Citrus Sinensis ID: 044309

---

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
YNYLCTLPLSIIYTYLHRKQQNAQHHTTLHCLADSLSGCLKTLILVPTPFEFSRENAKAKKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTREVKEIGPDGQEVTKVVPAVTEEVKDAL
Secondary Structure (PSIPRED)
cccEEEEEcccEEEEEEccccccccccccHHHHHHHcccccEEEEEcEEEEccccccccccccccccccccccHHHHHHHHHcccccccEEEEEEEEEEccEEEEEEEEcccEEEEEEHHHHHHHHHcccHHHHccccEEEEEEEEEEccccEEEEEcccccHHHHHHHHHHcccccEEHHHHHHHHHHHcccHHHHHHHHHHHHHHHHccHHHHHHHHHHccccccccccccHHcccccccccccccccccHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEccccccccccccccccccccccccccccccccEEEcccccccccEEEEEEEEHHHccEEEEEEcccccccEEEHHHHHHHHHHHHHHHHHccccEEEEEEEEcccccEEEcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHcHHHHHHHHHHHccHHHHccccHHHHHHHHHHHccccccccccHHHHHHc
Coil and Loop (DISEMBL)
ynylctlpLSIIYTYLHrkqqnaqhHTTLHCLADSLSGCLKTlilvptpfefsRENAKakklseqpimashspnlecrmyearypevDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLikvgriepvmVLRVdkekgyidlskrrvsEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGwplywkyghafeAFKIivtdpdsvlNSLTREvkeigpdgqevtkVVPAVTEEVKDAL
Flexible Loop (DISEMBL)
YNYLCTLPLSIIYTYLHRKQQNAQHHTTLHCLADSLSGCLKTLILVPTPFEFSRENAkakklseqpimashspnlECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVsslikvgriepvmvlrvdkekgyidlskrrvseediqACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTREvkeigpdgqevtkvvpavtEEVKDAL
Low Complexity Region (SEG)
YNYLCTLPLSIIYTYLHRKQQNAQHHTTLHCLADSLSGCLKTLILVPTPFEFSRENAKAKKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSElsrrrirsvssliKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTREVKEIGPDGQEVTKVVPAVTEEVKDAL
Disordered region (IsUnstruct)
**YLCTLPLSIIYTYLHRKQQNAQHHTTLHCLADSLSGCLKTLILVPTPFEF**********************LECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLT****************************
Disordered Region (DISOPRED)
YNYLCTLPLSIIYTYLHRKQQN**************SGCLKTLILVPTPFEFSREN*K**KL****IM***SP****RMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTREVKEIGPDGQEVTKVVPAV********
Disordered Region (DISEMBL)
YNYLCTLPLSIIYTYLHRKQQNAQHHTTLHCLADSLSGCLKTLILVPTPFEFSRENAKAKKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTREVKEIGPDGQEVTKVVPAVTEEVKDAL
Disordered Region (DISPRO)
YNYLCTLPLSIIYTYLHRKQQNAQHHTTLHCLADSLSGCLKTLILVPTPFEFS********LS**PIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTREVKEIGPDGQEVTKVVPAVTEEVK*AL
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
YNYLCTLPLSIIYTYLHRKQQNAQHHTTLHCLADSLSGCLKTLILVPTPFEFSRENAKAKKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTREVKEIGPDGQEVTKVVPAVTEEVKDAL
Positional Conservation
no confident homologs detected

---

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	259	2.2.26 [Sep-21-2011]
P56286	306	Eukaryotic translation in	yes	no	0.594	0.503	0.675	4e-58
P20459	304	Eukaryotic translation in	yes	no	0.563	0.480	0.671	4e-53
Q869N9	341	Eukaryotic translation in	yes	no	0.594	0.451	0.587	1e-47
Q6GL89	315	Eukaryotic translation in	yes	no	0.606	0.498	0.590	6e-47
P41374	341	Eukaryotic translation in	yes	no	0.625	0.475	0.563	1e-46
Q7ZTK4	315	Eukaryotic translation in	N/A	no	0.606	0.498	0.572	2e-46
Q5R493	315	Eukaryotic translation in	yes	no	0.606	0.498	0.584	2e-46
P68101	315	Eukaryotic translation in	yes	no	0.606	0.498	0.584	2e-46
Q6ZWX6	315	Eukaryotic translation in	yes	no	0.606	0.498	0.584	2e-46
P68102	315	Eukaryotic translation in	yes	no	0.606	0.498	0.584	2e-46

>sp|P56286|IF2A_SCHPO Eukaryotic translation initiation factor 2 subunit alpha OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=tif211 PE=1 SV=1

 Score =  224 bits (572), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 104/154 (67%), Positives = 124/154 (80%)

Query: 77  CRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKV 136
           CRMYE R+PEVD  V++ V+ I +MGAYV LLEY+NIEGM+L SELSRRRIRSV   I+V
Sbjct: 6   CRMYENRFPEVDELVVVNVRQIQEMGAYVKLLEYDNIEGMVLLSELSRRRIRSVQKHIRV 65

Query: 137 GRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEE 196
           GR E V+VLRVDKEKGYIDLSKRRVS ED+  CEER+NKSK VHSIMRH+AE   + LE 
Sbjct: 66  GRNEVVVVLRVDKEKGYIDLSKRRVSPEDVVKCEERFNKSKAVHSIMRHIAEKHNVPLET 125

Query: 197 LYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSL 230
           +Y  IGWPLY KYGHA++AFK+ +++PD V   L
Sbjct: 126 MYTTIGWPLYRKYGHAYDAFKLAISNPDHVFEGL 159

eIF-2 functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. This complex binds to a 40S ribosomal subunit, followed by mRNA binding to form a 43S preinitiation complex. Junction of the 60S ribosomal subunit to form the 80S initiation complex is preceded by hydrolysis of the GTP bound to eIF-2 and release of an eIF-2-GDP binary complex. In order for eIF-2 to recycle and catalyze another round of initiation, the GDP bound to eIF-2 must exchange with GTP by way of a reaction catalyzed by eIF-2B.
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|P20459|IF2A_YEAST Eukaryotic translation initiation factor 2 subunit alpha OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SUI2 PE=1 SV=1

 Score =  207 bits (528), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 98/146 (67%), Positives = 116/146 (79%)

Query: 77  CRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKV 136
           CR YE +YPE+D  VM+ V+ IA+MGAYV LLEY+NIEGMIL SELSRRRIRS+  LI+V
Sbjct: 6   CRFYENKYPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRV 65

Query: 137 GRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEE 196
           G+ +  +VLRVDKEKGYIDLSKRRVS EDI  CEE+Y KSK VHSI+R+ AE   I LEE
Sbjct: 66  GKNDVAVVLRVDKEKGYIDLSKRRVSSEDIIKCEEKYQKSKTVHSILRYCAEKFQIPLEE 125

Query: 197 LYVNIGWPLYWKYGHAFEAFKIIVTD 222
           LY  I WPL  K+GHA+EAFK+ + D
Sbjct: 126 LYKTIAWPLSRKFGHAYEAFKLSIID 151

eIF-2 functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. This complex binds to a 40S ribosomal subunit, followed by mRNA binding to form a 43S preinitiation complex. Junction of the 60S ribosomal subunit to form the 80S initiation complex is preceded by hydrolysis of the GTP bound to eIF-2 and release of an eIF-2-GDP binary complex. In order for eIF-2 to recycle and catalyze another round of initiation, the GDP bound to eIF-2 must exchange with GTP by way of a reaction catalyzed by eIF-2B.

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

>sp|Q869N9|IF2A_DICDI Eukaryotic translation initiation factor 2 subunit 1 OS=Dictyostelium discoideum GN=eif2s1 PE=1 SV=1

 Score =  189 bits (481), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 94/160 (58%), Positives = 123/160 (76%), Gaps = 6/160 (3%)

Query: 76  ECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIK 135
           +CRMYE +YPE +  VM+++++I DMG YVSLLEYNNIEGMIL SE+SRRRIRS++ L++
Sbjct: 6   DCRMYEKKYPEENELVMVRIESIGDMGVYVSLLEYNNIEGMILLSEISRRRIRSINKLVR 65

Query: 136 VGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLG---- 191
           VG+ E V+V+RVDK+KGYIDLSKRRV+ E+   CEER++KSK VH I+R+VA  L     
Sbjct: 66  VGKTEAVVVVRVDKDKGYIDLSKRRVTPEEYAQCEERFHKSKAVHGIVRYVATKLSTEDN 125

Query: 192 -IDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSL 230
            +  + LY    WPLY KYGHA+EAFK+ +T+P SV N  
Sbjct: 126 VVKTKHLYTKFVWPLYTKYGHAYEAFKLSITEP-SVFNGF 164

eIF-2 functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. This complex binds to a 40S ribosomal subunit, followed by mRNA binding to form a 43S preinitiation complex. Junction of the 60S ribosomal subunit to form the 80S initiation complex is preceded by hydrolysis of the GTP bound to eIF-2 and release of an eIF-2-GDP binary complex. In order for eIF-2 to recycle and catalyze another round of initiation, the GDP bound to eIF-2 must exchange with GTP by way of a reaction catalyzed by eIF-2B.

Dictyostelium discoideum (taxid: 44689)

>sp|Q6GL89|IF2A_XENTR Eukaryotic translation initiation factor 2 subunit 1 OS=Xenopus tropicalis GN=eif2s1 PE=2 SV=1

 Score =  187 bits (475), Expect = 6e-47,   Method: Compositional matrix adjust.
 Identities = 98/166 (59%), Positives = 122/166 (73%), Gaps = 9/166 (5%)

Query: 73  PNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSS 132
           P L CR Y+ ++PEVD  VM+ V++IA+MGAYVSLLEYNNIEGMIL SELSRRRIRS++ 
Sbjct: 2   PALSCRFYQHKFPEVDDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINK 61

Query: 133 LIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGI 192
           LI++GR E V+V+RVDK+KGYIDLSKRRVS E+   CE+++ KSK V+SI+RHVAE L  
Sbjct: 62  LIRIGRNECVVVIRVDKDKGYIDLSKRRVSPEEALKCEDKFTKSKTVYSILRHVAEVLEY 121

Query: 193 ----DLEELYVNIGWPLYWKYGH----AFEAFKIIVTDPDSVLNSL 230
                LE LY    W    KY      A++AFK  V+DPD VL+ L
Sbjct: 122 TKDEQLESLYQRTAWVFDEKYKKPGYGAYDAFKHAVSDPD-VLDGL 166

Functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. This complex binds to a 40S ribosomal subunit, followed by mRNA binding to form a 43S preinitiation complex. Junction of the 60S ribosomal subunit to form the 80S initiation complex is preceded by hydrolysis of the GTP bound to eIF-2 and release of an eIF-2-GDP binary complex. In order for eIF-2 to recycle and catalyze another round of initiation, the GDP bound to eIF-2 must exchange with GTP by way of a reaction catalyzed by eIF-2B.

Xenopus tropicalis (taxid: 8364)

>sp|P41374|IF2A_DROME Eukaryotic translation initiation factor 2 subunit 1 OS=Drosophila melanogaster GN=eIF-2alpha PE=2 SV=1

 Score =  186 bits (473), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 97/172 (56%), Positives = 126/172 (73%), Gaps = 10/172 (5%)

Query: 75  LECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLI 134
           L  R Y  RYPE++  VM+ V +IA+MGAYV LLEYNNIEGMIL SELSRRRIRS++ LI
Sbjct: 3   LTSRFYNERYPEIEDVVMVNVLSIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLI 62

Query: 135 KVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGID- 193
           +VG+ EPV+V+RVDKEKGYIDLSKRRVS ED++ C ER+ K+K ++S++RHVA+ LG + 
Sbjct: 63  RVGKTEPVVVIRVDKEKGYIDLSKRRVSPEDVEKCTERFAKAKAINSLLRHVADILGFEG 122

Query: 194 ---LEELYVNIGWPLYWKYGH---AFEAFKIIVTDPDSVLN--SLTREVKEI 237
              LE+LY    W    KY +   A++ FK  VTDP +V +  +L  E KE+
Sbjct: 123 NEKLEDLYQKTAWHFEKKYNNKTVAYDIFKQSVTDP-TVFDECNLEPETKEV 173

eIF-2 functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. This preinitiation complex mediates ribosomal recognition of a start codon during the scanning process of the leader region.

Drosophila melanogaster (taxid: 7227)

>sp|Q7ZTK4|IF2A_XENLA Eukaryotic translation initiation factor 2 subunit 1 OS=Xenopus laevis GN=eif2s1 PE=2 SV=1

 Score =  186 bits (472), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 95/166 (57%), Positives = 122/166 (73%), Gaps = 9/166 (5%)

Query: 73  PNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSS 132
           P L CR Y+ ++PEVD  VM+ V++IA+MGAYVSLLEYNNIEGMIL SELSRRRIRS++ 
Sbjct: 2   PGLNCRFYQHKFPEVDDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINK 61

Query: 133 LIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGI 192
           LI++GR E V+V+RVDK+KGYIDLSKRRVS E+   CE+++ KSK V+SI+RHVAE L  
Sbjct: 62  LIRIGRNECVVVIRVDKDKGYIDLSKRRVSPEEALKCEDKFTKSKTVYSILRHVAEVLDY 121

Query: 193 ----DLEELYVNIGWPLYWKYGH----AFEAFKIIVTDPDSVLNSL 230
                L+ L+    W    KY      A++AFK  V+DPD +L+ L
Sbjct: 122 TKDEQLDSLFQRTAWVFDEKYKKPGYGAYDAFKNAVSDPD-ILDGL 166

Functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. This complex binds to a 40S ribosomal subunit, followed by mRNA binding to form a 43S preinitiation complex. Junction of the 60S ribosomal subunit to form the 80S initiation complex is preceded by hydrolysis of the GTP bound to eIF-2 and release of an eIF-2-GDP binary complex. In order for eIF-2 to recycle and catalyze another round of initiation, the GDP bound to eIF-2 must exchange with GTP by way of a reaction catalyzed by eIF-2B.

Xenopus laevis (taxid: 8355)

>sp|Q5R493|IF2A_PONAB Eukaryotic translation initiation factor 2 subunit 1 OS=Pongo abelii GN=EIF2S1 PE=2 SV=1

 Score =  186 bits (472), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 97/166 (58%), Positives = 123/166 (74%), Gaps = 9/166 (5%)

Query: 73  PNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSS 132
           P L CR Y+ ++PEV+  VM+ V++IA+MGAYVSLLEYNNIEGMIL SELSRRRIRS++ 
Sbjct: 2   PGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINK 61

Query: 133 LIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGI 192
           LI++GR E V+V+RVDKEKGYIDLSKRRVS E+   CE+++ KSK V+SI+RHVAE L  
Sbjct: 62  LIRIGRNERVVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEY 121

Query: 193 ----DLEELYVNIGWPLYWKYGH----AFEAFKIIVTDPDSVLNSL 230
                LE L+    W    KY      A++AFK  V+DP S+L+SL
Sbjct: 122 TKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDP-SILDSL 166

Functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. This complex binds to a 40S ribosomal subunit, followed by mRNA binding to form a 43S preinitiation complex. Junction of the 60S ribosomal subunit to form the 80S initiation complex is preceded by hydrolysis of the GTP bound to eIF-2 and release of an eIF-2-GDP binary complex. In order for eIF-2 to recycle and catalyze another round of initiation, the GDP bound to eIF-2 must exchange with GTP by way of a reaction catalyzed by eIF-2B.

Pongo abelii (taxid: 9601)

>sp|P68101|IF2A_RAT Eukaryotic translation initiation factor 2 subunit 1 OS=Rattus norvegicus GN=Eif2s1 PE=1 SV=2

 Score =  186 bits (471), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 97/166 (58%), Positives = 123/166 (74%), Gaps = 9/166 (5%)

Query: 73  PNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSS 132
           P L CR Y+ ++PEV+  VM+ V++IA+MGAYVSLLEYNNIEGMIL SELSRRRIRS++ 
Sbjct: 2   PGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINK 61

Query: 133 LIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGI 192
           LI++GR E V+V+RVDKEKGYIDLSKRRVS E+   CE+++ KSK V+SI+RHVAE L  
Sbjct: 62  LIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEY 121

Query: 193 ----DLEELYVNIGWPLYWKYGH----AFEAFKIIVTDPDSVLNSL 230
                LE L+    W    KY      A++AFK  V+DP S+L+SL
Sbjct: 122 TKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDP-SILDSL 166

Functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. This complex binds to a 40S ribosomal subunit, followed by mRNA binding to form a 43S preinitiation complex. Junction of the 60S ribosomal subunit to form the 80S initiation complex is preceded by hydrolysis of the GTP bound to eIF-2 and release of an eIF-2-GDP binary complex. In order for eIF-2 to recycle and catalyze another round of initiation, the GDP bound to eIF-2 must exchange with GTP by way of a reaction catalyzed by eIF-2B.

Rattus norvegicus (taxid: 10116)

>sp|Q6ZWX6|IF2A_MOUSE Eukaryotic translation initiation factor 2 subunit 1 OS=Mus musculus GN=Eif2s1 PE=1 SV=3

 Score =  186 bits (471), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 97/166 (58%), Positives = 123/166 (74%), Gaps = 9/166 (5%)

Query: 73  PNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSS 132
           P L CR Y+ ++PEV+  VM+ V++IA+MGAYVSLLEYNNIEGMIL SELSRRRIRS++ 
Sbjct: 2   PGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINK 61

Query: 133 LIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGI 192
           LI++GR E V+V+RVDKEKGYIDLSKRRVS E+   CE+++ KSK V+SI+RHVAE L  
Sbjct: 62  LIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEY 121

Query: 193 ----DLEELYVNIGWPLYWKYGH----AFEAFKIIVTDPDSVLNSL 230
                LE L+    W    KY      A++AFK  V+DP S+L+SL
Sbjct: 122 TKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDP-SILDSL 166

Functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. This complex binds to a 40S ribosomal subunit, followed by mRNA binding to form a 43S preinitiation complex. Junction of the 60S ribosomal subunit to form the 80S initiation complex is preceded by hydrolysis of the GTP bound to eIF-2 and release of an eIF-2-GDP binary complex. In order for eIF-2 to recycle and catalyze another round of initiation, the GDP bound to eIF-2 must exchange with GTP by way of a reaction catalyzed by eIF-2B.

Mus musculus (taxid: 10090)

>sp|P68102|IF2A_BOVIN Eukaryotic translation initiation factor 2 subunit 1 OS=Bos taurus GN=EIF2S1 PE=2 SV=2

 Score =  186 bits (471), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 97/166 (58%), Positives = 123/166 (74%), Gaps = 9/166 (5%)

Query: 73  PNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSS 132
           P L CR Y+ ++PEV+  VM+ V++IA+MGAYVSLLEYNNIEGMIL SELSRRRIRS++ 
Sbjct: 2   PGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINK 61

Query: 133 LIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGI 192
           LI++GR E V+V+RVDKEKGYIDLSKRRVS E+   CE+++ KSK V+SI+RHVAE L  
Sbjct: 62  LIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEY 121

Query: 193 ----DLEELYVNIGWPLYWKYGH----AFEAFKIIVTDPDSVLNSL 230
                LE L+    W    KY      A++AFK  V+DP S+L+SL
Sbjct: 122 TKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDP-SILDSL 166

Functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. This complex binds to a 40S ribosomal subunit, followed by mRNA binding to form a 43S preinitiation complex. Junction of the 60S ribosomal subunit to form the 80S initiation complex is preceded by hydrolysis of the GTP bound to eIF-2 and release of an eIF-2-GDP binary complex. In order for eIF-2 to recycle and catalyze another round of initiation, the GDP bound to eIF-2 must exchange with GTP by way of a reaction catalyzed by eIF-2B.

Bos taurus (taxid: 9913)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	259
388503894	340	unknown [Lotus japonicus]	0.725	0.552	0.925	1e-97
224101189	343	predicted protein [Populus trichocarpa]	0.741	0.559	0.942	2e-95
224109264	343	predicted protein [Populus trichocarpa]	0.741	0.559	0.937	5e-95
449444100	344	PREDICTED: eukaryotic translation initia	0.741	0.558	0.927	3e-94
297827659	344	hypothetical protein ARALYDRAFT_483081 [	0.741	0.558	0.932	3e-94
18405334	344	Eukaryotic translation initiation factor	0.741	0.558	0.927	5e-94
225448536	344	PREDICTED: eukaryotic translation initia	0.741	0.558	0.916	1e-93
13549160	343	protein synthesis initiation factor eIF2	0.741	0.559	0.859	1e-93
21537411	344	putative eukaryotic translation initiati	0.741	0.558	0.921	1e-93
42571149	241	Eukaryotic translation initiation factor	0.741	0.796	0.927	2e-93

>gi|388503894|gb|AFK40013.1| unknown [Lotus japonicus]

 Score =  362 bits (928), Expect = 1e-97,   Method: Compositional matrix adjust.
 Identities = 174/188 (92%), Positives = 183/188 (97%)

Query: 72  SPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVS 131
           +PNLECRMYE +YPEVDMAVMI+VKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSV+
Sbjct: 2   APNLECRMYETKYPEVDMAVMIRVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVN 61

Query: 132 SLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLG 191
           SLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQ CEERYNKSKLVHSIMRHVAETL 
Sbjct: 62  SLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQTCEERYNKSKLVHSIMRHVAETLN 121

Query: 192 IDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTREVKEIGPDGQEVTKVVPAV 251
           IDLEELYV+IGWPLY KYGHAFEAFKI+VTDPDSVLN LTREVKE+GPDGQEVTKVVPAV
Sbjct: 122 IDLEELYVHIGWPLYRKYGHAFEAFKIVVTDPDSVLNLLTREVKEVGPDGQEVTKVVPAV 181

Query: 252 TEEVKDAL 259
           +EEVKD+L
Sbjct: 182 SEEVKDSL 189

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224101189|ref|XP_002312178.1| predicted protein [Populus trichocarpa] gi|222851998|gb|EEE89545.1| predicted protein [Populus trichocarpa]

 Score =  354 bits (909), Expect = 2e-95,   Method: Compositional matrix adjust.
 Identities = 181/192 (94%), Positives = 188/192 (97%)

Query: 68  MASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI 127
           MA+HSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI
Sbjct: 1   MATHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI 60

Query: 128 RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVA 187
           RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQ CEERYNKSKLVHSIMRHVA
Sbjct: 61  RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQTCEERYNKSKLVHSIMRHVA 120

Query: 188 ETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTREVKEIGPDGQEVTKV 247
           ETLGIDLEELYVNIGWPLY K+GHAFEAFKI+VTDPDSV+ SLTREVKE GPDGQEVTKV
Sbjct: 121 ETLGIDLEELYVNIGWPLYRKHGHAFEAFKIMVTDPDSVVGSLTREVKETGPDGQEVTKV 180

Query: 248 VPAVTEEVKDAL 259
           VPAV+EE+K+AL
Sbjct: 181 VPAVSEEIKEAL 192

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224109264|ref|XP_002315141.1| predicted protein [Populus trichocarpa] gi|222864181|gb|EEF01312.1| predicted protein [Populus trichocarpa]

 Score =  353 bits (905), Expect = 5e-95,   Method: Compositional matrix adjust.
 Identities = 180/192 (93%), Positives = 187/192 (97%)

Query: 68  MASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI 127
           MA+HSPNLECRMYE+RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI
Sbjct: 1   MATHSPNLECRMYESRYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI 60

Query: 128 RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVA 187
           RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQ CEERYNKSKLVHSIMRHVA
Sbjct: 61  RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQTCEERYNKSKLVHSIMRHVA 120

Query: 188 ETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTREVKEIGPDGQEVTKV 247
           ETLGIDLEELYVNIGWPLY KYGHAFEAFKI+V DPDSVL+ LTREVKE GPDGQEVTKV
Sbjct: 121 ETLGIDLEELYVNIGWPLYRKYGHAFEAFKIMVNDPDSVLDPLTREVKETGPDGQEVTKV 180

Query: 248 VPAVTEEVKDAL 259
           VPAV+EE+K+AL
Sbjct: 181 VPAVSEEIKEAL 192

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449444100|ref|XP_004139813.1| PREDICTED: eukaryotic translation initiation factor 2 subunit alpha-like [Cucumis sativus] gi|449492599|ref|XP_004159044.1| PREDICTED: eukaryotic translation initiation factor 2 subunit alpha-like [Cucumis sativus]

 Score =  350 bits (898), Expect = 3e-94,   Method: Compositional matrix adjust.
 Identities = 178/192 (92%), Positives = 188/192 (97%)

Query: 68  MASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI 127
           MASHSPNLECRMYEA+YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI
Sbjct: 1   MASHSPNLECRMYEAKYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI 60

Query: 128 RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVA 187
           RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVA
Sbjct: 61  RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVA 120

Query: 188 ETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTREVKEIGPDGQEVTKV 247
           ET+ IDLE+LY+++GWPLY KYGHAFEAFKIIVTDPDSVLNSLTREVKE GPDGQE TK+
Sbjct: 121 ETMNIDLEDLYIHVGWPLYRKYGHAFEAFKIIVTDPDSVLNSLTREVKEAGPDGQEETKI 180

Query: 248 VPAVTEEVKDAL 259
           VPA++E+VKDAL
Sbjct: 181 VPAMSEDVKDAL 192

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297827659|ref|XP_002881712.1| hypothetical protein ARALYDRAFT_483081 [Arabidopsis lyrata subsp. lyrata] gi|297327551|gb|EFH57971.1| hypothetical protein ARALYDRAFT_483081 [Arabidopsis lyrata subsp. lyrata]

 Score =  350 bits (898), Expect = 3e-94,   Method: Compositional matrix adjust.
 Identities = 179/192 (93%), Positives = 186/192 (96%)

Query: 68  MASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI 127
           MAS +PNLECRMYEA+YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI
Sbjct: 1   MASQTPNLECRMYEAKYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI 60

Query: 128 RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVA 187
           RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQ CEERYNKSKLVHSIMRHVA
Sbjct: 61  RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQTCEERYNKSKLVHSIMRHVA 120

Query: 188 ETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTREVKEIGPDGQEVTKV 247
           ETL IDLEELYVNIGWPLY ++GHAFEAFKI+VTDPDSVL  LTRE+KE+GPDGQEVTKV
Sbjct: 121 ETLSIDLEELYVNIGWPLYRRHGHAFEAFKILVTDPDSVLGPLTREIKEVGPDGQEVTKV 180

Query: 248 VPAVTEEVKDAL 259
           VPAVTEEVKDAL
Sbjct: 181 VPAVTEEVKDAL 192

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18405334|ref|NP_565927.1| Eukaryotic translation initiation factor 2 subunit 1 [Arabidopsis thaliana] gi|19347786|gb|AAL86344.1| putative eukaryotic translation initiation factor 2 alpha subunit eIF2 [Arabidopsis thaliana] gi|20198018|gb|AAD25664.2| putative eukaryotic translation initiation factor 2 alpha subunit, eIF2 [Arabidopsis thaliana] gi|21436249|gb|AAM51263.1| putative eukaryotic translation initiation factor 2 alpha subunit eIF2 [Arabidopsis thaliana] gi|330254713|gb|AEC09807.1| Eukaryotic translation initiation factor 2 subunit 1 [Arabidopsis thaliana]

 Score =  349 bits (896), Expect = 5e-94,   Method: Compositional matrix adjust.
 Identities = 178/192 (92%), Positives = 186/192 (96%)

Query: 68  MASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI 127
           MAS +PNLECRMYEA+YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI
Sbjct: 1   MASQTPNLECRMYEAKYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI 60

Query: 128 RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVA 187
           RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQ CEERYNKSKLVHSIMRHVA
Sbjct: 61  RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQTCEERYNKSKLVHSIMRHVA 120

Query: 188 ETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTREVKEIGPDGQEVTKV 247
           ETL IDLE+LYVNIGWPLY ++GHAFEAFKI+VTDPDSVL  LTRE+KE+GPDGQEVTKV
Sbjct: 121 ETLSIDLEDLYVNIGWPLYRRHGHAFEAFKILVTDPDSVLGPLTREIKEVGPDGQEVTKV 180

Query: 248 VPAVTEEVKDAL 259
           VPAVTEEVKDAL
Sbjct: 181 VPAVTEEVKDAL 192

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225448536|ref|XP_002276751.1| PREDICTED: eukaryotic translation initiation factor 2 subunit alpha [Vitis vinifera]

 Score =  348 bits (894), Expect = 1e-93,   Method: Compositional matrix adjust.
 Identities = 176/192 (91%), Positives = 189/192 (98%)

Query: 68  MASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI 127
           MA+++PNLECRMYEA+YPEVDMAVMIQV NIADMGAYVSLLEYNNIEGMILFSELSRRRI
Sbjct: 1   MATNTPNLECRMYEAKYPEVDMAVMIQVNNIADMGAYVSLLEYNNIEGMILFSELSRRRI 60

Query: 128 RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVA 187
           RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVA
Sbjct: 61  RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVA 120

Query: 188 ETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTREVKEIGPDGQEVTKV 247
           ET+ +DLE+LY+++GWPLY KYGHAFEAFKIIVTDPDSVLNSLTREVKE+GPDGQEVTKV
Sbjct: 121 ETMQLDLEDLYIHVGWPLYRKYGHAFEAFKIIVTDPDSVLNSLTREVKEVGPDGQEVTKV 180

Query: 248 VPAVTEEVKDAL 259
           VPA++EEVKDAL
Sbjct: 181 VPAISEEVKDAL 192

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|13549160|gb|AAK29673.1|AF353096_1 protein synthesis initiation factor eIF2 alpha [Arabidopsis thaliana]

 Score =  348 bits (894), Expect = 1e-93,   Method: Compositional matrix adjust.
 Identities = 165/192 (85%), Positives = 182/192 (94%)

Query: 68  MASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI 127
           MA+ +PNLECRMYE+RYP+VDMAVMIQVK IADMGAYVSLLEYNNIEGMILFSELSRRRI
Sbjct: 1   MANPAPNLECRMYESRYPDVDMAVMIQVKTIADMGAYVSLLEYNNIEGMILFSELSRRRI 60

Query: 128 RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVA 187
            S+SSLIKVGR EPVMVLRVD+E+GYIDLSKRRVS+ED +ACEERYNKSKLVHSIMRHVA
Sbjct: 61  GSISSLIKVGRTEPVMVLRVDRERGYIDLSKRRVSDEDKEACEERYNKSKLVHSIMRHVA 120

Query: 188 ETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTREVKEIGPDGQEVTKV 247
           ET+G+DLEELYVNIGWPLY K+GHAFEAFKI+VTDPDSV ++LTREVKE GPDG EVTKV
Sbjct: 121 ETVGVDLEELYVNIGWPLYKKHGHAFEAFKIVVTDPDSVFDALTREVKETGPDGVEVTKV 180

Query: 248 VPAVTEEVKDAL 259
           VPAV+EE+KDA 
Sbjct: 181 VPAVSEELKDAF 192

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|21537411|gb|AAM61752.1| putative eukaryotic translation initiation factor 2 alpha subunit, eIF2 [Arabidopsis thaliana]

 Score =  348 bits (893), Expect = 1e-93,   Method: Compositional matrix adjust.
 Identities = 177/192 (92%), Positives = 186/192 (96%)

Query: 68  MASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI 127
           MAS +PNLECRMYEA+YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI
Sbjct: 1   MASQTPNLECRMYEAKYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI 60

Query: 128 RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVA 187
           RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR+VSEEDIQ CEERYNKSKLVHSIMRHVA
Sbjct: 61  RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRKVSEEDIQTCEERYNKSKLVHSIMRHVA 120

Query: 188 ETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTREVKEIGPDGQEVTKV 247
           ETL IDLE+LYVNIGWPLY ++GHAFEAFKI+VTDPDSVL  LTRE+KE+GPDGQEVTKV
Sbjct: 121 ETLSIDLEDLYVNIGWPLYRRHGHAFEAFKILVTDPDSVLGPLTREIKEVGPDGQEVTKV 180

Query: 248 VPAVTEEVKDAL 259
           VPAVTEEVKDAL
Sbjct: 181 VPAVTEEVKDAL 192

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42571149|ref|NP_973648.1| Eukaryotic translation initiation factor 2 subunit 1 [Arabidopsis thaliana] gi|79324819|ref|NP_001031518.1| Eukaryotic translation initiation factor 2 subunit 1 [Arabidopsis thaliana] gi|124300956|gb|ABN04730.1| At2g40290 [Arabidopsis thaliana] gi|330254714|gb|AEC09808.1| Eukaryotic translation initiation factor 2 subunit 1 [Arabidopsis thaliana] gi|330254715|gb|AEC09809.1| Eukaryotic translation initiation factor 2 subunit 1 [Arabidopsis thaliana]

 Score =  347 bits (891), Expect = 2e-93,   Method: Compositional matrix adjust.
 Identities = 178/192 (92%), Positives = 186/192 (96%)

Query: 68  MASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI 127
           MAS +PNLECRMYEA+YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI
Sbjct: 1   MASQTPNLECRMYEAKYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI 60

Query: 128 RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVA 187
           RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQ CEERYNKSKLVHSIMRHVA
Sbjct: 61  RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQTCEERYNKSKLVHSIMRHVA 120

Query: 188 ETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTREVKEIGPDGQEVTKV 247
           ETL IDLE+LYVNIGWPLY ++GHAFEAFKI+VTDPDSVL  LTRE+KE+GPDGQEVTKV
Sbjct: 121 ETLSIDLEDLYVNIGWPLYRRHGHAFEAFKILVTDPDSVLGPLTREIKEVGPDGQEVTKV 180

Query: 248 VPAVTEEVKDAL 259
           VPAVTEEVKDAL
Sbjct: 181 VPAVTEEVKDAL 192

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

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	259
TAIR|locus:2063093	344	AT2G40290 [Arabidopsis thalian	0.741	0.558	0.859	1.3e-84
TAIR|locus:2153464	344	EIF2 ALPHA "eukaryotic transla	0.737	0.555	0.806	1.2e-79
POMBASE|SPAC3G9.09c	306	tif211 "translation initiation	0.594	0.503	0.610	7.7e-48
CGD|CAL0000442	300	SUI2 [Candida albicans (taxid:	0.617	0.533	0.596	4.8e-46
ASPGD|ASPL0000040948	308	AN3156 [Emericella nidulans (t	0.571	0.480	0.635	1e-45
SGD|S000003767	304	SUI2 "Alpha subunit of the tra	0.617	0.526	0.559	9.3e-43
DICTYBASE|DDB_G0271862	341	eif2s1 "eukaryotic translation	0.586	0.445	0.544	2.2e-41
GENEDB_PFALCIPARUM|PF07_0117	329	PF07_0117 "eukaryotictranslati	0.617	0.486	0.518	6.8e-40
UNIPROTKB|Q8IBH7	329	PF07_0117 "Eukaryotic translat	0.617	0.486	0.518	6.8e-40
FB|FBgn0261609	341	eIF-2alpha "eukaryotic transla	0.625	0.475	0.505	7e-38

TAIR|locus:2063093 AT2G40290 [Arabidopsis thaliana (taxid:3702)]

 Score = 847 (303.2 bits), Expect = 1.3e-84, P = 1.3e-84
 Identities = 165/192 (85%), Positives = 173/192 (90%)

Query:    68 MASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSEXXXXXX 127
             MAS +PNLECRMYEA+YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSE      
Sbjct:     1 MASQTPNLECRMYEAKYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI 60

Query:   128 XXXXXXXKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVA 187
                    KVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQ CEERYNKSKLVHSIMRHVA
Sbjct:    61 RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQTCEERYNKSKLVHSIMRHVA 120

Query:   188 ETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTREVKEIGPDGQEVTKV 247
             ETL IDLE+LYVNIGWPLY ++GHAFEAFKI+VTDPDSVL  LTRE+KE+GPDGQEVTKV
Sbjct:   121 ETLSIDLEDLYVNIGWPLYRRHGHAFEAFKILVTDPDSVLGPLTREIKEVGPDGQEVTKV 180

Query:   248 VPAVTEEVKDAL 259
             VPAVTEEVKDAL
Sbjct:   181 VPAVTEEVKDAL 192

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

GO:0003743 "translation initiation factor activity" evidence=IEA

GO:0005850 "eukaryotic translation initiation factor 2 complex" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

GO:0005634 "nucleus" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0009165 "nucleotide biosynthetic process" evidence=RCA

TAIR|locus:2153464 EIF2 ALPHA "eukaryotic translation initiation factor 2 alpha subunit" [Arabidopsis thaliana (taxid:3702)]

 Score = 800 (286.7 bits), Expect = 1.2e-79, P = 1.2e-79
 Identities = 154/191 (80%), Positives = 170/191 (89%)

Query:    68 MASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSEXXXXXX 127
             MA+ +PNLECRMYE+RYP+VDMAVMIQVK IADMGAYVSLLEYNNIEGMILFSE      
Sbjct:     1 MANPAPNLECRMYESRYPDVDMAVMIQVKTIADMGAYVSLLEYNNIEGMILFSELSRRRI 60

Query:   128 XXXXXXXKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVA 187
                    KVGR EPVMVLRVD+E+GYIDLSKRRVS+ED +ACEERYNKSKLVHSIMRHVA
Sbjct:    61 RSISSLIKVGRTEPVMVLRVDRERGYIDLSKRRVSDEDKEACEERYNKSKLVHSIMRHVA 120

Query:   188 ETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTREVKEIGPDGQEVTKV 247
             ET+G+DLEELYVNIGWPLY K+GHAFEAFKI+VTDPDSV ++LTREVKE GPDG EVTKV
Sbjct:   121 ETVGVDLEELYVNIGWPLYKKHGHAFEAFKIVVTDPDSVFDALTREVKETGPDGVEVTKV 180

Query:   248 VPAVTEEVKDA 258
             VPAV+EE+KDA
Sbjct:   181 VPAVSEELKDA 191

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

GO:0003743 "translation initiation factor activity" evidence=IEA;ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0005850 "eukaryotic translation initiation factor 2 complex" evidence=IEA

GO:0005829 "cytosol" evidence=IDA

GO:0009220 "pyrimidine ribonucleotide biosynthetic process" evidence=RCA

GO:0009640 "photomorphogenesis" evidence=RCA

GO:0010388 "cullin deneddylation" evidence=RCA

POMBASE|SPAC3G9.09c tif211 "translation initiation factor eIF2 alpha subunit" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 500 (181.1 bits), Expect = 7.7e-48, P = 7.7e-48
 Identities = 94/154 (61%), Positives = 114/154 (74%)

Query:    77 CRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSEXXXXXXXXXXXXXKV 136
             CRMYE R+PEVD  V++ V+ I +MGAYV LLEY+NIEGM+L SE             +V
Sbjct:     6 CRMYENRFPEVDELVVVNVRQIQEMGAYVKLLEYDNIEGMVLLSELSRRRIRSVQKHIRV 65

Query:   137 GRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEE 196
             GR E V+VLRVDKEKGYIDLSKRRVS ED+  CEER+NKSK VHSIMRH+AE   + LE 
Sbjct:    66 GRNEVVVVLRVDKEKGYIDLSKRRVSPEDVVKCEERFNKSKAVHSIMRHIAEKHNVPLET 125

Query:   197 LYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSL 230
             +Y  IGWPLY KYGHA++AFK+ +++PD V   L
Sbjct:   126 MYTTIGWPLYRKYGHAYDAFKLAISNPDHVFEGL 159

GO:0002183 "cytoplasmic translational initiation" evidence=NAS

GO:0003743 "translation initiation factor activity" evidence=ISO

GO:0005634 "nucleus" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0005850 "eukaryotic translation initiation factor 2 complex" evidence=ISO

GO:0007093 "mitotic cell cycle checkpoint" evidence=IMP

GO:0043561 "regulation of translational initiation in response to osmotic stress" evidence=IMP

CGD|CAL0000442 SUI2 [Candida albicans (taxid:5476)]

 Score = 483 (175.1 bits), Expect = 4.8e-46, P = 4.8e-46
 Identities = 96/161 (59%), Positives = 115/161 (71%)

Query:    77 CRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSEXXXXXXXXXXXXXKV 136
             CR YE +YPEVD  VM+ V+ IA+MGAYV LLEY+NIEGM+L SE             +V
Sbjct:     6 CRFYENKYPEVDEVVMVNVQEIAEMGAYVKLLEYDNIEGMVLLSELSRRRIRSIQKLIRV 65

Query:   137 GRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEE 196
             G+ E  +VLRVDKEKGYIDLSK+ VS EDI  C+ERYNKSK VHSI+RH AE   I LE 
Sbjct:    66 GKNEVAVVLRVDKEKGYIDLSKKVVSAEDIVKCDERYNKSKAVHSILRHCAEKFNIPLER 125

Query:   197 LYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTREVKEI 237
             LY  IGWPL  KYGHA++AFKI +TDP SV +S+    K++
Sbjct:   126 LYETIGWPLSRKYGHAYDAFKISITDP-SVFDSVDVPSKDV 165

GO:0043614 "multi-eIF complex" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

GO:0005850 "eukaryotic translation initiation factor 2 complex" evidence=IEA

GO:0043561 "regulation of translational initiation in response to osmotic stress" evidence=IEA

GO:0007093 "mitotic cell cycle checkpoint" evidence=IEA

ASPGD|ASPL0000040948 AN3156 [Emericella nidulans (taxid:162425)]

 Score = 480 (174.0 bits), Expect = 1.0e-45, P = 1.0e-45
 Identities = 94/148 (63%), Positives = 108/148 (72%)

Query:    77 CRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSEXXXXXXXXXXXXXKV 136
             CR YE +YPEVD  VM+ VK IA+MGAYV LLEY+NI+GMIL SE             ++
Sbjct:     6 CRFYEEKYPEVDSYVMVNVKQIAEMGAYVKLLEYDNIDGMILLSELSRRRIRSIQKLIRI 65

Query:   137 GRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEE 196
             GR E V+VLRVDKEKGYIDLSKRRVS ED+  CEERYNKSK VHSI+RHVAE     LE 
Sbjct:    66 GRNEVVIVLRVDKEKGYIDLSKRRVSPEDVIKCEERYNKSKAVHSILRHVAEATQTPLET 125

Query:   197 LYVNIGWPLYWKYGHAFEAFKIIVTDPD 224
             LY  I WPL  KYGH+ +AFKI +T+PD
Sbjct:   126 LYQQIAWPLNRKYGHSHDAFKISITNPD 153

GO:0007093 "mitotic cell cycle checkpoint" evidence=IEA

GO:0043561 "regulation of translational initiation in response to osmotic stress" evidence=IEA

GO:0043614 "multi-eIF complex" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

GO:0005850 "eukaryotic translation initiation factor 2 complex" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0003743 "translation initiation factor activity" evidence=IEA

