Citrus Sinensis ID: 047168

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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-------26
Protein Sequence
MAQLTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAPGGAPVHSSKNNNTNNNSGYNNNRGGRGGGGAGFGGYWKGNNDSRRNNGGGYGPGGVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGAGGAGGGGSCFNCGKPGHFARECTKVAN
Secondary Structure (PSIPRED)
cccccccccEEEEEEcccEEEEEEcccccccEEEEEcccccccccccccccEEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHcEEEEEEEEEccccEEEEEEccccccEEEEHHHEccccccccccccEEEEEEEccccccccEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEcccccccccccccccccccccEcEccccccccccccccccc
Coil and Loop (DISEMBL)
maqltrstgkvtwfdgakgygfirpddggadlfvhqksiksdgyrtlyenqsvEFDVQLeadgkyqaldvtapggapvhssknnntnnnsgynnnrggrggggagfggywkgnndsrrnngggygpggvvcyncdgvghvarectsnrrnsnynnnsggcyncgdpehfardcprqqggsnsynnnsggcfkcggyghlardcitrgsggggggrcyncgksghlardcgaggaggggscfncgkpghfaRECTKVAN
Flexible Loop (DISEMBL)
maqltrstgkvtwfdgakGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAPGgapvhssknnntnnnsgynnnRGGRGGGGAGFGGYWKGNNDSRRNNGGGYGPGGVVCYNCDGVGHVARECtsnrrnsnynnNSGGCYNCGDPEHFARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGAGGAGGGGSCFNCGKPGHFARECTKVAN
Low Complexity Region (SEG)
MAQLTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAPGGAPVHSSKnnntnnnsgynnnrggrggggagfggywkgnndsrrnngggygpggvvcyncDGVGHVARECTsnrrnsnynnnsggcyncgDPEHFARDCPRQQggsnsynnnsggCFKCGGYGHLARDCITrgsggggggrcyncgksgHLARDCgaggaggggSCFNCGKPGHFARECTKVAN
Disordered region (IsUnstruct)
*********KVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQAL************************************GFGGYWKG********GGGYGPGGVVCYNCDGVGHVARECTS***********GGCYNCGD*********************SGGCFKCGGYGHLARDCI******************GHLARDCGAGGAGGGGSCFNCGKPGHFA********
Disordered Region (DISOPRED)
******S****TWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAPGGAPVHSSKNNNTNNNSGYNNNRGGRGGGGAGFGGYW***************PGGVVCYNCDG********************************************************CGGY******************RCYNCGKSGHLARDC**********CFNCGKPGHF**EC*****
Disordered Region (DISEMBL)
********GKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAPGGAPVHSSKNNNTNNNSGYNNNRGGRGGGGAGFGGYWKGNNDSRRNNGGGYGPGGVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGAGGAGGGGSCFNCGKPGHFARECTKVAN
Disordered Region (DISPRO)
****TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAP**************************************************************GVGHVARECT**************************************************YGHLARDCITR*******GRC*****SGHLARDCGAGGAGGGGSC*****P*HFAR*C*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAQLTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAPGGAPVHSSKNNNTNNNSGYNNNRGGRGGGGAGFGGYWKGNNDSRRNNGGGYGPGGVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGAGGAGGGGSCFNCGKPGHFARECTKVAN
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	258	2.2.26 [Sep-21-2011]
O65639	299	Cold shock protein 1 OS=A	yes	no	0.957	0.826	0.420	6e-44
Q94C69	301	Cold shock domain-contain	no	no	0.961	0.823	0.429	5e-38
Q38896	201	Cold shock domain-contain	no	no	0.647	0.830	0.393	7e-21
Q04832	271	DNA-binding protein HEXBP	yes	no	0.492	0.468	0.401	4e-19
P36627	179	Cellular nucleic acid-bin	yes	no	0.441	0.636	0.401	1e-15
P53849	153	Zinc finger protein GIS2	yes	no	0.449	0.758	0.345	4e-14
P53996	178	Cellular nucleic acid-bin	no	no	0.403	0.584	0.356	1e-13
P62634	177	Cellular nucleic acid-bin	yes	no	0.403	0.587	0.356	1e-13
Q5R5R5	177	Cellular nucleic acid-bin	yes	no	0.403	0.587	0.356	1e-13
P62633	177	Cellular nucleic acid-bin	yes	no	0.403	0.587	0.356	1e-13

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

 Score =  177 bits (449), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 124/295 (42%), Positives = 151/295 (51%), Gaps = 48/295 (16%)

Query: 6   RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKY 65
           RSTGKV WF+ +KGYGFI PDDG  +LFVHQ SI S+GYR+L    +VEF +   +DGK 
Sbjct: 10  RSTGKVNWFNASKGYGFITPDDGSVELFVHQSSIVSEGYRSLTVGDAVEFAITQGSDGKT 69

Query: 66  QALDVTAPGGAPVHSSKNNNTNNNSGYNNNRGGRGGGGAGFGGYWKG-NNDSRRNNGGGY 124
           +A++VTAPGG  +   K NN+  N       G         G   K          G   
Sbjct: 70  KAVNVTAPGGGSL--KKENNSRGNGARRGGGGSGCYNCGELGHISKDCGIGGGGGGGERR 127

Query: 125 GPGGVVCYNCDGVGHVARECTS----NRRNSNYNNNSG---------------------- 158
             GG  CYNC   GH AR+CTS    ++R +    N G                      
Sbjct: 128 SRGGEGCYNCGDTGHFARDCTSAGNGDQRGATKGGNDGCYTCGDVGHVARDCTQKSVGNG 187

Query: 159 -----------GCYNCGDPEHFARDCPRQQGGSNSYN--NNSGGCFKCGGYGHLARDCIT 205
                      GCY CGD  HFARDC ++    N  +    SG C+ CGG GH+ARDC T
Sbjct: 188 DQRGAVKGGNDGCYTCGDVGHFARDCTQKVAAGNVRSGGGGSGTCYSCGGVGHIARDCAT 247

Query: 206 RGSGGGGGGRCYNCGKSGHLARDCGAGGAGGGG---SCFNCGKPGHFARECTKVA 257
           +     G   CY CG SGHLARDC   G+GGGG   +C+ CGK GHFAREC+ VA
Sbjct: 248 KRQPSRG---CYQCGGSGHLARDCDQRGSGGGGNDNACYKCGKEGHFARECSSVA 299

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

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

 Score =  157 bits (398), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 127/296 (42%), Positives = 159/296 (53%), Gaps = 48/296 (16%)

Query: 6   RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKY 65
           RS GKV+WF   KGYGFI PDDGG +LFVHQ SI SDG+R+L   +SVE+++ L +DGK 
Sbjct: 10  RSIGKVSWFSDGKGYGFITPDDGGEELFVHQSSIVSDGFRSLTLGESVEYEIALGSDGKT 69

Query: 66  QALDVTAPGGAPVHSSKNNNTNNNSGYNNNRGGRGGGGAG-------------------- 105
           +A++VTAPGG  ++  K  N++  SG N    G  G  A                     
Sbjct: 70  KAIEVTAPGGGSLN--KKENSSRGSGGNCFNCGEVGHMAKDCDGGSGGKSFGGGGGRRSG 127

Query: 106 ----------FGGYWKGNNDSRRNNGGGYGPGGVVCYNCDGVGHVAREC------TSNRR 149
                      G + +    S   N GG G GG  CY+C  VGH+A++C           
Sbjct: 128 GEGECYMCGDVGHFARDCRQSGGGNSGGGGGGGRPCYSCGEVGHLAKDCRGGSGGNRYGG 187

Query: 150 NSNYNNNSGGCYNCGDPEHFARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITR-GS 208
                +   GCY CG   HFARDC  +Q G  +       C+ CGG GH+A+ C ++  S
Sbjct: 188 GGGRGSGGDGCYMCGGVGHFARDC--RQNGGGNVGGGGSTCYTCGGVGHIAKVCTSKIPS 245

Query: 209 GGGGGGR-CYNCGKSGHLARDC------GAGGAGGGGSCFNCGKPGHFARECTKVA 257
           GGGGGGR CY CG +GHLARDC       +GG GG   CF CGK GHFARECT VA
Sbjct: 246 GGGGGGRACYECGGTGHLARDCDRRGSGSSGGGGGSNKCFICGKEGHFARECTSVA 301

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  100 bits (250), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 72/183 (39%), Positives = 95/183 (51%), Gaps = 16/183 (8%)

Query: 6   RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKY 65
           R  G V WFD  KG+GFI P DGG DLFVHQ SI+S+G+R+L   +SVEFDV+++  G+ 
Sbjct: 14  RRKGTVKWFDTQKGFGFITPSDGGDDLFVHQSSIRSEGFRSLAAEESVEFDVEVDNSGRP 73

Query: 66  QALDVTAPGGAPVHSSKNNNTNNNSGYNNNRGGRGGGGAGFGGYWKGNNDSRRNNGGGYG 125
           +A++V+ P GAPV  +     ++        GG  GGG G G Y  G         GG G
Sbjct: 74  KAIEVSGPDGAPVQGNSGGGGSSGGRGGFGGGGGRGGGRGGGSYGGGYGGRGSGGRGGGG 133

Query: 126 PGGVVCYNCDGVGHVARECTSNRRNSNYNNNSG---------------GCYNCGDPEHFA 170
                C+ C   GH+AREC+      +     G                CY+CG+  HFA
Sbjct: 134 GDN-SCFKCGEPGHMARECSQGGGGYSGGGGGGRYGSGGGGGGGGGGLSCYSCGESGHFA 192

Query: 171 RDC 173
           RDC
Sbjct: 193 RDC 195

Arabidopsis thaliana (taxid: 3702)

>sp|Q04832|HEXP_LEIMA DNA-binding protein HEXBP OS=Leishmania major GN=HEXBP PE=4 SV=1

 Score = 95.5 bits (236), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 59/147 (40%), Positives = 82/147 (55%), Gaps = 20/147 (13%)

Query: 128 GVVCYNCDGVGHVARECTSNRRNSN--YNNNSG------------GCYNCGDPEHFARDC 173
           G  CY C   GH++R+C S++  S   Y    G             CY CGD  H +RDC
Sbjct: 96  GFECYKCGQEGHLSRDCPSSQGGSRGGYGQKRGRSGAQGGYSGDRTCYKCGDAGHISRDC 155

Query: 174 PRQQGGSNSYNNNSGGCFKCGGYGHLARDCI--TRGSGGGGGGRCYNCGKSGHLARDCGA 231
           P  QGG +   + +  C+KCG  GH++RDC     G  G G  +CY CG+SGH++R+C +
Sbjct: 156 PNGQGGYSGAGDRT--CYKCGDAGHISRDCPNGQGGYSGAGDRKCYKCGESGHMSRECPS 213

Query: 232 GGAGGGG--SCFNCGKPGHFARECTKV 256
            G+ G G  +C+ CGKPGH +REC + 
Sbjct: 214 AGSTGSGDRACYKCGKPGHISRECPEA 240

Binds to single-stranded DNA located in the 5' hexanucleotide repeat region of the L.major leishmanolysin (GP63) gene.

Leishmania major (taxid: 5664)

>sp|P36627|BYR3_SCHPO Cellular nucleic acid-binding protein homolog OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=byr3 PE=4 SV=1

 Score = 83.6 bits (205), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 61/152 (40%), Positives = 70/152 (46%), Gaps = 38/152 (25%)

Query: 128 GVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQQGGSNSYNNNS 187
           G +CYNC+  GH A ECT  ++          CY CG   H  RDCP      +S N   
Sbjct: 35  GSICYNCNQTGHKASECTEPQQEKT-------CYACGTAGHLVRDCP------SSPNPRQ 81

Query: 188 GG-CFKCGGYGHLARDCITRG--SGGGGGGR-----CYNCGKSGHLARDCGAG------- 232
           G  C+KCG  GH+ARDC T G  SGG  GG      CY CG  GH ARDC  G       
Sbjct: 82  GAECYKCGRVGHIARDCRTNGQQSGGRFGGHRSNMNCYACGSYGHQARDCTMGVKCYSCG 141

Query: 233 ----------GAGGGGSCFNCGKPGHFARECT 254
                      A  G  C+ C +PGH A  CT
Sbjct: 142 KIGHRSFECQQASDGQLCYKCNQPGHIAVNCT 173

Acts in the sexual differentiation pathway. Is required for efficient conjugation. Double stranded DNA-binding protein.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|P53849|GIS2_YEAST Zinc finger protein GIS2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=GIS2 PE=1 SV=1

 Score = 78.6 bits (192), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 48/139 (34%), Positives = 70/139 (50%), Gaps = 23/139 (16%)

Query: 130 VCYNCDGVGHVARECTSNRR---NSNYNNNSGG----------CYNCGDPEHFARDCPRQ 176
           +CYNC+  GHV  +CT  R       YN    G          C+NC    H +R+CP  
Sbjct: 24  LCYNCNKPGHVQTDCTMPRTVEFKQCYNCGETGHVRSECTVQRCFNCNQTGHISRECPEP 83

Query: 177 QGGSNSYNNNSGGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGAGGAGG 236
           +  S     +   C+KCGG  H+A+DC+     G  G +CY CG++GH++RDC       
Sbjct: 84  KKTSRF---SKVSCYKCGGPNHMAKDCM--KEDGISGLKCYTCGQAGHMSRDC-----QN 133

Query: 237 GGSCFNCGKPGHFARECTK 255
              C+NC + GH +++C K
Sbjct: 134 DRLCYNCNETGHISKDCPK 152

May act in the sexual differentiation pathway.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|P53996|CNBP_MOUSE Cellular nucleic acid-binding protein OS=Mus musculus GN=Cnbp PE=2 SV=2

 Score = 77.4 bits (189), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 46/129 (35%), Positives = 64/129 (49%), Gaps = 25/129 (19%)

Query: 130 VCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQQGGSNSYNNNSGG 189
            CYNC   GH+A++C   +R          CYNCG P H ARDC          + +   
Sbjct: 74  ACYNCGRGGHIAKDCKEPKRE-----REQCCYNCGKPGHLARDCD---------HADEQK 119

Query: 190 CFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGAGGAGGGGSCFNCGKPGHF 249
           C+ CG +GH+ +DC           +CY CG++GH+A +C         +C+ CG+ GH 
Sbjct: 120 CYSCGEFGHIQKDCTK--------VKCYRCGETGHVAINCSKTSEV---NCYRCGESGHL 168

Query: 250 ARECTKVAN 258
           ARECT  A 
Sbjct: 169 ARECTIEAT 177

Single stranded DNA-binding protein, with specificity to the sterol regulatory element (SRE). Involved in sterol-mediated repression.

Mus musculus (taxid: 10090)

>sp|P62634|CNBP_RAT Cellular nucleic acid-binding protein OS=Rattus norvegicus GN=Cnbp PE=2 SV=1

 Score = 77.0 bits (188), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 46/129 (35%), Positives = 64/129 (49%), Gaps = 25/129 (19%)

Query: 130 VCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQQGGSNSYNNNSGG 189
            CYNC   GH+A++C   +R          CYNCG P H ARDC          + +   
Sbjct: 73  ACYNCGRGGHIAKDCKEPKRE-----REQCCYNCGKPGHLARDCD---------HADEQK 118

Query: 190 CFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGAGGAGGGGSCFNCGKPGHF 249
           C+ CG +GH+ +DC           +CY CG++GH+A +C         +C+ CG+ GH 
Sbjct: 119 CYSCGEFGHIQKDCTK--------VKCYRCGETGHVAINCSKTSEV---NCYRCGESGHL 167

Query: 250 ARECTKVAN 258
           ARECT  A 
Sbjct: 168 ARECTIEAT 176

Single stranded DNA-binding protein, with specificity to the sterol regulatory element (SRE). Involved in sterol-mediated repression.

Rattus norvegicus (taxid: 10116)

>sp|Q5R5R5|CNBP_PONAB Cellular nucleic acid-binding protein OS=Pongo abelii GN=CNBP PE=2 SV=1

 Score = 77.0 bits (188), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 46/129 (35%), Positives = 64/129 (49%), Gaps = 25/129 (19%)

Query: 130 VCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQQGGSNSYNNNSGG 189
            CYNC   GH+A++C   +R          CYNCG P H ARDC          + +   
Sbjct: 73  ACYNCGRGGHIAKDCKEPKRE-----REQCCYNCGKPGHLARDCD---------HADEQK 118

Query: 190 CFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGAGGAGGGGSCFNCGKPGHF 249
           C+ CG +GH+ +DC           +CY CG++GH+A +C         +C+ CG+ GH 
Sbjct: 119 CYSCGEFGHIQKDCTK--------VKCYRCGETGHVAINCSKTSEV---NCYRCGESGHL 167

Query: 250 ARECTKVAN 258
           ARECT  A 
Sbjct: 168 ARECTIEAT 176

Single stranded DNA-binding protein, with specificity to the sterol regulatory element (SRE). Involved in sterol-mediated repression.

Pongo abelii (taxid: 9601)

>sp|P62633|CNBP_HUMAN Cellular nucleic acid-binding protein OS=Homo sapiens GN=CNBP PE=1 SV=1

 Score = 77.0 bits (188), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 46/129 (35%), Positives = 64/129 (49%), Gaps = 25/129 (19%)

Query: 130 VCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQQGGSNSYNNNSGG 189
            CYNC   GH+A++C   +R          CYNCG P H ARDC          + +   
Sbjct: 73  ACYNCGRGGHIAKDCKEPKRE-----REQCCYNCGKPGHLARDCD---------HADEQK 118

Query: 190 CFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGAGGAGGGGSCFNCGKPGHF 249
           C+ CG +GH+ +DC           +CY CG++GH+A +C         +C+ CG+ GH 
Sbjct: 119 CYSCGEFGHIQKDCTK--------VKCYRCGETGHVAINCSKTSEV---NCYRCGESGHL 167

Query: 250 ARECTKVAN 258
           ARECT  A 
Sbjct: 168 ARECTIEAT 176

Single stranded DNA-binding protein, with specificity to the sterol regulatory element (SRE). Involved in sterol-mediated repression.

Homo sapiens (taxid: 9606)

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	258
15233440	299	cellular nucleic acid-binding protein [A	0.957	0.826	0.420	4e-42
297798314	257	hypothetical protein ARALYDRAFT_491032 [	0.922	0.926	0.465	3e-41
224134074	235	predicted protein [Populus trichocarpa]	0.806	0.885	0.424	7e-41
255586301	266	cellular nucleic acid binding protein, p	0.899	0.872	0.514	4e-40
356559280	250	PREDICTED: DNA-binding protein HEXBP-lik	0.895	0.924	0.458	3e-39
294470718	263	cold shock domain protein 1 [Eutrema sal	0.914	0.897	0.433	7e-39
224074255	225	predicted protein [Populus trichocarpa]	0.794	0.911	0.423	8e-38
357518027	329	Major cold-shock protein [Medicago trunc	0.895	0.702	0.383	1e-36
18398546	301	cold shock domain protein 3 [Arabidopsis	0.961	0.823	0.429	3e-36
297836502	299	hypothetical protein ARALYDRAFT_480687 [	0.961	0.829	0.415	6e-36

>gi|15233440|ref|NP_195326.1| cellular nucleic acid-binding protein [Arabidopsis thaliana] gi|75318587|sp|O65639.1|CSP1_ARATH RecName: Full=Cold shock protein 1; Short=AtCSP1; AltName: Full=Cold shock domain-containing protein 1 gi|3036806|emb|CAA18496.1| glycine-rich protein [Arabidopsis thaliana] gi|7270554|emb|CAB81511.1| glycine-rich protein [Arabidopsis thaliana] gi|110741941|dbj|BAE98911.1| glycine-rich protein [Arabidopsis thaliana] gi|332661203|gb|AEE86603.1| cellular nucleic acid-binding protein [Arabidopsis thaliana]

 Score =  177 bits (449), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 124/295 (42%), Positives = 151/295 (51%), Gaps = 48/295 (16%)

Query: 6   RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKY 65
           RSTGKV WF+ +KGYGFI PDDG  +LFVHQ SI S+GYR+L    +VEF +   +DGK 
Sbjct: 10  RSTGKVNWFNASKGYGFITPDDGSVELFVHQSSIVSEGYRSLTVGDAVEFAITQGSDGKT 69

Query: 66  QALDVTAPGGAPVHSSKNNNTNNNSGYNNNRGGRGGGGAGFGGYWKG-NNDSRRNNGGGY 124
           +A++VTAPGG  +   K NN+  N       G         G   K          G   
Sbjct: 70  KAVNVTAPGGGSL--KKENNSRGNGARRGGGGSGCYNCGELGHISKDCGIGGGGGGGERR 127

Query: 125 GPGGVVCYNCDGVGHVARECTS----NRRNSNYNNNSG---------------------- 158
             GG  CYNC   GH AR+CTS    ++R +    N G                      
Sbjct: 128 SRGGEGCYNCGDTGHFARDCTSAGNGDQRGATKGGNDGCYTCGDVGHVARDCTQKSVGNG 187

Query: 159 -----------GCYNCGDPEHFARDCPRQQGGSNSYN--NNSGGCFKCGGYGHLARDCIT 205
                      GCY CGD  HFARDC ++    N  +    SG C+ CGG GH+ARDC T
Sbjct: 188 DQRGAVKGGNDGCYTCGDVGHFARDCTQKVAAGNVRSGGGGSGTCYSCGGVGHIARDCAT 247

Query: 206 RGSGGGGGGRCYNCGKSGHLARDCGAGGAGGGG---SCFNCGKPGHFARECTKVA 257
           +     G   CY CG SGHLARDC   G+GGGG   +C+ CGK GHFAREC+ VA
Sbjct: 248 KRQPSRG---CYQCGGSGHLARDCDQRGSGGGGNDNACYKCGKEGHFARECSSVA 299

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297798314|ref|XP_002867041.1| hypothetical protein ARALYDRAFT_491032 [Arabidopsis lyrata subsp. lyrata] gi|297312877|gb|EFH43300.1| hypothetical protein ARALYDRAFT_491032 [Arabidopsis lyrata subsp. lyrata]

 Score =  174 bits (441), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 121/260 (46%), Positives = 149/260 (57%), Gaps = 22/260 (8%)

Query: 5   TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGK 64
            RSTGKV WF+ +KGYGFI PDD   +LFVHQ SI S+GYR+L E  SVEF +   +DGK
Sbjct: 9   VRSTGKVNWFNDSKGYGFITPDDRSEELFVHQSSIVSEGYRSLAEGDSVEFAITQGSDGK 68

Query: 65  YQALDVTAPGGAPVHSSKNNNTNNNSGYNNNRGGRGGGGAGFGGYWKGNNDSRRNNGGGY 124
            +A++VTA GG  +   +NN+  N +      G    G  G        +    + GG  
Sbjct: 69  TKAVEVTALGGGAL-KKENNSRGNGARRGGGSGCYNCGELG--------HIGGGSGGGER 119

Query: 125 GPGGVVCYNCDGVGHVARECTSNRR-NSNYNNNSG----GCYNCGDPEHFARDCPRQQ-- 177
           G     CYNC   GH AR+CT     N +    +G    GCYNCGD  HFARDC  Q+  
Sbjct: 120 GSRREGCYNCGDAGHFARDCTQKSVGNGDQRGAAGAGKDGCYNCGDIGHFARDCGNQKVT 179

Query: 178 GGSNSYNNNSGGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDC---GAGGA 234
            GS      SG C+ CGG GH+AR+C T+     G   CY CG SGHLARDC    +GG 
Sbjct: 180 AGSVRSGGGSGSCYTCGGVGHIARECATKRQPSRG---CYQCGGSGHLARDCDQRASGGN 236

Query: 235 GGGGSCFNCGKPGHFARECT 254
           GGG  C++CGK GHFAREC+
Sbjct: 237 GGGNKCYSCGKEGHFARECS 256

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224134074|ref|XP_002327749.1| predicted protein [Populus trichocarpa] gi|222836834|gb|EEE75227.1| predicted protein [Populus trichocarpa]

 Score =  173 bits (438), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 116/273 (42%), Positives = 141/273 (51%), Gaps = 65/273 (23%)

Query: 2   AQLTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDG-YRTLYENQSVEFDVQLE 60
            +  RSTG+V  F   KG+GFI+PD G  DLFVH  +IKSDG YRTLYE+  VEF + L 
Sbjct: 9   TKEERSTGRVVRFSDKKGFGFIKPDAGDKDLFVHHSAIKSDGGYRTLYEDDVVEFTILLN 68

Query: 61  ADGKYQALDVTAPGGAPVHSSKNNNTNNNSGYNNNRGGRGGGGAGFGGYWKGNNDSRRNN 120
            D KYQA+DVTAPGG P+       T  + G+N       GGG                 
Sbjct: 69  -DDKYQAVDVTAPGGGPI----KRRTTFSGGFNRRNSNTNGGG----------------- 106

Query: 121 GGGYGPGGVVCYNCDGVGHVARECTSNRR----------NSNYNNNSGGCYNCGDPEHFA 170
                     C+NC   GH+AREC +N             +       GCY CG+  HFA
Sbjct: 107 ----------CFNCGNPGHIARECNNNSSKSYNYNNNNNRTGGGGGDFGCYKCGNSGHFA 156

Query: 171 RDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCG 230
           R+C +         NN+ GC+ CGG+GH+ARDC       GG G CYNCG  GHLARDC 
Sbjct: 157 RECTK--------GNNNNGCYSCGGFGHVARDCP------GGSGACYNCGGHGHLARDCT 202

Query: 231 AGGAGGG--------GSCFNCGKPGHFARECTK 255
           +    GG        G CFNCGK GHFAR+C +
Sbjct: 203 SARGSGGGRFGSGNTGGCFNCGKDGHFARDCPE 235

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255586301|ref|XP_002533802.1| cellular nucleic acid binding protein, putative [Ricinus communis] gi|223526275|gb|EEF28589.1| cellular nucleic acid binding protein, putative [Ricinus communis]

 Score =  171 bits (432), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 138/268 (51%), Positives = 159/268 (59%), Gaps = 36/268 (13%)

Query: 5   TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDG-YRTLYENQSVEFDVQLEADG 63
            RS GKV  F   KG+GFI+PDDGG DLFVH  +IKSDG YR+L E+  VEF V L  D 
Sbjct: 12  VRSRGKVVRFSDRKGFGFIKPDDGGEDLFVHHSAIKSDGRYRSLAEDDVVEFTVSLSDDN 71

Query: 64  KYQALDVTAPGGAPVHSSKNNNTNNNSGYNNNRGGRGGGGAGFGGYWKGNNDSRRNNGGG 123
           KYQA+DVTAPGG P+ ++ +N        NN RGG G G A  GG + G+  S       
Sbjct: 72  KYQAVDVTAPGGGPIQANHSN--------NNKRGGGGDGPAKRGGGFGGSWSSSSTRRNN 123

Query: 124 YGPGGVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPR--QQGGSN 181
            G GG  CYNC G GH+AREC +   N+N N+N GGC+ CG+  HFARDC        +N
Sbjct: 124 NGGGGGGCYNCGGSGHIARECNN---NNNSNSNGGGCFKCGNTGHFARDCTTRGNNNNNN 180

Query: 182 SYNNNSGGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDC------------ 229
              +   GCF CGGYGHLARDC       GGGG CYNCG  GHLARDC            
Sbjct: 181 GGGDRDRGCFNCGGYGHLARDC------AGGGGACYNCGGFGHLARDCTSARGASGGGAG 234

Query: 230 ----GAGGAGGGGSCFNCGKPGHFAREC 253
               G  G  GGG CFNCG+ GHFAREC
Sbjct: 235 GGRFGGKGGSGGGGCFNCGEEGHFAREC 262

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356559280|ref|XP_003547928.1| PREDICTED: DNA-binding protein HEXBP-like [Glycine max]

 Score =  167 bits (424), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 126/275 (45%), Positives = 153/275 (55%), Gaps = 44/275 (16%)

Query: 1   MAQLTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLE 60
           MA+  R TG V WF+  KG+GFI+PDDGG DLFVHQ SI+SDGYRTL E   VEF +   
Sbjct: 1   MAE-ERFTGVVQWFNNGKGFGFIKPDDGGEDLFVHQSSIRSDGYRTLLEGDRVEFAIATG 59

Query: 61  ADGKYQALDVTAPGGAPVHSSKNNNTNNNSGYNNNRGGRGGGGAGFGGYWKGNNDSRRNN 120
            + K +A+DVT   GAP+           +   NNR G    G+GFG        +RRN 
Sbjct: 60  DNDKTKAVDVTGVDGAPLQP--------RASAANNRAG----GSGFG--------ARRNG 99

Query: 121 GGGYGPGGVVCYNCDGVGHVAREC-TSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQQGG 179
           G G       CY C   GH+AR+C  S+        + GGC+NCG   H ARDC R  GG
Sbjct: 100 GSG-----AACYQCGDFGHLARDCNRSSNTGGGGGGSGGGCFNCGGFGHLARDCVRGGGG 154

Query: 180 SNSYNNNSGG--CFKCGGYGHLARDCIT---RGSGGGGGGRCYNCGKSGHLARDCGAGG- 233
           +       G   CF+CGG+GH+ARDC T      GG  GG C+ CG+ GHLARDCG  G 
Sbjct: 155 NVGVGGGGGSGSCFRCGGFGHMARDCATGKGNIGGGSSGGGCFRCGEVGHLARDCGMEGG 214

Query: 234 -----------AGGGGSCFNCGKPGHFARECTKVA 257
                       GG  +CFNCGKPGHFAREC + +
Sbjct: 215 RYGDGGNSGGGGGGKSTCFNCGKPGHFARECVEAS 249

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|294470718|gb|ADE80751.1| cold shock domain protein 1 [Eutrema salsugineum]

 Score =  166 bits (421), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 115/265 (43%), Positives = 148/265 (55%), Gaps = 29/265 (10%)

Query: 6   RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKY 65
           RSTGKV WF+ +KGYGFI PDD G +LFVHQ +I S+G+R+L    SVEF V    DGK 
Sbjct: 10  RSTGKVNWFNDSKGYGFITPDDDGEELFVHQSAILSEGFRSLTVGDSVEFAVTQGTDGKT 69

Query: 66  QALDVTAPGGAPVHSSKNNNTNNNSGYNNNRGGRGGGGAGFGGYWKGNNDSRRNNGGGYG 125
           +A++VTAPGGAP+H  + ++  N        G R GG     G   G+     ++     
Sbjct: 70  KAVNVTAPGGAPLHRKEISSRGN--------GARRGGSCYHCGEV-GHMAKDCSSSDRGD 120

Query: 126 PGGVVCYNCDGVGHVARECTSNRRNSNYNNNSGG-----CYNCGDPEHFARDCPRQQGGS 180
                CY C   GH AR+C      +  +    G     CYNCG+  HFARDC ++  G+
Sbjct: 121 RSSGGCYTCGDTGHFARDCVQKSSGNGGSGGERGGAGGECYNCGNTGHFARDCVQKSVGN 180

Query: 181 NSYNNNSGG--CFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDC--------- 229
                + GG  C+ CGG GH+ARDC T+   G     CY CG +GH+ARDC         
Sbjct: 181 VGDRGSGGGGVCYNCGGAGHMARDCPTKRQPGA----CYECGGTGHMARDCDRRGSGGGR 236

Query: 230 GAGGAGGGGSCFNCGKPGHFARECT 254
           G  G GGGG+CF CG+ GHFAREC+
Sbjct: 237 GNAGGGGGGNCFKCGQGGHFARECS 261

Source: Eutrema salsugineum

Species: Eutrema salsugineum

Genus: Eutrema

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224074255|ref|XP_002304323.1| predicted protein [Populus trichocarpa] gi|222841755|gb|EEE79302.1| predicted protein [Populus trichocarpa]

 Score =  163 bits (412), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 113/267 (42%), Positives = 138/267 (51%), Gaps = 62/267 (23%)

Query: 6   RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSD-GYRTLYENQSVEFDVQLEADGK 64
           RSTG+V  F   KG+GFI+PD G  DLFVH  +IKSD GYRTLYE+  VEF + L  D K
Sbjct: 2   RSTGRVVRFSDKKGFGFIKPDVGDKDLFVHHSAIKSDGGYRTLYEDDVVEFTILLTED-K 60

Query: 65  YQALDVTAPGGAPVHSSKNNNTNNNSGYNNNRGGRGGGGAGFGGYWKGNNDSRRNNGGGY 124
           YQA++VTAPGG P+       T  + G++         G G                   
Sbjct: 61  YQAIEVTAPGGGPI----KRRTTTSGGFSRRNNNNNNNGVG------------------- 97

Query: 125 GPGGVVCYNCDGVGHVARECTSNRRNSNYNNNSG--------GCYNCGDPEHFARDCPRQ 176
                 C+NC   GH+AR+C +N   S  N N+         GCY CG   HFAR+C + 
Sbjct: 98  ------CFNCGNPGHIARDCNNNSSKSYNNYNNNNNNRGADFGCYKCGSSGHFARECTK- 150

Query: 177 QGGSNSYNNNSGGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGAG---- 232
                    N+ GC+ CGG GH+ARDC       GG G CYNCG  GHLARDC +     
Sbjct: 151 --------GNNNGCYSCGGIGHVARDC------PGGSGACYNCGGYGHLARDCTSARVTG 196

Query: 233 ----GAGGGGSCFNCGKPGHFARECTK 255
               G G  G CFNCG  GHFAR+C +
Sbjct: 197 GGRFGGGNSGGCFNCGNEGHFARDCPE 223

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357518027|ref|XP_003629302.1| Major cold-shock protein [Medicago truncatula] gi|355523324|gb|AET03778.1| Major cold-shock protein [Medicago truncatula]

 Score =  159 bits (401), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 115/300 (38%), Positives = 147/300 (49%), Gaps = 69/300 (23%)

Query: 1   MAQLTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLE 60
           MA+  R +G V WF+  KG+GFI+PDD   DLFVHQ  I+S+G+R+L E   VEF +   
Sbjct: 1   MAE-ERISGVVQWFNNTKGFGFIKPDDDSEDLFVHQSDIRSEGFRSLSEGDRVEFTIADG 59

Query: 61  ADGKYQALDVTAPGGAPVHSSKNNNTNNNSGYNNNRGGRGGGGAGFGGYWKGNNDSRRNN 120
            +GK +A+DVT P G P+   ++N+     G     G R  GG G               
Sbjct: 60  DNGKTKAVDVTGPKGEPLQVRQDNHGGGGGGRGFRGGERRNGGGG--------------- 104

Query: 121 GGGYGPGGVVCYNCDGVGHVARECTSNRRNSN--------YNNNSGGCYNCGDPEHFARD 172
                     CY C   GH+AR+C  + RN            +    CY CG  EHFARD
Sbjct: 105 ----------CYTCGDTGHIARDCDRSDRNDRNDRSGGGGGGDRDRACYTCGSFEHFARD 154

Query: 173 CPRQQGGSNSYNNNSG----GCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARD 228
           C R  G +N+     G     C++CGG GH+ARDC T  SGGGGGG CY CG+ GH+ARD
Sbjct: 155 CMRGGGNNNNGGGGYGGGGTSCYRCGGVGHIARDCATPSSGGGGGGACYKCGEVGHIARD 214

Query: 229 CG-AGGAGGGG------------------------------SCFNCGKPGHFARECTKVA 257
           C   GG   GG                              +CFNCGK GHFAR+C + +
Sbjct: 215 CSNEGGRFDGGNGRYDDGNGRFGGGNRRFGSGGGGHDGGKGTCFNCGKAGHFARDCVEAS 274

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18398546|ref|NP_565427.1| cold shock domain protein 3 [Arabidopsis thaliana] gi|75165198|sp|Q94C69.1|CSP3_ARATH RecName: Full=Cold shock domain-containing protein 3; Short=AtCSP3 gi|14334920|gb|AAK59638.1| putative glycine-rich, zinc-finger DNA-binding protein [Arabidopsis thaliana] gi|17104541|gb|AAL34159.1| putative glycine-rich, zinc-finger DNA-binding protein [Arabidopsis thaliana] gi|148726892|dbj|BAF63841.1| cold shock domain protein 3 [Arabidopsis thaliana] gi|330251603|gb|AEC06697.1| cold shock domain protein 3 [Arabidopsis thaliana]

 Score =  157 bits (398), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 127/296 (42%), Positives = 159/296 (53%), Gaps = 48/296 (16%)

Query: 6   RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKY 65
           RS GKV+WF   KGYGFI PDDGG +LFVHQ SI SDG+R+L   +SVE+++ L +DGK 
Sbjct: 10  RSIGKVSWFSDGKGYGFITPDDGGEELFVHQSSIVSDGFRSLTLGESVEYEIALGSDGKT 69

Query: 66  QALDVTAPGGAPVHSSKNNNTNNNSGYNNNRGGRGGGGAG-------------------- 105
           +A++VTAPGG  ++  K  N++  SG N    G  G  A                     
Sbjct: 70  KAIEVTAPGGGSLN--KKENSSRGSGGNCFNCGEVGHMAKDCDGGSGGKSFGGGGGRRSG 127

Query: 106 ----------FGGYWKGNNDSRRNNGGGYGPGGVVCYNCDGVGHVAREC------TSNRR 149
                      G + +    S   N GG G GG  CY+C  VGH+A++C           
Sbjct: 128 GEGECYMCGDVGHFARDCRQSGGGNSGGGGGGGRPCYSCGEVGHLAKDCRGGSGGNRYGG 187

Query: 150 NSNYNNNSGGCYNCGDPEHFARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITR-GS 208
                +   GCY CG   HFARDC  +Q G  +       C+ CGG GH+A+ C ++  S
Sbjct: 188 GGGRGSGGDGCYMCGGVGHFARDC--RQNGGGNVGGGGSTCYTCGGVGHIAKVCTSKIPS 245

Query: 209 GGGGGGR-CYNCGKSGHLARDC------GAGGAGGGGSCFNCGKPGHFARECTKVA 257
           GGGGGGR CY CG +GHLARDC       +GG GG   CF CGK GHFARECT VA
Sbjct: 246 GGGGGGRACYECGGTGHLARDCDRRGSGSSGGGGGSNKCFICGKEGHFARECTSVA 301

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297836502|ref|XP_002886133.1| hypothetical protein ARALYDRAFT_480687 [Arabidopsis lyrata subsp. lyrata] gi|297331973|gb|EFH62392.1| hypothetical protein ARALYDRAFT_480687 [Arabidopsis lyrata subsp. lyrata]

 Score =  156 bits (395), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 123/296 (41%), Positives = 154/296 (52%), Gaps = 48/296 (16%)

Query: 6   RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKY 65
           R  GKV WF   KGYGFI PDDGG +LFVHQ SI SDGYR+L   +SVE+ + L +DGK 
Sbjct: 8   RYIGKVNWFGDGKGYGFITPDDGGEELFVHQSSIVSDGYRSLTVGESVEYSITLGSDGKT 67

Query: 66  QALDVTAPGGAPVHSSKNNNTNNNSGYNNNRGGRGGGG---------------------- 103
           +A++VTAPGG  + + K N++  N G   N G  G                         
Sbjct: 68  KAVNVTAPGGGSL-NKKENSSRGNGGSCFNCGEVGHMAKDCDGGGGGRSYGGGGGRRSGG 126

Query: 104 ------AGFGGYWKGNNDSRRNNGGGYGPGGVVCYNCDGVGHVAREC-----TSNRRNSN 152
                  G  G++  +         G G GG  CY+C  VGH+A++C      +      
Sbjct: 127 EGTCYVCGDVGHFARDCRQSGGGNSGGGGGGGPCYSCGEVGHLAKDCRGGSGGNRYGGGG 186

Query: 153 YNNNSGGCYNCGDPEHFARDCPRQQGGSNSYNNNSGG-CFKCGGYGHLARDCITRGSGGG 211
             + S GCY CG   HFARDC +  GG+       G  C+ CGG GH+AR C ++   GG
Sbjct: 187 RGSGSDGCYLCGGVGHFARDCRQNGGGNVGGGGGGGNTCYTCGGVGHIARVCTSKRPSGG 246

Query: 212 GGGRCYNCGKSGHLARDC----------GAGGAGGGGSCFNCGKPGHFARECTKVA 257
               CY CG++GHLARDC          G GG GG G CFNCGK GHFAREC+ VA
Sbjct: 247 A---CYECGETGHLARDCDRRGSGSSGGGGGGGGGSGKCFNCGKEGHFARECSSVA 299

