Psyllid ID: psy3660

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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----
Protein Sequence
MSGSPLPFENKKPALSSPMLSPQEPHLHSNNTLSLPSPIITRRTRTESMDFKATAQRSKGSKEQPNFLISNRALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKALQGSKTCNSCNISSVELGTS
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHcccccccccccccccccccccccEEcEEEEEcccccEEEEccccccccEEEEEEccEEccccEEEEEEEEEccccccccccEEEccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccEEEccccccccccccccccccccccccccccccccccHHHHHHcccEEEEEEEEEEccccEEEEEEccccccEEEEHHccccccHHHHHHHHHHccccccccccEEEEEcccc
Coil and Loop (DISEMBL)
msgsplpfenkkpalsspmlspqephlhsnntlslpspiitrrtrtesmdfkataqrskgskeqpnflisnralqnpvetgkIKEFcrskghgfitpdsgepavfvhisdyvimPKLISQINKAlqgsktcnscnissvelgts
Flexible Loop (DISEMBL)
msgsplpfenkkpalsspMLSPQEPhlhsnntlslpspiiTRRTRTESMDFKataqrskgskeqpnflisnralqnpvetGKIKEFCRSKGHgfitpdsgepAVFVHISDYVIMPKLISQINKAlqgsktcnscnissvelgts
Low Complexity Region (SEG)
MSGSPLPFENKKPALSSPMLSPQEPHLHSNNTLSLPSPIITRRTRTESMDFKATAQRSKGSKEQPNFLISNRALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKALQGSKTCNSCNISSVELGTS
Disordered region (IsUnstruct)
******************************************************************************ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKALQGSKTCNSC**********
Disordered Region (DISOPRED)
**************************************IITRRTR***********************************GKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKL***************SCNI**V*****
Disordered Region (DISEMBL)
*********NKKPALSSPMLSPQEPHLHSNNTLSLPSPIITRRTRTES**************EQPNFLISNRALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKALQGSKTCNSCNISSVELGTS
Disordered Region (DISPRO)
*****************************NNTLSLPSPIITRRTRTE*MDF***********EQPNFLISNRALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKALQGSKTCNSCNISSV*L***
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSGSPLPFENKKPALSSPMLSPQEPHLHSNNTLSLPSPIITRRTRTESMDFKATAQRSKGSKEQPNFLISNRALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKALQGSKTCNSCNISSVELGTS
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	144	2.2.26 [Sep-21-2011]
Q9VVA0	143	Cold shock domain-contain	yes	N/A	0.534	0.538	0.462	5e-15
Q9Y2V2	147	Calcium-regulated heat st	yes	N/A	0.388	0.380	0.5	8e-11
Q9WU49	147	Calcium-regulated heat st	yes	N/A	0.388	0.380	0.5	9e-11
Q9CR86	148	Calcium-regulated heat st	yes	N/A	0.388	0.378	0.5	1e-10
Q63430	154	Cold shock domain-contain	no	N/A	0.569	0.532	0.355	7e-09
Q9Y534	153	Cold shock domain-contain	no	N/A	0.388	0.366	0.447	1e-08
Q91YQ3	154	Cold shock domain-contain	no	N/A	0.388	0.363	0.447	1e-08

>sp|Q9VVA0|Y9705_DROME Cold shock domain-containing protein CG9705 OS=Drosophila melanogaster GN=CG9705 PE=1 SV=1

 Score = 79.7 bits (195), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 49/106 (46%), Positives = 60/106 (56%), Gaps = 29/106 (27%)

Query: 19  MLSPQEPHLHSNN-----TLSLPSPIITRRTRTESMDFKATAQRSKGSKEQPNFLISNRA 73
           +L+ + P LH N+     +L LPSPIITRRTRT S                     S RA
Sbjct: 10  LLAAKPPVLHHNSHSPNASLQLPSPIITRRTRTAST--------------------SARA 49

Query: 74  LQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISD----YVIMP 115
           L+NPV TG +K F R+KGHGFITP++G   VF H+SD    YV MP
Sbjct: 50  LENPVVTGMVKSFSRTKGHGFITPNAGGEDVFCHVSDIEGEYVPMP 95

Drosophila melanogaster (taxid: 7227)

>sp|Q9Y2V2|CHSP1_HUMAN Calcium-regulated heat stable protein 1 OS=Homo sapiens GN=CARHSP1 PE=1 SV=2

 Score = 65.9 bits (159), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 38/76 (50%), Positives = 42/76 (55%), Gaps = 20/76 (26%)

Query: 35  LPSPIITRRTRTESMDFKATAQRSKGSKEQPNFLISNRALQNPVETGKIKEFCRSKGHGF 94
           +PSP+ TRRTRT    F AT                 RA Q PV  G  K FCRSKGHGF
Sbjct: 39  VPSPLPTRRTRT----FSATV----------------RASQGPVYKGVCKCFCRSKGHGF 78

Query: 95  ITPDSGEPAVFVHISD 110
           ITP  G P +F+HISD
Sbjct: 79  ITPADGGPDIFLHISD 94

Binds mRNA and regulates the stability of target mRNA. Binds single-stranded DNA (in vitro).

Homo sapiens (taxid: 9606)

>sp|Q9WU49|CHSP1_RAT Calcium-regulated heat stable protein 1 OS=Rattus norvegicus GN=Carhsp1 PE=1 SV=1

 Score = 65.5 bits (158), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 38/76 (50%), Positives = 42/76 (55%), Gaps = 20/76 (26%)

Query: 35  LPSPIITRRTRTESMDFKATAQRSKGSKEQPNFLISNRALQNPVETGKIKEFCRSKGHGF 94
           +PSP+ TRRTRT    F AT                 RA Q PV  G  K FCRSKGHGF
Sbjct: 39  VPSPLPTRRTRT----FSATV----------------RASQGPVYKGVCKCFCRSKGHGF 78

Query: 95  ITPDSGEPAVFVHISD 110
           ITP  G P +F+HISD
Sbjct: 79  ITPADGGPDIFLHISD 94

Binds mRNA and regulates the stability of target mRNA.

Rattus norvegicus (taxid: 10116)

>sp|Q9CR86|CHSP1_MOUSE Calcium-regulated heat stable protein 1 OS=Mus musculus GN=Carhsp1 PE=1 SV=1

 Score = 65.5 bits (158), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 38/76 (50%), Positives = 42/76 (55%), Gaps = 20/76 (26%)

Query: 35  LPSPIITRRTRTESMDFKATAQRSKGSKEQPNFLISNRALQNPVETGKIKEFCRSKGHGF 94
           +PSP+ TRRTRT    F AT                 RA Q PV  G  K FCRSKGHGF
Sbjct: 40  VPSPLPTRRTRT----FSATV----------------RASQGPVYKGVCKCFCRSKGHGF 79

Query: 95  ITPDSGEPAVFVHISD 110
           ITP  G P +F+HISD
Sbjct: 80  ITPADGGPDIFLHISD 95

Binds mRNA and regulates the stability of target mRNA.

Mus musculus (taxid: 10090)

>sp|Q63430|CSDC2_RAT Cold shock domain-containing protein C2 OS=Rattus norvegicus GN=Csdc2 PE=2 SV=3

 Score = 59.3 bits (142), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 42/118 (35%), Positives = 57/118 (48%), Gaps = 36/118 (30%)

Query: 9   ENKKPALSSPMLSPQEP-------HLHSNNTL---------SLPSPIITRRTRTESMDFK 52
           E+  P +  P+ SP+ P       H  S+             LPSP+ T+RTRT    + 
Sbjct: 4   ESTSPPVVPPLHSPKSPVWPTFPFHRESSRIWERGGGVSPRDLPSPLPTKRTRT----YS 59

Query: 53  ATAQRSKGSKEQPNFLISNRALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISD 110
           ATA+ S G                PV  G  K+F RS+GHGFITP++G   +FVH+SD
Sbjct: 60  ATARASAG----------------PVFKGVCKQFSRSQGHGFITPENGSEDIFVHVSD 101

RNA-binding factor which binds specifically to the very 3'-UTR ends of both histone H1 and H3.3 mRNAs, encompassing the polyadenylation signal. Might play a central role in the negative regulation of histone variant synthesis in the developing brain.

Rattus norvegicus (taxid: 10116)

>sp|Q9Y534|CSDC2_HUMAN Cold shock domain-containing protein C2 OS=Homo sapiens GN=CSDC2 PE=2 SV=1

 Score = 58.9 bits (141), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 34/76 (44%), Positives = 44/76 (57%), Gaps = 20/76 (26%)

Query: 35  LPSPIITRRTRTESMDFKATAQRSKGSKEQPNFLISNRALQNPVETGKIKEFCRSKGHGF 94
           LPSP+ T+RTRT    + ATA+ S G                PV  G  K+F RS+GHGF
Sbjct: 45  LPSPLPTKRTRT----YSATARASAG----------------PVFKGVCKQFSRSQGHGF 84

Query: 95  ITPDSGEPAVFVHISD 110
           ITP++G   +FVH+SD
Sbjct: 85  ITPENGSEDIFVHVSD 100

RNA-binding factor which binds specifically to the very 3'-UTR ends of both histone H1 and H3.3 mRNAs, encompassing the polyadenylation signal. Might play a central role in the negative regulation of histone variant synthesis in the developing brain.

Homo sapiens (taxid: 9606)

>sp|Q91YQ3|CSDC2_MOUSE Cold shock domain-containing protein C2 OS=Mus musculus GN=Csdc2 PE=2 SV=2

 Score = 58.5 bits (140), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 34/76 (44%), Positives = 44/76 (57%), Gaps = 20/76 (26%)

Query: 35  LPSPIITRRTRTESMDFKATAQRSKGSKEQPNFLISNRALQNPVETGKIKEFCRSKGHGF 94
           LPSP+ T+RTRT    + ATA+ S G                PV  G  K+F RS+GHGF
Sbjct: 46  LPSPLPTKRTRT----YSATARASAG----------------PVFKGVCKQFSRSQGHGF 85

Query: 95  ITPDSGEPAVFVHISD 110
           ITP++G   +FVH+SD
Sbjct: 86  ITPENGSEDIFVHVSD 101

RNA-binding factor which binds specifically to the very 3'-UTR ends of both histone H1 and H3.3 mRNAs, encompassing the polyadenylation signal. Might play a central role in the negative regulation of histone variant synthesis in the developing brain.