SGD|S000003767 SUI2 "Alpha subunit of the translation initiation factor eIF2" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 452 (164.2 bits), Expect = 9.3e-43, P = 9.3e-43
 Identities = 90/161 (55%), Positives = 112/161 (69%)

Query:    77 CRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSEXXXXXXXXXXXXXKV 136
             CR YE +YPE+D  VM+ V+ IA+MGAYV LLEY+NIEGMIL SE             +V
Sbjct:     6 CRFYENKYPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRV 65

Query:   137 GRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEE 196
             G+ +  +VLRVDKEKGYIDLSKRRVS EDI  CEE+Y KSK VHSI+R+ AE   I LEE
Sbjct:    66 GKNDVAVVLRVDKEKGYIDLSKRRVSSEDIIKCEEKYQKSKTVHSILRYCAEKFQIPLEE 125

Query:   197 LYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTREVKEI 237
             LY  I WPL  K+GHA+EAFK+ + D ++V   +    K++
Sbjct:   126 LYKTIAWPLSRKFGHAYEAFKLSIID-ETVWEGIEPPSKDV 165

GO:0043614 "multi-eIF complex" evidence=IDA

GO:0005840 "ribosome" evidence=TAS

GO:0003723 "RNA binding" evidence=IEA

GO:0003743 "translation initiation factor activity" evidence=IEA;TAS

GO:0006412 "translation" evidence=IEA

GO:0005850 "eukaryotic translation initiation factor 2 complex" evidence=IEA;ISS;IMP

GO:0006413 "translational initiation" evidence=IEA;TAS

GO:0005737 "cytoplasm" evidence=IDA

DICTYBASE|DDB_G0271862 eif2s1 "eukaryotic translation initiation factor 2 (eIF2) subunit 1" [Dictyostelium discoideum (taxid:44689)]

 Score = 439 (159.6 bits), Expect = 2.2e-41, P = 2.2e-41
 Identities = 86/158 (54%), Positives = 111/158 (70%)

Query:    76 ECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSEXXXXXXXXXXXXXK 135
             +CRMYE +YPE +  VM+++++I DMG YVSLLEYNNIEGMIL SE             +
Sbjct:     6 DCRMYEKKYPEENELVMVRIESIGDMGVYVSLLEYNNIEGMILLSEISRRRIRSINKLVR 65

Query:   136 VGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLG---- 191
             VG+ E V+V+RVDK+KGYIDLSKRRV+ E+   CEER++KSK VH I+R+VA  L     
Sbjct:    66 VGKTEAVVVVRVDKDKGYIDLSKRRVTPEEYAQCEERFHKSKAVHGIVRYVATKLSTEDN 125

Query:   192 -IDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLN 228
              +  + LY    WPLY KYGHA+EAFK+ +T+P SV N
Sbjct:   126 VVKTKHLYTKFVWPLYTKYGHAYEAFKLSITEP-SVFN 162

GO:0006446 "regulation of translational initiation" evidence=ISS

GO:0005850 "eukaryotic translation initiation factor 2 complex" evidence=IEA;ISS

GO:0005844 "polysome" evidence=ISS

GO:0005525 "GTP binding" evidence=ISS

GO:0003743 "translation initiation factor activity" evidence=IEA;ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0006417 "regulation of translation" evidence=IEA

GO:0006413 "translational initiation" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

GENEDB_PFALCIPARUM|PF07_0117 PF07_0117 "eukaryotictranslation initiation factor 2 alpha subunit, putative" [Plasmodium falciparum (taxid:5833)]

 Score = 425 (154.7 bits), Expect = 6.8e-40, P = 6.8e-40
 Identities = 84/162 (51%), Positives = 111/162 (68%)

Query:    76 ECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSEXXXXXXXXXXXXXK 135
             +CR Y+ ++PEVD  +M++V  I DMGAYVS+LEYN++EGMIL SE             +
Sbjct:    12 DCRFYKKKFPEVDDLIMVKVNRIEDMGAYVSILEYNDMEGMILMSELSKRRFRSVNKLIR 71

Query:   136 VGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLE 195
             VGR E V+VLRVD +KGYIDLSKRRVS +DI  CEE+++KSK VH  +RHVA+  GI +E
Sbjct:    72 VGRHEVVLVLRVDSQKGYIDLSKRRVSPKDIIKCEEKFSKSKKVHQTVRHVAKEHGITVE 131

Query:   196 ELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSL--TREVK 235
             EL     WPLY +YGHA +A K    +P++V   L  + E+K
Sbjct:   132 ELNEKAIWPLYERYGHALDALKEATMNPENVFKGLDISEEIK 173

GO:0006413 "translational initiation" evidence=ISS

UNIPROTKB|Q8IBH7 PF07_0117 "Eukaryotic translation initiation factor 2 alpha subunit, putative" [Plasmodium falciparum 3D7 (taxid:36329)]

 Score = 425 (154.7 bits), Expect = 6.8e-40, P = 6.8e-40
 Identities = 84/162 (51%), Positives = 111/162 (68%)

Query:    76 ECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSEXXXXXXXXXXXXXK 135
             +CR Y+ ++PEVD  +M++V  I DMGAYVS+LEYN++EGMIL SE             +
Sbjct:    12 DCRFYKKKFPEVDDLIMVKVNRIEDMGAYVSILEYNDMEGMILMSELSKRRFRSVNKLIR 71

Query:   136 VGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLE 195
             VGR E V+VLRVD +KGYIDLSKRRVS +DI  CEE+++KSK VH  +RHVA+  GI +E
Sbjct:    72 VGRHEVVLVLRVDSQKGYIDLSKRRVSPKDIIKCEEKFSKSKKVHQTVRHVAKEHGITVE 131

Query:   196 ELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSL--TREVK 235
             EL     WPLY +YGHA +A K    +P++V   L  + E+K
Sbjct:   132 ELNEKAIWPLYERYGHALDALKEATMNPENVFKGLDISEEIK 173

GO:0006413 "translational initiation" evidence=ISS

FB|FBgn0261609 eIF-2alpha "eukaryotic translation Initiation Factor 2alpha" [Drosophila melanogaster (taxid:7227)]

 Score = 406 (148.0 bits), Expect = 7.0e-38, P = 7.0e-38
 Identities = 87/172 (50%), Positives = 114/172 (66%)

Query:    75 LECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSEXXXXXXXXXXXXX 134
             L  R Y  RYPE++  VM+ V +IA+MGAYV LLEYNNIEGMIL SE             
Sbjct:     3 LTSRFYNERYPEIEDVVMVNVLSIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLI 62

Query:   135 KVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGID- 193
             +VG+ EPV+V+RVDKEKGYIDLSKRRVS ED++ C ER+ K+K ++S++RHVA+ LG + 
Sbjct:    63 RVGKTEPVVVIRVDKEKGYIDLSKRRVSPEDVEKCTERFAKAKAINSLLRHVADILGFEG 122

Query:   194 ---LEELYVNIGWPLYWKYGH---AFEAFKIIVTDPDSVLN--SLTREVKEI 237
                LE+LY    W    KY +   A++ FK  VTDP +V +  +L  E KE+
Sbjct:   123 NEKLEDLYQKTAWHFEKKYNNKTVAYDIFKQSVTDP-TVFDECNLEPETKEV 173

GO:0003743 "translation initiation factor activity" evidence=IGI;ISS;NAS

GO:0005829 "cytosol" evidence=ISS

GO:0006413 "translational initiation" evidence=ISS

GO:0005850 "eukaryotic translation initiation factor 2 complex" evidence=ISS;NAS

GO:0005525 "GTP binding" evidence=NAS

GO:0000049 "tRNA binding" evidence=NAS

GO:0001677 "formation of translation initiation ternary complex" evidence=NAS

GO:0005851 "eukaryotic translation initiation factor 2B complex" evidence=ISS

GO:0007052 "mitotic spindle organization" evidence=IMP

GO:0000022 "mitotic spindle elongation" evidence=IMP

GO:0005875 "microtubule associated complex" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

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	259
PTZ00248	319	PTZ00248, PTZ00248, eukaryotic translation initiat	1e-86
COG1093	269	COG1093, SUI2, Translation initiation factor 2, al	3e-57
cd04452	76	cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha sub	9e-40
PRK03987	262	PRK03987, PRK03987, translation initiation factor	2e-28
pfam00575	74	pfam00575, S1, S1 RNA binding domain	2e-12
smart00316	72	smart00316, S1, Ribosomal protein S1-like RNA-bind	7e-11
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	9e-10
cd05688	68	cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: R	1e-08
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	2e-08
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	2e-08
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	2e-08
cd04472	68	cd04472, S1_PNPase, S1_PNPase: Polynucleotide phos	2e-08
COG1185	692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	8e-08
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	8e-08
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	1e-07
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	2e-07
cd00164	65	cd00164, S1_like, S1_like: Ribosomal protein S1-li	2e-07
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	4e-07
cd05685	68	cd05685, S1_Tex, S1_Tex: The C-terminal S1 domain	9e-07
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	2e-06
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	2e-06
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	2e-06
cd05692	69	cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: R	2e-06
pfam07541	112	pfam07541, EIF_2_alpha, Eukaryotic translation ini	4e-06
cd05687	70	cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec	4e-06
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	4e-06
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	7e-06
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	7e-06
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	7e-06
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	2e-05
COG2183	780	COG2183, Tex, Transcriptional accessory protein [T	6e-05
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	1e-04
cd05690	69	cd05690, S1_RPS1_repeat_ec5, S1_RPS1_repeat_ec5: R	2e-04
PRK12269	863	PRK12269, PRK12269, bifunctional cytidylate kinase	2e-04
cd05684	79	cd05684, S1_DHX8_helicase, S1_DHX8_helicase: The N	4e-04
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	5e-04
cd05689	72	cd05689, S1_RPS1_repeat_ec4, S1_RPS1_repeat_ec4: R	5e-04
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	5e-04
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	6e-04
PRK08059	123	PRK08059, PRK08059, general stress protein 13; Val	6e-04
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	8e-04
cd05691	73	cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: R	8e-04
cd05708	77	cd05708, S1_Rrp5_repeat_sc12, S1_Rrp5_repeat_sc12:	0.001
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	0.002
PRK07899	486	PRK07899, rpsA, 30S ribosomal protein S1; Reviewed	0.003
PRK07400	318	PRK07400, PRK07400, 30S ribosomal protein S1; Revi	0.004

>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2 subunit 1; Provisional

 Score =  260 bits (666), Expect = 1e-86
 Identities = 105/166 (63%), Positives = 132/166 (79%), Gaps = 2/166 (1%)

Query: 73  PNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSS 132
             L+CR YE ++PE D  VM++V  I +MGAYVSLLEY++IEGMIL SELS+RRIRS++ 
Sbjct: 3   DLLDCRFYEQKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINK 62

Query: 133 LIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGI 192
           LI+VGR E V+VLRVDKEKGYIDLSK+RVS EDI+ACEE+++KSK VHSIMRH+A+  G+
Sbjct: 63  LIRVGRHEVVVVLRVDKEKGYIDLSKKRVSPEDIEACEEKFSKSKKVHSIMRHIAQKHGM 122

Query: 193 DLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLN--SLTREVKE 236
            +EELY  I WPLY KYGHA +A K  +T+PD+V     +  EVKE
Sbjct: 123 SVEELYTKIIWPLYKKYGHALDALKEALTNPDNVFEGLDIPEEVKE 168

Length = 319

>gnl|CDD|224018 COG1093, SUI2, Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]

 Score =  183 bits (467), Expect = 3e-57
 Identities = 56/170 (32%), Positives = 86/170 (50%), Gaps = 10/170 (5%)

Query: 77  CRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKV 136
            RM    YPE    V+  VK +AD GAYV L EY   EG I  SE++   ++++   +K 
Sbjct: 1   MRMKRREYPEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKE 60

Query: 137 GRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEE 196
           G+     VLRVD ++G+IDLS +RV+E   +   + + K +    ++   AE LG DLEE
Sbjct: 61  GQKVVAKVLRVDPKRGHIDLSLKRVTEHQRRKKIQEWKKEQKADKLLELAAEKLGKDLEE 120

Query: 197 LYVNIGWPLYWKYGHAFEAFKIIVTD----------PDSVLNSLTREVKE 236
            Y  +GW L  ++G  ++AF+    +          P+     L    +E
Sbjct: 121 AYEEVGWKLEEEFGSLYDAFEAAAKEGGEVLDDEGVPEEWKEVLKEIARE 170

Length = 269

>gnl|CDD|239899 cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain

 Score =  132 bits (334), Expect = 9e-40
 Identities = 57/76 (75%), Positives = 64/76 (84%)

Query: 85  PEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMV 144
           PE    V++ VK+IADMGAYVSLLEY NIEGMIL SELSRRRIRS+  L+KVGR E V V
Sbjct: 1   PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKV 60

Query: 145 LRVDKEKGYIDLSKRR 160
           +RVDKEKGYIDLSK+R
Sbjct: 61  IRVDKEKGYIDLSKKR 76

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to complete the initiation complex, which is competent to begin translation. The IF2a subunit is a major site of control of the translation initiation process, via phosphorylation of a specific serine residue. This alpha subunit is well conserved in eukaryotes and archaea but is not present in bacteria. IF2 is a cold-shock-inducible protein. Length = 76

>gnl|CDD|235188 PRK03987, PRK03987, translation initiation factor IF-2 subunit alpha; Validated

 Score =  108 bits (272), Expect = 2e-28
 Identities = 52/151 (34%), Positives = 82/151 (54%), Gaps = 8/151 (5%)

Query: 84  YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVM 143
           +PE    V+  VK + D GA+V+L EY   EG I  SE++   ++++   +K G+     
Sbjct: 5   WPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCK 64

Query: 144 VLRVDKEKGYIDLSKRRVSE----EDIQACEERYNKSKLVHSIMRHVAETLGIDLEELYV 199
           V+RVD  KG+IDLS +RV+E    E IQ   E  N+ K     +   AE LG  LEE + 
Sbjct: 65  VIRVDPRKGHIDLSLKRVNEHQRREKIQ---EWKNEQK-ADKWLELAAEKLGKSLEEAWE 120

Query: 200 NIGWPLYWKYGHAFEAFKIIVTDPDSVLNSL 230
            +G+ L  ++G  ++AF+    + +  L+ L
Sbjct: 121 EVGYKLEDEFGDLYDAFEEAAIEGEEALDDL 151

Length = 262

>gnl|CDD|216000 pfam00575, S1, S1 RNA binding domain

 Score = 60.7 bits (148), Expect = 2e-12
 Identities = 31/76 (40%), Positives = 40/76 (52%), Gaps = 2/76 (2%)

Query: 84  YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVM 143
            PE    V   V  +   GA+V L   N +EG I  SE+S  R+     ++KVG    V 
Sbjct: 1   KPEEGDVVKGTVTRVTKGGAFVDLG--NGVEGFIPISEISDDRVEDPDEVLKVGDEVEVK 58

Query: 144 VLRVDKEKGYIDLSKR 159
           VL+VDKE+G I LS R
Sbjct: 59  VLKVDKERGRIILSIR 74

The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure. Length = 74

>gnl|CDD|197648 smart00316, S1, Ribosomal protein S1-like RNA-binding domain

 Score = 56.5 bits (137), Expect = 7e-11
 Identities = 29/65 (44%), Positives = 39/65 (60%), Gaps = 2/65 (3%)

Query: 95  VKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYI 154
           V  I   GA+V L   N +EG+I  SELS +R++    ++KVG    V VL VD+EKG I
Sbjct: 10  VTEITPGGAFVDL--GNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRI 67

Query: 155 DLSKR 159
            LS +
Sbjct: 68  ILSLK 72

Length = 72

>gnl|CDD|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 58.3 bits (142), Expect = 9e-10
 Identities = 36/100 (36%), Positives = 55/100 (55%), Gaps = 4/100 (4%)

Query: 81  EARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELS-RRRIRSVSSLIKVGRI 139
           E +YP V   V  +V NI D GA+V L E   IEG++  SE+S  ++ +  S ++ VG+ 
Sbjct: 281 EKKYP-VGSKVKGKVTNITDYGAFVELEE--GIEGLVHVSEMSWTKKNKHPSKVVSVGQE 337

Query: 140 EPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLV 179
             VMVL +D+EK  I L  ++  E   +   E+Y    +V
Sbjct: 338 VEVMVLEIDEEKRRISLGLKQCKENPWEEFAEKYPVGDVV 377

Length = 565

>gnl|CDD|240193 cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain

 Score = 50.3 bits (121), Expect = 1e-08
 Identities = 23/63 (36%), Positives = 38/63 (60%), Gaps = 3/63 (4%)

Query: 95  VKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYI 154
           VK+I D GA+V L     ++G++  S++S  R++  S ++ VG    V VL++DKE+  I
Sbjct: 9   VKSITDFGAFVDL---GGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRI 65

Query: 155 DLS 157
            L 
Sbjct: 66  SLG 68

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 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Length = 68

>gnl|CDD|234623 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed

 Score = 54.6 bits (132), Expect = 2e-08
 Identities = 27/88 (30%), Positives = 48/88 (54%), Gaps = 3/88 (3%)

Query: 86  EVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVL 145
           E    V  +VK + D GA+V +     ++G++  SE+S  R+   S ++KVG    V +L
Sbjct: 476 EEGDVVEGEVKRLTDFGAFVDI---GGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYIL 532

Query: 146 RVDKEKGYIDLSKRRVSEEDIQACEERY 173
            +DKE   + LS +++  +  +  EE+Y
Sbjct: 533 DIDKENKKLSLSLKKLLPDPWENVEEKY 560

Length = 647

>gnl|CDD|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase

 Score = 54.4 bits (132), Expect = 2e-08
 Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 3/72 (4%)

Query: 85  PEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMV 144
           PEV      +V  I D GA+V +L     +G++  SE++  R+  V  ++K G    V V
Sbjct: 616 PEVGKIYEGKVVRIMDFGAFVEIL--PGKDGLVHISEIANERVEKVEDVLKEGDEVKVKV 673

Query: 145 LRVDKEKGYIDL 156
           L +DK +G I L
Sbjct: 674 LEIDK-QGRIKL 684

Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family) [Transcription, Degradation of RNA]. Length = 684

>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional

 Score = 54.3 bits (132), Expect = 2e-08
 Identities = 24/67 (35%), Positives = 38/67 (56%), Gaps = 3/67 (4%)

Query: 95  VKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYI 154
           V  I D GA+V +L     +G++  SE++  R+  V  ++K G    V VL +DK +G I
Sbjct: 629 VVRIVDFGAFVEIL--PGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDK-RGRI 685

Query: 155 DLSKRRV 161
            LS++ V
Sbjct: 686 RLSRKAV 692

Length = 693

>gnl|CDD|239918 cd04472, S1_PNPase, S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain

 Score = 49.5 bits (119), Expect = 2e-08
 Identities = 25/64 (39%), Positives = 36/64 (56%), Gaps = 3/64 (4%)

Query: 95  VKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYI 154
           V  I D GA+V +L     +G++  SELS  R+  V  ++KVG    V V+ VD  +G I
Sbjct: 8   VVKIKDFGAFVEILP--GKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD-RGRI 64

Query: 155 DLSK 158
            LS+
Sbjct: 65  SLSR 68

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. Length = 68

>gnl|CDD|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]

 Score = 52.6 bits (127), Expect = 8e-08
 Identities = 27/82 (32%), Positives = 42/82 (51%), Gaps = 3/82 (3%)

Query: 82  ARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEP 141
            R  EV       V  I D GA+V LL     +G++  S+L++ R+  V  ++K G    
Sbjct: 614 TREVEVGEVYEGTVVRIVDFGAFVELL--PGKDGLVHISQLAKERVEKVEDVLKEGDEVK 671

Query: 142 VMVLRVDKEKGYIDLSKRRVSE 163
           V V+ +D ++G I LS + V E
Sbjct: 672 VKVIEID-KQGRIRLSIKAVLE 692

Length = 692

>gnl|CDD|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

 Score = 52.3 bits (126), Expect = 8e-08
 Identities = 24/63 (38%), Positives = 40/63 (63%), Gaps = 3/63 (4%)

Query: 95  VKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYI 154
           VKNI D GA+V +     ++G++  SE+S +R+   S ++KVG    V V+ +D+E+G +
Sbjct: 200 VKNITDYGAFVDI---GGVDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRV 256

Query: 155 DLS 157
            LS
Sbjct: 257 SLS 259

Length = 541

>gnl|CDD|234623 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed

 Score = 51.5 bits (124), Expect = 1e-07
 Identities = 27/93 (29%), Positives = 45/93 (48%), Gaps = 3/93 (3%)

Query: 81  EARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIE 140
           E +YP   + V+ +V  IA  GA+V L     ++G++  S++S +RI     ++  G   
Sbjct: 557 EEKYPVGSI-VLGKVVRIAPFGAFVELEP--GVDGLVHISQISWKRIDKPEDVLSEGEEV 613

Query: 141 PVMVLRVDKEKGYIDLSKRRVSEEDIQACEERY 173
              +L VD E+  I LS + V EE     +   
Sbjct: 614 KAKILEVDPEEKRIRLSIKEVEEEPGDIEKVEL 646

Length = 647

>gnl|CDD|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

 Score = 51.1 bits (123), Expect = 2e-07
 Identities = 27/98 (27%), Positives = 48/98 (48%), Gaps = 3/98 (3%)

Query: 78  RMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVG 137
              E +YP  D      V N+ D GA+V +     +EG++  SE+S  +    S ++KVG
Sbjct: 269 EGIEKKYPVGDKVEGK-VTNLTDYGAFVEI--EEGVEGLVHVSEISWTKKNVPSEVVKVG 325

Query: 138 RIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNK 175
           +   V VL +D E+  I L  +++ E   +   +++  
Sbjct: 326 QEVEVKVLDIDPERRRISLGLKQLKENPWEEFADKHPV 363

Length = 541

>gnl|CDD|238094 cd00164, S1_like, S1_like: Ribosomal protein S1-like RNA-binding domain

 Score = 47.0 bits (112), Expect = 2e-07
 Identities = 26/64 (40%), Positives = 37/64 (57%), Gaps = 2/64 (3%)

Query: 94  QVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGY 153
           +V +I   G +V L +   +EG++  SELS + ++  S + KVG    V VL VD EKG 
Sbjct: 4   KVVSITKFGVFVELED--GVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGR 61

Query: 154 IDLS 157
           I LS
Sbjct: 62  ISLS 65

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. Length = 65

>gnl|CDD|233102 TIGR00717, rpsA, ribosomal protein S1

 Score = 50.1 bits (120), Expect = 4e-07
 Identities = 29/79 (36%), Positives = 52/79 (65%), Gaps = 3/79 (3%)

Query: 95  VKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYI 154
           VKNI D GA+V L     ++G++  +++S +R++  S  +KVG+   V V++ DKEKG I
Sbjct: 195 VKNITDFGAFVDL---GGVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRI 251

Query: 155 DLSKRRVSEEDIQACEERY 173
            LS +++ E+  +A E+++
Sbjct: 252 SLSLKQLGEDPWEAIEKKF 270

This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by PFAM model pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 516

>gnl|CDD|240190 cd05685, S1_Tex, S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa

 Score = 44.9 bits (107), Expect = 9e-07
 Identities = 22/63 (34%), Positives = 37/63 (58%), Gaps = 2/63 (3%)

Query: 95  VKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYI 154
           V N+ D GA+V +    +  G+I  S+++ R +   S ++ VG I  V V+ +D+E+G I
Sbjct: 8   VTNVTDFGAFVDIGVKQD--GLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRI 65

Query: 155 DLS 157
            LS
Sbjct: 66  SLS 68

The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea. Length = 68

>gnl|CDD|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 47.9 bits (115), Expect = 2e-06
 Identities = 30/96 (31%), Positives = 51/96 (53%), Gaps = 4/96 (4%)

Query: 81  EARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELS-RRRIRSVSSLIKVGRI 139
             +YP  D+ V  +VKNI D GA+V L     I+G++  S++S  ++      L K G  
Sbjct: 368 AEKYPVGDV-VEGKVKNITDFGAFVGLEG--GIDGLVHLSDISWDKKGEEAVELYKKGDE 424

Query: 140 EPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNK 175
              +VL+VD EK  I L  +++ E+  +   +++ K
Sbjct: 425 VEAVVLKVDVEKERISLGIKQLEEDPFEEFAKKHKK 460

Length = 565

>gnl|CDD|234623 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed

 Score = 48.4 bits (116), Expect = 2e-06
 Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 1/74 (1%)

Query: 114 EGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQAC-EER 172
           EG+I   EL+   I S+   +KVG    V VL+++ E GY+ LSK+    E      EE 
Sbjct: 327 EGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSKKEADREKAWKELEEA 386

Query: 173 YNKSKLVHSIMRHV 186
           +   + V   ++ V
Sbjct: 387 FENGEPVKGKVKEV 400

Length = 647

>gnl|CDD|233102 TIGR00717, rpsA, ribosomal protein S1

 Score = 48.2 bits (115), Expect = 2e-06
 Identities = 26/96 (27%), Positives = 49/96 (51%), Gaps = 4/96 (4%)

Query: 81  EARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELS-RRRIRSVSSLIKVGRI 139
           E ++P  D  +  +V N+ D G +V + E   IEG++  SE+S  ++    S ++K G  
Sbjct: 267 EKKFPVGD-KITGRVTNLTDYGVFVEIEE--GIEGLVHVSEMSWVKKNSHPSKVVKKGDE 323

Query: 140 EPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNK 175
             VM+L +D E+  + L  ++      +  EE++  
Sbjct: 324 VEVMILDIDPERRRLSLGLKQCKANPWEQFEEKHPV 359

This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by PFAM model pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 516

>gnl|CDD|240197 cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain

 Score = 44.2 bits (105), Expect = 2e-06
 Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 3/63 (4%)

Query: 95  VKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYI 154
           V  +   GA+V L     I G++  S+++ +R++ V  ++K G    V VL +D  +G I
Sbjct: 8   VTRLKPFGAFVELG--GGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID-ARGRI 64

Query: 155 DLS 157
            LS
Sbjct: 65  SLS 67

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. Length = 69

>gnl|CDD|219460 pfam07541, EIF_2_alpha, Eukaryotic translation initiation factor 2 alpha subunit

 Score = 44.4 bits (106), Expect = 4e-06
 Identities = 19/42 (45%), Positives = 24/42 (57%), Gaps = 2/42 (4%)

Query: 197 LYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLT--REVKE 236
           LY  I WPL  KYGHA++AF+      + VL+ L    E KE
Sbjct: 1   LYEEIAWPLEEKYGHAYDAFEAAAIPGEEVLDDLGIPEEWKE 42

These proteins share a region of similarity that falls towards the C terminus from pfam00575. Length = 112

>gnl|CDD|240192 cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain

 Score = 43.3 bits (103), Expect = 4e-06
 Identities = 21/46 (45%), Positives = 27/46 (58%)

Query: 114 EGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR 159
           EG+I  SE S   I +    +KVG    V VLRV+ E+G + LSKR
Sbjct: 25  EGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Length = 70

>gnl|CDD|235851 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 46.8 bits (112), Expect = 4e-06
 Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 3/63 (4%)

Query: 95  VKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYI 154
           V  + D GA+V +     ++G++  SELS  R+   S ++ VG+   V VL +D E   I
Sbjct: 200 VARLTDFGAFVDI---GGVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERI 256

Query: 155 DLS 157
            LS
Sbjct: 257 SLS 259

Length = 390

>gnl|CDD|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 46.3 bits (111), Expect = 7e-06
 Identities = 23/63 (36%), Positives = 37/63 (58%), Gaps = 3/63 (4%)

Query: 95  VKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYI 154
           VKNI D GA+V L     ++G++  +++S +R+   S ++ VG    V VL+ DKEK  +
Sbjct: 209 VKNITDYGAFVDL---GGVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRV 265

Query: 155 DLS 157
            L 
Sbjct: 266 SLG 268

Length = 565

>gnl|CDD|233102 TIGR00717, rpsA, ribosomal protein S1

 Score = 46.3 bits (110), Expect = 7e-06
 Identities = 32/101 (31%), Positives = 51/101 (50%), Gaps = 4/101 (3%)

Query: 80  YEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELS-RRRIRSVSSLIKVGR 138
           +E ++P V   V  ++K I D GA+V L     I+G+I  S++S  +  R    L K G 
Sbjct: 353 FEEKHP-VGDRVTGKIKKITDFGAFVEL--EGGIDGLIHLSDISWDKDGREADHLYKKGD 409

Query: 139 IEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLV 179
               +VL VDKEK  I L  ++++E   +    +Y    +V
Sbjct: 410 EIEAVVLAVDKEKKRISLGVKQLTENPWEKFAAKYKVGSVV 450

This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by PFAM model pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 516

>gnl|CDD|235851 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 46.4 bits (111), Expect = 7e-06
 Identities = 24/83 (28%), Positives = 46/83 (55%), Gaps = 2/83 (2%)

Query: 95  VKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYI 154
           VK + D GA+V +L    +EG++  S++S + I + S +++ G+   V VL V++E+  I
Sbjct: 285 VKRLTDFGAFVEVLP--GVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRI 342

Query: 155 DLSKRRVSEEDIQACEERYNKSK 177
            LS + + E   +  + R    +
Sbjct: 343 SLSIKALEEAPAEEEDRREEYRQ 365

Length = 390

>gnl|CDD|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 45.2 bits (108), Expect = 2e-05
 Identities = 31/117 (26%), Positives = 53/117 (45%), Gaps = 13/117 (11%)

Query: 60  KKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILF 119
           K+L E P             +  ++      V   V  + D GA+V L   + +EG+I  
Sbjct: 444 KQLEEDPFEE----------FAKKHK-KGSIVTGTVTEVKDKGAFVEL--EDGVEGLIRA 490

Query: 120 SELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKS 176
           SELSR R+   + ++KVG      V+ +D++   I LS + + E + +     YN +
Sbjct: 491 SELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKALDEAEEKEAIAEYNSA 547

Length = 565

>gnl|CDD|225094 COG2183, Tex, Transcriptional accessory protein [Transcription]

 Score = 43.8 bits (104), Expect = 6e-05
 Identities = 25/80 (31%), Positives = 44/80 (55%), Gaps = 2/80 (2%)

Query: 86  EVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVL 145
           +  M +   V+N+ D GA+V +  +   +G++  S+LS + ++  + ++KVG I  V V+
Sbjct: 657 KPGMILEGTVRNVVDFGAFVDIGVHQ--DGLVHISQLSDKFVKDPNEVVKVGDIVKVKVI 714

Query: 146 RVDKEKGYIDLSKRRVSEED 165
            VD  +  I LS R   EE 
Sbjct: 715 EVDTARKRIALSMRLDEEEG 734

Length = 780

>gnl|CDD|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

 Score = 42.3 bits (100), Expect = 1e-04
 Identities = 33/100 (33%), Positives = 49/100 (49%), Gaps = 3/100 (3%)

Query: 81  EARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIE 140
             ++P V   V  +VK+I D GA+V L     I+G++  S+LS  R    +   K G   
Sbjct: 358 ADKHP-VGDVVEGKVKSITDFGAFVELEG--GIDGLVHLSDLSWDRPGEEAEKYKKGDEV 414

Query: 141 PVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVH 180
              VL VDKEK  I L  +++ E   +   E+Y K  +V 
Sbjct: 415 EAKVLAVDKEKERISLGIKQLEESPWEEFSEKYKKGSVVK 454

Length = 541

>gnl|CDD|240195 cd05690, S1_RPS1_repeat_ec5, S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain

 Score = 38.2 bits (89), Expect = 2e-04
 Identities = 21/63 (33%), Positives = 36/63 (57%), Gaps = 3/63 (4%)

Query: 95  VKNIADMGAYVSLLEYNNIEGMILFSELS-RRRIRSVSSLIKVGRIEPVMVLRVDKEKGY 153
           +K+I D G +V L     I+G++  S++S  +R+R  S + K G+    +VL +D E+  
Sbjct: 8   IKSITDFGIFVGLDG--GIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERER 65

Query: 154 IDL 156
           I L
Sbjct: 66  ISL 68

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. Length = 69

>gnl|CDD|105491 PRK12269, PRK12269, bifunctional cytidylate kinase/ribosomal protein S1; Provisional

 Score = 41.6 bits (97), Expect = 2e-04
 Identities = 32/112 (28%), Positives = 55/112 (49%), Gaps = 4/112 (3%)

Query: 87  VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELS-RRRIRSVSSLIKVGRIEPVMVL 145
           V+  V  +V  IAD GA++ L E   IEG+   SE S  ++    S ++K+G     M+L
Sbjct: 578 VNDVVKGRVTKIADFGAFIELAE--GIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMIL 635

Query: 146 RVDKEKGYIDLSKRRVSEEDIQACEERYN-KSKLVHSIMRHVAETLGIDLEE 196
             D + G + L  ++V+    +  E RY   ++    I++       I++EE
Sbjct: 636 GYDIQAGRVSLGLKQVTANPWEEIEARYPVGARFTRRIVKVTNAGAFIEMEE 687

Length = 863

>gnl|CDD|240189 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

 Score = 38.0 bits (89), Expect = 4e-04
 Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 4/69 (5%)

Query: 95  VKNIADMGAYVSLLEYN-NIEGMILFSELS-RRRIRSVSSLIKVGRIEPVMVLRVDKEKG 152
           V +I D G +V L       EG++  S+LS   R+ + S ++K G+   V V+ +   K 
Sbjct: 8   VTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQNGK- 66

Query: 153 YIDLSKRRV 161
            I LS + V
Sbjct: 67  -ISLSMKDV 74

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. Length = 79

>gnl|CDD|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

 Score = 40.7 bits (96), Expect = 5e-04
 Identities = 29/96 (30%), Positives = 47/96 (48%), Gaps = 9/96 (9%)

Query: 80  YEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRI 139
             +   +    V  +VK++ D GA+V L     +EG+I  SELSR  +       KVG  
Sbjct: 442 EFSEKYKKGSVVKGKVKSVKDKGAFVEL--GGGVEGLIRLSELSRDVL-------KVGDE 492

Query: 140 EPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNK 175
              +V+ +DK+   I LS + +  ++ +   E YNK
Sbjct: 493 VEAVVVSIDKKNRKILLSIKALERKEEKEALESYNK 528

Length = 541

>gnl|CDD|240194 cd05689, S1_RPS1_repeat_ec4, S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain

 Score = 37.6 bits (87), Expect = 5e-04
 Identities = 22/65 (33%), Positives = 37/65 (56%), Gaps = 5/65 (7%)

Query: 94  QVKNIADMGAYVSLLEYNNIEGMILFSEL--SRRRIRSVSSLIKVGRIEPVMVLRVDKEK 151
           +V N+ D G +V L E   +EG++  SE+  + + I   S ++ +G    VMVL +D+E+
Sbjct: 10  KVTNLTDYGCFVELEE--GVEGLVHVSEMDWTNKNIHP-SKVVSLGDEVEVMVLDIDEER 66

Query: 152 GYIDL 156
             I L
Sbjct: 67  RRISL 71

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. Length = 72

>gnl|CDD|237516 PRK13806, rpsA, 30S ribosomal protein S1; Provisional

 Score = 40.9 bits (96), Expect = 5e-04
 Identities = 26/96 (27%), Positives = 42/96 (43%), Gaps = 3/96 (3%)

Query: 94  QVKNIADMGAYVSLLEYNNIEGMILFSELS-RRRIRSVSSLIKVGRIEPVMVLRVDKEKG 152
           +V  +A  GA+V +L    IEG++  SE+S  RR+     ++  G    V +  +D  K 
Sbjct: 299 KVVRLAPFGAFVEILP--GIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKR 356

Query: 153 YIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAE 188
            I LS R    +      ER+     V   +   A+
Sbjct: 357 RISLSLRDAEGDPWADVAERFAPGTTVTGTVEKRAQ 392

Length = 491

>gnl|CDD|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

 Score = 40.4 bits (95), Expect = 6e-04
 Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 3/68 (4%)

Query: 109 EYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV-SEEDIQ 167
           +   +   +  S +  R +R +  LI  G+     +L +DK++  + LS+R V  EE  +
Sbjct: 124 DIEGVRAFLPGSLVDVRPVRDLDPLI--GKELEFKILELDKKRNNVVLSRRAVLEEERSE 181

Query: 168 ACEERYNK 175
             EE  NK
Sbjct: 182 QREELLNK 189

Length = 541

>gnl|CDD|181215 PRK08059, PRK08059, general stress protein 13; Validated

 Score = 38.5 bits (90), Expect = 6e-04
 Identities = 25/70 (35%), Positives = 38/70 (54%), Gaps = 2/70 (2%)

Query: 94  QVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGY 153
           +V  I   GA+V+L E    +G++  SE++   ++ +   + VG    V VL VD+EKG 
Sbjct: 14  KVTGIQPYGAFVALDE--ETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGK 71

Query: 154 IDLSKRRVSE 163
           I LS R   E
Sbjct: 72  ISLSIRATEE 81

Length = 123

>gnl|CDD|237516 PRK13806, rpsA, 30S ribosomal protein S1; Provisional

 Score = 40.1 bits (94), Expect = 8e-04
 Identities = 25/84 (29%), Positives = 40/84 (47%), Gaps = 6/84 (7%)

Query: 95  VKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDK-EKGY 153
           V  +A  GA+V L     +EGM+  SELS  R++     + VG    V VL +++ +KG 
Sbjct: 210 VTRLAPFGAFVELAP--GVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGK 267

Query: 154 ---IDLSKRRVSEEDIQACEERYN 174
              I LS ++   +      +R  
Sbjct: 268 GLRISLSIKQAGGDPWDTVGDRLK 291

Length = 491

>gnl|CDD|240196 cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain

 Score = 36.9 bits (86), Expect = 8e-04
 Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 2/67 (2%)

Query: 91  VMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKE 150
           V  +V  +   GA V L +   +EG +  +ELSR R+   +   KVG      +  VD++
Sbjct: 4   VTGKVTEVDAKGATVKLGD--GVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRK 61

Query: 151 KGYIDLS 157
              I LS
Sbjct: 62  NRKISLS 68

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. Length = 73

>gnl|CDD|240213 cd05708, S1_Rrp5_repeat_sc12, S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

 Score = 36.2 bits (84), Expect = 0.001
 Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 95  VKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYI 154
           V+ + D G ++ + +  N+ G+   SE+S  R+   S L +VG      VL++D EK  I
Sbjct: 10  VRRVEDYGVFIDI-DGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRI 68

Query: 155 DLS 157
            L 
Sbjct: 69  SLG 71

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 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Length = 77

>gnl|CDD|235851 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 38.3 bits (90), Expect = 0.002
 Identities = 22/51 (43%), Positives = 32/51 (62%)

Query: 114 EGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEE 164
           EG+I  SELS   I  ++ ++KVG    V VL+V+  +G + LSKRR+  E
Sbjct: 43  EGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRLEAE 93

Length = 390

>gnl|CDD|236126 PRK07899, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 38.5 bits (90), Expect = 0.003
 Identities = 25/69 (36%), Positives = 38/69 (55%), Gaps = 9/69 (13%)

Query: 102 GAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV 161
           GA+V + E   IEG++  SEL+ R +     +++VG  + V V  +D     IDL +RR+
Sbjct: 308 GAFVRVEE--GIEGLVHISELAERHVEVPEQVVQVG--DEVFVKVID-----IDLERRRI 358

Query: 162 SEEDIQACE 170
           S    QA E
Sbjct: 359 SLSLKQANE 367

Length = 486

>gnl|CDD|180960 PRK07400, PRK07400, 30S ribosomal protein S1; Reviewed

 Score = 37.5 bits (87), Expect = 0.004
 Identities = 23/79 (29%), Positives = 41/79 (51%), Gaps = 3/79 (3%)

Query: 86  EVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVL 145
           EV   V+  V+ I   GA++ +     + G++  SE+S   I +  S+  V     VM++
Sbjct: 195 EVGEVVVGTVRGIKPYGAFIDI---GGVSGLLHISEISHEHIETPHSVFNVNDEMKVMII 251