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	258
TAIR|locus:2135139	299	CSDP1 "cold shock domain prote	0.271	0.234	0.614	6.4e-37
TAIR|locus:2827810	301	CSP3 "cold shock domain protei	0.298	0.255	0.571	3.1e-35
TAIR|locus:2121219	203	GRP2 "AT4G38680" [Arabidopsis	0.294	0.374	0.526	1.1e-31
TAIR|locus:2047092	201	GRP2B "glycine-rich protein 2B	0.294	0.378	0.539	1.3e-31
FB|FBgn0035626	195	lin-28 "lin-28" [Drosophila me	0.279	0.369	0.424	3.5e-15
ZFIN|ZDB-GENE-040426-747	202	lin28a "lin-28 homolog A (C. e	0.286	0.366	0.373	1.5e-14
UNIPROTKB|Q6ZN17	250	LIN28B "Protein lin-28 homolog	0.310	0.32	0.363	1.6e-13
TIGR_CMR|SO_1648	69	SO_1648 "cold shock domain fam	0.255	0.956	0.492	4.4e-13
UNIPROTKB|F1P7H7	251	LIN28B "Uncharacterized protei	0.310	0.318	0.352	5.1e-13
UNIPROTKB|D4A0Q1	247	Lin28b "Protein Lin28b" [Rattu	0.310	0.323	0.363	5.8e-13

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

 Score = 233 (87.1 bits), Expect = 6.4e-37, Sum P(2) = 6.4e-37
 Identities = 43/70 (61%), Positives = 54/70 (77%)

Query:     6 RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKY 65
             RSTGKV WF+ +KGYGFI PDDG  +LFVHQ SI S+GYR+L    +VEF +   +DGK 
Sbjct:    10 RSTGKVNWFNASKGYGFITPDDGSVELFVHQSSIVSEGYRSLTVGDAVEFAITQGSDGKT 69

Query:    66 QALDVTAPGG 75
             +A++VTAPGG
Sbjct:    70 KAVNVTAPGG 79

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

GO:0003677 "DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

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

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

GO:0003723 "RNA binding" evidence=IDA

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

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

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

GO:0032508 "DNA duplex unwinding" evidence=IDA

GO:0009631 "cold acclimation" evidence=IGI

GO:0009165 "nucleotide biosynthetic process" evidence=RCA

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

 Score = 245 (91.3 bits), Expect = 3.1e-35, Sum P(2) = 3.1e-35
 Identities = 44/77 (57%), Positives = 59/77 (76%)

Query:     6 RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKY 65
             RS GKV+WF   KGYGFI PDDGG +LFVHQ SI SDG+R+L   +SVE+++ L +DGK 
Sbjct:    10 RSIGKVSWFSDGKGYGFITPDDGGEELFVHQSSIVSDGFRSLTLGESVEYEIALGSDGKT 69

Query:    66 QALDVTAPGGAPVHSSK 82
             +A++VTAPGG  ++  +
Sbjct:    70 KAIEVTAPGGGSLNKKE 86

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

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0005737 "cytoplasm" evidence=IDA

GO:0009631 "cold acclimation" evidence=IMP

GO:0032508 "DNA duplex unwinding" evidence=IDA

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

 Score = 229 (85.7 bits), Expect = 1.1e-31, Sum P(3) = 1.1e-31
 Identities = 40/76 (52%), Positives = 57/76 (75%)

Query:     6 RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKY 65
             R  G V WFD  KG+GFI PDDGG DLFVHQ SI+S+G+R+L   ++VEF+V+++ + + 
Sbjct:    10 RRKGSVKWFDTQKGFGFITPDDGGDDLFVHQSSIRSEGFRSLAAEEAVEFEVEIDNNNRP 69

Query:    66 QALDVTAPGGAPVHSS 81
             +A+DV+ P GAPV  +
Sbjct:    70 KAIDVSGPDGAPVQGN 85

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0009409 "response to cold" evidence=IEP

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

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

GO:0003729 "mRNA binding" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

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

GO:0048316 "seed development" evidence=IMP

GO:0048443 "stamen development" evidence=IMP

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

GO:0032508 "DNA duplex unwinding" evidence=IDA

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

GO:0005886 "plasma membrane" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0009631 "cold acclimation" evidence=IGI

GO:0005829 "cytosol" evidence=IDA

GO:0009269 "response to desiccation" evidence=IEP

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

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

 Score = 229 (85.7 bits), Expect = 1.3e-31, Sum P(3) = 1.3e-31
 Identities = 41/76 (53%), Positives = 56/76 (73%)

Query:     6 RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKY 65
             R  G V WFD  KG+GFI P DGG DLFVHQ SI+S+G+R+L   +SVEFDV+++  G+ 
Sbjct:    14 RRKGTVKWFDTQKGFGFITPSDGGDDLFVHQSSIRSEGFRSLAAEESVEFDVEVDNSGRP 73

Query:    66 QALDVTAPGGAPVHSS 81
             +A++V+ P GAPV  +
Sbjct:    74 KAIEVSGPDGAPVQGN 89

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

GO:0003677 "DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009409 "response to cold" evidence=IEP

GO:0005634 "nucleus" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0009790 "embryo development" evidence=IMP

GO:0010154 "fruit development" evidence=IMP

FB|FBgn0035626 lin-28 "lin-28" [Drosophila melanogaster (taxid:7227)]

 Score = 156 (60.0 bits), Expect = 3.5e-15, Sum P(2) = 3.5e-15
 Identities = 31/73 (42%), Positives = 46/73 (63%)

Query:     9 GKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQAL 68
             GK  WF+ AKG+GF+ P+DGG ++FVHQ  I+  G+R+L E + VEF+ Q  + G  +A 
Sbjct:    41 GKCKWFNVAKGWGFLTPNDGGQEVFVHQSVIQMSGFRSLGEQEEVEFECQRTSRG-LEAT 99

Query:    69 DVTAPGGAPVHSS 81
              V++  G     S
Sbjct:   100 RVSSRHGGSCQGS 112

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

GO:0003677 "DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISS

GO:0001708 "cell fate specification" evidence=ISS

ZFIN|ZDB-GENE-040426-747 lin28a "lin-28 homolog A (C. elegans)" [Danio rerio (taxid:7955)]

 Score = 131 (51.2 bits), Expect = 1.5e-14, Sum P(2) = 1.5e-14
 Identities = 31/83 (37%), Positives = 46/83 (55%)

Query:     8 TGKVTWFDGAKGYGFIRPD-------DGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLE 60
             +G   WF+   G+GF+          D   D+FVHQ  +  +G+R+L E ++VEF  +  
Sbjct:    35 SGVCKWFNVRMGFGFLSMTHREGICLDSPVDVFVHQSKLHMEGFRSLKEGEAVEFTFKRS 94

Query:    61 ADGKYQALDVTAPGGAP-VHSSK 82
             + G  ++L VT PGGAP V S K
Sbjct:    95 SKG-LESLQVTGPGGAPCVGSEK 116

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0010629 "negative regulation of gene expression" evidence=IMP

GO:0005634 "nucleus" evidence=ISS

GO:0010494 "cytoplasmic stress granule" evidence=ISS

GO:0031054 "pre-miRNA processing" evidence=ISS

GO:0031123 "RNA 3'-end processing" evidence=ISS

GO:0019827 "stem cell maintenance" evidence=ISS

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

GO:0003723 "RNA binding" evidence=IEA;ISS

GO:0010587 "miRNA catabolic process" evidence=ISS

GO:0031047 "gene silencing by RNA" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|Q6ZN17 LIN28B "Protein lin-28 homolog B" [Homo sapiens (taxid:9606)]

 Score = 139 (54.0 bits), Expect = 1.6e-13, Sum P(2) = 1.6e-13
 Identities = 32/88 (36%), Positives = 49/88 (55%)

Query:     2 AQLTRSTGKVTWFDGAKGYGFIR-------PDDGGADLFVHQKSIKSDGYRTLYENQSVE 54
             +Q+ R TG   WF+   G+GFI        P D   D+FVHQ  +  +G+R+L E + VE
Sbjct:    25 SQVLRGTGHCKWFNVRMGFGFISMINREGSPLDIPVDVFVHQSKLFMEGFRSLKEGEPVE 84

Query:    55 FDVQLEADGKYQALDVTAPGGAPVHSSK 82
             F  +  + G  +++ VT PGG+P   S+
Sbjct:    85 FTFKKSSKG-LESIRVTGPGGSPCLGSE 111

GO:0003677 "DNA binding" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IDA

GO:0031054 "pre-miRNA processing" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0031123 "RNA 3'-end processing" evidence=IMP

GO:0010587 "miRNA catabolic process" evidence=IMP

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005739 "mitochondrion" evidence=IDA

TIGR_CMR|SO_1648 SO_1648 "cold shock domain family protein" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 172 (65.6 bits), Expect = 4.4e-13, P = 4.4e-13
 Identities = 33/67 (49%), Positives = 48/67 (71%)

Query:     4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADG 63
             ++++TG V WF+  KG+GFI PD+GGAD FVH ++I SDG++TL E Q V ++V+    G
Sbjct:     1 MSKTTGVVKWFNEDKGFGFISPDNGGADAFVHFRAIVSDGFKTLAEGQKVSYEVEQGQKG 60

Query:    64 KYQALDV 70
               QA +V
Sbjct:    61 P-QAANV 66

GO:0003677 "DNA binding" evidence=ISS

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

GO:0009409 "response to cold" evidence=ISS

UNIPROTKB|F1P7H7 LIN28B "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 135 (52.6 bits), Expect = 5.1e-13, Sum P(2) = 5.1e-13
 Identities = 31/88 (35%), Positives = 48/88 (54%)

Query:     2 AQLTRSTGKVTWFDGAKGYGFIR-------PDDGGADLFVHQKSIKSDGYRTLYENQSVE 54
             +Q+   TG   WF+   G+GFI        P D   D+FVHQ  +  +G+R+L E + VE
Sbjct:    24 SQILHGTGHCKWFNVRMGFGFISMINREGSPLDIPVDVFVHQSKLFMEGFRSLKEGEPVE 83

Query:    55 FDVQLEADGKYQALDVTAPGGAPVHSSK 82
             F  +  + G  +++ VT PGG+P   S+
Sbjct:    84 FTFKKSSKG-LESIRVTGPGGSPCLGSE 110

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|D4A0Q1 Lin28b "Protein Lin28b" [Rattus norvegicus (taxid:10116)]

 Score = 135 (52.6 bits), Expect = 5.8e-13, Sum P(2) = 5.8e-13
 Identities = 32/88 (36%), Positives = 47/88 (53%)

Query:     2 AQLTRSTGKVTWFDGAKGYGFI-------RPDDGGADLFVHQKSIKSDGYRTLYENQSVE 54
             +Q+ R TG   WF+   G+GFI        P D   D+FVHQ  +  +G+R+L E + VE
Sbjct:    23 SQVLRGTGHCKWFNVRMGFGFISMISREGNPLDIPVDVFVHQSKLFMEGFRSLKEGEPVE 82

Query:    55 FDVQLEADGKYQALDVTAPGGAPVHSSK 82
             F  +    G  +++ VT PGG P   S+
Sbjct:    83 FTFKKSPKG-LESIRVTGPGGNPCLGSE 109

GO:0003677 "DNA binding" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O65639	CSP1_ARATH	No assigned EC number	0.4203	0.9573	0.8260	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	CSDP1	CSDP1 (cold shock domain protein 1); RNA binding / double-stranded DNA binding / nucleic acid binding / single-stranded DNA binding; Encodes a cold shock domain protein. Involved in cold acclimation by blocking the secondary structure of mRNA which in turn facilitates translation at cold temperature. (299 aa)
		(Arabidopsis thaliana)
Predicted Functional Partners:
	SRZ-22	SRZ-22; protein binding; Encodes a Serine/arginine-rich (SR) protein RSZp22. SR proteins are sp [...] (200 aa)				•		•		•	0.943
	AT2G17870	cold-shock DNA-binding family protein; cold-shock DNA-binding family protein; FUNCTIONS IN- DNA [...] (301 aa)			•	•		•	•	•	0.928
	SmD3	SmD3 (snRNP core protein SmD3); snRNP core protein SmD3 (SmD3); FUNCTIONS IN- molecular_functio [...] (128 aa)				•		•			0.921
	NRPB12	NRPB12; DNA binding / DNA-directed RNA polymerase; Non-catalytic subunit common to nuclear DNA- [...] (51 aa)				•		•			0.918
	AT2G24590	splicing factor, putative; splicing factor, putative; FUNCTIONS IN- zinc ion binding, nucleotid [...] (196 aa)				•		•		•	0.916
	ATGRP2B	ATGRP2B (GLYCINE-RICH PROTEIN 2B); DNA binding / nucleic acid binding / zinc ion binding; glyci [...] (201 aa)			•			•	•	•	0.913
	GRP2	GRP2 (GLYCINE RICH PROTEIN 2); double-stranded DNA binding / mRNA binding / nucleic acid bindin [...] (203 aa)			•			•	•	•	0.912
	NRPB5	NRPB5; DNA binding / DNA-directed RNA polymerase; Non-catalytic subunit common to DNA-dependent [...] (205 aa)				•		•			0.912
	EMB2770	EMB2770 (EMBRYO DEFECTIVE 2770); RNA splicing factor, transesterification mechanism; Encodes a [...] (1029 aa)				•		•			0.909
	NRPB7	NRPB7; DNA-directed RNA polymerase/ RNA binding; Non-catalytic subunit specific to DNA-directed [...] (176 aa)				•		•			0.909

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	258
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	8e-30
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	5e-27
pfam00313	66	pfam00313, CSD, 'Cold-shock' DNA-binding domain	2e-23
cd04458	65	cd04458, CSP_CDS, Cold-Shock Protein (CSP) contain	3e-23
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	2e-22
COG1278	67	COG1278, CspC, Cold shock proteins [Transcription]	6e-20
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	9e-20
COG5082	190	COG5082, AIR1, Arginine methyltransferase-interact	4e-16
smart00357	64	smart00357, CSP, Cold shock protein domain	2e-15
TIGR02381	68	TIGR02381, cspD, cold shock domain protein CspD	7e-15
PRK09890	70	PRK09890, PRK09890, cold shock protein CspG; Provi	8e-15
PRK09507	69	PRK09507, cspE, cold shock protein CspE; Reviewed	3e-14
PRK14998	73	PRK14998, PRK14998, cold shock-like protein CspD;	3e-13
PRK10354	70	PRK10354, PRK10354, RNA chaperone/anti-terminator;	3e-13
PRK09937	74	PRK09937, PRK09937, stationary phase/starvation in	3e-13
PRK10943	69	PRK10943, PRK10943, cold shock-like protein CspC;	5e-13
COG5082	190	COG5082, AIR1, Arginine methyltransferase-interact	4e-10
COG5082	190	COG5082, AIR1, Arginine methyltransferase-interact	5e-10
COG5082	190	COG5082, AIR1, Arginine methyltransferase-interact	6e-10
COG5082	190	COG5082, AIR1, Arginine methyltransferase-interact	4e-07
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	4e-06
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	1e-05
pfam00098	18	pfam00098, zf-CCHC, Zinc knuckle	7e-04
smart00343	17	smart00343, ZnF_C2HC, zinc finger	0.002
PRK15463	70	PRK15463, PRK15463, cold shock-like protein CspF;	0.003
pfam00098	18	pfam00098, zf-CCHC, Zinc knuckle	0.004

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

 Score =  108 bits (272), Expect = 8e-30
 Identities = 52/129 (40%), Positives = 68/129 (52%), Gaps = 11/129 (8%)

Query: 127 GGVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQQGGSNSYNNN 186
               CY C   GH++REC S             CYNCG   H +R+CP    GS   +  
Sbjct: 26  KARPCYKCGEPGHLSRECPSAPGGRG----ERSCYNCGKTGHLSRECPEAPPGSGPRS-- 79

Query: 187 SGGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDC-GAGGAGGGG-SCFNCG 244
              C+ CG  GH++R+C  R  GG     CYNCG  GH++RDC  AG   GG  +C+NCG
Sbjct: 80  ---CYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCPNAGKRPGGDKTCYNCG 136

Query: 245 KPGHFAREC 253
           + GH +R+C
Sbjct: 137 QTGHLSRDC 145

Length = 148

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

 Score =  101 bits (254), Expect = 5e-27
 Identities = 51/126 (40%), Positives = 71/126 (56%), Gaps = 10/126 (7%)

Query: 130 VCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQQGGSNSYNNNSGG 189
           VCY C GVGH +REC ++         +  CY CG+P H +R+CP   GG    +     
Sbjct: 2   VCYRCGGVGHQSRECPNSAPAG--AAKARPCYKCGEPGHLSRECPSAPGGRGERS----- 54

Query: 190 CFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDC--GAGGAGGGGSCFNCGKPG 247
           C+ CG  GHL+R+C      G G   CYNCG++GH++R+C   A G     +C+NCG  G
Sbjct: 55  CYNCGKTGHLSRECPEA-PPGSGPRSCYNCGQTGHISRECPNRAKGGAARRACYNCGGEG 113

Query: 248 HFAREC 253
           H +R+C
Sbjct: 114 HISRDC 119

Length = 148

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

 Score = 89.6 bits (223), Expect = 2e-23
 Identities = 33/66 (50%), Positives = 43/66 (65%), Gaps = 1/66 (1%)

Query: 8  TGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQA 67
          TG V WF+  KG+GFI P+DG  D+FVH  +I+ DG+R+L E Q VEFD+  E     QA
Sbjct: 2  TGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQRVEFDIV-EGTKGPQA 60

Query: 68 LDVTAP 73
           +VT  
Sbjct: 61 ANVTLL 66

Length = 66

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

 Score = 89.2 bits (222), Expect = 3e-23
 Identities = 33/64 (51%), Positives = 45/64 (70%), Gaps = 1/64 (1%)

Query: 8  TGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQA 67
          TG V WFD  KG+GFI PDDGG D+FVH  +++ DG+R+L E   VEF+++ E D   QA
Sbjct: 2  TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELE-EGDKGPQA 60

Query: 68 LDVT 71
          ++V 
Sbjct: 61 VNVR 64

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

 Score = 89.5 bits (222), Expect = 2e-22
 Identities = 45/105 (42%), Positives = 57/105 (54%), Gaps = 8/105 (7%)

Query: 125 GPGGVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQQGGSNSYN 184
           G G   CYNC   GH++REC      S        CYNCG   H +R+CP +  G  +  
Sbjct: 49  GRGERSCYNCGKTGHLSRECPEAPPGS----GPRSCYNCGQTGHISRECPNRAKGGAA-- 102

Query: 185 NNSGGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDC 229
                C+ CGG GH++RDC   G   GG   CYNCG++GHL+RDC
Sbjct: 103 --RRACYNCGGEGHISRDCPNAGKRPGGDKTCYNCGQTGHLSRDC 145

Length = 148

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

 Score = 80.3 bits (199), Expect = 6e-20
 Identities = 32/67 (47%), Positives = 44/67 (65%), Gaps = 1/67 (1%)

Query: 6  RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKY 65
           +TG V WF+  KG+GFI P+DGG D+FVH  +I+  G+RTL E Q VEF+V+ +     
Sbjct: 1  MATGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRAGFRTLREGQKVEFEVE-QGRKGP 59

Query: 66 QALDVTA 72
           A +V A
Sbjct: 60 SAANVRA 66

Length = 67

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

 Score = 82.5 bits (204), Expect = 9e-20
 Identities = 43/96 (44%), Positives = 57/96 (59%), Gaps = 5/96 (5%)

Query: 160 CYNCGDPEHFARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITRGSGGGGGGRCYNC 219
           CY CG   H +R+CP     + +    +  C+KCG  GHL+R+C     GG G   CYNC
Sbjct: 3   CYRCGGVGHQSRECPNS---APAGAAKARPCYKCGEPGHLSREC-PSAPGGRGERSCYNC 58

Query: 220 GKSGHLARDCGAGGAGGGG-SCFNCGKPGHFARECT 254
           GK+GHL+R+C     G G  SC+NCG+ GH +REC 
Sbjct: 59  GKTGHLSRECPEAPPGSGPRSCYNCGQTGHISRECP 94

Length = 148

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

 Score = 73.7 bits (181), Expect = 4e-16
 Identities = 37/136 (27%), Positives = 54/136 (39%), Gaps = 35/136 (25%)

Query: 130 VCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQQGGSNSYNNNSGG 189
           VC+NC   GH+ R+C  +            CYNC    H +  CP+ +            
Sbjct: 62  VCFNCGQNGHLRRDCPHSI-----------CYNCSWDGHRSNHCPKPK-----------K 99

Query: 190 CFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDC----------GAGGAGGGGS 239
           C+ CG  GHL+RDC            C++C  + H + DC             G      
Sbjct: 100 CYNCGETGHLSRDCNPSKD---QQKSCFDCNSTRHSSEDCPSIWKHYVLNNGDGHPIKKF 156

Query: 240 CFNCGKPGHFARECTK 255
           C++CG  GHF  +C +
Sbjct: 157 CYSCGSAGHFGDDCKE 172

Length = 190

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

 Score = 68.4 bits (168), Expect = 2e-15
 Identities = 32/67 (47%), Positives = 40/67 (59%), Gaps = 4/67 (5%)

Query: 8  TGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQL-EADGKYQ 66
          TG V WF+  KG+GFIRPDDGG D+FVH   I+  G ++L E   VEF V   E   K +
Sbjct: 1  TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQ-GGLKSLREGDEVEFKVVSPEGGEKPE 57

Query: 67 ALDVTAP 73
          A +V   
Sbjct: 58 AENVVKL 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|131434 TIGR02381, cspD, cold shock domain protein CspD

 Score = 67.2 bits (164), Expect = 7e-15
 Identities = 25/50 (50%), Positives = 33/50 (66%)

Query: 8  TGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDV 57
           G V WF+ AKG+GFI P+    D+F H  +I+ DGYRTL   Q V+F+V
Sbjct: 3  IGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDGYRTLKAGQKVQFEV 52

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

 Score = 67.1 bits (163), Expect = 8e-15
 Identities = 33/66 (50%), Positives = 43/66 (65%)

Query: 6  RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKY 65
          + TG V WF+  KG+GFI PDDG  D+FVH  +I+S+ +RTL ENQ VEF ++    G  
Sbjct: 4  KMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRGPA 63

Query: 66 QALDVT 71
           A  VT
Sbjct: 64 AANVVT 69

Length = 70

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

 Score = 65.8 bits (160), Expect = 3e-14
 Identities = 30/69 (43%), Positives = 47/69 (68%), Gaps = 1/69 (1%)

Query: 4  LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADG 63
          +++  G V WF+ +KG+GFI P+DG  D+FVH  +I+++G++TL E Q VEF++   A G
Sbjct: 1  MSKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKG 60

Query: 64 KYQALDVTA 72
             A +V A
Sbjct: 61 P-SAANVIA 68

Length = 69

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

 Score = 63.1 bits (153), Expect = 3e-13
 Identities = 32/63 (50%), Positives = 41/63 (65%)

Query: 8  TGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQA 67
          TG V WF+ AKG+GFI P+ GG D+F H  +I+ DGYRTL   QSV FDV     G + +
Sbjct: 3  TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHAS 62

Query: 68 LDV 70
          + V
Sbjct: 63 VIV 65

Length = 73

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

 Score = 63.1 bits (153), Expect = 3e-13
 Identities = 29/58 (50%), Positives = 40/58 (68%)

Query: 6  RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADG 63
          + TG V WF+  KG+GFI PDDG  D+FVH  +I++DGY++L E Q V F ++  A G
Sbjct: 4  KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKG 61

Length = 70

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

 Score = 63.2 bits (153), Expect = 3e-13
 Identities = 31/62 (50%), Positives = 41/62 (66%)

Query: 9  GKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQAL 68
          G V WF+ AKG+GFI P+ GG D+F H  +I+ DGYRTL   QSV+FDV     G + ++
Sbjct: 4  GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKGNHASV 63

Query: 69 DV 70
           V
Sbjct: 64 IV 65

Length = 74

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

 Score = 62.4 bits (151), Expect = 5e-13
 Identities = 31/69 (44%), Positives = 48/69 (69%), Gaps = 1/69 (1%)

Query: 4  LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADG 63
          + +  G+V WF+ +KG+GFI P DG  D+FVH  +I+ +G++TL E Q+VEF++Q    G
Sbjct: 1  MAKIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKG 60

Query: 64 KYQALDVTA 72
             A++VTA
Sbjct: 61 P-AAVNVTA 68

Length = 69

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

 Score = 57.6 bits (139), Expect = 4e-10
 Identities = 29/103 (28%), Positives = 40/103 (38%), Gaps = 14/103 (13%)

Query: 126 PGGVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQQGGSNSYNN 185
           P    CYNC   GH++R+C  ++           C++C    H + DCP         N 
Sbjct: 95  PKPKKCYNCGETGHLSRDCNPSKDQQKS------CFDCNSTRHSSEDCPSIWKHYVLNNG 148

Query: 186 N----SGGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGH 224
           +       C+ CG  GH   DC    S        Y CGK G+
Sbjct: 149 DGHPIKKFCYSCGSAGHFGDDCKEPRS----SRVPYVCGKKGY 187

Length = 190

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

 Score = 57.2 bits (138), Expect = 5e-10
 Identities = 37/132 (28%), Positives = 51/132 (38%), Gaps = 27/132 (20%)

Query: 128 GVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQQGGSNSYNNNS 187
             +CYNC   GH +  C   ++          CYNCG+  H +RDC   +    S     
Sbjct: 78  HSICYNCSWDGHRSNHCPKPKK----------CYNCGETGHLSRDCNPSKDQQKS----- 122

Query: 188 GGCFKCGGYGHLARDC--ITRGSGGGGGGR------CYNCGKSGHLARDCGAGGAGGGGS 239
             CF C    H + DC  I +      G        CY+CG +GH   DC          
Sbjct: 123 --CFDCNSTRHSSEDCPSIWKHYVLNNGDGHPIKKFCYSCGSAGHFGDDCKE--PRSSRV 178

Query: 240 CFNCGKPGHFAR 251
            + CGK G+ + 
Sbjct: 179 PYVCGKKGYVSF 190

Length = 190

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

 Score = 56.8 bits (137), Expect = 6e-10
 Identities = 32/103 (31%), Positives = 43/103 (41%), Gaps = 20/103 (19%)

Query: 151 SNYNNNSGGCYNCGDPEHFARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITRGSGG 210
           S     +  C+NCG   H  RDCP               C+ C   GH +  C       
Sbjct: 54  SAIREENPVCFNCGQNGHLRRDCPHSI------------CYNCSWDGHRSNHCPKPK--- 98

Query: 211 GGGGRCYNCGKSGHLARDCGAGGAGGGGSCFNCGKPGHFAREC 253
               +CYNCG++GHL+RDC         SCF+C    H + +C
Sbjct: 99  ----KCYNCGETGHLSRDCNPSKD-QQKSCFDCNSTRHSSEDC 136

Length = 190

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

 Score = 48.7 bits (116), Expect = 4e-07
 Identities = 25/74 (33%), Positives = 33/74 (44%), Gaps = 13/74 (17%)

Query: 180 SNSYNNNSGGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGAGGAGGGGS 239
            ++    +  CF CG  GHL RDC            CYNC   GH +  C          
Sbjct: 53  VSAIREENPVCFNCGQNGHLRRDCPHS--------ICYNCSWDGHRSNHCPK-----PKK 99

Query: 240 CFNCGKPGHFAREC 253
           C+NCG+ GH +R+C
Sbjct: 100 CYNCGETGHLSRDC 113

Length = 190

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

 Score = 45.2 bits (107), Expect = 4e-06
 Identities = 19/43 (44%), Positives = 24/43 (55%), Gaps = 3/43 (6%)

Query: 216 CYNCGKSGHLARDC---GAGGAGGGGSCFNCGKPGHFARECTK 255
           CY CG  GH +R+C      GA     C+ CG+PGH +REC  
Sbjct: 3   CYRCGGVGHQSRECPNSAPAGAAKARPCYKCGEPGHLSRECPS 45

Length = 148

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

 Score = 43.6 bits (103), Expect = 1e-05
 Identities = 21/55 (38%), Positives = 27/55 (49%), Gaps = 3/55 (5%)

Query: 120 NGGGYGPGGVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCP 174
           N    G     CYNC G GH++R+C +  +          CYNCG   H +RDCP
Sbjct: 95  NRAKGGAARRACYNCGGEGHISRDCPNAGKRPG---GDKTCYNCGQTGHLSRDCP 146

Length = 148

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

 Score = 35.9 bits (84), Expect = 7e-04
 Identities = 10/16 (62%), Positives = 13/16 (81%)

Query: 240 CFNCGKPGHFARECTK 255
           C+NCGK GH AR+C +
Sbjct: 3   CYNCGKEGHLARDCPE 18

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

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

 Score = 34.3 bits (80), Expect = 0.002
 Identities = 10/16 (62%), Positives = 12/16 (75%)

Query: 240 CFNCGKPGHFARECTK 255
           C+NCGK GH AR+C  
Sbjct: 2   CYNCGKEGHIARDCPS 17

Length = 17

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

 Score = 35.3 bits (81), Expect = 0.003
 Identities = 19/50 (38%), Positives = 23/50 (46%)

Query: 6  RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEF 55
          + TG V  FDG  G G I P DG  D+ VH  ++       L     VEF
Sbjct: 4  KMTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEF 53

Length = 70

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

 Score = 33.6 bits (78), Expect = 0.004
 Identities = 13/16 (81%), Positives = 14/16 (87%)

Query: 214 GRCYNCGKSGHLARDC 229
            +CYNCGK GHLARDC
Sbjct: 1   RKCYNCGKEGHLARDC 16

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	258
PTZ00368	148	universal minicircle sequence binding protein (UMS	99.96
COG1278	67	CspC Cold shock proteins [Transcription]	99.92
PRK10943	69	cold shock-like protein CspC; Provisional	99.9
PRK15464	70	cold shock-like protein CspH; Provisional	99.9
PTZ00368	148	universal minicircle sequence binding protein (UMS	99.89
PRK15463	70	cold shock-like protein CspF; Provisional	99.89
PRK09507	69	cspE cold shock protein CspE; Reviewed	99.89
PRK09890	70	cold shock protein CspG; Provisional	99.89
PRK10354	70	RNA chaperone/anti-terminator; Provisional	99.89
PRK14998	73	cold shock-like protein CspD; Provisional	99.89
PRK09937	74	stationary phase/starvation inducible regulatory p	99.89
TIGR02381	68	cspD cold shock domain protein CspD. This model re	99.88
PF00313	66	CSD: 'Cold-shock' DNA-binding domain; InterPro: IP	99.84
cd04458	65	CSP_CDS Cold-Shock Protein (CSP) contains an S1-li	99.82
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	99.8
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	99.8
KOG3070	235	consensus Predicted RNA-binding protein containing	99.74
KOG4400	261	consensus E3 ubiquitin ligase interacting with arg	99.58
KOG4400	261	consensus E3 ubiquitin ligase interacting with arg	99.53
smart00357	64	CSP Cold shock protein domain. RNA-binding domain	98.94
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	98.2
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	98.03
PF08206	58	OB_RNB: Ribonuclease B OB domain; InterPro: IPR013	97.7
PF14444	58	S1-like: S1-like	97.21
PF13696	32	zf-CCHC_2: Zinc knuckle	96.65
PF13696	32	zf-CCHC_2: Zinc knuckle	96.65
PF07497	78	Rho_RNA_bind: Rho termination factor, RNA-binding	96.37
cd04459	68	Rho_CSD Rho_CSD: Rho protein cold-shock domain (CS	96.14
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	95.5
PF13917	42	zf-CCHC_3: Zinc knuckle	95.19
KOG0119	554	consensus Splicing factor 1/branch point binding p	94.65
smart00343	26	ZnF_C2HC zinc finger.	94.41
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	93.94
KOG0119	554	consensus Splicing factor 1/branch point binding p	93.46
PRK11642	813	exoribonuclease R; Provisional	93.4
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	92.95
smart00343	26	ZnF_C2HC zinc finger.	92.84
PF13917	42	zf-CCHC_3: Zinc knuckle	92.76
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	92.76
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	91.57
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	91.31
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	90.76
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	90.67
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	90.6
PRK07252	120	hypothetical protein; Provisional	90.03
PF14392	49	zf-CCHC_4: Zinc knuckle	89.62
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	89.42
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	89.34
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	89.22
PRK05054	644	exoribonuclease II; Provisional	89.14
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	89.14
PRK12608	380	transcription termination factor Rho; Provisional	88.99
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	88.91
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	88.72
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	88.54
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	88.46
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	88.25
PRK08582	139	hypothetical protein; Provisional	87.93
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	87.76
PRK09376	416	rho transcription termination factor Rho; Provisio	87.46
PF15288	40	zf-CCHC_6: Zinc knuckle	87.42
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	86.83
COG5222	427	Uncharacterized conserved protein, contains RING Z	86.7
PRK12678	672	transcription termination factor Rho; Provisional	86.69
KOG0314	448	consensus Predicted E3 ubiquitin ligase [Posttrans	86.48
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	86.12
PF14392	49	zf-CCHC_4: Zinc knuckle	85.94
COG1158	422	Rho Transcription termination factor [Transcriptio	85.36
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	84.95
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	84.93
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	84.71
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	84.63
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	84.32
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	83.07
COG5222	427	Uncharacterized conserved protein, contains RING Z	82.49
PF15288	40	zf-CCHC_6: Zinc knuckle	82.01
KOG0314	448	consensus Predicted E3 ubiquitin ligase [Posttrans	80.76
PF14787	36	zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB:	80.7
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	80.57

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

Probab=99.96  E-value=5.3e-29  Score=203.47  Aligned_cols=145  Identities=36%  Similarity=0.906  Sum_probs=118.6

Q ss_pred             CCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCccccccccccCCCCCCCCCCCcccCCCCCCC
Q 047168           90 SGYNNNRGGRGGGGAGFGGYWKGNNDSRRNNGGGYGPGGVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHF  169 (258)
Q Consensus        90 ~c~~c~~~g~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~C~~Cg~~GH~a~~Cp~~~~~~~~~~~~~~C~~Cg~~GH~  169 (258)
                      +|+||++.||++         .+||+....    ...+...||+|++.||++++||....    ......|++|++.||+
T Consensus         2 ~C~~C~~~GH~~---------~~c~~~~~~----~~~~~~~C~~Cg~~GH~~~~Cp~~~~----~~~~~~C~~Cg~~GH~   64 (148)
T PTZ00368          2 VCYRCGGVGHQS---------RECPNSAPA----GAAKARPCYKCGEPGHLSRECPSAPG----GRGERSCYNCGKTGHL   64 (148)
T ss_pred             cCCCCCCCCcCc---------ccCcCCCCC----CCCCCccCccCCCCCcCcccCcCCCC----CCCCcccCCCCCcCcC
Confidence            699999999998         899975431    12347899999999999999998432    1235689999999999


Q ss_pred             CCCCCCCCCCCCCCCCCCCcccccCCcccCcccCCCCCCCCCCCCccccCCCCCccCCCCCCCCC--CCCCccccCCCCC
Q 047168          170 ARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGAGGA--GGGGSCFNCGKPG  247 (258)
Q Consensus       170 ~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~--~~~~~C~~Cg~~G  247 (258)
                      +++||+...     ......|++|++.||++++||+..........||+|++.||++++||+.+.  .....||+|++.|
T Consensus        65 ~~~Cp~~~~-----~~~~~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~gH~~~~C~~~~~~~~~~~~C~~Cg~~g  139 (148)
T PTZ00368         65 SRECPEAPP-----GSGPRSCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCPNAGKRPGGDKTCYNCGQTG  139 (148)
T ss_pred             cccCCCccc-----CCCCcccCcCCCCCcccccCCCcccccccchhhcccCcCCcchhcCCCccccCCCCCccccCCCcC
Confidence            999998742     124578999999999999999975444455689999999999999999632  2356999999999


Q ss_pred             ccCCCCCCC
Q 047168          248 HFARECTKV  256 (258)
Q Consensus       248 H~~~~Cp~~  256 (258)
                      ||++|||++
T Consensus       140 H~~~dCp~~  148 (148)
T PTZ00368        140 HLSRDCPDK  148 (148)
T ss_pred             cccccCCCC
Confidence            999999985

>COG1278 CspC Cold shock proteins [Transcription]

Probab=99.92  E-value=1.5e-25  Score=156.74  Aligned_cols=66  Identities=50%  Similarity=0.928  Sum_probs=63.4

Q ss_pred             ccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeecccc
Q 047168            6 RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTA   72 (258)
Q Consensus         6 ~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~   72 (258)
                      +++|+|||||.+||||||+++++++|||||+|+|...++++|.+|++|+|+++.+++| ++|.+|++
T Consensus         1 ~~~GtVKwfn~~KGfGFI~p~~G~~DvFVH~Sai~~~g~~~L~eGQ~V~f~~~~g~kg-p~A~nv~~   66 (67)
T COG1278           1 MATGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRAGFRTLREGQKVEFEVEQGRKG-PSAANVRA   66 (67)
T ss_pred             CCcceEEEeeCCCcceEcCCCCCCcCEEEEeeeeccCCCcccCCCCEEEEEEecCCCC-CceeEEEe
Confidence            4689999999999999999999999999999999999999999999999999999998 89999975

>PRK10943 cold shock-like protein CspC; Provisional

Probab=99.90  E-value=5.9e-24  Score=151.72  Aligned_cols=68  Identities=46%  Similarity=0.868  Sum_probs=64.3

Q ss_pred             cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccC
Q 047168            5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAP   73 (258)
Q Consensus         5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~   73 (258)
                      ++++|+|||||.+||||||+++++++|||||+|+|...+++.|.+|++|+|+++.+++| ++|++|+.+
T Consensus         2 ~~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~g~~~l~~G~~V~f~~~~~~~g-~~A~~V~~~   69 (69)
T PRK10943          2 AKIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKG-PAAVNVTAI   69 (69)
T ss_pred             CccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHccccCCCCCCCCCEEEEEEEECCCC-ceeEEEEcC
Confidence            47899999999999999999999999999999999999999999999999999999998 899999864

>PRK15464 cold shock-like protein CspH; Provisional

Probab=99.90  E-value=7.5e-24  Score=151.18  Aligned_cols=66  Identities=32%  Similarity=0.391  Sum_probs=62.8

Q ss_pred             ccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeecccc
Q 047168            6 RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTA   72 (258)
Q Consensus         6 ~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~   72 (258)
                      +++|+|||||.+||||||+++++++|||||+++|...+++.|.+|++|+|+++++++| ++|++|..
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 KMTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRG-PTAANVYL   69 (70)
T ss_pred             cceEEEEEEECCCCeEEEccCCCCccEEEEehhehhcCCCCCCCCCEEEEEEEECCCC-ceeEEEEc
Confidence            4699999999999999999999999999999999999998999999999999999999 79999974

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

Probab=99.89  E-value=2.1e-23  Score=170.41  Aligned_cols=120  Identities=41%  Similarity=1.090  Sum_probs=98.4

Q ss_pred             CcccccCCCCccccccccccCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCcccCcccCCCCCC
Q 047168          129 VVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITRGS  208 (258)
Q Consensus       129 ~~C~~Cg~~GH~a~~Cp~~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~~~~  208 (258)
                      +.||+|++.||++++||+...  ........|++|++.||++++||++..     ......||+|++.||++++||+...
T Consensus         1 ~~C~~C~~~GH~~~~c~~~~~--~~~~~~~~C~~Cg~~GH~~~~Cp~~~~-----~~~~~~C~~Cg~~GH~~~~Cp~~~~   73 (148)
T PTZ00368          1 MVCYRCGGVGHQSRECPNSAP--AGAAKARPCYKCGEPGHLSRECPSAPG-----GRGERSCYNCGKTGHLSRECPEAPP   73 (148)
T ss_pred             CcCCCCCCCCcCcccCcCCCC--CCCCCCccCccCCCCCcCcccCcCCCC-----CCCCcccCCCCCcCcCcccCCCccc
Confidence            479999999999999998332  234456799999999999999998742     1245689999999999999998643


Q ss_pred             CCCCCCccccCCCCCccCCCCCCCCCC--CCCccccCCCCCccCCCCCCC
Q 047168          209 GGGGGGRCYNCGKSGHLARDCGAGGAG--GGGSCFNCGKPGHFARECTKV  256 (258)
Q Consensus       209 ~~~~~~~C~~Cg~~GH~~~~Cp~~~~~--~~~~C~~Cg~~GH~~~~Cp~~  256 (258)
                      .. ....|++|++.||++++||+....  ....||+|+++||++++||+.
T Consensus        74 ~~-~~~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~gH~~~~C~~~  122 (148)
T PTZ00368         74 GS-GPRSCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCPNA  122 (148)
T ss_pred             CC-CCcccCcCCCCCcccccCCCcccccccchhhcccCcCCcchhcCCCc
Confidence            22 345799999999999999996632  345899999999999999985