Mus musculus (taxid: 10090)

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	144
242022944	132	calcium-regulated heat stable protein, p	0.576	0.628	0.445	7e-14
158294527	157	AGAP005641-PA [Anopheles gambiae str. PE	0.437	0.401	0.505	2e-13
195328232	143	GM25657 [Drosophila sechellia] gi|195590	0.534	0.538	0.462	3e-13
21356601	143	CG9705, isoform A [Drosophila melanogast	0.534	0.538	0.462	3e-13
389609929	129	similar to CG9705 [Papilio xuthus]	0.465	0.519	0.483	5e-13
125977582	142	GA21978 [Drosophila pseudoobscura pseudo	0.534	0.542	0.471	6e-13
357603731	127	hypothetical protein KGM_10424 [Danaus p	0.493	0.559	0.474	7e-13
195376475	142	GJ13199 [Drosophila virilis] gi|19415418	0.534	0.542	0.462	9e-13
157121173	159	hypothetical protein AaeL_AAEL009235 [Ae	0.437	0.396	0.494	1e-12
195495012	143	GE19874 [Drosophila yakuba] gi|194181187	0.534	0.538	0.452	2e-12

>gi|242022944|ref|XP_002431897.1| calcium-regulated heat stable protein, putative [Pediculus humanus corporis] gi|212517238|gb|EEB19159.1| calcium-regulated heat stable protein, putative [Pediculus humanus corporis]

 Score = 82.0 bits (201), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 49/110 (44%), Positives = 61/110 (55%), Gaps = 27/110 (24%)

Query: 10  NKKPALSSPMLSPQEPHLHSNNTLSLPSPIITRRTRTESMDFKATAQRSKGSKEQPNFLI 69
           NKK +LS  + +P EP++     LSLPSPIITRRTRT S                     
Sbjct: 2   NKKASLSDSITTPTEPYI---KHLSLPSPIITRRTRTNST-------------------- 38

Query: 70  SNRALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISD----YVIMP 115
           S +A +NP+E G +K FCR KGHGFIT +     +FVHISD    YV +P
Sbjct: 39  SAKAFENPIEKGTVKMFCREKGHGFITSNRTGEDIFVHISDIEGEYVPLP 88

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|158294527|ref|XP_315660.4| AGAP005641-PA [Anopheles gambiae str. PEST] gi|157015604|gb|EAA11357.4| AGAP005641-PA [Anopheles gambiae str. PEST]

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 44/87 (50%), Positives = 53/87 (60%), Gaps = 24/87 (27%)

Query: 33  LSLPSPIITRRTRTESMDFKATAQRSKGSKEQPNFLISNRALQNPVETGKIKEFCRSKGH 92
           L LPSPIITRRTRT S                     S+RA++NP+E GK+K F RSKGH
Sbjct: 42  LQLPSPIITRRTRTAST--------------------SDRAMRNPIEEGKVKSFSRSKGH 81

Query: 93  GFITPDSGEPAVFVHISD----YVIMP 115
           GFITP++G   +FVHISD    YV +P
Sbjct: 82  GFITPNAGGDDIFVHISDIEGEYVPLP 108

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195328232|ref|XP_002030820.1| GM25657 [Drosophila sechellia] gi|195590920|ref|XP_002085192.1| GD14664 [Drosophila simulans] gi|194119763|gb|EDW41806.1| GM25657 [Drosophila sechellia] gi|194197201|gb|EDX10777.1| GD14664 [Drosophila simulans]

 Score = 79.7 bits (195), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 49/106 (46%), Positives = 60/106 (56%), Gaps = 29/106 (27%)

Query: 19  MLSPQEPHLHSNN-----TLSLPSPIITRRTRTESMDFKATAQRSKGSKEQPNFLISNRA 73
           +L+ + P LH N+     +L LPSPIITRRTRT S                     S RA
Sbjct: 10  LLAAKPPVLHHNSHSPNASLQLPSPIITRRTRTAS--------------------TSARA 49

Query: 74  LQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISD----YVIMP 115
           L+NPV TG +K F R+KGHGFITP++G   VF H+SD    YV MP
Sbjct: 50  LENPVVTGMVKSFSRTKGHGFITPNAGGEDVFCHVSDIEGEYVPMP 95

Source: Drosophila sechellia

Species: Drosophila sechellia

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|21356601|ref|NP_648920.1| CG9705, isoform A [Drosophila melanogaster] gi|24665520|ref|NP_730197.1| CG9705, isoform B [Drosophila melanogaster] gi|442632925|ref|NP_001261972.1| CG9705, isoform C [Drosophila melanogaster] gi|75027588|sp|Q9VVA0.1|Y9705_DROME RecName: Full=Cold shock domain-containing protein CG9705 gi|7294059|gb|AAF49414.1| CG9705, isoform A [Drosophila melanogaster] gi|16648430|gb|AAL25480.1| LD47312p [Drosophila melanogaster] gi|23093318|gb|AAN11740.1| CG9705, isoform B [Drosophila melanogaster] gi|220956110|gb|ACL90598.1| CG9705-PA [synthetic construct] gi|440215920|gb|AGB94665.1| CG9705, isoform C [Drosophila melanogaster]

 Score = 79.7 bits (195), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 49/106 (46%), Positives = 60/106 (56%), Gaps = 29/106 (27%)

Query: 19  MLSPQEPHLHSNN-----TLSLPSPIITRRTRTESMDFKATAQRSKGSKEQPNFLISNRA 73
           +L+ + P LH N+     +L LPSPIITRRTRT S                     S RA
Sbjct: 10  LLAAKPPVLHHNSHSPNASLQLPSPIITRRTRTAST--------------------SARA 49

Query: 74  LQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISD----YVIMP 115
           L+NPV TG +K F R+KGHGFITP++G   VF H+SD    YV MP
Sbjct: 50  LENPVVTGMVKSFSRTKGHGFITPNAGGEDVFCHVSDIEGEYVPMP 95

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|389609929|dbj|BAM18576.1| similar to CG9705 [Papilio xuthus]

 Score = 79.3 bits (194), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 44/91 (48%), Positives = 52/91 (57%), Gaps = 24/91 (26%)

Query: 29  SNNTLSLPSPIITRRTRTESMDFKATAQRSKGSKEQPNFLISNRALQNPVETGKIKEFCR 88
           +N+ L LPSPIITRR RT S                     S RAL NPVE GKIK FCR
Sbjct: 15  TNSHLQLPSPIITRRNRTAST--------------------SERALGNPVENGKIKSFCR 54

Query: 89  SKGHGFITPDSGEPAVFVHISD----YVIMP 115
            +GHG++TP+ G   +FVHISD    YV +P
Sbjct: 55  ERGHGYVTPEKGGEDLFVHISDIEGEYVPLP 85

Source: Papilio xuthus

Species: Papilio xuthus

Genus: Papilio

Family: Papilionidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|125977582|ref|XP_001352824.1| GA21978 [Drosophila pseudoobscura pseudoobscura] gi|195169856|ref|XP_002025730.1| GL20690 [Drosophila persimilis] gi|54641575|gb|EAL30325.1| GA21978 [Drosophila pseudoobscura pseudoobscura] gi|194109223|gb|EDW31266.1| GL20690 [Drosophila persimilis]

 Score = 79.0 bits (193), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 50/106 (47%), Positives = 57/106 (53%), Gaps = 29/106 (27%)

Query: 19  MLSPQEPHLHSNN-----TLSLPSPIITRRTRTESMDFKATAQRSKGSKEQPNFLISNRA 73
           MLS + P  H +N     +L LPSPIITRRTRT S                     S RA
Sbjct: 10  MLSAKPPVFHHHNNSPNASLQLPSPIITRRTRTAST--------------------SARA 49

Query: 74  LQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISD----YVIMP 115
           L+NPV TG +K F RSKGHGFI P +G   VF H+SD    YV MP
Sbjct: 50  LENPVVTGVVKSFSRSKGHGFIIPTAGGEDVFCHVSDIEGEYVPMP 95

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357603731|gb|EHJ63898.1| hypothetical protein KGM_10424 [Danaus plexippus]

 Score = 79.0 bits (193), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 47/99 (47%), Positives = 54/99 (54%), Gaps = 28/99 (28%)

Query: 21  SPQEPHLHSNNTLSLPSPIITRRTRTESMDFKATAQRSKGSKEQPNFLISNRALQNPVET 80
           SP + H H    L LPSPIITRR RT S                     S +ALQNP+E 
Sbjct: 12  SPNKSHTH----LQLPSPIITRRNRTAST--------------------SEKALQNPIEY 47

Query: 81  GKIKEFCRSKGHGFITPDSGEPAVFVHISD----YVIMP 115
           GKIK FCR KGHGF+TP  G   +F+HISD    YV +P
Sbjct: 48  GKIKSFCREKGHGFVTPLKGGEDLFLHISDIEGEYVPLP 86

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195376475|ref|XP_002047022.1| GJ13199 [Drosophila virilis] gi|194154180|gb|EDW69364.1| GJ13199 [Drosophila virilis]

 Score = 78.6 bits (192), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 49/106 (46%), Positives = 57/106 (53%), Gaps = 29/106 (27%)

Query: 19  MLSPQEPHLHSNN-----TLSLPSPIITRRTRTESMDFKATAQRSKGSKEQPNFLISNRA 73
           MLS + P  H N+     TL LPSPIITRRTRT S                     S RA
Sbjct: 10  MLSAKPPVYHQNSHSPNATLQLPSPIITRRTRTAS--------------------TSARA 49

Query: 74  LQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISD----YVIMP 115
           ++NPV +G +K F R+KGHGFITP  G   VF H+SD    YV MP
Sbjct: 50  MENPVVSGVVKSFSRTKGHGFITPHGGGEDVFCHVSDIEGEYVPMP 95

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157121173|ref|XP_001659860.1| hypothetical protein AaeL_AAEL009235 [Aedes aegypti] gi|108874689|gb|EAT38914.1| AAEL009235-PA [Aedes aegypti]

 Score = 78.2 bits (191), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 43/87 (49%), Positives = 52/87 (59%), Gaps = 24/87 (27%)

Query: 33  LSLPSPIITRRTRTESMDFKATAQRSKGSKEQPNFLISNRALQNPVETGKIKEFCRSKGH 92
           L LPSPIITRRTRT S                     S+RA++NP+E GK+K F RSKGH
Sbjct: 39  LQLPSPIITRRTRTAST--------------------SDRAMRNPIEEGKVKSFSRSKGH 78

Query: 93  GFITPDSGEPAVFVHISD----YVIMP 115
           GFI+P +G   +FVHISD    YV +P
Sbjct: 79  GFISPTAGGDDIFVHISDIEGEYVPLP 105

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195495012|ref|XP_002095086.1| GE19874 [Drosophila yakuba] gi|194181187|gb|EDW94798.1| GE19874 [Drosophila yakuba]

 Score = 77.4 bits (189), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 48/106 (45%), Positives = 58/106 (54%), Gaps = 29/106 (27%)