Query: 146 RVDKEKGYIDLSKRRVSEE 164
            +D E+G I LS +++  E
Sbjct: 252 DLDAERGRISLSTKQLEPE 270

Length = 318

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	259
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	100.0
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	100.0
KOG2916	304	consensus Translation initiation factor 2, alpha s	99.96
PRK03987	262	translation initiation factor IF-2 subunit alpha;	99.96
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	99.94
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	99.94
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	99.89
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	99.88
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	99.86
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	99.85
PHA02945	88	interferon resistance protein; Provisional	99.83
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	99.82
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	99.81
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	99.8
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	99.8
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	99.78
COG1098	129	VacB Predicted RNA binding protein (contains ribos	99.78
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	99.77
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	99.73
PRK07400	318	30S ribosomal protein S1; Reviewed	99.69
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	99.68
PRK07400	318	30S ribosomal protein S1; Reviewed	99.68
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	99.67
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	99.67
PRK08582	139	hypothetical protein; Provisional	99.65
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	99.63
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	99.63
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	99.62
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	99.62
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	99.62
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	99.6
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	99.6
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	99.6
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	99.59
PRK07252	120	hypothetical protein; Provisional	99.59
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	99.59
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	99.58
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	99.58
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	99.57
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	99.57
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	99.57
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	99.56
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	99.56
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	99.54
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	99.53
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	99.53
PRK05807	136	hypothetical protein; Provisional	99.53
PRK08059	123	general stress protein 13; Validated	99.52
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	99.51
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	99.49
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	99.48
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	99.46
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	99.45
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	99.44
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	99.42
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	99.4
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	99.4
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	99.39
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	99.39
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	99.38
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	99.38
PHA02858	86	EIF2a-like PKR inhibitor; Provisional	99.36
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	99.36
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	99.35
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	99.26
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	99.24
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	99.24
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	99.23
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	99.23
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	99.2
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	99.19
COG2183	780	Tex Transcriptional accessory protein [Transcripti	99.16
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	99.09
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	99.09
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	99.04
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	99.01
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	98.92
PRK11642	813	exoribonuclease R; Provisional	98.91
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	98.88
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	98.87
PRK09202	470	nusA transcription elongation factor NusA; Validat	98.71
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.69
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	98.68
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	98.66
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.57
PRK05054	644	exoribonuclease II; Provisional	98.48
TIGR01953	341	NusA transcription termination factor NusA. This m	98.41
PRK12327	362	nusA transcription elongation factor NusA; Provisi	98.39
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	98.35
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	98.3
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	98.29
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	98.23
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	98.17
COG0557	706	VacB Exoribonuclease R [Transcription]	98.09
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	98.05
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	98.04
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	98.0
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	97.92
PRK12328	374	nusA transcription elongation factor NusA; Provisi	97.88
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	97.82
PF07541	114	EIF_2_alpha: Eukaryotic translation initiation fac	97.77
COG1107	715	Archaea-specific RecJ-like exonuclease, contains D	97.66
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	97.65
PRK11712	489	ribonuclease G; Provisional	97.52
PRK12329	449	nusA transcription elongation factor NusA; Provisi	97.49
PRK10811	1068	rne ribonuclease E; Reviewed	97.35
KOG1856	1299	consensus Transcription elongation factor SPT6 [RN	97.23
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	96.68
KOG3409	193	consensus Exosomal 3'-5' exoribonuclease complex,	95.98
KOG3298	170	consensus DNA-directed RNA polymerase subunit E' [	95.19
PF08292	122	RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I	94.81
COG1530	487	CafA Ribonucleases G and E [Translation, ribosomal	94.42
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	92.77
PRK12442	87	translation initiation factor IF-1; Reviewed	92.49
COG1098	129	VacB Predicted RNA binding protein (contains ribos	91.31
TIGR00008	68	infA translation initiation factor IF-1. This fami	91.22
PF00313	66	CSD: 'Cold-shock' DNA-binding domain; InterPro: IP	90.41
KOG3013	301	consensus Exosomal 3'-5' exoribonuclease complex,	90.31
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	89.58
PF10246	104	MRP-S35: Mitochondrial ribosomal protein MRP-S35;	89.12
PRK15463	70	cold shock-like protein CspF; Provisional	89.05
PRK15464	70	cold shock-like protein CspH; Provisional	88.55
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	87.64
PRK10943	69	cold shock-like protein CspC; Provisional	87.24
PRK09507	69	cspE cold shock protein CspE; Reviewed	86.65
PRK09890	70	cold shock protein CspG; Provisional	85.81
PRK09937	74	stationary phase/starvation inducible regulatory p	85.53
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	84.81
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	84.53
COG4776	645	Rnb Exoribonuclease II [Transcription]	83.97
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	82.81
PRK09202	470	nusA transcription elongation factor NusA; Validat	82.51
PRK10354	70	RNA chaperone/anti-terminator; Provisional	82.04
cd04458	65	CSP_CDS Cold-Shock Protein (CSP) contains an S1-li	81.71
TIGR02381	68	cspD cold shock domain protein CspD. This model re	81.41
PRK14998	73	cold shock-like protein CspD; Provisional	81.2
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	81.18
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	80.89
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	80.63
cd05700	65	S1_Rrp5_repeat_hs9 S1_Rrp5_repeat_hs9: Rrp5 is a t	80.55
KOG1004	230	consensus Exosomal 3'-5' exoribonuclease complex s	80.42

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=100.00  E-value=9e-38  Score=288.27  Aligned_cols=164  Identities=62%  Similarity=1.017  Sum_probs=158.5

Q ss_pred             CchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCC
Q 044309           73 PNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKG  152 (259)
Q Consensus        73 ~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~g  152 (259)
                      +.+.|||+.++||++|++|.|+|++|.+|||||+|.+|+|++||||+||+||+|++++++++++||.+.|+|++||+++|
T Consensus         3 ~~~~cr~~~~~~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg   82 (319)
T PTZ00248          3 DLLDCRFYEQKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKG   82 (319)
T ss_pred             CcccccchhhhCCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCC
Confidence            46789999999998999999999999999999999999899999999999999999999999999999999999999999


Q ss_pred             eEEEEEeecchhhHHHHHHhccccceEEEEEEecccccCCchHHHHHhhchhhHHhhcCHHHHHHHHhcCcchhhccCCC
Q 044309          153 YIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTR  232 (259)
Q Consensus       153 kI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fve~~~~~~sw~l~~~~~~~~~~fk~a~~~~~~~l~~l~~  232 (259)
                      +|+||+|++.++||..+.++|+.|++++|+|.+++++||+|++++|..++||+.+.|+|+|+||+.++.+|.++|.++++
T Consensus        83 ~IdLS~K~v~~~pw~~~~e~~~~g~~v~~~V~~ia~~~g~~~eely~~i~~pl~~~~gh~y~af~~~v~~~~evl~~l~i  162 (319)
T PTZ00248         83 YIDLSKKRVSPEDIEACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYGHALDALKEALTNPDNVFEGLDI  162 (319)
T ss_pred             EEEEEeeecccchHHHHHHhCcCCCEEEEEEEEchhhcCCCHHHHHHHHHHHHHHhcCCHHHHHHHHhcCchhhhccCCC
Confidence            99999999999999999999999999999999999889999999999999999999999999999999999999999998


Q ss_pred             cccc
Q 044309          233 EVKE  236 (259)
Q Consensus       233 ~~~~  236 (259)
                      .+..
T Consensus       163 ~~ev  166 (319)
T PTZ00248        163 PEEV  166 (319)
T ss_pred             CHHH
Confidence            7543

>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=5.2e-35  Score=260.41  Aligned_cols=163  Identities=34%  Similarity=0.512  Sum_probs=156.9

Q ss_pred             hhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEE
Q 044309           77 CRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDL  156 (259)
Q Consensus        77 ~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~L  156 (259)
                      ||+..+.||++|++|.|+|++|.+|||||.|+||+|.+||+|+||++.+|++|+++++++||.+.|+|++||+.+|.|+|
T Consensus         1 m~~~~~~~PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDL   80 (269)
T COG1093           1 MRMKRREYPEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDL   80 (269)
T ss_pred             CcccccCCCCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEee
Confidence            67788899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeecchhhHHHHHHhccccceEEEEEEecccccCCchHHHHHhhchhhHHhhcCHHHHHHHHhcCcchhhccCCCcccc
Q 044309          157 SKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTREVKE  236 (259)
Q Consensus       157 SlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fve~~~~~~sw~l~~~~~~~~~~fk~a~~~~~~~l~~l~~~~~~  236 (259)
                      |+|++.+++..++.+.|+..+.+..+++.+++++|.+++++|.+++|+|.+.||++|+||+.|+.+|.++|.++..++..
T Consensus        81 SlkrV~~~q~~~k~~~wk~~qka~klle~aaekl~~~~ee~~~~vg~~L~e~fG~~y~aFE~aa~~g~~~l~~~~~~~~~  160 (269)
T COG1093          81 SLKRVTEHQRRKKIQEWKKEQKADKLLELAAEKLGKDLEEAYEEVGWKLEEEFGSLYDAFEAAAKEGGEVLDDEGVPEEW  160 (269)
T ss_pred             ehhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHhHHHHHHhCCHHHHHHHHHhcCCcccccCCCCHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999987665


Q ss_pred             CCC
Q 044309          237 IGP  239 (259)
Q Consensus       237 ~~~  239 (259)
                      +++
T Consensus       161 ~~~  163 (269)
T COG1093         161 KEV  163 (269)
T ss_pred             HHH
Confidence            544

>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]

Probab=99.96  E-value=5e-31  Score=234.55  Aligned_cols=158  Identities=73%  Similarity=1.166  Sum_probs=153.9

Q ss_pred             CchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCC
Q 044309           73 PNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKG  152 (259)
Q Consensus        73 ~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~g  152 (259)
                      +.+.|||+..+||+++++|.+.|.+|.+.||||.|.||++++|||-+||||.+|++++++..++|..-.|.|++||+++|
T Consensus         2 ~~~~cR~ye~kyPev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekG   81 (304)
T KOG2916|consen    2 STLECRFYENKYPEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKG   81 (304)
T ss_pred             CcceeehhhccCCCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCCC
Confidence            35789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEEeecchhhHHHHHHhccccceEEEEEEecccccCCchHHHHHhhchhhHHhhcCHHHHHHHHhcCcchhhccCC
Q 044309          153 YIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLT  231 (259)
Q Consensus       153 kI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fve~~~~~~sw~l~~~~~~~~~~fk~a~~~~~~~l~~l~  231 (259)
                      +|+||.+++.+++..+|.++|.+...++.++.++++++|..+++||..++||++++|||+|+|||+++.+|. +|..|+
T Consensus        82 YIDLSkrrVs~ed~~kC~Er~~ksK~v~sIlrhvAe~~g~~LeeLY~~igW~~~rk~g~aYdaFK~~vtd~t-V~d~l~  159 (304)
T KOG2916|consen   82 YIDLSKRRVSPEDKEKCEERFAKSKLVYSILRHVAEKLGYELEELYQRIGWPLERKYGHAYDAFKIAVTDPT-VLDELD  159 (304)
T ss_pred             ceechhccCCHHHHHHHHHHHHHhHHHHHHHHHHHHHhCCcHHHHHHHhCCchhhhhchHHHHHHHhccCcc-cccccC
Confidence            999999999999999999999999999999999999999999999999999999999999999999999955 999888

>PRK03987 translation initiation factor IF-2 subunit alpha; Validated

Probab=99.96  E-value=2.1e-29  Score=228.23  Aligned_cols=158  Identities=29%  Similarity=0.457  Sum_probs=149.3

Q ss_pred             hcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeec
Q 044309           82 ARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV  161 (259)
Q Consensus        82 ~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~  161 (259)
                      +.+|++|++|.|+|++|.++|+||+|.+|++++||||+|+++++++.++++.+++||.+.|+|+++|+++++|+||+|++
T Consensus         3 ~~~P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~v   82 (262)
T PRK03987          3 KEWPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKRV   82 (262)
T ss_pred             CCCCCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEEec
Confidence            46888999999999999999999999987789999999999999999999999999999999999999999999999999


Q ss_pred             chhhHHHHHHhccccceEEEEEEecccccCCchHHHHHhhchhhHHhhcCHHHHHHHHhcCcchhhccCCCccccCCC
Q 044309          162 SEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTREVKEIGP  239 (259)
Q Consensus       162 ~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fve~~~~~~sw~l~~~~~~~~~~fk~a~~~~~~~l~~l~~~~~~~~~  239 (259)
                      .+++..++.++|+..+.++.++..+++++|..++++|..++|||.++|||+|+||+.|+.+++++|.++++++...++
T Consensus        83 ~~~e~~~~~~~~~~~~~~~~il~~~a~~~~~~~e~~~~~~~~~l~~~yg~~y~af~~~~~~~~~~l~~~~~~~~~~~~  160 (262)
T PRK03987         83 NEHQRREKIQEWKNEQKADKWLELAAEKLGKSLEEAWEEVGYKLEDEFGDLYDAFEEAAIEGEEALDDLGVPEEWADA  160 (262)
T ss_pred             ccchHHHHHHHHHHHhhHhhHHHHHHHHcCCCHHHHHHHHHHHHHHHhCcHHHHHHHHHhcChhhhccCCCCHHHHHH
Confidence            998888899999999999999999999999999999999999999999999999999998778899999988766554

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

Probab=99.94  E-value=2.5e-27  Score=231.20  Aligned_cols=179  Identities=25%  Similarity=0.389  Sum_probs=152.4

Q ss_pred             Cccccchhhhh----hhhcccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccc
Q 044309           48 TPFEFSRENAK----AKKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELS  123 (259)
Q Consensus        48 ~~~eid~e~~r----iK~l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls  123 (259)
                      .++++|++++|    ||++.++||..          +.+++| +|+.+.|+|+++++|||||++.  +|++||+|+||+|
T Consensus       245 kVi~~D~e~~RVsLSlK~l~~dPw~~----------i~~~~~-~g~~v~G~Vt~i~~~GafVei~--~GvEGlvhvSEis  311 (541)
T COG0539         245 KVISLDEERGRVSLSLKQLEEDPWEG----------IEKKYP-VGDKVEGKVTNLTDYGAFVEIE--EGVEGLVHVSEIS  311 (541)
T ss_pred             EEEEEccCCCeEEEEehhcccCcHHH----------HhhhcC-CCCEEEEEEEEeecCcEEEEec--CCccceeechhhc
Confidence            44689999999    59999999998          889999 9999999999999999999998  6999999999999


Q ss_pred             cccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHHhccccceEEEEEEecccccCCch------HHH
Q 044309          124 RRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDL------EEL  197 (259)
Q Consensus       124 ~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fv------e~~  197 (259)
                      |.+...|++++++||+|.|+|+++|++++||+||+|++..+||+...+.|+.|+.++|.|.++++ +|+|+      +++
T Consensus       312 w~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~~~~~~~g~~v~g~v~~~t~-~g~fv~le~gidG~  390 (541)
T COG0539         312 WTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFADKHPVGDVVEGKVKSITD-FGAFVELEGGIDGL  390 (541)
T ss_pred             ccccCCHHHhcccCCEEEEEEEeeCchhceEEeeehhhhcChhhhhhhhcCCCCeEEEEEeeecc-cceEEccCCCccce
Confidence            99988899999999999999999999999999999999999999999999999999999999987 99997      344


Q ss_pred             --HHhhchhhHHhhcCHHHHHHHHh--------cCcchhhccCCCccccCCCCCcc
Q 044309          198 --YVNIGWPLYWKYGHAFEAFKIIV--------TDPDSVLNSLTREVKEIGPDGQE  243 (259)
Q Consensus       198 --~~~~sw~l~~~~~~~~~~fk~a~--------~~~~~~l~~l~~~~~~~~~~~~~  243 (259)
                        .+++||.   +-+....-||..-        -++..--.+|+++.-+-+|+...
T Consensus       391 vh~~d~sw~---~~~~~~~~~k~Gd~v~~~vl~vd~~~~~isLgiKql~~~p~~~~  443 (541)
T COG0539         391 VHLSDLSWD---RPGEEAEKYKKGDEVEAKVLAVDKEKERISLGIKQLEESPWEEF  443 (541)
T ss_pred             EEHHhcCcc---ccCcHHHhhccCcEEEEEEEEEecccceeeeehhhhccCchhhh
Confidence              8999995   3334444555432        12222344566666666776543

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

Probab=99.94  E-value=9e-27  Score=227.31  Aligned_cols=192  Identities=26%  Similarity=0.365  Sum_probs=150.0

Q ss_pred             cccccceeEEEeecCCccccchhhhhh----hhcccCccccCCCCchhhhh-hhhcCCCCCcEEEEEEEEEeCceEEEEE
Q 044309           33 ADSLSGCLKTLILVPTPFEFSRENAKA----KKLSEQPIMASHSPNLECRM-YEARYPEVDMAVMIQVKNIADMGAYVSL  107 (259)
Q Consensus        33 ~~~l~g~~~~~~~~~~~~eid~e~~ri----K~l~~~pw~~~~~~~~~~R~-~~~~~~~~G~iv~G~V~~I~~~GafV~L  107 (259)
                      .+.+.|.....    .++++|++++++    +.+.+.       .....|. +.+.++ +|+++.|+|+++++|||||+|
T Consensus       145 ~~~~~Gk~~~~----kiie~d~~~n~vv~SrR~~~e~-------~~~~~r~e~~~~l~-~G~vV~G~V~~It~~GafVdi  212 (541)
T COG0539         145 LDPLIGKELEF----KILELDKKRNNVVLSRRAVLEE-------ERSEQREELLNKLE-VGEVVEGVVKNITDYGAFVDI  212 (541)
T ss_pred             ccccCCceEEE----EEEEEccccCcEEEEhHHHhhH-------HHHHHHHHHHhcCC-CCceEEEEEEEeecCcEEEEe
Confidence            45566766664    457999999985    222210       0111111 345677 999999999999999999999


Q ss_pred             ccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHHhccccceEEEEEEecc
Q 044309          108 LEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVA  187 (259)
Q Consensus       108 ~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~  187 (259)
                      .   |++||||+|||||.++.+|+++|++||+|+|+|+++|++++||+||+|++.++||+...++|++|+.+.|+|+++.
T Consensus       213 g---GvdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~l~~dPw~~i~~~~~~g~~v~G~Vt~i~  289 (541)
T COG0539         213 G---GVDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQLEEDPWEGIEKKYPVGDKVEGKVTNLT  289 (541)
T ss_pred             c---CeeeEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehhcccCcHHHHhhhcCCCCEEEEEEEEee
Confidence            4   7999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cccCCch------HHH--HHhhchhhHHhhcCHHHHHHHHh--------cCcchhhccCCCccccCCCCCcc
Q 044309          188 ETLGIDL------EEL--YVNIGWPLYWKYGHAFEAFKIIV--------TDPDSVLNSLTREVKEIGPDGQE  243 (259)
Q Consensus       188 ~~~G~fv------e~~--~~~~sw~l~~~~~~~~~~fk~a~--------~~~~~~l~~l~~~~~~~~~~~~~  243 (259)
                      + ||+|+      ++|  .+++||.   +...+.+.++.-=        .++++--.+|++++-.-+|+.+.
T Consensus       290 ~-~GafVei~~GvEGlvhvSEisw~---~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~  357 (541)
T COG0539         290 D-YGAFVEIEEGVEGLVHVSEISWT---KKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEF  357 (541)
T ss_pred             c-CcEEEEecCCccceeechhhccc---ccCCHHHhcccCCEEEEEEEeeCchhceEEeeehhhhcChhhhh
Confidence            7 99997      456  9999995   5555777774211        22333344555555555664443

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=99.89  E-value=2.9e-23  Score=213.35  Aligned_cols=143  Identities=23%  Similarity=0.434  Sum_probs=131.4

Q ss_pred             Cccccchhhhhh----hhcccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccc
Q 044309           48 TPFEFSRENAKA----KKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELS  123 (259)
Q Consensus        48 ~~~eid~e~~ri----K~l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls  123 (259)
                      .++++|++++|+    |++.++||..          +.+.++ +|+++.|+|+++++||+||+|.  +|++||+|+||++
T Consensus       546 kVi~iD~e~~rI~LSlK~l~~~p~~~----------~~~~~~-vG~iV~G~V~~I~~fG~fVeL~--~gveGLvhiSEls  612 (863)
T PRK12269        546 KVIRLDQAEKRINLSLKHFQPDPWLE----------FENKFG-VNDVVKGRVTKIADFGAFIELA--EGIEGLAHISEFS  612 (863)
T ss_pred             EEEEEecCCCeEEEEEeccccchhhh----------hhccCC-CCCEEEEEEEEEeCCeEEEEec--CCceeeeEHHHhc
Confidence            346889998884    8899999997          777888 9999999999999999999997  5899999999999


Q ss_pred             c-ccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHHhccccceEEEEEEecccccCCch------HH
Q 044309          124 R-RRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDL------EE  196 (259)
Q Consensus       124 ~-~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fv------e~  196 (259)
                      | .++.+|.+.|++||+|+|+|+++|+++++|.||+|++.++||....++|+.|++++|+|.++.+ ||+|+      ++
T Consensus       613 ~~~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw~~~~~~~~vG~~v~G~V~~i~~-~G~fV~l~~gV~G  691 (863)
T PRK12269        613 WVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIEARYPVGARFTRRIVKVTN-AGAFIEMEEGIDG  691 (863)
T ss_pred             CccccCCHHHcCCCCCEEEEEEEEEecccCceEEEehhcccCchHHHHHhCCCCCEEEEEEEEEec-ceEEEEeCCCcEE
Confidence            9 6889999999999999999999999999999999999999999999999999999999999987 99997      33


Q ss_pred             H--HHhhchh
Q 044309          197 L--YVNIGWP  204 (259)
Q Consensus       197 ~--~~~~sw~  204 (259)
                      +  .++++|.
T Consensus       692 lIh~sels~~  701 (863)
T PRK12269        692 FLHVDDLSWV  701 (863)
T ss_pred             EEEhHHhhcc
Confidence            4  8899994

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=99.88  E-value=1.1e-22  Score=198.96  Aligned_cols=151  Identities=23%  Similarity=0.327  Sum_probs=131.9

Q ss_pred             ccccchhh----hh----hhhcccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcc
Q 044309           49 PFEFSREN----AK----AKKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFS  120 (259)
Q Consensus        49 ~~eid~e~----~r----iK~l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhis  120 (259)
                      ++++|.++    +|    +|++.++||..          +.+.++ +|+++.|+|+++++||+||++.  +|++||+|+|
T Consensus       257 Vl~id~~~~~~~~ri~lS~K~~~~~p~~~----------~~~~~~-~G~~v~G~V~~v~~~G~fV~l~--~gv~Glvh~s  323 (491)
T PRK13806        257 VLGIERAKKGKGLRISLSIKQAGGDPWDT----------VGDRLK-AGDKVTGKVVRLAPFGAFVEIL--PGIEGLVHVS  323 (491)
T ss_pred             EEEEecccCCcceEEEEEehhhhcccchh----------hhccCC-CCCEEEEEEEEEeCceEEEEeC--CCcEEEEEHH
Confidence            34677776    35    38889999997          777888 9999999999999999999997  5899999999


Q ss_pred             cccc-ccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHHhccccceEEEEEEecccccCCch-----
Q 044309          121 ELSR-RRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDL-----  194 (259)
Q Consensus       121 Els~-~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fv-----  194 (259)
                      +++| .++.++.+.+++||.|.|+|+++|+++++|.||+|++..+||....+.|++|++++|+|+++.+ ||+|+     
T Consensus       324 els~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~~~p~~~~~~~~~vG~~v~G~V~~i~~-~G~FV~l~~g  402 (491)
T PRK13806        324 EMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAERFAPGTTVTGTVEKRAQ-FGLFVNLAPG  402 (491)
T ss_pred             HcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEeecccChhHHhhhhCCCCCEEEEEEEEEec-CceEEEcCCC
Confidence            9999 6788899999999999999999999999999999999999999999999999999999999976 99997     


Q ss_pred             -HHH--HHhhchhhHHhhcCHHHHH
Q 044309          195 -EEL--YVNIGWPLYWKYGHAFEAF  216 (259)
Q Consensus       195 -e~~--~~~~sw~l~~~~~~~~~~f  216 (259)
                       ++|  .++++|.   +...+.+.|
T Consensus       403 v~Gli~~se~s~~---~~~~~~~~~  424 (491)
T PRK13806        403 VTGLLPASVISRA---GKPATYEKL  424 (491)
T ss_pred             cEEEEEHHHcCcc---cccchhhcC
Confidence             234  8899984   334444444

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.86  E-value=9e-22  Score=191.85  Aligned_cols=150  Identities=19%  Similarity=0.259  Sum_probs=128.9

Q ss_pred             ccceeEEEeecCCccccchhhhhh----hh----cccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEE
Q 044309           36 LSGCLKTLILVPTPFEFSRENAKA----KK----LSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSL  107 (259)
Q Consensus        36 l~g~~~~~~~~~~~~eid~e~~ri----K~----l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L  107 (259)
                      ..|.....    .++++|++++++    |.    ....+|..          +...++ +|+++.|+|+++++||+||+|
T Consensus       164 ~vGq~V~v----kVleid~~~~~ivLSrr~~l~~~~~~~~~~----------~~~~lk-~G~iv~G~V~~i~~~G~FVdl  228 (486)
T PRK07899        164 YIGQEIEA----KIIELDKNRNNVVLSRRAWLEQTQSEVRSE----------FLNQLQ-KGQVRKGVVSSIVNFGAFVDL  228 (486)
T ss_pred             cCCCEEEE----EEEEEECCCCEEEEEhHHHHHhhhHHHHHH----------HHHhcc-CCCEEEEEEEEEECCeEEEEE
Confidence            45665554    346788888874    32    23356665          556777 999999999999999999999


Q ss_pred             ccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHHhccccceEEEEEEecc
Q 044309          108 LEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVA  187 (259)
Q Consensus       108 ~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~  187 (259)
                      .   +++||||+|+++|.++.++.+.|++||.|+|+|+++|+++++|.||+|++.++||....++++.|+++.|+|+++.
T Consensus       229 g---gv~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~~~~~~vG~vv~G~V~~I~  305 (486)
T PRK07899        229 G---GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKATQEDPWQQFARTHAIGQIVPGKVTKLV  305 (486)
T ss_pred             C---CEEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeeccccchhhhHHhcCCCCEEEEEEEEEe
Confidence            4   7999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             cccCCchH------HH--HHhhchh
Q 044309          188 ETLGIDLE------EL--YVNIGWP  204 (259)
Q Consensus       188 ~~~G~fve------~~--~~~~sw~  204 (259)
                      + +|+|++      +|  .++++|.
T Consensus       306 ~-fGvFVeL~~gieGLvh~SeLs~~  329 (486)
T PRK07899        306 P-FGAFVRVEEGIEGLVHISELAER  329 (486)
T ss_pred             c-cEEEEEeCCCcEEEEEHHHcCcc
Confidence            6 999972      34  8888884

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=99.85  E-value=2.2e-21  Score=199.61  Aligned_cols=143  Identities=22%  Similarity=0.375  Sum_probs=128.1

Q ss_pred             Cccccchhhhh----hhhcccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccc
Q 044309           48 TPFEFSRENAK----AKKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELS  123 (259)
Q Consensus        48 ~~~eid~e~~r----iK~l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls  123 (259)
                      .++.+|.+++|    +|++.++||..          +.+.++ +|+++.|+|+++++||+||+|.  +|++||||.||++
T Consensus       633 kVl~iD~e~~rIsLS~K~l~~~Pw~~----------~~~~~~-vG~~v~G~V~~i~~~G~fV~l~--~gV~GlIh~sels  699 (863)
T PRK12269        633 MILGYDIQAGRVSLGLKQVTANPWEE----------IEARYP-VGARFTRRIVKVTNAGAFIEME--EGIDGFLHVDDLS  699 (863)
T ss_pred             EEEEEecccCceEEEehhcccCchHH----------HHHhCC-CCCEEEEEEEEEecceEEEEeC--CCcEEEEEhHHhh
Confidence            44678999888    48999999998          778888 9999999999999999999997  6999999999999


Q ss_pred             cccc-cCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHHhccccceEEEEEEecccccCCch------HH
Q 044309          124 RRRI-RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDL------EE  196 (259)
Q Consensus       124 ~~~v-~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fv------e~  196 (259)
                      |.+. .++...|++||.|+|+|+++|+++++|.||+|++..+||....+.|+.|++++|+|..+.+ +|+|+      ++
T Consensus       700 ~~~~~~~~~~~~kvGq~VkvkVl~ID~e~rrI~LS~K~l~~dpw~~~~~~~~vG~iV~GkV~~v~~-~GvFVeL~~gVeG  778 (863)
T PRK12269        700 WVKRTRPADHELEVGKEIECMVIECDPQARRIRLGVKQLSDNPWQVFANAYGVGSTVEGEVSSVTD-FGIFVRVPGGVEG  778 (863)
T ss_pred             ccccccchhhccCCCCEEEEEEEEEeccCCEEEEEecccccChHHHHHhhCCCCCEEEEEEEEEec-CeEEEEcCCCeEE
Confidence            9664 4455689999999999999999999999999999999999999999999999999999976 99997      23


Q ss_pred             H--HHhhchh
Q 044309          197 L--YVNIGWP  204 (259)
Q Consensus       197 ~--~~~~sw~  204 (259)
                      +  .++++|.
T Consensus       779 lI~~s~lsdd  788 (863)
T PRK12269        779 LVRKQHLVEN  788 (863)
T ss_pred             EEEHHHcCCc
Confidence            3  8888885

>PHA02945 interferon resistance protein; Provisional

Probab=99.83  E-value=3.6e-20  Score=140.69  Aligned_cols=79  Identities=28%  Similarity=0.451  Sum_probs=75.4

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccc--ccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEee
Q 044309           83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSEL--SRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRR  160 (259)
Q Consensus        83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEl--s~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~  160 (259)
                      .+|++|+++.|+|+. .+|||||.|+||+|.+||||+||+  +.+|+++ ++++ .||++.|+|+++|+.+|.|+||+|+
T Consensus         7 ~~P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~-rd~l-~GqkvV~KVirVd~~kg~IDlSlK~   83 (88)
T PHA02945          7 SLPNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY-RDKL-VGKTVKVKVIRVDYTKGYIDVNYKR   83 (88)
T ss_pred             cCCCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEee-eeEe-cCCEEEEEEEEECCCCCEEEeEeeE
Confidence            588899999999999 999999999999999999999955  9999999 9999 9999999999999999999999999


Q ss_pred             cchh
Q 044309          161 VSEE  164 (259)
Q Consensus       161 ~~~~  164 (259)
                      +.++
T Consensus        84 V~~~   87 (88)
T PHA02945         84 MCRH   87 (88)
T ss_pred             cccC
Confidence            8764

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=99.82  E-value=2.2e-20  Score=182.66  Aligned_cols=162  Identities=21%  Similarity=0.301  Sum_probs=132.4

Q ss_pred             ccceeEEEeecCCccccchhhhhh----hhcc----cCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEE
Q 044309           36 LSGCLKTLILVPTPFEFSRENAKA----KKLS----EQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSL  107 (259)
Q Consensus        36 l~g~~~~~~~~~~~~eid~e~~ri----K~l~----~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L  107 (259)
                      +.|+....    .++++|++++++    +++.    +.+|..          +...+. +|+++.|+|+++.++|+||+|
T Consensus       158 ~vG~~i~~----~V~~id~~~~~v~lSrk~~~~~~~~~~~~~----------~~~~l~-~G~iv~G~V~~v~~~G~fV~l  222 (491)
T PRK13806        158 YVGQTFQF----LITRVEENGRNIVVSRRALLEREQKEALEA----------FMETVK-EGDVVEGTVTRLAPFGAFVEL  222 (491)
T ss_pred             cCCCeEEE----EEEEEECCCCeEEEEeehhhhhhhHHHHHH----------HHhhCC-CCCEEEEEEEEEeCCeEEEEc
Confidence            45665554    235788888774    3332    244554          445566 999999999999999999999


Q ss_pred             ccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCC----CeEEEEEeecchhhHHHHHHhccccceEEEEE
Q 044309          108 LEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEK----GYIDLSKRRVSEEDIQACEERYNKSKLVHSIM  183 (259)
Q Consensus       108 ~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~----gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V  183 (259)
                      .  ++++||||+|+++|.++.++.+.|++||.|.|+|+++|.++    ++|.||+|++.++||....++|+.|+++.|+|
T Consensus       223 ~--~gv~g~v~~sels~~~~~~~~~~~~vGd~i~vkVl~id~~~~~~~~ri~lS~K~~~~~p~~~~~~~~~~G~~v~G~V  300 (491)
T PRK13806        223 A--PGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVGDRLKAGDKVTGKV  300 (491)
T ss_pred             C--CCcEEEEEHHHCCCccccChhHhcCCCCEEEEEEEEEecccCCcceEEEEEehhhhcccchhhhccCCCCCEEEEEE
Confidence            6  58999999999999999999999999999999999999875    47999999999999999999999999999999


Q ss_pred             EecccccCCchH------HH--HHhhchhhHHhhcCHHHHHH
Q 044309          184 RHVAETLGIDLE------EL--YVNIGWPLYWKYGHAFEAFK  217 (259)
Q Consensus       184 ~~i~~~~G~fve------~~--~~~~sw~l~~~~~~~~~~fk  217 (259)
                      +.+.+ +|+|++      ++  .++++|.  ++..++.+.|+
T Consensus       301 ~~v~~-~G~fV~l~~gv~Glvh~sels~~--~~~~~~~~~~~  339 (491)
T PRK13806        301 VRLAP-FGAFVEILPGIEGLVHVSEMSWT--RRVNKPEDVVA  339 (491)
T ss_pred             EEEeC-ceEEEEeCCCcEEEEEHHHcCcc--cccCCHHHcCC
Confidence            99976 999972      34  8899994  34455555553

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.81  E-value=1.6e-19  Score=178.81  Aligned_cols=161  Identities=24%  Similarity=0.377  Sum_probs=133.1

Q ss_pred             cccceeEEEeecCCccccchhhhhh----hhcccC----ccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEE
Q 044309           35 SLSGCLKTLILVPTPFEFSRENAKA----KKLSEQ----PIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVS  106 (259)
Q Consensus        35 ~l~g~~~~~~~~~~~~eid~e~~ri----K~l~~~----pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~  106 (259)
                      .+.|+....    .++++|++++++    |++.+.    +|..          +...+. +|+++.|+|++++++|+||+
T Consensus       156 ~~vG~~i~~----~V~~~d~~~~~i~lS~k~~~~~~~~~~~~~----------~~~~l~-~G~iv~g~V~~v~~~G~~V~  220 (565)
T PRK06299        156 PLEGKELEF----KVIKLDKKRNNIVVSRRAVLEEERAEEREE----------LLENLE-EGQVVEGVVKNITDYGAFVD  220 (565)
T ss_pred             HhCCCEEEE----EEEEEECCCCEEEEEhHHhhhhhhhhHHHH----------HHhcCC-CCCEEEEEEEEEeCCeEEEE
Confidence            346666654    335889888884    555443    3433          445666 99999999999999999999


Q ss_pred             EccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHHhccccceEEEEEEec
Q 044309          107 LLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHV  186 (259)
Q Consensus       107 L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i  186 (259)
                      ++   |.+||+|++|++|.++.++.+.|++||.|.|+|+++|++++++.||+|++.++||....+.|+.|+++.|+|..+
T Consensus       221 i~---g~~glv~~se~s~~~~~~~~~~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~i  297 (565)
T PRK06299        221 LG---GVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEKKYPVGSKVKGKVTNI  297 (565)
T ss_pred             EC---CEEEEEEHHHhcccccCCHhhcCCCCCEEEEEEEEEeCCCCeEEEEEEecccChhHHHHhhCCCCCEEEEEEEEE
Confidence            94   899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCchH------HH--HHhhchhhHHhhcCHHHHH
Q 044309          187 AETLGIDLE------EL--YVNIGWPLYWKYGHAFEAF  216 (259)
Q Consensus       187 ~~~~G~fve------~~--~~~~sw~l~~~~~~~~~~f  216 (259)
                      .+ +|+|++      ++  .++++|.  ....++.+.|
T Consensus       298 ~~-~G~fV~l~~~v~Glv~~sel~~~--~~~~~~~~~~  332 (565)
T PRK06299        298 TD-YGAFVELEEGIEGLVHVSEMSWT--KKNKHPSKVV  332 (565)
T ss_pred             eC-CeEEEEeCCCCEEEEEHHHcCcc--ccccCHHHhc
Confidence            66 999973      33  7889885  3334554444

>TIGR00717 rpsA ribosomal protein S1

Probab=99.80  E-value=1.3e-19  Score=177.44  Aligned_cols=141  Identities=26%  Similarity=0.481  Sum_probs=125.2

Q ss_pred             cccchhhhhh----hhcccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccc
Q 044309           50 FEFSRENAKA----KKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRR  125 (259)
Q Consensus        50 ~eid~e~~ri----K~l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~  125 (259)
                      +.+|++++++    |++.++||+.          +...++ +|+++.|+|+++.++|+||++.  ++++||+|+|+++|.
T Consensus       242 l~~d~~~~~i~lS~k~~~~~p~~~----------~~~~~~-~G~i~~g~V~~v~~~G~fV~l~--~~v~g~v~~sels~~  308 (516)
T TIGR00717       242 IKFDKEKGRISLSLKQLGEDPWEA----------IEKKFP-VGDKITGRVTNLTDYGVFVEIE--EGIEGLVHVSEMSWV  308 (516)
T ss_pred             EEEECCCCcEEEEEEecchhHHHH----------HHhhcc-CCCEEEEEEEEeeCCcEEEEeC--CCCEEEEEHHHcCCc
Confidence            4678888874    6777899987          666777 8999999999999999999997  589999999999985


Q ss_pred             -cccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHHhccccceEEEEEEecccccCCch------HHH-
Q 044309          126 -RIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDL------EEL-  197 (259)
Q Consensus       126 -~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fv------e~~-  197 (259)
                       ...++.+.+++||.+.|+|+++|++++++.||+|++..+||....+.+..|+++.|+|..+.+ +|+|+      +++ 
T Consensus       309 ~~~~~~~~~~~vG~~v~v~V~~id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~-~G~fV~l~~~v~glv  387 (516)
T TIGR00717       309 KKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEKHPVGDRVTGKIKKITD-FGAFVELEGGIDGLI  387 (516)
T ss_pred             cccCCHHHhccCCCEEEEEEEEEcCCCCEEEEEehhcccCcHHHHHHhCCCCCEEEEEEEEEec-ceEEEECCCCCEEEE
Confidence             466777889999999999999999999999999999999999999999999999999999966 99997      233 


Q ss_pred             -HHhhchh
Q 044309          198 -YVNIGWP  204 (259)
Q Consensus       198 -~~~~sw~  204 (259)
                       .++++|.
T Consensus       388 ~~s~ls~~  395 (516)
T TIGR00717       388 HLSDISWD  395 (516)
T ss_pred             EHHHCcCc
Confidence             8899995

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

>TIGR00717 rpsA ribosomal protein S1

Probab=99.80  E-value=1.5e-19  Score=176.91  Aligned_cols=141  Identities=27%  Similarity=0.427  Sum_probs=124.8

Q ss_pred             cccchhhhhh----hhcccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccc
Q 044309           50 FEFSRENAKA----KKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRR  125 (259)
Q Consensus        50 ~eid~e~~ri----K~l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~  125 (259)
                      +++|++++|+    |++.++||..          +.+.++ +|+++.|+|++++++|+||+|+  ++++||+|+++++|.
T Consensus       329 ~~id~~~~~i~lS~k~~~~~p~~~----------~~~~~~-~G~~v~g~V~~v~~~G~fV~l~--~~v~glv~~s~ls~~  395 (516)
T TIGR00717       329 LDIDPERRRLSLGLKQCKANPWEQ----------FEEKHP-VGDRVTGKIKKITDFGAFVELE--GGIDGLIHLSDISWD  395 (516)
T ss_pred             EEEcCCCCEEEEEehhcccCcHHH----------HHHhCC-CCCEEEEEEEEEecceEEEECC--CCCEEEEEHHHCcCc
Confidence            4688888884    7788899987          666777 8999999999999999999997  589999999999986


Q ss_pred             cc-cCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHHhccccceEEEEEEecccccCCch------HHH-
Q 044309          126 RI-RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDL------EEL-  197 (259)
Q Consensus       126 ~v-~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fv------e~~-  197 (259)
                      +. .++...|++||.|.|+|+++|+++++|.||+|++.++||....+.++.|++++|+|+++.+ +|+|+      +++ 
T Consensus       396 ~~~~~~~~~~~~G~~V~~~Vl~vd~~~~~i~ls~K~~~~~p~~~~~~~~~~G~~v~g~V~~v~~-~G~fV~l~~~~~Glv  474 (516)
T TIGR00717       396 KDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQLTENPWEKFAAKYKVGSVVKGKVTEIKD-FGAFVELPGGVEGLI  474 (516)
T ss_pred             ccCCCHhHccCCCCEEEEEEEEEeCcCCEEEEeeccccCCchhhhhhccCcceEEEEEEEEEec-ceEEEEcCCCeEEEE
Confidence            53 4567889999999999999999999999999999999999998899999999999999976 99997      233 


Q ss_pred             -HHhhchh
Q 044309          198 -YVNIGWP  204 (259)
Q Consensus       198 -~~~~sw~  204 (259)
                       .++++|.
T Consensus       475 ~~s~l~~~  482 (516)
T TIGR00717       475 RNSELSEN  482 (516)
T ss_pred             EHHHcCcc
Confidence             7888884

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

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.78  E-value=7.9e-19  Score=173.88  Aligned_cols=132  Identities=29%  Similarity=0.464  Sum_probs=121.0

Q ss_pred             ccccchhhhhh----hhcccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccccc
Q 044309           49 PFEFSRENAKA----KKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSR  124 (259)
Q Consensus        49 ~~eid~e~~ri----K~l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~  124 (259)
                      ++++|++++|+    |++..+||..          +...++ +|+++.|+|++++++|+||+|+  .+++||+|+++++|
T Consensus       342 V~~id~~~~~i~ls~k~~~~~p~~~----------~~~~~~-~G~~v~g~V~~v~~~G~fV~l~--~~v~g~i~~s~l~~  408 (565)
T PRK06299        342 VLEIDEEKRRISLGLKQCKENPWEE----------FAEKYP-VGDVVEGKVKNITDFGAFVGLE--GGIDGLVHLSDISW  408 (565)
T ss_pred             EEEEcCCCCEEEEehHHhccchhhh----------HHHhCC-CCCEEEEEEEEEecceEEEECC--CCCEEEEEHHHcCc
Confidence            35788888884    7788899987          666777 8999999999999999999997  48999999999999


Q ss_pred             ccc-cCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHHhccccceEEEEEEecccccCCch
Q 044309          125 RRI-RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDL  194 (259)
Q Consensus       125 ~~v-~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fv  194 (259)
                      .+. .++.+.|++||.|.|+|+++|+++++|.||+|+...+||....+.++.|+++.|+|.++.+ +|+|+
T Consensus       409 ~~~~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~k~~~~~p~~~~~~~~~~G~vV~G~V~~v~~-~G~fV  478 (565)
T PRK06299        409 DKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQLEEDPFEEFAKKHKKGSIVTGTVTEVKD-KGAFV  478 (565)
T ss_pred             cccccChHhhCCCCCEEEEEEEEEeCCCCEEEEEEehhhcCchhHHHhhcCCCCEEEEEEEEEec-CceEE
Confidence            876 8888999999999999999999999999999999999999999999999999999999976 89987

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

Probab=99.78  E-value=1.3e-19  Score=145.65  Aligned_cols=78  Identities=29%  Similarity=0.460  Sum_probs=74.1

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhH
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDI  166 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~  166 (259)
                      +|++++|+|++|++|||||+|+  ++..|||||||++.++++++.+++++||.|.|+|+++|. +|+|+||+|.+.+.|-
T Consensus         5 vG~~l~GkItgI~~yGAFV~l~--~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide-~GKisLSIr~~~e~pe   81 (129)
T COG1098           5 VGSKLKGKITGITPYGAFVELE--GGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDE-NGKISLSIRKLEEEPE   81 (129)
T ss_pred             ccceEEEEEEeeEecceEEEec--CCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeecc-CCCcceehHHhhhCcc
Confidence            8999999999999999999998  689999999999999999999999999999999999998 8999999999877554


Q ss_pred             H
Q 044309          167 Q  167 (259)
Q Consensus       167 ~  167 (259)
                      .
T Consensus        82 ~   82 (129)
T COG1098          82 K   82 (129)
T ss_pred             c
Confidence            3

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.77  E-value=8.6e-19  Score=166.28  Aligned_cols=149  Identities=22%  Similarity=0.338  Sum_probs=123.7