>PRK15463 cold shock-like protein CspF; Provisional

Probab=99.89  E-value=1.7e-23  Score=149.65  Aligned_cols=67  Identities=33%  Similarity=0.411  Sum_probs=63.2

Q ss_pred             cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeecccc
Q 047168            5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTA   72 (258)
Q Consensus         5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~   72 (258)
                      .+++|+|||||.+||||||+++++++|||||+++|...+++.|.+|++|+|+++.+++| ++|++|.+
T Consensus         3 ~~~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~g~~~l~~G~~V~f~v~~~~~G-~~A~~V~~   69 (70)
T PRK15463          3 RKMTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRINGLRG-PTAANVYL   69 (70)
T ss_pred             ccceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhcCCCCCCCCCEEEEEEEECCCC-ceeEEEEc
Confidence            34699999999999999999999999999999999988899999999999999999999 89999974

>PRK09507 cspE cold shock protein CspE; Reviewed

Probab=99.89  E-value=2e-23  Score=148.96  Aligned_cols=67  Identities=45%  Similarity=0.886  Sum_probs=63.9

Q ss_pred             cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeecccc
Q 047168            5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTA   72 (258)
Q Consensus         5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~   72 (258)
                      .+++|+|||||.+||||||+++++++|||||+++|...+++.|.+|++|+|+++.+++| ++|++|..
T Consensus         2 ~~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f~~~~~~~G-~~A~~V~~   68 (69)
T PRK09507          2 SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKG-PSAANVIA   68 (69)
T ss_pred             CccceEEEEEeCCCCcEEEecCCCCeeEEEEeecccccCCCCCCCCCEEEEEEEECCCC-cccEEEEe
Confidence            57889999999999999999999999999999999999999999999999999999999 89999975

>PRK09890 cold shock protein CspG; Provisional

Probab=99.89  E-value=2.4e-23  Score=149.01  Aligned_cols=68  Identities=47%  Similarity=0.844  Sum_probs=63.8

Q ss_pred             cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccC
Q 047168            5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAP   73 (258)
Q Consensus         5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~   73 (258)
                      .+++|+|||||.+||||||+++++++|||||+++|...+++.|.+|++|+|+++.+++| ++|.+|..+
T Consensus         3 ~~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~~~~~l~~G~~V~f~~~~~~~G-~~A~~V~~~   70 (70)
T PRK09890          3 NKMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRG-PAAANVVTL   70 (70)
T ss_pred             ccceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccCCCCCCCCCCEEEEEEEECCCC-ceeEEEEeC
Confidence            35799999999999999999999999999999999999999999999999999999999 899999753

>PRK10354 RNA chaperone/anti-terminator; Provisional

Probab=99.89  E-value=2.5e-23  Score=149.01  Aligned_cols=67  Identities=48%  Similarity=0.866  Sum_probs=63.4

Q ss_pred             ccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccC
Q 047168            6 RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAP   73 (258)
Q Consensus         6 ~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~   73 (258)
                      +|+|+|||||.+||||||+++++++|||||+++|...+++.|.+|++|+|+++.+++| ++|++|+.+
T Consensus         4 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f~~~~~~~G-~~A~~V~~~   70 (70)
T PRK10354          4 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKG-PAAGNVTSL   70 (70)
T ss_pred             cceEEEEEEeCCCCcEEEecCCCCccEEEEEeeccccCCCCCCCCCEEEEEEEECCCC-ceeEEEEeC
Confidence            4599999999999999999999999999999999999999999999999999999999 899999863

>PRK14998 cold shock-like protein CspD; Provisional

Probab=99.89  E-value=4.4e-23  Score=148.56  Aligned_cols=69  Identities=46%  Similarity=0.840  Sum_probs=64.5

Q ss_pred             cceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccCCCC
Q 047168            7 STGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAPGGA   76 (258)
Q Consensus         7 ~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~~g~   76 (258)
                      .+|+|||||.+||||||+++++++|||||+|+|...+++.|.+|++|+|+++.+++| ++|.+|..++.+
T Consensus         2 ~~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~g~~~l~~G~~V~f~~~~~~~G-~~A~~V~~~~~~   70 (73)
T PRK14998          2 ETGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKG-NHASVIVPIEAE   70 (73)
T ss_pred             CCeEEEEEeCCCceEEEecCCCCccEEEEeeeecccCCCCCCCCCEEEEEEEECCCC-ceeEEEEECccc
Confidence            479999999999999999999999999999999999999999999999999999999 799999876543

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

Probab=99.89  E-value=4.5e-23  Score=148.80  Aligned_cols=68  Identities=46%  Similarity=0.832  Sum_probs=64.2

Q ss_pred             cceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccCCC
Q 047168            7 STGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAPGG   75 (258)
Q Consensus         7 ~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~~g   75 (258)
                      .+|+|||||.+||||||+++++++|||||+|+|...+++.|.+|++|+|+++.+++| ++|++|..++.
T Consensus         2 ~~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~g~~~l~~G~~V~f~~~~~~~G-~~A~~V~~~~~   69 (74)
T PRK09937          2 EKGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKG-NHASVIVPVEV   69 (74)
T ss_pred             CCeEEEEEeCCCCeEEEeeCCCCccEEEEEeeccccCCCCCCCCCEEEEEEEECCCC-ceeeEEEECCc
Confidence            379999999999999999999999999999999999999999999999999999999 79999998743

>TIGR02381 cspD cold shock domain protein CspD

Probab=99.88  E-value=5.7e-23  Score=146.32  Aligned_cols=66  Identities=41%  Similarity=0.766  Sum_probs=62.6

Q ss_pred             cceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccC
Q 047168            7 STGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAP   73 (258)
Q Consensus         7 ~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~   73 (258)
                      .+|+|||||.+||||||+++++++|||||+|+|...+++.|.+|++|+|+++.+++| ++|.+|..+
T Consensus         2 ~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~g~~~l~~G~~V~f~~~~~~~G-~~A~~V~~~   67 (68)
T TIGR02381         2 AIGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDGYRTLKAGQKVQFEVVQGPKG-AHATHIVPI   67 (68)
T ss_pred             CCeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhcCCCCCCCCCEEEEEEEECCCC-ceeEEEEEC
Confidence            479999999999999999999999999999999999999999999999999999999 899999854

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.

>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=99.84  E-value=9.1e-21  Score=134.10  Aligned_cols=66  Identities=47%  Similarity=0.887  Sum_probs=60.0

Q ss_pred             cceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccC
Q 047168            7 STGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAP   73 (258)
Q Consensus         7 ~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~   73 (258)
                      |+|+|+|||+.+|||||+++++.+|||||+++|...+++.|.+|++|+|++..++++ ++|++|+.+
T Consensus         1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~~~~~l~~G~~V~F~~~~~~~g-~~A~~V~~~   66 (66)
T PF00313_consen    1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGNGFRSLKEGDRVEFEVEEGKKG-PQAVNVRKI   66 (66)
T ss_dssp             EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSSSSTS--TTSEEEEEEEECTTS-EEEEEEEE-
T ss_pred             CeEEEEEEECCCCceEEEEcccceeEEeccccccccccccCCCCCEEEEEEEECCCC-CEEEEEECc
Confidence            689999999999999999999989999999999999889999999999999998887 899999853

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=99.82  E-value=3.6e-20  Score=130.67  Aligned_cols=65  Identities=49%  Similarity=0.957  Sum_probs=61.1

Q ss_pred             cceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeecccc
Q 047168            7 STGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTA   72 (258)
Q Consensus         7 ~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~   72 (258)
                      ++|+|||||.+||||||+++++++|||||+++|...++..|.+|+.|+|++..+++| ++|++|+.
T Consensus         1 ~~G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~~~~~~~~G~~V~f~~~~~~~g-~~A~~V~~   65 (65)
T cd04458           1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKG-PQAVNVRL   65 (65)
T ss_pred             CcEEEEEEECCCCeEEEecCCCCcCEEEEhhHhhccCCCcCCCCCEEEEEEEECCCC-CeEEEeEC
Confidence            579999999999999999999889999999999988889999999999999999887 89999863

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.

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

Probab=99.80  E-value=1.3e-19  Score=150.76  Aligned_cols=126  Identities=30%  Similarity=0.689  Sum_probs=95.4

Q ss_pred             CCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCccccccccccCCCCCCCCCCCccc
Q 047168           83 NNNTNNNSGYNNNRGGRGGGGAGFGGYWKGNNDSRRNNGGGYGPGGVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYN  162 (258)
Q Consensus        83 ~~~~g~~~c~~c~~~g~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~C~~Cg~~GH~a~~Cp~~~~~~~~~~~~~~C~~  162 (258)
                      .....++.|+||++.||+.         ++||             ...||+|...+|.+..||.          .+.|++
T Consensus        55 ~~~~~~~~C~nCg~~GH~~---------~DCP-------------~~iC~~C~~~~H~s~~C~~----------~~~C~~  102 (190)
T COG5082          55 AIREENPVCFNCGQNGHLR---------RDCP-------------HSICYNCSWDGHRSNHCPK----------PKKCYN  102 (190)
T ss_pred             cccccccccchhcccCccc---------ccCC-------------hhHhhhcCCCCcccccCCc----------cccccc
Confidence            4444566799999999988         8888             3588999778899999887          378999


Q ss_pred             CCCCCCCCCCC-CCCCCCCCCCCCCCCcccccCCcccCcccCCCCCCCCC--------CCCccccCCCCCccCCCCCCCC
Q 047168          163 CGDPEHFARDC-PRQQGGSNSYNNNSGGCFKCGGYGHLARDCITRGSGGG--------GGGRCYNCGKSGHLARDCGAGG  233 (258)
Q Consensus       163 Cg~~GH~~~~C-p~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~~~~~~~--------~~~~C~~Cg~~GH~~~~Cp~~~  233 (258)
                      |++.||++++| |.+        .....|+.|....|++++||+.+....        ....||+|+..+|++++|++++
T Consensus       103 Cg~~GH~~~dC~P~~--------~~~~~C~~C~s~~H~s~~Cp~~~k~y~~~~~~~~~~~~~cy~c~~~~H~~~dc~~~~  174 (190)
T COG5082         103 CGETGHLSRDCNPSK--------DQQKSCFDCNSTRHSSEDCPSIWKHYVLNNGDGHPIKKFCYSCGSAGHFGDDCKEPR  174 (190)
T ss_pred             ccccCccccccCccc--------ccCcceeccCCCccccccCcccccccccccCCCcceeeeccccCCccccCCCCCCCc
Confidence            99999999999 454        335688999999999999988743221        1345888888888888888877


Q ss_pred             CCCCCccccCCCCCccC
Q 047168          234 AGGGGSCFNCGKPGHFA  250 (258)
Q Consensus       234 ~~~~~~C~~Cg~~GH~~  250 (258)
                      .....  |.|+..+|+.
T Consensus       175 ~s~~~--~~~~~~~~~~  189 (190)
T COG5082         175 SSRVP--YVCGKKGYVS  189 (190)
T ss_pred             ccccc--ccccccccCC
Confidence            65444  7777776653

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

Probab=99.80  E-value=4.3e-20  Score=153.66  Aligned_cols=104  Identities=35%  Similarity=0.912  Sum_probs=92.0

Q ss_pred             CCcccccCCCCccccccccccCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCcccCcccC-CCC
Q 047168          128 GVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDC-ITR  206 (258)
Q Consensus       128 ~~~C~~Cg~~GH~a~~Cp~~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C-~~~  206 (258)
                      ..+||+|++.||++++||.           .+|++|...+|.+..||.+           .+|++|++.||++++| |..
T Consensus        60 ~~~C~nCg~~GH~~~DCP~-----------~iC~~C~~~~H~s~~C~~~-----------~~C~~Cg~~GH~~~dC~P~~  117 (190)
T COG5082          60 NPVCFNCGQNGHLRRDCPH-----------SICYNCSWDGHRSNHCPKP-----------KKCYNCGETGHLSRDCNPSK  117 (190)
T ss_pred             ccccchhcccCcccccCCh-----------hHhhhcCCCCcccccCCcc-----------cccccccccCccccccCccc
Confidence            6899999999999999996           8999997799999999987           5999999999999999 554


Q ss_pred             CCCCCCCCccccCCCCCccCCCCCCCCCCC----------CCccccCCCCCccCCCCCCCc
Q 047168          207 GSGGGGGGRCYNCGKSGHLARDCGAGGAGG----------GGSCFNCGKPGHFARECTKVA  257 (258)
Q Consensus       207 ~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~----------~~~C~~Cg~~GH~~~~Cp~~~  257 (258)
                      ...    ..|+.|...+|++++||+.|+..          ...||+|+..+||+.+|+++.
T Consensus       118 ~~~----~~C~~C~s~~H~s~~Cp~~~k~y~~~~~~~~~~~~~cy~c~~~~H~~~dc~~~~  174 (190)
T COG5082         118 DQQ----KSCFDCNSTRHSSEDCPSIWKHYVLNNGDGHPIKKFCYSCGSAGHFGDDCKEPR  174 (190)
T ss_pred             ccC----cceeccCCCccccccCcccccccccccCCCcceeeeccccCCccccCCCCCCCc
Confidence            332    37999999999999999988541          358999999999999999764

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

Probab=99.74  E-value=1.2e-17  Score=145.38  Aligned_cols=85  Identities=47%  Similarity=0.821  Sum_probs=78.7

Q ss_pred             CccccceEEEEeeCCCceeEEecCCCCCceEEecccccc----CCccccCCCCcEEEEEEeCCCccceeeccccCCCCcc
Q 047168            3 QLTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKS----DGYRTLYENQSVEFDVQLEADGKYQALDVTAPGGAPV   78 (258)
Q Consensus         3 ~~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~----~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~~g~~~   78 (258)
                      ++...+|+|||||+.+|||||+++|+.+||||||++|..    .+|++|.+++.|.|+++...++ .+|++|+.+++.++
T Consensus        53 ~~~~~~G~~k~fnv~~G~gFi~~~d~~~D~fvhQs~i~~~~~~~~~rs~~~~e~v~f~~~~~~~g-~~a~~vt~p~g~~~  131 (235)
T KOG3070|consen   53 QGARVKGTVKWFNVGKGYGFITRDDGPEDVFVHQSAITKYTPSEGFRSLKEGEAVPFDIQEGNKG-TEAANVTGPDGVPV  131 (235)
T ss_pred             ccccccCcceeEeccCCcceecccCCCCceeEEeeeecccccccchhhcccCCCccceecccCcc-ceeeeecCCCCccc
Confidence            456889999999999999999999999999999999999    8899999999999999999999 89999999999999


Q ss_pred             cCCCCCCCCC
Q 047168           79 HSSKNNNTNN   88 (258)
Q Consensus        79 ~~s~~~~~g~   88 (258)
                      ..+++..+..
T Consensus       132 ~~s~~~~~~~  141 (235)
T KOG3070|consen  132 RGSKGAVKGN  141 (235)
T ss_pred             cccccccccc
Confidence            8887766543

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

Probab=99.58  E-value=9.2e-15  Score=129.94  Aligned_cols=136  Identities=30%  Similarity=0.698  Sum_probs=87.1

Q ss_pred             CCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCccccccccccCCCCCCCCCCCcccCCC
Q 047168           86 TNNNSGYNNNRGGRGGGGAGFGGYWKGNNDSRRNNGGGYGPGGVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGD  165 (258)
Q Consensus        86 ~g~~~c~~c~~~g~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~C~~Cg~~GH~a~~Cp~~~~~~~~~~~~~~C~~Cg~  165 (258)
                      ....+|++|++.+|..         .+|+..           ...|++|++.||++++||.......   ....|+.|+.
T Consensus        70 ~~~~~c~~~g~~~~~~---------~~~~~~-----------~~~c~~C~~~gH~~~~c~~~~~~~~---~~~~~~~c~~  126 (261)
T KOG4400|consen   70 CPEVSCYICGEKGHLG---------RRCTRI-----------AAACFNCGEGGHIERDCPEAGKEGS---SETSCYSCGK  126 (261)
T ss_pred             CCCceeeecCCCCchh---------hcCccc-----------chhhhhCCCCccchhhCCcccCccc---ccceeeccCC
Confidence            3355788888888776         666641           4688888888888888886332111   3456788888


Q ss_pred             CCCCC-CCCCCCCCCCCCCCCCCCcccccCCcccCcccCCCCCCCCCCCCccccCCCCCccCCCCCCCCCCC--------
Q 047168          166 PEHFA-RDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGAGGAGG--------  236 (258)
Q Consensus       166 ~GH~~-~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~--------  236 (258)
                      .+|.. +++....     .... ..||+|++.||++.+||++     ....||.|++.+|.+++||......        
T Consensus       127 ~gh~~~~~~~~~~-----~~~~-~~Cy~Cg~~GH~s~~C~~~-----~~~~c~~c~~~~h~~~~C~~~~~~~~~~~~~~~  195 (261)
T KOG4400|consen  127 TGHRGCPDADPVD-----GPKP-AKCYSCGEQGHISDDCPEN-----KGGTCFRCGKVGHGSRDCPSKQKSKSKQGGQRK  195 (261)
T ss_pred             CccccCccccccc-----CCCC-CccCCCCcCCcchhhCCCC-----CCCccccCCCcceecccCCccccccccCccccc
Confidence            88887 3322221     1122 6688888888888888864     1237888888888888888765331        


Q ss_pred             -CCccccCCCCCccCCCCCCC
Q 047168          237 -GGSCFNCGKPGHFARECTKV  256 (258)
Q Consensus       237 -~~~C~~Cg~~GH~~~~Cp~~  256 (258)
                       ...|+ +...+|+.++|+..
T Consensus       196 ~~~~~~-~~~~~~~~~~~~~~  215 (261)
T KOG4400|consen  196 GFGACY-DYPQGHKQRACGGS  215 (261)
T ss_pred             ccccCc-cccccccccccCCC
Confidence             11233 44677777777653

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

Probab=99.53  E-value=3e-14  Score=126.68  Aligned_cols=111  Identities=40%  Similarity=1.017  Sum_probs=90.0

Q ss_pred             CCcccccCCCCccccccccccCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCcccCcccCCCCC
Q 047168          128 GVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITRG  207 (258)
Q Consensus       128 ~~~C~~Cg~~GH~a~~Cp~~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~~~  207 (258)
                      ...|+.|++.+|.++.|+.         ....|++|++.||++++|+......    .....||.|+..+|..  |+...
T Consensus        72 ~~~c~~~g~~~~~~~~~~~---------~~~~c~~C~~~gH~~~~c~~~~~~~----~~~~~~~~c~~~gh~~--~~~~~  136 (261)
T KOG4400|consen   72 EVSCYICGEKGHLGRRCTR---------IAAACFNCGEGGHIERDCPEAGKEG----SSETSCYSCGKTGHRG--CPDAD  136 (261)
T ss_pred             CceeeecCCCCchhhcCcc---------cchhhhhCCCCccchhhCCcccCcc----cccceeeccCCCcccc--Ccccc
Confidence            6899999999999999984         4588999999999999999885321    1456899999999999  33322


Q ss_pred             C--CCCCCCccccCCCCCccCCCCCCCCCCCCCccccCCCCCccCCCCCCCc
Q 047168          208 S--GGGGGGRCYNCGKSGHLARDCGAGGAGGGGSCFNCGKPGHFARECTKVA  257 (258)
Q Consensus       208 ~--~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~C~~Cg~~GH~~~~Cp~~~  257 (258)
                      .  .... +.||+|++.||++++||++   ....||.|++.+|.+++||++.
T Consensus       137 ~~~~~~~-~~Cy~Cg~~GH~s~~C~~~---~~~~c~~c~~~~h~~~~C~~~~  184 (261)
T KOG4400|consen  137 PVDGPKP-AKCYSCGEQGHISDDCPEN---KGGTCFRCGKVGHGSRDCPSKQ  184 (261)
T ss_pred             cccCCCC-CccCCCCcCCcchhhCCCC---CCCccccCCCcceecccCCccc
Confidence            1  1112 5799999999999999976   2568999999999999999875

>smart00357 CSP Cold shock protein domain

Probab=98.94  E-value=2.7e-09  Score=73.75  Aligned_cols=62  Identities=52%  Similarity=0.945  Sum_probs=50.3

Q ss_pred             ceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeC-CCccceeecccc
Q 047168            8 TGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLE-ADGKYQALDVTA   72 (258)
Q Consensus         8 ~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~-~~G~~~A~~V~~   72 (258)
                      +|+|+|++  +|||||.+++...|||||.+.|.. ++..+.+|+.|.|.+... .+++++|..|.+
T Consensus         1 ~G~i~~~~--~g~gfv~~~~~~~~i~v~~~~~~~-~~~~~~~Gd~V~~~i~~~~~~~~~~a~~v~~   63 (64)
T smart00357        1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQG-GLKSLREGDEVEFKVVSPRGGGKPEAENVVK   63 (64)
T ss_pred             CeEEEEEc--CCeeEEecCCCCccEEEEhHHhhc-CCCcCCCCCEEEEEEEEccCCCCcEEEEEEe
Confidence            58999997  799999998765799999999876 566789999999999872 233478887654

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.

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

Probab=98.20  E-value=7.5e-07  Score=46.72  Aligned_cols=17  Identities=71%  Similarity=1.712  Sum_probs=10.1

Q ss_pred             ccccCCCCCccCCCCCC
Q 047168          239 SCFNCGKPGHFARECTK  255 (258)
Q Consensus       239 ~C~~Cg~~GH~~~~Cp~  255 (258)
                      .||+|++.||++++||+
T Consensus         2 ~C~~C~~~GH~~~~Cp~   18 (18)
T PF00098_consen    2 KCFNCGEPGHIARDCPK   18 (18)
T ss_dssp             BCTTTSCSSSCGCTSSS
T ss_pred             cCcCCCCcCcccccCcc
Confidence            46666666666666653

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

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

Probab=98.03  E-value=3e-06  Score=44.40  Aligned_cols=16  Identities=63%  Similarity=1.661  Sum_probs=9.7

Q ss_pred             ccccCCCCCccCCCCC
Q 047168          215 RCYNCGKSGHLARDCG  230 (258)
Q Consensus       215 ~C~~Cg~~GH~~~~Cp  230 (258)
                      .||+|++.||++++||
T Consensus         2 ~C~~C~~~GH~~~~Cp   17 (18)
T PF00098_consen    2 KCFNCGEPGHIARDCP   17 (18)
T ss_dssp             BCTTTSCSSSCGCTSS
T ss_pred             cCcCCCCcCcccccCc
Confidence            4666666666666665

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

>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=97.70  E-value=7.8e-05  Score=51.14  Aligned_cols=48  Identities=25%  Similarity=0.578  Sum_probs=33.9

Q ss_pred             CCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCC-Cccceeec
Q 047168           17 AKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEA-DGKYQALD   69 (258)
Q Consensus        17 ~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~-~G~~~A~~   69 (258)
                      .+||||+.+++..+|||+....+..     .-.||.|...+.... .+++++.-
T Consensus         7 ~~GfGFv~~~~~~~DifIp~~~l~~-----A~~gD~V~v~i~~~~~~~~~eg~v   55 (58)
T PF08206_consen    7 PKGFGFVIPDDGGEDIFIPPRNLNG-----AMDGDKVLVRITPPSRGKRPEGEV   55 (58)
T ss_dssp             SSS-EEEEECT-TEEEEE-HHHHTT-----S-TT-EEEEEEEESSSEEEEEEEE
T ss_pred             cCCCEEEEECCCCCCEEECHHHHCC-----CCCCCEEEEEEecCCCCCCCCEEE
Confidence            8999999999988999999999965     478999999998833 33344443

; PDB: 2ID0_D 2IX1_A 2IX0_A.

>PF14444 S1-like: S1-like

Probab=97.21  E-value=0.00099  Score=45.36  Aligned_cols=47  Identities=26%  Similarity=0.400  Sum_probs=40.0

Q ss_pred             ccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCC
Q 047168            6 RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEAD   62 (258)
Q Consensus         6 ~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~   62 (258)
                      .++|.|+.+  ...||||.     +||||..+++...   .|++||+|..+....+.
T Consensus         3 ~~~GvVTkl--~~~yG~ID-----e~vFF~~~vv~G~---~P~vGdrV~v~A~~n~~   49 (58)
T PF14444_consen    3 VFTGVVTKL--CDDYGFID-----EDVFFQTDVVKGN---VPKVGDRVLVEAIYNPN   49 (58)
T ss_pred             eEEEEEEEE--eCCcceEc-----ccEEEEcccEecC---CCccCCEEEEEEEeCCC
Confidence            468999999  47899997     7999999998744   47999999999888754

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=96.65  E-value=0.0014  Score=39.35  Aligned_cols=17  Identities=41%  Similarity=1.079  Sum_probs=8.6

Q ss_pred             ccccCCCCCccCCCCCC
Q 047168          215 RCYNCGKSGHLARDCGA  231 (258)
Q Consensus       215 ~C~~Cg~~GH~~~~Cp~  231 (258)
                      .|+.|++.||+.+|||+
T Consensus        10 ~C~~C~~~GH~i~dCP~   26 (32)
T PF13696_consen   10 VCHRCGQKGHWIQDCPT   26 (32)
T ss_pred             EeecCCCCCccHhHCCC
Confidence            35555555555555554

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=96.65  E-value=0.0013  Score=39.42  Aligned_cols=21  Identities=38%  Similarity=0.798  Sum_probs=15.9

Q ss_pred             CCCcccccCCcccCcccCCCC
Q 047168          186 NSGGCFKCGGYGHLARDCITR  206 (258)
Q Consensus       186 ~~~~C~~Cg~~GH~~~~C~~~  206 (258)
                      ...+|++|++.||+.++||++
T Consensus         7 ~~Y~C~~C~~~GH~i~dCP~~   27 (32)
T PF13696_consen    7 PGYVCHRCGQKGHWIQDCPTN   27 (32)
T ss_pred             CCCEeecCCCCCccHhHCCCC
Confidence            456788888888888888874

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

Probab=96.37  E-value=0.0066  Score=44.13  Aligned_cols=63  Identities=29%  Similarity=0.480  Sum_probs=39.2

Q ss_pred             ceEEEEeeCCCceeEEecC-----CCCCceEEeccccccCCccccCCCCcEEEEEEeCCCcc--ceeeccccCCC
Q 047168            8 TGKVTWFDGAKGYGFIRPD-----DGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGK--YQALDVTAPGG   75 (258)
Q Consensus         8 ~G~vk~f~~~kGfGFI~~~-----~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~--~~A~~V~~~~g   75 (258)
                      .|++--  ..+|||||..+     .+.+||||-.+.|+..+   |+.|+.|+=.+.....+.  +..+.|..+.+
T Consensus         4 ~GvLei--~~dGyGFLR~~~~~y~~~~~DvYVs~~qIrrf~---LR~GD~V~G~vr~p~~~ek~~aL~~V~~VNg   73 (78)
T PF07497_consen    4 EGVLEI--LPDGYGFLRSPDNNYLPSPDDVYVSPSQIRRFG---LRTGDLVEGQVRPPREGEKYFALLRVESVNG   73 (78)
T ss_dssp             EEEEEE---TTS-EEEE-GGGTTS-STTSEEE-CCCCCCTT-----TTEEEEEEEE--STTSSSEEECEECEETT
T ss_pred             EEEEEE--CCCCcEEeECCCcCCCCCCCCEEECHHHHHHcC---CCCCCEEEEEEeCCCCCCcceeeEEEEeECC
Confidence            455553  25799999987     35799999999998875   899999998888865442  23445554444

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=96.14  E-value=0.011  Score=41.85  Aligned_cols=48  Identities=23%  Similarity=0.467  Sum_probs=37.7

Q ss_pred             eEEEEeeCCCceeEEecC-----CCCCceEEeccccccCCccccCCCCcEEEEEEeCC
Q 047168            9 GKVTWFDGAKGYGFIRPD-----DGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEA   61 (258)
Q Consensus         9 G~vk~f~~~kGfGFI~~~-----~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~   61 (258)
                      |++--.  ..|||||...     .+.+||||..+.|+..+   |+.|+.|+=.+....
T Consensus         3 GiLdi~--~~g~GFLR~~~~~y~~~~~DvyVs~~~Irr~~---LR~GD~V~G~vr~p~   55 (68)
T cd04459           3 GVLEIL--PDGFGFLRSSGYNYLPGPDDIYVSPSQIRRFN---LRTGDTVVGQIRPPK   55 (68)
T ss_pred             EEEEEc--CCCceEEecCCcCCCCCCCCEEECHHHHHHhC---CCCCCEEEEEEeCCC
Confidence            444433  3499999866     36799999999998875   899999998887643

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.

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=95.50  E-value=0.04  Score=37.97  Aligned_cols=55  Identities=24%  Similarity=0.360  Sum_probs=34.4

Q ss_pred             cceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceee
Q 047168            7 STGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQAL   68 (258)
Q Consensus         7 ~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~   68 (258)
                      .+-+|+..+   .+|++-..+...+||++.+.+..    .+.+|+.|+.-+..+.++++.|+
T Consensus         5 ~~L~V~~~~---~~g~fL~~~~~~~vlLp~~e~~~----~~~~Gd~v~VFvY~D~~~rl~AT   59 (61)
T PF13509_consen    5 NTLKVVDKN---EFGYFLDDGEGKEVLLPKSEVPE----PLKVGDEVEVFVYLDKEGRLVAT   59 (61)
T ss_dssp             ----EEEE----SSEEEEEETT-EEEEEEGGG----------TTSEEEEEEEE-TTS-EEEE
T ss_pred             cceEEEEEe---CCEEEEECCCCCEEEechHHcCC----CCCCCCEEEEEEEECCCCCEEEe
Confidence            345677765   46766666666999999999964    38999999999999998888776

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=95.19  E-value=0.011  Score=37.70  Aligned_cols=16  Identities=44%  Similarity=1.221  Sum_probs=8.2

Q ss_pred             ccccCCCCCccCCCCC
Q 047168          239 SCFNCGKPGHFARECT  254 (258)
Q Consensus       239 ~C~~Cg~~GH~~~~Cp  254 (258)
                      .|.+|++.||+..+||
T Consensus         6 ~CqkC~~~GH~tyeC~   21 (42)
T PF13917_consen    6 RCQKCGQKGHWTYECP   21 (42)
T ss_pred             cCcccCCCCcchhhCC
Confidence            4555555555555555

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

Probab=94.65  E-value=0.025  Score=53.90  Aligned_cols=42  Identities=36%  Similarity=0.752  Sum_probs=18.4

Q ss_pred             CcccccCCcccCcccCCCCCCCCCCCCccccCCCCCccCCCCCC
Q 047168          188 GGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGA  231 (258)
Q Consensus       188 ~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~  231 (258)
                      ..|..|+..+|-.-+||......  ...|..|+..||++.||+.
T Consensus       262 ~~c~~cg~~~H~q~~cp~r~~~~--~n~c~~cg~~gH~~~dc~~  303 (554)
T KOG0119|consen  262 RACRNCGSTGHKQYDCPGRIPNT--TNVCKICGPLGHISIDCKV  303 (554)
T ss_pred             ccccccCCCccccccCCcccccc--cccccccCCcccccccCCC
Confidence            44555555555555555431000  0144444444444444443

>smart00343 ZnF_C2HC zinc finger

Probab=94.41  E-value=0.02  Score=32.42  Aligned_cols=15  Identities=67%  Similarity=1.690  Sum_probs=9.7

Q ss_pred             cccCCCCCccCCCCC
Q 047168          240 CFNCGKPGHFARECT  254 (258)
Q Consensus       240 C~~Cg~~GH~~~~Cp  254 (258)
                      |++|++.||++++||
T Consensus         2 C~~CG~~GH~~~~C~   16 (26)
T smart00343        2 CYNCGKEGHIARDCP   16 (26)
T ss_pred             CccCCCCCcchhhCC
Confidence            666666666666665

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

Probab=93.94  E-value=0.14  Score=46.02  Aligned_cols=22  Identities=41%  Similarity=0.596  Sum_probs=18.8

Q ss_pred             ccceEEEEeeCCCceeEEecCC
Q 047168            6 RSTGKVTWFDGAKGYGFIRPDD   27 (258)
Q Consensus         6 ~~~G~vk~f~~~kGfGFI~~~~   27 (258)
                      ...|+|..-|..|-|||+-.+|
T Consensus        24 e~ygkVlECDIvKNYgFVHiEd   45 (346)
T KOG0109|consen   24 EQYGKVLECDIVKNYGFVHIED   45 (346)
T ss_pred             HhhCceEeeeeecccceEEeec
Confidence            3579999999999999997664

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

Probab=93.46  E-value=0.075  Score=50.79  Aligned_cols=44  Identities=30%  Similarity=0.670  Sum_probs=23.3

Q ss_pred             CCcccccCCCCccccccccccCCCCCCCCCCCcccCCCCCCCCCCCCCC
Q 047168          128 GVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQ  176 (258)
Q Consensus       128 ~~~C~~Cg~~GH~a~~Cp~~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~  176 (258)
                      ..+|.+|+..||...+||..-     ......|..|+..||++.+|+..
T Consensus       261 ~~~c~~cg~~~H~q~~cp~r~-----~~~~n~c~~cg~~gH~~~dc~~~  304 (554)
T KOG0119|consen  261 NRACRNCGSTGHKQYDCPGRI-----PNTTNVCKICGPLGHISIDCKVN  304 (554)
T ss_pred             cccccccCCCccccccCCccc-----ccccccccccCCcccccccCCCc
Confidence            356666666666666666410     00111566666666666666544

>PRK11642 exoribonuclease R; Provisional

Probab=93.40  E-value=0.11  Score=53.33  Aligned_cols=62  Identities=23%  Similarity=0.290  Sum_probs=45.8

Q ss_pred             ccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeC-CCccceeeccccCC
Q 047168            6 RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLE-ADGKYQALDVTAPG   74 (258)
Q Consensus         6 ~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~-~~G~~~A~~V~~~~   74 (258)
                      .+.|+|..=  .+||||+.+++..+|||+....+..     .-.||.|...+... .+++++|.-|.++.
T Consensus        84 ~~~G~v~~~--~~GfgFv~~e~~~~difI~~~~l~~-----A~~GD~V~v~i~~~~~~~r~eg~Vv~Ile  146 (813)
T PRK11642         84 LLKGTVIGH--RDGYGFLRVEGRKDDLYLSSEQMKT-----CIHGDQVLAQPLGADRKGRREARIVRVLV  146 (813)
T ss_pred             eEEEEEEEC--CCccEEEEECCCCCCEEEChHHHcc-----CCCCCEEEEEEccCCCCCCcEEEEEEEEe
Confidence            367888843  8999999998767899998887754     35699998887652 34556777666655

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

Probab=92.95  E-value=0.2  Score=50.41  Aligned_cols=63  Identities=27%  Similarity=0.397  Sum_probs=46.5

Q ss_pred             cccceEEEEeeCCCceeEEecCC-CCCceEEeccccccCCccccCCCCcEEEEEEe-CCCccceeeccccCC
Q 047168            5 TRSTGKVTWFDGAKGYGFIRPDD-GGADLFVHQKSIKSDGYRTLYENQSVEFDVQL-EADGKYQALDVTAPG   74 (258)
Q Consensus         5 ~~~~G~vk~f~~~kGfGFI~~~~-~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~-~~~G~~~A~~V~~~~   74 (258)
                      ..+.|+|+.=  .+||||+.+++ ..+|||+.-..+..     .-.||.|...+.. ..+++++|.-|.++.
T Consensus        15 ~~~~G~i~~~--~~gfgFv~~~~~~~~difI~~~~~~~-----a~~GD~V~v~i~~~~~~~~~~g~v~~il~   79 (654)
T TIGR00358        15 DLVKGVVKAH--NKGFGFLRPDDDDKKDYFIPPPQMKK-----VMHGDLVEACPLSQPQRGRFEAEVERILE   79 (654)
T ss_pred             CeEEEEEEEC--CCccEEEEeCCCCCCcEEEchHHhCc-----CCCCCEEEEEEeecCCCCCceEEEEEEec
Confidence            3578999964  89999999886 36899998877754     4679999988754 334545676666554

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.

>smart00343 ZnF_C2HC zinc finger

Probab=92.84  E-value=0.052  Score=30.71  Aligned_cols=17  Identities=71%  Similarity=1.644  Sum_probs=14.6

Q ss_pred             ccccCCCCCccCCCCCC
Q 047168          215 RCYNCGKSGHLARDCGA  231 (258)
Q Consensus       215 ~C~~Cg~~GH~~~~Cp~  231 (258)
                      .|++|++.||++++||+
T Consensus         1 ~C~~CG~~GH~~~~C~~   17 (26)
T smart00343        1 KCYNCGKEGHIARDCPK   17 (26)
T ss_pred             CCccCCCCCcchhhCCc
Confidence            48899999999999984

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=92.76  E-value=0.059  Score=34.44  Aligned_cols=18  Identities=39%  Similarity=1.012  Sum_probs=16.0

Q ss_pred             CccccCCCCCccCCCCCC
Q 047168          214 GRCYNCGKSGHLARDCGA  231 (258)
Q Consensus       214 ~~C~~Cg~~GH~~~~Cp~  231 (258)
                      ..|.+|++.||++.+||.
T Consensus         5 ~~CqkC~~~GH~tyeC~~   22 (42)
T PF13917_consen    5 VRCQKCGQKGHWTYECPN   22 (42)
T ss_pred             CcCcccCCCCcchhhCCC
Confidence            489999999999999993

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

Probab=92.76  E-value=0.4  Score=33.55  Aligned_cols=56  Identities=20%  Similarity=0.195  Sum_probs=44.0

Q ss_pred             ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccC----CccccCCCCcEEEEEEeCCC
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSD----GYRTLYENQSVEFDVQLEAD   62 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~----~~~~l~~G~~V~F~v~~~~~   62 (258)
                      .+.+.|+|...+.   ||++.....+-+.|+|.+.|...    ....+.+|+.|++.+..-+.
T Consensus         5 G~iv~g~V~~v~~---~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~   64 (74)
T PF00575_consen    5 GDIVEGKVTSVED---FGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDK   64 (74)
T ss_dssp             TSEEEEEEEEEET---TEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEET
T ss_pred             CCEEEEEEEEEEC---CEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEEC
Confidence            4678999999975   66655555678999999999853    45678999999999887543

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 ....

>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=91.57  E-value=0.67  Score=33.42  Aligned_cols=56  Identities=20%  Similarity=0.088  Sum_probs=42.6

Q ss_pred             ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeCCC
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLEAD   62 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~~~   62 (258)
                      .+.+.|+|+...   -||++.....+.+.|+|.+.|....+    ..+.+|+.|++.+..-+.
T Consensus        15 G~i~~g~V~~v~---~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~   74 (83)
T cd04461          15 GMVVHGYVRNIT---PYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDE   74 (83)
T ss_pred             CCEEEEEEEEEe---eceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcC
Confidence            467889999886   37777766556899999999965533    247789999999877543

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.

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

Probab=91.31  E-value=0.84  Score=30.14  Aligned_cols=51  Identities=24%  Similarity=0.328  Sum_probs=37.4

Q ss_pred             cceEEEEeeCCCcee-EEecCCCCCceEEeccccccCC----ccccCCCCcEEEEEEeCC
Q 047168            7 STGKVTWFDGAKGYG-FIRPDDGGADLFVHQKSIKSDG----YRTLYENQSVEFDVQLEA   61 (258)
Q Consensus         7 ~~G~vk~f~~~kGfG-FI~~~~~~~dvF~H~s~l~~~~----~~~l~~G~~V~F~v~~~~   61 (258)
                      ++|+|+..+   .+| ||..+ ...+.|+|.+.+....    ...+++|+.|+..+..-+
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            468999996   344 45544 4589999999996531    245899999999988754

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.