Query: 19  MLSPQEPHLHSNN-----TLSLPSPIITRRTRTESMDFKATAQRSKGSKEQPNFLISNRA 73
           +L+ + P  H N+     +L LPSPIITRRTRT S                     S RA
Sbjct: 10  LLAAKPPVFHHNSHSPNASLQLPSPIITRRTRTAST--------------------SARA 49

Query: 74  LQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISD----YVIMP 115
           L+NPV TG +K F R+KGHGFITP +G   VF H+SD    YV MP
Sbjct: 50  LENPVVTGIVKSFSRTKGHGFITPHAGGEDVFCHVSDIEGEYVPMP 95

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	144
FB|FBgn0036661	143	CG9705 [Drosophila melanogaste	0.319	0.321	0.6	5.5e-18
UNIPROTKB|E1C8P8	152	CARHSP1 "Uncharacterized prote	0.666	0.631	0.398	3.5e-11
UNIPROTKB|I3LCU9	158	CARHSP1 "Uncharacterized prote	0.687	0.626	0.358	2e-10
MGI|MGI:1196368	148	Carhsp1 "calcium regulated hea	0.631	0.614	0.402	2e-10
UNIPROTKB|Q2NKU4	147	CARHSP1 "Uncharacterized prote	0.652	0.639	0.385	5.2e-10
RGD|708415	147	Carhsp1 "calcium regulated hea	0.652	0.639	0.385	5.2e-10
UNIPROTKB|H3BNU9	131	CARHSP1 "Calcium-regulated hea	0.652	0.717	0.385	6.6e-10
UNIPROTKB|H3BPY5	126	CARHSP1 "Calcium-regulated hea	0.652	0.746	0.385	6.6e-10
UNIPROTKB|H3BSW7	112	CARHSP1 "Calcium-regulated hea	0.652	0.839	0.385	6.6e-10
UNIPROTKB|H3BUY4	124	CARHSP1 "Calcium-regulated hea	0.652	0.758	0.385	6.6e-10

FB|FBgn0036661 CG9705 [Drosophila melanogaster (taxid:7227)]

 Score = 146 (56.5 bits), Expect = 5.5e-18, Sum P(2) = 5.5e-18
 Identities = 30/50 (60%), Positives = 36/50 (72%)

Query:    70 SNRALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISD----YVIMP 115
             S RAL+NPV TG +K F R+KGHGFITP++G   VF H+SD    YV MP
Sbjct:    46 SARALENPVVTGMVKSFSRTKGHGFITPNAGGEDVFCHVSDIEGEYVPMP 95

GO:0005575 "cellular_component" evidence=ND

GO:0003677 "DNA binding" evidence=IEA

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

UNIPROTKB|E1C8P8 CARHSP1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 154 (59.3 bits), Expect = 3.5e-11, P = 3.5e-11
 Identities = 41/103 (39%), Positives = 55/103 (53%)

Query:    10 NKKPALSSPMLSPQEPHLHSNNTLSLPSPIITRRTRTESMD-FKATAQRSK-GSKEQPNF 67
             + +PA S+   SP    LHS ++L LP     RRTR  S    +     S   ++    +
Sbjct:     2 SSEPAASASEQSPSS--LHSPSSLHLPE---NRRTRDRSPSPMRGYLIPSPLPTRRTRTY 56

Query:    68 LISNRALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISD 110
               + RA + P+  G  K FCRSKGHGFI+P  G P +FVHISD
Sbjct:    57 SATVRASEGPIYKGVCKCFCRSKGHGFISPADGGPDIFVHISD 99

GO:0003677 "DNA binding" evidence=IEA

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

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

UNIPROTKB|I3LCU9 CARHSP1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 147 (56.8 bits), Expect = 2.0e-10, P = 2.0e-10
 Identities = 38/106 (35%), Positives = 52/106 (49%)

Query:     7 PFENKKPALSSPMLSPQEPHLHSNNTLSLPSPIITRRTRTESMD-FKATAQRSK-GSKEQ 64
             P    + A+SS    P +P  H ++       + T+R R  S    +     S   ++  
Sbjct:     5 PLSLSRSAMSSEPPPPSQPPTHQSSV-----GLDTQRARDRSPSPLRGNVVPSPLPTRRT 59

Query:    65 PNFLISNRALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISD 110
               F  + RA Q P+  G  K FCRSKGHGFITP  G P +F+HISD
Sbjct:    60 RTFSATVRASQGPIYKGVCKCFCRSKGHGFITPADGGPDIFLHISD 105

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

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

GO:0003677 "DNA binding" evidence=IEA

MGI|MGI:1196368 Carhsp1 "calcium regulated heat stable protein 1" [Mus musculus (taxid:10090)]

 Score = 147 (56.8 bits), Expect = 2.0e-10, P = 2.0e-10
 Identities = 39/97 (40%), Positives = 48/97 (49%)

Query:    16 SSPMLSPQEPHLHSNNTLSLPSPIITRRTRTESMD-FKATAQRSK-GSKEQPNFLISNRA 73
             S P   P +P  H  +   L +P    RTR  S    +     S   ++    F  + RA
Sbjct:     3 SEPPPPPLQPPTHQTSVGLLDTP----RTRDRSPSPLRGNVVPSPLPTRRTRTFSATVRA 58

Query:    74 LQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISD 110
              Q PV  G  K FCRSKGHGFITP  G P +F+HISD
Sbjct:    59 SQGPVYKGVCKCFCRSKGHGFITPADGGPDIFLHISD 95

GO:0000177 "cytoplasmic exosome (RNase complex)" evidence=IDA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

GO:0005515 "protein binding" evidence=IPI

GO:0005737 "cytoplasm" evidence=ISO

GO:0005829 "cytosol" evidence=IDA

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

GO:0043186 "P granule" evidence=IDA

GO:0043488 "regulation of mRNA stability" evidence=IMP

UNIPROTKB|Q2NKU4 CARHSP1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 143 (55.4 bits), Expect = 5.2e-10, P = 5.2e-10
 Identities = 37/96 (38%), Positives = 48/96 (50%)

Query:    15 LSSPMLSPQEPHLHSNNTLSLPSPIITRRTRTESMDFKATAQRSKGSKEQPNFLISNRAL 74
             +SS    P +P  H ++T  L +     R R+ S            ++    F  + RA 
Sbjct:     1 MSSEPPPPSQPPTHQSSTGLLDTQ--QARDRSPSPLRGNVVPSPLPTRRTRTFSATVRAS 58

Query:    75 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISD 110
             Q PV  G  K FCRSKGHGFITP  G P +F+HISD
Sbjct:    59 QGPVYKGVCKCFCRSKGHGFITPADGGPDIFLHISD 94

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

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

GO:0003677 "DNA binding" evidence=IEA

RGD|708415 Carhsp1 "calcium regulated heat stable protein 1" [Rattus norvegicus (taxid:10116)]

 Score = 143 (55.4 bits), Expect = 5.2e-10, P = 5.2e-10
 Identities = 37/96 (38%), Positives = 47/96 (48%)

Query:    15 LSSPMLSPQEPHLHSNNTLSLPSPIITRRTRTESMDFKATAQRSKGSKEQPNFLISNRAL 74
             +SS    P +P  H  +   L +P    R R+ S            ++    F  + RA 
Sbjct:     1 MSSEPPPPPQPPTHQTSIGLLDTP--RARDRSPSPLRGNVVPSPLPTRRTRTFSATVRAS 58

Query:    75 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISD 110
             Q PV  G  K FCRSKGHGFITP  G P +F+HISD
Sbjct:    59 QGPVYKGVCKCFCRSKGHGFITPADGGPDIFLHISD 94

GO:0000177 "cytoplasmic exosome (RNase complex)" evidence=ISO;ISS

GO:0000932 "cytoplasmic mRNA processing body" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005737 "cytoplasm" evidence=IDA

GO:0005829 "cytosol" evidence=ISO;ISS

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

GO:0019722 "calcium-mediated signaling" evidence=NAS

GO:0043186 "P granule" evidence=ISO;ISS

GO:0043488 "regulation of mRNA stability" evidence=ISO;ISS

UNIPROTKB|H3BNU9 CARHSP1 "Calcium-regulated heat stable protein 1" [Homo sapiens (taxid:9606)]

 Score = 142 (55.0 bits), Expect = 6.6e-10, P = 6.6e-10
 Identities = 37/96 (38%), Positives = 47/96 (48%)

Query:    15 LSSPMLSPQEPHLHSNNTLSLPSPIITRRTRTESMDFKATAQRSKGSKEQPNFLISNRAL 74
             +SS    P +P  H  +   L +P    R R+ S            ++    F  + RA 
Sbjct:     1 MSSEPPPPPQPPTHQASVGLLDTP--RSRERSPSPLRGNVVPSPLPTRRTRTFSATVRAS 58

Query:    75 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISD 110
             Q PV  G  K FCRSKGHGFITP  G P +F+HISD
Sbjct:    59 QGPVYKGVCKCFCRSKGHGFITPADGGPDIFLHISD 94

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005737 "cytoplasm" evidence=IEA

UNIPROTKB|H3BPY5 CARHSP1 "Calcium-regulated heat stable protein 1" [Homo sapiens (taxid:9606)]

 Score = 142 (55.0 bits), Expect = 6.6e-10, P = 6.6e-10
 Identities = 37/96 (38%), Positives = 47/96 (48%)

Query:    15 LSSPMLSPQEPHLHSNNTLSLPSPIITRRTRTESMDFKATAQRSKGSKEQPNFLISNRAL 74
             +SS    P +P  H  +   L +P    R R+ S            ++    F  + RA 
Sbjct:     1 MSSEPPPPPQPPTHQASVGLLDTP--RSRERSPSPLRGNVVPSPLPTRRTRTFSATVRAS 58

Query:    75 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISD 110
             Q PV  G  K FCRSKGHGFITP  G P +F+HISD
Sbjct:    59 QGPVYKGVCKCFCRSKGHGFITPADGGPDIFLHISD 94

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005737 "cytoplasm" evidence=IEA

UNIPROTKB|H3BSW7 CARHSP1 "Calcium-regulated heat stable protein 1" [Homo sapiens (taxid:9606)]

 Score = 142 (55.0 bits), Expect = 6.6e-10, P = 6.6e-10
 Identities = 37/96 (38%), Positives = 47/96 (48%)

Query:    15 LSSPMLSPQEPHLHSNNTLSLPSPIITRRTRTESMDFKATAQRSKGSKEQPNFLISNRAL 74
             +SS    P +P  H  +   L +P    R R+ S            ++    F  + RA 
Sbjct:     1 MSSEPPPPPQPPTHQASVGLLDTP--RSRERSPSPLRGNVVPSPLPTRRTRTFSATVRAS 58