Q ss_pred             cccchhhhhh----hhccc----CccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccc
Q 044309           50 FEFSRENAKA----KKLSE----QPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSE  121 (259)
Q Consensus        50 ~eid~e~~ri----K~l~~----~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisE  121 (259)
                      +++|++++++    |++..    ++|..          ....+. +|+++.|+|+++.++|+||++.   +++||||+|+
T Consensus       158 l~~d~~~~~i~lS~k~~~~~~~~~~~~~----------~~~~~~-~G~~v~g~V~~v~~~G~fV~l~---~v~g~v~~se  223 (390)
T PRK06676        158 IELDPEKNRVILSRRAVVEEERAAKKEE----------LLSSLK-EGDVVEGTVARLTDFGAFVDIG---GVDGLVHISE  223 (390)
T ss_pred             EEEECCCCEEEEEeHHHhhhhhhhHHHH----------HHhhCC-CCCEEEEEEEEEecceEEEEeC---CeEEEEEHHH
Confidence            4678877774    44322    34443          444566 8999999999999999999994   7999999999


Q ss_pred             cccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHHhccccceEEEEEEecccccCCchH------
Q 044309          122 LSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLE------  195 (259)
Q Consensus       122 ls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fve------  195 (259)
                      ++|.++.++.+.|++||.|.|+|+++|+++++|.||+|++..+||....+.+..|+++.|.|+.+.+ +|+|++      
T Consensus       224 ls~~~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~~~~G~~v~g~V~~i~~-~G~fV~l~~gi~  302 (390)
T PRK06676        224 LSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEEKLPEGDVIEGTVKRLTD-FGAFVEVLPGVE  302 (390)
T ss_pred             cCccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEeecccCccccchhhhcCCcEEEEEEEEEeC-ceEEEEECCCCe
Confidence            9999999999999999999999999999999999999999999999999999999999999999976 999973      


Q ss_pred             HH--HHhhchhhHHhhcCHHHHH
Q 044309          196 EL--YVNIGWPLYWKYGHAFEAF  216 (259)
Q Consensus       196 ~~--~~~~sw~l~~~~~~~~~~f  216 (259)
                      ++  .++++|.   +..++.+.|
T Consensus       303 Glv~~se~~~~---~~~~~~~~~  322 (390)
T PRK06676        303 GLVHISQISHK---HIATPSEVL  322 (390)
T ss_pred             EEEEhHHcCcc---ccCChhhcc
Confidence            23  7788774   333444444

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

Probab=99.73  E-value=9.2e-18  Score=169.11  Aligned_cols=149  Identities=26%  Similarity=0.420  Sum_probs=124.5

Q ss_pred             cccchhhhh-h----hhcc----cCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcc
Q 044309           50 FEFSRENAK-A----KKLS----EQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFS  120 (259)
Q Consensus        50 ~eid~e~~r-i----K~l~----~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhis  120 (259)
                      +++|+++++ +    |.+.    ..+|..          ..+.+. +|+++.|+|+++.++|+||++   ++++||||+|
T Consensus       442 l~vd~e~~~~l~lS~k~~~~~~~~~~~~~----------~~~~l~-~G~iV~g~V~~v~~~G~fV~l---~gv~Gll~~s  507 (647)
T PRK00087        442 IEFNRKRRKKVVLSRKAILEEEKEKKKEE----------TWNSLE-EGDVVEGEVKRLTDFGAFVDI---GGVDGLLHVS  507 (647)
T ss_pred             EEEEcCCCcEEEEEeHHHhhhhhhhHHHH----------HHHhCC-CCCEEEEEEEEEeCCcEEEEE---CCEEEEEEHH
Confidence            577888777 4    3321    233333          334465 899999999999999999999   3899999999


Q ss_pred             ccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHHhccccceEEEEEEecccccCCchH-----
Q 044309          121 ELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLE-----  195 (259)
Q Consensus       121 Els~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fve-----  195 (259)
                      +++|.++.++.+.|++||.+.|+|+++|++++++.||+|++.++||....++++.|+++.|+|.++.+ +|+|++     
T Consensus       508 els~~~~~~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~~~~~~~G~~v~g~V~~i~~-~G~fV~l~~~i  586 (647)
T PRK00087        508 EISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEKYPVGSIVLGKVVRIAP-FGAFVELEPGV  586 (647)
T ss_pred             HcCccccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEeeccccChhhhhhhhccCCeEEEEEEEEEEC-CeEEEEECCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999976 999982     


Q ss_pred             -HH--HHhhchhhHHhhcCHHHHH
Q 044309          196 -EL--YVNIGWPLYWKYGHAFEAF  216 (259)
Q Consensus       196 -~~--~~~~sw~l~~~~~~~~~~f  216 (259)
                       ++  .++++|.   +..++.+.|
T Consensus       587 ~Gli~~sel~~~---~~~~~~~~~  607 (647)
T PRK00087        587 DGLVHISQISWK---RIDKPEDVL  607 (647)
T ss_pred             EEEEEhhhcCcc---ccCCHhhcC
Confidence             33  7888884   344555555

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=99.69  E-value=1.2e-16  Score=148.75  Aligned_cols=117  Identities=24%  Similarity=0.372  Sum_probs=98.8

Q ss_pred             cccccceeEEEeecCCccccchhhhhh----hhcccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEc
Q 044309           33 ADSLSGCLKTLILVPTPFEFSRENAKA----KKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLL  108 (259)
Q Consensus        33 ~~~l~g~~~~~~~~~~~~eid~e~~ri----K~l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~  108 (259)
                      .+.+.|.....    .++++|++++|+    |+....   .          ....++ +|+++.|+|+++++||+||++ 
T Consensus       156 ~~~~vG~~i~~----kVl~id~~~~~i~lS~K~~~~~---~----------~~~~~k-~G~vv~G~V~~I~~~G~fV~i-  216 (318)
T PRK07400        156 KEELVGEELPL----KFLEVDEERNRLVLSHRRALVE---R----------KMNRLE-VGEVVVGTVRGIKPYGAFIDI-  216 (318)
T ss_pred             ccccCCCEEEE----EEEEEEcccCEEEEEhhHhhhh---h----------hhccCC-CCCEEEEEEEEEECCeEEEEE-
Confidence            34567777764    447899999995    433221   1          223566 899999999999999999999 


Q ss_pred             cCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHH
Q 044309          109 EYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACE  170 (259)
Q Consensus       109 ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~  170 (259)
                        ++++||||+++++|.++.++.+.|++||.|+|+|+++|.++++|.||+|++.++||+...
T Consensus       217 --~gv~Gllhisels~~~~~~~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K~l~~~P~~~~~  276 (318)
T PRK07400        217 --GGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQLEPEPGDMLK  276 (318)
T ss_pred             --CCEEEEEEHHHcccccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeccccChhhhhh
Confidence              489999999999999999999999999999999999999999999999999999998653

>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=99.68  E-value=1.6e-16  Score=118.08  Aligned_cols=69  Identities=22%  Similarity=0.384  Sum_probs=64.8

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCc---cccccCCCeEEEEEEEEeCCCCeEEEE
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSV---SSLIKVGRIEPVMVLRVDKEKGYIDLS  157 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~---~~~~kvGd~V~vkVi~vD~~~gkI~LS  157 (259)
                      +|+++.|+|++++++|+||+|.  ++++|+||+++++|.++.++   .+.|++||.+.|+|+++|+++++|.||
T Consensus         3 ~G~~V~g~V~~i~~~G~fV~l~--~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~LS   74 (74)
T cd05705           3 EGQLLRGYVSSVTKQGVFFRLS--SSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS   74 (74)
T ss_pred             CCCEEEEEEEEEeCCcEEEEeC--CCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence            8999999999999999999997  58999999999999987775   588999999999999999999999986

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.

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=99.68  E-value=2.5e-16  Score=146.61  Aligned_cols=118  Identities=15%  Similarity=0.177  Sum_probs=107.7

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecc
Q 044309           83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVS  162 (259)
Q Consensus        83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~  162 (259)
                      .+. .|+++.|+|+++.++|+||+|+  ++.+||||.+|+++.++.++.+.+++||.+.|+|++++.+++++.||+|++.
T Consensus        28 ~~~-~G~iv~G~V~~i~~~g~~Vdig--~k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i~lS~k~~~  104 (318)
T PRK07400         28 HFK-PGDIVNGTVFSLEPRGALIDIG--AKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQLTLSIRRIE  104 (318)
T ss_pred             hcC-CCCEEEEEEEEEECCEEEEEEC--CCeEEEEEHHHhccccccCHHHccCCCCEEEEEEEEEeCCCCeEEEehhhhh
Confidence            355 8999999999999999999996  5799999999999999999999999999999999999999999999999986


Q ss_pred             h-hhHHHHHHhccccceEEEEEEecccccCCchH-----HH--HHhhchh
Q 044309          163 E-EDIQACEERYNKSKLVHSIMRHVAETLGIDLE-----EL--YVNIGWP  204 (259)
Q Consensus       163 ~-~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fve-----~~--~~~~sw~  204 (259)
                      . ++|+...+.+..|+.+.|+|..+.+ +|+|++     +|  .++++|.
T Consensus       105 ~~~~w~~l~~~~~~~~~V~g~V~~~~~-~G~~V~l~Gv~gfip~s~ls~~  153 (318)
T PRK07400        105 YMRAWERVRQLQKEDATVRSEVFATNR-GGALVRIEGLRGFIPGSHISTR  153 (318)
T ss_pred             hhhHHHHHHHhccCCCEEEEEEEEEEC-CeEEEEECCEEEEEEHHHcCcc
Confidence            4 8999999999999999999999976 899873     33  7889984

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.67  E-value=1.6e-16  Score=155.14  Aligned_cols=146  Identities=17%  Similarity=0.280  Sum_probs=121.5

Q ss_pred             ccchhhhhh----hhc-ccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccc
Q 044309           51 EFSRENAKA----KKL-SEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRR  125 (259)
Q Consensus        51 eid~e~~ri----K~l-~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~  125 (259)
                      .++.+++++    |++ .+++|..          +.+.+. .|+++.|+|+++.++|+||++    |++||||.|++++.
T Consensus        92 ~~~~~~g~liLS~k~~~~~~~w~~----------ie~~~e-~g~~V~G~V~~v~k~G~~Vdl----Gi~gflP~Sel~~~  156 (486)
T PRK07899         92 QKEDKEGRLILSKKRAQYERAWGT----------IEKIKE-KDGVVTGTVIEVVKGGLILDI----GLRGFLPASLVEMR  156 (486)
T ss_pred             EEECCCCeEEEEehhhcccchHHH----------HHHHhc-CCCEEEEEEEEEECCeEEEEE----CCEEEEEhhHhccc
Confidence            456666663    433 3688987          766665 799999999999999999999    58999999999998


Q ss_pred             cccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecc----hhhHHHHHHhccccceEEEEEEecccccCCch-----HH
Q 044309          126 RIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVS----EEDIQACEERYNKSKLVHSIMRHVAETLGIDL-----EE  196 (259)
Q Consensus       126 ~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~----~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fv-----e~  196 (259)
                      ++.++..+  +||.|.|+|+++|++++++.||+|.+.    ..+|......++.|+++.|+|+.+.+ +|+|+     ++
T Consensus       157 ~~~~~~~~--vGq~V~vkVleid~~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~-~G~FVdlggv~G  233 (486)
T PRK07899        157 RVRDLQPY--IGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVN-FGAFVDLGGVDG  233 (486)
T ss_pred             ccCChhhc--CCCEEEEEEEEEECCCCEEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEEC-CeEEEEECCEEE
Confidence            88887764  899999999999999999999999653    36788888999999999999999976 99997     34


Q ss_pred             H--HHhhchhhHHhhcCHHHHHH
Q 044309          197 L--YVNIGWPLYWKYGHAFEAFK  217 (259)
Q Consensus       197 ~--~~~~sw~l~~~~~~~~~~fk  217 (259)
                      +  .++++|.   ++.++.+.|+
T Consensus       234 lv~~Sels~~---~v~~~~~~~k  253 (486)
T PRK07899        234 LVHVSELSWK---HIDHPSEVVE  253 (486)
T ss_pred             EEEHHHCCCc---ccCCHHHhcC
Confidence            4  8999994   5667766664

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

Probab=99.67  E-value=6.5e-16  Score=113.57  Aligned_cols=75  Identities=75%  Similarity=1.064  Sum_probs=70.3

Q ss_pred             CCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEee
Q 044309           86 EVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRR  160 (259)
Q Consensus        86 ~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~  160 (259)
                      +.|+++.|+|+++.++|+||++.++++.+||||+|+++++++.++.+.|++||.+.|+|+++|.+++++.||+|+
T Consensus         2 ~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls~k~   76 (76)
T cd04452           2 EEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR   76 (76)
T ss_pred             CCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence            479999999999999999999975456999999999999999999999999999999999999989999999984

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

>PRK08582 hypothetical protein; Provisional

Probab=99.65  E-value=8.7e-16  Score=127.30  Aligned_cols=80  Identities=26%  Similarity=0.433  Sum_probs=75.8

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhH
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDI  166 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~  166 (259)
                      +|++|.|+|++|++||+||+|+  ++++||||+|++++.++.++.+.|++||.|.|+|+++|. +++|.||++++.++||
T Consensus         5 vG~iv~G~V~~I~~fG~fV~L~--~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~-~gkI~LSlk~~~~~~~   81 (139)
T PRK08582          5 VGSKLQGKVTGITNFGAFVELP--EGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVED-DGKIGLSIKKAKDRPK   81 (139)
T ss_pred             CCCEEEEEEEEEECCeEEEEEC--CCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECC-CCcEEEEEEecccCch
Confidence            8999999999999999999998  589999999999999999999999999999999999997 5999999999999998


Q ss_pred             HHH
Q 044309          167 QAC  169 (259)
Q Consensus       167 ~~~  169 (259)
                      ...
T Consensus        82 ~~~   84 (139)
T PRK08582         82 RQH   84 (139)
T ss_pred             hhc
Confidence            754

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.63  E-value=1.5e-15  Score=144.23  Aligned_cols=110  Identities=26%  Similarity=0.421  Sum_probs=99.8

Q ss_pred             cccchhhhhh----hhcccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccc
Q 044309           50 FEFSRENAKA----KKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRR  125 (259)
Q Consensus        50 ~eid~e~~ri----K~l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~  125 (259)
                      +++|++++|+    |++.++||..          +.+.+. +|+++.|+|+++.++|+||++.  ++++||+|+|++++.
T Consensus       247 l~vd~~~~~i~lS~k~~~~~~~~~----------~~~~~~-~G~~v~g~V~~i~~~G~fV~l~--~gi~Glv~~se~~~~  313 (390)
T PRK06676        247 LSIDWETERISLSLKDTLPGPWEG----------VEEKLP-EGDVIEGTVKRLTDFGAFVEVL--PGVEGLVHISQISHK  313 (390)
T ss_pred             EEEeCCCCEEEEEEeecccCcccc----------chhhhc-CCcEEEEEEEEEeCceEEEEEC--CCCeEEEEhHHcCcc
Confidence            4778888884    7788899987          666777 8999999999999999999997  589999999999999


Q ss_pred             cccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHHh
Q 044309          126 RIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEER  172 (259)
Q Consensus       126 ~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~~  172 (259)
                      ++.++.+.|++||.|.|+|+++|++++++.||+|++..+||+...++
T Consensus       314 ~~~~~~~~~~~Gd~v~v~V~~id~e~~~i~ls~k~~~~~~~~~~~~~  360 (390)
T PRK06676        314 HIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIKALEEAPAEEEDRR  360 (390)
T ss_pred             ccCChhhccCCCCEEEEEEEEEECCCCEEEEEEEecccChhhhhhhh
Confidence            98899999999999999999999999999999999999999987654

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

Probab=99.63  E-value=2.4e-15  Score=110.83  Aligned_cols=71  Identities=21%  Similarity=0.288  Sum_probs=65.1

Q ss_pred             CCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEE
Q 044309           86 EVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSK  158 (259)
Q Consensus        86 ~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSl  158 (259)
                      ++|+++.|+|+++++||+||++.++ +.+||+|+|++++.++.++.+.+++||.+.|+|+++|.++ ++.||+
T Consensus         2 ~~g~~~~g~V~~i~~fG~fv~l~~~-~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~-ki~ls~   72 (73)
T cd05686           2 ALYQIFKGEVASVTEYGAFVKIPGC-RKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKD-KMKLSL   72 (73)
T ss_pred             cCCCEEEEEEEEEEeeeEEEEECCC-CeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCC-cEEEEe
Confidence            4899999999999999999999531 3799999999999999999999999999999999999964 999986

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.

>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=99.62  E-value=2.1e-15  Score=109.41  Aligned_cols=70  Identities=29%  Similarity=0.376  Sum_probs=66.8

Q ss_pred             CcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309           88 DMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR  159 (259)
Q Consensus        88 G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK  159 (259)
                      |+++.|+|+++.++|+||++.  ++.+||+|+|+++++++.++.+.+++||.++|+|+++|++++++.||+|
T Consensus         1 g~~~~g~V~~v~~~G~~V~l~--~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~k   70 (70)
T cd05698           1 GLKTHGTIVKVKPNGCIVSFY--NNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK   70 (70)
T ss_pred             CCEEEEEEEEEecCcEEEEEC--CCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence            789999999999999999997  5799999999999988999999999999999999999999999999986

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.

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

Probab=99.62  E-value=3.6e-15  Score=109.16  Aligned_cols=71  Identities=44%  Similarity=0.573  Sum_probs=68.6

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR  159 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK  159 (259)
                      +|+++.|+|+++.++|+||+|.  ++++||||.+++++.+..++.+.+++||.+.|+|+++|++++++.||+|
T Consensus         4 ~G~iv~g~V~~v~~~g~~V~l~--~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS~k   74 (74)
T PF00575_consen    4 EGDIVEGKVTSVEDFGVFVDLG--NGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK   74 (74)
T ss_dssp             TTSEEEEEEEEEETTEEEEEES--TSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred             CCCEEEEEEEEEECCEEEEEEC--CcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence            8999999999999999999997  5899999999999999999999999999999999999999999999986

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 ....

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

Probab=99.62  E-value=3.2e-15  Score=110.63  Aligned_cols=70  Identities=23%  Similarity=0.306  Sum_probs=66.1

Q ss_pred             CcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccccccc--ccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309           88 DMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRR--IRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR  159 (259)
Q Consensus        88 G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~--v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK  159 (259)
                      |+++.|+|+++.++|+||+|.  ++++|+||++++++..  .+++.+.|++||.++|+|+++|+++++|.||+|
T Consensus         1 G~~V~g~V~~i~~~g~~V~l~--~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~k   72 (73)
T cd05703           1 GQEVTGFVNNVSKEFVWLTIS--PDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR   72 (73)
T ss_pred             CCEEEEEEEEEeCCEEEEEeC--CCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence            789999999999999999997  5899999999999864  888999999999999999999999999999987

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

>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=99.60  E-value=4.1e-15  Score=109.59  Aligned_cols=69  Identities=22%  Similarity=0.198  Sum_probs=65.2

Q ss_pred             CCcEEEEEEEEEeC-ceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309           87 VDMAVMIQVKNIAD-MGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR  159 (259)
Q Consensus        87 ~G~iv~G~V~~I~~-~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK  159 (259)
                      +|++|.|+|+++.+ +|+||+|.  ++.+|++|+|+++++++.++.+.|++||.++|+|+++|.  +++.||+|
T Consensus         3 ~G~iv~G~V~~i~~~~g~~v~l~--~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~--~~i~LSl~   72 (72)
T cd05704           3 EGAVTLGMVTKVIPHSGLTVQLP--FGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD--GKYQLSLR   72 (72)
T ss_pred             CCCEEEEEEEEeeCCcEEEEECC--CCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecC--CEEEEEeC
Confidence            79999999999985 89999997  689999999999999999999999999999999999984  89999986

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.

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=99.60  E-value=2.7e-15  Score=154.14  Aligned_cols=108  Identities=26%  Similarity=0.314  Sum_probs=91.0

Q ss_pred             EEeecCCccccchhhhhhhhcccCccccCCCCchhhhhhhhcCCCCCcEEE-EEEEEEeCceEEEEEccCCCEEEEEEcc
Q 044309           42 TLILVPTPFEFSRENAKAKKLSEQPIMASHSPNLECRMYEARYPEVDMAVM-IQVKNIADMGAYVSLLEYNNIEGMILFS  120 (259)
Q Consensus        42 ~~~~~~~~~eid~e~~riK~l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~-G~V~~I~~~GafV~L~ey~~~eGllhis  120 (259)
                      ..+++++...++..+.+|+++..                   .+++|++|. |+|++|.+||+||+|.  ++.+||||+|
T Consensus       727 V~I~a~d~~~i~~A~~~I~~l~~-------------------~~~vG~iy~~g~V~~I~~FGaFVeL~--~g~EGLVHIS  785 (891)
T PLN00207        727 VKITAKDLSSLEKSKAIISSLTM-------------------VPTVGDIYRNCEIKSIAPYGAFVEIA--PGREGLCHIS  785 (891)
T ss_pred             EEEEeCCHHHHHHHHHHHHHHhc-------------------CcCCCcEEECcEEEEEeccEEEEEeC--CCCEEEEEhh
Confidence            33455555555555555655531                   234899995 6999999999999997  5899999999


Q ss_pred             ccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHH
Q 044309          121 ELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEE  171 (259)
Q Consensus       121 Els~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~  171 (259)
                      +++|+++.++.+.|++||.|+|+|+++|+ +++|.||+|++.++||++..+
T Consensus       786 eLs~~rv~~~~dv~kvGD~V~VkVi~ID~-~grI~LSlK~l~~~Pw~~~~~  835 (891)
T PLN00207        786 ELSSNWLAKPEDAFKVGDRIDVKLIEVND-KGQLRLSRRALLPEANSEKSS  835 (891)
T ss_pred             hcCCccccCHHHhcCCCCEEEEEEEEECC-CCcEEEEEeccccCchhhhhh
Confidence            99999999999999999999999999997 799999999999999998764

>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=99.60  E-value=5.9e-15  Score=107.12  Aligned_cols=69  Identities=22%  Similarity=0.305  Sum_probs=65.7

Q ss_pred             CcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEE
Q 044309           88 DMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSK  158 (259)
Q Consensus        88 G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSl  158 (259)
                      |+++.|+|+++.++|+||+|+  ++++||+|++++++.+..++.+.+++||.+.|+|+++|++++++.||+
T Consensus         1 G~~v~g~V~~v~~~Gv~V~l~--~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~~~~~i~ls~   69 (69)
T cd05697           1 GQVVKGTIRKLRPSGIFVKLS--DHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL   69 (69)
T ss_pred             CCEEEEEEEEEeccEEEEEec--CCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence            789999999999999999997  579999999999999888899999999999999999999999999985

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.

>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=99.59  E-value=5.2e-15  Score=111.35  Aligned_cols=72  Identities=29%  Similarity=0.277  Sum_probs=68.5

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEE
Q 044309           84 YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSK  158 (259)
Q Consensus        84 ~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSl  158 (259)
                      +. +|+++.|+|+++.++|+||+|.  ++.+||+|+++++++++.++.+.|++||.+.|+|+++|.++++|.||+
T Consensus        12 ~~-~G~i~~g~V~~v~~~G~fv~l~--~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i~lsl   83 (83)
T cd04461          12 LK-PGMVVHGYVRNITPYGVFVEFL--GGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL   83 (83)
T ss_pred             CC-CCCEEEEEEEEEeeceEEEEcC--CCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEeC
Confidence            45 8999999999999999999997  589999999999999999999999999999999999999999999986

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.

>PRK07252 hypothetical protein; Provisional

Probab=99.59  E-value=8.1e-15  Score=118.71  Aligned_cols=80  Identities=29%  Similarity=0.376  Sum_probs=74.1

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecch-hh
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSE-ED  165 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~-~~  165 (259)
                      +|+++.|+|++|+++|+||+|.  ++.+||+|++++++.++.++.+.+++||.|.|+|+++|.+++++.||++++.+ .+
T Consensus         3 vG~iv~G~V~~V~~~G~fVei~--~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~~~~~   80 (120)
T PRK07252          3 IGDKLKGTITGIKPYGAFVALE--NGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLEEEKQ   80 (120)
T ss_pred             CCCEEEEEEEEEeCcEEEEEEC--CCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeecccCcc
Confidence            7999999999999999999997  57999999999999999999999999999999999999999999999999986 34


Q ss_pred             HHH
Q 044309          166 IQA  168 (259)
Q Consensus       166 ~~~  168 (259)
                      |..
T Consensus        81 ~~~   83 (120)
T PRK07252         81 HFP   83 (120)
T ss_pred             ccC
Confidence            443

>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=99.59  E-value=1.3e-14  Score=106.21  Aligned_cols=71  Identities=24%  Similarity=0.195  Sum_probs=67.4

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR  159 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK  159 (259)
                      +|+++.|+|++++++|+||+|+  ++++|++|++++++++..++.+.|++||.++|+|+++|..++++.||++
T Consensus         3 ~G~iv~g~V~~v~~~gi~v~l~--~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls~~   73 (73)
T cd05706           3 VGDILPGRVTKVNDRYVLVQLG--NKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR   73 (73)
T ss_pred             CCCEEEEEEEEEeCCeEEEEeC--CCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence            8999999999999999999998  5899999999999988888889999999999999999998999999985

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.

>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=99.58  E-value=1e-14  Score=107.25  Aligned_cols=69  Identities=23%  Similarity=0.386  Sum_probs=65.2

Q ss_pred             CcEEE-EEEEEE-eCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEE
Q 044309           88 DMAVM-IQVKNI-ADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSK  158 (259)
Q Consensus        88 G~iv~-G~V~~I-~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSl  158 (259)
                      |++|. |+|+++ .++|+||+|.  ++++||+|+|++++.++.++.+.|++||.+.|+|+++|+.+++|.||+
T Consensus         1 G~v~~~g~V~~v~~~~G~~V~l~--~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS~   71 (71)
T cd05696           1 GAVVDSVKVTKVEPDLGAVFELK--DGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL   71 (71)
T ss_pred             CcEeeeeEEEEEccCceEEEEeC--CCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence            78999 999999 6999999997  589999999999999999999999999999999999999999999985

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.

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

Probab=99.58  E-value=1.8e-14  Score=104.81  Aligned_cols=72  Identities=29%  Similarity=0.377  Sum_probs=68.5

Q ss_pred             CcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeec
Q 044309           88 DMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV  161 (259)
Q Consensus        88 G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~  161 (259)
                      |+++.|+|+++.++|+||+|.  ++++|++|+++++++++.++.+.|++||.+.|+|+++|++++++.||+|+.
T Consensus         1 G~~v~g~V~~v~~~g~~v~l~--~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k~~   72 (73)
T cd05691           1 GSIVTGKVTEVDAKGATVKLG--DGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAK   72 (73)
T ss_pred             CCEEEEEEEEEECCeEEEEeC--CCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEc
Confidence            789999999999999999997  579999999999999999999999999999999999999889999999975

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=99.57  E-value=9.2e-15  Score=105.81  Aligned_cols=68  Identities=28%  Similarity=0.417  Sum_probs=65.0

Q ss_pred             CcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEE
Q 044309           88 DMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLS  157 (259)
Q Consensus        88 G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LS  157 (259)
                      |+++.|+|+++.++|+||++.  ++++||+|++++++++..++.+.+++||.+.|+|+++|+++++|.||
T Consensus         1 G~~v~g~V~~v~~~Gv~V~l~--~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls   68 (68)
T cd05707           1 GDVVRGFVKNIANNGVFVTLG--RGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT   68 (68)
T ss_pred             CCEEEEEEEEEECccEEEEeC--CCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence            789999999999999999997  57999999999999999999999999999999999999999999886

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.

>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=99.57  E-value=1.7e-14  Score=107.41  Aligned_cols=75  Identities=28%  Similarity=0.394  Sum_probs=68.6

Q ss_pred             CcEEEEEEEEEeCceEEEEEccC-CCEEEEEEccccccccc-cCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchh
Q 044309           88 DMAVMIQVKNIADMGAYVSLLEY-NNIEGMILFSELSRRRI-RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEE  164 (259)
Q Consensus        88 G~iv~G~V~~I~~~GafV~L~ey-~~~eGllhisEls~~~v-~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~  164 (259)
                      |+++.|+|+++++||+||+|.++ ++.+||+|++++++.+. .++.+.|++||.|.|+|+++|  ++++.||+|++.++
T Consensus         1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd--~~~i~~s~k~~~~~   77 (79)
T cd05684           1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ--NGKISLSMKDVDQD   77 (79)
T ss_pred             CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe--CCEEEEEEEecccC
Confidence            78999999999999999999743 26999999999999886 899999999999999999999  79999999998764

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.

>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.57  E-value=2.2e-14  Score=105.23  Aligned_cols=74  Identities=28%  Similarity=0.439  Sum_probs=69.2

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeec
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV  161 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~  161 (259)
                      +|+++.|+|++++++|+||++.+ .+.+|++|++++++.+..++.+.|++||.|.|+|+++|.+++++.||+|+.
T Consensus         2 ~g~~v~g~V~~i~~~g~~v~l~~-~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k~~   75 (77)
T cd05708           2 VGQKIDGTVRRVEDYGVFIDIDG-TNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS   75 (77)
T ss_pred             CCCEEEEEEEEEEcceEEEEECC-CCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence            69999999999999999999973 369999999999999888899999999999999999999999999999974

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 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

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

Probab=99.56  E-value=1.5e-14  Score=104.33  Aligned_cols=68  Identities=32%  Similarity=0.530  Sum_probs=63.5

Q ss_pred             CcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccccc-ccccCccccccCCCeEEEEEEEEeCCCCeEEEE
Q 044309           88 DMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSR-RRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLS  157 (259)
Q Consensus        88 G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~-~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LS  157 (259)
                      |+++.|+|+++++||+||+|+  ++.+||+|+++++| .+..++.+.|++||.+.|+|+++|.++++|+||
T Consensus         1 G~~~~g~V~~i~~~G~fv~l~--~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~~~~i~l~   69 (69)
T cd05690           1 GTVVSGKIKSITDFGIFVGLD--GGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISLG   69 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEeC--CCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCcCEEeCC
Confidence            789999999999999999997  58999999999997 577888899999999999999999999999885

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.

>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=99.56  E-value=3.8e-14  Score=105.30  Aligned_cols=70  Identities=19%  Similarity=0.209  Sum_probs=64.4

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecch
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSE  163 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~  163 (259)
                      +|+++.|+|++|+++|+||+++ +++++||+|.+++++.      +.+++||.+.|+|+++|++++++.||+|+..+
T Consensus         4 ~G~~v~g~V~si~d~G~~v~~g-~~gv~Gfl~~~~~~~~------~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~~~~   73 (74)
T cd05694           4 EGMVLSGCVSSVEDHGYILDIG-IPGTTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV   73 (74)
T ss_pred             CCCEEEEEEEEEeCCEEEEEeC-CCCcEEEEEHHHCCcc------cccCCCCEEEEEEEEEECCCCEEEEEEeeccc
Confidence            8999999999999999999995 2589999999999976      77999999999999999999999999998653

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.

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

Probab=99.54  E-value=4.4e-14  Score=102.54  Aligned_cols=70  Identities=36%  Similarity=0.387  Sum_probs=66.6

Q ss_pred             CcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309           88 DMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR  159 (259)
Q Consensus        88 G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK  159 (259)
                      |++|.|+|.++.++|+||+|.  ++.+|+||.+|+++.+..++.+.+++||.++|+|+++|++.+++.||+|
T Consensus         1 G~iv~g~V~~i~~~~~~v~l~--~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~   70 (70)
T cd05687           1 GDIVKGTVVSVDDDEVLVDIG--YKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR   70 (70)
T ss_pred             CCEEEEEEEEEeCCEEEEEeC--CCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence            789999999999999999996  5799999999999999999999999999999999999988899999985

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

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

Probab=99.53  E-value=4.8e-14  Score=100.52  Aligned_cols=69  Identities=30%  Similarity=0.512  Sum_probs=65.5

Q ss_pred             CcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309           88 DMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR  159 (259)
Q Consensus        88 G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK  159 (259)
                      |+++.|+|+++.++|+||++.  ++.+||+|.++++++++.++.+.+++||.+.|+|+++|. ++++.||+|
T Consensus         1 G~~~~g~V~~i~~~g~~v~i~--~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~~-~~~i~ls~k   69 (69)
T cd05692           1 GSVVEGTVTRLKPFGAFVELG--GGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA-RGRISLSIK   69 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEEC--CCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECC-CCcEEEEEC
Confidence            789999999999999999997  589999999999999999999999999999999999998 899999986

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.

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

Probab=99.53  E-value=4.8e-14  Score=102.88  Aligned_cols=71  Identities=31%  Similarity=0.531  Sum_probs=64.0

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccc-cccCccccccCCCeEEEEEEEEeCCCCeEEEE
Q 044309           84 YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRR-RIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLS  157 (259)
Q Consensus        84 ~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~-~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LS  157 (259)
                      || +|+++.|+|++++++|+||+|.  ++.+||+|+++++|. +..++.+.|++||.+.|+|+++|.+++++.||
T Consensus         1 ~~-~g~~~~g~V~~i~~~G~fv~l~--~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~~   72 (72)
T cd05689           1 YP-EGTRLFGKVTNLTDYGCFVELE--EGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISLG   72 (72)
T ss_pred             Cc-CCCEEEEEEEEEEeeEEEEEcC--CCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCcCEEeCC
Confidence            45 8999999999999999999998  479999999999975 55577788999999999999999999999875

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.

>PRK05807 hypothetical protein; Provisional

Probab=99.53  E-value=6.6e-14  Score=115.64  Aligned_cols=72  Identities=24%  Similarity=0.367  Sum_probs=69.1

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecc
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVS  162 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~  162 (259)
                      +|++|.|+|++++++|+||+|+   +.+||||+|++++.++.++.+.+++||.|.|+|+++|. +++|.||+|++.
T Consensus         5 vG~vv~G~Vt~i~~~GafV~L~---~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~-~gkI~LSlk~~~   76 (136)
T PRK05807          5 AGSILEGTVVNITNFGAFVEVE---GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD-NGKISLSIKQAM   76 (136)
T ss_pred             CCCEEEEEEEEEECCeEEEEEC---CEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECC-CCcEEEEEEecc
Confidence            8999999999999999999994   68999999999999999999999999999999999998 799999999986

>PRK08059 general stress protein 13; Validated

Probab=99.52  E-value=6.9e-14  Score=113.44  Aligned_cols=80  Identities=34%  Similarity=0.509  Sum_probs=74.7

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecc
Q 044309           83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVS  162 (259)
Q Consensus        83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~  162 (259)
                      .+. +|++|.|+|+++.++|+||++.  ++.+|++|++++++.++.++.+.+++||.|.|+|+++|.+++++.||++++.
T Consensus         4 ~~k-~G~iv~G~V~~i~~~G~fV~i~--~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk~~~   80 (123)
T PRK08059          4 QYE-VGSVVTGKVTGIQPYGAFVALD--EETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATE   80 (123)
T ss_pred             cCC-CCCEEEEEEEEEecceEEEEEC--CCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEEcc
Confidence            355 8999999999999999999997  5899999999999999999999999999999999999999999999999998


Q ss_pred             hhh
Q 044309          163 EED  165 (259)
Q Consensus       163 ~~~  165 (259)
                      .+|
T Consensus        81 ~~~   83 (123)
T PRK08059         81 EAP   83 (123)
T ss_pred             cCc
Confidence            766

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

Probab=99.51  E-value=4.7e-14  Score=142.38  Aligned_cols=103  Identities=34%  Similarity=0.515  Sum_probs=94.5

Q ss_pred             cccchhhhh----hhhcccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccc
Q 044309           50 FEFSRENAK----AKKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRR  125 (259)
Q Consensus        50 ~eid~e~~r----iK~l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~  125 (259)
                      +++|+++++    +|++.++||..          +.+.++ +|+++.|+|++++++|+||++.  ++++||+|++++++.
T Consensus       532 ~~id~~~~~I~lS~K~~~~~p~~~----------~~~~~~-~G~~v~g~V~~i~~~G~fV~l~--~~i~Gli~~sel~~~  598 (647)
T PRK00087        532 LDIDKENKKLSLSLKKLLPDPWEN----------VEEKYP-VGSIVLGKVVRIAPFGAFVELE--PGVDGLVHISQISWK  598 (647)
T ss_pred             EEEECCCCEEEEEeeccccChhhh----------hhhhcc-CCeEEEEEEEEEECCeEEEEEC--CCCEEEEEhhhcCcc
Confidence            467888888    38888999997          666777 8999999999999999999997  689999999999999


Q ss_pred             cccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhh
Q 044309          126 RIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEED  165 (259)
Q Consensus       126 ~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~  165 (259)
                      ++.++.+.|++||.|+|+|+++|++++++.||+|++.++|
T Consensus       599 ~~~~~~~~~kvGd~V~vkV~~id~e~~rI~lslk~~~~~~  638 (647)
T PRK00087        599 RIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEEEP  638 (647)
T ss_pred             ccCCHhhcCCCCCEEEEEEEEEeCCCCEEEEEEeecccCc
Confidence            9999999999999999999999999999999999999877

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

Probab=99.49  E-value=1.4e-13  Score=98.01  Aligned_cols=68  Identities=34%  Similarity=0.545  Sum_probs=64.2

Q ss_pred             CcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEE
Q 044309           88 DMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLS  157 (259)
Q Consensus        88 G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LS  157 (259)
                      |+++.|+|++++++|+||++.  ++.+||+|.+++++.++.++.+.+++||.+.|+|+++|++++++.||
T Consensus         1 g~~~~g~V~~i~~~G~fv~l~--~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls   68 (68)
T cd05685           1 GMVLEGVVTNVTDFGAFVDIG--VKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS   68 (68)
T ss_pred             CCEEEEEEEEEecccEEEEcC--CCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence            789999999999999999997  57999999999999888899999999999999999999989999886

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

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

Probab=99.48  E-value=2e-13  Score=103.15  Aligned_cols=76  Identities=21%  Similarity=0.269  Sum_probs=67.7

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccccc----ccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309           84 YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSR----RRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR  159 (259)
Q Consensus        84 ~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~----~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK  159 (259)
                      .|++|++|.|+|+++.++|++|++.  ++.+|+||++++++    .+..++.+.+++||.+.|+|+++|++ +++.||++
T Consensus         3 ~p~~GdiV~g~V~~i~~~g~~v~i~--~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~-~~i~LS~~   79 (86)
T cd05789           3 IPEVGDVVIGRVTEVGFKRWKVDIN--SPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSD-GSVSLHTR   79 (86)
T ss_pred             cCCCCCEEEEEEEEECCCEEEEECC--CCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCC-CCEEEEeC
Confidence            3458999999999999999999997  58999999999996    45567788899999999999999885 99999999


Q ss_pred             ecc
Q 044309          160 RVS  162 (259)
Q Consensus       160 ~~~  162 (259)
                      +..
T Consensus        80 ~~~   82 (86)
T cd05789          80 SLK   82 (86)
T ss_pred             ccc
Confidence            753

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

>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain

Probab=99.46  E-value=3.8e-13  Score=96.04  Aligned_cols=68  Identities=35%  Similarity=0.538  Sum_probs=64.1

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEE
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLS  157 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LS  157 (259)
                      +|+++.|+|+++.++|+||++.   +.+|++|.+++++.++.++.+.|++||.+.|+|+++|.+++++.||
T Consensus         1 ~g~~~~g~V~~v~~~g~~v~l~---~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls   68 (68)
T cd05688           1 EGDVVEGTVKSITDFGAFVDLG---GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG   68 (68)
T ss_pred             CCCEEEEEEEEEEeeeEEEEEC---CeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECCCCEEecC
Confidence            4899999999999999999994   6999999999999889899999999999999999999999999986

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 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

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

Probab=99.45  E-value=4.5e-13  Score=95.80  Aligned_cols=68  Identities=37%  Similarity=0.566  Sum_probs=64.1

Q ss_pred             CcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEE
Q 044309           88 DMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSK  158 (259)
Q Consensus        88 G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSl  158 (259)
                      |+++.|+|+++.++|+||++.  ++.+||+|++++++.++.++.+.|++||.+.|+|+++|+ ++++.||+
T Consensus         1 g~~~~g~V~~v~~~G~~v~l~--~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d~-~~~i~ls~   68 (68)
T cd04472           1 GKIYEGKVVKIKDFGAFVEIL--PGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD-RGRISLSR   68 (68)
T ss_pred             CCEEEEEEEEEEEeEEEEEeC--CCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECC-CCcEEeeC
Confidence            789999999999999999997  579999999999999988889999999999999999999 89999985

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.

>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.44  E-value=5.3e-13  Score=96.77  Aligned_cols=66  Identities=26%  Similarity=0.340  Sum_probs=59.7

Q ss_pred             CcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEE
Q 044309           88 DMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLS  157 (259)
Q Consensus        88 G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LS  157 (259)
                      |+++.|+|+++.++|+||+|.  ++++|++|.++++..+..  .+.|++||.+.|+|+++|+++++|.||
T Consensus         1 G~~V~g~V~~i~~~G~~v~l~--~~v~g~v~~~~l~~~~~~--~~~~~~G~~i~~kVi~id~~~~~i~LS   66 (66)
T cd05695           1 GMLVNARVKKVLSNGLILDFL--SSFTGTVDFLHLDPEKSS--KSTYKEGQKVRARILYVDPSTKVVGLS   66 (66)
T ss_pred             CCEEEEEEEEEeCCcEEEEEc--CCceEEEEHHHcCCccCc--ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence            789999999999999999997  579999999999765443  778999999999999999999999886

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 3 (hs3). 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=99.42  E-value=1.5e-12  Score=93.97  Aligned_cols=67  Identities=21%  Similarity=0.340  Sum_probs=61.5

Q ss_pred             CcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309           88 DMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR  159 (259)
Q Consensus        88 G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK  159 (259)
                      |+++.|+|+++.++|+||++   ++++||||.|++++.+..++.+.  +||.+.|+|+++|.++++|.||+|
T Consensus         1 G~iv~g~V~~v~~~G~~v~l---~g~~gfip~s~~~~~~~~~~~~~--vG~~i~~~i~~vd~~~~~i~lS~k   67 (67)
T cd04465           1 GEIVEGKVTEKVKGGLIVDI---EGVRAFLPASQVDLRPVEDLDEY--VGKELKFKIIEIDRERNNIVLSRR   67 (67)
T ss_pred             CCEEEEEEEEEECCeEEEEE---CCEEEEEEHHHCCCcccCChHHh--CCCEEEEEEEEEeCCCCEEEEEcC
Confidence            78999999999999999999   37999999999998887777663  899999999999998999999975

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.