>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=90.76  E-value=0.66  Score=32.05  Aligned_cols=55  Identities=13%  Similarity=0.064  Sum_probs=39.8

Q ss_pred             cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCC----ccccCCCCcEEEEEEeCCC
Q 047168            5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDG----YRTLYENQSVEFDVQLEAD   62 (258)
Q Consensus         5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~----~~~l~~G~~V~F~v~~~~~   62 (258)
                      +.+.|+|+...+   ||.+...++.-+-|+|.+.|....    ...+++|+.|++.+..-+.
T Consensus         2 ~~~~g~V~~v~~---~G~~V~l~~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~   60 (70)
T cd05698           2 LKTHGTIVKVKP---NGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDP   60 (70)
T ss_pred             CEEEEEEEEEec---CcEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcC
Confidence            357899999853   565555554589999999996432    2247899999999887544

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

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

Probab=90.67  E-value=1.4  Score=31.00  Aligned_cols=61  Identities=18%  Similarity=0.070  Sum_probs=43.0

Q ss_pred             CccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCcc----ccCCCCcEEEEEEeCCCccc
Q 047168            3 QLTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYR----TLYENQSVEFDVQLEADGKY   65 (258)
Q Consensus         3 ~~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~----~l~~G~~V~F~v~~~~~G~~   65 (258)
                      ..+.+.|+|+.....  ||.+.....+.+-|+|+|.+...-..    .+++||.|...+..-+++++
T Consensus         3 ~G~iv~G~V~~i~~~--~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~~~i   67 (72)
T cd05704           3 EGAVTLGMVTKVIPH--SGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKDGKY   67 (72)
T ss_pred             CCCEEEEEEEEeeCC--cEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecCCEE
Confidence            346789999997433  55555455568999999999664322    35789999988877655543

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.

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

Probab=90.60  E-value=0.89  Score=33.57  Aligned_cols=57  Identities=21%  Similarity=0.145  Sum_probs=40.4

Q ss_pred             ccccceEEEEeeCCCceeEEecCCCCCceEEecccccc-------CCccccCCCCcEEEEEEeCC
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKS-------DGYRTLYENQSVEFDVQLEA   61 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~-------~~~~~l~~G~~V~F~v~~~~   61 (258)
                      ...+.|+|+...+.-.==||...+ +.+-|+|++.+..       .--..|++||.|...+...+
T Consensus         8 G~iy~g~V~~i~~~~~GaFV~l~~-g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~   71 (88)
T cd04453           8 GNIYLGRVKKIVPGLQAAFVDIGL-GKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEP   71 (88)
T ss_pred             CCEEEEEEEEeccCCcEEEEEeCC-CCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEec
Confidence            356889999995332334556554 5899999999954       11235899999999988854

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

>PRK07252 hypothetical protein; Provisional

Probab=90.03  E-value=1.8  Score=33.98  Aligned_cols=57  Identities=19%  Similarity=0.152  Sum_probs=43.6

Q ss_pred             CCccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeCC
Q 047168            2 AQLTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLEA   61 (258)
Q Consensus         2 ~~~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~~   61 (258)
                      .....+.|+|....   -||++...+...+-|+|++.|....+    ..+..||.|+..|..-+
T Consensus         2 kvG~iv~G~V~~V~---~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD   62 (120)
T PRK07252          2 KIGDKLKGTITGIK---PYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFD   62 (120)
T ss_pred             CCCCEEEEEEEEEe---CcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEe
Confidence            34567899999985   38877766666899999999965432    34788999999988854

>PF14392 zf-CCHC_4: Zinc knuckle

Probab=89.62  E-value=0.14  Score=33.70  Aligned_cols=20  Identities=35%  Similarity=0.858  Sum_probs=12.2

Q ss_pred             CCCCcccccCCcccCcccCC
Q 047168          185 NNSGGCFKCGGYGHLARDCI  204 (258)
Q Consensus       185 ~~~~~C~~Cg~~GH~~~~C~  204 (258)
                      ..+..|+.|+..||..++||
T Consensus        29 ~lp~~C~~C~~~gH~~~~C~   48 (49)
T PF14392_consen   29 RLPRFCFHCGRIGHSDKECP   48 (49)
T ss_pred             CcChhhcCCCCcCcCHhHcC
Confidence            34456666666666666665

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

Probab=89.42  E-value=1.6  Score=29.37  Aligned_cols=54  Identities=24%  Similarity=0.267  Sum_probs=39.2

Q ss_pred             cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeCC
Q 047168            5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLEA   61 (258)
Q Consensus         5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~~   61 (258)
                      ..+.|+|+....   ||++...+...+.|+|.+.+.....    ..++.||.|+..+..-+
T Consensus         2 ~~~~g~V~~i~~---~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~   59 (69)
T cd05692           2 SVVEGTVTRLKP---FGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID   59 (69)
T ss_pred             CEEEEEEEEEEe---eeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEEC
Confidence            356789988763   6766655556899999999965422    34789999998876543

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.

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

Probab=89.34  E-value=0.2  Score=45.06  Aligned_cols=21  Identities=38%  Similarity=1.088  Sum_probs=14.4

Q ss_pred             CccccCCCCCccCCCCCCCCC
Q 047168          214 GRCYNCGKSGHLARDCGAGGA  234 (258)
Q Consensus       214 ~~C~~Cg~~GH~~~~Cp~~~~  234 (258)
                      ..||+|++.||.+++||..+.
T Consensus       161 ~~cyrcGkeghwskEcP~~~~  181 (346)
T KOG0109|consen  161 SGCYRCGKEGHWSKECPVDRT  181 (346)
T ss_pred             HHheeccccccccccCCccCC
Confidence            357777777777777776553

>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=89.22  E-value=1.9  Score=30.03  Aligned_cols=57  Identities=12%  Similarity=-0.142  Sum_probs=40.3

Q ss_pred             CccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeCCC
Q 047168            3 QLTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLEAD   62 (258)
Q Consensus         3 ~~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~~~   62 (258)
                      ..+.+.|+|+....   ||.+-..+..-+-|+|+++|.....    ..+++||.|+..+..-+.
T Consensus         3 ~G~iv~g~V~~v~~---~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~   63 (73)
T cd05706           3 VGDILPGRVTKVND---RYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDV   63 (73)
T ss_pred             CCCEEEEEEEEEeC---CeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeC
Confidence            45678899999843   4544444445899999999975421    237899999998877543

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.

>PRK05054 exoribonuclease II; Provisional

Probab=89.14  E-value=0.65  Score=46.67  Aligned_cols=60  Identities=20%  Similarity=0.257  Sum_probs=42.5

Q ss_pred             cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccC
Q 047168            5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAP   73 (258)
Q Consensus         5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~   73 (258)
                      ..+.|+|+.=  .+||||+.+++ .+|||+....+...     -.||.|...+... +++.+|.-+.++
T Consensus        20 ~~~~G~~~~~--~~gfgFv~~~~-~~difI~~~~l~~a-----~~GD~V~v~i~~~-~~r~~g~v~~il   79 (644)
T PRK05054         20 PRVEGVVKAT--EKGFGFLEVDA-QKSYFIPPPQMKKV-----MHGDRIIAVIHTE-KDREIAEPEELI   79 (644)
T ss_pred             CeEEEEEEEC--CCccEEEEECC-CCcEEEChHHHccC-----CCCCEEEEEEecC-CCCcEEEEEEEE
Confidence            4577999854  89999998755 46999998888653     5699998887653 233455544443

>TIGR02063 RNase_R ribonuclease R

Probab=89.14  E-value=0.69  Score=46.96  Aligned_cols=62  Identities=19%  Similarity=0.412  Sum_probs=44.5

Q ss_pred             ccceEEEEeeCCCceeEEecCC-CCCceEEeccccccCCccccCCCCcEEEEEEeCC--CccceeeccccCC
Q 047168            6 RSTGKVTWFDGAKGYGFIRPDD-GGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEA--DGKYQALDVTAPG   74 (258)
Q Consensus         6 ~~~G~vk~f~~~kGfGFI~~~~-~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~--~G~~~A~~V~~~~   74 (258)
                      .+.|+++.  ..+||||+.+++ ..+|||+....+.     .+..||.|...+....  +++++|.-|.+++
T Consensus        68 ~~~G~i~~--~~~g~gFv~~~~~~~~di~I~~~~~~-----~a~~GD~Vlv~I~~~~~~~~~~eg~Vv~Il~  132 (709)
T TIGR02063        68 LVKGTVIA--HRDGFGFLRPEDDDEDDIFIPPRQMN-----GAMHGDRVLVRITGKPDGGDRFEARVIKILE  132 (709)
T ss_pred             eEEEEEEE--CCCccEEEEECCCCCCcEEEChHHhC-----cCCCCCEEEEEEecccCCCCCceEEEEEEEe
Confidence            46788875  489999999886 4579999876653     3578999999986532  3445666665554

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.

>PRK12608 transcription termination factor Rho; Provisional

Probab=88.99  E-value=0.54  Score=44.16  Aligned_cols=51  Identities=24%  Similarity=0.334  Sum_probs=41.3

Q ss_pred             ccccceEEEEeeCCCceeEEecC-----CCCCceEEeccccccCCccccCCCCcEEEEEEe
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPD-----DGGADLFVHQKSIKSDGYRTLYENQSVEFDVQL   59 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~-----~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~   59 (258)
                      .....|++--..  .||||+...     .+.+||||..+.|+..+   |..|+.|.-....
T Consensus        16 ~~~~~g~l~~~~--~g~gflr~~~~~~~~~~~d~yv~~~~i~~~~---l~~Gd~V~~~~r~   71 (380)
T PRK12608         16 TEEVLGVLEILG--DGFGFLRSARRNYLPSPDDVFVPPALIRRFN---LRTGDVVEGVARP   71 (380)
T ss_pred             CCcceEEEEEcC--CCceEeecCccCCCCCCCCeeeCHHHHHHhC---CCCCCEEEeccCC
Confidence            356778888664  499999985     45799999999998875   8999999987655

>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=88.91  E-value=1.3  Score=31.07  Aligned_cols=52  Identities=17%  Similarity=0.079  Sum_probs=36.0

Q ss_pred             cc-eEEEEeeCCCceeEEecCCCCCceEEeccccccCC----ccccCCCCcEEEEEEeC
Q 047168            7 ST-GKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDG----YRTLYENQSVEFDVQLE   60 (258)
Q Consensus         7 ~~-G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~----~~~l~~G~~V~F~v~~~   60 (258)
                      +. |+|+...  ..||.+.....+-+-|+|+|.|....    ...+++|+.|++.+..-
T Consensus         4 ~~~g~V~~v~--~~~G~~V~l~~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~i   60 (71)
T cd05696           4 VDSVKVTKVE--PDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGY   60 (71)
T ss_pred             eeeeEEEEEc--cCceEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEE
Confidence            45 8888874  34665444433589999999995432    33488999999987653

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.

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

Probab=88.72  E-value=2  Score=30.15  Aligned_cols=56  Identities=18%  Similarity=0.097  Sum_probs=40.4

Q ss_pred             ccccceEEEEeeCCCceeEEecCCC-CCceEEeccccccCCccc----cCCCCcEEEEEEeCCC
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPDDG-GADLFVHQKSIKSDGYRT----LYENQSVEFDVQLEAD   62 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~~~-~~dvF~H~s~l~~~~~~~----l~~G~~V~F~v~~~~~   62 (258)
                      ...+.|+|+...   -||++...++ ..+-|+|++.|....+..    ++.||.|+..+..-+.
T Consensus         4 g~~~~g~V~~i~---~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~   64 (73)
T cd05686           4 YQIFKGEVASVT---EYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREM   64 (73)
T ss_pred             CCEEEEEEEEEE---eeeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECC
Confidence            467889999986   3776655543 369999999997654322    5789999988776443

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.

>TIGR02062 RNase_B exoribonuclease II

Probab=88.54  E-value=0.83  Score=45.87  Aligned_cols=61  Identities=20%  Similarity=0.244  Sum_probs=42.8

Q ss_pred             ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccC
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAP   73 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~   73 (258)
                      ...+.|+|+.=  .+||||+.+++ .+|||+.-..+...     -.||.|...+.... ++.+|.-+.++
T Consensus        16 ~~~~~G~i~~~--~kGfgFv~~~~-~~difI~~~~l~~A-----~~GD~V~v~i~~~~-~r~~~~v~~iv   76 (639)
T TIGR02062        16 TPRVEGVVKAT--EKGFGFLEVDA-QKSYFIPPPQMKKV-----MHGDKIIAVIHSEK-ERESAEPEELI   76 (639)
T ss_pred             CceEEEEEEEC--CCccEEEEECC-CCcEEEChHHHccC-----CCCCEEEEEEecCC-CCcEEEEEEEE
Confidence            34677999854  89999997654 57999999888654     56999988876543 33454444433

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.

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

Probab=88.46  E-value=1.2  Score=30.06  Aligned_cols=56  Identities=14%  Similarity=0.117  Sum_probs=40.9

Q ss_pred             ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCC----ccccCCCCcEEEEEEeCCC
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDG----YRTLYENQSVEFDVQLEAD   62 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~----~~~l~~G~~V~F~v~~~~~   62 (258)
                      .+.+.|+|+..+.   +|++-..+...+.|+|.+.+....    ...+++|+.|.+.+..-+.
T Consensus         3 G~~v~g~V~~v~~---~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~   62 (72)
T smart00316        3 GDVVEGTVTEITP---FGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDE   62 (72)
T ss_pred             CCEEEEEEEEEEc---cEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeC
Confidence            3567899999975   455544444589999999997541    2348999999999887543

>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=88.25  E-value=1.7  Score=29.94  Aligned_cols=55  Identities=9%  Similarity=0.009  Sum_probs=40.5

Q ss_pred             cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeCCC
Q 047168            5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLEAD   62 (258)
Q Consensus         5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~~~   62 (258)
                      +.+.|+|+...   .||.+-..+.+-+-|+|.+.|....+    ..++.|+.|++.+..-+.
T Consensus         2 ~~v~g~V~~v~---~~Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~   60 (69)
T cd05697           2 QVVKGTIRKLR---PSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEP   60 (69)
T ss_pred             CEEEEEEEEEe---ccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEEC
Confidence            35789999985   36766555555899999999965432    348899999999877543

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.

>PRK08582 hypothetical protein; Provisional

Probab=87.93  E-value=2.7  Score=33.79  Aligned_cols=65  Identities=25%  Similarity=0.293  Sum_probs=45.2

Q ss_pred             cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeCC-CccceeeccccC
Q 047168            5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLEA-DGKYQALDVTAP   73 (258)
Q Consensus         5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~~-~G~~~A~~V~~~   73 (258)
                      ..+.|+|+...   .||++...+...+-|||++.|...-+    ..+.+||.|+..|..-+ ++++ ...+..+
T Consensus         7 ~iv~G~V~~I~---~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~~gkI-~LSlk~~   76 (139)
T PRK08582          7 SKLQGKVTGIT---NFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKI-GLSIKKA   76 (139)
T ss_pred             CEEEEEEEEEE---CCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECCCCcE-EEEEEec
Confidence            57889999874   46766555556899999999964432    35789999998887754 4543 3334333

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

Probab=87.76  E-value=2.9  Score=28.92  Aligned_cols=56  Identities=25%  Similarity=0.233  Sum_probs=40.1

Q ss_pred             ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc-----cccCCCCcEEEEEEeCCC
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY-----RTLYENQSVEFDVQLEAD   62 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~-----~~l~~G~~V~F~v~~~~~   62 (258)
                      .+.+.|+|+...   -||+....+.+.+-|+|++.|.....     ..++.||.|+..+..-+.
T Consensus         4 g~~~~g~V~~i~---~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~   64 (72)
T cd05689           4 GTRLFGKVTNLT---DYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDE   64 (72)
T ss_pred             CCEEEEEEEEEE---eeEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeC
Confidence            456889999885   48877666556899999999963211     236789999888766543

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.

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=87.46  E-value=0.84  Score=43.24  Aligned_cols=66  Identities=26%  Similarity=0.507  Sum_probs=46.6

Q ss_pred             ccceEEEEeeCCCceeEEecCC-----CCCceEEeccccccCCccccCCCCcEEEEEEeCCCcc--ceeeccccCCCC
Q 047168            6 RSTGKVTWFDGAKGYGFIRPDD-----GGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGK--YQALDVTAPGGA   76 (258)
Q Consensus         6 ~~~G~vk~f~~~kGfGFI~~~~-----~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~--~~A~~V~~~~g~   76 (258)
                      ...|++--..  .||||+...+     +.+||||-.+.|+..+   |+.|+.|+=.+....++.  +..+.|..+.+.
T Consensus        50 ~~~g~le~~~--~g~gflr~~~~~y~~~~~d~yvs~~~ir~~~---lr~gd~v~g~~r~~~~~e~~~~l~~v~~vng~  122 (416)
T PRK09376         50 FGEGVLEILP--DGFGFLRSPDANYLPGPDDIYVSPSQIRRFN---LRTGDTVEGKIRPPKEGERYFALLKVETVNGE  122 (416)
T ss_pred             EEEEEEEEcC--CCCeEEeCCCcCCCCCCCCeeeCHHHHHhcC---CCCCCEEEEEeeCCCCCCCccceEEEeeeCCC
Confidence            3556666553  4999999853     4689999999998875   899999998887754331  234455555543

>PF15288 zf-CCHC_6: Zinc knuckle

Probab=87.42  E-value=0.32  Score=30.69  Aligned_cols=20  Identities=35%  Similarity=0.798  Sum_probs=15.2

Q ss_pred             CccccCCCCCccC--CCCCCCC
Q 047168          214 GRCYNCGKSGHLA--RDCGAGG  233 (258)
Q Consensus       214 ~~C~~Cg~~GH~~--~~Cp~~~  233 (258)
                      ++|.+|+..||+.  +.||...
T Consensus         2 ~kC~~CG~~GH~~t~k~CP~~~   23 (40)
T PF15288_consen    2 VKCKNCGAFGHMRTNKRCPMYC   23 (40)
T ss_pred             ccccccccccccccCccCCCCC
Confidence            4788888888886  6788743

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

Probab=86.83  E-value=2.4  Score=30.04  Aligned_cols=56  Identities=16%  Similarity=0.013  Sum_probs=40.7

Q ss_pred             CccccceEEEEeeCCCcee-EEecCCCCCceEEeccccccCCc-------cccCCCCcEEEEEEeCCC
Q 047168            3 QLTRSTGKVTWFDGAKGYG-FIRPDDGGADLFVHQKSIKSDGY-------RTLYENQSVEFDVQLEAD   62 (258)
Q Consensus         3 ~~~~~~G~vk~f~~~kGfG-FI~~~~~~~dvF~H~s~l~~~~~-------~~l~~G~~V~F~v~~~~~   62 (258)
                      ..+.+.|+|+...   .|| |++.. .+-+-|+|+++|.....       ..+++|+.|++.|..-+.
T Consensus         3 ~G~~V~g~V~~i~---~~G~fV~l~-~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~   66 (74)
T cd05705           3 EGQLLRGYVSSVT---KQGVFFRLS-SSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNS   66 (74)
T ss_pred             CCCEEEEEEEEEe---CCcEEEEeC-CCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEEC
Confidence            3467889999984   444 45544 46899999999976541       346999999999887543

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

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

Probab=86.70  E-value=0.38  Score=43.42  Aligned_cols=23  Identities=30%  Similarity=0.742  Sum_probs=19.5

Q ss_pred             CCCCCcccccCCcccCcccCCCC
Q 047168          184 NNNSGGCFKCGGYGHLARDCITR  206 (258)
Q Consensus       184 ~~~~~~C~~Cg~~GH~~~~C~~~  206 (258)
                      ......||+||+.|||..+||.+
T Consensus       173 pPpgY~CyRCGqkgHwIqnCpTN  195 (427)
T COG5222         173 PPPGYVCYRCGQKGHWIQNCPTN  195 (427)
T ss_pred             CCCceeEEecCCCCchhhcCCCC
Confidence            34567899999999999999876

>PRK12678 transcription termination factor Rho; Provisional

Probab=86.69  E-value=0.92  Score=45.04  Aligned_cols=52  Identities=23%  Similarity=0.501  Sum_probs=41.1

Q ss_pred             ccceEEEEeeCCCceeEEecC---CCCCceEEeccccccCCccccCCCCcEEEEEEeCCCc
Q 047168            6 RSTGKVTWFDGAKGYGFIRPD---DGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADG   63 (258)
Q Consensus         6 ~~~G~vk~f~~~kGfGFI~~~---~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G   63 (258)
                      .+.|++--.   .|||||...   .+..||||..+.|...+   |..|+.|.=.|.....+
T Consensus       295 ~~~GiLdi~---dg~gFlR~~~y~~~~~Dvyvs~~qirr~~---Lr~Gd~v~G~vr~p~~~  349 (672)
T PRK12678        295 PVAGILDVL---DNYAFVRTSGYLPGPNDVYVSMNQVRKNG---LRKGDAVTGAVRAPREG  349 (672)
T ss_pred             EeeEEEEec---CCeeEeeCCCCCCCCCCeeeCHHHHHHcC---CCCCCEEEEeecCCCCC
Confidence            356766655   499999876   46799999999998875   89999999887765444

>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=86.48  E-value=1.6  Score=41.75  Aligned_cols=66  Identities=26%  Similarity=0.387  Sum_probs=54.1

Q ss_pred             CCcccccCCCCccccccccccCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCcccCcccCCCC
Q 047168          128 GVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITR  206 (258)
Q Consensus       128 ~~~C~~Cg~~GH~a~~Cp~~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~~  206 (258)
                      ...+..++..+|..+.+..        .....|..|-.++|+...|....     .+.....|++|...|||.+.||..
T Consensus       112 ~q~~~~~~~~~~~~~~~t~--------~~~~~~~~~~~~~~~iq~~~~~g-----~Pppsy~c~rc~~~g~wikacptv  177 (448)
T KOG0314|consen  112 IQMNGRMGGRGFGMRRQTP--------PPGYVCHRCNSPGHFIQHCSTNG-----SPPPSYKCVKCPTPGPWIKACPTV  177 (448)
T ss_pred             hhhccccccCCcccccCCC--------cccceeeecccCccccccccccC-----CCCCCcceecCCCCCccceecccc
Confidence            4578889999999888853        44578999999999999888763     345678999999999999999876

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

Probab=86.12  E-value=2.8  Score=28.32  Aligned_cols=53  Identities=21%  Similarity=0.182  Sum_probs=39.8

Q ss_pred             ccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeCC
Q 047168            6 RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLEA   61 (258)
Q Consensus         6 ~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~~   61 (258)
                      .+.|+|.....   ||++.......+-|+|++.|...-+    ..++.|+.|...+...+
T Consensus         3 ~~~g~V~~v~~---~G~~v~l~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d   59 (68)
T cd04472           3 IYEGKVVKIKD---FGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVD   59 (68)
T ss_pred             EEEEEEEEEEE---eEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEEC
Confidence            46788888864   8888776556899999999965432    23688999998877644

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.

>PF14392 zf-CCHC_4: Zinc knuckle

Probab=85.94  E-value=0.31  Score=32.00  Aligned_cols=19  Identities=32%  Similarity=0.891  Sum_probs=11.0

Q ss_pred             CCCCcccCCCCCCCCCCCC
Q 047168          156 NSGGCYNCGDPEHFARDCP  174 (258)
Q Consensus       156 ~~~~C~~Cg~~GH~~~~Cp  174 (258)
                      .+..|+.|+..||..++||
T Consensus        30 lp~~C~~C~~~gH~~~~C~   48 (49)
T PF14392_consen   30 LPRFCFHCGRIGHSDKECP   48 (49)
T ss_pred             cChhhcCCCCcCcCHhHcC
Confidence            3455666666666666554

>COG1158 Rho Transcription termination factor [Transcription]

Probab=85.36  E-value=0.8  Score=42.40  Aligned_cols=68  Identities=28%  Similarity=0.518  Sum_probs=47.7

Q ss_pred             eEEEEeeCCCceeEEecCC-----CCCceEEeccccccCCccccCCCCcEEEEEEeCCCcc--ceeeccccCCCCcccCC
Q 047168            9 GKVTWFDGAKGYGFIRPDD-----GGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGK--YQALDVTAPGGAPVHSS   81 (258)
Q Consensus         9 G~vk~f~~~kGfGFI~~~~-----~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~--~~A~~V~~~~g~~~~~s   81 (258)
                      |++--.  ..||||+.+.+     +.+||||--|.|...+   |..||.|+=.|.....|.  ..-+.|..+.+.+....
T Consensus        56 GvLeil--~dGfGFLR~~~~~yl~~~~DiYvSpSQIRrf~---LrtGD~v~G~vR~Pke~Ery~aLl~ve~vN~~~pe~~  130 (422)
T COG1158          56 GVLEIL--PDGFGFLRSADSSYLPGPDDIYVSPSQIRRFN---LRTGDTVEGKVRPPKEGERYFALLKVEAVNGDDPEKA  130 (422)
T ss_pred             eEEEec--cCCcceeecCccccCCCCCceEECHHHHhhcc---CccCCEEeeeecCCCcccceeeeEEEeecCCCCHHHh
Confidence            444444  48999998775     5699999999998774   889999998888776553  22345555555443333

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

Probab=84.95  E-value=3.2  Score=28.59  Aligned_cols=54  Identities=22%  Similarity=0.204  Sum_probs=39.8

Q ss_pred             ccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeCCC
Q 047168            6 RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLEAD   62 (258)
Q Consensus         6 ~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~~~   62 (258)
                      .+.|+|+...   .+|++...+..-+-|+|.+.+....+    ..+++||.|++.+..-+.
T Consensus         3 ~v~g~V~~v~---~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~   60 (73)
T cd05691           3 IVTGKVTEVD---AKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDR   60 (73)
T ss_pred             EEEEEEEEEE---CCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeC
Confidence            4679999985   46666555555899999999876433    236899999999887554

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.

>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=84.93  E-value=2.9  Score=28.65  Aligned_cols=54  Identities=15%  Similarity=0.053  Sum_probs=38.2

Q ss_pred             cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCcc----ccCCCCcEEEEEEeCC
Q 047168            5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYR----TLYENQSVEFDVQLEA   61 (258)
Q Consensus         5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~----~l~~G~~V~F~v~~~~   61 (258)
                      ..+.|+|+...   .||.+......-+-|+|++.|......    .+.+||.|+..+..-+
T Consensus         2 ~~v~g~V~~v~---~~Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d   59 (68)
T cd05707           2 DVVRGFVKNIA---NNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSID   59 (68)
T ss_pred             CEEEEEEEEEE---CccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEe
Confidence            35789999985   355544444458999999999654322    3789999999877654

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.

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

Probab=84.71  E-value=1.8  Score=29.65  Aligned_cols=53  Identities=19%  Similarity=0.158  Sum_probs=37.6

Q ss_pred             cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCcc--ccCCCCcEEEEEEeCC
Q 047168            5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYR--TLYENQSVEFDVQLEA   61 (258)
Q Consensus         5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~--~l~~G~~V~F~v~~~~   61 (258)
                      +.+.|+|+.+++   +|++... .+-+.|+|.+.+......  ...+|+.+++.+..-+
T Consensus         2 ~iv~g~V~~v~~---~G~~v~l-~g~~gfip~s~~~~~~~~~~~~~vG~~i~~~i~~vd   56 (67)
T cd04465           2 EIVEGKVTEKVK---GGLIVDI-EGVRAFLPASQVDLRPVEDLDEYVGKELKFKIIEID   56 (67)
T ss_pred             CEEEEEEEEEEC---CeEEEEE-CCEEEEEEHHHCCCcccCChHHhCCCEEEEEEEEEe
Confidence            346899999963   5666555 458999999999754322  1247999999887754

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

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

Probab=84.63  E-value=3.8  Score=29.11  Aligned_cols=55  Identities=20%  Similarity=0.120  Sum_probs=41.2

Q ss_pred             CccccceEEEEeeCCCceeEEecCC-CCCceEEeccccccCCccccCCCCcEEEEEEeCCC
Q 047168            3 QLTRSTGKVTWFDGAKGYGFIRPDD-GGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEAD   62 (258)
Q Consensus         3 ~~~~~~G~vk~f~~~kGfGFI~~~~-~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~   62 (258)
                      ..+.+.|+|+...   -||++.... .+-+-|+|.+++...  ..+.+|+.|...+..-++
T Consensus         4 ~G~~v~g~V~si~---d~G~~v~~g~~gv~Gfl~~~~~~~~--~~~~~Gq~v~~~V~~vd~   59 (74)
T cd05694           4 EGMVLSGCVSSVE---DHGYILDIGIPGTTGFLPKKDAGNF--SKLKVGQLLLCVVEKVKD   59 (74)
T ss_pred             CCCEEEEEEEEEe---CCEEEEEeCCCCcEEEEEHHHCCcc--cccCCCCEEEEEEEEEEC
Confidence            3456889999985   567655443 346899999999765  569999999999875443

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

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

Probab=84.32  E-value=4.4  Score=28.77  Aligned_cols=50  Identities=16%  Similarity=0.100  Sum_probs=39.0

Q ss_pred             ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeC
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLE   60 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~   60 (258)
                      .+.+.|+|....   -||+...-+...+-|+|.+.+..    .++.||.|...+..-
T Consensus        17 G~~~~g~V~~i~---~~G~fV~l~~~~~Glv~~se~~~----~~~iGd~v~v~I~~i   66 (77)
T cd04473          17 GKLYKGKVNGVA---KYGVFVDLNDHVRGLIHRSNLLR----DYEVGDEVIVQVTDI   66 (77)
T ss_pred             CCEEEEEEEeEe---cceEEEEECCCcEEEEEchhccC----cCCCCCEEEEEEEEE
Confidence            356889998874   47777666666899999999853    489999999887664

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.

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

Probab=83.07  E-value=4.3  Score=27.63  Aligned_cols=53  Identities=26%  Similarity=0.263  Sum_probs=38.4

Q ss_pred             ccceEEEEeeCCCceeEEecCCCCCceEEecccccc-CC----ccccCCCCcEEEEEEeCC
Q 047168            6 RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKS-DG----YRTLYENQSVEFDVQLEA   61 (258)
Q Consensus         6 ~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~-~~----~~~l~~G~~V~F~v~~~~   61 (258)
                      .+.|+|+...   -||+....+...+-|+|++.|.. ..    ...++.||.|+..+..-+
T Consensus         3 ~~~g~V~~i~---~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id   60 (69)
T cd05690           3 VVSGKIKSIT---DFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNID   60 (69)
T ss_pred             EEEEEEEEEE---eeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEE
Confidence            5678888874   58777666556899999999963 11    124688999998876643

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.

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

Probab=82.49  E-value=0.86  Score=41.20  Aligned_cols=23  Identities=43%  Similarity=1.063  Sum_probs=17.3

Q ss_pred             CCCCcccccCCCCcccccccccc
Q 047168          126 PGGVVCYNCDGVGHVARECTSNR  148 (258)
Q Consensus       126 ~~~~~C~~Cg~~GH~a~~Cp~~~  148 (258)
                      ..+..||.||+.|||..+||.+.
T Consensus       174 PpgY~CyRCGqkgHwIqnCpTN~  196 (427)
T COG5222         174 PPGYVCYRCGQKGHWIQNCPTNQ  196 (427)
T ss_pred             CCceeEEecCCCCchhhcCCCCC
Confidence            44667888888888888888744

>PF15288 zf-CCHC_6: Zinc knuckle

Probab=82.01  E-value=0.84  Score=28.79  Aligned_cols=19  Identities=37%  Similarity=0.850  Sum_probs=16.3

Q ss_pred             CccccCCCCCccC--CCCCCC
Q 047168          238 GSCFNCGKPGHFA--RECTKV  256 (258)
Q Consensus       238 ~~C~~Cg~~GH~~--~~Cp~~  256 (258)
                      +.|.+|+..||+.  +.||..
T Consensus         2 ~kC~~CG~~GH~~t~k~CP~~   22 (40)
T PF15288_consen    2 VKCKNCGAFGHMRTNKRCPMY   22 (40)
T ss_pred             ccccccccccccccCccCCCC
Confidence            4699999999998  779864

>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=80.76  E-value=3  Score=39.97  Aligned_cols=69  Identities=20%  Similarity=0.319  Sum_probs=54.8

Q ss_pred             CCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCcccCcccCCCCCCCCCCCCccccCCCCCccCCCCCCCC
Q 047168          155 NNSGGCYNCGDPEHFARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGAGG  233 (258)
Q Consensus       155 ~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~  233 (258)
                      +....+..++..+|..+.+...         ...+|..|...+|+...|...... -....|++|...||....||...
T Consensus       110 p~~q~~~~~~~~~~~~~~~t~~---------~~~~~~~~~~~~~~iq~~~~~g~P-ppsy~c~rc~~~g~wikacptv~  178 (448)
T KOG0314|consen  110 PLIQMNGRMGGRGFGMRRQTPP---------PGYVCHRCNSPGHFIQHCSTNGSP-PPSYKCVKCPTPGPWIKACPTVS  178 (448)
T ss_pred             chhhhccccccCCcccccCCCc---------ccceeeecccCccccccccccCCC-CCCcceecCCCCCccceeccccC
Confidence            3445799999999999988554         368999999999999999876331 12347999999999999999854

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

Probab=80.70  E-value=0.86  Score=27.99  Aligned_cols=19  Identities=37%  Similarity=0.770  Sum_probs=9.4

Q ss_pred             CcccccCCcccCcccCCCC
Q 047168          188 GGCFKCGGYGHLARDCITR  206 (258)
Q Consensus       188 ~~C~~Cg~~GH~~~~C~~~  206 (258)
                      ..|++|++--|++.+|-..
T Consensus         3 ~~CprC~kg~Hwa~~C~sk   21 (36)
T PF14787_consen    3 GLCPRCGKGFHWASECRSK   21 (36)
T ss_dssp             -C-TTTSSSCS-TTT---T
T ss_pred             ccCcccCCCcchhhhhhhh
Confidence            3577777777777777554

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

Probab=80.57  E-value=5.9  Score=28.00  Aligned_cols=55  Identities=24%  Similarity=0.299  Sum_probs=38.6

Q ss_pred             ccceEEEEeeCCCceeEEecCC---CCCceEEeccccccCCc-----cccCCCCcEEEEEEeCCCc
Q 047168            6 RSTGKVTWFDGAKGYGFIRPDD---GGADLFVHQKSIKSDGY-----RTLYENQSVEFDVQLEADG   63 (258)
Q Consensus         6 ~~~G~vk~f~~~kGfGFI~~~~---~~~dvF~H~s~l~~~~~-----~~l~~G~~V~F~v~~~~~G   63 (258)
                      .+.|+|+...   -||+....+   .+.+-|+|++.|...-+     ..++.|+.|...+...+++
T Consensus         3 ~~~g~V~~v~---~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd~~   65 (79)
T cd05684           3 IYKGKVTSIM---DFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQNG   65 (79)
T ss_pred             EEEEEEEEEE---eeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEeCC
Confidence            4678888885   367665444   25799999999965432     2458999998887775544

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	258
3i2z_B	71	Structure Of Cold Shock Protein E From Salmonella T		2e-12
3cam_A	67	Crystal Structure Of The Cold Shock Domain Protein		2e-12
2l15_A	70	Solution Structure Of Cold Shock Protein Cspa Using		1e-11
1mjc_A	69	Crystal Structure Of Cspa, The Major Cold Shock Pro		2e-11
3mef_A	69	Major Cold-Shock Protein From Escherichia Coli Solu		2e-11
1g6p_A	66	Solution Nmr Structure Of The Cold Shock Protein Fr		4e-11
4a4i_A	90	Crystal Structure Of The Human Lin28b Cold Shock Do		9e-10
2lss_A	70	Solution Structure Of The R. Rickettsii Cold Shock-		1e-09
3ulj_A	90	Crystal Structure Of Apo Lin28b Cold Shock Domain L		1e-09
1hza_A	67	Bacillus Caldolyticus Cold-Shock Protein Mutants To		3e-09
1hz9_A	66	Bacillus Caldolyticus Cold-Shock Protein Mutants To		3e-09
3a0j_A	73	Crystal Structure Of Cold Shock Protein 1 From Ther		3e-09
1i5f_A	66	Bacillus Caldolyticus Cold-Shock Protein Mutants To		4e-09
1hzc_A	66	Bacillus Caldolyticus Cold-Shock Protein Mutants To		4e-09
1c9o_A	66	Crystal Structure Analysis Of The Bacillus Caldolyt		4e-09
1h95_A	79	Solution Structure Of The Single-Stranded Dna-Bindi		4e-09
1hzb_A	66	Bacillus Caldolyticus Cold-Shock Protein Mutants To		6e-09
2i5l_X	67	Crystal Structure Of Bacillus Subtilis Cold Shock P		1e-08
2es2_A	67	Crystal Structure Analysis Of The Bacillus Subtilis		2e-08
2i5m_X	67	Crystal Structure Of Bacillus Subtilis Cold Shock P		3e-08
3trz_A	148	Mouse Lin28a In Complex With Let-7d Microrna Pre-El		1e-07
3ts0_A	146	Mouse Lin28a In Complex With Let-7f-1 Microrna Pre-		1e-07
2bh8_A	101	Combinatorial Protein 1b11 Length = 101		5e-05

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

Iteration: 1
 Score = 69.3 bits (168), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 31/71 (43%), Positives = 49/71 (69%), Gaps = 1/71 (1%)
Query: 2  AQLTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEA 61
          + +++  G V WF+ +KG+GFI P+DG  D+FVH  +I+++G++TL E Q VEF++   A
Sbjct: 1  SHMSKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGA 60
Query: 62 DGKYQALDVTA 72
           G   A +VTA
Sbjct: 61 KGP-SAANVTA 70

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

Iteration: 1
 Score = 69.3 bits (168), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 34/66 (51%), Positives = 44/66 (66%), Gaps = 1/66 (1%)
Query: 7  STGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQ 66
          +TG V WF+ AKG+GFI PD+GG DLF H  +I  +G++TL E Q V FDV     GK Q
Sbjct: 2  ATGIVKWFNDAKGFGFITPDEGGEDLFAHFSAINXEGFKTLKEGQRVSFDVTTGPKGK-Q 60
Query: 67 ALDVTA 72
          A ++ A
Sbjct: 61 AANIQA 66

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

Iteration: 1
 Score = 66.6 bits (161), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 29/58 (50%), Positives = 40/58 (68%)
Query: 6  RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADG 63
          + TG V WF+  KG+GFI PDDG  D+FVH  +I++DGY++L E Q V F ++  A G
Sbjct: 4  KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKG 61

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

Iteration: 1
 Score = 66.2 bits (160), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 29/58 (50%), Positives = 40/58 (68%)
Query: 6  RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADG 63
          + TG V WF+  KG+GFI PDDG  D+FVH  +I++DGY++L E Q V F ++  A G
Sbjct: 3  KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKG 60

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

Iteration: 1
 Score = 66.2 bits (160), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 29/58 (50%), Positives = 40/58 (68%)
Query: 6  RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADG 63
          + TG V WF+  KG+GFI PDDG  D+FVH  +I++DGY++L E Q V F ++  A G
Sbjct: 3  KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKG 60

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

Iteration: 1
 Score = 65.1 bits (157), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 29/50 (58%), Positives = 38/50 (76%), Gaps = 1/50 (2%)
Query: 9  GKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQ 58
          GKV WFD  KGYGFI  D+GG D+FVH  +I+ +G++TL E Q VEF++Q
Sbjct: 3  GKVKWFDSKKGYGFITKDEGG-DVFVHWSAIEMEGFKTLKEGQVVEFEIQ 51

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

Iteration: 1
 Score = 60.5 bits (145), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 31/83 (37%), Positives = 47/83 (56%), Gaps = 8/83 (9%)
Query: 2  AQLTRSTGKVTWFDGAKGYGFIR-------PDDGGADLFVHQKSIKSDGYRTLYENQSVE 54
          +Q+ R TG   WF+   G+GFI        P D   D+FVHQ  +  +G+R+L E + VE
Sbjct: 4  SQVLRGTGHCKWFNVRMGFGFISMINREGSPLDIPVDVFVHQSKLFMEGFRSLKEGEPVE 63
Query: 55 FDVQLEADGKYQALDVTAPGGAP 77
          F  +  + G  +++ VT PGG+P
Sbjct: 64 FTFKKSSKG-LESIRVTGPGGSP 85

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

Iteration: 1
 Score = 60.5 bits (145), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 27/66 (40%), Positives = 42/66 (63%), Gaps = 1/66 (1%)
Query: 5  TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGK 64
          T   GKV W++  K +GFI  D+GG D+FVH+ ++ + G  +L E Q V FD++ E  GK
Sbjct: 3  TNIVGKVKWYNSTKNFGFIEQDNGGKDVFVHKSAVDAAGLHSLEEGQDVIFDLE-EKQGK 61
Query: 65 YQALDV 70
            A+++
Sbjct: 62 AYAVNL 67