Query:    75 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISD 110
             Q PV  G  K FCRSKGHGFITP  G P +F+HISD
Sbjct:    59 QGPVYKGVCKCFCRSKGHGFITPADGGPDIFLHISD 94

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005737 "cytoplasm" evidence=IEA

UNIPROTKB|H3BUY4 CARHSP1 "Calcium-regulated heat stable protein 1" [Homo sapiens (taxid:9606)]

 Score = 142 (55.0 bits), Expect = 6.6e-10, P = 6.6e-10
 Identities = 37/96 (38%), Positives = 47/96 (48%)

Query:    15 LSSPMLSPQEPHLHSNNTLSLPSPIITRRTRTESMDFKATAQRSKGSKEQPNFLISNRAL 74
             +SS    P +P  H  +   L +P    R R+ S            ++    F  + RA 
Sbjct:     1 MSSEPPPPPQPPTHQASVGLLDTP--RSRERSPSPLRGNVVPSPLPTRRTRTFSATVRAS 58

Query:    75 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISD 110
             Q PV  G  K FCRSKGHGFITP  G P +F+HISD
Sbjct:    59 QGPVYKGVCKCFCRSKGHGFITPADGGPDIFLHISD 94

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005737 "cytoplasm" evidence=IEA

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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	144
cd04458	65	cd04458, CSP_CDS, Cold-Shock Protein (CSP) contain	1e-11
COG1278	67	COG1278, CspC, Cold shock proteins [Transcription]	3e-09
pfam00313	66	pfam00313, CSD, 'Cold-shock' DNA-binding domain	3e-08
smart00357	64	smart00357, CSP, Cold shock protein domain	4e-06
PRK10354	70	PRK10354, PRK10354, RNA chaperone/anti-terminator;	4e-05
PRK09507	69	PRK09507, cspE, cold shock protein CspE; Reviewed	8e-05
TIGR02381	68	TIGR02381, cspD, cold shock domain protein CspD	8e-05
PRK10943	69	PRK10943, PRK10943, cold shock-like protein CspC;	1e-04
PRK09890	70	PRK09890, PRK09890, cold shock protein CspG; Provi	3e-04
PRK14998	73	PRK14998, PRK14998, cold shock-like protein CspD;	0.001
PRK15464	70	PRK15464, PRK15464, cold shock-like protein CspH;	0.003

>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 = 56.0 bits (136), Expect = 1e-11
 Identities = 19/31 (61%), Positives = 20/31 (64%)

Query: 80  TGKIKEFCRSKGHGFITPDSGEPAVFVHISD 110
           TG +K F   KG GFITPD G   VFVHIS 
Sbjct: 2   TGTVKWFDDEKGFGFITPDDGGEDVFVHISA 32

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 = 49.8 bits (120), Expect = 3e-09
 Identities = 18/31 (58%), Positives = 21/31 (67%)

Query: 79  ETGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
            TG +K F  +KG GFITP+ G   VFVHIS
Sbjct: 2   ATGTVKWFNATKGFGFITPEDGGKDVFVHIS 32

Length = 67

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

 Score = 47.2 bits (113), Expect = 3e-08
 Identities = 17/33 (51%), Positives = 20/33 (60%)

Query: 79  ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDY 111
            TG +K F   KG GFITP+ G+  VFVH S  
Sbjct: 1   MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAI 33

Length = 66

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

 Score = 41.4 bits (98), Expect = 4e-06
 Identities = 17/32 (53%), Positives = 19/32 (59%), Gaps = 2/32 (6%)

Query: 80  TGKIKEFCRSKGHGFITPDSGEPAVFVHISDY 111
           TG +K F  +KG GFI PD G   VFVH S  
Sbjct: 1   TGVVKWF--NKGFGFIRPDDGGKDVFVHPSQI 30

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

 Score = 39.2 bits (91), Expect = 4e-05
 Identities = 18/30 (60%), Positives = 19/30 (63%)

Query: 80  TGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
           TG +K F   KG GFITPD G   VFVH S
Sbjct: 6   TGIVKWFNADKGFGFITPDDGSKDVFVHFS 35

Length = 70

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

 Score = 38.5 bits (89), Expect = 8e-05
 Identities = 17/29 (58%), Positives = 19/29 (65%)

Query: 81  GKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
           G +K F  SKG GFITP+ G   VFVH S
Sbjct: 6   GNVKWFNESKGFGFITPEDGSKDVFVHFS 34

Length = 69

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

 Score = 38.3 bits (89), Expect = 8e-05
 Identities = 12/32 (37%), Positives = 18/32 (56%)

Query: 78  VETGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
           +  G +K F  +KG GFI P+  +  +F H S
Sbjct: 1   MAIGIVKWFNNAKGFGFICPEGVDGDIFAHYS 32

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

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

 Score = 37.7 bits (87), Expect = 1e-04
 Identities = 17/29 (58%), Positives = 19/29 (65%)

Query: 81  GKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
           G++K F  SKG GFITP  G   VFVH S
Sbjct: 6   GQVKWFNESKGFGFITPADGSKDVFVHFS 34

Length = 69

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

 Score = 37.1 bits (85), Expect = 3e-04
 Identities = 17/30 (56%), Positives = 19/30 (63%)

Query: 80  TGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
           TG +K F   KG GFITPD G   VFVH +
Sbjct: 6   TGLVKWFNADKGFGFITPDDGSKDVFVHFT 35

Length = 70

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

 Score = 35.4 bits (81), Expect = 0.001
 Identities = 15/32 (46%), Positives = 20/32 (62%)

Query: 78  VETGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
           +ETG +K F  +KG GFI P+ G   +F H S
Sbjct: 1   METGTVKWFNNAKGFGFICPEGGGEDIFAHYS 32

Length = 73

>gnl|CDD|185361 PRK15464, PRK15464, cold shock-like protein CspH; Provisional

 Score = 34.3 bits (78), Expect = 0.003
 Identities = 19/44 (43%), Positives = 23/44 (52%), Gaps = 6/44 (13%)

Query: 80  TGKIKEFCRSKGHGFITPDSGEPAVFVHISDY------VIMPKL 117
           TG +K F R  G GFI P  G   V VHIS +      V++P L
Sbjct: 6   TGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGL 49

Length = 70

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	144
COG1278	67	CspC Cold shock proteins [Transcription]	99.82
PRK09937	74	stationary phase/starvation inducible regulatory p	99.8
PRK14998	73	cold shock-like protein CspD; Provisional	99.8
TIGR02381	68	cspD cold shock domain protein CspD. This model re	99.79
PRK09507	69	cspE cold shock protein CspE; Reviewed	99.78
PRK15464	70	cold shock-like protein CspH; Provisional	99.78
PRK10943	69	cold shock-like protein CspC; Provisional	99.78
PRK15463	70	cold shock-like protein CspF; Provisional	99.78
PRK09890	70	cold shock protein CspG; Provisional	99.77
PRK10354	70	RNA chaperone/anti-terminator; Provisional	99.75
cd04458	65	CSP_CDS Cold-Shock Protein (CSP) contains an S1-li	99.64
PF00313	66	CSD: 'Cold-shock' DNA-binding domain; InterPro: IP	99.63
KOG3070|consensus	235		99.21
smart00357	64	CSP Cold shock protein domain. RNA-binding domain	98.37
PF08206	58	OB_RNB: Ribonuclease B OB domain; InterPro: IPR013	96.61
PF14444	58	S1-like: S1-like	96.07
PF07497	78	Rho_RNA_bind: Rho termination factor, RNA-binding	95.0
cd04459	68	Rho_CSD Rho_CSD: Rho protein cold-shock domain (CS	94.51
PRK11642	813	exoribonuclease R; Provisional	89.41
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	88.77
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	84.29
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	83.87
PRK05054	644	exoribonuclease II; Provisional	82.83
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	81.62

>COG1278 CspC Cold shock proteins [Transcription]

Probab=99.82  E-value=1.5e-20  Score=130.00  Aligned_cols=61  Identities=36%  Similarity=0.499  Sum_probs=51.4

Q ss_pred             ccccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceec-----eeeeCCccccccccee
Q psy3660          78 VETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQIN-----KALQGSKTCNSCNISS  138 (144)
Q Consensus        78 ~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~G-----d~V~g~kg~~a~~i~~  138 (144)
                      |.+|+|||||..||||||+++++++|||||+|+|+...-..+..|     ++++|.||.+|.||..
T Consensus         1 ~~~GtVKwfn~~KGfGFI~p~~G~~DvFVH~Sai~~~g~~~L~eGQ~V~f~~~~g~kgp~A~nv~~   66 (67)
T COG1278           1 MATGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRAGFRTLREGQKVEFEVEQGRKGPSAANVRA   66 (67)
T ss_pred             CCcceEEEeeCCCcceEcCCCCCCcCEEEEeeeeccCCCcccCCCCEEEEEEecCCCCCceeEEEe
Confidence            468999999999999999999999999999999987643444444     5668899999999864

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

Probab=99.80  E-value=6.1e-20  Score=128.10  Aligned_cols=64  Identities=31%  Similarity=0.508  Sum_probs=54.8

Q ss_pred             ccccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceee-----eCCcccccccceeeec
Q psy3660          78 VETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKAL-----QGSKTCNSCNISSVEL  141 (144)
Q Consensus        78 ~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V-----~g~kg~~a~~i~~~~~  141 (144)
                      |.+|+|||||..||||||+++++++|||||+++|+....+.++.||.|     ++++|.+|.+|..++.
T Consensus         1 M~~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~g~~~l~~G~~V~f~~~~~~~G~~A~~V~~~~~   69 (74)
T PRK09937          1 MEKGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKGNHASVIVPVEV   69 (74)
T ss_pred             CCCeEEEEEeCCCCeEEEeeCCCCccEEEEEeeccccCCCCCCCCCEEEEEEEECCCCceeeEEEECCc
Confidence            457999999999999999999999999999999987633667777655     7889999999987753

>PRK14998 cold shock-like protein CspD; Provisional

Probab=99.80  E-value=8.9e-20  Score=126.87  Aligned_cols=65  Identities=31%  Similarity=0.492  Sum_probs=55.2

Q ss_pred             ccccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceee-----eCCcccccccceeeecC
Q psy3660          78 VETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKAL-----QGSKTCNSCNISSVELG  142 (144)
Q Consensus        78 ~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V-----~g~kg~~a~~i~~~~~~  142 (144)
                      |.+|+|||||..||||||+++++++|||||+++|+...-+.+..|+.|     ++.+|.+|.+|..++.+
T Consensus         1 M~~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~g~~~l~~G~~V~f~~~~~~~G~~A~~V~~~~~~   70 (73)
T PRK14998          1 METGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASVIVPIEAE   70 (73)
T ss_pred             CCCeEEEEEeCCCceEEEecCCCCccEEEEeeeecccCCCCCCCCCEEEEEEEECCCCceeEEEEECccc
Confidence            458999999999999999999999999999999987633666666655     78899999999877654

>TIGR02381 cspD cold shock domain protein CspD

Probab=99.79  E-value=8.8e-20  Score=124.60  Aligned_cols=63  Identities=27%  Similarity=0.450  Sum_probs=53.0

Q ss_pred             ccccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceee-----eCCcccccccceeee
Q psy3660          78 VETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKAL-----QGSKTCNSCNISSVE  140 (144)
Q Consensus        78 ~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V-----~g~kg~~a~~i~~~~  140 (144)
                      |.+|+|||||..||||||.++++++|||||+++|+....+.++.||.|     ++.+|.+|.+|+.++
T Consensus         1 m~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~g~~~l~~G~~V~f~~~~~~~G~~A~~V~~~~   68 (68)
T TIGR02381         1 MAIGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDGYRTLKAGQKVQFEVVQGPKGAHATHIVPIE   68 (68)
T ss_pred             CCCeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhcCCCCCCCCCEEEEEEEECCCCceeEEEEECC
Confidence            457999999999999999999999999999999987633666777766     678888998887653

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.