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

Probab=99.40  E-value=2.3e-12  Score=91.55  Aligned_cols=71  Identities=44%  Similarity=0.571  Sum_probs=66.5

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR  159 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK  159 (259)
                      +|+++.|+|++++++|+||++.  ++.+|++|.+++++.+..++.+.|++||.+.|+|++++..++++.||++
T Consensus         2 ~G~~v~g~V~~v~~~g~~v~i~--~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~~   72 (72)
T smart00316        2 VGDVVEGTVTEITPFGAFVDLG--NGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK   72 (72)
T ss_pred             CCCEEEEEEEEEEccEEEEEeC--CCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence            6999999999999999999997  5899999999999888888888899999999999999998899999975

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=99.40  E-value=8.9e-13  Score=133.24  Aligned_cols=70  Identities=29%  Similarity=0.528  Sum_probs=65.1

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccc----cccccCccccccCCCeEEEEEEEEeCCCCeEEEE
Q 044309           85 PEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELS----RRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLS  157 (259)
Q Consensus        85 ~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls----~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LS  157 (259)
                      |++|++|.|+|++|++||+||+|.  +|.+||||+||++    ++++.++.+++++||.|+|+|+++|. ++||.|+
T Consensus       645 ~~vG~i~~GkV~~I~dfGaFVel~--~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID~-~gKI~L~  718 (719)
T TIGR02696       645 PEVGERFLGTVVKTTAFGAFVSLL--PGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDD-RGKLSLV  718 (719)
T ss_pred             CCCCCEEEEEEEEEECceEEEEec--CCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEECC-CCCeeec
Confidence            459999999999999999999997  6899999999996    47899999999999999999999996 7999986

Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=99.39  E-value=1.6e-12  Score=132.15  Aligned_cols=73  Identities=36%  Similarity=0.549  Sum_probs=69.6

Q ss_pred             CCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeec
Q 044309           86 EVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV  161 (259)
Q Consensus        86 ~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~  161 (259)
                      ++|+++.|+|++|.+||+||+|.  ++.+||+|+|++++++++++.+.|++||.|+|+|+++|.+ +++.||+|.+
T Consensus       620 ~vG~v~~G~V~~I~~fGafVei~--~~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD~~-grI~LS~k~~  692 (693)
T PRK11824        620 EVGEIYEGKVVRIVDFGAFVEIL--PGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKR-GRIRLSRKAV  692 (693)
T ss_pred             cCCeEEEEEEEEEECCeEEEEEC--CCCEEEEEeeeccCccccCccceeCCCCEEEEEEEEECCC-CcEEEEEEec
Confidence            38999999999999999999997  6899999999999999999999999999999999999986 9999999975

>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.39  E-value=1.2e-12  Score=102.82  Aligned_cols=72  Identities=29%  Similarity=0.408  Sum_probs=65.4

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc-------------------cCccccccCCCeEEEEEEEE
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI-------------------RSVSSLIKVGRIEPVMVLRV  147 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v-------------------~~~~~~~kvGd~V~vkVi~v  147 (259)
                      +|++|.|+|++|.++|+||+|.  ++++|++|++++++.+.                   .++.+.|++||.|.|+|+++
T Consensus         3 ~G~vV~G~V~~v~~~gl~v~L~--~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~   80 (100)
T cd05693           3 EGMLVLGQVKEITKLDLVISLP--NGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSL   80 (100)
T ss_pred             CCCEEEEEEEEEcCCCEEEECC--CCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEc
Confidence            7999999999999999999997  58999999999998652                   34778899999999999999


Q ss_pred             eCC---CCeEEEEEee
Q 044309          148 DKE---KGYIDLSKRR  160 (259)
Q Consensus       148 D~~---~gkI~LSlK~  160 (259)
                      |++   +++|.||+|.
T Consensus        81 d~~~~~~~~i~LSlr~   96 (100)
T cd05693          81 DKSKSGKKRIELSLEP   96 (100)
T ss_pred             cCCcCCCcEEEEEecH
Confidence            997   7899999984

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 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=99.38  E-value=2.9e-12  Score=111.03  Aligned_cols=122  Identities=16%  Similarity=0.159  Sum_probs=96.1

Q ss_pred             cceeEEEeecCCccccchhhhhhhhcccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccC------
Q 044309           37 SGCLKTLILVPTPFEFSRENAKAKKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEY------  110 (259)
Q Consensus        37 ~g~~~~~~~~~~~~eid~e~~riK~l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey------  110 (259)
                      .|++...++.  .+++|.++++++-   +||..          +. ..|++|++|.|+|+++.++|+||+|..+      
T Consensus        30 ~~~i~as~~G--~~~id~~~~~Isv---~P~~~----------~~-~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~   93 (189)
T PRK09521         30 NGEVYASVVG--KVFIDDINRKISV---IPFKK----------TP-PLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERE   93 (189)
T ss_pred             CCEEEEEeeE--EEEEcCCCCEEEE---ecCcC----------CC-CCCCCCCEEEEEEEEEcCCeEEEEEEEecccccc
Confidence            3555554442  3467887777543   58875          33 3444999999999999999999999632      


Q ss_pred             --CCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHHhccccceEEEEEEeccc
Q 044309          111 --NNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAE  188 (259)
Q Consensus       111 --~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~  188 (259)
                        .+.+|++|.+++++.+..++.+.|++||.|.|+|++++   +++.||+|+..                 -|.|...+.
T Consensus        94 l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~---~~i~LS~k~~~-----------------lGvv~a~~~  153 (189)
T PRK09521         94 LATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT---DPLQLSTKGKD-----------------LGVIYAMCS  153 (189)
T ss_pred             cCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC---CcEEEEEecCC-----------------ceEEEEEcc
Confidence              26899999999999888889999999999999999998   78999998532                 388888888


Q ss_pred             ccCCch
Q 044309          189 TLGIDL  194 (259)
Q Consensus       189 ~~G~fv  194 (259)
                      .+|..+
T Consensus       154 ~~g~~~  159 (189)
T PRK09521        154 RCRTPL  159 (189)
T ss_pred             ccCCce
Confidence            788865

>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain

Probab=99.38  E-value=2.5e-12  Score=96.49  Aligned_cols=75  Identities=13%  Similarity=0.120  Sum_probs=69.2

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeec
Q 044309           84 YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV  161 (259)
Q Consensus        84 ~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~  161 (259)
                      +|++|++|.|+|+++.+.|++|++.  .+.+|++|.++++..+..++.+.|++||.+.|+|+++|.+ +++.||++..
T Consensus         3 ~p~~GdiV~G~V~~v~~~~~~V~i~--~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~-~~i~LS~~~~   77 (82)
T cd04454           3 LPDVGDIVIGIVTEVNSRFWKVDIL--SRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVLLTTADN   77 (82)
T ss_pred             CCCCCCEEEEEEEEEcCCEEEEEeC--CCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC-CCEEEEECCC
Confidence            4569999999999999999999997  5899999999999888888899999999999999999986 8999999863

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

>PHA02858 EIF2a-like PKR inhibitor; Provisional

Probab=99.36  E-value=2.1e-12  Score=97.52  Aligned_cols=73  Identities=29%  Similarity=0.563  Sum_probs=69.4

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEE-ccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEE
Q 044309           83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMIL-FSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSK  158 (259)
Q Consensus        83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllh-isEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSl  158 (259)
                      .||++|+++. .|+.+.+.|+||.|.||+ .+|+|. .+|++.++++++++.+ +|..+.|+|+++|+++|.|+||.
T Consensus        12 ~~P~v~dvv~-~Vv~i~d~~~YV~LleY~-iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~KGYIDLs~   85 (86)
T PHA02858         12 VFPNINEVTK-GIVFVKDNIFYVKLIDYG-LEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKGYIDVRH   85 (86)
T ss_pred             ecCCCCeEEE-EEEEEeccEEEEEEecCc-cceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCCCEEEeEc
Confidence            5899999999 777999999999999996 999998 9999999999999999 99999999999999999999985

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

Probab=99.36  E-value=3.9e-12  Score=97.58  Aligned_cols=70  Identities=20%  Similarity=0.240  Sum_probs=61.3

Q ss_pred             CCcEEEEEEEEEeCc--eEEEEEccCCCEEEEEEcccccc---ccccCccccccCCCeEEEEEEEEeCCCCeEEEEE
Q 044309           87 VDMAVMIQVKNIADM--GAYVSLLEYNNIEGMILFSELSR---RRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSK  158 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~--GafV~L~ey~~~eGllhisEls~---~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSl  158 (259)
                      +|+++.|+|+++.++  ||||+|.  ++.+||||+||++|   .++.++.+.+++||.|.|+|++......-..||.
T Consensus         7 ~G~iy~g~V~~i~~~~~GaFV~l~--~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~lt~   81 (88)
T cd04453           7 VGNIYLGRVKKIVPGLQAAFVDIG--LGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLTT   81 (88)
T ss_pred             CCCEEEEEEEEeccCCcEEEEEeC--CCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCceEEE
Confidence            899999999999997  9999998  58999999999999   6788899999999999999999776544444443

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

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

Probab=99.35  E-value=6.1e-12  Score=93.54  Aligned_cols=71  Identities=23%  Similarity=0.361  Sum_probs=62.1

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccccccccc-----------CccccccCCCeEEEEEEEEeCCCCeEE
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIR-----------SVSSLIKVGRIEPVMVLRVDKEKGYID  155 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~-----------~~~~~~kvGd~V~vkVi~vD~~~gkI~  155 (259)
                      +|+++.|+|++++++|+||+|..| +.+|++|++++++.++.           +..+.+++||.|+|+|.++|.+++++.
T Consensus         1 ~g~~~~g~V~~v~~~G~fv~l~~~-~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~~i~   79 (83)
T cd04471           1 VGEEFDGVISGVTSFGLFVELDNL-TVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKID   79 (83)
T ss_pred             CCCEEEEEEEeEEeeeEEEEecCC-CEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccCEEE
Confidence            389999999999999999999742 79999999999875422           345789999999999999999899999


Q ss_pred             EEE
Q 044309          156 LSK  158 (259)
Q Consensus       156 LSl  158 (259)
                      +++
T Consensus        80 ~~l   82 (83)
T cd04471          80 FEL   82 (83)
T ss_pred             EEE
Confidence            986

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

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

Probab=99.26  E-value=6e-12  Score=113.62  Aligned_cols=113  Identities=20%  Similarity=0.219  Sum_probs=99.6

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhH
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDI  166 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~  166 (259)
                      .|+.+.|+|++....|.||-++  ++.-||||-||..        ...+.|+++.++|+++.+ +|+|.||++....+..
T Consensus       155 ~nq~v~~tVYr~~~~G~fv~~e--~~~~GfIh~sEr~--------~~prlG~~l~~rVi~~re-Dg~lnLSl~p~~~E~l  223 (287)
T COG2996         155 KNQEVDATVYRLLESGTFVITE--NGYLGFIHKSERF--------AEPRLGERLTARVIGVRE-DGKLNLSLRPRAHEML  223 (287)
T ss_pred             hcCeeeeEEEEEeccceEEEEc--CCeEEEEcchhhc--------ccccCCceEEEEEEEEcc-CCeeecccccccHHhh
Confidence            4999999999999999999996  7999999999976        457899999999999998 8999999999988777


Q ss_pred             HHHHHhccccceEEEEEEecccccCCchHHHHHhhchh--hHHhhcCHHHHHHHHhcC
Q 044309          167 QACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGWP--LYWKYGHAFEAFKIIVTD  222 (259)
Q Consensus       167 ~~~~~~~~~g~~v~g~V~~i~~~~G~fve~~~~~~sw~--l~~~~~~~~~~fk~a~~~  222 (259)
                      +..+         +.+++.+.+ .|-|+.  |+|.|-|  |.+.|+.++.+||+|+|.
T Consensus       224 ~~da---------q~Il~yL~~-~gG~mp--f~DKSsPEdIk~~FgiSKg~FKrAiGg  269 (287)
T COG2996         224 DEDA---------QMILTYLES-NGGFMP--FNDKSSPEDIKATFGISKGQFKRAIGG  269 (287)
T ss_pred             hhhH---------HHHHHHHHH-cCCccc--cCCCCCHHHHHHHhCcCHHHHHHHHHH
Confidence            7665         356677766 555678  9999999  999999999999999985

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

Probab=99.24  E-value=2.9e-11  Score=84.30  Aligned_cols=65  Identities=42%  Similarity=0.590  Sum_probs=60.2

Q ss_pred             EEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEE
Q 044309           91 VMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLS  157 (259)
Q Consensus        91 v~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LS  157 (259)
                      +.|+|+++.++|+||++.  ++.+|++|.+++++.+..++.+.+++||.+.|+|+++|++++++.||
T Consensus         1 v~g~V~~v~~~g~~v~l~--~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~~~~i~ls   65 (65)
T cd00164           1 VTGKVVSITKFGVFVELE--DGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS   65 (65)
T ss_pred             CEEEEEEEEeeeEEEEec--CCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence            479999999999999997  58999999999999888888899999999999999999988999876

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.

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

Probab=99.24  E-value=8.2e-11  Score=87.62  Aligned_cols=64  Identities=30%  Similarity=0.352  Sum_probs=58.1

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEE
Q 044309           83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSK  158 (259)
Q Consensus        83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSl  158 (259)
                      .+. +|+.+.|+|++++++|+||++.  ++.+||+|.+++.        +.+++||.++++|.++ .+++++++|+
T Consensus        13 ~~~-~G~~~~g~V~~i~~~G~fV~l~--~~~~Glv~~se~~--------~~~~iGd~v~v~I~~i-~e~~~i~l~~   76 (77)
T cd04473          13 DLE-VGKLYKGKVNGVAKYGVFVDLN--DHVRGLIHRSNLL--------RDYEVGDEVIVQVTDI-PENGNIDLIP   76 (77)
T ss_pred             hCC-CCCEEEEEEEeEecceEEEEEC--CCcEEEEEchhcc--------CcCCCCCEEEEEEEEE-CCCCcEEEEE
Confidence            455 8999999999999999999998  5799999999974        5699999999999999 7789999986

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.

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

Probab=99.23  E-value=4.2e-11  Score=87.30  Aligned_cols=62  Identities=24%  Similarity=0.216  Sum_probs=57.5

Q ss_pred             CcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccccccc--ccCccccccCCCeEEEEEEEEeCCC
Q 044309           88 DMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRR--IRSVSSLIKVGRIEPVMVLRVDKEK  151 (259)
Q Consensus        88 G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~--v~~~~~~~kvGd~V~vkVi~vD~~~  151 (259)
                      |++|.|+|+++.++|+||++.  ++++|++|++++++++  ..++.+.|++||.+.|+|+++|.++
T Consensus         1 G~iV~g~V~~i~~~gi~v~l~--~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~   64 (70)
T cd05702           1 GDLVKAKVKSVKPTQLNVQLA--DNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAK   64 (70)
T ss_pred             CCEEEEEEEEEECCcEEEEeC--CCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCcc
Confidence            789999999999999999997  5899999999999874  7888899999999999999999854

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

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=99.23  E-value=2.5e-11  Score=123.38  Aligned_cols=69  Identities=36%  Similarity=0.578  Sum_probs=64.5

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEE
Q 044309           85 PEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDL  156 (259)
Q Consensus        85 ~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~L  156 (259)
                      +++|++|.|+|++|.+||+||++.  ++.+||||+|++++.++.++.+.|++||.|.|+|+++|. +|+|+|
T Consensus       616 ~~~G~i~~G~V~~I~~~GafVei~--~g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id~-~gki~L  684 (684)
T TIGR03591       616 PEVGKIYEGKVVRIMDFGAFVEIL--PGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDK-QGRIKL  684 (684)
T ss_pred             cccCcEEEEEEEEEeCCEEEEEEC--CCcEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEECC-CCCccC
Confidence            348999999999999999999997  689999999999999999999999999999999999998 788765

Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).

>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]

Probab=99.20  E-value=3e-11  Score=120.50  Aligned_cols=79  Identities=32%  Similarity=0.464  Sum_probs=72.5

Q ss_pred             hhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309           80 YEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR  159 (259)
Q Consensus        80 ~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK  159 (259)
                      +...+. +|+++.|+|+++.+|||||+|.  ++.+||+|+|++++.|+.+..+++++||.+.|||+.+|+ +|+++||++
T Consensus       613 i~~e~e-vg~iy~G~V~ri~~fGaFv~l~--~gkdgl~hiS~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD~-~Gri~ls~~  688 (692)
T COG1185         613 ITREVE-VGEVYEGTVVRIVDFGAFVELL--PGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEIDK-QGRIRLSIK  688 (692)
T ss_pred             HHhhcc-cccEEEEEEEEEeecceEEEec--CCcceeEEehhhhhhhhhcccceeecCceEEEEEeeecc-cCCccceeh
Confidence            344444 9999999999999999999998  789999999999999999999999999999999999997 799999998


Q ss_pred             ecc
Q 044309          160 RVS  162 (259)
Q Consensus       160 ~~~  162 (259)
                      ...
T Consensus       689 ~~~  691 (692)
T COG1185         689 AVL  691 (692)
T ss_pred             hcc
Confidence            753

>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]

Probab=99.19  E-value=3e-11  Score=117.93  Aligned_cols=81  Identities=25%  Similarity=0.321  Sum_probs=73.7

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecc
Q 044309           83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVS  162 (259)
Q Consensus        83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~  162 (259)
                      .+. .|.+++|+|+++.++|+||+|.  ++.+||+|+|||+..++.+|.+.+.+||.|.|+.++.|+ ++.+.+|.|.+.
T Consensus       665 ~l~-~g~vy~~tIt~~rd~G~~V~l~--p~~~~Llh~sqL~~e~iakpsd~levGq~I~vk~ie~d~-~g~~~ls~ralL  740 (760)
T KOG1067|consen  665 DLE-FGGVYTATITEIRDTGVMVELY--PMQQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDP-RGGIMLSSRALL  740 (760)
T ss_pred             ceE-eeeEEEEEEeeecccceEEEec--CCchhhccchhcccccccChHHHHhhcceeEEEEEeecC-ccceeehhhhhc
Confidence            344 7999999999999999999995  799999999999999999999999999999999999998 688888888888


Q ss_pred             hhhHH
Q 044309          163 EEDIQ  167 (259)
Q Consensus       163 ~~~~~  167 (259)
                      ++|..
T Consensus       741 p~p~~  745 (760)
T KOG1067|consen  741 PDPAT  745 (760)
T ss_pred             CCccc
Confidence            87654

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=99.16  E-value=5.8e-11  Score=120.02  Aligned_cols=78  Identities=31%  Similarity=0.454  Sum_probs=73.6

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecc
Q 044309           83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVS  162 (259)
Q Consensus        83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~  162 (259)
                      .+. +|.++.|+|+++.+||+||+|+  -+.+|+||+|+++.+++.+|.+++++||.|+|+|+++|..+++|.||++.-.
T Consensus       655 dLk-~Gm~leg~Vrnv~~fgafVdIg--v~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~~  731 (780)
T COG2183         655 DLK-PGMILEGTVRNVVDFGAFVDIG--VHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMRLDE  731 (780)
T ss_pred             hcc-CCCEEEEEEEEeeeccceEEec--cccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEeeccC
Confidence            455 8999999999999999999997  5899999999999999999999999999999999999999999999999765


Q ss_pred             h
Q 044309          163 E  163 (259)
Q Consensus       163 ~  163 (259)
                      .
T Consensus       732 ~  732 (780)
T COG2183         732 E  732 (780)
T ss_pred             C
Confidence            4

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

Probab=99.09  E-value=6.5e-10  Score=86.45  Aligned_cols=78  Identities=21%  Similarity=0.335  Sum_probs=66.2

Q ss_pred             cEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccC-----------ccccccCCCeEEEEEEEEeCCC-----C
Q 044309           89 MAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRS-----------VSSLIKVGRIEPVMVLRVDKEK-----G  152 (259)
Q Consensus        89 ~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~-----------~~~~~kvGd~V~vkVi~vD~~~-----g  152 (259)
                      +++.|+|+++.++|+||+|.   +++|++|++++++++...           ..+.|++||.+.|+|.++|.+.     +
T Consensus         1 ~vv~g~V~~i~~~GifV~l~---~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~   77 (99)
T cd04460           1 EVVEGEVVEVVDFGAFVRIG---PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRES   77 (99)
T ss_pred             CEEEEEEEEEEeccEEEEEc---CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCc
Confidence            47999999999999999995   599999999999866543           3477999999999999999763     5


Q ss_pred             eEEEEEeecchhhHHHH
Q 044309          153 YIDLSKRRVSEEDIQAC  169 (259)
Q Consensus       153 kI~LSlK~~~~~~~~~~  169 (259)
                      ++.||+|+....+|.=.
T Consensus        78 ~i~ls~k~~~~g~~~~~   94 (99)
T cd04460          78 KIGLTMRQPGLGKLEWI   94 (99)
T ss_pred             eEEEEEecCCCCcHHHh
Confidence            89999999877666543

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

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=99.09  E-value=4.2e-10  Score=100.81  Aligned_cols=76  Identities=18%  Similarity=0.211  Sum_probs=68.7

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc----cCccccccCCCeEEEEEEEEeCCCCeEEEEE
Q 044309           83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI----RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSK  158 (259)
Q Consensus        83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v----~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSl  158 (259)
                      ..|++||+|.|+|+++.++|+||+|.  ++.+|+||++++++.++    .++++.|++||.|.|+|++++++ +.+.||+
T Consensus        59 y~P~vGDiViG~V~~i~~~~~~vdI~--~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~-~~~~LS~  135 (235)
T PRK04163         59 YIPKVGDLVIGKVTDVTFSGWEVDIN--SPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRT-RDVVLTL  135 (235)
T ss_pred             ccCCCCCEEEEEEEEEeCceEEEEeC--CCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCC-CcEEEEE
Confidence            45679999999999999999999997  47999999999999887    78899999999999999999974 5699999


Q ss_pred             eec
Q 044309          159 RRV  161 (259)
Q Consensus       159 K~~  161 (259)
                      ++.
T Consensus       136 k~~  138 (235)
T PRK04163        136 KGK  138 (235)
T ss_pred             cCC
Confidence            864

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

Probab=99.04  E-value=1.6e-09  Score=78.54  Aligned_cols=63  Identities=24%  Similarity=0.146  Sum_probs=55.4

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCC--CeEEEEE
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEK--GYIDLSK  158 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~--gkI~LSl  158 (259)
                      .|+++.|+|.++.+.|+||+++   +.+|+||.+|++.      .+.+++||.++|.|++++.++  ++|.||+
T Consensus         3 ~g~iV~G~V~~~~~~~~~vdig---~~eg~lp~~e~~~------~~~~~~Gd~v~v~v~~v~~~~~~~~i~lSr   67 (67)
T cd04455           3 EGEIVTGIVKRVDRGNVIVDLG---KVEAILPKKEQIP------GESYRPGDRIKAYVLEVRKTSKGPQIILSR   67 (67)
T ss_pred             CCCEEEEEEEEEcCCCEEEEcC---CeEEEeeHHHCCC------CCcCCCCCEEEEEEEEEecCCCCCEEEEeC
Confidence            7999999999999999999995   5999999999973      467899999999999999643  5788874

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

>TIGR02063 RNase_R ribonuclease R

Probab=99.01  E-value=1.4e-09  Score=111.11  Aligned_cols=81  Identities=20%  Similarity=0.340  Sum_probs=68.6

Q ss_pred             chhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc-----------cCccccccCCCeEEE
Q 044309           74 NLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI-----------RSVSSLIKVGRIEPV  142 (259)
Q Consensus        74 ~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v-----------~~~~~~~kvGd~V~v  142 (259)
                      ...|+++...   +|+++.|+|++|++||+||+|.+ .+++||+|+|++++++.           ++..+.+++||.|.|
T Consensus       617 ~~~~~yl~~~---iG~~~~g~V~~v~~fGifV~L~~-~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~V  692 (709)
T TIGR02063       617 WKKAEYMSEK---IGEEFEGVISGVTSFGLFVELEN-NTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKV  692 (709)
T ss_pred             HHHHHhhhcc---CCcEEEEEEEEEEeCCEEEEecC-CceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEE
Confidence            4466766654   79999999999999999999984 26999999999986543           334577999999999


Q ss_pred             EEEEEeCCCCeEEEEE
Q 044309          143 MVLRVDKEKGYIDLSK  158 (259)
Q Consensus       143 kVi~vD~~~gkI~LSl  158 (259)
                      +|.++|..+++|++++
T Consensus       693 kv~~vd~~~~~I~~~l  708 (709)
T TIGR02063       693 RVVKADLDTGKIDFEL  708 (709)
T ss_pred             EEEEEecccCeEEEEE
Confidence            9999999999999986

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.

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

Probab=98.92  E-value=5.3e-09  Score=106.03  Aligned_cols=81  Identities=22%  Similarity=0.370  Sum_probs=69.2

Q ss_pred             chhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc-----------cCccccccCCCeEEE
Q 044309           74 NLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI-----------RSVSSLIKVGRIEPV  142 (259)
Q Consensus        74 ~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v-----------~~~~~~~kvGd~V~v  142 (259)
                      ...|+++.+.   +|+.+.|+|++|+++|+||+|++ .+++||+|++++.+++.           ++....|++||.|+|
T Consensus       562 ~~~~~yl~~~---iG~~~~g~I~~v~~~GifV~L~~-~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~V  637 (654)
T TIGR00358       562 WLKCRYLLDK---VGTEFSGEISSVTRFGMFVRLDD-NGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTV  637 (654)
T ss_pred             HHHHHhhhhC---CCcEEEEEEEeEEcCcEEEEecC-CceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEE
Confidence            3457776665   79999999999999999999986 47999999999997641           334577999999999


Q ss_pred             EEEEEeCCCCeEEEEE
Q 044309          143 MVLRVDKEKGYIDLSK  158 (259)
Q Consensus       143 kVi~vD~~~gkI~LSl  158 (259)
                      +|.++|.++++|++++
T Consensus       638 ki~~vd~~~~~I~f~l  653 (654)
T TIGR00358       638 KLTEVNMETRSIIFEL  653 (654)
T ss_pred             EEEEEecccCeEEEEE
Confidence            9999999999999985

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.

>PRK11642 exoribonuclease R; Provisional

Probab=98.91  E-value=5.6e-09  Score=108.04  Aligned_cols=82  Identities=22%  Similarity=0.294  Sum_probs=69.2

Q ss_pred             hhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc-----------cCccccccCCCeEEEE
Q 044309           75 LECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI-----------RSVSSLIKVGRIEPVM  143 (259)
Q Consensus        75 ~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v-----------~~~~~~~kvGd~V~vk  143 (259)
                      +.|+++.+.   +|+++.|+|++|++||+||+|++ .+++||||++++.+++.           ++....|++||.|.|+
T Consensus       634 ~~~~~m~~~---iGe~f~G~Is~V~~fGifVeL~~-~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~Vk  709 (813)
T PRK11642        634 LKCDFMLDQ---VGNVFKGVISSVTGFGFFVRLDD-LFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVR  709 (813)
T ss_pred             HHHhhhhcc---CCcEEEEEEEEeecCceEEEECC-CCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEE
Confidence            456666653   79999999999999999999974 35999999999987532           1235779999999999


Q ss_pred             EEEEeCCCCeEEEEEee
Q 044309          144 VLRVDKEKGYIDLSKRR  160 (259)
Q Consensus       144 Vi~vD~~~gkI~LSlK~  160 (259)
                      |.++|.++++|+|++..
T Consensus       710 V~~vD~~~rkI~f~l~~  726 (813)
T PRK11642        710 VEAVNMDERKIDFSLIS  726 (813)
T ss_pred             EEEeecCCCeEEEEEec
Confidence            99999999999999853

>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain

Probab=98.88  E-value=8.2e-09  Score=79.82  Aligned_cols=75  Identities=19%  Similarity=0.213  Sum_probs=65.1

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEE--------ccCCCEEEEEEcccccccccc--CccccccCCCeEEEEEEEEeCCCCe
Q 044309           84 YPEVDMAVMIQVKNIADMGAYVSL--------LEYNNIEGMILFSELSRRRIR--SVSSLIKVGRIEPVMVLRVDKEKGY  153 (259)
Q Consensus        84 ~~~~G~iv~G~V~~I~~~GafV~L--------~ey~~~eGllhisEls~~~v~--~~~~~~kvGd~V~vkVi~vD~~~gk  153 (259)
                      .|++|++|.|+|++++...|.|++        .  ....|++|++++......  ++.+.|++||.|.|+|++++. ...
T Consensus         3 ~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~--~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~-~~~   79 (92)
T cd05791           3 LPKVGSIVIARVTRINPRFAKVDILCVGGRPLK--ESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGD-ASS   79 (92)
T ss_pred             CCCCCCEEEEEEEEEcCCEEEEEEEEecCeecC--CCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCC-CCC
Confidence            467999999999999999999999        5  368999999999876665  678999999999999999975 366


Q ss_pred             EEEEEeec
Q 044309          154 IDLSKRRV  161 (259)
Q Consensus       154 I~LSlK~~  161 (259)
                      +.||+++-
T Consensus        80 ~~Lst~~~   87 (92)
T cd05791          80 YYLSTAEN   87 (92)
T ss_pred             cEEEecCC
Confidence            88998753

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".

>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form

Probab=98.87  E-value=1.3e-08  Score=87.53  Aligned_cols=74  Identities=20%  Similarity=0.267  Sum_probs=63.5

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccccccccc-----------CccccccCCCeEEEEEEEEe-----CC
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIR-----------SVSSLIKVGRIEPVMVLRVD-----KE  150 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~-----------~~~~~~kvGd~V~vkVi~vD-----~~  150 (259)
                      +|+++.|+|++++++|+||+++   ..+|++|.+++.+.+..           +....++.||.|+++|.++|     ++
T Consensus        81 ~gEvv~G~V~~v~~~GifV~lg---~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~  157 (179)
T TIGR00448        81 LGEIVEGEVIEIVEFGAFVSLG---PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRPE  157 (179)
T ss_pred             CCCEEEEEEEEEEeeEEEEEeC---CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCCC
Confidence            7999999999999999999994   69999999999865431           23577999999999999998     55


Q ss_pred             CCeEEEEEeecch
Q 044309          151 KGYIDLSKRRVSE  163 (259)
Q Consensus       151 ~gkI~LSlK~~~~  163 (259)
                      ..+|.||+|+...
T Consensus       158 ~~~I~lt~k~~~L  170 (179)
T TIGR00448       158 GSKIGLTMRQPLL  170 (179)
T ss_pred             cceEEEEeccCcC
Confidence            6799999998644

This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=98.71  E-value=9.1e-08  Score=93.62  Aligned_cols=67  Identities=22%  Similarity=0.157  Sum_probs=61.2

Q ss_pred             CCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCC--eEEEEEeec
Q 044309           86 EVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKG--YIDLSKRRV  161 (259)
Q Consensus        86 ~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~g--kI~LSlK~~  161 (259)
                      ++|++|.|+|.++.++|+||+|   ++++||||.++++      |++.|++||.++|.|++|+++++  +|.||++..
T Consensus       133 ~~GeIV~G~V~ri~~~giiVDL---ggvea~LP~sE~i------p~E~~~~GdrIka~I~~Vd~~~kg~qIilSRt~p  201 (470)
T PRK09202        133 RVGEIITGVVKRVERGNIIVDL---GRAEAILPRKEQI------PRENFRPGDRVRAYVYEVRKEARGPQIILSRTHP  201 (470)
T ss_pred             hcCCEEEEEEEEEecCCEEEEE---CCeEEEecHHHcC------CCccCCCCCEEEEEEEEEecCCCCCeEEEEeCcH
Confidence            3899999999999999999999   4899999999996      67889999999999999999766  899998854

>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]

Probab=98.69  E-value=1.3e-07  Score=100.12  Aligned_cols=110  Identities=20%  Similarity=0.247  Sum_probs=97.1

Q ss_pred             hhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEee
Q 044309           81 EARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRR  160 (259)
Q Consensus        81 ~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~  160 (259)
                      .+.+. .|+++.|.|.++.+.|+|+.|.  .+++|++++|+++......+++.|.+|+.+.++|.+++...+++.||+|.
T Consensus      1157 ~eDlk-~g~iv~G~V~nv~~~glfi~ls--~~v~a~v~is~~~ds~~k~w~k~~~~gklv~~rv~~ve~~s~riel~Lk~ 1233 (1710)
T KOG1070|consen 1157 IEDLK-IGDIVRGFVKNVETKGLFIALS--RKVEAFVPISGLSDSFEKEWEKHLPVGKLVTGRVLSVEEDSKRIELSLKN 1233 (1710)
T ss_pred             hhhcc-cCceeEEEEEEecCCcEEEEEc--cceEEEEEccccccchhhhhhccCCccceeeeEEEEeeccCceEEEEEec
Confidence            45666 8999999999999999999998  68999999999999999999999999999999999999999999999998


Q ss_pred             cchhhH---HHHHHhccccceEEEEEEecccccCCch
Q 044309          161 VSEEDI---QACEERYNKSKLVHSIMRHVAETLGIDL  194 (259)
Q Consensus       161 ~~~~~~---~~~~~~~~~g~~v~g~V~~i~~~~G~fv  194 (259)
                      .....-   .......++|+...|+|..+.+ +|.|+
T Consensus      1234 s~~~d~~~~~~~~~~l~~gd~~~g~v~~~~~-~G~fi 1269 (1710)
T KOG1070|consen 1234 SDIKDTVKLLKDSKDLKKGDREDGTVEVVDP-FGLFI 1269 (1710)
T ss_pred             cccCCchhhhhhhhhhhccccccceEEEecC-CceEE
Confidence            654222   2234667899999999999965 99987

>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional

Probab=98.68  E-value=1.3e-07  Score=81.55  Aligned_cols=75  Identities=23%  Similarity=0.421  Sum_probs=63.2

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccccccccc-----------CccccccCCCeEEEEEEEEeCCC--
Q 044309           85 PEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIR-----------SVSSLIKVGRIEPVMVLRVDKEK--  151 (259)
Q Consensus        85 ~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~-----------~~~~~~kvGd~V~vkVi~vD~~~--  151 (259)
                      |.+|+++.|+|++++++|+||+++   ..+|++|.+++.+++..           +....+++||.|+++|.+++.+.  
T Consensus        79 P~~GEVv~g~V~~v~~~Gi~V~lg---~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~  155 (187)
T PRK08563         79 PELQEVVEGEVVEVVEFGAFVRIG---PVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERR  155 (187)
T ss_pred             ccCCCEEEEEEEEEEccEEEEEEe---CceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCC
Confidence            347999999999999999999995   59999999999875432           34567999999999999999754  


Q ss_pred             ---CeEEEEEeecc
Q 044309          152 ---GYIDLSKRRVS  162 (259)
Q Consensus       152 ---gkI~LSlK~~~  162 (259)
                         .+|.+|+++..
T Consensus       156 ~~~~~I~ls~~~~~  169 (187)
T PRK08563        156 PRGSKIGLTMRQPG  169 (187)
T ss_pred             CCCCEEEEEecCCC
Confidence               37899999754

>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]

Probab=98.66  E-value=9.2e-08  Score=82.40  Aligned_cols=81  Identities=20%  Similarity=0.283  Sum_probs=65.7

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccccccc----------ccC-ccccccCCCeEEEEEEEEeCCC--
Q 044309           85 PEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRR----------IRS-VSSLIKVGRIEPVMVLRVDKEK--  151 (259)
Q Consensus        85 ~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~----------v~~-~~~~~kvGd~V~vkVi~vD~~~--  151 (259)
                      |..|++|.|.|+++.+||+||.+.   ..+||+|.|++.+..          +.+ -...+++||.|.+||+.++...  
T Consensus        79 P~~gEVV~GeVv~~~~~G~fV~ig---p~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~  155 (183)
T COG1095          79 PFRGEVVEGEVVEVVEFGAFVRIG---PLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRR  155 (183)
T ss_pred             eccccEEEEEEEEEeecceEEEec---cccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCc
Confidence            447999999999999999999995   799999999999862          222 3447999999999999998654  


Q ss_pred             ---CeEEEEEeecch--hhHHH
Q 044309          152 ---GYIDLSKRRVSE--EDIQA  168 (259)
Q Consensus       152 ---gkI~LSlK~~~~--~~~~~  168 (259)
                         .+|.+++|+.-.  -+|-.
T Consensus       156 ~~~~~I~lTmrq~~LGklew~~  177 (183)
T COG1095         156 PRESKIGLTMRQPGLGKLEWIE  177 (183)
T ss_pred             cccceEEEEeccccCCcchhhh
Confidence               578999998653  34543

>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]

Probab=98.57  E-value=1.6e-07  Score=99.51  Aligned_cols=79  Identities=25%  Similarity=0.301  Sum_probs=73.3

Q ss_pred             hhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309           80 YEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR  159 (259)
Q Consensus        80 ~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK  159 (259)
                      +....  +|.++.|+|.++.++||||.+.  ++++||.|.|+++..++.++++.|.+||.+.|+|.++|.++.+|.||+|
T Consensus       594 ~~~~~--pg~~~~G~l~~~~~~g~~V~F~--g~lsGf~p~s~~sd~~v~~~~ehf~vGqTv~~~i~nvd~ek~rm~l~~r  669 (1710)
T KOG1070|consen  594 FEQAI--PGKITKGTLCAIKENGAFVTFT--GGLSGFAPVSEMSDDFVLSDSEHFPVGQTVRAKIVNVDDEKRRMPLGLR  669 (1710)
T ss_pred             hhhcC--CCceEEEEEeeeccCCeEEEec--CccccccchhhhhhhhhcChhhhcccccEEEEEEEecCchhceeehhhh
Confidence            44444  4999999999999999999996  7999999999999999999999999999999999999999999999999


Q ss_pred             ecc
Q 044309          160 RVS  162 (259)
Q Consensus       160 ~~~  162 (259)
                      ...
T Consensus       670 ~s~  672 (1710)
T KOG1070|consen  670 ASS  672 (1710)
T ss_pred             hhh
Confidence            764

>PRK05054 exoribonuclease II; Provisional

Probab=98.48  E-value=6.6e-07  Score=90.79  Aligned_cols=83  Identities=24%  Similarity=0.202  Sum_probs=65.5

Q ss_pred             chhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc-----cC-------ccccccCCCeEE
Q 044309           74 NLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI-----RS-------VSSLIKVGRIEP  141 (259)
Q Consensus        74 ~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v-----~~-------~~~~~kvGd~V~  141 (259)
                      .+.|+++.+..- .|+.+.|.|++|+++|+||+|.+ .+++||||++.+...+.     .+       -+..|++||.|.
T Consensus       549 ~~~~~y~~~~~G-~~~~f~g~I~~v~~~G~fV~l~~-~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~  626 (644)
T PRK05054        549 WLYARYLKDKAG-TDTRFAAEIIDISRGGMRVRLLE-NGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVID  626 (644)
T ss_pred             HHHHHHHhhccC-CCeEEEEEEEeeecCcEEEEEeC-CceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEE
Confidence            446666665521 24599999999999999999987 58999999999965311     01       125799999999


Q ss_pred             EEEEEEeCCCCeEEEEE
Q 044309          142 VMVLRVDKEKGYIDLSK  158 (259)
Q Consensus       142 vkVi~vD~~~gkI~LSl  158 (259)
                      |+|.++|..+++|++++
T Consensus       627 V~v~~vd~~~~~i~~~~  643 (644)
T PRK05054        627 VTLAEVRMETRSIIARP  643 (644)
T ss_pred             EEEEEEccccCeEEEEE
Confidence            99999999999999875

>TIGR01953 NusA transcription termination factor NusA

Probab=98.41  E-value=2.3e-06  Score=80.77  Aligned_cols=67  Identities=24%  Similarity=0.252  Sum_probs=58.7

Q ss_pred             CCCcEEEEEEEEEeCce-EEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCC--CCeEEEEEeec
Q 044309           86 EVDMAVMIQVKNIADMG-AYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKE--KGYIDLSKRRV  161 (259)
Q Consensus        86 ~~G~iv~G~V~~I~~~G-afV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~--~gkI~LSlK~~  161 (259)
                      ++|++++|+|.++.+.| +||++   ++.+|+||.+|+.      +++.|++||.++|.|++++..  ..+|.||++..
T Consensus       130 k~GeiV~G~V~~v~~~g~v~Vdi---G~~ea~LP~~E~i------p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~~  199 (341)
T TIGR01953       130 KEGEIISGTVKRVNRRGNLYVEL---GKTEGILPKKEQI------PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHP  199 (341)
T ss_pred             hcCCEEEEEEEEEecCCcEEEEE---CCeEEEecHHHcC------CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCcH
Confidence            38999999999999988 69999   4899999999988      456699999999999999954  35899998864

This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=98.39  E-value=2.4e-06  Score=81.20  Aligned_cols=66  Identities=24%  Similarity=0.190  Sum_probs=56.9

Q ss_pred             CCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCC--eEEEEEee
Q 044309           86 EVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKG--YIDLSKRR  160 (259)
Q Consensus        86 ~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~g--kI~LSlK~  160 (259)
                      +.|++++|+|.++.+.|+||++   ++++|+||.+++.      +++.|++||.++|.|++|+.+++  +|.||+..
T Consensus       133 k~GeiV~G~V~~~~~~~~~Vdl---g~vEa~LP~~E~i------p~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt~  200 (362)
T PRK12327        133 REGDIVTGVVQRRDNRFVYVNL---GKIEAVLPPAEQI------PGETYKHGDRIKVYVVKVEKTTKGPQIFVSRTH  200 (362)
T ss_pred             hcCCEEEEEEEEEeCCcEEEEe---CCeEEEecHHHcC------CCCCCCCCCEEEEEEEEEecCCCCCeEEEEeCC
Confidence            3899999999999999999999   4799999999886      36789999999999999996543  57777653

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=98.35  E-value=5.7e-06  Score=79.98  Aligned_cols=58  Identities=21%  Similarity=0.217  Sum_probs=51.3

Q ss_pred             CCcEEEEEEEEEeCc--eEEEEEccCCCEEEEEEccccccc------------cccCccccccCCCeEEEEEEE
Q 044309           87 VDMAVMIQVKNIADM--GAYVSLLEYNNIEGMILFSELSRR------------RIRSVSSLIKVGRIEPVMVLR  146 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~--GafV~L~ey~~~eGllhisEls~~------------~v~~~~~~~kvGd~V~vkVi~  146 (259)
                      +|++|.|+|+++.+.  ||||+|+  .+..||||++++.+.            +..++.+.+++||.|.|.|.+
T Consensus        25 vGnIY~GrV~~i~p~l~aAFVdiG--~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~K   96 (414)
T TIGR00757        25 KGNIYKGRVTRILPSLQAAFVDIG--LEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVK   96 (414)
T ss_pred             CCCEEEEEEeeecCCCceEEEEcC--CCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEee
Confidence            899999999999999  9999998  579999999999752            244567789999999999997

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

>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]

Probab=98.30  E-value=3e-06  Score=75.86  Aligned_cols=77  Identities=21%  Similarity=0.385  Sum_probs=67.6

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc----cCccccccCCCeEEEEEEEEeCCCCeEEEEE
Q 044309           83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI----RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSK  158 (259)
Q Consensus        83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v----~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSl  158 (259)
                      ..|++||+|.|+|..+...|+.|+|.  +.+.|++|+|++.++.+    .+.+.+|++||.|.|+|..+|+ .+.+.|++
T Consensus        60 YiP~~gD~VIG~I~~v~~~~W~VDI~--sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~-~~~~~L~~  136 (239)
T COG1097          60 YIPEVGDVVIGKIIEVGPSGWKVDIG--SPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDR-DGEVELTL  136 (239)
T ss_pred             ccCCCCCEEEEEEEEEcccceEEEcC--CccceEeehhhhhcccccccccccccccccCCEEEEEEEEccC-CCceEEEe
Confidence            45779999999999999999999997  56999999999976553    4578899999999999999998 68999999


Q ss_pred             eecc
Q 044309          159 RRVS  162 (259)
Q Consensus       159 K~~~  162 (259)
                      |...
T Consensus       137 k~~~  140 (239)
T COG1097         137 KDEG  140 (239)
T ss_pred             ecCC
Confidence            7643

>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain

Probab=98.29  E-value=5e-06  Score=63.72  Aligned_cols=74  Identities=14%  Similarity=0.036  Sum_probs=62.4

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeec
Q 044309           84 YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV  161 (259)
Q Consensus        84 ~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~  161 (259)
                      .|++||.|.|+|+++...+.+|+|.  +...|+||.+++... .+..+..+++||.|-|+|.++|+ .....||+...
T Consensus         3 ~P~~gD~VIG~V~~~~~~~~~VdI~--s~~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV~~~~~-~~~~eLtc~~~   76 (86)
T cd05790           3 VPAKGDHVIGIVVAKAGDFFKVDIG--GSEPASLSYLAFEGA-TKRNRPNLNVGDLVYARVVKANR-DMEPELSCVDS   76 (86)
T ss_pred             cCCCCCEEEEEEEEEcCCeEEEEcC--CCcceEechHHcccc-cccccccCCCCCEEEEEEEecCC-CCCeEEEEeCC
Confidence            4669999999999999999999997  468999999887533 34456789999999999999998 46788988763

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

>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]

Probab=98.23  E-value=8.1e-06  Score=70.59  Aligned_cols=94  Identities=16%  Similarity=0.175  Sum_probs=78.9

Q ss_pred             hcCCCCCcEEEEEEEEEeCceEEEEEcc-----C---CCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCe
Q 044309           82 ARYPEVDMAVMIQVKNIADMGAYVSLLE-----Y---NNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGY  153 (259)
Q Consensus        82 ~~~~~~G~iv~G~V~~I~~~GafV~L~e-----y---~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gk  153 (259)
                      ..+|+.|++|.|.|+++....+.|++-.     +   +...|-+|+|+.+...+++.++.|++||.|.++|++.-   ..
T Consensus        59 ~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~---~~  135 (188)
T COG1096          59 PPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG---DP  135 (188)
T ss_pred             CCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccEEEEEEEecC---CC
Confidence            3577799999999999999999999851     0   02567899999999999999999999999999999974   46


Q ss_pred             EEEEEeecchhhHHHHHHhccccceEEEEEEecccccCCchH
Q 044309          154 IDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLE  195 (259)
Q Consensus       154 I~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fve  195 (259)
                      +.||.+.-.                 -|.|...|.++|.+|.
T Consensus       136 ~~Lst~~~d-----------------lGVI~A~CsrC~~~L~  160 (188)
T COG1096         136 IQLSTKGND-----------------LGVIYARCSRCRAPLV  160 (188)
T ss_pred             eEEEecCCc-----------------ceEEEEEccCCCcceE
Confidence            889888543                 3999999999999773

>TIGR02062 RNase_B exoribonuclease II

Probab=98.17  E-value=7e-06  Score=83.33  Aligned_cols=82  Identities=21%  Similarity=0.236  Sum_probs=63.7

Q ss_pred             chhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccccc--ccc---c-C-----c-cccccCCCeEE
Q 044309           74 NLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSR--RRI---R-S-----V-SSLIKVGRIEP  141 (259)
Q Consensus        74 ~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~--~~v---~-~-----~-~~~~kvGd~V~  141 (259)
                      .+.|+++.++.- .|+.+.|.|++++.+|+||+|.+ .+++||||++.+..  ...   . .     . ...|++||.|+
T Consensus       545 ~~~~~yl~~~~g-~~~~f~g~I~~v~~~g~~v~l~~-~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~  622 (639)
T TIGR02062       545 WLYARFLADKAA-KNTRFAAEIVDISRGGMRVRLLE-NGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVID  622 (639)
T ss_pred             HHHHHHHhhccC-CCcEEEEEEEeeeCCcEEEEEec-CceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEE
Confidence            345666666521 25599999999999999999986 68999999999965  111   0 1     1 23699999999


Q ss_pred             EEEEEEeCCCCeEEEE
Q 044309          142 VMVLRVDKEKGYIDLS  157 (259)
Q Consensus       142 vkVi~vD~~~gkI~LS  157 (259)
                      |+|.++|.++++|++.
T Consensus       623 V~v~~vd~~~~~i~~~  638 (639)
T TIGR02062       623 VVLTEVRMETRSIIAR  638 (639)
T ss_pred             EEEEEeccccCcEeee
Confidence            9999999999999874

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.

