccccCCCCCCEEEEEEEe
Q psy547           31 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNN-PRKLYKTLAEGETVEFDIMQ   90 (282)
Q Consensus        31 ~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~-~~~g~~~l~~Gd~V~f~v~~   90 (282)
                      .+.+.|+|+--..   ||....-+++-+-|+|.+++.... .......+++||.|.+.+..
T Consensus         6 Gd~V~G~V~~v~~---~g~~V~i~~~~~g~l~~se~s~~~~~~~~~~~~~vGd~V~~kV~~   63 (83)
T d2ba0a1           6 GDVVIGIIREVAA---NGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLN   63 (83)
T ss_dssp             TCEEEEEEEEECS---SEEEEECSSSSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEE
T ss_pred             CCEEEEEEEEEEC---CEEEEecCCCeeEEEecccccccccccChhhhcccccEEEEEEEE
Confidence            3457899998754   344444444778999999996431 01113458999999999875

>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=80.98  E-value=1.8  Score=31.06  Aligned_cols=56  Identities=20%  Similarity=0.157  Sum_probs=40.1

Q ss_pred             eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCC-----------cccccCCCCCCEEEEEEEEc
Q psy547          199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNP-----------RKLYKTLAEGETVEFDIMQG  258 (282)
Q Consensus       199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~-----------r~g~~~l~~Gd~V~F~i~~~  258 (282)
                      ..+.|+|+..+   .|||...-+ +-+-|+|.++|....-           +.--..++.||.|...|..-
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            34568998875   478777665 5899999999985320           00114689999999998863

>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=80.83  E-value=5.4  Score=28.93  Aligned_cols=69  Identities=9%  Similarity=0.112  Sum_probs=44.9

Q ss_pred             eeeeeeeEEEEeeCCCceEEEeCC-CCCCcEEEEeeccccCC-CcccccCCCCCCEEEEEEEeCCCCceEEEEe
Q psy547           30 LATKVCGVVKWFSVKSGYGFIATP-SSNEDVFVHSKRIKYNN-PRKLYKTLAEGETVEFDIMQGDKGHEAINVT  101 (282)
Q Consensus        30 ~~~~~~G~Vkwfn~~kGfGFI~~~-d~~~dvF~H~s~l~~~~-~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~  101 (282)
                      .-+.+.|+|+...   -||++..- ..+-+-|+|+++|.... .......+++||.|.+.|..-+..-.-+.+.
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 PGMLLTGTVSSLE---DHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLS   91 (119)
T ss_dssp             TTCEEEEEEEEEC---SSEEEEECCCSSCEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCTTSCEEEEE
T ss_pred             CCCEEEEEEEEEe---ccEEEEEEeccccceEEeHHHhccccccCCHHHhcccceEEEEEEEEEeCCCCEEEEE
Confidence            3566899999984   34555544 34568999999985420 0001357899999999998765543333343