>PRK09507 cspE cold shock protein CspE; Reviewed

Probab=99.78  E-value=2.4e-19  Score=123.00  Aligned_cols=61  Identities=33%  Similarity=0.458  Sum_probs=51.7

Q ss_pred             ccccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceee-----eCCccccccccee
Q psy3660          78 VETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKAL-----QGSKTCNSCNISS  138 (144)
Q Consensus        78 ~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V-----~g~kg~~a~~i~~  138 (144)
                      ..+|+|||||..||||||+++++++|||||+++|+...-+.++.||.|     ++.+|.+|.+|..
T Consensus         3 ~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f~~~~~~~G~~A~~V~~   68 (69)
T PRK09507          3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIA   68 (69)
T ss_pred             ccceEEEEEeCCCCcEEEecCCCCeeEEEEeecccccCCCCCCCCCEEEEEEEECCCCcccEEEEe
Confidence            468999999999999999999999999999999987633677777766     6677788887754

>PRK15464 cold shock-like protein CspH; Provisional

Probab=99.78  E-value=2e-19  Score=124.45  Aligned_cols=58  Identities=31%  Similarity=0.465  Sum_probs=49.2

Q ss_pred             cccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceee-----eCCcccccccc
Q psy3660          79 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKAL-----QGSKTCNSCNI  136 (144)
Q Consensus        79 ~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V-----~g~kg~~a~~i  136 (144)
                      ++|+|||||..||||||+++++++|||||+++|+...-+.++.||.|     ++.+|.+|.+|
T Consensus         5 ~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~g~~~l~~G~~V~f~v~~~~kG~~A~~v   67 (70)
T PRK15464          5 MTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAANV   67 (70)
T ss_pred             ceEEEEEEECCCCeEEEccCCCCccEEEEehhehhcCCCCCCCCCEEEEEEEECCCCceeEEE
Confidence            48999999999999999999999999999999987734467777766     56677777776

>PRK10943 cold shock-like protein CspC; Provisional

Probab=99.78  E-value=1.9e-19  Score=123.55  Aligned_cols=60  Identities=33%  Similarity=0.432  Sum_probs=50.6

Q ss_pred             ccccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceee-----eCCcccccccce
Q psy3660          78 VETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKAL-----QGSKTCNSCNIS  137 (144)
Q Consensus        78 ~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V-----~g~kg~~a~~i~  137 (144)
                      +++|+|||||..||||||+++++++|||||+++|+....+.++.||.|     ++.+|.+|.+|.
T Consensus         3 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~g~~~l~~G~~V~f~~~~~~~g~~A~~V~   67 (69)
T PRK10943          3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKGPAAVNVT   67 (69)
T ss_pred             ccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHccccCCCCCCCCCEEEEEEEECCCCceeEEEE
Confidence            578999999999999999999999999999999987733667777766     667777777774

>PRK15463 cold shock-like protein CspF; Provisional

Probab=99.78  E-value=1.9e-19  Score=124.22  Aligned_cols=58  Identities=29%  Similarity=0.398  Sum_probs=48.2

Q ss_pred             cccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceee-----eCCcccccccc
Q psy3660          79 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKAL-----QGSKTCNSCNI  136 (144)
Q Consensus        79 ~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V-----~g~kg~~a~~i  136 (144)
                      ++|+|||||..||||||+++++++|||||+++|+....+.|+.||.|     ++.+|.+|.+|
T Consensus         5 ~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~g~~~l~~G~~V~f~v~~~~~G~~A~~V   67 (70)
T PRK15463          5 MTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRINGLRGPTAANV   67 (70)
T ss_pred             ceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhcCCCCCCCCCEEEEEEEECCCCceeEEE
Confidence            48999999999999999999999999999999987655667777766     55556666555

>PRK09890 cold shock protein CspG; Provisional

Probab=99.77  E-value=5e-19  Score=121.73  Aligned_cols=60  Identities=35%  Similarity=0.496  Sum_probs=50.9

Q ss_pred             cccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceee-----eCCccccccccee
Q psy3660          79 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKAL-----QGSKTCNSCNISS  138 (144)
Q Consensus        79 ~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V-----~g~kg~~a~~i~~  138 (144)
                      ++|+|||||..||||||+++++++|||||+++|+....+.++.||.|     ++.+|.+|.+|..
T Consensus         5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~~~~~l~~G~~V~f~~~~~~~G~~A~~V~~   69 (70)
T PRK09890          5 MTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRGPAAANVVT   69 (70)
T ss_pred             ceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccCCCCCCCCCCEEEEEEEECCCCceeEEEEe
Confidence            48999999999999999999999999999999987744667777766     6677888888753

>PRK10354 RNA chaperone/anti-terminator; Provisional

Probab=99.75  E-value=1.3e-18  Score=119.36  Aligned_cols=59  Identities=36%  Similarity=0.460  Sum_probs=49.7

Q ss_pred             cccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceee-----eCCcccccccce
Q psy3660          79 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKAL-----QGSKTCNSCNIS  137 (144)
Q Consensus        79 ~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V-----~g~kg~~a~~i~  137 (144)
                      ++|+|||||..||||||.++++++|||||+++|+....+.++.||.|     ++.+|.+|.+|.
T Consensus         5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f~~~~~~~G~~A~~V~   68 (70)
T PRK10354          5 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVT   68 (70)
T ss_pred             ceEEEEEEeCCCCcEEEecCCCCccEEEEEeeccccCCCCCCCCCEEEEEEEECCCCceeEEEE
Confidence            38999999999999999999999999999999988744677888877     456666777664

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

Probab=99.64  E-value=2.3e-16  Score=104.80  Aligned_cols=58  Identities=36%  Similarity=0.413  Sum_probs=48.8

Q ss_pred             cccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceeeeC-----Ccccccccc
Q psy3660          79 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKALQG-----SKTCNSCNI  136 (144)
Q Consensus        79 ~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V~g-----~kg~~a~~i  136 (144)
                      .+|+|||||..||||||+++++++|||||++++.....+.++.||.|++     .+|.+|.+|
T Consensus         1 ~~G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~~~~~~~~G~~V~f~~~~~~~g~~A~~V   63 (65)
T cd04458           1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNV   63 (65)
T ss_pred             CcEEEEEEECCCCeEEEecCCCCcCEEEEhhHhhccCCCcCCCCCEEEEEEEECCCCCeEEEe
Confidence            3799999999999999999998899999999999875677888887755     555566555

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=99.63  E-value=2.7e-16  Score=104.74  Aligned_cols=60  Identities=33%  Similarity=0.426  Sum_probs=48.4

Q ss_pred             cccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceeee-----CCccccccccee
Q psy3660          79 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKALQ-----GSKTCNSCNISS  138 (144)
Q Consensus        79 ~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V~-----g~kg~~a~~i~~  138 (144)
                      ++|+||||+..||||||.++++++|||||++++....-+.+..||.|+     +.+|.+|.+|..
T Consensus         1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~~~~~l~~G~~V~F~~~~~~~g~~A~~V~~   65 (66)
T PF00313_consen    1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGNGFRSLKEGDRVEFEVEEGKKGPQAVNVRK   65 (66)
T ss_dssp             EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSSSSTS--TTSEEEEEEEECTTSEEEEEEEE
T ss_pred             CeEEEEEEECCCCceEEEEcccceeEEeccccccccccccCCCCCEEEEEEEECCCCCEEEEEEC
Confidence            479999999999999999999999999999999888336777777775     566677776643

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 ....

>KOG3070|consensus

Probab=99.21  E-value=1.5e-11  Score=102.01  Aligned_cols=65  Identities=31%  Similarity=0.376  Sum_probs=50.7

Q ss_pred             cccCCcccccEEEEccCCCceeEecCCCCCCcEEEEeecccc----CC-----CccceeceeeeCCcccccccc
Q psy3660          72 RALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVI----MP-----KLISQINKALQGSKTCNSCNI  136 (144)
Q Consensus        72 r~~~~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~----~~-----g~~p~~Gd~V~g~kg~~a~~i  136 (144)
                      +.......+|+|||||..+|||||.++|+.+|||||+++|..    ..     .+....-+++.+.+|..|.++
T Consensus        50 ~~~~~~~~~G~~k~fnv~~G~gFi~~~d~~~D~fvhQs~i~~~~~~~~~rs~~~~e~v~f~~~~~~~g~~a~~v  123 (235)
T KOG3070|consen   50 KKVQGARVKGTVKWFNVGKGYGFITRDDGPEDVFVHQSAITKYTPSEGFRSLKEGEAVPFDIQEGNKGTEAANV  123 (235)
T ss_pred             cccccccccCcceeEeccCCcceecccCCCCceeEEeeeecccccccchhhcccCCCccceecccCccceeeee
Confidence            455667889999999999999999999999999999999988    21     122234467778888555554

>smart00357 CSP Cold shock protein domain

Probab=98.37  E-value=3.7e-07  Score=58.21  Aligned_cols=46  Identities=37%  Similarity=0.446  Sum_probs=35.1

Q ss_pred             ccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceeeeCC
Q psy3660          80 TGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKALQGS  128 (144)
Q Consensus        80 ~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V~g~  128 (144)
                      +|+|+|++  +|||||.+++...|+|||.+.++. ....+..||.|.+.
T Consensus         1 ~G~i~~~~--~g~gfv~~~~~~~~i~v~~~~~~~-~~~~~~~Gd~V~~~   46 (64)
T smart00357        1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQG-GLKSLREGDEVEFK   46 (64)
T ss_pred             CeEEEEEc--CCeeEEecCCCCccEEEEhHHhhc-CCCcCCCCCEEEEE
Confidence            58999998  799999998766799999998755 23445556666554

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=96.61  E-value=0.0013  Score=43.31  Aligned_cols=39  Identities=26%  Similarity=0.439  Sum_probs=26.0

Q ss_pred             cEEEEccCCCceeEecCCCCCCcEEEEeeccccC-CCcccee
Q psy3660          81 GKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIM-PKLISQI  121 (144)
Q Consensus        81 GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~-~g~~p~~  121 (144)
                      |+++.  ..+||||+.+++.++||||....+... .|+++.+
T Consensus         1 G~~~~--~~~GfGFv~~~~~~~DifIp~~~l~~A~~gD~V~v   40 (58)
T PF08206_consen    1 GTLKI--HPKGFGFVIPDDGGEDIFIPPRNLNGAMDGDKVLV   40 (58)
T ss_dssp             EEEEE---SSS-EEEEECT-TEEEEE-HHHHTTS-TT-EEEE
T ss_pred             CEEEE--EcCCCEEEEECCCCCCEEECHHHHCCCCCCCEEEE
Confidence            44444  479999999999889999999998764 3555544

; PDB: 2ID0_D 2IX1_A 2IX0_A.