>COG0557 VacB Exoribonuclease R [Transcription]

Probab=98.09  E-value=1.2e-05  Score=82.52  Aligned_cols=81  Identities=23%  Similarity=0.295  Sum_probs=67.5

Q ss_pred             hhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccccccc-----------ccCccccccCCCeEEEE
Q 044309           75 LECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRR-----------IRSVSSLIKVGRIEPVM  143 (259)
Q Consensus        75 ~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~-----------v~~~~~~~kvGd~V~vk  143 (259)
                      +.|+++.+.   +|+.+.|.|++++.+|+||.|.+ .+++|++|++.+...+           .......++.||.|+|+
T Consensus       613 ~~~~~m~~~---vg~~f~g~V~~v~~~g~~V~l~~-~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~  688 (706)
T COG0557         613 LKAEYMKKR---VGEEFDGVVTGVTSFGFFVELPE-LGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVK  688 (706)
T ss_pred             HHHHHHHHh---cCCEEEEEEEEEEeccEEEEecc-cccccceEcccCCCceeeeccccceeeccccccccccCCEEEEE
Confidence            355666655   79999999999999999999986 4699999999999532           23345679999999999


Q ss_pred             EEEEeCCCCeEEEEEe
Q 044309          144 VLRVDKEKGYIDLSKR  159 (259)
Q Consensus       144 Vi~vD~~~gkI~LSlK  159 (259)
                      |.+++...++|++++-
T Consensus       689 v~~v~~~~~~i~~~~v  704 (706)
T COG0557         689 VTSVDLDERKIDFELV  704 (706)
T ss_pred             EEEEcccccceEEEec
Confidence            9999999999998864

>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []

Probab=98.05  E-value=1.7e-05  Score=60.26  Aligned_cols=64  Identities=19%  Similarity=0.269  Sum_probs=43.7

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEEccC----------------CCEEEEEEccccccccccC--ccccccCCCeEEEEEE
Q 044309           84 YPEVDMAVMIQVKNIADMGAYVSLLEY----------------NNIEGMILFSELSRRRIRS--VSSLIKVGRIEPVMVL  145 (259)
Q Consensus        84 ~~~~G~iv~G~V~~I~~~GafV~L~ey----------------~~~eGllhisEls~~~v~~--~~~~~kvGd~V~vkVi  145 (259)
                      +|++|++|.|+|+++++.-|+++|.--                ....|+|+.+++.......  +.+.|++||.|.|+|+
T Consensus         1 lP~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~Vi   80 (82)
T PF10447_consen    1 LPKVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVI   80 (82)
T ss_dssp             ---TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEE
T ss_pred             CCCCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhccCCCCEEEEEEe
Confidence            367999999999999999999998632                1467999999987644433  5788999999999999


Q ss_pred             EE
Q 044309          146 RV  147 (259)
Q Consensus       146 ~v  147 (259)
                      +.
T Consensus        81 Sl   82 (82)
T PF10447_consen   81 SL   82 (82)
T ss_dssp             EE
T ss_pred             eC
Confidence            74

The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.

>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain

Probab=98.04  E-value=4e-05  Score=58.80  Aligned_cols=63  Identities=10%  Similarity=0.030  Sum_probs=50.5

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc-----------cCccccccCCCeEEEEEEEEeCCCC
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI-----------RSVSSLIKVGRIEPVMVLRVDKEKG  152 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v-----------~~~~~~~kvGd~V~vkVi~vD~~~g  152 (259)
                      +|+++.|+|++++++|+||.++   .+++|+|.+.+.....           .+-...++.|+.|++||+.+..+.+
T Consensus         1 kgEVi~g~V~~v~~~G~~v~~G---pl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~   74 (88)
T cd04462           1 KGEVVDAIVTSVNKTGFFAEVG---PLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVDAT   74 (88)
T ss_pred             CCcEEEEEEEEEeccEEEEEEc---CceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEccC
Confidence            4899999999999999999994   7999999988864322           1124558999999999998876533

RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.

>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=98.00  E-value=3e-05  Score=57.53  Aligned_cols=68  Identities=24%  Similarity=0.257  Sum_probs=57.6

Q ss_pred             CcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccC---ccccccCCCeE-EEEEEEEeCCCCeEEEEEe
Q 044309           88 DMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRS---VSSLIKVGRIE-PVMVLRVDKEKGYIDLSKR  159 (259)
Q Consensus        88 G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~---~~~~~kvGd~V-~vkVi~vD~~~gkI~LSlK  159 (259)
                      |++|.|+|..-++.+++|++.+ .++.|+||...+++ .+.+   .-..+++||++ .+.|+  +...+.|.||.|
T Consensus         1 G~lV~~~V~EKt~D~l~v~l~~-~~l~a~l~~~HLsD-~~~k~~~~~~klrvG~~L~~~lvL--~~~~r~i~lt~K   72 (72)
T cd05699           1 GKLVDARVLKKTLNGLEVAILP-EEIRAFLPTMHLSD-HVSNCPLLWHCLQEGDTIPNLMCL--SNYKGRIILTKK   72 (72)
T ss_pred             CceEEEEEEEEcCCcEEEEecC-CCcEEEEEccccCC-chhhCHHHHhhhhcCCCccceEEE--eccccEEEEecC
Confidence            7899999999999999999996 58999999999998 4433   33558999999 89999  777788888865

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 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional

Probab=97.92  E-value=7.2e-05  Score=64.46  Aligned_cols=72  Identities=11%  Similarity=0.051  Sum_probs=56.3

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccc-----------cc-cCccccccCCCeEEEEEEEEeCCC--C
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRR-----------RI-RSVSSLIKVGRIEPVMVLRVDKEK--G  152 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~-----------~v-~~~~~~~kvGd~V~vkVi~vD~~~--g  152 (259)
                      .|+++.|+|++++++|+||.++   -.++|||.+.+...           |. ++-+..++.|+.|++||..+..+.  .
T Consensus        81 ~gEVv~g~V~~v~~~G~~v~~G---p~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~~  157 (176)
T PTZ00162         81 KDEVLDAIVTDVNKLGFFAQAG---PLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASNL  157 (176)
T ss_pred             CCCEEEEEEEEEecceEEEEee---CeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCCc
Confidence            7999999999999999999995   58899999999842           11 222456999999999998886543  3


Q ss_pred             eEEEEEeec
Q 044309          153 YIDLSKRRV  161 (259)
Q Consensus       153 kI~LSlK~~  161 (259)
                      ++..|+|+.
T Consensus       158 ~~i~T~~~~  166 (176)
T PTZ00162        158 FAIATINSD  166 (176)
T ss_pred             EEEEEecCC
Confidence            455566654

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=97.88  E-value=9.4e-05  Score=70.50  Aligned_cols=68  Identities=19%  Similarity=0.329  Sum_probs=57.6

Q ss_pred             CCCCCcEEEEEEEEEeCc-eEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCC---eEEEEEe
Q 044309           84 YPEVDMAVMIQVKNIADM-GAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKG---YIDLSKR  159 (259)
Q Consensus        84 ~~~~G~iv~G~V~~I~~~-GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~g---kI~LSlK  159 (259)
                      ..++|+++.|+|.++... ++||+|   ++.+|+||.+|..      +++.|++||.+.|.|.+|+...+   +|.||+.
T Consensus       135 ~~~~Geiv~g~V~r~~~~~~i~vdl---g~~ea~LP~~eqi------p~E~~~~Gdrik~~i~~V~~~~k~gp~IilSRt  205 (374)
T PRK12328        135 KKKVGKIVFGTVVRVDNEENTFIEI---DEIRAVLPMKNRI------KGEKFKVGDVVKAVLKRVKIDKNNGILIELSRT  205 (374)
T ss_pred             HHhcCcEEEEEEEEEecCCCEEEEc---CCeEEEeCHHHcC------CCCcCCCCCEEEEEEEEEecCCCCCCEEEEEcC
Confidence            344899999999999864 599999   4899999999876      56889999999999999998654   7888876


Q ss_pred             e
Q 044309          160 R  160 (259)
Q Consensus       160 ~  160 (259)
                      .
T Consensus       206 ~  206 (374)
T PRK12328        206 S  206 (374)
T ss_pred             C
Confidence            4

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=97.82  E-value=0.00014  Score=51.94  Aligned_cols=61  Identities=21%  Similarity=0.293  Sum_probs=35.8

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR  159 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK  159 (259)
                      +|++.+.+|++++++|+|++.+  .+.+-+||.+|+.        ..+++||.+.|-| ..|. ++++..|+|
T Consensus         1 iG~~~~L~V~~~~~~g~fL~~~--~~~~vlLp~~e~~--------~~~~~Gd~v~VFv-Y~D~-~~rl~AT~k   61 (61)
T PF13509_consen    1 IGQINTLKVVDKNEFGYFLDDG--EGKEVLLPKSEVP--------EPLKVGDEVEVFV-YLDK-EGRLVATTK   61 (61)
T ss_dssp             --------EEEE-SSEEEEEET--T-EEEEEEGGG--------------TTSEEEEEE-EE-T-TS-EEEE--
T ss_pred             CCCCcceEEEEEeCCEEEEECC--CCCEEEechHHcC--------CCCCCCCEEEEEE-EECC-CCCEEEecC
Confidence            4899999999999999999986  3699999999986        3488999999985 4566 568887764

>PF07541 EIF_2_alpha: Eukaryotic translation initiation factor 2 alpha subunit; InterPro: IPR011488 In Eukaryota and Archaea, translation initiation factor 2 (eIF2/aIF2), which contains three subunits (alpha, beta and gamma), is pivotal for binding of charged initiator tRNA to the small ribosomal subunit

Probab=97.77  E-value=2e-05  Score=63.31  Aligned_cols=44  Identities=39%  Similarity=0.710  Sum_probs=37.3

Q ss_pred             HHHHhhchhhHHhhcCHHHHHH-HHhcCcchhhccCCCccccCCC
Q 044309          196 ELYVNIGWPLYWKYGHAFEAFK-IIVTDPDSVLNSLTREVKEIGP  239 (259)
Q Consensus       196 ~~~~~~sw~l~~~~~~~~~~fk-~a~~~~~~~l~~l~~~~~~~~~  239 (259)
                      ++|.+++|||+++|||+|+||+ .++.+++++|.++++++....+
T Consensus         1 ely~~i~w~l~~~yg~~y~aFe~~~~~~~~~vl~~l~i~~~~~~~   45 (114)
T PF07541_consen    1 ELYEKIGWPLYKKYGSLYDAFELSAADNGEEVLKKLGIPEEVKEA   45 (114)
T ss_dssp             HHHHHTHHHHHHHCSSHHHHHHHHHHHHGGGGGBTTTBSCCHHHH
T ss_pred             ChHHHHHHHHHHHhCcHHHHHHHHHcCCCcceeccCCCCHHHHHH
Confidence            4799999999999999999999 6667666899999988665443

This entry represents the alpha subunit of both eukaryota and archaeal translation initiator factor 2.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0005850 eukaryotic translation initiation factor 2 complex; PDB: 2QN6_B 3CW2_C 2AHO_B 3QSY_B 3V11_B 2QMU_B 1YZ7_A 1YZ6_A 3AEV_A 1KL9_A ....

>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]

Probab=97.66  E-value=6.6e-05  Score=74.57  Aligned_cols=101  Identities=21%  Similarity=0.200  Sum_probs=76.9

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecc
Q 044309           83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVS  162 (259)
Q Consensus        83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~  162 (259)
                      .+. .|..+.|+|+++..||+||+|.  ..+.||+|-++++..      .-+.+|+.+.|.|..+.+.+|.|++....+.
T Consensus       119 Dve-~g~~Y~g~v~~v~~~GvFv~Ln--~~v~GL~~~~d~~~~------~~~~vgdeiiV~v~~vr~~~geidf~~~~~~  189 (715)
T COG1107         119 DVE-AGKYYKGIVSRVEKYGVFVELN--SHVRGLIHRRDLGGD------PDYAVGDEIIVQVSDVRPEKGEIDFEPVGLD  189 (715)
T ss_pred             hcc-cceeeeccccchhhhcceeecC--hhhhccccccccCCC------CCCCCCCeEEEEeeccCCCCCccceeecCCc
Confidence            444 8999999999999999999998  479999999999852      3478999999999999998899999887765


Q ss_pred             hhhHHHHHHhc----------cccc--eEEEEEEecccccCC
Q 044309          163 EEDIQACEERY----------NKSK--LVHSIMRHVAETLGI  192 (259)
Q Consensus       163 ~~~~~~~~~~~----------~~g~--~v~g~V~~i~~~~G~  192 (259)
                      ...-.+..+++          ..|+  .+.|.|+.+..--|-
T Consensus       190 ~Y~~~~~~ke~~r~~i~~id~~ig~tV~I~GeV~qikqT~GP  231 (715)
T COG1107         190 RYREVQVEKELPRTLIDDLDEMIGKTVRIEGEVTQIKQTSGP  231 (715)
T ss_pred             cchhhhhhhhcccccHHHHHhhcCceEEEEEEEEEEEEcCCC
Confidence            32111111111          4455  567889888664443

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

Probab=97.65  E-value=0.00029  Score=64.34  Aligned_cols=97  Identities=22%  Similarity=0.179  Sum_probs=76.9

Q ss_pred             CCcEEEEEEEEEe-CceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhh
Q 044309           87 VDMAVMIQVKNIA-DMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEED  165 (259)
Q Consensus        87 ~G~iv~G~V~~I~-~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~  165 (259)
                      +|+.=.++|+.+. +.||||+.+  -..+-++|++++...+    .--+++||.+-|. +.+|. ++||.-.++  .+..
T Consensus        73 vg~~g~~~Vv~v~~~lGaFlD~G--l~KDl~vp~~elp~~~----~~wpq~Gd~l~v~-l~~Dk-k~Ri~g~~a--~~~~  142 (287)
T COG2996          73 VGEYGWLKVVEVNKDLGAFLDWG--LPKDLLVPLDELPTLK----SLWPQKGDKLLVY-LYVDK-KGRIWGTLA--IEKI  142 (287)
T ss_pred             ecceeEEEEEEEcCCcceEEecC--CCcceeeehhhccccc----ccCCCCCCEEEEE-EEEcc-CCcEEEEec--chhH
Confidence            8999999999998 999999997  3599999999998310    1127899999999 56887 578877665  3455


Q ss_pred             HHHHHHhccc---cceEEEEEEecccccCCch
Q 044309          166 IQACEERYNK---SKLVHSIMRHVAETLGIDL  194 (259)
Q Consensus       166 ~~~~~~~~~~---g~~v~g~V~~i~~~~G~fv  194 (259)
                      .++....+..   ++.++|+|.++.+ .|.|+
T Consensus       143 l~~l~~~~~~~l~nq~v~~tVYr~~~-~G~fv  173 (287)
T COG2996         143 LENLATPAYNNLKNQEVDATVYRLLE-SGTFV  173 (287)
T ss_pred             HHhcCCccchhhhcCeeeeEEEEEec-cceEE
Confidence            5566656655   9999999999966 89987

>PRK11712 ribonuclease G; Provisional

Probab=97.52  E-value=0.001  Score=65.71  Aligned_cols=126  Identities=20%  Similarity=0.225  Sum_probs=79.4

Q ss_pred             CCcEEEEEEEEEeC--ceEEEEEccCCCEEEEEEccccccc------------cccCccccccCCCeEEEEEEEEe----
Q 044309           87 VDMAVMIQVKNIAD--MGAYVSLLEYNNIEGMILFSELSRR------------RIRSVSSLIKVGRIEPVMVLRVD----  148 (259)
Q Consensus        87 ~G~iv~G~V~~I~~--~GafV~L~ey~~~eGllhisEls~~------------~v~~~~~~~kvGd~V~vkVi~vD----  148 (259)
                      +|.+|.|+|.+|.+  .+|||+|+  .+..||+|++++...            ...++.+.+++||.|-|.|.+--    
T Consensus        38 vGnIY~G~V~~v~pg~~AAFVdIG--~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke~~~~K  115 (489)
T PRK11712         38 VGNIYKGRVSRVLPGMQAAFVDIG--LDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKDPLGTK  115 (489)
T ss_pred             cccEEEEEEeecCCCCceeEEeeC--CCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeCCcCCC
Confidence            79999999999964  37999998  589999999998320            12234667999999999998742    


Q ss_pred             ------------------CCCCeEEEEEeecchhhHHH---HHHhccccceEEEEEEecccccCCchHHHHHhhchhhHH
Q 044309          149 ------------------KEKGYIDLSKRRVSEEDIQA---CEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGWPLYW  207 (259)
Q Consensus       149 ------------------~~~gkI~LSlK~~~~~~~~~---~~~~~~~g~~v~g~V~~i~~~~G~fve~~~~~~sw~l~~  207 (259)
                                        |...++.+|.|=..++....   ....+....  .|.+.+-+- -|+..+++..|+.. |.+
T Consensus       116 G~~lT~~Isl~GrylVl~P~~~~vgiSrKI~de~~R~rLk~i~~~~~~~~--~GvIiRT~A-~~a~~eel~~dl~~-L~~  191 (489)
T PRK11712        116 GARLTTDITLPSRYLVFMPGASHVGVSQRIESEEERERLKKIVAPYCDEQ--GGFIIRTAA-EGVGEEELAQDAAF-LKR  191 (489)
T ss_pred             CCeEEEEEEeccceEEEECCCCCeeEecCCCChHHHHHHHHHHHhhCCCC--ceEEEEccC-CCCCHHHHHHHHHH-HHH
Confidence                              22334455555333333332   233433333  477777644 57776666555543 444


Q ss_pred             hhcCHHHHHHH
Q 044309          208 KYGHAFEAFKI  218 (259)
Q Consensus       208 ~~~~~~~~fk~  218 (259)
                      .+....+.++.
T Consensus       192 ~w~~i~~~~~~  202 (489)
T PRK11712        192 LWTKVMERKKR  202 (489)
T ss_pred             HHHHHHHHHhc
Confidence            44444444443

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=97.49  E-value=0.00086  Score=65.21  Aligned_cols=70  Identities=10%  Similarity=0.081  Sum_probs=57.8

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEEcc-CC--CEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCC---CeEEEEE
Q 044309           85 PEVDMAVMIQVKNIADMGAYVSLLE-YN--NIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEK---GYIDLSK  158 (259)
Q Consensus        85 ~~~G~iv~G~V~~I~~~GafV~L~e-y~--~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~---gkI~LSl  158 (259)
                      .++|+++.|+|.++...+++|+|.. ++  +++|+||.+|..      +++.|++||.++|.|.+|+...   -+|.||+
T Consensus       150 ~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqi------p~E~y~~Gdrika~i~~V~~~~~kGpqIilSR  223 (449)
T PRK12329        150 DLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQL------PNDNYRANATFKVFLKEVSEGPRRGPQLFVSR  223 (449)
T ss_pred             HhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcC------CCCcCCCCCEEEEEEEEeecCCCCCCEEEEEc
Confidence            3489999999999999999999941 12  399999999876      5688999999999999998752   3688887


Q ss_pred             ee
Q 044309          159 RR  160 (259)
Q Consensus       159 K~  160 (259)
                      ..
T Consensus       224 t~  225 (449)
T PRK12329        224 AN  225 (449)
T ss_pred             CC
Confidence            64

>PRK10811 rne ribonuclease E; Reviewed

Probab=97.35  E-value=0.002  Score=67.66  Aligned_cols=59  Identities=14%  Similarity=0.201  Sum_probs=47.7

Q ss_pred             CCcEEEEEEEEEeC--ceEEEEEccCCCEEEEEEccccccccc---------cCccccccCCCeEEEEEEEE
Q 044309           87 VDMAVMIQVKNIAD--MGAYVSLLEYNNIEGMILFSELSRRRI---------RSVSSLIKVGRIEPVMVLRV  147 (259)
Q Consensus        87 ~G~iv~G~V~~I~~--~GafV~L~ey~~~eGllhisEls~~~v---------~~~~~~~kvGd~V~vkVi~v  147 (259)
                      +|.||.|+|.+|.+  .+|||+|+  .+..||||++++.....         .++...+++||.|.|.|.+-
T Consensus        38 vGnIYkGkVenIvPGInAAFVDIG--~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KE  107 (1068)
T PRK10811         38 KANIYKGKITRIEPSLEAAFVDYG--AERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKE  107 (1068)
T ss_pred             ccceEEEEEecccCCcceeEEEec--CCcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeec
Confidence            79999999999953  47899998  58999999999963221         13456799999999999873

>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]

Probab=97.23  E-value=0.00037  Score=73.60  Aligned_cols=75  Identities=29%  Similarity=0.409  Sum_probs=65.3

Q ss_pred             CCCCCcEEEEEEEEEeCc-e--EEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEee
Q 044309           84 YPEVDMAVMIQVKNIADM-G--AYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRR  160 (259)
Q Consensus        84 ~~~~G~iv~G~V~~I~~~-G--afV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~  160 (259)
                      +- +|.+|.++|++|+.. |  +=|.++  +|++|+||.+++|.+.+.+|...+++||.|.++|+++|.++=.+.||++.
T Consensus       983 ~~-~g~iV~~~V~~vt~rr~~Cv~v~ld--~G~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~id~e~f~v~Ls~r~ 1059 (1299)
T KOG1856|consen  983 FY-EGAIVPVTVTKVTHRRGICVRVRLD--CGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVELSCRT 1059 (1299)
T ss_pred             hc-cCceEEEeeeEEEecccceeEEEec--CCCceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhhhhhhhh
Confidence            44 799999999999743 3  356676  79999999999999999999999999999999999999987788888876


Q ss_pred             c
Q 044309          161 V  161 (259)
Q Consensus       161 ~  161 (259)
                      .
T Consensus      1060 s 1060 (1299)
T KOG1856|consen 1060 S 1060 (1299)
T ss_pred             H
Confidence            4

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=96.68  E-value=0.00012  Score=68.59  Aligned_cols=92  Identities=14%  Similarity=0.166  Sum_probs=72.7

Q ss_pred             cceeEEEeecCCccccchhhhhh----hhcccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEe-CceEEEE-----
Q 044309           37 SGCLKTLILVPTPFEFSRENAKA----KKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIA-DMGAYVS-----  106 (259)
Q Consensus        37 ~g~~~~~~~~~~~~eid~e~~ri----K~l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~-~~GafV~-----  106 (259)
                      .|.....    .++++|++++++    |++.++||..          ..+.|+ .|+++.|+|..+. .+|+|++     
T Consensus        66 vGd~v~v----kVl~VD~ekg~IdLS~K~v~~~pw~~----------~~e~~~-~g~~v~~~V~~ia~~~g~~~eely~~  130 (319)
T PTZ00248         66 VGRHEVV----VVLRVDKEKGYIDLSKKRVSPEDIEA----------CEEKFS-KSKKVHSIMRHIAQKHGMSVEELYTK  130 (319)
T ss_pred             CCCEEEE----EEEEEeCCCCEEEEEeeecccchHHH----------HHHhCc-CCCEEEEEEEEchhhcCCCHHHHHHH
Confidence            3544443    446889999994    8999999998          888999 9999999999994 6999998     


Q ss_pred             -EccCCCEEEEEEccccccccccCcccccc---CCCeEEEEEE
Q 044309          107 -LLEYNNIEGMILFSELSRRRIRSVSSLIK---VGRIEPVMVL  145 (259)
Q Consensus       107 -L~ey~~~eGllhisEls~~~v~~~~~~~k---vGd~V~vkVi  145 (259)
                       ..  +..+++.|++++....+.++.+.|.   +|+.+...++
T Consensus       131 i~~--pl~~~~gh~y~af~~~v~~~~evl~~l~i~~ev~~~l~  171 (319)
T PTZ00248        131 IIW--PLYKKYGHALDALKEALTNPDNVFEGLDIPEEVKESLL  171 (319)
T ss_pred             HHH--HHHHhcCCHHHHHHHHhcCchhhhccCCCCHHHHHHHH
Confidence             22  5789999999998887888776766   6666555443

>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]

Probab=95.98  E-value=0.035  Score=47.81  Aligned_cols=97  Identities=18%  Similarity=0.162  Sum_probs=67.2

Q ss_pred             hhhcCCCCCcEEEEEEEEEeCceEEEEEcc-----C-CCEEEEEEccccccc--cccCccccccCCCeEEEEEEEEeCCC
Q 044309           80 YEARYPEVDMAVMIQVKNIADMGAYVSLLE-----Y-NNIEGMILFSELSRR--RIRSVSSLIKVGRIEPVMVLRVDKEK  151 (259)
Q Consensus        80 ~~~~~~~~G~iv~G~V~~I~~~GafV~L~e-----y-~~~eGllhisEls~~--~v~~~~~~~kvGd~V~vkVi~vD~~~  151 (259)
                      +...+|.+|++|.++|.++..-=|=|+|.-     | ....|+||..++..-  .--.+-+.|++||.|.++|++... .
T Consensus        61 ~~~~LP~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~-~  139 (193)
T KOG3409|consen   61 FNELLPFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGD-G  139 (193)
T ss_pred             hhhcCCccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCC-C
Confidence            345688899999999999987777777641     1 257899998888641  112356779999999999999554 4


Q ss_pred             CeEEEEEeecchhhHHHHHHhccccceEEEEEEecccccCCch
Q 044309          152 GYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDL  194 (259)
Q Consensus       152 gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fv  194 (259)
                      ....||.-+-.                 -|.|..-+..+|..|
T Consensus       140 ~~y~LTtAene-----------------LGVV~a~as~~g~~M  165 (193)
T KOG3409|consen  140 SNYLLTTAENE-----------------LGVVFARASETGEPM  165 (193)
T ss_pred             CcEEEEEeccc-----------------ceEEEEeccccCCce
Confidence            55666654211                 266665554577755

>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]

Probab=95.19  E-value=0.072  Score=45.40  Aligned_cols=62  Identities=13%  Similarity=0.031  Sum_probs=43.7

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccc----cccccC-------ccccccCCCeEEEEEEEEeCCC
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELS----RRRIRS-------VSSLIKVGRIEPVMVLRVDKEK  151 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls----~~~v~~-------~~~~~kvGd~V~vkVi~vD~~~  151 (259)
                      .|+++.|+|+.+...|+|++.+   .++.++.---+.    ....+|       -...++.|.+|+++|+...-+.
T Consensus        81 KGEVvdgvV~~Vnk~G~F~~~G---Pl~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr~~~  153 (170)
T KOG3298|consen   81 KGEVVDGVVTKVNKMGVFARSG---PLEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTRVDE  153 (170)
T ss_pred             CCcEEEEEEEEEeeeeEEEecc---ceEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEEEee
Confidence            5999999999999999999995   566665322222    111222       1226889999999999876543

>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit

Probab=94.81  E-value=0.21  Score=40.61  Aligned_cols=61  Identities=18%  Similarity=-0.025  Sum_probs=44.7

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccc---------c---c-cCccccccCCCeEEEEEEEEeC
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRR---------R---I-RSVSSLIKVGRIEPVMVLRVDK  149 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~---------~---v-~~~~~~~kvGd~V~vkVi~vD~  149 (259)
                      +|+++.|+|++.+..|+.|.|+=  =-+-+||.+.|...         +   . ..-.-++..|+.|++||.++..
T Consensus         3 ~gEvl~g~I~~~~~~Gi~vslgF--FddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~f   76 (122)
T PF08292_consen    3 VGEVLTGKIKSSTAEGIRVSLGF--FDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEIF   76 (122)
T ss_dssp             TT-EEEEEEEEEETTEEEEEECC--EEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEEE
T ss_pred             CCCEEEEEEEecCCCcEEEEecc--cccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEEE
Confidence            69999999999999999999962  35788888888731         1   1 3334558999999999998865

Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.

>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]

Probab=94.42  E-value=0.06  Score=53.38  Aligned_cols=59  Identities=19%  Similarity=0.244  Sum_probs=49.0

Q ss_pred             CCcEEEEEEEEEeCc--eEEEEEccCCCEEEEEEccccccccccC-----ccccccCCCeEEEEEEEEe
Q 044309           87 VDMAVMIQVKNIADM--GAYVSLLEYNNIEGMILFSELSRRRIRS-----VSSLIKVGRIEPVMVLRVD  148 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~--GafV~L~ey~~~eGllhisEls~~~v~~-----~~~~~kvGd~V~vkVi~vD  148 (259)
                      +|.++.|+|++|.+.  .|||+++  .+..||+|++++.+ +.+.     +...++.||.+-|.|..-.
T Consensus        37 ~gniy~grv~~i~p~~~aafvdig--~~r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv~ke~  102 (487)
T COG1530          37 VGNIYKGRVTRVLPSLEAAFVDIG--LERNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQVVKEP  102 (487)
T ss_pred             ecCceEEEecccCccchhheeecc--CCccceEEecccch-hhhhcccccceeeecCCceEEEEEEeec
Confidence            699999999999764  5899998  58999999999998 3332     3458999999999988753

>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=92.77  E-value=0.036  Score=40.80  Aligned_cols=31  Identities=13%  Similarity=0.208  Sum_probs=25.8

Q ss_pred             ccccceEEEEEEecccccCCch------HHH--HHhhchh
Q 044309          173 YNKSKLVHSIMRHVAETLGIDL------EEL--YVNIGWP  204 (259)
Q Consensus       173 ~~~g~~v~g~V~~i~~~~G~fv------e~~--~~~~sw~  204 (259)
                      +++|+++.|+|.++.+ +|+|+      +++  ++++||.
T Consensus         1 ~k~G~~V~g~V~~i~~-~G~fV~l~~~v~G~v~~~~ls~~   39 (74)
T cd05705           1 IKEGQLLRGYVSSVTK-QGVFFRLSSSIVGRVLFQNVTKY   39 (74)
T ss_pred             CCCCCEEEEEEEEEeC-CcEEEEeCCCCEEEEEHHHccCc
Confidence            4789999999999976 99997      334  8999995

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.

>PRK12442 translation initiation factor IF-1; Reviewed

Probab=92.49  E-value=0.88  Score=34.99  Aligned_cols=65  Identities=18%  Similarity=0.132  Sum_probs=49.8

Q ss_pred             EEEEEEEEEeCceEEE-EEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEee
Q 044309           90 AVMIQVKNIADMGAYV-SLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRR  160 (259)
Q Consensus        90 iv~G~V~~I~~~GafV-~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~  160 (259)
                      .+.|+|+.+-+.+.|. .|+  +|.+-+.|+|-=    .+.-.-.+.+||.|.|.+--.|..+|+|..-.+.
T Consensus         8 e~~G~V~e~Lp~~~frV~Le--nG~~vla~isGK----mR~~rIrIl~GD~V~VE~spYDltkGRIiyR~~~   73 (87)
T PRK12442          8 ELDGIVDEVLPDSRFRVTLE--NGVEVGAYASGR----MRKHRIRILAGDRVTLELSPYDLTKGRINFRHKD   73 (87)
T ss_pred             EEEEEEEEECCCCEEEEEeC--CCCEEEEEeccc----eeeeeEEecCCCEEEEEECcccCCceeEEEEecC
Confidence            5899999998888765 776  688888887732    1111122679999999999999999999987763

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

Probab=91.31  E-value=0.1  Score=42.73  Aligned_cols=55  Identities=11%  Similarity=0.041  Sum_probs=38.0

Q ss_pred             hccccceEEEEEEecccccCCchH------HH--HHhhchhhHHhhcCHHHHHHHHhcCcchh-hccCCCcc
Q 044309          172 RYNKSKLVHSIMRHVAETLGIDLE------EL--YVNIGWPLYWKYGHAFEAFKIIVTDPDSV-LNSLTREV  234 (259)
Q Consensus       172 ~~~~g~~v~g~V~~i~~~~G~fve------~~--~~~~sw~l~~~~~~~~~~fk~a~~~~~~~-l~~l~~~~  234 (259)
                      .++.|++++|+|+.|.+ ||+||+      +|  +++++....+.+       ...+..|+++ .+-|++++
T Consensus         2 ~~kvG~~l~GkItgI~~-yGAFV~l~~g~tGLVHISEIa~~fVkdI-------~d~L~vG~eV~vKVl~ide   65 (129)
T COG1098           2 SMKVGSKLKGKITGITP-YGAFVELEGGKTGLVHISEIADGFVKDI-------HDHLKVGQEVKVKVLDIDE   65 (129)
T ss_pred             CccccceEEEEEEeeEe-cceEEEecCCCcceEEehHhhhhhHHhH-------HHHhcCCCEEEEEEEeecc
Confidence            46899999999999976 999993      34  777777533332       2344566666 55566555

>TIGR00008 infA translation initiation factor IF-1

Probab=91.22  E-value=1.2  Score=32.68  Aligned_cols=60  Identities=22%  Similarity=0.093  Sum_probs=45.6

Q ss_pred             EEEEEEEEEeCceEEE-EEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEE
Q 044309           90 AVMIQVKNIADMGAYV-SLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYID  155 (259)
Q Consensus        90 iv~G~V~~I~~~GafV-~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~  155 (259)
                      .+.|+|+..-+.|.|- .|+  +|.+-+.|+|-=    .+.-+-.+.+||.|.|.+-..|..+|+|.
T Consensus         6 e~~G~V~e~L~~~~f~V~l~--ng~~vla~i~GK----mr~~rI~I~~GD~V~Ve~spyd~tkgrIi   66 (68)
T TIGR00008         6 EMEGKVTESLPNAMFRVELE--NGHEVLAHISGK----IRMHYIRILPGDKVKVELSPYDLTRGRIT   66 (68)
T ss_pred             EEEEEEEEECCCCEEEEEEC--CCCEEEEEecCc----chhccEEECCCCEEEEEECcccCCcEeEE
Confidence            5889999998888765 776  688888887742    22112237799999999998888888875

This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).

>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=90.41  E-value=4.6  Score=28.44  Aligned_cols=50  Identities=20%  Similarity=0.166  Sum_probs=36.1

Q ss_pred             EEEEEEEEeC---ceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEE
Q 044309           91 VMIQVKNIAD---MGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLR  146 (259)
Q Consensus        91 v~G~V~~I~~---~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~  146 (259)
                      .+|+|+...+   || |+.-++ ++-+-|+|.|++....    -..++.|+.|.+.+..
T Consensus         1 ~~G~V~~~~~~kgyG-FI~~~~-~~~diFfh~s~~~~~~----~~~l~~G~~V~F~~~~   53 (66)
T PF00313_consen    1 MTGTVKWFDDEKGYG-FITSDD-GGEDIFFHISDLSGNG----FRSLKEGDRVEFEVEE   53 (66)
T ss_dssp             EEEEEEEEETTTTEE-EEEETT-SSSEEEEEGGGBCSSS----STS--TTSEEEEEEEE
T ss_pred             CeEEEEEEECCCCce-EEEEcc-cceeEEeccccccccc----cccCCCCCEEEEEEEE
Confidence            4799999864   55 555553 4569999999998643    2457899999999887

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 ....

>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]

Probab=90.31  E-value=0.27  Score=44.92  Aligned_cols=76  Identities=22%  Similarity=0.264  Sum_probs=61.6

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccc----cc------cCccccccCCCeEEEEEEEEeCCCC
Q 044309           83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRR----RI------RSVSSLIKVGRIEPVMVLRVDKEKG  152 (259)
Q Consensus        83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~----~v------~~~~~~~kvGd~V~vkVi~vD~~~g  152 (259)
                      ..|++||+|.|+|..|...-+=|++.  ...++.+.+|.+.-.    |-      ...+++|+.||.+.+.|-.+-. +|
T Consensus        81 Y~pEvGDvVVgRV~eVq~KRWkvd~n--sk~d~vL~LsSvNLPGg~~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~~-dG  157 (301)
T KOG3013|consen   81 YAPEVGDVVVGRVIEVQQKRWKVDLN--SKQDAVLMLSSVNLPGGIQRRKSEEDELQMRSFLKEGDLIVAEVQNVFH-DG  157 (301)
T ss_pred             cCCccCCEEEEEeeeeecceeEEecc--cccceEEEeecccCCchhhhccchhhHHHHHHHhhccCeehHHHHHhcc-CC
Confidence            35779999999999999999999997  589999999977631    11      1368899999999999988865 68


Q ss_pred             eEEEEEeec
Q 044309          153 YIDLSKRRV  161 (259)
Q Consensus       153 kI~LSlK~~  161 (259)
                      -+.|-.|..
T Consensus       158 s~sLhTRS~  166 (301)
T KOG3013|consen  158 SLSLHTRSL  166 (301)
T ss_pred             eEEEEecch
Confidence            888876644

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

Probab=89.58  E-value=0.12  Score=39.32  Aligned_cols=46  Identities=4%  Similarity=-0.033  Sum_probs=33.9

Q ss_pred             HhccccceEEEEEEecccc-cCCchH------HH--HHhhchhhHHhhcCHHHHH
Q 044309          171 ERYNKSKLVHSIMRHVAET-LGIDLE------EL--YVNIGWPLYWKYGHAFEAF  216 (259)
Q Consensus       171 ~~~~~g~~v~g~V~~i~~~-~G~fve------~~--~~~~sw~l~~~~~~~~~~f  216 (259)
                      .++..|+++.|+|+.+.+. +|+|++      +|  ++++||..+++..++.+.|
T Consensus         3 ~~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~   57 (88)
T cd04453           3 REPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLL   57 (88)
T ss_pred             CcCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcC
Confidence            3567999999999999873 399983      34  8999996545565665555

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

>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=89.12  E-value=2.3  Score=33.69  Aligned_cols=52  Identities=8%  Similarity=0.046  Sum_probs=42.7

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEE
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRV  147 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~v  147 (259)
                      .|.+|.|+|..+.+.-+||+++  ....+.++..+...       +.+..|.+|.+++...
T Consensus        23 ~gk~V~G~I~hvv~ddLYIDfG--~KFhcVc~rp~~~~-------~~y~~G~rV~lrLkdl   74 (104)
T PF10246_consen   23 EGKIVIGKIFHVVDDDLYIDFG--GKFHCVCKRPAVNG-------EKYVRGSRVRLRLKDL   74 (104)
T ss_pred             cCCEEEEEEEEEecCceEEEeC--CceeEEEecccccc-------cccccCCEEEEEECCH
Confidence            7999999999999889999997  67999998665542       4577899999887543

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 [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].