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

Iteration: 1
 Score = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/82 (36%), Positives = 46/82 (56%), Gaps = 8/82 (9%)
Query: 3  QLTRSTGKVTWFDGAKGYGFIR-------PDDGGADLFVHQKSIKSDGYRTLYENQSVEF 55
          Q+ R +G   WF+   G+GFI        P +   D+FVHQ  +  +G+R+L E + VEF
Sbjct: 5  QVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEF 64
Query: 56 DVQLEADGKYQALDVTAPGGAP 77
            +  + G +++L VT PGG P
Sbjct: 65 TFKKSSKG-FESLRVTGPGGNP 85

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

Iteration: 1
 Score = 58.9 bits (141), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 29/63 (46%), Positives = 44/63 (69%), Gaps = 2/63 (3%)
Query: 9  GKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQAL 68
          GKV WF+  KGYGFI  + GG+D+FVH  +I+ +G++TL E Q V F++ ++ +   QA 
Sbjct: 4  GKVKWFNNEKGYGFIEVE-GGSDVFVHFTAIQGEGFKTLEEGQEVSFEI-VQGNRGPQAA 61
Query: 69 DVT 71
          +VT
Sbjct: 62 NVT 64

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

Iteration: 1
 Score = 58.9 bits (141), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 25/49 (51%), Positives = 37/49 (75%), Gaps = 1/49 (2%)
Query: 9  GKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDV 57
          GKV WF+  KGYGFI  + GG+D+FVH  +I+ +G++TL E Q+V F++
Sbjct: 4  GKVKWFNNEKGYGFIEVE-GGSDVFVHFTAIQGEGFKTLEEGQAVSFEI 51

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

Iteration: 1
 Score = 58.9 bits (141), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 31/64 (48%), Positives = 42/64 (65%), Gaps = 2/64 (3%)
Query: 9  GKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGK-YQA 67
          G+V WF+  KGYGFI   +G  D+FVH  +I + G+RTL E   V FDV+   +GK  QA
Sbjct: 4  GRVKWFNAEKGYGFIE-REGDTDVFVHYTAINAKGFRTLNEGDIVTFDVEPGRNGKGPQA 62
Query: 68 LDVT 71
          ++VT
Sbjct: 63 VNVT 66

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 25/49 (51%), Positives = 36/49 (73%), Gaps = 1/49 (2%)
Query: 9  GKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDV 57
          GKV WF+  KGYGFI  + GG+D+FVH  +I+ +G++TL E Q V F++
Sbjct: 4  GKVKWFNNEKGYGFIEVE-GGSDVFVHFTAIQGEGFKTLEEGQEVSFEI 51

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 25/49 (51%), Positives = 37/49 (75%), Gaps = 1/49 (2%)
Query: 9  GKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDV 57
          GKV WF+  KGYGFI  + GG+D+FVH  +I+ +G++TL E Q+V F++
Sbjct: 4  GKVKWFNNEKGYGFIEVE-GGSDVFVHFTAIQGEGFKTLEEGQAVSFEI 51

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 25/49 (51%), Positives = 36/49 (73%), Gaps = 1/49 (2%)
Query: 9  GKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDV 57
          GKV WF+  KGYGFI  + GG+D+FVH  +I+ +G++TL E Q V F++
Sbjct: 4  GKVKWFNNEKGYGFIEVE-GGSDVFVHFTAIQGEGFKTLEEGQEVSFEI 51

>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 = 58.5 bits (140), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 30/74 (40%), Positives = 45/74 (60%), Gaps = 5/74 (6%)
Query: 5  TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDG----YRTLYENQSVEFDVQLE 60
          T+  G V WF+   GYGFI  +D   D+FVHQ +IK +      R++ + ++VEFDV +E
Sbjct: 7  TKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDV-VE 65
Query: 61 ADGKYQALDVTAPG 74
           +   +A +VT PG
Sbjct: 66 GEKGAEAANVTGPG 79

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

Iteration: 1
 Score = 57.8 bits (138), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 25/49 (51%), Positives = 36/49 (73%), Gaps = 1/49 (2%)
Query: 9  GKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDV 57
          GKV WF+  KGYGFI  + GG+D+FVH  +I+ +G++TL E Q V F++
Sbjct: 4  GKVKWFNNEKGYGFIEVE-GGSDVFVHFTAIQGEGFKTLEEGQEVSFEI 51

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 29/66 (43%), Positives = 44/66 (66%), Gaps = 2/66 (3%)
Query: 6  RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKY 65
          R  GKV WF+  KG+GFI  + G  D+FVH  +I+ +G++TL E Q+V F++ +E +   
Sbjct: 1  RLKGKVKWFNSEKGFGFIEVE-GQDDVFVHFSAIQGEGFKTLEEGQAVSFEI-VEGNRGP 58
Query: 66 QALDVT 71
          QA +VT
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 = 55.8 bits (133), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 28/63 (44%), Positives = 43/63 (68%), Gaps = 2/63 (3%)
Query: 9  GKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQAL 68
          GKV WF+  KG+GFI  + G  D+FVH  +I+ +G++TL E Q+V F++ +E +   QA 
Sbjct: 4  GKVKWFNSEKGFGFIEVE-GQDDVFVHFSAIQGEGFKTLEEGQAVSFEI-VEGNRGPQAA 61
Query: 69 DVT 71
          +VT
Sbjct: 62 NVT 64

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

Iteration: 1
 Score = 55.5 bits (132), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 28/63 (44%), Positives = 42/63 (66%), Gaps = 2/63 (3%)
Query: 9  GKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQAL 68
          GKV WF+  KG+GFI  + G  D+FVH  +I+ +G++TL E Q V F++ +E +   QA 
Sbjct: 4  GKVKWFNSEKGFGFIEVE-GQDDVFVHFSAIQGEGFKTLEEGQKVRFEI-VEGNRGPQAA 61
Query: 69 DVT 71
          +VT
Sbjct: 62 NVT 64

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 28/81 (34%), Positives = 42/81 (51%), Gaps = 8/81 (9%)
Query: 3  QLTRSTGKVTWFDGAKGYGFIRPD-------DGGADLFVHQKSIKSDGYRTLYENQSVEF 55
          QL    G   WF+   G+GF+          D   D+FVHQ  +  +G+R+L E ++VEF
Sbjct: 6  QLLHGAGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEGFRSLKEGEAVEF 65
Query: 56 DVQLEADGKYQALDVTAPGGA 76
            +  A G  +++ VT PGG 
Sbjct: 66 TFKKSAKG-LESIRVTGPGGV 85

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 28/81 (34%), Positives = 42/81 (51%), Gaps = 8/81 (9%)
Query: 3  QLTRSTGKVTWFDGAKGYGFIRPD-------DGGADLFVHQKSIKSDGYRTLYENQSVEF 55
          QL    G   WF+   G+GF+          D   D+FVHQ  +  +G+R+L E ++VEF
Sbjct: 4  QLLHGAGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEGFRSLKEGEAVEF 63
Query: 56 DVQLEADGKYQALDVTAPGGA 76
            +  A G  +++ VT PGG 
Sbjct: 64 TFKKSAKG-LESIRVTGPGGV 83

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 19/33 (57%), Positives = 23/33 (69%)
Query: 3  QLTRSTGKVTWFDGAKGYGFIRPDDGGADLFVH 35
          Q  + TG V WF+  KG+GFI PDDG  D+FVH
Sbjct: 13 QSGKMTGIVKWFNADKGFGFITPDDGSKDVFVH 45

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	258
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	6e-27
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	2e-08
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	7e-08
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	8e-05
3ulj_A	90	LIN28B, DNA-binding protein; beta barrel, cold sho	3e-26
2lss_A	70	Cold shock-like protein; CSD, CSP, oligonucleotide	2e-24
3i2z_B	71	RNA chaperone, negative regulator of CSPA transcri	3e-24
3cam_A	67	Cold-shock domain family protein; cold shock prote	3e-24
1h95_A	79	CSD, Y-box binding protein; translation factor, tr	1e-23
3aqq_A	147	Calcium-regulated heat stable protein 1; compact b	5e-22
1g6p_A	66	Cold shock protein TMCSP; greek-KEY, beta barrel,	1e-20
1c9o_A	66	CSPB, cold-shock protein; beta barrel, homodimer,	2e-20
3a0j_A	73	Cold shock protein; OB-fold, cytoplasm, transcript	3e-20
2kcm_A	74	Cold shock domain family protein; nucleic acid bin	7e-20
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	1e-17
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	2e-10
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	4e-05
2bh8_A	101	1B11; transcription, molecular evolution, unique a	7e-17
2k5n_A	74	Putative cold-shock protein; GFT protein structure	1e-15
2ytx_A	97	Cold shock domain-containing protein E1; cell-free	1e-13
2yty_A	88	Cold shock domain-containing protein E1; cell-free	9e-13
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	2e-10
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	2e-09
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	1e-08
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	3e-08
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	3e-10
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	9e-10
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	4e-08
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	4e-07
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	3e-08
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	1e-06
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	2e-05
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	1e-04
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	4e-08
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	5e-07
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	3e-06
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	1e-06
1x65_A	89	UNR protein; cell-free protein synthesis, beta-bar	4e-06
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	8e-06
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	4e-04
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	8e-06
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	4e-04
1qzv_F	154	Plant photosystem I: subunit PSAF; photosynthesis,	2e-05
1wfq_A	89	UNR protein; beta-barrel, translational regulation	3e-05
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	5e-05
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	7e-04
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	5e-05
3gv2_A	342	Ca, fusion protein consisting of capsid protein P2	3e-04

>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 =  100 bits (251), Expect = 6e-27
 Identities = 43/181 (23%), Positives = 63/181 (34%), Gaps = 55/181 (30%)

Query: 3   QLTRSTGKVTWFDGAKGYGFIRPD-------DGGADLFVHQKSIKSDGYRTLYENQSVEF 55
           QL    G   WF+   G+GF+          D   D+FVHQ  +  +G+R+L E ++VEF
Sbjct: 6   QLLHGAGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEGFRSLKEGEAVEF 65

Query: 56  DVQLEADGKYQALDVTAPGGAPVHSSKNNNTNNNSGYNNNRGGRGGGGAGFGGYWKGNND 115
             +  A G  +++ VT PGG                                    G+  
Sbjct: 66  TFKKSAKG-LESIRVTGPGGVFC--------------------------------IGSER 92

Query: 116 SRRNNGGGYGPGGVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPR 175
             +            CYNC G+ H A+EC               C+ C    H    CP 
Sbjct: 93  RPKGGDR--------CYNCGGLDHHAKEC-------KLPPQPKKCHFCQSINHMVASCPL 137

Query: 176 Q 176
           +
Sbjct: 138 K 138

>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 = 51.2 bits (122), Expect = 2e-08
 Identities = 13/51 (25%), Positives = 19/51 (37%), Gaps = 4/51 (7%)

Query: 179 GSNSYNNNSGGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDC 229
           GS         C+ CGG  H A++C           +C+ C    H+   C
Sbjct: 89  GSERRPKGGDRCYNCGGLDHHAKEC----KLPPQPKKCHFCQSINHMVASC 135

>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 = 49.6 bits (118), Expect = 7e-08
 Identities = 17/52 (32%), Positives = 19/52 (36%), Gaps = 2/52 (3%)

Query: 203 CITRGSGGGGGGRCYNCGKSGHLARDCGAGGAGGGGSCFNCGKPGHFARECT 254
           CI       GG RCYNCG   H A++C          C  C    H    C 
Sbjct: 87  CIGSERRPKGGDRCYNCGGLDHHAKECKLP--PQPKKCHFCQSINHMVASCP 136

>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 = 40.8 bits (95), Expect = 8e-05
 Identities = 13/66 (19%), Positives = 19/66 (28%), Gaps = 8/66 (12%)

Query: 148 RRNSNYNNNSGGCYNCGDPEHFARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITRG 207
             +         CYNCG  +H A++C                C  C    H+   C  + 
Sbjct: 88  IGSERRPKGGDRCYNCGGLDHHAKECKLPPQP--------KKCHFCQSINHMVASCPLKA 139

Query: 208 SGGGGG 213
             G   
Sbjct: 140 QQGPSS 145

>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 = 97.5 bits (243), Expect = 3e-26
 Identities = 30/88 (34%), Positives = 47/88 (53%), Gaps = 8/88 (9%)

Query: 2  AQLTRSTGKVTWFDGAKGYGFI-------RPDDGGADLFVHQKSIKSDGYRTLYENQSVE 54
           Q+ R +G   WF+   G+GFI        P +   D+FVHQ  +  +G+R+L E + VE
Sbjct: 4  PQVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVE 63

Query: 55 FDVQLEADGKYQALDVTAPGGAPVHSSK 82
          F  +  + G  ++L VT PGG P   ++
Sbjct: 64 FTFKKSSKGF-ESLRVTGPGGNPCLGNE 90

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

 Score = 91.5 bits (228), Expect = 2e-24
 Identities = 27/67 (40%), Positives = 42/67 (62%), Gaps = 1/67 (1%)

Query: 5  TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGK 64
          T   GKV W++  K +GFI  D+GG D+FVH+ ++ + G  +L E Q V FD++ E  GK
Sbjct: 3  TNIVGKVKWYNSTKNFGFIEQDNGGKDVFVHKSAVDAAGLHSLEEGQDVIFDLE-EKQGK 61

Query: 65 YQALDVT 71
            A+++ 
Sbjct: 62 AYAVNLR 68

>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 = 91.2 bits (227), Expect = 3e-24
 Identities = 31/68 (45%), Positives = 47/68 (69%), Gaps = 1/68 (1%)

Query: 5  TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGK 64
          ++  G V WF+ +KG+GFI P+DG  D+FVH  +I+++G++TL E Q VEF++   A G 
Sbjct: 4  SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGP 63

Query: 65 YQALDVTA 72
            A +VTA
Sbjct: 64 -SAANVTA 70

>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 = 91.1 bits (227), Expect = 3e-24
 Identities = 34/66 (51%), Positives = 44/66 (66%), Gaps = 1/66 (1%)

Query: 7  STGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQ 66
          +TG V WF+ AKG+GFI PD+GG DLF H  +I  +G++TL E Q V FDV     GK Q
Sbjct: 2  ATGIVKWFNDAKGFGFITPDEGGEDLFAHFSAINMEGFKTLKEGQRVSFDVTTGPKGK-Q 60

Query: 67 ALDVTA 72
          A ++ A
Sbjct: 61 AANIQA 66

>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 = 90.1 bits (224), Expect = 1e-23
 Identities = 30/74 (40%), Positives = 43/74 (58%), Gaps = 5/74 (6%)

Query: 5  TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDG----YRTLYENQSVEFDVQLE 60
          T+  G V WF+   GYGFI  +D   D+FVHQ +IK +      R++ + ++VEFDV   
Sbjct: 7  TKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEG 66

Query: 61 ADGKYQALDVTAPG 74
            G  +A +VT PG
Sbjct: 67 EKGA-EAANVTGPG 79

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

 Score = 88.2 bits (218), Expect = 5e-22
 Identities = 23/75 (30%), Positives = 34/75 (45%), Gaps = 4/75 (5%)

Query: 5   TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQL--EAD 62
               G    F  +KG+GFI P DGG D+F+H   +  +G     E   V + +      +
Sbjct: 61  PVYKGVCKCFCRSKGHGFITPADGGPDIFLHISDV--EGEYVPVEGDEVTYKMCSIPPKN 118

Query: 63  GKYQALDVTAPGGAP 77
            K QA++V     AP
Sbjct: 119 EKLQAVEVVITHLAP 133

>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 = 81.9 bits (203), Expect = 1e-20
 Identities = 33/65 (50%), Positives = 42/65 (64%), Gaps = 2/65 (3%)

Query: 8  TGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQA 67
           GKV WFD  KGYGFI  D+GG D+FVH  +I+ +G++TL E Q VEF++Q    G  QA
Sbjct: 2  RGKVKWFDSKKGYGFITKDEGG-DVFVHWSAIEMEGFKTLKEGQVVEFEIQEGKKGP-QA 59

Query: 68 LDVTA 72
            V  
Sbjct: 60 AHVKV 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 = 81.1 bits (201), Expect = 2e-20
 Identities = 29/66 (43%), Positives = 41/66 (62%), Gaps = 2/66 (3%)

Query: 7  STGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQ 66
            GKV WF+  KGYGFI  + GG+D+FVH  +I+ +G++TL E Q V F++     G  Q
Sbjct: 2  QRGKVKWFNNEKGYGFIEVE-GGSDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGNRGP-Q 59

Query: 67 ALDVTA 72
          A +V  
Sbjct: 60 AANVVK 65

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

 Score = 81.2 bits (201), Expect = 3e-20
 Identities = 32/72 (44%), Positives = 43/72 (59%), Gaps = 2/72 (2%)

Query: 7  STGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGK-Y 65
            G+V WF+  KGYGFI  + G  D+FVH  +I + G+RTL E   V FDV+   +GK  
Sbjct: 2  QKGRVKWFNAEKGYGFIERE-GDTDVFVHYTAINAKGFRTLNEGDIVTFDVEPGRNGKGP 60

Query: 66 QALDVTAPGGAP 77
          QA++VT    A 
Sbjct: 61 QAVNVTVVEPAR 72

>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 = 80.0 bits (198), Expect = 7e-20
 Identities = 21/67 (31%), Positives = 28/67 (41%), Gaps = 3/67 (4%)

Query: 8  TGKVTWFDGAKGYGFIRPDDGGADLFVHQKSI-KSDGYRTLYENQSVEFDVQLEADGKYQ 66
           GKV  +  AK YGFI+ DD G   F+H   +        L +   V FD      G   
Sbjct: 2  KGKVVSYLAAKKYGFIQGDD-GESYFLHFSELLDKKDEGKLVKGSMVHFDPTPTPKGL-A 59

Query: 67 ALDVTAP 73
          A  ++ P
Sbjct: 60 AKAISLP 66

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Length = 124

 Score = 76.0 bits (186), Expect = 1e-17
 Identities = 31/146 (21%), Positives = 43/146 (29%), Gaps = 44/146 (30%)

Query: 128 GVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPE-HFARDCPRQQGGSNSYNNN 186
              C NC   GH+ ++C               C  CG  + H++R CP+           
Sbjct: 4   APKCNNCSQRGHLKKDCPHII-----------CSYCGATDDHYSRHCPKAI--------- 43

Query: 187 SGGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDC----------------- 229
              C KC   GH    C  +        +C  C    H    C                 
Sbjct: 44  --QCSKCDEVGHYRSQCPHKWK----KVQCTLCKSKKHSKERCPSIWRAYILVDDNEKAK 97

Query: 230 GAGGAGGGGSCFNCGKPGHFARECTK 255
                     C+NCG  GHF  +C +
Sbjct: 98  PKVLPFHTIYCYNCGGKGHFGDDCKE 123

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Length = 124

 Score = 56.3 bits (135), Expect = 2e-10
 Identities = 24/104 (23%), Positives = 30/104 (28%), Gaps = 22/104 (21%)

Query: 126 PGGVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQQGGSNSYNN 185
           P  + C  CD VGH   +C    +          C  C   +H    CP         ++
Sbjct: 40  PKAIQCSKCDEVGHYRSQCPHKWKK-------VQCTLCKSKKHSKERCPSIWRAYILVDD 92

Query: 186 NSGGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDC 229
           N     K                       CYNCG  GH   DC
Sbjct: 93  NEKAKPKV---------------LPFHTIYCYNCGGKGHFGDDC 121

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Length = 124

 Score = 41.3 bits (96), Expect = 4e-05
 Identities = 16/65 (24%), Positives = 21/65 (32%), Gaps = 12/65 (18%)

Query: 124 YGPGGVVCYNCDGVGHVARECTSNRRNSNYNNNSGG------------CYNCGDPEHFAR 171
           +    V C  C    H    C S  R     +++              CYNCG   HF  
Sbjct: 60  HKWKKVQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGD 119

Query: 172 DCPRQ 176
           DC  +
Sbjct: 120 DCKEK 124

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

 Score = 72.9 bits (179), Expect = 7e-17
 Identities = 22/62 (35%), Positives = 30/62 (48%), Gaps = 2/62 (3%)

Query: 5  TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDG--YRTLYENQSVEFDVQLEAD 62
           + TG V WF+  KG+GFI PDDG  D+FVH  +  S         +   VE  ++   D
Sbjct: 15 GKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAGSSGAAVRGNPQQGDRVEGKIKSITD 74

Query: 63 GK 64
            
Sbjct: 75 FG 76

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

 Score = 68.9 bits (169), Expect = 1e-15
 Identities = 13/64 (20%), Positives = 28/64 (43%), Gaps = 4/64 (6%)

Query: 8  TGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQA 67
           G +T +   KG+GFI+ ++ G + + H   +       + ++ +V F+     +    A
Sbjct: 4  NGTITTWFKDKGFGFIKDEN-GDNRYFHVIKVA--NPDLIKKDAAVTFEPT-TNNKGLSA 59

Query: 68 LDVT 71
            V 
Sbjct: 60 YAVK 63

>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 = 64.1 bits (156), Expect = 1e-13
 Identities = 22/74 (29%), Positives = 31/74 (41%), Gaps = 5/74 (6%)

Query: 6  RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKY 65
          R  G V      + +GFI   D   ++F H    K     TL     VEF ++ + +GK 
Sbjct: 18 RCQGVVCAMK--EAFGFIERGDVVKEIFFHYSEFK-GDLETLQPGDDVEFTIK-DRNGKE 73

Query: 66 QALDVT-APGGAPV 78
           A DV   P G  +
Sbjct: 74 VATDVRLLPQGTVI 87

>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 = 61.4 bits (149), Expect = 9e-13
 Identities = 16/70 (22%), Positives = 23/70 (32%), Gaps = 3/70 (4%)

Query: 6  RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKY 65
          R  G V        +GFI   +   ++F H      D   +L     VE+ +      K 
Sbjct: 18 RLLGYVATLK--DNFGFIETANHDKEIFFHYSEFSGDV-DSLELGDMVEYSLSKGKGNKV 74

Query: 66 QALDVTAPGG 75
           A  V    G
Sbjct: 75 SAEKVNKTSG 84

>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A Length = 60

 Score = 54.6 bits (131), Expect = 2e-10
 Identities = 17/51 (33%), Positives = 23/51 (45%), Gaps = 5/51 (9%)

Query: 213 GGRCYNCGKSGHLARDC-----GAGGAGGGGSCFNCGKPGHFARECTKVAN 258
           GG C+ CGK GH A++C             G C  C +  H+A EC    +
Sbjct: 1   GGSCFKCGKKGHFAKNCHEHAHNNAEPKVPGLCPRCKRGKHWANECKSKTD 51

>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A Length = 60

 Score = 51.5 bits (123), Expect = 2e-09
 Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 1/54 (1%)

Query: 158 GGCYNCGDPEHFARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITRGSGGG 211
           G C+ CG   HFA++C  +   +N+     G C +C    H A +C ++    G
Sbjct: 2   GSCFKCGKKGHFAKNCH-EHAHNNAEPKVPGLCPRCKRGKHWANECKSKTDNQG 54

>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A Length = 60

 Score = 49.6 bits (118), Expect = 1e-08
 Identities = 16/45 (35%), Positives = 21/45 (46%), Gaps = 3/45 (6%)

Query: 188 GGCFKCGGYGHLARDC---ITRGSGGGGGGRCYNCGKSGHLARDC 229
           G CFKCG  GH A++C       +     G C  C +  H A +C
Sbjct: 2   GSCFKCGKKGHFAKNCHEHAHNNAEPKVPGLCPRCKRGKHWANEC 46

>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A Length = 60

 Score = 48.4 bits (115), Expect = 3e-08
 Identities = 14/53 (26%), Positives = 22/53 (41%)

Query: 128 GVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQQGGS 180
           G  C+ C   GH A+ C  +  N+      G C  C   +H+A +C  +    
Sbjct: 1   GGSCFKCGKKGHFAKNCHEHAHNNAEPKVPGLCPRCKRGKHWANECKSKTDNQ 53

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} Length = 61

 Score = 54.1 bits (130), Expect = 3e-10
 Identities = 16/48 (33%), Positives = 18/48 (37%), Gaps = 2/48 (4%)

Query: 210 GGGGGRCYNCGKSGHLARDC--GAGGAGGGGSCFNCGKPGHFARECTK 255
           G   G CY CG  GH    C            C  C   GH A++C K
Sbjct: 1   GRARGLCYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQCRK 48

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} Length = 61

 Score = 52.6 bits (126), Expect = 9e-10
 Identities = 16/52 (30%), Positives = 19/52 (36%)

Query: 187 SGGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGAGGAGGGG 238
            G C+ CG  GH    C  +   G    RC  C   GH A+ C       G 
Sbjct: 4   RGLCYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQCRKRDGNQGQ 55

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} Length = 61

 Score = 47.9 bits (114), Expect = 4e-08
 Identities = 19/56 (33%), Positives = 25/56 (44%), Gaps = 4/56 (7%)

Query: 157 SGGCYNCGDPEHFARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITRGSGGGG 212
            G CY CG P H+   CP+++       N+   C  C G GH A+ C  R    G 
Sbjct: 4   RGLCYTCGSPGHYQAQCPKKRKS----GNSRERCQLCNGMGHNAKQCRKRDGNQGQ 55

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} Length = 61

 Score = 45.3 bits (107), Expect = 4e-07
 Identities = 15/58 (25%), Positives = 23/58 (39%), Gaps = 3/58 (5%)

Query: 125 GPGGVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQQGGSNS 182
           G    +CY C   GH   +C   R++    N+   C  C    H A+ C ++ G    
Sbjct: 1   GRARGLCYTCGSPGHYQAQCPKKRKS---GNSRERCQLCNGMGHNAKQCRKRDGNQGQ 55

>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 63

 Score = 48.4 bits (115), Expect = 3e-08
 Identities = 17/49 (34%), Positives = 19/49 (38%), Gaps = 2/49 (4%)

Query: 207 GSGGGGGGRCYNCGKSGHLARDCGAGGAGGGGSCFNCGKPGHFARECTK 255
           GS G  G RCYNCG   H A++C          C  C    H    C  
Sbjct: 1   GSSGSSGDRCYNCGGLDHHAKECKLPPQPKK--CHFCQSISHMVASCPL 47

>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 63

 Score = 44.2 bits (104), Expect = 1e-06
 Identities = 18/66 (27%), Positives = 24/66 (36%), Gaps = 7/66 (10%)

Query: 122 GGYGPGGVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQQGGSN 181
           G  G  G  CYNC G+ H A+EC    +          C+ C    H    CP +     
Sbjct: 1   GSSGSSGDRCYNCGGLDHHAKECKLPPQP-------KKCHFCQSISHMVASCPLKAQQGP 53

Query: 182 SYNNNS 187
           S   + 
Sbjct: 54  SAQGSG 59

>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 63

 Score = 40.3 bits (94), Expect = 2e-05
 Identities = 12/48 (25%), Positives = 20/48 (41%), Gaps = 4/48 (8%)

Query: 182 SYNNNSGGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDC 229
           S  ++   C+ CGG  H A++C           +C+ C    H+   C
Sbjct: 2   SSGSSGDRCYNCGGLDHHAKEC----KLPPQPKKCHFCQSISHMVASC 45

>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 63

 Score = 38.4 bits (89), Expect = 1e-04
 Identities = 13/61 (21%), Positives = 20/61 (32%), Gaps = 8/61 (13%)

Query: 153 YNNNSGGCYNCGDPEHFARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITRGSGGGG 212
             ++   CYNCG  +H A++C                C  C    H+   C  +   G  
Sbjct: 3   SGSSGDRCYNCGGLDHHAKECKLPPQP--------KKCHFCQSISHMVASCPLKAQQGPS 54

Query: 213 G 213
            
Sbjct: 55  A 55

>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens} Length = 74

 Score = 48.4 bits (115), Expect = 4e-08
 Identities = 14/51 (27%), Positives = 17/51 (33%), Gaps = 2/51 (3%)

Query: 205 TRGSGGGGGGRCYNCGKSGHLARDCGAGGAGGGGSCFNCGKPGHFARECTK 255
           +       G RCYNCG   H A++C          C  C    H    C  
Sbjct: 16  SMQKRRSKGDRCYNCGGLDHHAKECKLPPQPKK--CHFCQSISHMVASCPL 64

>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens} Length = 74

 Score = 45.4 bits (107), Expect = 5e-07
 Identities = 17/72 (23%), Positives = 27/72 (37%), Gaps = 7/72 (9%)

Query: 111 KGNNDSRRNNGGGYGPGGVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFA 170
           +G++  +  +       G  CYNC G+ H A+EC    +          C+ C    H  
Sbjct: 7   RGSHMPKGKSMQKRRSKGDRCYNCGGLDHHAKECKLPPQP-------KKCHFCQSISHMV 59

Query: 171 RDCPRQQGGSNS 182
             CP +     S
Sbjct: 60  ASCPLKAQQGPS 71

>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens} Length = 74

 Score = 43.0 bits (101), Expect = 3e-06
 Identities = 12/50 (24%), Positives = 19/50 (38%), Gaps = 4/50 (8%)

Query: 190 CFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGAGGAGGGGS 239
           C+ CGG  H A++C           +C+ C    H+   C      G  +
Sbjct: 27  CYNCGGLDHHAKEC----KLPPQPKKCHFCQSISHMVASCPLKAQQGPSA 72

>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus} Length = 37

 Score = 43.0 bits (101), Expect = 1e-06
 Identities = 19/40 (47%), Positives = 24/40 (60%), Gaps = 5/40 (12%)

Query: 215 RCYNCGKSGHLARDCGAGGAGGGGSCFNCGKPGHFARECT 254
            CYNCGK GHL+  C A        CF C +PGHF+++C 
Sbjct: 2   TCYNCGKPGHLSSQCRAPKV-----CFKCKQPGHFSKQCR 36

>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 = 43.4 bits (102), Expect = 4e-06
 Identities = 18/74 (24%), Positives = 28/74 (37%), Gaps = 7/74 (9%)

Query: 5  TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLE--AD 62
           R  G +       G+GFI+  D    +F H   I       L+    VEF V  +  + 
Sbjct: 7  GREMGVIAAMR--DGFGFIKCVDRDVRMFFHFSEILDG--NQLHIADEVEFTVVPDMLSA 62

Query: 63 GKYQALDVT-APGG 75
           +  A+ +   P G
Sbjct: 63 QRNHAIRIKKLPKG 76

>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic} Length = 39

 Score = 41.0 bits (96), Expect = 8e-06
 Identities = 18/41 (43%), Positives = 21/41 (51%), Gaps = 3/41 (7%)

Query: 215 RCYNCGKSGHLARDCGAGGAGGGGSCFNCGKPGHFARECTK 255
            C+NCGK GH AR C      G   C+NCG   H   +C K
Sbjct: 2   TCFNCGKPGHTARMCRQPRQEG---CWNCGSKEHRFAQCPK 39

>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic} Length = 39

 Score = 36.4 bits (84), Expect = 4e-04
 Identities = 18/47 (38%), Positives = 23/47 (48%), Gaps = 8/47 (17%)

Query: 129 VVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPR 175
           + C+NC   GH AR C   R+         GC+NCG  EH    CP+
Sbjct: 1   LTCFNCGKPGHTARMCRQPRQE--------GCWNCGSKEHRFAQCPK 39

>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae} Length = 83

 Score = 42.3 bits (99), Expect = 8e-06
 Identities = 16/60 (26%), Positives = 20/60 (33%), Gaps = 12/60 (20%)

Query: 129 VVCYNCDGVGHVARECTSNRRNSNYNNNSGG------------CYNCGDPEHFARDCPRQ 176
           V C  C    H    C S  R     +++              CYNCG   HF  DC  +
Sbjct: 6   VQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEK 65

>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae} Length = 83

 Score = 37.3 bits (86), Expect = 4e-04
 Identities = 14/66 (21%), Positives = 19/66 (28%), Gaps = 9/66 (13%)

Query: 190 CFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGAGGAGGGGSCFNCGKPGHF 249
           C  C    H    C +         R Y         +            C+NCG  GHF
Sbjct: 8   CTLCKSKKHSKERCPSIW-------RAYILVDDNE--KAKPKVLPFHTIYCYNCGGKGHF 58

Query: 250 ARECTK 255
             +C +
Sbjct: 59  GDDCKE 64

>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant photosynthetic reaction center, peripheral antenna; HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1 Length = 154

 Score = 43.0 bits (100), Expect = 2e-05
 Identities = 8/29 (27%), Positives = 15/29 (51%), Gaps = 8/29 (27%)

Query: 49 ENQSVEFDVQLEADGKYQALDVTAPGGAP 77
          E Q+++   +L+A     +L + A   AP
Sbjct: 18 EKQALK---KLQA-----SLKLYADDSAP 38

>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 = 40.7 bits (95), Expect = 3e-05
 Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 2/55 (3%)

Query: 18 KGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEA-DGKYQALDVT 71
            YGFI+  +  A LF H      +  + L     VEF+V  +   GK  A+ + 
Sbjct: 28 TSYGFIQCSERQARLFFHCSQYNGN-LQDLKVGDDVEFEVSSDRRTGKPIAVKLV 81

>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1 Length = 49

 Score = 39.2 bits (91), Expect = 5e-05
 Identities = 20/41 (48%), Positives = 24/41 (58%), Gaps = 3/41 (7%)

Query: 215 RCYNCGKSGHLARDCGAGGAGGGGSCFNCGKPGHFARECTK 255
           RC+NCGK GH AR C A    G   C+ CGK GH   +C +
Sbjct: 8   RCWNCGKEGHSARQCRAPRRQG---CWKCGKTGHVMAKCPE 45

>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1 Length = 49

 Score = 36.1 bits (83), Expect = 7e-04
 Identities = 19/51 (37%), Positives = 25/51 (49%), Gaps = 8/51 (15%)

Query: 129 VVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQQGG 179
           + C+NC   GH AR+C + RR         GC+ CG   H    CP +Q G
Sbjct: 7   IRCWNCGKEGHSARQCRAPRRQ--------GCWKCGKTGHVMAKCPERQAG 49

>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A Length = 55

 Score = 39.2 bits (91), Expect = 5e-05
 Identities = 19/41 (46%), Positives = 28/41 (68%), Gaps = 3/41 (7%)

Query: 215 RCYNCGKSGHLARDCGAGGAGGGGSCFNCGKPGHFARECTK 255
           +C+NCGK GH+A++C A    G   C+ CGK GH  ++CT+
Sbjct: 14  KCFNCGKEGHIAKNCRAPRKKG---CWKCGKEGHQMKDCTE 51

>3gv2_A Ca, fusion protein consisting of capsid protein P24, linker and carbon dioxide-concentrating...; hexameric retroviral capsid; 7.00A {Human immunodeficiency virus type 1} Length = 342

 Score = 40.7 bits (95), Expect = 3e-04
 Identities = 8/78 (10%), Positives = 12/78 (15%), Gaps = 19/78 (24%)

Query: 190 CFKCGGYGHLARDC----------ITRGSGGGGGG--RCYNCGKSGHLARDCGAGGAGGG 237
           C   GG                     G         +       G++        AG  
Sbjct: 218 CQGVGGTRPELMSAQSAVGSIETIGFPGILAAADAMVKAGRITIVGYIR-------AGSA 270

Query: 238 GSCFNCGKPGHFARECTK 255
               N        +    
Sbjct: 271 RFTLNIRGDVQEVKTAMA 288

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	258
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	100.0
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	99.94
3ulj_A	90	LIN28B, DNA-binding protein; beta barrel, cold sho	99.93
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	99.91
3i2z_B	71	RNA chaperone, negative regulator of CSPA transcri	99.91
3cam_A	67	Cold-shock domain family protein; cold shock prote	99.9
1h95_A	79	CSD, Y-box binding protein; translation factor, tr	99.9
1c9o_A	66	CSPB, cold-shock protein; beta barrel, homodimer,	99.89
3a0j_A	73	Cold shock protein; OB-fold, cytoplasm, transcript	99.89
2kcm_A	74	Cold shock domain family protein; nucleic acid bin	99.89
1g6p_A	66	Cold shock protein TMCSP; greek-KEY, beta barrel,	99.89
2lss_A	70	Cold shock-like protein; CSD, CSP, oligonucleotide	99.81
2k5n_A	74	Putative cold-shock protein; GFT protein structure	99.88
1wfq_A	89	UNR protein; beta-barrel, translational regulation	99.87
2yty_A	88	Cold shock domain-containing protein E1; cell-free	99.85
1x65_A	89	UNR protein; cell-free protein synthesis, beta-bar	99.83
3aqq_A	147	Calcium-regulated heat stable protein 1; compact b	99.82
2ytx_A	97	Cold shock domain-containing protein E1; cell-free	99.81
2ytv_A	79	Cold shock domain-containing protein E1; cell-free	99.79
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	99.65
2bh8_A	101	1B11; transcription, molecular evolution, unique a	99.64
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	99.52
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	99.51
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	99.45
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	99.34
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	99.28
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	99.24
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	99.23
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	99.22
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	99.19
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	99.19
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	99.19
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	99.18
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	99.17
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	99.13
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	99.11
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	99.05
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	99.02
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	98.99
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	97.99
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	97.94
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	97.8
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	97.78
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	97.74
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	97.51
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	97.44
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	97.28
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	97.19
1a62_A	130	RHO; transcription termination, termination, RNA b	96.97
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	96.65
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	93.15
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	93.01
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	93.0
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	91.04
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	91.01
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	90.8
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	90.44
3l0o_A	427	Transcription termination factor RHO; helicase, RH	89.26
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	88.19
2l55_A	82	SILB,silver efflux protein, MFP component of the c	88.12
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	87.45
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	86.54
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	85.55
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	85.11
2vb2_X	88	Copper protein, cation efflux system protein CUSF;	85.02
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	84.44
2qcp_X	80	Cation efflux system protein CUSF; silver-binding,	84.35
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	82.15
3ice_A	422	Transcription termination factor RHO; transcriptio	80.97
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	80.95

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

Probab=100.00  E-value=5.7e-37  Score=248.94  Aligned_cols=99  Identities=31%  Similarity=0.583  Sum_probs=84.8

Q ss_pred             CCccccceEEEEeeCCCceeEEecC-------CCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccCC
Q 047168            2 AQLTRSTGKVTWFDGAKGYGFIRPD-------DGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAPG   74 (258)
Q Consensus         2 ~~~~~~~G~vk~f~~~kGfGFI~~~-------~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~~   74 (258)
                      .+.++++|+|||||.+||||||+++       ++++|||||+|+|...+|++|.+|++|+|+++.+++| ++|++|+.++
T Consensus         5 ~~l~~~~G~Vkwfn~~kGfGFI~~~~~~g~p~~~g~DvFvH~s~i~~~g~~~l~eG~~V~f~~~~g~kG-~~A~~V~~pg   83 (148)
T 3ts2_A            5 PQLLHGAGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEGFRSLKEGEAVEFTFKKSAKG-LESIRVTGPG   83 (148)
T ss_dssp             -CCEEEEEEEEEEETTTTEEEEEEEEETTEEEEEEEEEEEEGGGBCSSSSCCCCTTCEEEEEEEEETTE-EEEEEEESGG
T ss_pred             cccccceeEEEEEECCCCeeEEeeCccccccCCCCccEEEEhHHhcccCCccCCCCCEEEEEEEEcccc-chhhcccccC
Confidence            3567899999999999999999987       4679999999999999999999999999999999999 8999999999


Q ss_pred             CCcccCCCCCCCCCCCCccCCCCCCCC
Q 047168           75 GAPVHSSKNNNTNNNSGYNNNRGGRGG  101 (258)
Q Consensus        75 g~~~~~s~~~~~g~~~c~~c~~~g~~~  101 (258)
                      +++++++++++++...||||++.||++
T Consensus        84 g~pv~GS~rrp~~~~~C~~Cg~~GH~a  110 (148)
T 3ts2_A           84 GVFCIGSERRPKGGDRCYNCGGLDHHA  110 (148)
T ss_dssp             GCCCCCCTTSCCCSCCCTTTCCSSCCG
T ss_pred             CccccccccccCCCCcccEeCCccchh
Confidence            999999887775544455555444444

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

Probab=99.94  E-value=5.1e-27  Score=185.18  Aligned_cols=103  Identities=30%  Similarity=0.732  Sum_probs=85.3