>PF14444 S1-like: S1-like

Probab=96.07  E-value=0.006  Score=41.46  Aligned_cols=45  Identities=22%  Similarity=0.369  Sum_probs=35.8

Q ss_pred             ccccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceeeeCCcccc
Q psy3660          78 VETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKALQGSKTCN  132 (144)
Q Consensus        78 ~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V~g~kg~~  132 (144)
                      ..+|.|..++  ..||||.     +||||+.++++   |..|++||.|...-.+|
T Consensus         3 ~~~GvVTkl~--~~yG~ID-----e~vFF~~~vv~---G~~P~vGdrV~v~A~~n   47 (58)
T PF14444_consen    3 VFTGVVTKLC--DDYGFID-----EDVFFQTDVVK---GNVPKVGDRVLVEAIYN   47 (58)
T ss_pred             eEEEEEEEEe--CCcceEc-----ccEEEEcccEe---cCCCccCCEEEEEEEeC
Confidence            3589999997  5799995     68999999966   67889999997654443

>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=95.00  E-value=0.02  Score=40.68  Aligned_cols=37  Identities=19%  Similarity=0.334  Sum_probs=24.8

Q ss_pred             CCceeEecCC-----CCCCcEEEEeeccccCCCccceeceeeeCC
Q psy3660          89 SKGHGFITPD-----SGEPAVFVHISDYVIMPKLISQINKALQGS  128 (144)
Q Consensus        89 ~KGfGFI~~d-----~gg~DVFVHiSai~~~~g~~p~~Gd~V~g~  128 (144)
                      .+||||+...     .+.+||||-.+.|+.- +  ++.||.|.|.
T Consensus        11 ~dGyGFLR~~~~~y~~~~~DvYVs~~qIrrf-~--LR~GD~V~G~   52 (78)
T PF07497_consen   11 PDGYGFLRSPDNNYLPSPDDVYVSPSQIRRF-G--LRTGDLVEGQ   52 (78)
T ss_dssp             TTS-EEEE-GGGTTS-STTSEEE-CCCCCCT-T----TTEEEEEE
T ss_pred             CCCcEEeECCCcCCCCCCCCEEECHHHHHHc-C--CCCCCEEEEE
Confidence            4799999987     3568999999999876 3  5667777654

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 ....

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

Probab=94.51  E-value=0.02  Score=39.60  Aligned_cols=36  Identities=19%  Similarity=0.429  Sum_probs=28.5

Q ss_pred             CceeEecCC-----CCCCcEEEEeeccccCCCccceeceeeeCC
Q psy3660          90 KGHGFITPD-----SGEPAVFVHISDYVIMPKLISQINKALQGS  128 (144)
Q Consensus        90 KGfGFI~~d-----~gg~DVFVHiSai~~~~g~~p~~Gd~V~g~  128 (144)
                      +||||+...     .+.+||||..+-|+.- +  +..||.|.|.
T Consensus        10 ~g~GFLR~~~~~y~~~~~DvyVs~~~Irr~-~--LR~GD~V~G~   50 (68)
T cd04459          10 DGFGFLRSSGYNYLPGPDDIYVSPSQIRRF-N--LRTGDTVVGQ   50 (68)
T ss_pred             CCceEEecCCcCCCCCCCCEEECHHHHHHh-C--CCCCCEEEEE
Confidence            499999976     2568999999999887 4  5667888774

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.

>PRK11642 exoribonuclease R; Provisional

Probab=89.41  E-value=0.5  Score=45.65  Aligned_cols=44  Identities=9%  Similarity=0.160  Sum_probs=33.5

Q ss_pred             cccccEEEEccCCCceeEecCCCCCCcEEEEeeccccC-CCccceec
Q psy3660          77 PVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIM-PKLISQIN  122 (144)
Q Consensus        77 ~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~-~g~~p~~G  122 (144)
                      ..+.|+|+.  ..+||||+.++++++||||.-..+... .||++.+-
T Consensus        83 ~~~~G~v~~--~~~GfgFv~~e~~~~difI~~~~l~~A~~GD~V~v~  127 (813)
T PRK11642         83 DLLKGTVIG--HRDGYGFLRVEGRKDDLYLSSEQMKTCIHGDQVLAQ  127 (813)
T ss_pred             ceEEEEEEE--CCCccEEEEECCCCCCEEEChHHHccCCCCCEEEEE
Confidence            357899996  679999999987678999988776543 36666543

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

Probab=88.77  E-value=0.75  Score=43.09  Aligned_cols=43  Identities=21%  Similarity=0.403  Sum_probs=32.5

Q ss_pred             cccccEEEEccCCCceeEecCCC-CCCcEEEEeeccccC-CCcccee
Q psy3660          77 PVETGKIKEFCRSKGHGFITPDS-GEPAVFVHISDYVIM-PKLISQI  121 (144)
Q Consensus        77 ~~~~GtVK~Fd~~KGfGFI~~d~-gg~DVFVHiSai~~~-~g~~p~~  121 (144)
                      ....|++++  ..|||||+.+++ +++||||.-..+... .||++.+
T Consensus        15 ~~~~G~i~~--~~~gfgFv~~~~~~~~difI~~~~~~~a~~GD~V~v   59 (654)
T TIGR00358        15 DLVKGVVKA--HNKGFGFLRPDDDDKKDYFIPPPQMKKVMHGDLVEA   59 (654)
T ss_pred             CeEEEEEEE--CCCccEEEEeCCCCCCcEEEchHHhCcCCCCCEEEE
Confidence            457899997  579999999986 368999987776442 3666644

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.

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

Probab=84.29  E-value=1.3  Score=28.88  Aligned_cols=51  Identities=16%  Similarity=0.208  Sum_probs=38.1

Q ss_pred             cCCcccccEEEEccCCCceeEecCCCCCCcEEEEeecccc----CCCccceeceeeeC
Q psy3660          74 LQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVI----MPKLISQINKALQG  127 (144)
Q Consensus        74 ~~~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~----~~g~~p~~Gd~V~g  127 (144)
                      ..++.+.|+|...+.   +|++-.-+.+-+.|+|.+.+..    .+.....+||.|..
T Consensus         3 ~~G~iv~g~V~~v~~---~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v   57 (74)
T PF00575_consen    3 KEGDIVEGKVTSVED---FGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRV   57 (74)
T ss_dssp             STTSEEEEEEEEEET---TEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEE
T ss_pred             CCCCEEEEEEEEEEC---CEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEE
Confidence            457788999999876   5555544466899999999874    35677788887754

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=83.87  E-value=1  Score=42.23  Aligned_cols=44  Identities=23%  Similarity=0.317  Sum_probs=32.0

Q ss_pred             CCcccccEEEEccCCCceeEecCCCCCCcEEEEeeccccC-CCcccee
Q psy3660          75 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIM-PKLISQI  121 (144)
Q Consensus        75 ~~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~-~g~~p~~  121 (144)
                      ......|++++  ..|||||+..++ .+||||.-..+... .||++.+
T Consensus        15 ~~~~~~G~i~~--~~kGfgFv~~~~-~~difI~~~~l~~A~~GD~V~v   59 (639)
T TIGR02062        15 QTPRVEGVVKA--TEKGFGFLEVDA-QKSYFIPPPQMKKVMHGDKIIA   59 (639)
T ss_pred             cCceEEEEEEE--CCCccEEEEECC-CCcEEEChHHHccCCCCCEEEE
Confidence            34567799997  679999996554 46999988876543 3666644

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=82.83  E-value=1.2  Score=41.83  Aligned_cols=43  Identities=21%  Similarity=0.301  Sum_probs=31.9

Q ss_pred             CcccccEEEEccCCCceeEecCCCCCCcEEEEeeccccC-CCcccee
Q psy3660          76 NPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIM-PKLISQI  121 (144)
Q Consensus        76 ~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~-~g~~p~~  121 (144)
                      .....|++++  ..|||||+.+++ .+||||.-..+... .||++.+
T Consensus        19 ~~~~~G~~~~--~~~gfgFv~~~~-~~difI~~~~l~~a~~GD~V~v   62 (644)
T PRK05054         19 TPRVEGVVKA--TEKGFGFLEVDA-QKSYFIPPPQMKKVMHGDRIIA   62 (644)
T ss_pred             CCeEEEEEEE--CCCccEEEEECC-CCcEEEChHHHccCCCCCEEEE
Confidence            3457799997  579999998754 46999988887543 3666644

>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=81.62  E-value=1.4  Score=29.77  Aligned_cols=54  Identities=11%  Similarity=0.015  Sum_probs=38.9

Q ss_pred             ccCCcccccEEEEccCCCceeEecCCCCCCcEEEEeeccccC----CCccceeceeeeCCc
Q psy3660          73 ALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIM----PKLISQINKALQGSK  129 (144)
Q Consensus        73 ~~~~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~----~g~~p~~Gd~V~g~k  129 (144)
                      +..+..+.|+|+....   ||++-.-.++-+.|+|++.+...    +.+...+||.|....
T Consensus        12 ~~~G~i~~g~V~~v~~---~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV   69 (83)
T cd04461          12 LKPGMVVHGYVRNITP---YGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKV   69 (83)
T ss_pred             CCCCCEEEEEEEEEee---ceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEE
Confidence            5567889999998764   77766654557999999998543    244457788876543