>PRK15463 cold shock-like protein CspF; Provisional

Probab=89.05  E-value=1.9  Score=31.60  Aligned_cols=51  Identities=14%  Similarity=0.120  Sum_probs=38.8

Q ss_pred             EEEEEEEEeC-ceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEE
Q 044309           91 VMIQVKNIAD-MGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLR  146 (259)
Q Consensus        91 v~G~V~~I~~-~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~  146 (259)
                      ++|+|+...+ .|. |+.-+. ++-+.|+|+|.+.....    ..+++||.|.+.+..
T Consensus         5 ~~G~Vk~fn~~kGfGFI~~~~-g~~DvFvH~sal~~~g~----~~l~~G~~V~f~v~~   57 (70)
T PRK15463          5 MTGIVKTFDGKSGKGLITPSD-GRKDVQVHISALNLRDA----EELTTGLRVEFCRIN   57 (70)
T ss_pred             ceEEEEEEeCCCceEEEecCC-CCccEEEEehhhhhcCC----CCCCCCCEEEEEEEE
Confidence            4799998853 565 777764 56899999999975322    347899999998654

>PRK15464 cold shock-like protein CspH; Provisional

Probab=88.55  E-value=1.9  Score=31.63  Aligned_cols=51  Identities=14%  Similarity=0.150  Sum_probs=38.9

Q ss_pred             EEEEEEEEe-CceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEE
Q 044309           91 VMIQVKNIA-DMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLR  146 (259)
Q Consensus        91 v~G~V~~I~-~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~  146 (259)
                      ++|+|+... +.|. |+.-++ ++-+.|+|+|.+....    ...+.+||.|.+.|..
T Consensus         5 ~~G~Vk~fn~~KGfGFI~~~~-g~~DvFvH~s~l~~~g----~~~l~~G~~V~f~v~~   57 (70)
T PRK15464          5 MTGIVKTFDRKSGKGFIIPSD-GRKEVQVHISAFTPRD----AEVLIPGLRVEFCRVN   57 (70)
T ss_pred             ceEEEEEEECCCCeEEEccCC-CCccEEEEehhehhcC----CCCCCCCCEEEEEEEE
Confidence            479999885 4566 787764 5689999999996432    2348899999998765

>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain

Probab=87.64  E-value=2  Score=31.53  Aligned_cols=55  Identities=16%  Similarity=0.222  Sum_probs=38.5

Q ss_pred             ccCCCeEEEEEEEEeCCCCeEEE--------EEeecchhhHHHHHHhccccceEEEEEEeccc
Q 044309          134 IKVGRIEPVMVLRVDKEKGYIDL--------SKRRVSEEDIQACEERYNKSKLVHSIMRHVAE  188 (259)
Q Consensus       134 ~kvGd~V~vkVi~vD~~~gkI~L--------SlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~  188 (259)
                      .++||.|.++|++++.+.=.+++        ...++......+..+.++.|+.+.++|.++.+
T Consensus         4 p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~   66 (82)
T cd04454           4 PDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGD   66 (82)
T ss_pred             CCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCC
Confidence            37899999999999764222322        22333333455566779999999999999855

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

>PRK10943 cold shock-like protein CspC; Provisional

Probab=87.24  E-value=3  Score=30.36  Aligned_cols=52  Identities=13%  Similarity=0.208  Sum_probs=38.6

Q ss_pred             EEEEEEEEEeC-ceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEE
Q 044309           90 AVMIQVKNIAD-MGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLR  146 (259)
Q Consensus        90 iv~G~V~~I~~-~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~  146 (259)
                      .++|+|+...+ .|. |+.-++ ++-+-|+|+|.+.....    ..+.+||.|.+.+..
T Consensus         3 ~~~G~Vk~f~~~kGfGFI~~~~-g~~dvFvH~s~l~~~g~----~~l~~G~~V~f~~~~   56 (69)
T PRK10943          3 KIKGQVKWFNESKGFGFITPAD-GSKDVFVHFSAIQGNGF----KTLAEGQNVEFEIQD   56 (69)
T ss_pred             ccceEEEEEeCCCCcEEEecCC-CCeeEEEEhhHccccCC----CCCCCCCEEEEEEEE
Confidence            46799998853 555 777654 56899999999975322    447899999998765

>PRK09507 cspE cold shock protein CspE; Reviewed

Probab=86.65  E-value=3.4  Score=30.02  Aligned_cols=53  Identities=11%  Similarity=0.160  Sum_probs=38.6

Q ss_pred             EEEEEEEEEe-CceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEE
Q 044309           90 AVMIQVKNIA-DMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRV  147 (259)
Q Consensus        90 iv~G~V~~I~-~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~v  147 (259)
                      .++|+|+... +.|. |+.-++ ++-+-|+|+|.+.....    ..+.+||.|.+.+..-
T Consensus         3 ~~~G~Vk~f~~~kGyGFI~~~~-g~~dvfvH~s~l~~~g~----~~l~~G~~V~f~~~~~   57 (69)
T PRK09507          3 KIKGNVKWFNESKGFGFITPED-GSKDVFVHFSAIQTNGF----KTLAEGQRVEFEITNG   57 (69)
T ss_pred             ccceEEEEEeCCCCcEEEecCC-CCeeEEEEeecccccCC----CCCCCCCEEEEEEEEC
Confidence            4679999885 3455 677764 56899999999974321    4478999999987653

>PRK09890 cold shock protein CspG; Provisional

Probab=85.81  E-value=4.2  Score=29.62  Aligned_cols=51  Identities=10%  Similarity=0.164  Sum_probs=37.6

Q ss_pred             EEEEEEEEe-CceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEE
Q 044309           91 VMIQVKNIA-DMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLR  146 (259)
Q Consensus        91 v~G~V~~I~-~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~  146 (259)
                      ++|+|+... ..|. |+.-++ ++-+-|+|+|.+.....    ..+++||.|.+.+..
T Consensus         5 ~~G~Vk~f~~~kGfGFI~~~~-g~~dvFvH~s~l~~~~~----~~l~~G~~V~f~~~~   57 (70)
T PRK09890          5 MTGLVKWFNADKGFGFITPDD-GSKDVFVHFTAIQSNEF----RTLNENQKVEFSIEQ   57 (70)
T ss_pred             ceEEEEEEECCCCcEEEecCC-CCceEEEEEeeeccCCC----CCCCCCCEEEEEEEE
Confidence            479999875 3454 777764 56899999999975422    347899999997654

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

Probab=85.53  E-value=3.8  Score=30.35  Aligned_cols=63  Identities=16%  Similarity=0.053  Sum_probs=43.2

Q ss_pred             EEEEEEEe-CceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeec
Q 044309           92 MIQVKNIA-DMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV  161 (259)
Q Consensus        92 ~G~V~~I~-~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~  161 (259)
                      +|+|+-.. +.|. ||..++ ++.+.|+|+|.+...-    ...+..||.|.+.+..-  .+|+-...+..+
T Consensus         3 ~G~Vkwfn~~KGfGFI~~~~-gg~dVFvH~s~i~~~g----~~~l~~G~~V~f~~~~~--~~G~~A~~V~~~   67 (74)
T PRK09937          3 KGTVKWFNNAKGFGFICPEG-GGEDIFAHYSTIQMDG----YRTLKAGQSVQFDVHQG--PKGNHASVIVPV   67 (74)
T ss_pred             CeEEEEEeCCCCeEEEeeCC-CCccEEEEEeeccccC----CCCCCCCCEEEEEEEEC--CCCceeeEEEEC
Confidence            48888875 3565 777664 5799999999997432    24578999999997653  246544444443

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

Probab=84.81  E-value=0.47  Score=34.42  Aligned_cols=41  Identities=15%  Similarity=0.284  Sum_probs=30.2

Q ss_pred             cccceEEEEEEecccccCCchH------HH--HHhhchhhHHhhcCHHHHHH
Q 044309          174 NKSKLVHSIMRHVAETLGIDLE------EL--YVNIGWPLYWKYGHAFEAFK  217 (259)
Q Consensus       174 ~~g~~v~g~V~~i~~~~G~fve------~~--~~~~sw~l~~~~~~~~~~fk  217 (259)
                      +.|+++.|+|.++.+.+|+|++      ++  .++++|.   ...++.+.|+
T Consensus         2 ~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~---~~~~~~~~~~   50 (72)
T cd05704           2 EEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDS---YTENPLEGFK   50 (72)
T ss_pred             CCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCc---ccCCHHHhCC
Confidence            5789999999998755899873      33  8888885   4556666663

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.

>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=84.53  E-value=3.7  Score=29.17  Aligned_cols=53  Identities=23%  Similarity=0.352  Sum_probs=35.4

Q ss_pred             ccCCCeEEEEEEEEeCCCCeEEEEE----------eecchhhHHHHHHhccccceEEEEEEeccc
Q 044309          134 IKVGRIEPVMVLRVDKEKGYIDLSK----------RRVSEEDIQACEERYNKSKLVHSIMRHVAE  188 (259)
Q Consensus       134 ~kvGd~V~vkVi~vD~~~gkI~LSl----------K~~~~~~~~~~~~~~~~g~~v~g~V~~i~~  188 (259)
                      +++|+.+.++|.++...  .+.+.+          .++..+...+..+.|+.|+.+.++|..+..
T Consensus         1 ~~~G~iv~g~V~~v~~~--gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~   63 (73)
T cd05706           1 LKVGDILPGRVTKVNDR--YVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDV   63 (73)
T ss_pred             CCCCCEEEEEEEEEeCC--eEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeC
Confidence            36899999999999652  333333          222222223345679999999999999853

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.

>COG4776 Rnb Exoribonuclease II [Transcription]

Probab=83.97  E-value=0.37  Score=47.49  Aligned_cols=76  Identities=22%  Similarity=0.252  Sum_probs=58.4

Q ss_pred             hhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc------------cCccccccCCCeEEE
Q 044309           75 LECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI------------RSVSSLIKVGRIEPV  142 (259)
Q Consensus        75 ~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v------------~~~~~~~kvGd~V~v  142 (259)
                      +.||++.++-- ....+.+.|..|..-|.-|.|.+ +|..+|||-.-+-..+-            -+-...+++||.+.|
T Consensus       550 LY~r~L~~k~~-~~~~F~AEI~Di~R~G~RvrLle-NGA~~FIPa~lih~~reei~~n~e~gtv~I~ge~~Yk~~D~i~V  627 (645)
T COG4776         550 LYARFLADKAG-TNTRFAAEIQDISRGGMRVRLLE-NGAIAFIPAPLIHANREELVCNQENGTVQIKGETVYKVGDVIDV  627 (645)
T ss_pred             HHHHHhccccc-cCchhhhhhhhhccCceEEEecc-CCcceecchhhhccchhheEecCCCceEEEccEEEEeeccEEEE
Confidence            46888877655 67789999999999999999998 89999999876654321            122455788888888


Q ss_pred             EEEEEeCCCC
Q 044309          143 MVLRVDKEKG  152 (259)
Q Consensus       143 kVi~vD~~~g  152 (259)
                      ++.+|..+++
T Consensus       628 ~l~eVr~etR  637 (645)
T COG4776         628 TLAEVRMETR  637 (645)
T ss_pred             EeHHHHHhhh
Confidence            8888776544

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=82.81  E-value=5.9  Score=34.13  Aligned_cols=57  Identities=16%  Similarity=0.296  Sum_probs=38.3

Q ss_pred             cccccCCCeEEEEEEEEeCCCCeEEEEE------------------eecchhhHHHHHHhccccceEEEEEEecc
Q 044309          131 SSLIKVGRIEPVMVLRVDKEKGYIDLSK------------------RRVSEEDIQACEERYNKSKLVHSIMRHVA  187 (259)
Q Consensus       131 ~~~~kvGd~V~vkVi~vD~~~gkI~LSl------------------K~~~~~~~~~~~~~~~~g~~v~g~V~~i~  187 (259)
                      ...+++||.|.++|.++....=.+++--                  .++......+..+.|++|+.+..+|..+.
T Consensus        59 ~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~  133 (189)
T PRK09521         59 PPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT  133 (189)
T ss_pred             CCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC
Confidence            4557899999999999976433344421                  11112222334577999999999999985

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=82.51  E-value=0.37  Score=47.69  Aligned_cols=75  Identities=17%  Similarity=0.236  Sum_probs=52.4

Q ss_pred             EEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEE-Eeecchh-----hHHHHHHhcc--ccceEEEEEE
Q 044309          113 IEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLS-KRRVSEE-----DIQACEERYN--KSKLVHSIMR  184 (259)
Q Consensus       113 ~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LS-lK~~~~~-----~~~~~~~~~~--~g~~v~g~V~  184 (259)
                      -.+.|++++...     ....+.+||.+.+.|...+.  ||+.++ .|+....     .++...+.|+  .|+++.|+|.
T Consensus        71 ~~~eI~L~eAk~-----~~~~~~vGD~ie~~I~~~~f--gRia~q~aKq~i~Qkire~ere~i~~eyk~~~GeIV~G~V~  143 (470)
T PRK09202         71 PTKEISLEEARK-----IDPDAEVGDYIEEEIESVDF--GRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVK  143 (470)
T ss_pred             CcceeeHHHHhh-----hCccccCCCeEEEEEccccC--ChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEE
Confidence            456777776642     22347899999999988774  444433 3343333     3446778898  9999999999


Q ss_pred             ecccccCCchH
Q 044309          185 HVAETLGIDLE  195 (259)
Q Consensus       185 ~i~~~~G~fve  195 (259)
                      ++.+ +|++++
T Consensus       144 ri~~-~giiVD  153 (470)
T PRK09202        144 RVER-GNIIVD  153 (470)
T ss_pred             EEec-CCEEEE
Confidence            9964 899875

>PRK10354 RNA chaperone/anti-terminator; Provisional

Probab=82.04  E-value=6.5  Score=28.56  Aligned_cols=51  Identities=14%  Similarity=0.173  Sum_probs=37.3

Q ss_pred             EEEEEEEEe-CceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEE
Q 044309           91 VMIQVKNIA-DMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLR  146 (259)
Q Consensus        91 v~G~V~~I~-~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~  146 (259)
                      ..|+|+... +.|. |+.-++ ++-+-|+|+|.+....    ...+++||.|.+.+..
T Consensus         5 ~~G~Vk~f~~~kGfGFI~~~~-g~~dvfvH~s~l~~~g----~~~l~~G~~V~f~~~~   57 (70)
T PRK10354          5 MTGIVKWFNADKGFGFITPDD-GSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIES   57 (70)
T ss_pred             ceEEEEEEeCCCCcEEEecCC-CCccEEEEEeeccccC----CCCCCCCCEEEEEEEE
Confidence            379998874 3454 677654 5689999999997432    2457899999998665

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

Probab=81.71  E-value=11  Score=26.40  Aligned_cols=51  Identities=14%  Similarity=0.070  Sum_probs=37.1

Q ss_pred             EEEEEEEeC-ceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEE
Q 044309           92 MIQVKNIAD-MGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRV  147 (259)
Q Consensus        92 ~G~V~~I~~-~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~v  147 (259)
                      .|+|+...+ .|. |+..++ ++-+-|+|.+++...-    ...+++|+.|.+.+..-
T Consensus         2 ~G~Vk~~~~~kGfGFI~~~~-~g~diffh~~~~~~~~----~~~~~~G~~V~f~~~~~   54 (65)
T cd04458           2 TGTVKWFDDEKGFGFITPDD-GGEDVFVHISALEGDG----FRSLEEGDRVEFELEEG   54 (65)
T ss_pred             cEEEEEEECCCCeEEEecCC-CCcCEEEEhhHhhccC----CCcCCCCCEEEEEEEEC
Confidence            588888754 343 666653 4799999999998531    24578999999987654

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.

>TIGR02381 cspD cold shock domain protein CspD

Probab=81.41  E-value=5.5  Score=28.77  Aligned_cols=50  Identities=14%  Similarity=0.109  Sum_probs=36.9

Q ss_pred             EEEEEEEe-CceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEE
Q 044309           92 MIQVKNIA-DMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLR  146 (259)
Q Consensus        92 ~G~V~~I~-~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~  146 (259)
                      +|+|+-.. +.|. |+.-++ ++-+.|+|+|.+....    ...++.||.|.+.+..
T Consensus         3 ~G~Vk~f~~~kGfGFI~~~~-g~~dvfvH~s~~~~~g----~~~l~~G~~V~f~~~~   54 (68)
T TIGR02381         3 IGIVKWFNNAKGFGFICPEG-VDGDIFAHYSTIQMDG----YRTLKAGQKVQFEVVQ   54 (68)
T ss_pred             CeEEEEEeCCCCeEEEecCC-CCccEEEEHHHhhhcC----CCCCCCCCEEEEEEEE
Confidence            58888874 4565 777764 5789999999997432    2457899999998654

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

>PRK14998 cold shock-like protein CspD; Provisional

Probab=81.20  E-value=6.9  Score=28.86  Aligned_cols=61  Identities=15%  Similarity=0.041  Sum_probs=41.9

Q ss_pred             EEEEEEEe-CceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309           92 MIQVKNIA-DMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR  159 (259)
Q Consensus        92 ~G~V~~I~-~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK  159 (259)
                      +|+|+-.. +.|. |+.-++ ++-+.|+|+|.+....    ...+..|+.|.+.+..-+  +|.-...+.
T Consensus         3 ~G~Vkwfn~~kGfGFI~~~~-g~~dVFvH~s~l~~~g----~~~l~~G~~V~f~~~~~~--~G~~A~~V~   65 (73)
T PRK14998          3 TGTVKWFNNAKGFGFICPEG-GGEDIFAHYSTIQMDG----YRTLKAGQSVRFDVHQGP--KGNHASVIV   65 (73)
T ss_pred             CeEEEEEeCCCceEEEecCC-CCccEEEEeeeecccC----CCCCCCCCEEEEEEEECC--CCceeEEEE
Confidence            48888775 3565 777764 5789999999997432    245789999999976533  455444333

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

Probab=81.18  E-value=2.6  Score=30.60  Aligned_cols=50  Identities=18%  Similarity=0.272  Sum_probs=33.5

Q ss_pred             CCeEEEEEEEEeCCCCeEEEEEe----------ecchhh--HHHHHHhccccceEEEEEEeccc
Q 044309          137 GRIEPVMVLRVDKEKGYIDLSKR----------RVSEED--IQACEERYNKSKLVHSIMRHVAE  188 (259)
Q Consensus       137 Gd~V~vkVi~vD~~~gkI~LSlK----------~~~~~~--~~~~~~~~~~g~~v~g~V~~i~~  188 (259)
                      |+.|.++|.++...  -+.+++-          ++..+.  ..+..+.|+.|+.++++|..+..
T Consensus         1 G~~V~g~V~~i~~~--g~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~   62 (73)
T cd05703           1 GQEVTGFVNNVSKE--FVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDK   62 (73)
T ss_pred             CCEEEEEEEEEeCC--EEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeC
Confidence            78899999998753  3333331          122111  33466889999999999999854

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

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

Probab=80.89  E-value=0.45  Score=34.45  Aligned_cols=39  Identities=13%  Similarity=0.107  Sum_probs=28.5

Q ss_pred             cccceEEEEEEecccccCCchH-------HH--HHhhchhhHHhhcCHHHHH
Q 044309          174 NKSKLVHSIMRHVAETLGIDLE-------EL--YVNIGWPLYWKYGHAFEAF  216 (259)
Q Consensus       174 ~~g~~v~g~V~~i~~~~G~fve-------~~--~~~~sw~l~~~~~~~~~~f  216 (259)
                      ..|+++.|+|..+.+ ||+|++       ++  .++++|.   ++.++.+.|
T Consensus         2 ~~g~~~~g~V~~i~~-fG~fv~l~~~~~eGlvh~sel~~~---~~~~~~~~~   49 (73)
T cd05686           2 ALYQIFKGEVASVTE-YGAFVKIPGCRKQGLVHKSHMSSC---RVDDPSEVV   49 (73)
T ss_pred             cCCCEEEEEEEEEEe-eeEEEEECCCCeEEEEEchhhCCC---cccCHhhEE
Confidence            478999999999976 999873       23  6788884   555555554

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.

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=80.63  E-value=1.4  Score=45.83  Aligned_cols=81  Identities=7%  Similarity=0.088  Sum_probs=50.2

Q ss_pred             EEEeCCCCeEEEEEeecchh--h---HHHHHH--hccccceEEEEEEecccccCCch------HHH--HHhhc---hhhH
Q 044309          145 LRVDKEKGYIDLSKRRVSEE--D---IQACEE--RYNKSKLVHSIMRHVAETLGIDL------EEL--YVNIG---WPLY  206 (259)
Q Consensus       145 i~vD~~~gkI~LSlK~~~~~--~---~~~~~~--~~~~g~~v~g~V~~i~~~~G~fv------e~~--~~~~s---w~l~  206 (259)
                      +.++. +|++.++-.....-  .   .+....  ..+.|+++.|+|+++.+ ||+|+      ++|  .+++|   |.  
T Consensus       611 Idi~d-~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~~GkV~~I~d-fGaFVel~~G~eGLvHISeisdls~~--  686 (719)
T TIGR02696       611 ISIED-DGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLGTVVKTTA-FGAFVSLLPGKDGLLHISQIRKLAGG--  686 (719)
T ss_pred             EEEec-CcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEEEEEEEEEC-ceEEEEecCCceEEEEhhhccccccc--
Confidence            45554 68888766543221  1   111223  36899999999999987 99998      344  67665   64  


Q ss_pred             HhhcCHHHHHHHHhcCcchh-hccCCCc
Q 044309          207 WKYGHAFEAFKIIVTDPDSV-LNSLTRE  233 (259)
Q Consensus       207 ~~~~~~~~~fk~a~~~~~~~-l~~l~~~  233 (259)
                      ++..++.+.|    ..|+++ .+-++++
T Consensus       687 ~rv~~~~dv~----kvGd~V~VKVl~ID  710 (719)
T TIGR02696       687 KRVENVEDVL----SVGQKIQVEIADID  710 (719)
T ss_pred             cCcCCHHHcC----CCCCEEEEEEEEEC
Confidence            5667776666    445544 4444444

Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.

>cd05700 S1_Rrp5_repeat_hs9 S1_Rrp5_repeat_hs9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=80.55  E-value=7.4  Score=28.03  Aligned_cols=65  Identities=15%  Similarity=0.203  Sum_probs=40.0

Q ss_pred             CcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEE
Q 044309           88 DMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSK  158 (259)
Q Consensus        88 G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSl  158 (259)
                      |+..+-.|-.+++.|--+--.  +.+.|+-    +.-.|...-...+-+|+++++.|+.||.-+.++-+|+
T Consensus         1 G~~L~LvV~~~~edgsv~fs~--g~v~g~t----v~AtryH~~g~nl~pGqK~kaviLhvD~l~~~VhVSl   65 (65)
T cd05700           1 GDQLKLVVQDVTEDGSVMFSG--GQVSGLT----VLASRYHKEGVNVTPGCKLKAVILHVDFVKSQVHVSL   65 (65)
T ss_pred             CceEEEEEeeeccCCcEEEec--CCcCCcE----EEEEEEEecceecCCCceeEEEEEEEeeEEeEEEEeC
Confidence            556666777765555333232  3456651    1122333334557899999999999998777776664

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 Homo sapiens S1 repeat 9 (hs9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]

Probab=80.42  E-value=7.6  Score=34.72  Aligned_cols=63  Identities=13%  Similarity=0.064  Sum_probs=46.2

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeC
Q 044309           84 YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDK  149 (259)
Q Consensus        84 ~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~  149 (259)
                      .|.+||.|.|.|++-..-+.-|+|.  +.-.|.|+.-.+... .+.=+-.+++||.|-++|...++
T Consensus        62 iP~~~D~VIGiV~~~~gd~ykVDig--g~~~a~L~~laFe~A-tkrNrPnl~vGdliyakv~~a~~  124 (230)
T KOG1004|consen   62 IPVKGDHVIGIVTSKSGDIYKVDIG--GSEPASLSYLAFEGA-TKRNRPNLQVGDLIYAKVVDANK  124 (230)
T ss_pred             cCCCCCEEEEEEEeccCceEEEecC--CCCeeeeeeccccCc-cccCCCccccccEEEEEEEecCC
Confidence            5668999999999998888999996  346677665444321 11113448999999999998764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	259
1q46_A	175	Crystal Structure Of The Eif2 Alpha Subunit From Sa		4e-46
2a19_A	175	Pkr Kinase Domain- Eif2alpha- Amp-Pnp Complex. Leng		5e-46
1q8k_A	308	Solution Structure Of Alpha Subunit Of Human Eif2 L		2e-37
1kl9_A	182	Crystal Structure Of The N-Terminal Segment Of Huma		1e-34
3aev_A	275	Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex		2e-13
1yz6_A	274	Crystal Structure Of Intact Alpha Subunit Of Aif2 F		5e-13
2aho_B	266	Structure Of The Archaeal Initiation Factor Eif2 Al		2e-10

>pdb|1Q46|A Chain A, Crystal Structure Of The Eif2 Alpha Subunit From Saccharomyces Cerevisia Length = 175

Iteration: 1
 Score =  181 bits (459), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 88/146 (60%), Positives = 105/146 (71%)
Query: 77  CRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSEXXXXXXXXXXXXXKV 136
           CR YE +YPE+D  VM+ V+ IA+MGAYV LLEY+NIEGMIL SE             +V
Sbjct: 5   CRFYENKYPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRV 64
Query: 137 GRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEE 196
           G+ +  +VLRVDKEKGYIDLSKRRVS EDI  CEE+Y KSK VHSI+R+ AE   I LEE
Sbjct: 65  GKNDVAVVLRVDKEKGYIDLSKRRVSSEDIIKCEEKYQKSKTVHSILRYCAEKFQIPLEE 124
Query: 197 LYVNIGWPLYWKYGHAFEAFKIIVTD 222
           LY  I WPL  K+GHA+EAFK+ + D
Sbjct: 125 LYKTIAWPLSRKFGHAYEAFKLSIID 150

>pdb|2A19|A Chain A, Pkr Kinase Domain- Eif2alpha- Amp-Pnp Complex. Length = 175

Iteration: 1
 Score =  180 bits (457), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 88/146 (60%), Positives = 105/146 (71%)
Query: 77  CRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSEXXXXXXXXXXXXXKV 136
           CR YE +YPE+D  VM+ V+ IA+MGAYV LLEY+NIEGMIL SE             +V
Sbjct: 5   CRFYENKYPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRV 64
Query: 137 GRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEE 196
           G+ +  +VLRVDKEKGYIDLSKRRVS EDI  CEE+Y KSK VHSI+R+ AE   I LEE
Sbjct: 65  GKNDVAVVLRVDKEKGYIDLSKRRVSSEDIIKCEEKYQKSKTVHSILRYCAEKFQIPLEE 124
Query: 197 LYVNIGWPLYWKYGHAFEAFKIIVTD 222
           LY  I WPL  K+GHA+EAFK+ + D
Sbjct: 125 LYKTIAWPLSRKFGHAYEAFKLSIID 150

>pdb|1Q8K|A Chain A, Solution Structure Of Alpha Subunit Of Human Eif2 Length = 308

Iteration: 1
 Score =  152 bits (383), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 83/164 (50%), Positives = 107/164 (65%), Gaps = 9/164 (5%)
Query: 75  LECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSEXXXXXXXXXXXXX 134
           + CR Y+ ++PEV+  VM+ V++I +MGAYVSLLEYNNIEGMI  SE             
Sbjct: 1   MSCRFYQHKFPEVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLI 60
Query: 135 KVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGI-- 192
           ++GR E V V+RVDKEKGYIDLSKRRVS E+   CE+++ KSK V+SI+RHVAE L    
Sbjct: 61  RIGRNECVKVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTK 120
Query: 193 --DLEELYVNIGWPLYWKYGH----AFEAFKIIVTDPDSVLNSL 230
              LE L+    W    KY      A++AFK  V+DP S+L+SL
Sbjct: 121 DEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDP-SILDSL 163

>pdb|1KL9|A Chain A, Crystal Structure Of The N-Terminal Segment Of Human Eukaryotic Initiation Factor 2alpha Length = 182

Iteration: 1
 Score =  143 bits (360), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 87/180 (48%), Positives = 114/180 (63%), Gaps = 14/180 (7%)
Query: 73  PNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSEXXXXXXXXXXX 132
           P L CR Y+ ++PEV+  V + V++IA+ GAYVSLLEYNNIEG IL SE           
Sbjct: 1   PGLSCRFYQHKFPEVEDVVXVNVRSIAEXGAYVSLLEYNNIEGXILLSELSRRRIRSINK 60
Query: 133 XXKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGI 192
             ++GR E V+V+RVDKEKGYIDLSKRRVS E+   CE+++ KSK V+SI+RHVAE L  
Sbjct: 61  LIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEY 120
Query: 193 ----DLEELYVNIGWPLYWKYGH----AFEAFKIIVTDPDSVLNSLTREVKEIGPDGQEV 244
                LE L+    W    KY      A++AFK  V+DP S+L+SL     ++  D +EV
Sbjct: 121 TKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDP-SILDSL-----DLNEDEREV 174

>pdb|3AEV|A Chain A, Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex From Pyrococcus Horikoshii Ot3 Length = 275

Iteration: 1
 Score = 72.8 bits (177), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 46/146 (31%), Positives = 72/146 (49%)
Query: 84  YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSEXXXXXXXXXXXXXKVGRIEPVM 143
           YPE    V+  VK I + GA++ L EY   E  +  SE             K G+     
Sbjct: 8   YPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAK 67
Query: 144 VLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGW 203
           V+RVD  KG+IDLS RRV+++  +A  + + +++   +++R  AE LG D E  +  +  
Sbjct: 68  VIRVDPRKGHIDLSLRRVTQQQRKAKLQEFKRAQKAENLLRLAAEKLGKDFEAAWREVWV 127
Query: 204 PLYWKYGHAFEAFKIIVTDPDSVLNS 229
           PL  ++G  + AF+    D   VL  
Sbjct: 128 PLEEEWGEVYAAFEDAAKDGIEVLKG 153

>pdb|1YZ6|A Chain A, Crystal Structure Of Intact Alpha Subunit Of Aif2 From Pyrococcus Abyssi Length = 274

Iteration: 1
 Score = 71.2 bits (173), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 45/146 (30%), Positives = 72/146 (49%)
Query: 84  YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSEXXXXXXXXXXXXXKVGRIEPVM 143
           YPE    V+  VK I + GA++ L EY   E  +  SE             K G+     
Sbjct: 7   YPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAK 66
Query: 144 VLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGW 203
           V+RVD  KG+IDLS RRV+++  +A  + + +++   ++++  AE LG D E  +  +  
Sbjct: 67  VIRVDPRKGHIDLSLRRVTQQQRKAKLQEFKRAQKAENLLKLAAEKLGKDFETAWREVWV 126
Query: 204 PLYWKYGHAFEAFKIIVTDPDSVLNS 229
           PL  ++G  + AF+    D   VL  
Sbjct: 127 PLEEEWGEVYAAFEDAAKDGIDVLKG 152

>pdb|2AHO|B Chain B, Structure Of The Archaeal Initiation Factor Eif2 Alpha- Gamma Heterodimer From Sulfolobus Solfataricus Complexed With Gdpnp Length = 266

Iteration: 1
 Score = 62.8 bits (151), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 37/146 (25%), Positives = 74/146 (50%)
Query: 82  ARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSEXXXXXXXXXXXXXKVGRIEP 141
           ++ P     ++  VK + D G+YVSL EY  ++  + +SE             K  R   
Sbjct: 6   SKLPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVI 65
Query: 142 VMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEELYVNI 201
           V V+RVD+ KG +D+S ++V++++ +    ++ K + +  I+  V++ L +  ++ +  +
Sbjct: 66  VKVIRVDRRKGTVDVSLKKVTDDERRKKNLQWKKIQRLDKILELVSQKLKLSEKDAWEQV 125
Query: 202 GWPLYWKYGHAFEAFKIIVTDPDSVL 227
            W L  KYG    A +  V + + +L
Sbjct: 126 AWKLEAKYGDPITAIEKAVKEGEKIL 151

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	259
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	6e-68
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	1e-65
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	2e-57
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	1e-54
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	1e-50
1yz7_A	188	Probable translation initiation factor 2 alpha sub	1e-22
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	6e-14
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	3e-12
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	2e-10
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	1e-09
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	2e-09
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	2e-08
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	3e-08
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	4e-08
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	2e-07
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	2e-07
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	8e-07
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	2e-06
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	2e-06
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	1e-04
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	6e-04

>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 Length = 175

 Score =  206 bits (527), Expect = 6e-68
 Identities = 99/165 (60%), Positives = 122/165 (73%), Gaps = 2/165 (1%)

Query: 74  NLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSL 133
           +  CR YE +YPE+D  VM+ V+ IA+MGAYV LLEY+NIEGMIL SELSRRRIRS+  L
Sbjct: 2   SSHCRFYENKYPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKL 61

Query: 134 IKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGID 193
           I+VG+ +  +VLRVDKEKGYIDLSKRRVS EDI  CEE+Y KSK VHSI+R+ AE   I 
Sbjct: 62  IRVGKNDVAVVLRVDKEKGYIDLSKRRVSSEDIIKCEEKYQKSKTVHSILRYCAEKFQIP 121

Query: 194 LEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLN--SLTREVKE 236
           LEELY  I WPL  K+GHA+EAFK+ + D          +++V +
Sbjct: 122 LEELYKTIAWPLSRKFGHAYEAFKLSIIDETVWEGIEPPSKDVLD 166

>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 Length = 182

 Score =  201 bits (512), Expect = 1e-65
 Identities = 95/174 (54%), Positives = 124/174 (71%), Gaps = 9/174 (5%)

Query: 73  PNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSS 132
           P L CR Y+ ++PEV+  VM+ V++IA+MGAYVSLLEYNNIEGMIL SELSRRRIRS++ 
Sbjct: 1   PGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINK 60

Query: 133 LIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGI 192
           LI++GR E V+V+RVDKEKGYIDLSKRRVS E+   CE+++ KSK V+SI+RHVAE L  
Sbjct: 61  LIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEY 120

Query: 193 D----LEELYVNIGWPLYWKYGH----AFEAFKIIVTDPDSVLN-SLTREVKEI 237
                LE L+    W    KY      A++AFK  V+DP  + +  L  + +E+
Sbjct: 121 TKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREV 174

>3cw2_C Translation initiation factor 2 subunit alpha; AIF2, intact AIF2, initiation factor 2 alpha subunit, initiation factor 2 beta subunit; 2.80A {Sulfolobus solfataricus} PDB: 2aho_B 3v11_B* Length = 266

 Score =  183 bits (465), Expect = 2e-57
 Identities = 38/160 (23%), Positives = 84/160 (52%)

Query: 78  RMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVG 137
               ++ P     ++  VK + D G+YVSL EY  ++  + +SE+S + ++++  ++K  
Sbjct: 2   IYSRSKLPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKEN 61

Query: 138 RIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEEL 197
           R   V V+RVD+ KG +D+S ++V++++ +    ++ K + +  I+  V++ L +  ++ 
Sbjct: 62  RKVIVKVIRVDRRKGTVDVSLKKVTDDERRKKNLQWKKIQRLDKILELVSQKLKLSEKDA 121

Query: 198 YVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTREVKEI 237
           +  + W L  KYG    A +  V + + +L         +
Sbjct: 122 WEQVAWKLEAKYGDPITAIEKAVKEGEKILIDAGVPEIWV 161

>1q8k_A Eukaryotic translation initiation factor 2 subunit 1; NMR {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 d.58.51.1 Length = 308

 Score =  177 bits (450), Expect = 1e-54
 Identities = 89/160 (55%), Positives = 114/160 (71%), Gaps = 8/160 (5%)

Query: 75  LECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLI 134
           + CR Y+ ++PEV+  VM+ V++I +MGAYVSLLEYNNIEGMI  SELSRRRIRS++ LI
Sbjct: 1   MSCRFYQHKFPEVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLI 60

Query: 135 KVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGI-- 192
           ++GR E V V+RVDKEKGYIDLSKRRVS E+   CE+++ KSK V+SI+RHVAE L    
Sbjct: 61  RIGRNECVKVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTK 120

Query: 193 --DLEELYVNIGWPLYWKYGH----AFEAFKIIVTDPDSV 226
              LE L+    W    KY      A++AFK  V+DP  +
Sbjct: 121 DEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDPSIL 160

>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB: 1yz6_A Length = 275

 Score =  165 bits (420), Expect = 1e-50
 Identities = 47/154 (30%), Positives = 80/154 (51%)

Query: 80  YEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRI 139
               YPE    V+  VK I + GA++ L EY   E  +  SE++   +R++   +K G+ 
Sbjct: 4   KAREYPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQK 63

Query: 140 EPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEELYV 199
               V+RVD  KG+IDLS RRV+++  +A  + + +++   +++R  AE LG D E  + 
Sbjct: 64  VVAKVIRVDPRKGHIDLSLRRVTQQQRKAKLQEFKRAQKAENLLRLAAEKLGKDFEAAWR 123

Query: 200 NIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTRE 233
            +  PL  ++G  + AF+    D   VL     +
Sbjct: 124 EVWVPLEEEWGEVYAAFEDAAKDGIEVLKGHVPD 157

>1yz7_A Probable translation initiation factor 2 alpha subunit; helical domain, alpha-beta domain; 2.26A {Pyrococcus abyssi} Length = 188

 Score = 90.7 bits (225), Expect = 1e-22
 Identities = 15/64 (23%), Positives = 31/64 (48%)

Query: 167 QACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSV 226
           +A  + + +++   ++++  AE LG D E  +  +  PL  ++G  + AF+    D   V
Sbjct: 4   KAKLQEFKRAQKAENLLKLAAEKLGKDFETAWREVWVPLEEEWGEVYAAFEDAAKDGIDV 63

Query: 227 LNSL 230
           L   
Sbjct: 64  LKGH 67

>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis} Length = 130

 Score = 65.9 bits (161), Expect = 6e-14
 Identities = 29/112 (25%), Positives = 50/112 (44%), Gaps = 3/112 (2%)

Query: 85  PEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMV 144
            EV      +V  +   GA+V+L E    +G++  SE++   ++ ++  + VG    V V
Sbjct: 5   FEVGSVYTGKVTGLQAYGAFVALDE--ETQGLVHISEVTHGFVKDINEHLSVGDEVQVKV 62

Query: 145 LRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEE 196
           L VD+EKG I LS  R ++   +  E +  K K                L++
Sbjct: 63  LAVDEEKGKISLS-IRATQAAPEKKESKPRKPKAAQVSEEASTPQGFNTLKD 113

>1luz_A Protein K3, protein K2; stranded anti-parallel beta barrel, viral protein; 1.80A {Vaccinia virus} SCOP: b.40.4.5 Length = 88

 Score = 60.0 bits (145), Expect = 3e-12
 Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 3/79 (3%)

Query: 84  YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMIL-FSELSRRRIRSVSSLIKVGRIEPV 142
            P     +  +V    D   Y+ L +Y + E ++    ++   R       + VG+   V
Sbjct: 8   LPNAGDVIKGRVY-EKDYALYIYLFDYPHFEAILAESVKMHMDRYVEYRDKL-VGKTVKV 65

Query: 143 MVLRVDKEKGYIDLSKRRV 161
            V+RVD  KGYID++ +R+
Sbjct: 66  KVIRVDYTKGYIDVNYKRM 84

>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 115

 Score = 55.7 bits (135), Expect = 2e-10
 Identities = 26/94 (27%), Positives = 45/94 (47%), Gaps = 4/94 (4%)

Query: 81  EARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELS-RRRIRSVSSLIKVGRI 139
             RYP     +  +V N+ D G +V + E   +EG++  SE+    +    S ++ VG +
Sbjct: 25  AKRYP-EGTKLTGRVTNLTDYGCFVEIEE--GVEGLVHVSEMDWTNKNIHPSKVVNVGDV 81

Query: 140 EPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERY 173
             VMVL +D+E+  I L  ++      Q   E +
Sbjct: 82  VEVMVLDIDEERRRISLGLKQCKANPWQQFAETH 115

>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 109

 Score = 53.3 bits (129), Expect = 1e-09
 Identities = 25/87 (28%), Positives = 40/87 (45%), Gaps = 5/87 (5%)

Query: 80  YEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVG-R 138
           + A   +  + V  +V  +   GA V L +   +EG +  SE SR R+   + ++ VG  
Sbjct: 25  WVALNKKGAI-VTGKVTAVDAKGATVELAD--GVEGYLRASEASRDRVEDATLVLSVGDE 81

Query: 139 IEPVMVLRVDKEKGYIDLSKRRVSEED 165
           +E      VD++   I LS R   E D
Sbjct: 82  VE-AKFTGVDRKNRAISLSVRAKDEAD 107

>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii} Length = 80

 Score = 52.3 bits (126), Expect = 2e-09
 Identities = 17/80 (21%), Positives = 30/80 (37%), Gaps = 6/80 (7%)

Query: 85  PEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMV 144
            E        V  I   GA+++L E   + G++   ++   R+ ++     VG    V  
Sbjct: 3   VEPGKFYKGVVTRIEKYGAFINLNE--QVRGLLRPRDMISLRLENL----NVGDEIIVQA 56

Query: 145 LRVDKEKGYIDLSKRRVSEE 164
           + V  EK  ID     +   
Sbjct: 57  IDVRPEKREIDFKYIPLEHH 76

>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} Length = 119

 Score = 50.9 bits (122), Expect = 2e-08
 Identities = 15/82 (18%), Positives = 38/82 (46%), Gaps = 3/82 (3%)