Q ss_pred             CCcccccCCCCccccccccccCCCCCCCCCCCcccCCCC-CCCCCCCCCCCCCCCCCCCCCCcccccCCcccCcccCCCC
Q 047168          128 GVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDP-EHFARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITR  206 (258)
Q Consensus       128 ~~~C~~Cg~~GH~a~~Cp~~~~~~~~~~~~~~C~~Cg~~-GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~~  206 (258)
                      ...||+|++.||++++||+           ..||+|+++ ||++++||..           ..||+|++.||++++||+.
T Consensus         4 ~~~C~~C~~~GH~~~~Cp~-----------~~C~~Cg~~~gH~~~~C~~~-----------~~C~~Cg~~GH~~~~C~~~   61 (124)
T 2lli_A            4 APKCNNCSQRGHLKKDCPH-----------IICSYCGATDDHYSRHCPKA-----------IQCSKCDEVGHYRSQCPHK   61 (124)
T ss_dssp             SSCCSSCSSSSCCTTTTTS-----------CCCTTTCCTTTCCTTTGGGS-----------SCSSSSSCSSSSTTTSCCC
T ss_pred             CCcccCCCCCCcCcccCcC-----------CcCcCCCCcCCccCcccCCc-----------ccccccCCCCCccccCcCc
Confidence            4679999999999999987           579999998 8999999865           4799999999999999875


Q ss_pred             CCCCCCCCccccCCCCCccCCCCCCCCCC-----------------CCCccccCCCCCccCCCCCCC
Q 047168          207 GSGGGGGGRCYNCGKSGHLARDCGAGGAG-----------------GGGSCFNCGKPGHFARECTKV  256 (258)
Q Consensus       207 ~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~-----------------~~~~C~~Cg~~GH~~~~Cp~~  256 (258)
                      ..    ...||+|++.||++++||+.+..                 ..+.||+|++.|||++|||++
T Consensus        62 ~~----~~~C~~Cg~~GH~~~~Cp~~~~~y~~~~~~~~~~~~~~~~~~~~Cy~Cg~~GH~a~dCp~~  124 (124)
T 2lli_A           62 WK----KVQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEK  124 (124)
T ss_dssp             CC----CCSSSSSCSSCCCTTTCCCSTTSCCSSSCCCCCCCSCCCCCCCCTTTTSSSCTTTTTSCCC
T ss_pred             cc----CccCCCCCcCCcchhhCCCccccccccCccccccccccCCCCCCcCCCCCCCcCcccCcCC
Confidence            32    24799999999999999886531                 256899999999999999974

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

Probab=99.93  E-value=1.7e-26  Score=171.45  Aligned_cols=79  Identities=38%  Similarity=0.809  Sum_probs=73.0

Q ss_pred             CccccceEEEEeeCCCceeEEe-------cCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccCCC
Q 047168            3 QLTRSTGKVTWFDGAKGYGFIR-------PDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAPGG   75 (258)
Q Consensus         3 ~~~~~~G~vk~f~~~kGfGFI~-------~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~~g   75 (258)
                      +.+|.+|+|||||..||||||+       ++++++|||||+|+|...+|++|.+|++|+|+++.+++| ++|++|+.+++
T Consensus         5 ~~~r~tG~VKWFn~~KGfGFI~~~~~~~~p~dgg~DvFVH~s~i~~~g~~~L~eG~~V~f~v~~g~kG-~~A~~Vtg~~G   83 (90)
T 3ulj_A            5 QVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEFTFKKSSKG-FESLRVTGPGG   83 (90)
T ss_dssp             CCEEEEEEEEEEETTTTEEEEEEEEETTEEEEEEEEEEEEGGGBCCSSSCCCCTTCEEEEEEEEETTE-EEEEEEECGGG
T ss_pred             cccccceEEEEeeCCCCeEEeEecCcCcCCCCCCccEEEEeehhcccCCCccCCCCEEEEEEEECCCC-cEEEEEECCCC
Confidence            3568899999999999999998       456778999999999999999999999999999999999 89999999999


Q ss_pred             CcccCCC
Q 047168           76 APVHSSK   82 (258)
Q Consensus        76 ~~~~~s~   82 (258)
                      .++++++
T Consensus        84 ~p~~gse   90 (90)
T 3ulj_A           84 NPCLGNE   90 (90)
T ss_dssp             CCCCCCC
T ss_pred             ccccCCC
Confidence            9998764

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

Probab=99.91  E-value=4.1e-24  Score=168.48  Aligned_cols=103  Identities=25%  Similarity=0.559  Sum_probs=89.6

Q ss_pred             CCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCC-CccccccccccCCCCCCCCCCCcccCCCCC
Q 047168           89 NSGYNNNRGGRGGGGAGFGGYWKGNNDSRRNNGGGYGPGGVVCYNCDGV-GHVARECTSNRRNSNYNNNSGGCYNCGDPE  167 (258)
Q Consensus        89 ~~c~~c~~~g~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~C~~Cg~~-GH~a~~Cp~~~~~~~~~~~~~~C~~Cg~~G  167 (258)
                      ..||||++.||++         ++||+             ..||+|++. ||++++||.          ...|++|+++|
T Consensus         5 ~~C~~C~~~GH~~---------~~Cp~-------------~~C~~Cg~~~gH~~~~C~~----------~~~C~~Cg~~G   52 (124)
T 2lli_A            5 PKCNNCSQRGHLK---------KDCPH-------------IICSYCGATDDHYSRHCPK----------AIQCSKCDEVG   52 (124)
T ss_dssp             SCCSSCSSSSCCT---------TTTTS-------------CCCTTTCCTTTCCTTTGGG----------SSCSSSSSCSS
T ss_pred             CcccCCCCCCcCc---------ccCcC-------------CcCcCCCCcCCccCcccCC----------cccccccCCCC
Confidence            4699999999998         99994             489999998 999999997          37899999999


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCcccccCCcccCcccCCCCCCC---------------CCCCCccccCCCCCccCCCCCC
Q 047168          168 HFARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITRGSG---------------GGGGGRCYNCGKSGHLARDCGA  231 (258)
Q Consensus       168 H~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~~~~~---------------~~~~~~C~~Cg~~GH~~~~Cp~  231 (258)
                      |++++||++.        ....||+|++.||++++||+....               ....+.||+|++.||+++|||+
T Consensus        53 H~~~~C~~~~--------~~~~C~~Cg~~GH~~~~Cp~~~~~y~~~~~~~~~~~~~~~~~~~~Cy~Cg~~GH~a~dCp~  123 (124)
T 2lli_A           53 HYRSQCPHKW--------KKVQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKE  123 (124)
T ss_dssp             SSTTTSCCCC--------CCCSSSSSCSSCCCTTTCCCSTTSCCSSSCCCCCCCSCCCCCCCCTTTTSSSCTTTTTSCC
T ss_pred             CccccCcCcc--------cCccCCCCCcCCcchhhCCCccccccccCccccccccccCCCCCCcCCCCCCCcCcccCcC
Confidence            9999999873        347899999999999999986421               1135689999999999999996

>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=99.91  E-value=2e-24  Score=153.99  Aligned_cols=68  Identities=46%  Similarity=0.877  Sum_probs=64.2

Q ss_pred             cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccC
Q 047168            5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAP   73 (258)
Q Consensus         5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~   73 (258)
                      ++++|+|||||.+||||||+++++++|||||+|+|...++++|.+|++|+|+++.+++| ++|++|+++
T Consensus         4 ~~~~G~Vk~fn~~kGfGFI~~~~g~~dvFvH~s~i~~~g~~~l~~G~~V~f~~~~~~kG-~~A~~V~~~   71 (71)
T 3i2z_B            4 SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKG-PSAANVTAL   71 (71)
T ss_dssp             -CEEEEEEEEETTTTEEEEEETTCCCCEEEEGGGBCCSSCCCCCTTCEEEEEEEEETTE-EEEEEEEEC
T ss_pred             ccccEEEEEEECCCCcEEEecCCCCccEEEEhHHcccccCcCCCCCCEEEEEEEECCCC-CEeEEEEeC
Confidence            47899999999999999999999999999999999999999999999999999999999 899999863

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

Probab=99.90  E-value=2.5e-24  Score=151.82  Aligned_cols=65  Identities=51%  Similarity=0.939  Sum_probs=62.1

Q ss_pred             cceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeecccc
Q 047168            7 STGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTA   72 (258)
Q Consensus         7 ~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~   72 (258)
                      .+|+|||||.+||||||+++++++|||||+|+|...++++|.+|++|+|+++.+++| ++|++|++
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 ATGIVKWFNDAKGFGFITPDEGGEDLFAHFSAINMEGFKTLKEGQRVSFDVTTGPKG-KQAANIQA   66 (67)
T ss_dssp             EEEEEEEEETTTTEEEEEETTSCCCEEEEGGGBCGGGGSSCCTTCEEEEEEEEETTE-EEEEEEEE
T ss_pred             CCEEEEEEECCCCeEEEecCCCCccEEEEHHHccccCCCCCCCCCEEEEEEEECCCC-ccceEEEe
Confidence            579999999999999999999889999999999999999999999999999999999 69999985

>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=4.9e-24  Score=155.08  Aligned_cols=70  Identities=43%  Similarity=0.755  Sum_probs=64.9

Q ss_pred             ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccC----CccccCCCCcEEEEEEeCCCccceeeccccCC
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSD----GYRTLYENQSVEFDVQLEADGKYQALDVTAPG   74 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~----~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~~   74 (258)
                      +++++|+|||||.+||||||+++++++|||||+|+|...    ++++|.+|++|+|+++.+++| ++|++|+.++
T Consensus         6 ~~~~~G~Vkwfn~~kGfGFI~~~~gg~DvFvH~s~i~~~~~~~g~~~l~~G~~V~f~~~~~~kG-~~A~~V~~p~   79 (79)
T 1h95_A            6 ATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKG-AEAANVTGPG   79 (79)
T ss_dssp             EEEEEEEEEEEETTTTEEEEEEGGGTEEEEEEGGGBCSCCCSCCSCSCCSSCEEEEEEEECSSS-EEEESBCCCC
T ss_pred             ccccceEEEEEECCCCcEEEecCCCCccEEEEhHHccccccccccccCCCCCEEEEEEEECCCC-ceeEEEECcC
Confidence            356789999999999999999999889999999999876    789999999999999999999 7999999874

>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=99.89  E-value=7.5e-24  Score=149.01  Aligned_cols=65  Identities=43%  Similarity=0.814  Sum_probs=61.8

Q ss_pred             cceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccC
Q 047168            7 STGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAP   73 (258)
Q Consensus         7 ~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~   73 (258)
                      ++|+|||||.+||||||+++++ +|||||+|+|...++++|.+|++|+|+++.+++| ++|++|+++
T Consensus         2 ~~G~Vk~fn~~kGfGFI~~~~g-~dvFvH~s~i~~~g~~~l~~G~~V~f~~~~~~kG-~~A~~V~~~   66 (66)
T 1c9o_A            2 QRGKVKWFNNEKGYGFIEVEGG-SDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGNRG-PQAANVVKL   66 (66)
T ss_dssp             EEEEEEEEETTTTEEEEEETTE-EEEEEEGGGBCSSSCCCCCTTCEEEEEEEEETTE-EEEEEEEEC
T ss_pred             CceEEEEEECCCCeEEEecCCC-ccEEEEHHHccccCCCCCCCCCEEEEEEEECCCC-cEeEEEEeC
Confidence            5799999999999999999998 9999999999999999999999999999999999 899999853

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

Probab=99.89  E-value=1.1e-23  Score=151.01  Aligned_cols=67  Identities=43%  Similarity=0.795  Sum_probs=63.2

Q ss_pred             cceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCC--CccceeeccccCCC
Q 047168            7 STGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEA--DGKYQALDVTAPGG   75 (258)
Q Consensus         7 ~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~--~G~~~A~~V~~~~g   75 (258)
                      .+|+|||||.+||||||+++++ +|||||+|+|...++++|.+|++|+|++..++  +| ++|++|++++.
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-TDVFVHYTAINAKGFRTLNEGDIVTFDVEPGRNGKG-PQAVNVTVVEP   70 (73)
T ss_dssp             EEEEEEEEETTTTEEEEECTTS-CCEEEEGGGBCSSSCSSCCTTCEEEEEEECCSCCSS-SEEEEEEEEEC
T ss_pred             CCEEEEEEECCCCEEEEecCCC-CcEEEEhhhccccCCCCCCCCCEEEEEEEECCCCCC-CEEEEEEeCCC
Confidence            5799999999999999999998 99999999999999999999999999999999  88 89999998754

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

Probab=99.89  E-value=7.8e-24  Score=151.82  Aligned_cols=67  Identities=31%  Similarity=0.471  Sum_probs=63.5

Q ss_pred             cceEEEEeeCCCceeEEecCCCCCceEEeccccc-cCCccccCCCCcEEEEEEeCCCccceeeccccCCC
Q 047168            7 STGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIK-SDGYRTLYENQSVEFDVQLEADGKYQALDVTAPGG   75 (258)
Q Consensus         7 ~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~-~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~~g   75 (258)
                      |+|+|||||.+||||||+++++ +|||||+|+|. ..+|++|.+|++|+|+++.+++| ++|++|++++.
T Consensus         1 ~~G~Vkwfn~~KGfGFI~~~dG-~DvFvH~s~i~~~~g~~~l~~G~~V~F~~~~g~kG-~~A~~V~~~~~   68 (74)
T 2kcm_A            1 MKGKVVSYLAAKKYGFIQGDDG-ESYFLHFSELLDKKDEGKLVKGSMVHFDPTPTPKG-LAAKAISLPLE   68 (74)
T ss_dssp             CEEEEEEEETTTTEEEEEETTS-CEECCCGGGSSCSGGGTTCCTTSEEEEEEECTTTS-CEEEEEECCSC
T ss_pred             CCEEEEEEECCCCEEEEecCCC-ceEEEEhhhcccCCCCCCCCCCCEEEEEEEECCCC-ceeEEEEEcCc
Confidence            5799999999999999999998 99999999999 89999999999999999999999 79999998764

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

Probab=99.89  E-value=1e-23  Score=148.30  Aligned_cols=66  Identities=48%  Similarity=0.842  Sum_probs=62.2

Q ss_pred             cceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccCC
Q 047168            7 STGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAPG   74 (258)
Q Consensus         7 ~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~~   74 (258)
                      |+|+|||||.+||||||+++++ +|||||+|+|...++++|.+|++|+|+++.+++| ++|++|++++
T Consensus         1 m~G~Vk~fn~~kGfGFI~~~~g-~dvFvH~s~i~~~g~~~l~~G~~V~f~~~~~~~G-~~A~~V~~~~   66 (66)
T 1g6p_A            1 MRGKVKWFDSKKGYGFITKDEG-GDVFVHWSAIEMEGFKTLKEGQVVEFEIQEGKKG-PQAAHVKVVE   66 (66)
T ss_dssp             CCEEEEEEETTTTEEEEEETTS-CBCBBCSSSSCCSSCCCCCSSSEEEEEEECSSSC-CEEEEEEEEC
T ss_pred             CcEEEEEEECCCCEEEEecCCC-ceEEEEhHHccccCCCCCCCCCEEEEEEEECCCC-CEEEEEEECC
Confidence            6899999999999999999986 9999999999999999999999999999999999 8999998653

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

Probab=99.81  E-value=1.2e-24  Score=154.71  Aligned_cols=68  Identities=35%  Similarity=0.713  Sum_probs=64.5

Q ss_pred             ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeecccc
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTA   72 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~   72 (258)
                      +++++|+|||||.+||||||+++++++|||||+|+|...++++|.+|++|+|+++.+++| ++|++|++
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 ATNIVGKVKWYNSTKNFGFIEQDNGGKDVFVHKSAVDAAGLHSLEEGQDVIFDLEEKQGK-AYAVNLRI   69 (70)
Confidence            567999999999999999999999889999999999999999999999999999999998 89999975

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

Probab=99.88  E-value=6.5e-23  Score=147.10  Aligned_cols=68  Identities=21%  Similarity=0.393  Sum_probs=62.6

Q ss_pred             cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccCCCC
Q 047168            5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAPGGA   76 (258)
Q Consensus         5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~~g~   76 (258)
                      |+++|+|||||.+||||||+++++.+| |||+|+|...+  +|.+|++|+|+++.+++| ++|++|++++..
T Consensus         1 M~~~G~Vkwfn~~KGfGFI~~~dg~~d-FvH~s~i~~~g--~l~~G~~V~F~~~~g~kG-~~A~~V~~~~~~   68 (74)
T 2k5n_A            1 MAMNGTITTWFKDKGFGFIKDENGDNR-YFHVIKVANPD--LIKKDAAVTFEPTTNNKG-LSAYAVKVVPLE   68 (74)
T ss_dssp             CCEEEEEEEEETTTTEEEEEESSSCEE-EEEGGGBSSGG--GCCTTCEEEEEEEECSSS-EEEEEEEECCSS
T ss_pred             CCcceEEEEEECCCCeEEEecCCCCce-EEEHhHcccCC--CCCCCCEEEEEEEeCCCC-ceeEEEEeCCCc
Confidence            467899999999999999999998777 99999999887  799999999999999999 899999987653

>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=99.87  E-value=1.1e-22  Score=150.98  Aligned_cols=69  Identities=29%  Similarity=0.442  Sum_probs=63.7

Q ss_pred             ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCC-ccceeeccccCCC
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEAD-GKYQALDVTAPGG   75 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~-G~~~A~~V~~~~g   75 (258)
                      .++++|+|||||  ||||||+++++++|||||+++|... ++.|.+|++|+|+++.+++ |+++|++|++++.
T Consensus        16 ~~~~~G~Vkwf~--KGfGFI~~ddgg~DVFvH~s~i~~~-~~~L~~G~~V~F~v~~~~k~Gk~~A~~V~~~~~   85 (89)
T 1wfq_A           16 ALRETGVIEKLL--TSYGFIQCSERQARLFFHCSQYNGN-LQDLKVGDDVEFEVSSDRRTGKPIAVKLVKISG   85 (89)
T ss_dssp             CCEEEEEEEEEC--SSEEEEEETTTTEEEEEETTTCSSC-TTTCCTTCCEEEEEEECSSSCCEEEEEEEESSC
T ss_pred             ccccceEEEEEe--CCeeEEecCCCCccEEEEhHHhhCc-cCCCCCCCEEEEEEEECCCCCCcEEEEEEECCc
Confidence            478899999996  9999999999989999999999887 7899999999999999998 8789999998754

>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=99.85  E-value=6.4e-22  Score=146.58  Aligned_cols=69  Identities=23%  Similarity=0.377  Sum_probs=63.9

Q ss_pred             ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccCCC
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAPGG   75 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~~g   75 (258)
                      .++++|+||||+  ||||||+++++++|||||+|+|... ++.|.+|++|+|+++.+++|+++|++|++++.
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            578899999997  8999999999889999999999987 78999999999999999999789999998754

>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=99.83  E-value=2.2e-21  Score=143.79  Aligned_cols=69  Identities=25%  Similarity=0.371  Sum_probs=62.0

Q ss_pred             ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCC--ccceeeccccCCCC
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEAD--GKYQALDVTAPGGA   76 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~--G~~~A~~V~~~~g~   76 (258)
                      .++++|+||||+  ||||||+++++++|||||+|+|.. + +.|.+|++|+|+++.+++  |+++|++|++++..
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            368899999995  999999999988999999999987 5 789999999999999986  56899999987653

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

Probab=99.82  E-value=1.4e-20  Score=151.42  Aligned_cols=71  Identities=30%  Similarity=0.469  Sum_probs=62.9

Q ss_pred             ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeC---CCccceeeccccCCCCc
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLE---ADGKYQALDVTAPGGAP   77 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~---~~G~~~A~~V~~~~g~~   77 (258)
                      .++++|+|||||.+||||||+++++++|||||+++|...  ..|.+|++|+|+++.+   .+| ++|++|++++..+
T Consensus        60 g~m~~GtVKwFn~~KGfGFI~~ddGg~DVFVH~Sai~~~--~~L~eGq~V~Fev~~~~~~~~g-~qA~nV~~~~~~p  133 (147)
T 3aqq_A           60 GPVYKGVCKCFCRSKGHGFITPADGGPDIFLHISDVEGE--YVPVEGDEVTYKMCSIPPKNEK-LQAVEVVITHLAP  133 (147)
T ss_dssp             SCCEEEEEEEEETTTTEEEEEESSSCSCEEEEGGGEESS--BCCCTTCEEEEEEEEC--CCSC-EEEEEEEEEECCS
T ss_pred             CCccceEEEEEeCCCCeEEeccCCCCccEEEEeeeecCC--CcCCCCCEEEEEEEeccCCCCC-ceEEEEEeCCCCC
Confidence            367899999999999999999999999999999999855  4899999999999874   344 8999999987665

>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=99.81  E-value=1.6e-20  Score=141.49  Aligned_cols=71  Identities=28%  Similarity=0.378  Sum_probs=63.5

Q ss_pred             ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccCCCCcc
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAPGGAPV   78 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~~g~~~   78 (258)
                      .++.+|+||||  .||||||+++++++|||||+++|... ++.|.+|++|+|+++.++++ ++|++|++++...+
T Consensus        16 ~~~~~G~Vkwf--~KGfGFI~~ddg~~DvFvH~s~i~~~-~~~L~~G~~V~F~v~~~~~g-~~A~~V~~~~~~~~   86 (97)
T 2ytx_A           16 QARCQGVVCAM--KEAFGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIKDRNGK-EVATDVRLLPQGTV   86 (97)
T ss_dssp             CCCEEEEECCC--CSSEEEEECSSSCCCEEEETTTCCSC-TTSCCSCCEEEEEECCCSSS-CBEEEEEECCCSSC
T ss_pred             CcceeEEEEEE--eCCceEEecCCCCceEEEEehHhccc-cCCCCCCCEEEEEEEcCCCC-cEEEEEEECCCCcc
Confidence            46789999999  89999999999989999999999987 88999999999999877666 89999998876543

>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=99.79  E-value=8.4e-20  Score=132.53  Aligned_cols=67  Identities=31%  Similarity=0.450  Sum_probs=60.7

Q ss_pred             ccccceEEEEeeCCCceeEEecCCC-CCceEEeccccccCCccccCCCCcEEEEEEeCCC-ccceeeccccCC
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPDDG-GADLFVHQKSIKSDGYRTLYENQSVEFDVQLEAD-GKYQALDVTAPG   74 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~~~-~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~-G~~~A~~V~~~~   74 (258)
                      .++.+|+|+||  +||||||+++++ ++|||||+++|. .+ +.|.+|++|+|+++.+++ |+++|++|++++
T Consensus         6 ~~~~~G~V~~~--~KGfGFI~~ddg~g~DvFvH~s~i~-~g-~~l~~G~~V~F~v~~~~k~G~~~A~~V~~~~   74 (79)
T 2ytv_A            6 SGLRRATVECV--KDQFGFINYEVGDSKKLFFHVKEVQ-DG-IELQAGDEVEFSVILNQRTGKCSACNVWRVS   74 (79)
T ss_dssp             CSBCCEEEEEC--CSSEEEESCCCSSSSSEEEETTTCC-SS-CCCCTTCEEECBCEECSSSCCEECCSCEECS
T ss_pred             CCcccEEEEEe--cccceeEeCCCCCCCcEEEEhHHcC-CC-CcCCCCCEEEEEEEECCCCCCceeEEEEECC
Confidence            57899999999  699999999988 699999999999 66 789999999999999988 844999999875

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

Probab=99.65  E-value=4.7e-17  Score=118.90  Aligned_cols=60  Identities=25%  Similarity=0.421  Sum_probs=28.4

Q ss_pred             CcccccCCcccCcccCCCCCCCCCCCCccccCCCCCccCCCCCCCCCCCCCccccCCCCCccCCCCCCC
Q 047168          188 GGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGAGGAGGGGSCFNCGKPGHFARECTKV  256 (258)
Q Consensus       188 ~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~C~~Cg~~GH~~~~Cp~~  256 (258)
                      ..||+|++.||++++||+..       +||+|++.+|++++|+.+..  .+.||+|++.|||++|||++
T Consensus         6 ~~C~~Cg~~GH~~~~Cp~~~-------rcY~c~~~gh~~~~c~~p~~--~~~CYnCG~~GH~~rdC~~~   65 (83)
T 3nyb_B            6 VQCTLCKSKKHSKERCPSIW-------RAYILVDDNEKAKPKVLPFH--TIYCYNCGGKGHFGDDCKEK   65 (83)
T ss_dssp             -CCSSSCCSSSCGGGCGGGT-------CCCCBC-------------C--CCBCSSSSCBSSCGGGCSSC
T ss_pred             CCCCCCCCCCCccccCCCcc-------cccccccCCcccccccCCCC--CCeecccCCCCcCcccCCcc
Confidence            45666666666666666542       46666666666666655421  45666666666666666654

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

Probab=99.64  E-value=2.4e-16  Score=119.64  Aligned_cols=61  Identities=36%  Similarity=0.584  Sum_probs=54.9

Q ss_pred             ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc--cccCCCCcEEEEEEeCC-Ccc
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY--RTLYENQSVEFDVQLEA-DGK   64 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~--~~l~~G~~V~F~v~~~~-~G~   64 (258)
                      .++++|+|||||.+||||||+++++++|||||+|+|...++  +.|.+|+.|+|++.... .|.
T Consensus        14 ~~~~~G~Vk~fn~~kGfGFI~~~~gg~dvfvH~s~l~~~~~~~~~l~~Ge~V~g~V~~i~~fG~   77 (101)
T 2bh8_A           14 SGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAGSSGAAVRGNPQQGDRVEGKIKSITDFGI   77 (101)
T ss_dssp             --CEEEEEEEEEGGGTEEEEEESSSSCEEEEECCCSCSSSCCCCCCCTTCEEEEEEEECCSEEE
T ss_pred             cccceeEEEEEECCCCCEEEEeCCCCcEEEEEEEEEecCCccccCCCCCCEEEEEEEEeCCcEE
Confidence            45789999999999999999999999999999999999988  89999999999999865 464

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

Probab=99.52  E-value=8.6e-15  Score=104.66  Aligned_cols=62  Identities=23%  Similarity=0.552  Sum_probs=21.6

Q ss_pred             CCCCCCCCCCCCCCC-CCCCCCCCcccccCCcccCcccCCCCCCCCCCCCccccCCCCCccCCCCCC
Q 047168          166 PEHFARDCPRQQGGS-NSYNNNSGGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGA  231 (258)
Q Consensus       166 ~GH~~~~Cp~~~~~~-~~~~~~~~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~  231 (258)
                      .||+++||+++.... .........||+|++.||++++|+....    ...||+|++.||++++||+
T Consensus         2 ~gh~~rdc~~~~~~~~~~~~~r~~~C~~Cg~~GH~a~~C~~~~~----~~~C~~Cg~~GH~ar~Cp~   64 (74)
T 2li8_A            2 SGLVPRGSHMPKGKSMQKRRSKGDRCYNCGGLDHHAKECKLPPQ----PKKCHFCQSISHMVASCPL   64 (74)
T ss_dssp             ----------CCCCCCCSCCSTTSCCTTTCCSSSCTTTCSSCCC----CCCCTTTCCTTSCGGGCTT
T ss_pred             CccccCcCCCCCcCccccccCCCCcccccCCcCcCcccCCCCCC----CCccCCcCCcCCccCcCcC
Confidence            466677776654221 1111233445555555555555554211    1244444444444444443

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

Probab=99.51  E-value=8.5e-15  Score=106.88  Aligned_cols=61  Identities=28%  Similarity=0.507  Sum_probs=25.1

Q ss_pred             CCcccccCCCCccccccccccCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCcccCcccCCCC
Q 047168          128 GVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITR  206 (258)
Q Consensus       128 ~~~C~~Cg~~GH~a~~Cp~~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~~  206 (258)
                      .+.||+|++.||++++||+          ..+||+|+..+|++++|+.+.        ....||+|++.||++++||+.
T Consensus         5 ~~~C~~Cg~~GH~~~~Cp~----------~~rcY~c~~~gh~~~~c~~p~--------~~~~CYnCG~~GH~~rdC~~~   65 (83)
T 3nyb_B            5 KVQCTLCKSKKHSKERCPS----------IWRAYILVDDNEKAKPKVLPF--------HTIYCYNCGGKGHFGDDCKEK   65 (83)
T ss_dssp             --CCSSSCCSSSCGGGCGG----------GTCCCCBC---------------------CCCBCSSSSCBSSCGGGCSSC
T ss_pred             cCCCCCCCCCCCccccCCC----------cccccccccCCcccccccCCC--------CCCeecccCCCCcCcccCCcc
Confidence            4566666666666666665          224555555555555554431        134455555555555555443

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

Probab=99.45  E-value=7e-14  Score=99.94  Aligned_cols=40  Identities=30%  Similarity=0.806  Sum_probs=19.7

Q ss_pred             CCcccCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCcccCcccCCC
Q 047168          158 GGCYNCGDPEHFARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCIT  205 (258)
Q Consensus       158 ~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~  205 (258)
                      ..||+|+++||++++|+...        ....||+|++.||++++||+
T Consensus        25 ~~C~~Cg~~GH~a~~C~~~~--------~~~~C~~Cg~~GH~ar~Cp~   64 (74)
T 2li8_A           25 DRCYNCGGLDHHAKECKLPP--------QPKKCHFCQSISHMVASCPL   64 (74)
T ss_dssp             SCCTTTCCSSSCTTTCSSCC--------CCCCCTTTCCTTSCGGGCTT
T ss_pred             CcccccCCcCcCcccCCCCC--------CCCccCCcCCcCCccCcCcC
Confidence            44555555555555555331        12445555555555555554

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

Probab=99.34  E-value=7.8e-13  Score=82.93  Aligned_cols=38  Identities=45%  Similarity=1.014  Sum_probs=29.0

Q ss_pred             ccccCCCCCccCCCCCCCCCCCCCccccCCCCCccCCCCCC
Q 047168          215 RCYNCGKSGHLARDCGAGGAGGGGSCFNCGKPGHFARECTK  255 (258)
Q Consensus       215 ~C~~Cg~~GH~~~~Cp~~~~~~~~~C~~Cg~~GH~~~~Cp~  255 (258)
                      .||+|++.||++++||.++   ...||+|++.||++++||+
T Consensus         2 ~C~~Cg~~GH~a~~C~~~~---~~~C~~Cg~~GH~~~~C~~   39 (39)
T 2a51_A            2 TCFNCGKPGHTARMCRQPR---QEGCWNCGSKEHRFAQCPK   39 (39)
T ss_dssp             BCTTTCCBSSCTTTCCSCC---CSSCTTTCCSSSCTTTSCC
T ss_pred             eeeccCCCCcccccCCCCC---CCccccCCCCCCccCcCcC
Confidence            5777777777777777653   3568888888888888875

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

Probab=99.28  E-value=2.6e-12  Score=84.56  Aligned_cols=40  Identities=48%  Similarity=1.110  Sum_probs=24.1

Q ss_pred             ccccCCCCCccCCCCCCCCCCCCCccccCCCCCccCCCCCCCc
Q 047168          215 RCYNCGKSGHLARDCGAGGAGGGGSCFNCGKPGHFARECTKVA  257 (258)
Q Consensus       215 ~C~~Cg~~GH~~~~Cp~~~~~~~~~C~~Cg~~GH~~~~Cp~~~  257 (258)
                      .||+|++.||++++||.++   ...||+|++.||++++||++.
T Consensus         8 ~C~~Cg~~GH~a~~C~~~~---~~~C~~Cg~~GH~~~~C~~~~   47 (49)
T 2ec7_A            8 RCWNCGKEGHSARQCRAPR---RQGCWKCGKTGHVMAKCPERQ   47 (49)
T ss_dssp             BCTTTCCBTCCTTTCCCSS---CCSCSSSCCSSCCGGGCCSSC
T ss_pred             eeeecCCCCcChhhCcCCC---CCeeCcCCCcCCccCCCcCCC
Confidence            5666666666666665543   235666666666666666653

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

Probab=99.24  E-value=3.9e-12  Score=78.80  Aligned_cols=36  Identities=53%  Similarity=1.364  Sum_probs=26.4

Q ss_pred             ccccCCCCCccCCCCCCCCCCCCCccccCCCCCccCCCCCC
Q 047168          215 RCYNCGKSGHLARDCGAGGAGGGGSCFNCGKPGHFARECTK  255 (258)
Q Consensus       215 ~C~~Cg~~GH~~~~Cp~~~~~~~~~C~~Cg~~GH~~~~Cp~  255 (258)
                      .||+|++.||++++||.+     ..||+|++.||++++||+
T Consensus         2 ~C~~Cg~~GH~~~~C~~~-----~~C~~Cg~~GH~a~~C~~   37 (37)
T 2bl6_A            2 TCYNCGKPGHLSSQCRAP-----KVCFKCKQPGHFSKQCRS   37 (37)
T ss_dssp             CBSSSCCSSCCTTTSSCB-----TTCSSCCCTTGGGGTTCC
T ss_pred             cccccCCCCcchhhCcCc-----CeEccCCCcCCccCcCcC
Confidence            577777777777777763     468888888888888875

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

Probab=99.23  E-value=5.2e-12  Score=86.92  Aligned_cols=47  Identities=32%  Similarity=0.775  Sum_probs=30.8

Q ss_pred             CCcccccCCcccCcccCCCCCCCCCCCCccccCCCCCccCCCCCCCC
Q 047168          187 SGGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGAGG  233 (258)
Q Consensus       187 ~~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~  233 (258)
                      ...||+|++.||++++||+..........||+|+++||++++||+..
T Consensus         4 ~~~C~~Cg~~GH~a~~C~~~~~~~~~~~~C~~Cg~~GH~ar~C~~~~   50 (61)
T 2ihx_A            4 RGLCYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQCRKRD   50 (61)
T ss_dssp             TTBCSSSCCBTCCGGGCTTTTSSSCCCSBCTTTCCBSSCGGGCCCCC
T ss_pred             CCcccccCCCCeehhhCcCCcCCCCCCCeeCCCCCCCCCcCCCcCCC
Confidence            46788888888888888775332222346777777777777776644

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

Probab=99.22  E-value=9.3e-12  Score=85.64  Aligned_cols=46  Identities=39%  Similarity=1.015  Sum_probs=23.7

Q ss_pred             CCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCcccCcccCCCC
Q 047168          157 SGGCYNCGDPEHFARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITR  206 (258)
Q Consensus       157 ~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~~  206 (258)
                      +..||+|+++||++++||.....    ......||+|++.||++++||+.
T Consensus         4 ~~~C~~Cg~~GH~a~~C~~~~~~----~~~~~~C~~Cg~~GH~ar~C~~~   49 (61)
T 2ihx_A            4 RGLCYTCGSPGHYQAQCPKKRKS----GNSRERCQLCNGMGHNAKQCRKR   49 (61)
T ss_dssp             TTBCSSSCCBTCCGGGCTTTTSS----SCCCSBCTTTCCBSSCGGGCCCC
T ss_pred             CCcccccCCCCeehhhCcCCcCC----CCCCCeeCCCCCCCCCcCCCcCC
Confidence            34566666666666666554210    01234566666666666666554

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

Probab=99.19  E-value=8.1e-12  Score=84.11  Aligned_cols=39  Identities=46%  Similarity=1.199  Sum_probs=21.2

Q ss_pred             ccccCCCCCccCCCCCCCCCCCCCccccCCCCCccCCCCCCC
Q 047168          215 RCYNCGKSGHLARDCGAGGAGGGGSCFNCGKPGHFARECTKV  256 (258)
Q Consensus       215 ~C~~Cg~~GH~~~~Cp~~~~~~~~~C~~Cg~~GH~~~~Cp~~  256 (258)
                      .||+|++.||++++||.++   ...||+|++.||++++||+.
T Consensus        14 ~C~~Cg~~GH~a~~C~~~~---~~~C~~Cg~~GH~~~~C~~~   52 (55)
T 1a1t_A           14 KCFNCGKEGHIAKNCRAPR---KKGCWKCGKEGHQMKDCTER   52 (55)
T ss_dssp             BCTTTCCBSSCGGGCSSCS---CCBCTTTCCBSSCGGGCSSS
T ss_pred             ceeeeCCCCcChhhcCCCC---CCEeCCCCCcCCccCCCcCc
Confidence            4555555555555555432   23466666666666666654

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

Probab=99.19  E-value=1.8e-11  Score=84.71  Aligned_cols=45  Identities=24%  Similarity=0.693  Sum_probs=32.5

Q ss_pred             CCCCcccccCCcccCcccCCCCCCCCCCCCccccCCCCCccCCCCCCCC
Q 047168          185 NNSGGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGAGG  233 (258)
Q Consensus       185 ~~~~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~  233 (258)
                      .....||+|++.||++++||.+..    ...||+|++.||++++||+..
T Consensus         5 ~r~~~C~~Cg~~GH~a~~C~~~~~----~~~C~~Cg~~GH~ar~Cp~~~   49 (63)
T 2cqf_A            5 SSGDRCYNCGGLDHHAKECKLPPQ----PKKCHFCQSISHMVASCPLKA   49 (63)
T ss_dssp             CSCCCCSSSCCSSSCTTTCCSCCC----SSCCTTTCCSSSCTTTCTGGG
T ss_pred             CCCCcccccCCCCcChhhCCCCCC----CCccCCcCCcCCccCcCCCcc
Confidence            345678888888888888886421    237888888888888887754

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

Probab=99.19  E-value=5.3e-12  Score=86.54  Aligned_cols=44  Identities=34%  Similarity=0.848  Sum_probs=10.7

Q ss_pred             cccccCCcccCcccCCCCCCCCC---CCCccccCCCCCccCCCCCCC
Q 047168          189 GCFKCGGYGHLARDCITRGSGGG---GGGRCYNCGKSGHLARDCGAG  232 (258)
Q Consensus       189 ~C~~Cg~~GH~~~~C~~~~~~~~---~~~~C~~Cg~~GH~~~~Cp~~  232 (258)
                      .||+|++.||++++||+......   ....||+|++.||++++||+.
T Consensus         3 ~Cf~Cg~~GH~a~~C~~~~~~~~~~~~~~~C~~Cg~~GH~ar~C~~~   49 (60)
T 1cl4_A            3 SCFKCGKKGHFAKNCHEHAHNNAEPKVPGLCPRCKRGKHWANECKSK   49 (60)
T ss_dssp             --------------------------CCCSCSSCSSCSSCSTTCCCT
T ss_pred             ccccCCCCCcCHhhCcCCCCCccccCCCcceeECCCCCCccCcCCCc
Confidence            57777777777777776532110   123455555555555555553

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

Probab=99.18  E-value=2.5e-11  Score=84.00  Aligned_cols=44  Identities=27%  Similarity=0.770  Sum_probs=28.3

Q ss_pred             CCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCcccCcccCCCC
Q 047168          155 NNSGGCYNCGDPEHFARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITR  206 (258)
Q Consensus       155 ~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~~  206 (258)
                      .....||+|+++||++++||.+.        ....||+|++.||++++||+.
T Consensus         5 ~r~~~C~~Cg~~GH~a~~C~~~~--------~~~~C~~Cg~~GH~ar~Cp~~   48 (63)
T 2cqf_A            5 SSGDRCYNCGGLDHHAKECKLPP--------QPKKCHFCQSISHMVASCPLK   48 (63)
T ss_dssp             CSCCCCSSSCCSSSCTTTCCSCC--------CSSCCTTTCCSSSCTTTCTGG
T ss_pred             CCCCcccccCCCCcChhhCCCCC--------CCCccCCcCCcCCccCcCCCc
Confidence            34456777777777777776541        235677777777777777664

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

Probab=99.17  E-value=1.8e-11  Score=76.63  Aligned_cols=38  Identities=39%  Similarity=0.878  Sum_probs=26.5

Q ss_pred             cccccCCcccCcccCCCCCCCCCCCCccccCCCCCccCCCCCC
Q 047168          189 GCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGA  231 (258)
Q Consensus       189 ~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~  231 (258)
                      .||+|++.||++++||++.     ...||+|++.||++++||+
T Consensus         2 ~C~~Cg~~GH~a~~C~~~~-----~~~C~~Cg~~GH~~~~C~~   39 (39)
T 2a51_A            2 TCFNCGKPGHTARMCRQPR-----QEGCWNCGSKEHRFAQCPK   39 (39)
T ss_dssp             BCTTTCCBSSCTTTCCSCC-----CSSCTTTCCSSSCTTTSCC
T ss_pred             eeeccCCCCcccccCCCCC-----CCccccCCCCCCccCcCcC
Confidence            5777777777777777642     1367777777777777774

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

Probab=99.13  E-value=3e-11  Score=74.76  Aligned_cols=36  Identities=33%  Similarity=1.063  Sum_probs=26.6