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	144
3aqq_A	147	Crystal Structure Of Human Crhsp-24 Length = 147		8e-12
2bh8_A	101	Combinatorial Protein 1b11 Length = 101		1e-04
2l15_A	70	Solution Structure Of Cold Shock Protein Cspa Using		3e-04
1mjc_A	69	Crystal Structure Of Cspa, The Major Cold Shock Pro		3e-04
3mef_A	69	Major Cold-Shock Protein From Escherichia Coli Solu		3e-04
3i2z_B	71	Structure Of Cold Shock Protein E From Salmonella T		7e-04

>pdb|3AQQ|A Chain A, Crystal Structure Of Human Crhsp-24 Length = 147

Iteration: 1
 Score = 65.9 bits (159), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 38/76 (50%), Positives = 42/76 (55%), Gaps = 20/76 (26%)
Query: 35  LPSPIITRRTRTESMDFKATAQRSKGSKEQPNFLISNRALQNPVETGKIKEFCRSKGHGF 94
           +PSP+ TRRTRT    F AT                 RA Q PV  G  K FCRSKGHGF
Sbjct: 39  VPSPLPTRRTRT----FSATV----------------RASQGPVYKGVCKCFCRSKGHGF 78
Query: 95  ITPDSGEPAVFVHISD 110
           ITP  G P +F+HISD
Sbjct: 79  ITPADGGPDIFLHISD 94

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/36 (55%), Positives = 22/36 (61%)
Query: 74  LQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
           LQ+   TG +K F   KG GFITPD G   VFVH S
Sbjct: 12  LQSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFS 47

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

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 18/30 (60%), Positives = 19/30 (63%)
Query: 80  TGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
           TG +K F   KG GFITPD G   VFVH S
Sbjct: 6   TGIVKWFNADKGFGFITPDDGSKDVFVHFS 35

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

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 18/30 (60%), Positives = 19/30 (63%)
Query: 80  TGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
           TG +K F   KG GFITPD G   VFVH S
Sbjct: 5   TGIVKWFNADKGFGFITPDDGSKDVFVHFS 34

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

Iteration: 1
 Score = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 18/30 (60%), Positives = 19/30 (63%)
Query: 80  TGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
           TG +K F   KG GFITPD G   VFVH S
Sbjct: 5   TGIVKWFNADKGFGFITPDDGSKDVFVHFS 34

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

Iteration: 1
 Score = 39.7 bits (91), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 17/29 (58%), Positives = 19/29 (65%)
Query: 81  GKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
           G +K F  SKG GFITP+ G   VFVH S
Sbjct: 8   GNVKWFNESKGFGFITPEDGSKDVFVHFS 36

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	144
3aqq_A	147	Calcium-regulated heat stable protein 1; compact b	5e-18
2lss_A	70	Cold shock-like protein; CSD, CSP, oligonucleotide	9e-10
3cam_A	67	Cold-shock domain family protein; cold shock prote	2e-08
3i2z_B	71	RNA chaperone, negative regulator of CSPA transcri	3e-08
2k5n_A	74	Putative cold-shock protein; GFT protein structure	3e-08
1h95_A	79	CSD, Y-box binding protein; translation factor, tr	2e-07
2kcm_A	74	Cold shock domain family protein; nucleic acid bin	7e-07
2bh8_A	101	1B11; transcription, molecular evolution, unique a	8e-07
1c9o_A	66	CSPB, cold-shock protein; beta barrel, homodimer,	8e-07
1g6p_A	66	Cold shock protein TMCSP; greek-KEY, beta barrel,	9e-07
3a0j_A	73	Cold shock protein; OB-fold, cytoplasm, transcript	2e-06
2yty_A	88	Cold shock domain-containing protein E1; cell-free	4e-04
3ulj_A	90	LIN28B, DNA-binding protein; beta barrel, cold sho	5e-04
2ytx_A	97	Cold shock domain-containing protein E1; cell-free	7e-04

>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 = 74.3 bits (182), Expect = 5e-18
 Identities = 39/107 (36%), Positives = 47/107 (43%), Gaps = 20/107 (18%)

Query: 4   SPLPFENKKPALSSPMLSPQEPHLHSNNTLSLPSPIITRRTRTESMDFKATAQRSKGSKE 63
            P P  ++           +E          +PSP+ TRRTRT S               
Sbjct: 8   PPQPPTHQASVGLLDTPRSRERSPSPLRGNVVPSPLPTRRTRTFSA-------------- 53

Query: 64  QPNFLISNRALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISD 110
                 + RA Q PV  G  K FCRSKGHGFITP  G P +F+HISD
Sbjct: 54  ------TVRASQGPVYKGVCKCFCRSKGHGFITPADGGPDIFLHISD 94

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

 Score = 50.7 bits (122), Expect = 9e-10
 Identities = 14/30 (46%), Positives = 18/30 (60%)

Query: 80  TGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
            GK+K +  +K  GFI  D+G   VFVH S
Sbjct: 6   VGKVKWYNSTKNFGFIEQDNGGKDVFVHKS 35

>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 = 46.8 bits (112), Expect = 2e-08
 Identities = 16/31 (51%), Positives = 19/31 (61%)

Query: 79  ETGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
            TG +K F  +KG GFITPD G   +F H S
Sbjct: 2   ATGIVKWFNDAKGFGFITPDEGGEDLFAHFS 32

>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 = 46.9 bits (112), Expect = 3e-08
 Identities = 17/30 (56%), Positives = 19/30 (63%)

Query: 80  TGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
            G +K F  SKG GFITP+ G   VFVH S
Sbjct: 7   KGNVKWFNESKGFGFITPEDGSKDVFVHFS 36

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

 Score = 46.9 bits (112), Expect = 3e-08
 Identities = 9/31 (29%), Positives = 16/31 (51%), Gaps = 1/31 (3%)

Query: 80  TGKIKEFCRSKGHGFITPDSGEPAVFVHISD 110
            G I  + + KG GFI  ++G+   + H+  
Sbjct: 4   NGTITTWFKDKGFGFIKDENGDN-RYFHVIK 33

>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 = 44.7 bits (106), Expect = 2e-07
 Identities = 11/31 (35%), Positives = 16/31 (51%)

Query: 79  ETGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
             G +K F    G+GFI  +  +  VFVH +
Sbjct: 9   VLGTVKWFNVRNGYGFINRNDTKEDVFVHQT 39

>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 = 43.4 bits (103), Expect = 7e-07
 Identities = 12/30 (40%), Positives = 17/30 (56%), Gaps = 1/30 (3%)

Query: 80  TGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
            GK+  +  +K +GFI  D GE   F+H S
Sbjct: 2   KGKVVSYLAAKKYGFIQGDDGES-YFLHFS 30

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

 Score = 44.0 bits (104), Expect = 8e-07
 Identities = 18/30 (60%), Positives = 19/30 (63%)

Query: 80  TGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
           TG +K F   KG GFITPD G   VFVH S
Sbjct: 18  TGIVKWFNADKGFGFITPDDGSKDVFVHFS 47

>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 = 43.0 bits (102), Expect = 8e-07
 Identities = 14/31 (45%), Positives = 19/31 (61%), Gaps = 1/31 (3%)

Query: 79  ETGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
           + GK+K F   KG+GFI  + G   VFVH +
Sbjct: 2   QRGKVKWFNNEKGYGFIEVEGG-SDVFVHFT 31

>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 = 43.0 bits (102), Expect = 9e-07
 Identities = 17/30 (56%), Positives = 19/30 (63%), Gaps = 1/30 (3%)

Query: 80  TGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
            GK+K F   KG+GFIT D G   VFVH S
Sbjct: 2   RGKVKWFDSKKGYGFITKDEG-GDVFVHWS 30

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

 Score = 42.3 bits (100), Expect = 2e-06
 Identities = 12/31 (38%), Positives = 18/31 (58%), Gaps = 1/31 (3%)

Query: 79  ETGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
           + G++K F   KG+GFI  +     VFVH +
Sbjct: 2   QKGRVKWFNAEKGYGFIEREGD-TDVFVHYT 31

>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 = 36.3 bits (84), Expect = 4e-04
 Identities = 8/47 (17%), Positives = 17/47 (36%), Gaps = 2/47 (4%)

Query: 65  PNFLISNRALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDY 111
            +  +  R   +    G +         GFI   + +  +F H S++
Sbjct: 5   SSGRLLGRNSNSKRLLGYVATL--KDNFGFIETANHDKEIFFHYSEF 49

>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 = 35.9 bits (83), Expect = 5e-04
 Identities = 13/38 (34%), Positives = 15/38 (39%), Gaps = 7/38 (18%)

Query: 79  ETGKIKEFCRSKGHGFIT-------PDSGEPAVFVHIS 109
            +G  K F    G GFI+       P      VFVH S
Sbjct: 9   GSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQS 46

>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 = 36.0 bits (83), Expect = 7e-04
 Identities = 7/33 (21%), Positives = 12/33 (36%), Gaps = 2/33 (6%)

Query: 79  ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDY 111
             G +      +  GFI        +F H S++
Sbjct: 19  CQGVVCAM--KEAFGFIERGDVVKEIFFHYSEF 49

---

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	144
d1mjca_	69	b.40.4.5 (A:) Major cold shock protein {Escherichi	1e-09
d1h95a_	79	b.40.4.5 (A:) Y-box protein 1 cold shock domain (Y	2e-09
d1g6pa_	66	b.40.4.5 (A:) Major cold shock protein {Thermotoga	6e-08
d1c9oa_	66	b.40.4.5 (A:) Major cold shock protein {Bacillus c	8e-07
d1wfqa_	89	b.40.4.5 (A:) Cold shock domain protein E1 (UNR) {	1e-06

>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 = 49.0 bits (117), Expect = 1e-09
 Identities = 18/30 (60%), Positives = 19/30 (63%)

Query: 80  TGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
           TG +K F   KG GFITPD G   VFVH S
Sbjct: 5   TGIVKWFNADKGFGFITPDDGSKDVFVHFS 34

>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 = 49.0 bits (117), Expect = 2e-09
 Identities = 11/30 (36%), Positives = 16/30 (53%)

Query: 80  TGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
            G +K F    G+GFI  +  +  VFVH +
Sbjct: 10  LGTVKWFNVRNGYGFINRNDTKEDVFVHQT 39

>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 = 44.7 bits (106), Expect = 6e-08
 Identities = 17/31 (54%), Positives = 19/31 (61%), Gaps = 1/31 (3%)

Query: 80  TGKIKEFCRSKGHGFITPDSGEPAVFVHISD 110
            GK+K F   KG+GFIT D G   VFVH S 
Sbjct: 2   RGKVKWFDSKKGYGFITKDEGGD-VFVHWSA 31