Q ss_pred             cccccCCcccCcccCCCCCCCCCCCCccccCCCCCccCCCCCC
Q 047168          189 GCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGA  231 (258)
Q Consensus       189 ~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~  231 (258)
                      .||+|++.||++++||++       ..||+|++.||++++||+
T Consensus         2 ~C~~Cg~~GH~~~~C~~~-------~~C~~Cg~~GH~a~~C~~   37 (37)
T 2bl6_A            2 TCYNCGKPGHLSSQCRAP-------KVCFKCKQPGHFSKQCRS   37 (37)
T ss_dssp             CBSSSCCSSCCTTTSSCB-------TTCSSCCCTTGGGGTTCC
T ss_pred             cccccCCCCcchhhCcCc-------CeEccCCCcCCccCcCcC
Confidence            577777777777777764       267888888888887773

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

Probab=99.11  E-value=7.5e-11  Score=77.50  Aligned_cols=39  Identities=38%  Similarity=0.945  Sum_probs=20.5

Q ss_pred             CcccccCCcccCcccCCCCCCCCCCCCccccCCCCCccCCCCCC
Q 047168          188 GGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGA  231 (258)
Q Consensus       188 ~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~  231 (258)
                      ..||+|++.||++++||.+.     ...||+|++.||++++||+
T Consensus         7 ~~C~~Cg~~GH~a~~C~~~~-----~~~C~~Cg~~GH~~~~C~~   45 (49)
T 2ec7_A            7 IRCWNCGKEGHSARQCRAPR-----RQGCWKCGKTGHVMAKCPE   45 (49)
T ss_dssp             CBCTTTCCBTCCTTTCCCSS-----CCSCSSSCCSSCCGGGCCS
T ss_pred             CeeeecCCCCcChhhCcCCC-----CCeeCcCCCcCCccCCCcC
Confidence            45555555555555555431     1245555555555555554

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

Probab=99.05  E-value=8.6e-11  Score=79.04  Aligned_cols=41  Identities=39%  Similarity=0.999  Sum_probs=28.6

Q ss_pred             CCcccccCCcccCcccCCCCCCCCCCCCccccCCCCCccCCCCCCC
Q 047168          187 SGGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGAG  232 (258)
Q Consensus       187 ~~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~  232 (258)
                      ...||+|++.||++++||.+.     ...||+|++.||++++||+.
T Consensus        12 ~~~C~~Cg~~GH~a~~C~~~~-----~~~C~~Cg~~GH~~~~C~~~   52 (55)
T 1a1t_A           12 TVKCFNCGKEGHIAKNCRAPR-----KKGCWKCGKEGHQMKDCTER   52 (55)
T ss_dssp             TCBCTTTCCBSSCGGGCSSCS-----CCBCTTTCCBSSCGGGCSSS
T ss_pred             CcceeeeCCCCcChhhcCCCC-----CCEeCCCCCcCCccCCCcCc
Confidence            456777777777777777642     13677777777777777764

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

Probab=99.02  E-value=8.4e-11  Score=80.51  Aligned_cols=17  Identities=35%  Similarity=1.083  Sum_probs=0.0

Q ss_pred             cccccCCCCcccccccc
Q 047168          130 VCYNCDGVGHVARECTS  146 (258)
Q Consensus       130 ~C~~Cg~~GH~a~~Cp~  146 (258)
                      .||+|++.||++++||.
T Consensus         3 ~Cf~Cg~~GH~a~~C~~   19 (60)
T 1cl4_A            3 SCFKCGKKGHFAKNCHE   19 (60)
T ss_dssp             -----------------
T ss_pred             ccccCCCCCcCHhhCcC
Confidence            57777777777777765

>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=98.99  E-value=1.8e-10  Score=92.93  Aligned_cols=43  Identities=26%  Similarity=0.711  Sum_probs=30.2

Q ss_pred             CCcccccCCcccCcccCCCCCCCCCCCCccccCCCCCccCCCCCCCC
Q 047168          187 SGGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGAGG  233 (258)
Q Consensus       187 ~~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~  233 (258)
                      ...||+|++.||++++||.+..    ...||+|++.||++++||+..
T Consensus        97 ~~~C~~Cg~~GH~a~~C~~~~~----~~~C~~Cg~~GH~~r~Cp~~~  139 (148)
T 3ts2_A           97 GDRCYNCGGLDHHAKECKLPPQ----PKKCHFCQSINHMVASCPLKA  139 (148)
T ss_dssp             SCCCTTTCCSSCCGGGCCSCCC----CCCCTTTCCSSCCGGGCTTTT
T ss_pred             CCcccEeCCccchhhhCCCCCC----CCcccccCCcCCEeccCcCCC
Confidence            4578888888888888887432    136777777777777777643

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

Probab=97.99  E-value=2.6e-06  Score=48.15  Aligned_cols=18  Identities=50%  Similarity=1.337  Sum_probs=9.8

Q ss_pred             ccccCCCCCccCCCCCCC
Q 047168          215 RCYNCGKSGHLARDCGAG  232 (258)
Q Consensus       215 ~C~~Cg~~GH~~~~Cp~~  232 (258)
                      .||+|++.||++++||++
T Consensus         4 ~Cf~CG~~GH~ardC~~~   21 (26)
T 1dsq_A            4 VCFSCGKTGHIKRDCKEE   21 (26)
T ss_dssp             BCTTTCCBSSCTTTTTCC
T ss_pred             eeEeCCCCCcccccCCCc
Confidence            455555555555555543

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

Probab=97.94  E-value=4.3e-06  Score=47.19  Aligned_cols=18  Identities=50%  Similarity=1.318  Sum_probs=10.0

Q ss_pred             ccccCCCCCccCCCCCCC
Q 047168          239 SCFNCGKPGHFARECTKV  256 (258)
Q Consensus       239 ~C~~Cg~~GH~~~~Cp~~  256 (258)
                      .||+|++.||++++||++
T Consensus         4 ~Cf~CG~~GH~ardC~~~   21 (26)
T 1dsq_A            4 VCFSCGKTGHIKRDCKEE   21 (26)
T ss_dssp             BCTTTCCBSSCTTTTTCC
T ss_pred             eeEeCCCCCcccccCCCc
Confidence            455555555555555554

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

Probab=97.80  E-value=1.3e-05  Score=49.93  Aligned_cols=19  Identities=37%  Similarity=0.870  Sum_probs=11.8

Q ss_pred             ccccCCCCCccCCCCCCCC
Q 047168          215 RCYNCGKSGHLARDCGAGG  233 (258)
Q Consensus       215 ~C~~Cg~~GH~~~~Cp~~~  233 (258)
                      .||+|++.||++++||.+.
T Consensus        12 ~C~~Cgk~GH~ardCP~~~   30 (40)
T 1a6b_B           12 QCAYCKEKGHWAKDCPKKP   30 (40)
T ss_dssp             SCSSSCCTTCCTTSCSSSC
T ss_pred             eeeECCCCCcchhhCcCCc
Confidence            5666666666666666644

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

Probab=97.78  E-value=7.5e-06  Score=47.39  Aligned_cols=18  Identities=67%  Similarity=1.394  Sum_probs=9.1

Q ss_pred             ccccCCCCCccCCCCCCC
Q 047168          215 RCYNCGKSGHLARDCGAG  232 (258)
Q Consensus       215 ~C~~Cg~~GH~~~~Cp~~  232 (258)
                      .||||+++||++++||.+
T Consensus         8 ~C~nCgk~GH~ar~C~~p   25 (29)
T 1nc8_A            8 RCWNCGKEGHSARQCRAP   25 (29)
T ss_dssp             BCTTTSCBSSCGGGCCSS
T ss_pred             EEEECCccccCHhHCccc
Confidence            455555555555555443

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

Probab=97.74  E-value=1.4e-05  Score=46.27  Aligned_cols=18  Identities=44%  Similarity=0.979  Sum_probs=8.7

Q ss_pred             CcccccCCcccCcccCCC
Q 047168          188 GGCFKCGGYGHLARDCIT  205 (258)
Q Consensus       188 ~~C~~Cg~~GH~~~~C~~  205 (258)
                      ..||+|++.||++++|+.
T Consensus         7 ~~C~nCgk~GH~ar~C~~   24 (29)
T 1nc8_A            7 IRCWNCGKEGHSARQCRA   24 (29)
T ss_dssp             CBCTTTSCBSSCGGGCCS
T ss_pred             CEEEECCccccCHhHCcc
Confidence            345555555555555544

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

Probab=97.51  E-value=5.3e-05  Score=47.11  Aligned_cols=23  Identities=30%  Similarity=0.645  Sum_probs=18.5

Q ss_pred             CCCCcccccCCcccCcccCCCCC
Q 047168          185 NNSGGCFKCGGYGHLARDCITRG  207 (258)
Q Consensus       185 ~~~~~C~~Cg~~GH~~~~C~~~~  207 (258)
                      .....||+|++.|||+++||...
T Consensus         8 ~~~~~C~~Cgk~GH~ardCP~~~   30 (40)
T 1a6b_B            8 LDRDQCAYCKEKGHWAKDCPKKP   30 (40)
T ss_dssp             CCSSSCSSSCCTTCCTTSCSSSC
T ss_pred             CCCCeeeECCCCCcchhhCcCCc
Confidence            44678888988899999998863

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

Probab=97.44  E-value=5.6e-05  Score=50.50  Aligned_cols=20  Identities=35%  Similarity=0.828  Sum_probs=13.9

Q ss_pred             CccccCCCCCccCCCCCCCC
Q 047168          214 GRCYNCGKSGHLARDCGAGG  233 (258)
Q Consensus       214 ~~C~~Cg~~GH~~~~Cp~~~  233 (258)
                      ..||+|++.||+++|||.+.
T Consensus        24 ~~C~~Cge~GH~ardCp~~~   43 (56)
T 1u6p_A           24 DQCAYCKEKGHWAKDCPKKP   43 (56)
T ss_dssp             TBCSSSCCBSSCGGGCTTCC
T ss_pred             CcceeCCCCCcccccCcCCc
Confidence            46777777777777777654

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

Probab=97.28  E-value=0.00039  Score=46.36  Aligned_cols=21  Identities=29%  Similarity=0.673  Sum_probs=17.5

Q ss_pred             CCCcccccCCCCccccccccc
Q 047168          127 GGVVCYNCDGVGHVARECTSN  147 (258)
Q Consensus       127 ~~~~C~~Cg~~GH~a~~Cp~~  147 (258)
                      ....||+|++.||++++||.+
T Consensus        22 ~~~~C~~Cge~GH~ardCp~~   42 (56)
T 1u6p_A           22 DRDQCAYCKEKGHWAKDCPKK   42 (56)
T ss_dssp             CTTBCSSSCCBSSCGGGCTTC
T ss_pred             CCCcceeCCCCCcccccCcCC
Confidence            367899999999999999873

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

Probab=97.19  E-value=0.00016  Score=48.15  Aligned_cols=21  Identities=38%  Similarity=0.947  Sum_probs=17.1

Q ss_pred             CCCcccccCCcccCcccCCCC
Q 047168          186 NSGGCFKCGGYGHLARDCITR  206 (258)
Q Consensus       186 ~~~~C~~Cg~~GH~~~~C~~~  206 (258)
                      ....||+|+++||++++||..
T Consensus         6 ~~~~C~kCGk~GH~~k~Cp~~   26 (55)
T 2ysa_A            6 SGYTCFRCGKPGHYIKNCPTN   26 (55)
T ss_dssp             SSCCCTTTCCTTSCGGGCSGG
T ss_pred             CCCccccCCCcCcccccCCCC
Confidence            356899999999999999854

>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=96.97  E-value=0.00091  Score=52.33  Aligned_cols=65  Identities=22%  Similarity=0.456  Sum_probs=48.3

Q ss_pred             cceEEEEeeCCCceeEEecCC-----CCCceEEeccccccCCccccCCCCcEEEEEEeCCCcc--ceeeccccCCCC
Q 047168            7 STGKVTWFDGAKGYGFIRPDD-----GGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGK--YQALDVTAPGGA   76 (258)
Q Consensus         7 ~~G~vk~f~~~kGfGFI~~~~-----~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~--~~A~~V~~~~g~   76 (258)
                      +.|++.--  .+||||+.+++     +.+||||..+.|...+   |..||.|+-.+.....+.  ...+.|..+.+.
T Consensus        51 ~~Gvlei~--~dG~GFlr~~~~~y~~~~~DiyVs~~~irrf~---lr~GD~V~g~vr~~~~~ek~~~l~~v~~vng~  122 (130)
T 1a62_A           51 GDGVLEIL--QDGFGFLRSADSSYLAGPDDIYVSPSQIRRFN---LRTGDTISGKIRPPKEGERYFALLKVNEVNFD  122 (130)
T ss_dssp             EEEEEEEC--TTSCEEEECGGGTTCCCTTCEEECHHHHHHTT---CCTTCEEEEEEECCCTTCCSEEEEEEEEETTB
T ss_pred             EEEEEEEc--CCCeEEEecCCcCCCCCCCCEEECHHHHhHhC---CCCCCEEEEEEeCCCCCCcccceeEEEeECCC
Confidence            56776654  57999999883     6799999999998764   899999999998876542  133455555554

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

Probab=96.65  E-value=0.00098  Score=44.24  Aligned_cols=19  Identities=32%  Similarity=1.025  Sum_probs=14.4

Q ss_pred             CCcccccCCCCcccccccc
Q 047168          128 GVVCYNCDGVGHVARECTS  146 (258)
Q Consensus       128 ~~~C~~Cg~~GH~a~~Cp~  146 (258)
                      ...||.|++.||++++||+
T Consensus         7 ~~~C~kCGk~GH~~k~Cp~   25 (55)
T 2ysa_A            7 GYTCFRCGKPGHYIKNCPT   25 (55)
T ss_dssp             SCCCTTTCCTTSCGGGCSG
T ss_pred             CCccccCCCcCcccccCCC
Confidence            4578888888888888875

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

Probab=93.15  E-value=0.19  Score=35.14  Aligned_cols=53  Identities=17%  Similarity=0.172  Sum_probs=40.6

Q ss_pred             ccccceEEEEeeCCCcee-EEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeC
Q 047168            4 LTRSTGKVTWFDGAKGYG-FIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLE   60 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfG-FI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~   60 (258)
                      .+.+.|+|+...+   || ||..++ ..+-|+|+|.+...-+..+.+||.|...+..-
T Consensus         6 G~iv~G~V~~v~~---~G~fV~l~~-~~~Gllh~sel~~~~~~~~~~Gd~V~v~V~~v   59 (80)
T 2k52_A            6 GKFYKGVVTRIEK---YGAFINLNE-QVRGLLRPRDMISLRLENLNVGDEIIVQAIDV   59 (80)
T ss_dssp             TCEEEEEEEEEET---TEEEEEEET-TEEEEECGGGCSSCCGGGCCTTCEEEEEEEEE
T ss_pred             CCEEEEEEEEEeC---CEEEEEECC-CCEEEEEHHHCCcccceeeCCCCEEEEEEEEE
Confidence            3578999999854   66 555554 58999999999754334699999999988764

>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=93.01  E-value=0.069  Score=52.17  Aligned_cols=61  Identities=20%  Similarity=0.292  Sum_probs=46.5

Q ss_pred             cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccCC
Q 047168            5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAPG   74 (258)
Q Consensus         5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~~   74 (258)
                      ..+.|+|+-=  .+||||+.+++ .+|||+.-..+..     .-.||+|...+... +++++|.-|.+++
T Consensus        20 ~~~~G~~~~~--~~GfgF~~~d~-~~difi~~~~~~~-----a~~GD~V~v~i~~~-~~~~eg~v~~ile   80 (644)
T 2id0_A           20 PRAEGVVKAT--EKGFGFLEVDA-QKSYFIPPPQMKK-----VMHGDRIIAVIHSE-KERESAEPEELVE   80 (644)
T ss_dssp             CEEEEEEECC--SSSCEEEECSS-SCEEEECHHHHTT-----SCTTCEEEEEEECC-SSSCEEEEEEEEE
T ss_pred             CeEEEEEEEe--cCCcEEEEECC-CCCEEECHHHHhc-----CCCCCEEEEEEecC-CCCeEEEEEEEEe
Confidence            3578998864  79999999986 5899999887754     46899999988765 3456666665554

>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=93.00  E-value=0.22  Score=37.80  Aligned_cols=54  Identities=20%  Similarity=0.203  Sum_probs=39.8

Q ss_pred             ccccceEEEEeeCCCcee-EEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeC
Q 047168            4 LTRSTGKVTWFDGAKGYG-FIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLE   60 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfG-FI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~   60 (258)
                      ...+.|+|+...+   || ||..+....+-|+|++.|...-+    ..+++||.|...|..-
T Consensus        23 G~iv~G~V~~I~~---fGaFV~l~g~~~~Glvhisel~~~~~~~~~~~~~~Gd~V~VkV~~v   81 (119)
T 2cqo_A           23 YTIFQGEVAMVTD---YGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGR   81 (119)
T ss_dssp             TCEEEEEEEEEET---TEEEEECTTCSSCEEEEHHHHCSSCCSCHHHHCCTTCEEEEEEEEE
T ss_pred             CCEEEEEEEEEeC---ceEEEEECCCcEEEEEEHHHCCcccccChhhcCCCCCEEEEEEEEE
Confidence            3568999999954   66 66654334799999999965322    3488999999888764

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

Probab=91.04  E-value=0.63  Score=40.75  Aligned_cols=63  Identities=11%  Similarity=0.050  Sum_probs=45.1

Q ss_pred             ccccceEEEEeeCCCceeEEecCCC-CCceEEeccccccCCccccCCCCcEEEEEEeCCCccceee
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPDDG-GADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQAL   68 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~~~-~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~   68 (258)
                      .....|+|++.+  +.||....... +.|+|+|+|.+...--..+.+|+.|...+..++++++.|.
T Consensus        70 G~~~~g~V~~v~--~~~GaFVdiG~~~~d~lvp~sel~~~~~~~~~~Gd~v~v~l~iD~~~Ri~ls  133 (285)
T 3go5_A           70 DQFGWGRVTEVR--KDLGVFVDTGLPDKEIVVSLDILPELKELWPKKGDQLYIRLEVDKKDRIWGL  133 (285)
T ss_dssp             SSCEEEEEEEEE--TTTEEEEECSCTTCCEEEEGGGSCSSGGGSCCTTCEEEEEEEECTTSCEEEE
T ss_pred             CCEEEEEEEEEc--cCceEEEEECCCCcEEEEEHHHCCcccccccCCCCEEEEEEEECCCCcEEEE
Confidence            356789999884  44774443443 4799999999865322357999999888877777776665

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

Probab=91.01  E-value=0.37  Score=40.48  Aligned_cols=80  Identities=13%  Similarity=0.132  Sum_probs=45.9

Q ss_pred             cccceEEEEeeCCCceeEEecCCCCCceEEeccccccC------Cc--------cccCCCCcEEEEEEeCCC--ccceee
Q 047168            5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSD------GY--------RTLYENQSVEFDVQLEAD--GKYQAL   68 (258)
Q Consensus         5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~------~~--------~~l~~G~~V~F~v~~~~~--G~~~A~   68 (258)
                      +.+.|+|+....   ||+...... .|.|||+|.|...      ..        +.+++||.|++.|..-+.  ....++
T Consensus        85 ev~~G~V~~vt~---fG~FVelg~-~dGlVhiS~l~d~~~~d~~~~~w~~~~~~~~~~~Gd~VrVkV~~vd~~~~~i~~I  160 (215)
T 2b8k_G           85 EVVDGTVVSCSQ---HGFEVQVGP-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAI  160 (215)
T ss_dssp             EEEEEEEEEEET---TEEEEECTT-SEEEEEGGGSCSSCCCBSSCSSCEEECSSCEEETTCEEEEEEEEEEEETTEEEEE
T ss_pred             CEEEEEEEEEec---ceEEEEecC-cEEEEEHHHCCccceeccccccceeeccccEECCCCEEEEEEEEEEcCCCccEEE
Confidence            568899999863   787665555 8999999998532      00        348899999999877432  112222


Q ss_pred             -ccccCCCCcccCCCCCCCCC
Q 047168           69 -DVTAPGGAPVHSSKNNNTNN   88 (258)
Q Consensus        69 -~V~~~~g~~~~~s~~~~~g~   88 (258)
                       .+..+...++...+++-+.|
T Consensus       161 gSmk~~~LG~~~~~~~~~~~~  181 (215)
T 2b8k_G          161 GSIKEDYLGAISHEKRRWKKN  181 (215)
T ss_dssp             EECCSTTCEEC----------
T ss_pred             EEcCCCCCCCcchhhHHHHhh
Confidence             34444455566666665554

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

Probab=90.80  E-value=1.6  Score=32.54  Aligned_cols=55  Identities=24%  Similarity=0.225  Sum_probs=39.9

Q ss_pred             ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccC-----CccccCCCCcEEEEEEeCC
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSD-----GYRTLYENQSVEFDVQLEA   61 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~-----~~~~l~~G~~V~F~v~~~~   61 (258)
                      .+.+.|+|+...+   ||+....+.+.+.|+|++.|...     .-..+.+||.|...|..-+
T Consensus        31 G~~~~G~V~~v~~---~G~FV~l~~~~~Glvhisel~~~~~~~~~~~~~~vGd~V~vkV~~vd   90 (115)
T 2khi_A           31 GTKLTGRVTNLTD---YGCFVEIEEGVEGLVHVSEMDWTNKNIHPSKVVNVGDVVEVMVLDID   90 (115)
T ss_dssp             SCEEEEEEEEEET---TEEEEECSTTCEEEEETTSSSCSSTTCSSTTTCCTTCEEEEEEEEEE
T ss_pred             CCEEEEEEEEEEC---CEEEEEECCCCEEEEEHHHCCccccccCcccEECCCCEEEEEEEEEE
Confidence            3568999999864   67444444458999999999542     1235899999999887743

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

Probab=90.44  E-value=1  Score=32.99  Aligned_cols=57  Identities=23%  Similarity=0.304  Sum_probs=41.9

Q ss_pred             cccceEEEEeeCCCcee-EEecCC--CCCceEEeccccccCC-----ccccCCCCcEEEEEEeCCCcc
Q 047168            5 TRSTGKVTWFDGAKGYG-FIRPDD--GGADLFVHQKSIKSDG-----YRTLYENQSVEFDVQLEADGK   64 (258)
Q Consensus         5 ~~~~G~vk~f~~~kGfG-FI~~~~--~~~dvF~H~s~l~~~~-----~~~l~~G~~V~F~v~~~~~G~   64 (258)
                      +.+.|+|+...   -|| ||..++  ...+-|+|+|.|....     ...+++||.|...|..-+.++
T Consensus        14 ~i~~G~V~~v~---~fG~FV~l~~~~~~~~Glvhisel~~~~~~~~~~~~~~~Gd~V~VkV~~vd~~~   78 (103)
T 2eqs_A           14 DIYNGKVTSIM---QFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGTK   78 (103)
T ss_dssp             CEEEEEEEEEC---SSCEEEEECSSSSCCEEEECGGGTSSSSCCCCHHHHCCTTCEEEEEEEEEETTE
T ss_pred             CEEEEEEEEEe---ccEEEEEEcCCCCCeEEEEEHHHCCCCcccCCcccEeCCCCEEEEEEEEEECCe
Confidence            56899999984   377 667665  2689999999994321     135899999999988765553

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

Probab=89.26  E-value=0.3  Score=45.10  Aligned_cols=66  Identities=17%  Similarity=0.384  Sum_probs=47.6

Q ss_pred             cceEEEEeeCCCceeEEecC-----CCCCceEEeccccccCCccccCCCCcEEEEEEeCCCcc--ceeeccccCCCCc
Q 047168            7 STGKVTWFDGAKGYGFIRPD-----DGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGK--YQALDVTAPGGAP   77 (258)
Q Consensus         7 ~~G~vk~f~~~kGfGFI~~~-----~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~--~~A~~V~~~~g~~   77 (258)
                      ..|++--.  ..||||+.+.     .+.+||||-.+.|+..+   |+.||.|+=.+.....+.  .....|..+.+.+
T Consensus        58 ~~g~le~~--~~g~gflr~~~~~y~~~~~d~yvs~~~ir~~~---lr~gd~v~g~~r~~~~~e~~~~l~~v~~vng~~  130 (427)
T 3l0o_A           58 GEGVLEIH--PEGFGFLRRIEDNLLPSNDDIYISPSQIRKFN---LNTGDIISGVIRKPKEGEKYFAMIKIEAINYRP  130 (427)
T ss_dssp             EEEEEEEC--TTSCEEEECGGGTTCCCSSCEEECHHHHHHTT---CCTTCEEEEEEECCCSSSCSEEEEEEEEETTEE
T ss_pred             EEEEEEEc--CCCceEeeCCccCCCCCCCCeeeCHHHHHhcC---CCCCCEEEEEEeCCCCCcccccceEEEecCCCC
Confidence            44555544  5799999877     46899999999998875   899999999888765542  2234455555543

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

Probab=88.19  E-value=0.77  Score=35.26  Aligned_cols=53  Identities=25%  Similarity=0.224  Sum_probs=39.0

Q ss_pred             cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCC----ccccCCCCcEEEEEEeC
Q 047168            5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDG----YRTLYENQSVEFDVQLE   60 (258)
Q Consensus         5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~----~~~l~~G~~V~F~v~~~   60 (258)
                      +.+.|+|+...+   ||+....+.+.+-|+|++.|...-    ...+.+||.|...|..-
T Consensus         9 ~iv~G~V~~i~~---~G~FV~l~~~~~Glihisel~~~~~~~~~~~~~vGd~V~vkV~~v   65 (130)
T 2k4k_A            9 SVYTGKVTGLQA---YGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQVKVLAV   65 (130)
T ss_dssp             CEEEEEEEEEET---TEEEEEEETTEEEEEEGGGTSSSCCSCGGGTCCTTCEEEEEEEEE
T ss_pred             CEEEEEEEEEeC---CeEEEEECCCcEEEEEHHHCCcccccCccccCCCCCEEEEEEEEE
Confidence            568999999843   565444444589999999996432    14589999999888764

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

Probab=88.12  E-value=0.6  Score=33.11  Aligned_cols=63  Identities=13%  Similarity=0.165  Sum_probs=40.4

Q ss_pred             ccceEEEEeeCCCceeEEecCCCC--------CceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccCC
Q 047168            6 RSTGKVTWFDGAKGYGFIRPDDGG--------ADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAPG   74 (258)
Q Consensus         6 ~~~G~vk~f~~~kGfGFI~~~~~~--------~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~~   74 (258)
                      ..+|+|+.++...    |+...+.        .-.-|.+.+  ...+..|++|+.|+|+++..+.|.++-+.|+..+
T Consensus         5 ~~~G~V~~vd~~~----iTi~H~pI~~l~wPaMTM~F~v~~--~~~l~~lk~Gd~V~F~~~~~~~g~~~it~i~~~~   75 (82)
T 2l55_A            5 RAVGRIQSIGERS----LIIAHEAIPSAQWGAMTMEFAAPP--AGLPQGLKAGDRVAFSFRLDPHGMATLVTVAPQV   75 (82)
T ss_dssp             EEEEEEEECCSSE----EEEEECCCTTTTCCCEEEEEECCT--TCCCSSCSTTCEEEEEEEEETTTEEEEEEEEECC
T ss_pred             EEeEEEEEEcccc----EEEecCCccccCCCceEEEEEcCC--hhHhhcCCCCCEEEEEEEECCCCeEEEEEEEecC
Confidence            3579999998765    6543221        122233322  2235679999999999999887447777776543

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

Probab=87.45  E-value=0.89  Score=36.47  Aligned_cols=53  Identities=13%  Similarity=0.137  Sum_probs=38.3

Q ss_pred             cccceEEEEeeCCCceeEEecCCCCCceEEeccccccC------Cc--------cccCCCCcEEEEEEeCC
Q 047168            5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSD------GY--------RTLYENQSVEFDVQLEA   61 (258)
Q Consensus         5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~------~~--------~~l~~G~~V~F~v~~~~   61 (258)
                      +.+.|+|+....   ||+...... .|.|+|+|.|...      ..        +.++.||.|++.+..-+
T Consensus        85 ev~~G~V~~v~~---fG~FV~l~~-~dglvhis~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd  151 (171)
T 1y14_B           85 EVVDGTVVSCSQ---HGFEVQVGP-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCI  151 (171)
T ss_dssp             CEEEEEEEEEET---TEEEEEETT-EEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEE
T ss_pred             CEEEEEEEEEec---CEEEEEecC-eEEEEEHHHCCCCceECcccCceEEeccceEECCCCEEEEEEEEEE
Confidence            568899999863   776654444 8999999998422      00        34788999999887643

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

Probab=86.54  E-value=1.4  Score=32.54  Aligned_cols=54  Identities=24%  Similarity=0.201  Sum_probs=39.1

Q ss_pred             ccccceEEEEeeCCCcee-EEecCCCCCceEEeccccccCC----ccccCCCCcEEEEEEeCC
Q 047168            4 LTRSTGKVTWFDGAKGYG-FIRPDDGGADLFVHQKSIKSDG----YRTLYENQSVEFDVQLEA   61 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfG-FI~~~~~~~dvF~H~s~l~~~~----~~~l~~G~~V~F~v~~~~   61 (258)
                      .+.+.|+|+...+   || ||..++ +.+-|+|++.|...-    ...+.+||.|...|..-+
T Consensus        32 G~iv~G~V~~v~~---~G~fV~l~~-~~~Gll~~sel~~~~~~~~~~~~~vGd~V~v~V~~vd   90 (109)
T 2khj_A           32 GAIVTGKVTAVDA---KGATVELAD-GVEGYLRASEASRDRVEDATLVLSVGDEVEAKFTGVD   90 (109)
T ss_dssp             SSEEEEEEEEECS---SCEEEECST-TCBCCBCTTCCCSSSSSSGGGSCCTTCEEEEEEEEEE
T ss_pred             CCEEEEEEEEEEC---CeEEEEECC-CCEEEEEHHHcCcccccChhhccCCCCEEEEEEEEEE
Confidence            3568999999953   45 455444 589999999996432    235889999998887753

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

Probab=85.55  E-value=1.6  Score=38.20  Aligned_cols=56  Identities=9%  Similarity=-0.015  Sum_probs=43.3

Q ss_pred             ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeec
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALD   69 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~   69 (258)
                      ...++|+|+...   -||++...+ +.++|+|.+.+..      .+||.|++.+..+.++++.|+.
T Consensus         7 G~~v~g~V~~~~---~~G~fv~~~-g~egllp~se~~~------~vGdevev~v~~d~~~r~iat~   62 (285)
T 3go5_A            7 ASFIVGLIIDEN---DRFYFVQKD-GQTYALAKEEGQH------TVGDTVKGFAYTDMKQKLRLTT   62 (285)
T ss_dssp             TEEEEEEEEEEC---SSEEEEEET-TEEEEEEGGGCCC------CTTSEEEEEEEECTTSCEEEEC
T ss_pred             CCEEEEEEEEEE---CCEEEEEcC-CeEEEEEHHHCcc------ccCCEEEEEEEECCCCCEEEec
Confidence            356889999885   366555444 6899999999942      8999999998888888777754

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

Probab=85.11  E-value=1.8  Score=35.23  Aligned_cols=54  Identities=6%  Similarity=-0.070  Sum_probs=36.9

Q ss_pred             ccccceEEEEeeCCCcee-EEecC-CCCCceEEeccccccCC----ccccCCCCcEEEEEEeC
Q 047168            4 LTRSTGKVTWFDGAKGYG-FIRPD-DGGADLFVHQKSIKSDG----YRTLYENQSVEFDVQLE   60 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfG-FI~~~-~~~~dvF~H~s~l~~~~----~~~l~~G~~V~F~v~~~   60 (258)
                      .+.+.|+|+...   -|| ||..+ ..+.+=|+|+|.|...-    ...+++||.|...|..-
T Consensus        16 G~iv~G~V~~I~---~fGaFV~L~e~~g~eGLvhiSels~~~v~~~~~~~~vGd~V~VkVl~v   75 (182)
T 1kl9_A           16 EDVVMVNVRSIA---EMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRV   75 (182)
T ss_dssp             TCEEEEEEEEEC---SSEEEEEETTTTTEEEEEEGGGC------------CTTCEEEEEEEEE
T ss_pred             CCEEEEEEEEEe---ccEEEEEEccCCCcEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEE
Confidence            367899999984   577 66664 34689999999996432    23578999999888764

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

Probab=85.02  E-value=2.1  Score=30.67  Aligned_cols=61  Identities=13%  Similarity=0.082  Sum_probs=39.4

Q ss_pred             ccceEEEEeeCCCceeEEecCCCC--------CceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccc
Q 047168            6 RSTGKVTWFDGAKGYGFIRPDDGG--------ADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVT   71 (258)
Q Consensus         6 ~~~G~vk~f~~~kGfGFI~~~~~~--------~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~   71 (258)
                      ..+|+|+.++...+-  |+...+.        .-.-|.+.  ....+..|++|+.|.|+++..+.+ +.-+.|+
T Consensus        17 ~~~G~V~~id~~~~~--iTi~H~pI~~l~wpaMTM~F~v~--~~~~l~~lk~Gd~V~F~~~~~~~~-~~it~i~   85 (88)
T 2vb2_X           17 SATGVVKGIDLESKK--ITIHHDPIAAVNWPEMTMRFTIT--PQTKMSEIKTGDKVAFNFVQQGNL-SLLQDIK   85 (88)
T ss_dssp             EEEEEEEEEETTTTE--EEEEECCBGGGTBCSEEEEEECC--TTCEECCCCTTCEEEEEEEEETTE-EEEEEEE
T ss_pred             EEEEEEEEEcCCCCE--EEEecCCcccCCCCceEEEEEcC--ChhhhhcCCCCCEEEEEEEEeCCE-EEEEEEE
Confidence            478999999877655  5544221        11223332  222356799999999999988765 6665554

>2a19_A EIF-2- alpha, eukaryotic translation initiation factor 2 alpha; transferase, protein biosynthesis, protein synthesis transferase complex; HET: TPO ANP; 2.50A {Saccharomyces cerevisiae} PDB: 2a1a_A* 1q46_A

Probab=84.44  E-value=1.5  Score=35.48  Aligned_cols=54  Identities=6%  Similarity=-0.068  Sum_probs=36.6

Q ss_pred             ccccceEEEEeeCCCcee-EEecC-CCCCceEEeccccccCC----ccccCCCCcEEEEEEeC
Q 047168            4 LTRSTGKVTWFDGAKGYG-FIRPD-DGGADLFVHQKSIKSDG----YRTLYENQSVEFDVQLE   60 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfG-FI~~~-~~~~dvF~H~s~l~~~~----~~~l~~G~~V~F~v~~~   60 (258)
                      .+.+.|+|+...   -|| ||..+ ..+.+-|+|+|.|...-    -..+++||.|...|..-
T Consensus        16 G~iv~G~V~~i~---~fGaFV~L~e~~gveGLvhiSels~~~v~~~~~~~~vGd~V~vkVl~v   75 (175)
T 2a19_A           16 DDIVMVNVQQIA---EMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRV   75 (175)
T ss_dssp             TCEEEEEEEEEE---TTEEEEEETTTTTCEEEEECC--------CCCCCCCTTSEEEEEEEEE
T ss_pred             CCEEEEEEEEEe---cceEEEEEcCCCCcEEEEEHHHcCCcccCCHHHcCCCCCEEEEEEEEE
Confidence            356899999883   477 66664 25689999999996432    24588999999988764

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

Probab=84.35  E-value=2.4  Score=29.73  Aligned_cols=61  Identities=13%  Similarity=0.082  Sum_probs=39.4

Q ss_pred             ccceEEEEeeCCCceeEEecCCCC--------CceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccc
Q 047168            6 RSTGKVTWFDGAKGYGFIRPDDGG--------ADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVT   71 (258)
Q Consensus         6 ~~~G~vk~f~~~kGfGFI~~~~~~--------~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~   71 (258)
                      ..+|+|+.++...+-  |+...+.        .-.-|.+.  ....+..|++|+.|.|+++..+.+ +.-+.|+
T Consensus         9 ~~~G~V~~id~~~~~--iTi~H~pI~~l~wpaMTM~F~v~--~~~~l~~lk~Gd~V~F~~~~~~~~-~~it~i~   77 (80)
T 2qcp_X            9 SATGVVKGIDLESKK--ITIHHDPIAAVNWPEMTMRFTIT--PQTKMSEIKTGDKVAFNFVQQGNL-SLLQDIK   77 (80)
T ss_dssp             EEEEEEEEEETTTTE--EEEEECCBGGGTBCSEEEEEECC--TTCEECCCCTTCEEEEEEEEETTE-EEEEEEE
T ss_pred             EEEEEEEEEcCCCCE--EEEEcCCcccCCCCceEEEEEcc--ChhhhhcCCCCCEEEEEEEEeCCE-EEEEEEE
Confidence            578999999877655  5544322        12223332  222356799999999999988765 6655554

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

Probab=82.15  E-value=3  Score=36.21  Aligned_cols=55  Identities=25%  Similarity=0.289  Sum_probs=41.3

Q ss_pred             ccccceEEEEeeCCCcee-EEecCC-CCCceEEeccccccCCc----cccCCCCcEEEEEEeCC
Q 047168            4 LTRSTGKVTWFDGAKGYG-FIRPDD-GGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLEA   61 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfG-FI~~~~-~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~~   61 (258)
                      .+.+.|+|+...+   || ||..++ .+.+-|+|+|.|...-+    ..+++||.|...|..-+
T Consensus        12 Gdiv~G~V~~I~~---fGaFV~L~e~~gieGlIhiSels~~~v~~~~~~~kvGd~V~vkVi~vD   72 (275)
T 3aev_A           12 GEFVVATVKRIHN---YGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVD   72 (275)
T ss_dssp             TCEEEEEEEEEET---TEEEEEETTSTTCEEEEEGGGSCSSCCSCGGGTCCTTCEEEEEEEEEE
T ss_pred             CCEEEEEEEEEEC---cEEEEEECCCCCeEEEEEHHHcCcccccCHHhccCCCCEEEEEEEEEE
Confidence            3578999999953   56 666664 46899999999964322    35889999999887743

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

Probab=80.97  E-value=0.8  Score=42.22  Aligned_cols=52  Identities=21%  Similarity=0.496  Sum_probs=40.7

Q ss_pred             cceEEEEeeCCCceeEEecC-----CCCCceEEeccccccCCccccCCCCcEEEEEEeCCCc
Q 047168            7 STGKVTWFDGAKGYGFIRPD-----DGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADG   63 (258)
Q Consensus         7 ~~G~vk~f~~~kGfGFI~~~-----~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G   63 (258)
                      ..|++--.  ..||||+.+.     .+.+||||-.+.|+..+   |+.||.|+=.+.....+
T Consensus        54 ~~g~le~~--~~g~gflr~~~~~~~~~~~d~yvs~~~ir~~~---lr~gd~v~g~~r~~~~~  110 (422)
T 3ice_A           54 GDGVLEIL--QDGFGFLRSADSSYLAGPDDIYVSPSQIRRFN---LRTGDTISGKIRPPKEG  110 (422)
T ss_dssp             EEEEEEEC--TTSCEEEECGGGTTCCCTTCEEBCHHHHHHHT---CCTTCEEEEEEECCCSS
T ss_pred             EEEEEEEc--CCCceEeeCCCcCCCCCCCCeeeCHHHHHhcC---CCCCCEEEEEEeCCCcc
Confidence            45666544  5799999874     36799999999998874   89999999888776544

>1luz_A Protein K3, protein K2; stranded anti-parallel beta barrel, viral protein; 1.80A {Vaccinia virus} SCOP: b.40.4.5

Probab=80.95  E-value=1.1  Score=31.95  Aligned_cols=53  Identities=19%  Similarity=0.214  Sum_probs=38.4

Q ss_pred             ccccceEEEEeeCCCcee-EEecCC-CCCceEEecc-ccccCCc----cccCCCCcEEEEEEeCC
Q 047168            4 LTRSTGKVTWFDGAKGYG-FIRPDD-GGADLFVHQK-SIKSDGY----RTLYENQSVEFDVQLEA   61 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfG-FI~~~~-~~~dvF~H~s-~l~~~~~----~~l~~G~~V~F~v~~~~   61 (258)
                      .+.+.|+|+ ..   .|| ||..++ ++.+-|+|+| .|...-+    ..+ .||.|+..+..-+
T Consensus        12 G~~~~G~V~-v~---~fG~FVel~~~~~~eGLvhis~el~~~~~~~~~~~~-~Gd~V~VkV~~vd   71 (88)
T 1luz_A           12 GDVIKGRVY-EK---DYALYIYLFDYPHFEAILAESVKMHMDRYVEYRDKL-VGKTVKVKVIRVD   71 (88)
T ss_dssp             TCEEEEEEE-EE---TTEEEEEETTCTTSEEEEGGGSSCCHHHHHHHHHHH-TTCEEEEEEEEEE
T ss_pred             CCEEEEEEE-EE---ccEEEEEECCCCCeEEEEEeeHHhCcccccCHhHEe-CCCEEEEEEEEEE
Confidence            356899999 63   466 777765 3689999999 9854321    235 8999999887743

---

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	258
d1h95a_	79	b.40.4.5 (A:) Y-box protein 1 cold shock domain (Y	1e-22
d1mjca_	69	b.40.4.5 (A:) Major cold shock protein {Escherichi	3e-22
d1g6pa_	66	b.40.4.5 (A:) Major cold shock protein {Thermotoga	4e-18
d1c9oa_	66	b.40.4.5 (A:) Major cold shock protein {Bacillus c	2e-17
d1wfqa_	89	b.40.4.5 (A:) Cold shock domain protein E1 (UNR) {	1e-10
d2exfa1	42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	7e-09
d2exfa1	42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	7e-07
d2exfa1	42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	9e-07
d2exfa1	42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	1e-06

>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 = 86.4 bits (214), Expect = 1e-22
 Identities = 30/74 (40%), Positives = 44/74 (59%), Gaps = 5/74 (6%)

Query: 5  TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDG----YRTLYENQSVEFDVQLE 60
          T+  G V WF+   GYGFI  +D   D+FVHQ +IK +      R++ + ++VEFDV  E
Sbjct: 7  TKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVV-E 65

Query: 61 ADGKYQALDVTAPG 74
           +   +A +VT PG
Sbjct: 66 GEKGAEAANVTGPG 79

>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 = 85.2 bits (211), Expect = 3e-22
 Identities = 32/67 (47%), Positives = 45/67 (67%), Gaps = 1/67 (1%)

Query: 6  RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKY 65
          + TG V WF+  KG+GFI PDDG  D+FVH  +I++DGY++L E Q V F ++  A G  
Sbjct: 3  KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGP- 61

Query: 66 QALDVTA 72
           A +VT+
Sbjct: 62 AAGNVTS 68

>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 = 74.0 bits (182), Expect = 4e-18
 Identities = 33/65 (50%), Positives = 42/65 (64%), Gaps = 2/65 (3%)

Query: 8  TGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQA 67
           GKV WFD  KGYGFI  D+GG D+FVH  +I+ +G++TL E Q VEF++Q E     QA
Sbjct: 2  RGKVKWFDSKKGYGFITKDEGG-DVFVHWSAIEMEGFKTLKEGQVVEFEIQ-EGKKGPQA 59

Query: 68 LDVTA 72
            V  
Sbjct: 60 AHVKV 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 = 72.5 bits (178), Expect = 2e-17
 Identities = 29/65 (44%), Positives = 41/65 (63%), Gaps = 2/65 (3%)

Query: 8  TGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQA 67
           GKV WF+  KGYGFI  + GG+D+FVH  +I+ +G++TL E Q V F++     G  QA
Sbjct: 3  RGKVKWFNNEKGYGFIEVE-GGSDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGNRGP-QA 60

Query: 68 LDVTA 72
           +V  
Sbjct: 61 ANVVK 65

>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 = 54.9 bits (132), Expect = 1e-10
 Identities = 20/72 (27%), Positives = 27/72 (37%), Gaps = 4/72 (5%)

Query: 5  TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDV-QLEADG 63
           R TG +        YGFI+  +  A LF H         + L     VEF+V      G
Sbjct: 17 LRETGVIEKLL--TSYGFIQCSERQARLFFHCSQYN-GNLQDLKVGDDVEFEVSSDRRTG 73

Query: 64 KYQALDVTAPGG 75
          K  A+ +    G
Sbjct: 74 KPIAVKLVKISG 85

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Length = 42

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

 Score = 48.3 bits (115), Expect = 7e-09
 Identities = 19/41 (46%), Positives = 26/41 (63%), Gaps = 3/41 (7%)

Query: 215 RCYNCGKSGHLARDCGAGGAGGGGSCFNCGKPGHFARECTK 255
           +C+NCGK GH AR+C    A     C+ CGK GH  ++CT+
Sbjct: 3   KCFNCGKEGHTARNC---RAPRKKGCWKCGKEGHQMKDCTE 40

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Length = 42

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

 Score = 42.5 bits (100), Expect = 7e-07
 Identities = 18/47 (38%), Positives = 23/47 (48%), Gaps = 9/47 (19%)

Query: 160 CYNCGDPEHFARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITR 206
           C+NCG   H AR+C   +           GC+KCG  GH  +DC  R
Sbjct: 4   CFNCGKEGHTARNCRAPR---------KKGCWKCGKEGHQMKDCTER 41

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Length = 42

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

 Score = 42.5 bits (100), Expect = 9e-07
 Identities = 18/49 (36%), Positives = 23/49 (46%), Gaps = 8/49 (16%)

Query: 129 VVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQQ 177
           V C+NC   GH AR C + R          GC+ CG   H  +DC  +Q
Sbjct: 2   VKCFNCGKEGHTARNCRAPR--------KKGCWKCGKEGHQMKDCTERQ 42

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Length = 42

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

 Score = 42.5 bits (100), Expect = 1e-06
 Identities = 17/40 (42%), Positives = 20/40 (50%), Gaps = 5/40 (12%)

Query: 190 CFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDC 229
           CF CG  GH AR+C            C+ CGK GH  +DC
Sbjct: 4   CFNCGKEGHTARNC-----RAPRKKGCWKCGKEGHQMKDC 38

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	258
d1mjca_	69	Major cold shock protein {Escherichia coli [TaxId:	99.91
d1h95a_	79	Y-box protein 1 cold shock domain (YB1-CSD) {Human	99.9
d1g6pa_	66	Major cold shock protein {Thermotoga maritima [Tax	99.88
d1c9oa_	66	Major cold shock protein {Bacillus caldolyticus [T	99.87
d1wfqa_	89	Cold shock domain protein E1 (UNR) {Human (Homo sa	99.72
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	99.42
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	99.18
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	97.9
d2ix0a2	79	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	97.64
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	97.59
d1a62a2	78	Rho termination factor, RNA-binding domain {Escher	96.79
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	96.2
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	96.2
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	95.83
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	95.12
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	93.9
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	90.57
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	90.44
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	90.14
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	89.34
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	89.1
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	88.62
d1u0la1	66	Probable GTPase EngC (YjeQ), N-terminal domain {Th	86.22
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	84.16
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	83.9
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	82.91
d2ix0a1	90	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	82.44
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	82.4
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	82.06

>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=99.91  E-value=9.7e-25  Score=152.99  Aligned_cols=68  Identities=47%  Similarity=0.848  Sum_probs=64.7

Q ss_pred             cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccC
Q 047168            5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAP   73 (258)
Q Consensus         5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~   73 (258)
                      .+++|+|||||.+||||||+++++++|||||+|+|...+++.|.+|++|+|++..+++| ++|++|+.+
T Consensus         2 ~r~~G~Vk~f~~~kGfGFI~~d~g~~diFvH~s~l~~~~~~~L~~G~~V~f~~~~~~~G-~~A~~V~~l   69 (69)
T d1mjca_           2 GKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKG-PAAGNVTSL   69 (69)
T ss_dssp             CCEEEEEEEEETTTTEEEEEETTSCCCEEEEGGGBCCTTTCCCCTTCEEEEEEECCSSS-CEEEEEEEC
T ss_pred             CCEEEEEEEEeCCCCEEEEEEcCCCccEEEEhHHhcccCCCcCCCCCEEEEEEEeCCCC-cEEEEEEeC
Confidence            57999999999999999999999999999999999999999999999999999999999 899999864

>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=1.2e-24  Score=156.30  Aligned_cols=70  Identities=43%  Similarity=0.776  Sum_probs=65.1

Q ss_pred             ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCC----ccccCCCCcEEEEEEeCCCccceeeccccCC
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDG----YRTLYENQSVEFDVQLEADGKYQALDVTAPG   74 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~----~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~~   74 (258)
                      +.+++|+|||||.+||||||+++++++|||||+++|...+    +++|.+|+.|+|++..+++| ++|++|+.|+
T Consensus         6 ~~r~~G~VKwfn~~KGfGFI~~ddg~~DvFvH~s~i~~~g~~~~~~~L~~G~~V~f~~~~~~~G-~~A~~Vtgpg   79 (79)
T d1h95a_           6 ATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKG-AEAANVTGPG   79 (79)
T ss_dssp             EEEEEEEEEEEETTTTEEEEEEGGGTEEEEEEGGGBCSCCCSCCSCSCCSSCEEEEEEEECSSS-EEEESBCCCC
T ss_pred             cCcccEEEEEEcCCCCeEEEEECCCCccEEEEhhHcccCCCcceeeecCCCCEEEEEEEeCCCC-CeeEEEeCCC
Confidence            4688999999999999999999999999999999998876    78899999999999999999 7999999764

>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=99.88  E-value=1.5e-23  Score=145.63  Aligned_cols=66  Identities=48%  Similarity=0.842  Sum_probs=62.0

Q ss_pred             cceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccCC
Q 047168            7 STGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAPG   74 (258)
Q Consensus         7 ~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~~   74 (258)
                      |+|+|||||.+||||||+++++ +|||||+|+|...+++.|.+|++|+|++..+++| ++|.+|++++
T Consensus         1 l~G~Vk~f~~~kGfGFI~~~~g-~diFvH~s~l~~~g~~~l~~G~~V~f~~~~~~~G-~~A~~V~~id   66 (66)
T d1g6pa_           1 MRGKVKWFDSKKGYGFITKDEG-GDVFVHWSAIEMEGFKTLKEGQVVEFEIQEGKKG-PQAAHVKVVE   66 (66)
T ss_dssp             CCEEEEEEETTTTEEEEEETTS-CBCBBCSSSSCCSSCCCCCSSSEEEEEEECSSSC-CEEEEEEEEC
T ss_pred             CeEEEEEEeCCCCeeEEEecCC-ceEEEEhHHhcccCCCcCCCCCEEEEEEEECCCC-CEEEEEEecC
Confidence            5899999999999999999885 6999999999999999999999999999999999 7999998764

>d1c9oa_ b.40.4.5 (A:) Major cold shock protein {Bacillus caldolyticus [TaxId: 1394]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Major cold shock protein
species: Bacillus caldolyticus [TaxId: 1394]

Probab=99.87  E-value=5.5e-23  Score=142.77  Aligned_cols=65  Identities=43%  Similarity=0.814  Sum_probs=60.5

Q ss_pred             cceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccC
Q 047168            7 STGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAP   73 (258)
Q Consensus         7 ~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~   73 (258)
                      .+|+|||||.+||||||++++ ++|||||+|+|...+++.|.+|++|+|++..+++| ++|++|+.+
T Consensus         2 ~~G~Vk~fn~~kGfGFI~~d~-g~DiF~H~s~l~~~~~~~L~~G~~V~f~~~~~~~G-~~A~~V~~l   66 (66)
T d1c9oa_           2 QRGKVKWFNNEKGYGFIEVEG-GSDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGNRG-PQAANVVKL   66 (66)
T ss_dssp             EEEEEEEEETTTTEEEEEETT-EEEEEEEGGGBCSSSCCCCCTTCEEEEEEEEETTE-EEEEEEEEC
T ss_pred             CCeEEEEEECCCCEEEEEecC-CceEEEEehhcccccCCcCCCCCEEEEEEEECCCC-CEEEEEEEC
Confidence            479999999999999999976 58999999999999999999999999999999999 899999853

>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=99.72  E-value=7e-18  Score=123.32  Aligned_cols=71  Identities=28%  Similarity=0.420  Sum_probs=62.2

Q ss_pred             CccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCC-ccceeeccccCCCC
Q 047168            3 QLTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEAD-GKYQALDVTAPGGA   76 (258)
Q Consensus         3 ~~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~-G~~~A~~V~~~~g~   76 (258)
                      .+++.+|+|+||+  +|||||+++++.+|||||+++|. .+++.|.+|++|+|++..+++ ++++|++|..+.+.
T Consensus        15 ~~~r~~G~I~~~~--~gfGFI~~~~~~~dvF~H~s~~~-~~~~~l~~G~~VeF~v~~~~kg~k~~Av~V~~~~~p   86 (89)
T d1wfqa_          15 AALRETGVIEKLL--TSYGFIQCSERQARLFFHCSQYN-GNLQDLKVGDDVEFEVSSDRRTGKPIAVKLVKISGP   86 (89)
T ss_dssp             CCCEEEEEEEEEC--SSEEEEEETTTTEEEEEETTTCS-SCTTTCCTTCCEEEEEEECSSSCCEEEEEEEESSCC
T ss_pred             ccceEEEEEEEec--CccceEEeCCCCceEEEEeehhh-ccCCcccCCCEEEEEEEECCCCCceEEEEEEECCCC
Confidence            3578999999994  69999999999999999999997 467889999999999999976 67889999877643

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

Probab=99.42  E-value=6.4e-14  Score=87.64  Aligned_cols=41  Identities=46%  Similarity=1.095  Sum_probs=33.0

Q ss_pred             CccccCCCCCccCCCCCCCCCCCCCccccCCCCCccCCCCCCCc
Q 047168          214 GRCYNCGKSGHLARDCGAGGAGGGGSCFNCGKPGHFARECTKVA  257 (258)
Q Consensus       214 ~~C~~Cg~~GH~~~~Cp~~~~~~~~~C~~Cg~~GH~~~~Cp~~~  257 (258)
                      ++||+|++.||++++||.++   ...||+|++.||++++||+++
T Consensus         2 i~C~~Cg~~GH~~~~Cp~~~---~~~C~~Cg~~GH~~~~Cp~rq   42 (42)
T d2exfa1           2 VKCFNCGKEGHTARNCRAPR---KKGCWKCGKEGHQMKDCTERQ   42 (42)
T ss_dssp             CCCTTTCCSSSCTTTCSSCC---CSSCSSSCCSSSCTTTCCSSC
T ss_pred             CccccCCCcCcCcccCcCCC---cCccccCCCCCeecccCCCCC
Confidence            47888888888888888764   346999999999999998763

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

Probab=99.18  E-value=1e-11  Score=77.43  Aligned_cols=39  Identities=41%  Similarity=1.063  Sum_probs=18.2

Q ss_pred             CcccccCCCCccccccccccCCCCCCCCCCCcccCCCCCCCCCCCCC
Q 047168          129 VVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPR  175 (258)
Q Consensus       129 ~~C~~Cg~~GH~a~~Cp~~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~  175 (258)
                      +.||+|++.||++++||.+        ....|++|++.||++++||+
T Consensus         2 i~C~~Cg~~GH~~~~Cp~~--------~~~~C~~Cg~~GH~~~~Cp~   40 (42)
T d2exfa1           2 VKCFNCGKEGHTARNCRAP--------RKKGCWKCGKEGHQMKDCTE   40 (42)
T ss_dssp             CCCTTTCCSSSCTTTCSSC--------CCSSCSSSCCSSSCTTTCCS
T ss_pred             CccccCCCcCcCcccCcCC--------CcCccccCCCCCeecccCCC
Confidence            3455555555555555531        12334444444444444443

>d1nc8a_ g.40.1.1 (A:) HIV nucleocapsid {Human immunodeficiency virus type 2 [TaxId: 11709]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 2 [TaxId: 11709]

Probab=97.90  E-value=2.6e-06  Score=46.51  Aligned_cols=20  Identities=60%  Similarity=1.164  Sum_probs=11.7

Q ss_pred             CccccCCCCCccCCCCCCCC
Q 047168          214 GRCYNCGKSGHLARDCGAGG  233 (258)
Q Consensus       214 ~~C~~Cg~~GH~~~~Cp~~~  233 (258)
                      ++||||+++||++++|..|+
T Consensus         7 ikCfNCGkeGH~ar~CrAPR   26 (29)
T d1nc8a_           7 IRCWNCGKEGHSARQCRAPR   26 (29)
T ss_dssp             CBCTTTSCBSSCGGGCCSSS
T ss_pred             eEeecCCccchhhhhccCcc
Confidence            45666666666666665554

>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=97.64  E-value=1.4e-05  Score=55.68  Aligned_cols=61  Identities=20%  Similarity=0.289  Sum_probs=45.0

Q ss_pred             ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccC
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAP   73 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~   73 (258)
                      ...+.|+|.-=  .+||||+.+++ .+|||+....+..     .-.||.|+..+... +++++|.-|.++
T Consensus        16 ~~~~~G~i~~~--~~G~GFv~~d~-~~DifI~~~~~~~-----A~~GD~V~v~i~~~-~~r~eg~I~~il   76 (79)
T d2ix0a2          16 TPRAEGVVKAT--EKGFGFLEVDA-QKSYFIPPPQMKK-----VMHGDRIIAVIHSE-KERESAEPEELV   76 (79)
T ss_dssp             SCEEEEEEECC--C--CEEEEEET-TEEEEECHHHHTT-----CCTTCEEEEEEECC---CCEEEEEEEE
T ss_pred             CCEEEEEEEEe--CCCcEEEEECC-CCcEEECHHHHcC-----CCCCCEEEEEEEeC-CCcEEEEEEEEe
Confidence            35678888764  79999999987 5899999999865     47899999998654 566777766654

>d1nc8a_ g.40.1.1 (A:) HIV nucleocapsid {Human immunodeficiency virus type 2 [TaxId: 11709]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 2 [TaxId: 11709]

Probab=97.59  E-value=9.5e-06  Score=44.24  Aligned_cols=22  Identities=45%  Similarity=0.895  Sum_probs=19.1

Q ss_pred             CCccccCCCCCccCCCCCCCcC
Q 047168          237 GGSCFNCGKPGHFARECTKVAN  258 (258)
Q Consensus       237 ~~~C~~Cg~~GH~~~~Cp~~~~  258 (258)
                      .+.||||+++||++++|-.+.+
T Consensus         6 ~ikCfNCGkeGH~ar~CrAPRk   27 (29)
T d1nc8a_           6 VIRCWNCGKEGHSARQCRAPRR   27 (29)
T ss_dssp             CCBCTTTSCBSSCGGGCCSSSS
T ss_pred             eeEeecCCccchhhhhccCccc
Confidence            5689999999999999987653

>d1a62a2 b.40.4.5 (A:48-125) Rho termination factor, RNA-binding domain {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Rho termination factor, RNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=96.79  E-value=0.00066  Score=46.58  Aligned_cols=64  Identities=20%  Similarity=0.435  Sum_probs=47.2

Q ss_pred             ceEEEEeeCCCceeEEecC-----CCCCceEEeccccccCCccccCCCCcEEEEEEeCCCcc--ceeeccccCCCC
Q 047168            8 TGKVTWFDGAKGYGFIRPD-----DGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGK--YQALDVTAPGGA   76 (258)
Q Consensus         8 ~G~vk~f~~~kGfGFI~~~-----~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~--~~A~~V~~~~g~   76 (258)
                      .|++--.  ..|||||...     .+.+||||..+.|+..+   |+.|+.|+=.+.....+.  +..+.|..+.+.
T Consensus         5 ~GiLei~--~dGyGFLR~~~~~y~~~~~DiyVs~s~Irrfg---LR~GD~V~G~vr~p~~~ek~~~L~~V~~VNG~   75 (78)
T d1a62a2           5 DGVLEIL--QDGFGFLRSADSSYLAGPDDIYVSPSQIRRFN---LRTGDTISGKIRPPKEGERYFALLKVNEVNFD   75 (78)
T ss_dssp             EEEEEEC--TTSCEEEECGGGTTCCCTTCEEECHHHHHHTT---CCTTCEEEEEEECCCTTCCSEEEEEEEEETTB
T ss_pred             EEEEEEc--CCCcEEeECCccCCCCCCcceEECHHHHHHhC---CCcCcEEEEEEECCCCCCCceeeEEEeeeCCc
Confidence            3444333  6899999973     35789999999999875   899999999998876553  345566655543

>d1dsqa_ g.40.1.1 (A:) Nucleic acid binding protein p14 {Mouse mammary tumor virus [TaxId: 11757]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Nucleic acid binding protein p14
species: Mouse mammary tumor virus [TaxId: 11757]

Probab=96.20  E-value=0.0014  Score=33.95  Aligned_cols=17  Identities=53%  Similarity=1.431  Sum_probs=9.0

Q ss_pred             ccccCCCCCccCCCCCC
Q 047168          215 RCYNCGKSGHLARDCGA  231 (258)
Q Consensus       215 ~C~~Cg~~GH~~~~Cp~  231 (258)
                      .|+.|++.||+.+||.+
T Consensus         4 vcfscgktghikkdck~   20 (26)
T d1dsqa_           4 VCFSCGKTGHIKRDCKE   20 (26)
T ss_dssp             BCTTTCCBSSCTTTTTC
T ss_pred             EEEecCCcccchhhhhh
Confidence            45555555555555544

>d1dsqa_ g.40.1.1 (A:) Nucleic acid binding protein p14 {Mouse mammary tumor virus [TaxId: 11757]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Nucleic acid binding protein p14
species: Mouse mammary tumor virus [TaxId: 11757]

Probab=96.20  E-value=0.0013  Score=34.06  Aligned_cols=20  Identities=50%  Similarity=1.270  Sum_probs=18.0

Q ss_pred             CCccccCCCCCccCCCCCCC
Q 047168          237 GGSCFNCGKPGHFARECTKV  256 (258)
Q Consensus       237 ~~~C~~Cg~~GH~~~~Cp~~  256 (258)
                      .+.||.|++.||+.+||.+.
T Consensus         2 gpvcfscgktghikkdck~e   21 (26)
T d1dsqa_           2 GPVCFSCGKTGHIKRDCKEE   21 (26)
T ss_dssp             CCBCTTTCCBSSCTTTTTCC
T ss_pred             CCEEEecCCcccchhhhhhh
Confidence            46899999999999999875

>d1a6bb_ g.40.1.1 (B:) Zinc finger protein ncp10 {Moloney murine leukemia virus, MoMLV [TaxId: 11801]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Zinc finger protein ncp10
species: Moloney murine leukemia virus, MoMLV [TaxId: 11801]

Probab=95.83  E-value=0.004  Score=36.13  Aligned_cols=19  Identities=37%  Similarity=0.870  Sum_probs=11.3

Q ss_pred             ccccCCCCCccCCCCCCCC
Q 047168          215 RCYNCGKSGHLARDCGAGG  233 (258)
Q Consensus       215 ~C~~Cg~~GH~~~~Cp~~~  233 (258)
                      .|--|.+.||.++|||...
T Consensus        12 QCAyCke~GHW~~dCPkkp   30 (40)
T d1a6bb_          12 QCAYCKEKGHWAKDCPKKP   30 (40)
T ss_dssp             SCSSSCCTTCCTTSCSSSC
T ss_pred             hhHHHhhcCchhhhCccCC
Confidence            4666666666666666543

>d1a6bb_ g.40.1.1 (B:) Zinc finger protein ncp10 {Moloney murine leukemia virus, MoMLV [TaxId: 11801]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Zinc finger protein ncp10
species: Moloney murine leukemia virus, MoMLV [TaxId: 11801]

Probab=95.12  E-value=0.011  Score=34.29  Aligned_cols=22  Identities=32%  Similarity=0.699  Sum_probs=14.9

Q ss_pred             CCCCcccccCCcccCcccCCCC
Q 047168          185 NNSGGCFKCGGYGHLARDCITR  206 (258)
Q Consensus       185 ~~~~~C~~Cg~~GH~~~~C~~~  206 (258)
                      .....|-.|.+.|||+++||..
T Consensus         8 L~kDQCAyCke~GHW~~dCPkk   29 (40)
T d1a6bb_           8 LDRDQCAYCKEKGHWAKDCPKK   29 (40)
T ss_dssp             CCSSSCSSSCCTTCCTTSCSSS
T ss_pred             ccchhhHHHhhcCchhhhCccC
Confidence            3456677777777777777764

>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=93.90  E-value=0.092  Score=34.90  Aligned_cols=58  Identities=28%  Similarity=0.268  Sum_probs=43.6

Q ss_pred             ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeC-CCcc
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLE-ADGK   64 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~-~~G~   64 (258)
                      .+.+.|+|+.+.+   ||.+...+...+-|+|.+.|...-.    ..+++|+.|++.+..- ++++
T Consensus         6 G~iv~G~V~~v~~---~G~fV~l~~~~~Glv~~sels~~~~~~~~~~~~~G~~v~v~Vi~id~~~r   68 (76)
T d1sroa_           6 GRVYTGKVTRIVD---FGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDRQGR   68 (76)
T ss_dssp             TSEEEEEEEEEET---TEEEEECSSSCCCBCCTTSSCSSCCSCHHHHCCTTCEEEEEEEECCTTCC
T ss_pred             CCEEEEEEEEEeC---cEEEEEeCCCCEEEEEhHHhCccccCCHHHccCCCCEEEEEEEEECCCCC
Confidence            4678999999974   6766656556899999999975532    2378999999998884 4443

>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=90.57  E-value=0.57  Score=31.14  Aligned_cols=54  Identities=9%  Similarity=-0.095  Sum_probs=39.4

Q ss_pred             ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCC-----ccccCCCCcEEEEEEeC
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDG-----YRTLYENQSVEFDVQLE   60 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~-----~~~l~~G~~V~F~v~~~   60 (258)
                      .+.+.|+|+....   ||++..-....+-|+|.+++....     ...+++||.|...|..-
T Consensus         6 Gd~V~G~V~~v~~---~g~~V~i~~~~~g~l~~se~s~~~~~~~~~~~~~vGd~V~~kV~~v   64 (83)
T d2ba0a1           6 GDVVIGIIREVAA---NGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNI   64 (83)
T ss_dssp             TCEEEEEEEEECS---SEEEEECSSSSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEE
T ss_pred             CCEEEEEEEEEEC---CEEEEecCCCeeEEEecccccccccccChhhhcccccEEEEEEEEE
Confidence            3678899999853   455544555689999999996432     23488999999888764

>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=90.44  E-value=0.59  Score=31.81  Aligned_cols=58  Identities=22%  Similarity=0.282  Sum_probs=46.4

Q ss_pred             cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc-------------cccCCCCcEEEEEEeCCCc
Q 047168            5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY-------------RTLYENQSVEFDVQLEADG   63 (258)
Q Consensus         5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~-------------~~l~~G~~V~F~v~~~~~G   63 (258)
                      .-+.|+|+...+.-.=-||.-... .+-|+|++++....+             ..|++|+.|-.+|...+.+
T Consensus         2 NIY~G~V~~V~pgl~AAFVDiG~~-k~gFL~~~di~~~~~~~~~~~~~~~~i~~~l~~G~~ilVQV~Ke~~~   72 (87)
T d1smxa_           2 NIYKGKITRIEPSLEAAFVDYGAE-RHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERG   72 (87)
T ss_dssp             CCEEEEEEEEEGGGTEEEEESSSS-SCEEEEGGGSCGGGCSSCCCSSSCCCGGGTCCTTCEEEEEEEECCBT
T ss_pred             CcEEEEEEEecCCceEEEEEeCCC-ccceeEecccceeeeccccccccccchhhhccCCCeEEEEEeecccC
Confidence            357899999999999999997764 899999998754321             2478999999999997543

>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=90.14  E-value=0.28  Score=33.08  Aligned_cols=54  Identities=6%  Similarity=-0.036  Sum_probs=36.7

Q ss_pred             ccccceEEEEeeCCCcee-EEecCC-CCCceEEeccccccCC----ccccCCCCcEEEEEEeC
Q 047168            4 LTRSTGKVTWFDGAKGYG-FIRPDD-GGADLFVHQKSIKSDG----YRTLYENQSVEFDVQLE   60 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfG-FI~~~~-~~~dvF~H~s~l~~~~----~~~l~~G~~V~F~v~~~   60 (258)
                      .+.+.|+|+...   -|| ||..++ .+-+-|+|.+.|....    ...+.+||.|+..|..-
T Consensus        14 G~iv~G~V~~i~---~~G~fV~l~~~~~i~G~i~~sels~~~~~~~~~~~~~Gd~v~~kV~~v   73 (86)
T d1kl9a2          14 EDVVMVNVRSIA---EMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRV   73 (86)
T ss_dssp             TCEEEEEEEEEC---SSEEEEEETTTTTEEEEEEGGGC------------CTTCEEEEEEEEE
T ss_pred             CCEEEEEEEEEe---CCeEEEEEecCCCEEEEEEeeeccccccccceEEeecccEEEEEEEEE
Confidence            356889999984   478 677664 3579999999996543    23477899999888773

>d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=89.34  E-value=0.32  Score=32.55  Aligned_cols=53  Identities=25%  Similarity=0.290  Sum_probs=38.6

Q ss_pred             cccceEEEEeeCCCcee-EEecCC-CCCceEEeccccccCC----ccccCCCCcEEEEEEeC
Q 047168            5 TRSTGKVTWFDGAKGYG-FIRPDD-GGADLFVHQKSIKSDG----YRTLYENQSVEFDVQLE   60 (258)
Q Consensus         5 ~~~~G~vk~f~~~kGfG-FI~~~~-~~~dvF~H~s~l~~~~----~~~l~~G~~V~F~v~~~   60 (258)
                      +.++|+|+...+   || ||+.++ ++-+-|+|.+.|...-    ...+++|+.|++.|..-
T Consensus        13 ~iv~G~V~~v~~---~G~fV~l~~~~gi~Gli~~sels~~~~~~~~~~~~~G~~v~~kV~~v   71 (84)
T d2ahob2          13 EILIATVKQVFD---YGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRV   71 (84)
T ss_dssp             CCCEEEEEEEET---TEEEEEETTTTTEEEEECGGGCC-----CHHHHTCSSCEEECEEEEE
T ss_pred             CEEEEEEEEEEC---CEEEEEECCcCCEEEEEEccccccccccccceEeecccEEEEEEEEE
Confidence            578999999853   56 566554 4578999999997643    23478999999998774

>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=89.10  E-value=0.46  Score=33.41  Aligned_cols=52  Identities=17%  Similarity=0.073  Sum_probs=39.2

Q ss_pred             cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc---------------cccCCCCcEEEEEEeC
Q 047168            5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY---------------RTLYENQSVEFDVQLE   60 (258)
Q Consensus         5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~---------------~~l~~G~~V~F~v~~~   60 (258)
                      +.+.|+|+..+   -|||....+ +-|-|||++.|....+               ..+.+|+.|...|..-
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            56789999986   345444444 4899999999986543               5689999999888764

>d1y14b1 b.40.4.5 (B:81-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.62  E-value=0.59  Score=31.65  Aligned_cols=53  Identities=11%  Similarity=0.128  Sum_probs=38.1

Q ss_pred             ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCC--------------ccccCCCCcEEEEEEeC
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDG--------------YRTLYENQSVEFDVQLE   60 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~--------------~~~l~~G~~V~F~v~~~   60 (258)
                      .+.+.|+|+..+ ..|+ |++..  .-|.|+|.+.|..+-              -+.++.|+.|++.+..-
T Consensus         4 Gev~~g~I~~v~-~~G~-fv~lg--~~eg~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~v   70 (91)
T d1y14b1           4 GEVVDGTVVSCS-QHGF-EVQVG--PMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGC   70 (91)
T ss_dssp             TCEEEEEEEEEE-TTEE-EEEET--TEEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEE
T ss_pred             CCEEEEEEEEEE-eeEE-EEEEc--CeEEEEEhhhcCcceEEccccceeEecccCeEEeCCCEEEEEEEEE
Confidence            456789999996 5555 66663  469999999996431              12578888888887764

>d1u0la1 b.40.4.5 (A:3-68) Probable GTPase EngC (YjeQ), N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Probable GTPase EngC (YjeQ), N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=86.22  E-value=1.1  Score=28.76  Aligned_cols=56  Identities=16%  Similarity=0.331  Sum_probs=36.8

Q ss_pred             cccceEEEEeeCCCceeEEecCCCCCceEEeccc-cccCCccccCCCCcEEEEEEeCCCc
Q 047168            5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKS-IKSDGYRTLYENQSVEFDVQLEADG   63 (258)
Q Consensus         5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~-l~~~~~~~l~~G~~V~F~v~~~~~G   63 (258)
                      |+.+|+|...  ..+|=+|..++.++.+--+... |.... ..+.+||.|+|+......|
T Consensus         1 m~~~G~Vi~~--~~~~y~V~~~e~g~~~~c~~rG~lr~~~-~~~~VGD~V~~~~~~~~~g   57 (66)
T d1u0la1           1 LRRRGIVVSF--HSNMVTVEDEETGERILCKLRGKFRLQN-LKIYVGDRVEYTPDETGSG   57 (66)
T ss_dssp             CCEEEEEEEE--ETTEEEEEETTTCCEEEEEECGGGTTTT-CCCCTTCEEEEECCCSSSE
T ss_pred             CCeeEEEEEE--ECCEEEEEECCCCcEEEEEeeccccccC-CccccCCEEEEEECCCCeE
Confidence            4567888776  4666677766554555566654 33333 3489999999987655554

>d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=84.16  E-value=1.2  Score=29.83  Aligned_cols=54  Identities=13%  Similarity=0.055  Sum_probs=39.6

Q ss_pred             ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCC-------ccccCCCCcEEEEEEeC
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDG-------YRTLYENQSVEFDVQLE   60 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~-------~~~l~~G~~V~F~v~~~   60 (258)
                      .+.+.|+|+...   .||++..-...-+-|+|+++|...-       ...+++||.|+..|..-
T Consensus         8 Gdiv~G~V~~i~---~~g~fV~i~~~~~gll~~s~~~~~~~~~~~~~~~~~~~Gd~v~~kV~~v   68 (87)
T d2je6i1           8 NDIVIGLVEDVE---IYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENF   68 (87)
T ss_dssp             TCEEEEEEEEEC---SSEEEEECSSSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEE
T ss_pred             CCEEEEEEEEEE---CCEEEEEeCCCEEEEEehHHhCCceeccccccchhhcccceEEEEEEEE
Confidence            356889999985   3555554555689999999996431       23488999999998764

>d2c35b1 b.40.4.5 (B:78-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {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: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.90  E-value=1.1  Score=30.48  Aligned_cols=52  Identities=15%  Similarity=0.215  Sum_probs=36.6

Q ss_pred             ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCC-c---------------cccCCCCcEEEEEEe
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDG-Y---------------RTLYENQSVEFDVQL   59 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~-~---------------~~l~~G~~V~F~v~~   59 (258)
                      .+.+.|+|+..+ ..|+ |++. . .-|.|+|.+.|..+- |               ..++.|+.|.+.|..
T Consensus         5 Gev~~g~V~~v~-~~G~-fv~l-g-~~~~~v~~~~l~~d~~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV~~   72 (94)
T d2c35b1           5 GEVVDAVVTQVN-KVGL-FTEI-G-PMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVG   72 (94)
T ss_dssp             TCEEEEEEEEEE-TTEE-EEEE-T-TEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEE
T ss_pred             CCEEEEEEEEEE-eeEE-EEEe-c-CceEEEEhhhcCcceeecccccceEEEcccceEEEeCCCEEEEEEEE
Confidence            356789999986 4444 5555 3 469999999997653 2               246778888888775

>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=82.91  E-value=1.5  Score=31.23  Aligned_cols=56  Identities=16%  Similarity=0.072  Sum_probs=41.2

Q ss_pred             ccccceEEEEeeCCCceeEEecC-CCCCceEEeccccccC-----CccccCCCCcEEEEEEeCCC
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPD-DGGADLFVHQKSIKSD-----GYRTLYENQSVEFDVQLEAD   62 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~-~~~~dvF~H~s~l~~~-----~~~~l~~G~~V~F~v~~~~~   62 (258)
                      .+.++|+|+...   -||++... ...-+=|+|++.|...     ....|++|+.|+..|..-+.
T Consensus        22 G~iv~G~V~~i~---~~G~~V~lg~~~~~G~l~~~els~~~~~~~~~~~~~vGq~v~~~V~~vd~   83 (119)
T d1wi5a_          22 GMLLTGTVSSLE---DHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKG   83 (119)
T ss_dssp             TCEEEEEEEEEC---SSEEEEECCCSSCEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCT
T ss_pred             CCEEEEEEEEEe---ccEEEEEEeccccceEEeHHHhccccccCCHHHhcccceEEEEEEEEEeC
Confidence            467899999994   44665554 3456899999998532     23468999999999888654

>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=82.44  E-value=4.1  Score=27.34  Aligned_cols=65  Identities=15%  Similarity=0.051  Sum_probs=45.0

Q ss_pred             ccceEEEEeeCCCceeEEecCCCC--CceEEeccccccCCccccCCCCcEEEEEEeCC-C-cc-ceeeccccCCCC
Q 047168            6 RSTGKVTWFDGAKGYGFIRPDDGG--ADLFVHQKSIKSDGYRTLYENQSVEFDVQLEA-D-GK-YQALDVTAPGGA   76 (258)
Q Consensus         6 ~~~G~vk~f~~~kGfGFI~~~~~~--~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~-~-G~-~~A~~V~~~~g~   76 (258)
                      +..|++   -..++|+||.+|+..  .|||+--......   .+++|+.|.-++..=+ + .+ ++|.-+..++..
T Consensus         3 rfVGr~---~~~~~~~fVvPd~~ri~~~I~I~~~~~~~~---~ak~Gd~Vvvei~~~P~~~~~~~~g~I~evlG~~   72 (90)
T d2ix0a1           3 RFVGKV---QGKNDRLAIVPDHPLLKDAIPCRAARGLNH---EFKEGDWAVAEMRRHPLKGDRSFYAELTQYITFG   72 (90)
T ss_dssp             EEEEEE---ESCSSSEEEEESCTTCCSCEEEEECTTCCC---CCCTTCEEEEEEEECGGGTCSSCEEEEEEECCCT
T ss_pred             cEEEEE---EEeCCEEEEEeCCCcccccccccccccccc---cCCCCCEEEEEEEeCCCCCCCCceEEEEEEEecC
Confidence            445555   468899999999874  6788866554322   3799999999998854 2 22 467666666543

>d2z0sa1 b.40.4.5 (A:60-147) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

Probab=82.40  E-value=2  Score=28.55  Aligned_cols=57  Identities=5%  Similarity=-0.082  Sum_probs=41.0

Q ss_pred             ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc--------cccCCCCcEEEEEEeC-CCc
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY--------RTLYENQSVEFDVQLE-ADG   63 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~--------~~l~~G~~V~F~v~~~-~~G   63 (258)
                      .+.+.|+|+...   .||+.-.-....+-|+|.+++.....        ..+++||.|...|..- +++
T Consensus         8 GdvV~G~V~~v~---~~g~fV~i~~~~~g~l~~se~~~~~~~~~~~~~~~~~~vGd~V~~kV~~vd~~~   73 (88)
T d2z0sa1           8 GDVVIGLIQSVG---IMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDKTR   73 (88)
T ss_dssp             TCCEEEEEEEEC---SSEEEEECSSSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECTTS
T ss_pred             CCEEEEEEEEEE---CCeEEEEeCCCeEEEEehHHhCcccccccccchhhhcccCcEEEEEEEEECCCC
Confidence            356889999874   35555545556899999999965432        3478999999888874 444

>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=82.06  E-value=2.1  Score=28.98  Aligned_cols=54  Identities=19%  Similarity=0.109  Sum_probs=41.4

Q ss_pred             ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCC----ccccCCCCcEEEEEEeC
Q 047168            4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDG----YRTLYENQSVEFDVQLE   60 (258)
Q Consensus         4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~----~~~l~~G~~V~F~v~~~   60 (258)
                      .+.+.|+|+....   ||.+.....+-+-|+|.++|...-    ...+.+|+.|...|..-
T Consensus        19 G~iv~g~V~~v~~---~G~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~vGq~v~~~V~~i   76 (94)
T d3bzka4          19 GMVLEGVVTNVTN---FGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEV   76 (94)
T ss_dssp             TCEEEEEEEEEET---TEEEEECSSSSCEEEEGGGGCSSCCSCHHHHCCTTCEEEEEEEEE
T ss_pred             CCEEEEEEEEEEC---cEEEEEeCCCceEEeehhhhhcccccChhhhhccCcEEEEEEEEE
Confidence            4578999999973   677766666789999999996433    23577999999987774