>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 = 41.7 bits (98), Expect = 8e-07
 Identities = 14/32 (43%), Positives = 19/32 (59%), Gaps = 1/32 (3%)

Query: 79  ETGKIKEFCRSKGHGFITPDSGEPAVFVHISD 110
           + GK+K F   KG+GFI  + G   VFVH + 
Sbjct: 2   QRGKVKWFNNEKGYGFIEVEGGSD-VFVHFTA 32

>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 = 42.2 bits (99), Expect = 1e-06
 Identities = 11/37 (29%), Positives = 16/37 (43%), Gaps = 2/37 (5%)

Query: 79  ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMP 115
           ETG I++      +GFI     +  +F H S Y    
Sbjct: 19  ETGVIEKL--LTSYGFIQCSERQARLFFHCSQYNGNL 53

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	144
d1mjca_	69	Major cold shock protein {Escherichia coli [TaxId:	99.78
d1c9oa_	66	Major cold shock protein {Bacillus caldolyticus [T	99.74
d1h95a_	79	Y-box protein 1 cold shock domain (YB1-CSD) {Human	99.73
d1g6pa_	66	Major cold shock protein {Thermotoga maritima [Tax	99.72
d1wfqa_	89	Cold shock domain protein E1 (UNR) {Human (Homo sa	99.34
d2ix0a2	79	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	95.87
d1a62a2	78	Rho termination factor, RNA-binding domain {Escher	94.11

>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=99.78  E-value=6e-20  Score=123.51  Aligned_cols=61  Identities=36%  Similarity=0.447  Sum_probs=49.6

Q ss_pred             ccccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceee-----eCCccccccccee
Q psy3660          78 VETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKAL-----QGSKTCNSCNISS  138 (144)
Q Consensus        78 ~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V-----~g~kg~~a~~i~~  138 (144)
                      .++|+|||||..||||||.++++++|||||+++|+...-+.+..||.|     ++.+|.+|.||..
T Consensus         3 r~~G~Vk~f~~~kGfGFI~~d~g~~diFvH~s~l~~~~~~~L~~G~~V~f~~~~~~~G~~A~~V~~   68 (69)
T d1mjca_           3 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVTS   68 (69)
T ss_dssp             CEEEEEEEEETTTTEEEEEETTSCCCEEEEGGGBCCTTTCCCCTTCEEEEEEECCSSSCEEEEEEE
T ss_pred             CEEEEEEEEeCCCCEEEEEEcCCCccEEEEhHHhcccCCCcCCCCCEEEEEEEeCCCCcEEEEEEe
Confidence            479999999999999999999999999999999986533445556555     6677778877754

>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=99.74  E-value=3.3e-19  Score=118.81  Aligned_cols=60  Identities=27%  Similarity=0.388  Sum_probs=48.8

Q ss_pred             ccccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceee-----eCCccccccccee
Q psy3660          78 VETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKAL-----QGSKTCNSCNISS  138 (144)
Q Consensus        78 ~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V-----~g~kg~~a~~i~~  138 (144)
                      |.+|+|||||..||||||++++ ++|||||+++|+....+.+..||.|     ++.+|.+|.+|.+
T Consensus         1 M~~G~Vk~fn~~kGfGFI~~d~-g~DiF~H~s~l~~~~~~~L~~G~~V~f~~~~~~~G~~A~~V~~   65 (66)
T d1c9oa_           1 MQRGKVKWFNNEKGYGFIEVEG-GSDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGNRGPQAANVVK   65 (66)
T ss_dssp             CEEEEEEEEETTTTEEEEEETT-EEEEEEEGGGBCSSSCCCCCTTCEEEEEEEEETTEEEEEEEEE
T ss_pred             CCCeEEEEEECCCCEEEEEecC-CceEEEEehhcccccCCcCCCCCEEEEEEEECCCCCEEEEEEE
Confidence            5689999999999999999975 5799999999987644455556655     7788888888865

>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=99.73  E-value=4.7e-19  Score=122.07  Aligned_cols=61  Identities=23%  Similarity=0.312  Sum_probs=48.1

Q ss_pred             cccccEEEEccCCCceeEecCCCCCCcEEEEeeccccCC----Cccceeceee-----eCCcccccccce
Q psy3660          77 PVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMP----KLISQINKAL-----QGSKTCNSCNIS  137 (144)
Q Consensus        77 ~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~----g~~p~~Gd~V-----~g~kg~~a~~i~  137 (144)
                      .++.|+|||||..||||||+++++++|||||+++|+...    -+.++.||.|     ++.+|.+|.||+
T Consensus         7 ~r~~G~VKwfn~~KGfGFI~~ddg~~DvFvH~s~i~~~g~~~~~~~L~~G~~V~f~~~~~~~G~~A~~Vt   76 (79)
T d1h95a_           7 TKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVT   76 (79)
T ss_dssp             EEEEEEEEEEETTTTEEEEEEGGGTEEEEEEGGGBCSCCCSCCSCSCCSSCEEEEEEEECSSSEEEESBC
T ss_pred             CcccEEEEEEcCCCCeEEEEECCCCccEEEEhhHcccCCCcceeeecCCCCEEEEEEEeCCCCCeeEEEe
Confidence            467899999999999999999999999999999997752    1224445554     666777777774

>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=99.72  E-value=9.1e-19  Score=116.77  Aligned_cols=61  Identities=34%  Similarity=0.443  Sum_probs=50.0

Q ss_pred             cccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceee-----eCCcccccccceeee
Q psy3660          79 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKAL-----QGSKTCNSCNISSVE  140 (144)
Q Consensus        79 ~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V-----~g~kg~~a~~i~~~~  140 (144)
                      ++|+|||||..||||||+++++ +|||||+++|....-..+..||.|     ++.+|.+|.+|.-+|
T Consensus         1 l~G~Vk~f~~~kGfGFI~~~~g-~diFvH~s~l~~~g~~~l~~G~~V~f~~~~~~~G~~A~~V~~id   66 (66)
T d1g6pa_           1 MRGKVKWFDSKKGYGFITKDEG-GDVFVHWSAIEMEGFKTLKEGQVVEFEIQEGKKGPQAAHVKVVE   66 (66)
T ss_dssp             CCEEEEEEETTTTEEEEEETTS-CBCBBCSSSSCCSSCCCCCSSSEEEEEEECSSSCCEEEEEEEEC
T ss_pred             CeEEEEEEeCCCCeeEEEecCC-ceEEEEhHHhcccCCCcCCCCCEEEEEEEECCCCCEEEEEEecC
Confidence            4799999999999999999875 699999999986633445666655     778899999987665

>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=99.34  E-value=2.6e-13  Score=94.62  Aligned_cols=67  Identities=19%  Similarity=0.222  Sum_probs=52.0

Q ss_pred             ccccCCcccccEEEEccCCCceeEecCCCCCCcEEEEeeccccCCCccceeceeeeC-----Ccc--cccccceeee
Q psy3660          71 NRALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKALQG-----SKT--CNSCNISSVE  140 (144)
Q Consensus        71 ~r~~~~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~~g~~p~~Gd~V~g-----~kg--~~a~~i~~~~  140 (144)
                      .+...+.+.+|+|+||.  +|||||+++++++|||||++++... .+.+++||.|++     .|+  .+|.+|..+.
T Consensus        11 ~~~~~~~r~~G~I~~~~--~gfGFI~~~~~~~dvF~H~s~~~~~-~~~l~~G~~VeF~v~~~~kg~k~~Av~V~~~~   84 (89)
T d1wfqa_          11 NGTSAALRETGVIEKLL--TSYGFIQCSERQARLFFHCSQYNGN-LQDLKVGDDVEFEVSSDRRTGKPIAVKLVKIS   84 (89)
T ss_dssp             CSSSCCCEEEEEEEEEC--SSEEEEEETTTTEEEEEETTTCSSC-TTTCCTTCCEEEEEEECSSSCCEEEEEEEESS
T ss_pred             CCCCccceEEEEEEEec--CccceEEeCCCCceEEEEeehhhcc-CCcccCCCEEEEEEEECCCCCceEEEEEEECC
Confidence            34555667899999995  5999999999989999999999754 677888887765     455  4566665543

>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=95.87  E-value=0.0011  Score=44.18  Aligned_cols=54  Identities=20%  Similarity=0.295  Sum_probs=36.3

Q ss_pred             cCCcccccEEEEccCCCceeEecCCCCCCcEEEEeeccccC-CCccceeceeeeCCcccc
Q psy3660          74 LQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIM-PKLISQINKALQGSKTCN  132 (144)
Q Consensus        74 ~~~~~~~GtVK~Fd~~KGfGFI~~d~gg~DVFVHiSai~~~-~g~~p~~Gd~V~g~kg~~  132 (144)
                      .......|++..  ..+||||+.+++ ++|||+....+... .||++++  .+...+++.
T Consensus        14 ~~~~~~~G~i~~--~~~G~GFv~~d~-~~DifI~~~~~~~A~~GD~V~v--~i~~~~~r~   68 (79)
T d2ix0a2          14 SQTPRAEGVVKA--TEKGFGFLEVDA-QKSYFIPPPQMKKVMHGDRIIA--VIHSEKERE   68 (79)
T ss_dssp             HTSCEEEEEEEC--CC--CEEEEEET-TEEEEECHHHHTTCCTTCEEEE--EEECC--CC
T ss_pred             hcCCEEEEEEEE--eCCCcEEEEECC-CCcEEECHHHHcCCCCCCEEEE--EEEeCCCcE
Confidence            345678899987  679999999987 58999999987653 3777665  233444443

>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=94.11  E-value=0.0083  Score=40.01  Aligned_cols=36  Identities=19%  Similarity=0.447  Sum_probs=26.7

Q ss_pred             CCceeEecCCC-----CCCcEEEEeeccccCCCccceeceeeeC
Q psy3660          89 SKGHGFITPDS-----GEPAVFVHISDYVIMPKLISQINKALQG  127 (144)
Q Consensus        89 ~KGfGFI~~d~-----gg~DVFVHiSai~~~~g~~p~~Gd~V~g  127 (144)
                      .+|||||...+     +.+||||..+.|+.- +  ++.||.|.|
T Consensus        12 ~dGyGFLR~~~~~y~~~~~DiyVs~s~Irrf-g--LR~GD~V~G   52 (78)
T d1a62a2          12 QDGFGFLRSADSSYLAGPDDIYVSPSQIRRF-N--LRTGDTISG   52 (78)
T ss_dssp             TTSCEEEECGGGTTCCCTTCEEECHHHHHHT-T--CCTTCEEEE
T ss_pred             CCCcEEeECCccCCCCCCcceEECHHHHHHh-C--CCcCcEEEE
Confidence            47999999732     457999999999876 3  345666654