Query: 85  PEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMV 144
           P +      +V  + D GA++ +      +G++  + +S  R+   S ++ VG    V +
Sbjct: 20  PALYTIFQGEVAMVTDYGAFIKIPGCRK-QGLVHRTHMSSCRVDKPSEIVDVGDKVWVKL 78

Query: 145 LRVD--KEKGYIDLSKRRVSEE 164
           +  +   ++  + LS + V++ 
Sbjct: 79  IGREMKNDRIKVSLSMKVVNQG 100

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A Length = 723

 Score = 53.3 bits (129), Expect = 3e-08
 Identities = 24/78 (30%), Positives = 44/78 (56%), Gaps = 3/78 (3%)

Query: 95  VKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYI 154
           V  I D GA+V++      EG++  S+++ +R+  V+  +++G+  PV VL VD+ +G I
Sbjct: 635 VTRIVDFGAFVAIG--GGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDR-QGRI 691

Query: 155 DLSKRRVSEEDIQACEER 172
            LS +  +E+   A    
Sbjct: 692 RLSIKEATEQSQPAAAPE 709

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A Length = 726

 Score = 52.5 bits (127), Expect = 4e-08
 Identities = 20/70 (28%), Positives = 37/70 (52%), Gaps = 3/70 (4%)

Query: 95  VKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYI 154
           V  + D GA+V+       +G++  S++S  R+   S ++K G++  V +L  D  +G  
Sbjct: 645 VVKVVDFGAFVNFF--GAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFDD-RGKT 701

Query: 155 DLSKRRVSEE 164
            LS + V +E
Sbjct: 702 KLSMKVVDQE 711

>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae} Length = 1030

 Score = 51.0 bits (122), Expect = 2e-07
 Identities = 11/92 (11%), Positives = 36/92 (39%), Gaps = 6/92 (6%)

Query: 87  VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIR-SVSSLIKVGRIEPVMVL 145
               + ++V+         +    + +E ++     +  ++R   + + ++G+  P  V+
Sbjct: 905 KGSIIPVRVERFWHNDIICTT--NSEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVI 962

Query: 146 RVDKEKGYIDLSKRRVSEEDIQACEERYNKSK 177
            +D      ++S     + D++      + SK
Sbjct: 963 YIDYANITAEVSLL---DHDVKQQYVPISYSK 991

>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} Length = 103

 Score = 46.9 bits (112), Expect = 2e-07
 Identities = 22/82 (26%), Positives = 36/82 (43%), Gaps = 4/82 (4%)

Query: 85  PEVDMAVMIQVKNIADMGAYVSLLEY-NNIEGMILFSELS-RRRIRSVSSLIKVGRIEPV 142
           P +      +V +I   G +V L       EG++  SEL    R+ +V+ ++  G+   V
Sbjct: 10  PTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKV 69

Query: 143 MVLRVDKEKGYIDLSKRRVSEE 164
            VL     K    LS + V +E
Sbjct: 70  KVLSFTGTK--TSLSMKDVDQE 89

>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} SCOP: a.60.2.6 a.60.2.6 a.294.1.1 b.40.4.5 c.55.3.13 PDB: 3bzk_A 2oce_A Length = 785

 Score = 48.7 bits (117), Expect = 8e-07
 Identities = 22/96 (22%), Positives = 42/96 (43%), Gaps = 10/96 (10%)

Query: 86  EVDMAVMIQVKNIADMGAYVSLLEYNNI----EGMILFSELSRRRIRSVSSLIKVGRIEP 141
           +  M +   V N+ + GA+V      +I    +G++  S LS + ++    ++K G I  
Sbjct: 653 KPGMVLEGVVTNVTNFGAFV------DIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVK 706

Query: 142 VMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSK 177
           V V+ VD  +  + LS R       +   +R  +  
Sbjct: 707 VKVMEVDIPRNRVGLSMRMSDTPGEKVEGQRGGRPT 742

>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae} Length = 1219

 Score = 48.0 bits (114), Expect = 2e-06
 Identities = 11/90 (12%), Positives = 36/90 (40%), Gaps = 6/90 (6%)

Query: 89  MAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIR-SVSSLIKVGRIEPVMVLRV 147
             + ++V+         +    + +E ++     +  ++R   + + ++G+  P  V+ +
Sbjct: 904 SIIPVRVERFWHNDIICTT--NSEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYI 961

Query: 148 DKEKGYIDLSKRRVSEEDIQACEERYNKSK 177
           D      ++S     + D++      + SK
Sbjct: 962 DYANITAEVSLL---DHDVKQQYVPISYSK 988

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A Length = 757

 Score = 47.2 bits (113), Expect = 2e-06
 Identities = 19/74 (25%), Positives = 36/74 (48%), Gaps = 7/74 (9%)

Query: 95  VKNIADMGAYVSLLEYNNIEGMILFSELSR----RRIRSVSSLIKVGRIEPVMVLRVDKE 150
           V      GA+VSLL     +G++  S++ +    +R+ +V  ++ VG+   V +  +D  
Sbjct: 675 VVKTTTFGAFVSLL--PGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEID-S 731

Query: 151 KGYIDLSKRRVSEE 164
           +G + L      EE
Sbjct: 732 RGKLSLIPVIEGEE 745

>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae} Length = 285

 Score = 41.9 bits (98), Expect = 1e-04
 Identities = 18/92 (19%), Positives = 34/92 (36%), Gaps = 9/92 (9%)

Query: 81  EARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIE 140
            A     +      V  +   G +V L E NN+ G I  SE             ++G++ 
Sbjct: 146 PAYNNMQNQNWPAIVYRLKLSGTFVYLPE-NNMLGFIHPSERYAE--------PRLGQVL 196

Query: 141 PVMVLRVDKEKGYIDLSKRRVSEEDIQACEER 172
              V+   +    ++LS +  S E ++   + 
Sbjct: 197 DARVIGFREVDRTLNLSLKPRSFEMLENDAQM 228

>1wi5_A RRP5 protein homolog; S1 domain, OB-fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: b.40.4.5 Length = 119

 Score = 37.7 bits (87), Expect = 6e-04
 Identities = 14/70 (20%), Positives = 29/70 (41%), Gaps = 2/70 (2%)

Query: 89  MAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSR-RRIRSVSSLIKVGRIEPVMVLRV 147
           M +   V ++ D G  V +   +     +   +     R ++  + +KVG+    +V +V
Sbjct: 23  MLLTGTVSSLEDHGYLVDI-GVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKV 81

Query: 148 DKEKGYIDLS 157
               G + LS
Sbjct: 82  KGNGGVVSLS 91

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	259
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	100.0
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	100.0
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	99.97
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	99.97
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	99.96
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	99.85
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	99.84
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	99.8
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	99.79
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	99.75
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	99.72
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	99.7
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	99.7
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	99.61
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	99.52
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	99.48
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	99.45
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	99.45
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	99.44
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	99.44
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	99.4
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	99.37
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	99.35
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	99.32
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	99.31
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	99.26
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	99.23
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	99.22
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	99.22
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	99.18
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	99.14
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	99.09
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	98.96
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	98.77
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	98.71
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	98.68
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	98.65
1yz7_A	188	Probable translation initiation factor 2 alpha sub	98.59
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	98.58
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	98.55
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	98.53
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	98.52
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	98.45
2bh8_A	101	1B11; transcription, molecular evolution, unique a	98.39
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	98.27
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	97.9
2bh8_A	101	1B11; transcription, molecular evolution, unique a	97.13
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	96.63
1jjg_A	102	M156R; beta barrel, S1 motif, OB fold, MYXV156R, N	96.6
2r7d_A	469	Ribonuclease II family protein; structural genomic	96.46
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	96.37
3d0f_A	106	Penicillin-binding 1 transmembrane protein MRCA; B	95.43
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	95.41
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	95.18
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	94.27
2rf4_A	214	DNA-directed RNA polymerase I subunit RPA4; transf	94.05
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	90.68
1h95_A	79	CSD, Y-box binding protein; translation factor, tr	89.83
1wfq_A	89	UNR protein; beta-barrel, translational regulation	89.05
3h8z_A	128	FragIle X mental retardation syndrome-related Pro;	87.82
2yty_A	88	Cold shock domain-containing protein E1; cell-free	86.97
2k5n_A	74	Putative cold-shock protein; GFT protein structure	85.31
3i2z_B	71	RNA chaperone, negative regulator of CSPA transcri	84.78
3cam_A	67	Cold-shock domain family protein; cold shock prote	84.42
3aqq_A	147	Calcium-regulated heat stable protein 1; compact b	83.23
2ytx_A	97	Cold shock domain-containing protein E1; cell-free	83.09
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	82.49
1c9o_A	66	CSPB, cold-shock protein; beta barrel, homodimer,	82.45
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	82.14
3i4o_A	79	Translation initiation factor IF-1; cytoplasm, pro	80.43
3a0j_A	73	Cold shock protein; OB-fold, cytoplasm, transcript	80.02

>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=100.00  E-value=4.1e-36  Score=256.22  Aligned_cols=157  Identities=62%  Similarity=1.029  Sum_probs=142.6

Q ss_pred             hhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEE
Q 044309           76 ECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYID  155 (259)
Q Consensus        76 ~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~  155 (259)
                      .|||+.+.+|++|+++.|+|++|++|||||+|.+|++++||||+||++|.++.++++.+++||.|.|+|+++|+++++|+
T Consensus         4 ~~~~~~~~~p~~G~iv~G~V~~i~~fGaFV~L~e~~gveGLvhiSels~~~v~~~~~~~~vGd~V~vkVl~vd~~~~~I~   83 (175)
T 2a19_A            4 HCRFYENKYPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYID   83 (175)
T ss_dssp             CCCSSSSSSCCTTCEEEEEEEEEETTEEEEEETTTTTCEEEEECC--------CCCCCCCTTSEEEEEEEEEETTTTEEE
T ss_pred             ceEEhhhcCCCCCCEEEEEEEEEecceEEEEEcCCCCcEEEEEHHHcCCcccCCHHHcCCCCCEEEEEEEEEECCCCeEE
Confidence            48999999999999999999999999999999755789999999999999999999999999999999999999999999


Q ss_pred             EEEeecchhhHHHHHHhccccceEEEEEEecccccCCchHHHHHhhchhhHHhhcCHHHHHHHHhcCcchhhccCCCc
Q 044309          156 LSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTRE  233 (259)
Q Consensus       156 LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fve~~~~~~sw~l~~~~~~~~~~fk~a~~~~~~~l~~l~~~  233 (259)
                      ||+|++.++||..+.++|+.|+.+.|+|+++++.+|+.++++|..++|++.++||++|+||++|++ ++++|.+++++
T Consensus        84 LSlk~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~~~e~~~~~~~~~l~~~~g~~~~af~~a~~-~~~~l~~~~~~  160 (175)
T 2a19_A           84 LSKRRVSSEDIIKCEEKYQKSKTVHSILRYCAEKFQIPLEELYKTIAWPLSRKFGHAYEAFKLSII-DETVWEGIEPP  160 (175)
T ss_dssp             EESTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHTHHHHHHHHSSHHHHHHHHHH-CGGGGTTCCCS
T ss_pred             EEEEecCcChHHHHHHhccCCCcceEEEEEchhhcCCCHHHHHHHHHHHHHHHhCcHHHHHHHHhC-ChhhhhhcCCC
Confidence            999999999999999999999999999999997899999999999999999999999999999999 56799999974

>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=100.00  E-value=3.7e-34  Score=245.58  Aligned_cols=159  Identities=59%  Similarity=0.939  Sum_probs=136.7

Q ss_pred             hhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeE
Q 044309           75 LECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYI  154 (259)
Q Consensus        75 ~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI  154 (259)
                      ++|||+...+|++|+++.|+|++|++|||||+|.++++++||||+||++|.++.++++.+++||.|.|+|+++|+++++|
T Consensus         3 ~~~~~~~~~~p~~G~iv~G~V~~I~~fGaFV~L~e~~g~eGLvhiSels~~~v~~~~~~~~vGd~V~VkVl~vD~~~~rI   82 (182)
T 1kl9_A            3 LSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYI   82 (182)
T ss_dssp             CCCCSSSSSSCCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC------------CTTCEEEEEEEEEETTTTEE
T ss_pred             eeeEeccccCCCCCCEEEEEEEEEeccEEEEEEccCCCcEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEE
Confidence            67999999998899999999999999999999965578999999999999999999999999999999999999999999


Q ss_pred             EEEEeecchhhHHHHHHhccccceEEEEEEecccccCC----chHHHHHhhchhhHHhhcC----HHHHHHHHhcCcchh
Q 044309          155 DLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGI----DLEELYVNIGWPLYWKYGH----AFEAFKIIVTDPDSV  226 (259)
Q Consensus       155 ~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~----fve~~~~~~sw~l~~~~~~----~~~~fk~a~~~~~~~  226 (259)
                      +||+|++.++||..+.++|+.|+.+.|+|++++++||+    .+++|+...+|++.+++++    +|+||++|+. ++++
T Consensus        83 ~LSlk~~~~~p~~~~~~~~~~g~~v~g~v~~i~~~~gv~l~~giegl~h~s~~~~~~~~~~~~~~~~~~f~~~~~-~~~~  161 (182)
T 1kl9_A           83 DLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVS-DPSI  161 (182)
T ss_dssp             EEESTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSHHHHHHHHHHTHHHHHHHHTCTTHHHHHHHHHHHH-CGGG
T ss_pred             EEEEeecCcChHHHHHHhccCCCEEEEEEEEchhhcCCcccCChhheEEeeecchhhhcCCcchhHHHHHHHHhc-Chhh
Confidence            99999999999999999999999999999999888997    4577888888988899999    9999999999 5679


Q ss_pred             hccCCCcc
Q 044309          227 LNSLTREV  234 (259)
Q Consensus       227 l~~l~~~~  234 (259)
                      |.++++++
T Consensus       162 l~~~~~~~  169 (182)
T 1kl9_A          162 LDSLDLNE  169 (182)
T ss_dssp             GTTSSCCH
T ss_pred             hhhcCCCH
Confidence            99999754

>1q8k_A Eukaryotic translation initiation factor 2 subunit 1; NMR {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 d.58.51.1

Probab=99.97  E-value=1.4e-32  Score=252.74  Aligned_cols=163  Identities=56%  Similarity=0.868  Sum_probs=151.6

Q ss_pred             hhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEE
Q 044309           76 ECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYID  155 (259)
Q Consensus        76 ~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~  155 (259)
                      +|||+.+.+|++|++|.|+|++|++|||||+|.+|++++||||+|+++|+++.++++.|++||.|.|+|+++|+++++|+
T Consensus         2 ~~~f~~~~~~~vG~iv~G~V~~I~~fGaFV~L~ey~gveGLvhiSels~~~i~~~~~~~kvGd~V~VkVl~vD~~~~rI~   81 (308)
T 1q8k_A            2 SCRFYQHKFPEVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNECVKVIRVDKEKGYID   81 (308)
T ss_dssp             CCCSSSSCCCSSCCEEEEEEEEEETTEEEEESCTTTSCCEEECGGGTSCSSCSCCTTTCSSSCEEEEEEEEEETTTTEEE
T ss_pred             ceEehhhcCCCCCCEEEEEEEEEeCcEEEEEECCCCCeEEEEEhHHcCcccccCHHHhcCCCCEEEEEEEEEeCCCCEEE
Confidence            58999999999999999999999999999999877789999999999999999999999999999999999999999999


Q ss_pred             EEEeecchhhHHHHHHhccccceEEEEEEecccccCCch----HHHHHhhchhhHHhhcC----HHHHHHHHhcCcchhh
Q 044309          156 LSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDL----EELYVNIGWPLYWKYGH----AFEAFKIIVTDPDSVL  227 (259)
Q Consensus       156 LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fv----e~~~~~~sw~l~~~~~~----~~~~fk~a~~~~~~~l  227 (259)
                      ||+|++.++||..+.++|+.|+.+.|+|.++++.||+|+    +++|.+++|++.++|++    +|++|+.|+. ++++|
T Consensus        82 LSlK~~~~~p~~~~~~~~~~G~~v~G~V~~v~~~~G~fi~~~~e~l~~~i~~~l~~~~g~~~~~~y~af~~a~~-~~~~l  160 (308)
T 1q8k_A           82 LSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVS-DPSIL  160 (308)
T ss_dssp             EECSSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSSHHHHHHHHHTHHHHHHHTTCSSHHHHHHHHHTTT-CGGGG
T ss_pred             EEEEecccChHHHHHHHccCCCeeEEEEEEcccccCCccCCCHHHHHHHHHHHHHHHhCCcchhHHHHHHHHcC-Chhhh
Confidence            999999999999999999999999999999987679954    56899999999999999    9999999999 45699


Q ss_pred             ccCCCccccCCC
Q 044309          228 NSLTREVKEIGP  239 (259)
Q Consensus       228 ~~l~~~~~~~~~  239 (259)
                      .++++++...++
T Consensus       161 ~~~~i~~~~~~~  172 (308)
T 1q8k_A          161 DSLDLNEDEREV  172 (308)
T ss_dssp             GGCCCCHHHHHH
T ss_pred             hhcCCCHHHHHH
Confidence            999987654443

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

Probab=99.97  E-value=5e-32  Score=245.69  Aligned_cols=160  Identities=29%  Similarity=0.429  Sum_probs=147.2

Q ss_pred             hhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEE
Q 044309           78 RMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLS  157 (259)
Q Consensus        78 R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LS  157 (259)
                      +++.+.+|++|++|.|+|++|.+||+||+|++|++++||||+||++++++.++++.+++||.|.|+|+++|+++++|+||
T Consensus         2 ~~~~~~~p~~Gdiv~G~V~~I~~fGaFV~L~e~~gieGlIhiSels~~~v~~~~~~~kvGd~V~vkVi~vD~~~~~I~LS   81 (275)
T 3aev_A            2 PRKAREYPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVDPRKGHIDLS   81 (275)
T ss_dssp             -----CCCCTTCEEEEEEEEEETTEEEEEETTSTTCEEEEEGGGSCSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEEE
T ss_pred             CcccccCCCCCCEEEEEEEEEECcEEEEEECCCCCeEEEEEHHHcCcccccCHHhccCCCCEEEEEEEEEECCCCEEEEE
Confidence            45677888899999999999999999999987668999999999999999999999999999999999999999999999


Q ss_pred             EeecchhhHHHHHHhccccceEEEEEEecccccCCchHHHHHhhchhhHHhhcCHHHHHHHHhcCcchhhccCCCccccC
Q 044309          158 KRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTREVKEI  237 (259)
Q Consensus       158 lK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fve~~~~~~sw~l~~~~~~~~~~fk~a~~~~~~~l~~l~~~~~~~  237 (259)
                      +|++.++||....++|+.|+.+.|+|+++++++|+++++++..++|++.++||+++++|++|+++++++|.+| ++..+.
T Consensus        82 lk~~~~~~~~~~~~~~~~g~~v~g~v~~v~~~~G~~~ee~~~~~~w~l~~~~g~~~~afk~a~~~~~~~l~~l-i~~~~~  160 (275)
T 3aev_A           82 LRRVTQQQRKAKLQEFKRAQKAENLLRLAAEKLGKDFEAAWREVWVPLEEEWGEVYAAFEDAAKDGIEVLKGH-VPDEWL  160 (275)
T ss_dssp             STTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCHHHHHHHTHHHHHHHHSSHHHHHHHHHHHCGGGGBTT-BCGGGH
T ss_pred             EeecCcchhHHHHHhccCCCeEEEEEEEchhhcCCCHHHHHHHHHHHHHHHhCCHHHHHHHHhhcCcHHHHhh-CCHHHH
Confidence            9999999999999999999999999999997799999999999999999999999999999999777899999 876554


Q ss_pred             C
Q 044309          238 G  238 (259)
Q Consensus       238 ~  238 (259)
                      +
T Consensus       161 ~  161 (275)
T 3aev_A          161 P  161 (275)
T ss_dssp             H
T ss_pred             H
Confidence            4

>3cw2_C Translation initiation factor 2 subunit alpha; AIF2, intact AIF2, initiation factor 2 alpha subunit, initiation factor 2 beta subunit; 2.80A {Sulfolobus solfataricus} PDB: 2aho_B 3v11_B*

Probab=99.96  E-value=9.2e-31  Score=236.40  Aligned_cols=162  Identities=24%  Similarity=0.447  Sum_probs=151.0

Q ss_pred             hhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEE
Q 044309           78 RMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLS  157 (259)
Q Consensus        78 R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LS  157 (259)
                      ||+...++++|++|.|+|++|.+|||||+|++|++.+||||+||++++++.++++.+++||.|.|+|+++|+++++|+||
T Consensus         2 r~~~~~~~~vG~iv~G~V~~I~~~GaFV~l~e~~~~~GlihiSels~~~v~~~~~~~~vGd~V~VkVi~vd~~~g~I~LS   81 (266)
T 3cw2_C            2 IYSRSKLPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDVS   81 (266)
T ss_dssp             CCCSSSSCCTTCEEEEEEEECCSSSBEEEETTTTSEECBBCGGGSSCSSCCCHHHHSCTTCEEEEEECCCCSSSCCCBEE
T ss_pred             CccccccCCCCCEEEEEEEEEeccEEEEEEcCCCCeEEEEEhHHcCcccccCHHHhCcCCCEEEEEEEEEeCCCCEEEEE
Confidence            56777888899999999999999999999986678999999999999999999999999999999999999989999999


Q ss_pred             EeecchhhHHHHHHhccccceEEEEEEecccccCCchHHHHHhhchhhHHhhcCHHHHHHHHhcCcchhhccCCCccccC
Q 044309          158 KRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTREVKEI  237 (259)
Q Consensus       158 lK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fve~~~~~~sw~l~~~~~~~~~~fk~a~~~~~~~l~~l~~~~~~~  237 (259)
                      +|++.+++|..+.++|+.|+.+.++|+.+++.+|...++++.+++|+|.+.|++++++||+|+++++++|.++++++...
T Consensus        82 lk~~~~~~~~~~~~~~~~~~~~~~iv~~lae~~~~~~ee~~~~i~~~l~~~~~~~~~aFk~a~~~~~~~l~~~~i~~~~~  161 (266)
T 3cw2_C           82 LKKVTDDERRKKNLQWKKIQRLDKILELVSQKLKLSEKDAWEQVAWKLEAKYGDPITAIEKAVKEGEKILIDAGVPEIWV  161 (266)
T ss_dssp             STTSCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHTHHHHHTTSSCHHHHHHHHHHHCSHHHHTTTCCSTTH
T ss_pred             EEecchhhHHHHHHhccccCccceeeeehhhhCCCCHHHHHHHHHHHHHHHHhhHHHHHHHHhcCCchhhhhcCCCHHHH
Confidence            99999999999999999999999999999988998888899999999999999999999999996678999999876554


Q ss_pred             CC
Q 044309          238 GP  239 (259)
Q Consensus       238 ~~  239 (259)
                      ++
T Consensus       162 ~~  163 (266)
T 3cw2_C          162 KP  163 (266)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

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

Probab=99.85  E-value=1.6e-22  Score=184.10  Aligned_cols=138  Identities=17%  Similarity=0.121  Sum_probs=116.2

Q ss_pred             ccchhhhhh----hhc-ccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEE-EEccCCCEEEEEEcccccc
Q 044309           51 EFSRENAKA----KKL-SEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYV-SLLEYNNIEGMILFSELSR  124 (259)
Q Consensus        51 eid~e~~ri----K~l-~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV-~L~ey~~~eGllhisEls~  124 (259)
                      ++|+ ++||    |+. ..+||..          ....++ +|++|.|+|+++++||+|| .++  ++++||||.||++ 
T Consensus       123 ~iD~-~~Ri~ls~k~~~~~~~~~~----------~~~~~~-~G~~V~g~V~~i~~~G~fV~~i~--~g~~Glih~SEl~-  187 (285)
T 3go5_A          123 EVDK-KDRIWGLLAYQEDFQRLAR----------PAYNNM-QNQNWPAIVYRLKLSGTFVYLPE--NNMLGFIHPSERY-  187 (285)
T ss_dssp             EECT-TSCEEEEECCHHHHHHHCC----------CCCSCC-TTCEEEEEEEEEETTEEEEEETT--TTEEEEECGGGCS-
T ss_pred             EECC-CCcEEEEehhhhhcchhhh----------hhhhCC-CCCEEEEEEEEEeCCcEEEEEeC--CCeEEEEEHHHcc-
Confidence            6788 6785    443 4678986          566788 9999999999999999999 997  5899999999998 


Q ss_pred             ccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHHhccccceEEEEEEecccccCCchHHHHHhhchh
Q 044309          125 RRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGWP  204 (259)
Q Consensus       125 ~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fve~~~~~~sw~  204 (259)
                             +.+++||+|+|+|+++|++++||+||+|+....+++..++         .++..+.++.| +++  |+|.|.|
T Consensus       188 -------~~l~~Gd~v~~~V~~id~~d~kI~LSlk~~~~~~~~~~a~---------~il~~L~~~~G-~l~--~~DkS~p  248 (285)
T 3go5_A          188 -------AEPRLGQVLDARVIGFREVDRTLNLSLKPRSFEMLENDAQ---------MILTYLESNGG-FMT--LNDKSSP  248 (285)
T ss_dssp             -------SCCCTTCEEEEEEEEEETTTTEEEEECSCCCCCCCCHHHH---------HHHHHHHHTTT-EES--CCTTSCH
T ss_pred             -------ccCCCCCEEEEEEEEEECCCCeEEEEeChhhhhccchHHH---------HHHHHHHhcCC-eec--cCCCCCH
Confidence                   4689999999999999998999999999998776666553         23445655444 677  9999999


Q ss_pred             --hHHhhcCHHHHHHHHhcC
Q 044309          205 --LYWKYGHAFEAFKIIVTD  222 (259)
Q Consensus       205 --l~~~~~~~~~~fk~a~~~  222 (259)
                        |++.|+.++++||+|+|.
T Consensus       249 e~I~~~f~~SK~~FKrAiG~  268 (285)
T 3go5_A          249 DDIKATFGISKGQFKKALGG  268 (285)
T ss_dssp             HHHHHHHSSCHHHHHHHHHH
T ss_pred             HHHHHHhCcCHHHHHHHHHH
Confidence              999999999999999985

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

Probab=99.84  E-value=1.8e-21  Score=154.68  Aligned_cols=100  Identities=26%  Similarity=0.410  Sum_probs=83.9

Q ss_pred             hhhcccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccccc-ccccCccccccCC
Q 044309           59 AKKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSR-RRIRSVSSLIKVG  137 (259)
Q Consensus        59 iK~l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~-~~v~~~~~~~kvG  137 (259)
                      +|++..+||..          +...+. +|+++.|+|+++++||+||+|+  ++++||||+|++++ .++.++.+.+++|
T Consensus        13 ~k~~~~~p~~~----------~~~~~~-~G~~~~G~V~~v~~~G~FV~l~--~~~~Glvhisel~~~~~~~~~~~~~~vG   79 (115)
T 2khi_A           13 GLVPRGSHWVA----------IAKRYP-EGTKLTGRVTNLTDYGCFVEIE--EGVEGLVHVSEMDWTNKNIHPSKVVNVG   79 (115)
T ss_dssp             --------CCC----------SSCSSC-SSCEEEEEEEEEETTEEEEECS--TTCEEEEETTSSSCSSTTCSSTTTCCTT
T ss_pred             hhhcccCCHHH----------HhhcCC-CCCEEEEEEEEEECCEEEEEEC--CCCEEEEEHHHCCccccccCcccEECCC
Confidence            68899999997          555666 9999999999999999999997  58999999999998 4788899999999


Q ss_pred             CeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHH
Q 044309          138 RIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEE  171 (259)
Q Consensus       138 d~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~  171 (259)
                      |.|.|+|+++|.++++|.||+|++.++||++..+
T Consensus        80 d~V~vkV~~vd~~~~rI~lslk~~~~~p~~~~~~  113 (115)
T 2khi_A           80 DVVEVMVLDIDEERRRISLGLKQCKANPWQQFAE  113 (115)
T ss_dssp             CEEEEEEEEEETTTTEEEECCCCCCSSCCCCCCC
T ss_pred             CEEEEEEEEEECCCCEEEEEEEecCcCHHHHHHh
Confidence            9999999999998999999999999999986543

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

Probab=99.80  E-value=6.3e-20  Score=144.28  Aligned_cols=92  Identities=25%  Similarity=0.260  Sum_probs=79.2

Q ss_pred             hhhcccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCC
Q 044309           59 AKKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGR  138 (259)
Q Consensus        59 iK~l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd  138 (259)
                      +||+.++||..          +...+. +|++|.|+|+++++||+||+|+  ++++||||+|++++.++.++.+.|++||
T Consensus        14 iKq~~~~p~~~----------~~~~~~-~G~iv~G~V~~v~~~G~fV~l~--~~~~Gll~~sel~~~~~~~~~~~~~vGd   80 (109)
T 2khj_A           14 LVPRGSHMFNN----------WVALNK-KGAIVTGKVTAVDAKGATVELA--DGVEGYLRASEASRDRVEDATLVLSVGD   80 (109)
T ss_dssp             -------CHHH----------HTTTCC-SSSEEEEEEEEECSSCEEEECS--TTCBCCBCTTCCCSSSSSSGGGSCCTTC
T ss_pred             hhhcccCHHHH----------HhhcCC-CCCEEEEEEEEEECCeEEEEEC--CCCEEEEEHHHcCcccccChhhccCCCC
Confidence            78999999997          666676 9999999999999999999997  5899999999999999999999999999


Q ss_pred             eEEEEEEEEeCCCCeEEEEEeecch
Q 044309          139 IEPVMVLRVDKEKGYIDLSKRRVSE  163 (259)
Q Consensus       139 ~V~vkVi~vD~~~gkI~LSlK~~~~  163 (259)
                      .|.|+|+++|+++++|.||+|++.+
T Consensus        81 ~V~v~V~~vd~~~~ki~LS~k~~~~  105 (109)
T 2khj_A           81 EVEAKFTGVDRKNRAISLSVRAKDE  105 (109)
T ss_dssp             EEEEEEEEEETTTTEEEEETTSSSS
T ss_pred             EEEEEEEEEECCCCEEEEEEeecCh
Confidence            9999999999988899999998764

>1luz_A Protein K3, protein K2; stranded anti-parallel beta barrel, viral protein; 1.80A {Vaccinia virus} SCOP: b.40.4.5

Probab=99.79  E-value=1.3e-19  Score=137.97  Aligned_cols=79  Identities=28%  Similarity=0.460  Sum_probs=73.4

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcc-ccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecc
Q 044309           84 YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFS-ELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVS  162 (259)
Q Consensus        84 ~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhis-Els~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~  162 (259)
                      .+++|+++.|+|+ |++||+||+|.+|++++||||+| |++++++.++++.+ +||.|.|+|+++|+++++|+||+|++.
T Consensus         8 ~~~vG~~~~G~V~-v~~fG~FVel~~~~~~eGLvhis~el~~~~~~~~~~~~-~Gd~V~VkV~~vd~~~~kI~lslk~~~   85 (88)
T 1luz_A            8 LPNAGDVIKGRVY-EKDYALYIYLFDYPHFEAILAESVKMHMDRYVEYRDKL-VGKTVKVKVIRVDYTKGYIDVNYKRMC   85 (88)
T ss_dssp             CCCTTCEEEEEEE-EETTEEEEEETTCTTSEEEEGGGSSCCHHHHHHHHHHH-TTCEEEEEEEEEETTTTEEEEEEEEEC
T ss_pred             CCCCCCEEEEEEE-EEccEEEEEECCCCCeEEEEEeeHHhCcccccCHhHEe-CCCEEEEEEEEEECCCCEEEEEEeecC
Confidence            4458999999999 99999999998655899999999 99999999999999 999999999999999999999999987


Q ss_pred             hh
Q 044309          163 EE  164 (259)
Q Consensus       163 ~~  164 (259)
                      ++
T Consensus        86 ~~   87 (88)
T 1luz_A           86 RH   87 (88)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>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=99.75  E-value=1.4e-18  Score=139.06  Aligned_cols=96  Identities=16%  Similarity=0.179  Sum_probs=83.0

Q ss_pred             cccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEE
Q 044309           62 LSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEP  141 (259)
Q Consensus        62 l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~  141 (259)
                      +.+++|..          +...+. +|++|.|+|++|++|||||+|.. .+.+||||+|++++.++.++.+.|++||.|.
T Consensus         8 ~~~~~~~~----------~~~~~~-vG~iv~G~V~~I~~fGaFV~l~g-~~~~Glvhisel~~~~~~~~~~~~~~Gd~V~   75 (119)
T 2cqo_A            8 MNSGRPET----------MENLPA-LYTIFQGEVAMVTDYGAFIKIPG-CRKQGLVHRTHMSSCRVDKPSEIVDVGDKVW   75 (119)
T ss_dssp             SCCCCCCC----------SCCSCC-TTCEEEEEEEEEETTEEEEECTT-CSSCEEEEHHHHCSSCCSCHHHHCCTTCEEE
T ss_pred             ccccchhh----------hhcccC-CCCEEEEEEEEEeCceEEEEECC-CcEEEEEEHHHCCcccccChhhcCCCCCEEE
Confidence            45677775          554444 99999999999999999999952 1469999999999999999999999999999


Q ss_pred             EEEEEEeCCC--CeEEEEEeecchhhHHHH
Q 044309          142 VMVLRVDKEK--GYIDLSKRRVSEEDIQAC  169 (259)
Q Consensus       142 vkVi~vD~~~--gkI~LSlK~~~~~~~~~~  169 (259)
                      |+|+++|.++  ++|.||+|++.+++|+..
T Consensus        76 VkV~~vd~~~~~~~i~LSlk~~~~~~~~~~  105 (119)
T 2cqo_A           76 VKLIGREMKNDRIKVSLSMKVVNQGTGKDL  105 (119)
T ss_dssp             EEEEEEEECSSCEEEEEESTTBCSSSCCBS
T ss_pred             EEEEEEeccccCceEEEEEeecccCCcccc
Confidence            9999999754  799999999999888653

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

Probab=99.72  E-value=1.2e-17  Score=135.44  Aligned_cols=82  Identities=28%  Similarity=0.433  Sum_probs=76.7

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecc
Q 044309           83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVS  162 (259)
Q Consensus        83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~  162 (259)
                      .+. +|++|.|+|++|++|||||+|.  ++++||||+|++++.++.++.+.|++||.|.|+|+++|.++++|.||+|++.
T Consensus         4 ~~~-vG~iv~G~V~~i~~~G~FV~l~--~~~~Glihisel~~~~~~~~~~~~~vGd~V~vkV~~vd~~~~kI~LSlk~~~   80 (130)
T 2k4k_A            4 KFE-VGSVYTGKVTGLQAYGAFVALD--EETQGLVHISEVTHGFVKDINEHLSVGDEVQVKVLAVDEEKGKISLSIRATQ   80 (130)
T ss_dssp             CCC-TTCEEEEEEEEEETTEEEEEEE--TTEEEEEEGGGTSSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEEESHHHH
T ss_pred             cCC-CCCEEEEEEEEEeCCeEEEEEC--CCcEEEEEHHHCCcccccCccccCCCCCEEEEEEEEEeCCCCEEEEEEeecc
Confidence            344 8999999999999999999997  5899999999999999999999999999999999999998999999999998


Q ss_pred             hhhHH
Q 044309          163 EEDIQ  167 (259)
Q Consensus       163 ~~~~~  167 (259)
                      ++|+.
T Consensus        81 ~~p~~   85 (130)
T 2k4k_A           81 AAPEK   85 (130)
T ss_dssp             HSCCC
T ss_pred             cCccc
Confidence            87764

>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=99.70  E-value=3.7e-17  Score=127.40  Aligned_cols=81  Identities=25%  Similarity=0.331  Sum_probs=73.8

Q ss_pred             CCCcEEEEEEEEEeCceEEEEEccCC-CEEEEEEcccc-ccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecch
Q 044309           86 EVDMAVMIQVKNIADMGAYVSLLEYN-NIEGMILFSEL-SRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSE  163 (259)
Q Consensus        86 ~~G~iv~G~V~~I~~~GafV~L~ey~-~~eGllhisEl-s~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~  163 (259)
                      ++|+++.|+|++|++||+||+|.++. +++||||+||+ ++.++.++.+.|++||.|.|+|+++|.  ++|.||+|++.+
T Consensus        11 ~vG~i~~G~V~~v~~fG~FV~l~~~~~~~~Glvhisel~~~~~~~~~~~~~~~Gd~V~VkV~~vd~--~~i~LSlk~~~~   88 (103)
T 2eqs_A           11 TIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTG--TKTSLSMKDVDQ   88 (103)
T ss_dssp             CTTCEEEEEEEEECSSCEEEEECSSSSCCEEEECGGGTSSSSCCCCHHHHCCTTCEEEEEEEEEET--TEEEEESTTBCT
T ss_pred             CCCCEEEEEEEEEeccEEEEEEcCCCCCeEEEEEHHHCCCCcccCCcccEeCCCCEEEEEEEEEEC--CeeEEEEeeccc
Confidence            38999999999999999999997432 79999999999 677888999999999999999999997  699999999999


Q ss_pred             hhHHH
Q 044309          164 EDIQA  168 (259)
Q Consensus       164 ~~~~~  168 (259)
                      +||..
T Consensus        89 ~~~~~   93 (103)
T 2eqs_A           89 ETGED   93 (103)
T ss_dssp             TTCCB
T ss_pred             CCchh
Confidence            88864

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

Probab=99.70  E-value=1.2e-16  Score=118.92  Aligned_cols=71  Identities=21%  Similarity=0.256  Sum_probs=66.1

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecch
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSE  163 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~  163 (259)
                      +|+++.|+|+++++||+||+|+  ++++||||+||+++.++    +.+++||.|.|+|+++|+++++|+||++++.+
T Consensus         5 ~G~iv~G~V~~v~~~G~fV~l~--~~~~Gllh~sel~~~~~----~~~~~Gd~V~v~V~~vd~~~~~i~lsl~~~~~   75 (80)
T 2k52_A            5 PGKFYKGVVTRIEKYGAFINLN--EQVRGLLRPRDMISLRL----ENLNVGDEIIVQAIDVRPEKREIDFKYIPLEH   75 (80)
T ss_dssp             TTCEEEEEEEEEETTEEEEEEE--TTEEEEECGGGCSSCCG----GGCCTTCEEEEEEEEEETTTTEEEEEECSCC-
T ss_pred             CCCEEEEEEEEEeCCEEEEEEC--CCCEEEEEHHHCCcccc----eeeCCCCEEEEEEEEEECCCCEEEEEEeeccc
Confidence            8999999999999999999998  58999999999998765    78999999999999999988999999998875

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

Probab=99.61  E-value=6.9e-16  Score=140.38  Aligned_cols=99  Identities=17%  Similarity=0.040  Sum_probs=88.0

Q ss_pred             CCcEEEEEEEEEe-CceEEEEEccCC-CEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeec-ch
Q 044309           87 VDMAVMIQVKNIA-DMGAYVSLLEYN-NIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV-SE  163 (259)
Q Consensus        87 ~G~iv~G~V~~I~-~~GafV~L~ey~-~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~-~~  163 (259)
                      +|+++.|+|++++ +|||||+++  . +.+||||+||++|.+.    ..+++||.+.|. +.+|+ ++||.||+|+. ..
T Consensus        69 ~G~~~~g~V~~v~~~~GaFVdiG--~~~~d~lvp~sel~~~~~----~~~~~Gd~v~v~-l~iD~-~~Ri~ls~k~~~~~  140 (285)
T 3go5_A           69 QDQFGWGRVTEVRKDLGVFVDTG--LPDKEIVVSLDILPELKE----LWPKKGDQLYIR-LEVDK-KDRIWGLLAYQEDF  140 (285)
T ss_dssp             SSSCEEEEEEEEETTTEEEEECS--CTTCCEEEEGGGSCSSGG----GSCCTTCEEEEE-EEECT-TSCEEEEECCHHHH
T ss_pred             CCCEEEEEEEEEccCceEEEEEC--CCCcEEEEEHHHCCcccc----cccCCCCEEEEE-EEECC-CCcEEEEehhhhhc
Confidence            8999999999999 899999996  4 5899999999998644    346899999766 69998 79999999976 46


Q ss_pred             hhHHHHHHhccccceEEEEEEecccccCCch
Q 044309          164 EDIQACEERYNKSKLVHSIMRHVAETLGIDL  194 (259)
Q Consensus       164 ~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fv  194 (259)
                      ++|......|+.|+.++|+|.++++ +|+|+
T Consensus       141 ~~~~~~~~~~~~G~~V~g~V~~i~~-~G~fV  170 (285)
T 3go5_A          141 QRLARPAYNNMQNQNWPAIVYRLKL-SGTFV  170 (285)
T ss_dssp             HHHCCCCCSCCTTCEEEEEEEEEET-TEEEE
T ss_pred             chhhhhhhhCCCCCEEEEEEEEEeC-CcEEE
Confidence            8898888899999999999999987 99999

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=99.52  E-value=8.6e-16  Score=154.62  Aligned_cols=88  Identities=24%  Similarity=0.389  Sum_probs=0.0

Q ss_pred             hhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEee
Q 044309           81 EARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRR  160 (259)
Q Consensus        81 ~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~  160 (259)
                      ...+. +|++|.|+|++|++||+||+|.  ++++||||+||++++++.++.+.|++||.|.|+|+++|+ +++|+||+|+
T Consensus       632 ~~~~~-vG~v~~G~V~~I~~fGaFVel~--~g~eGLvHiSels~~rv~~~~d~~kvGD~V~VkVi~iD~-~grI~LS~K~  707 (726)
T 4aid_A          632 TDEAE-VGKIYDGKVVKVVDFGAFVNFF--GAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFDD-RGKTKLSMKV  707 (726)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hhhhc-CCcEEEEEEEEEeccEEEEEEC--CCcEEEEEHHHcCcccccCccccCCCCCEEEEEEEEECC-CCcEEEEEee
Confidence            33455 9999999999999999999997  689999999999999999999999999999999999998 7999999999


Q ss_pred             cchhhHHHHHHh
Q 044309          161 VSEEDIQACEER  172 (259)
Q Consensus       161 ~~~~~~~~~~~~  172 (259)
                      +.+++++...++
T Consensus       708 ~~~~~G~~~~~k  719 (726)
T 4aid_A          708 VDQETGEDLSKK  719 (726)
T ss_dssp             ------------
T ss_pred             cccCcchhhhhh
Confidence            999888776544

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A

Probab=99.48  E-value=8.6e-16  Score=155.48  Aligned_cols=86  Identities=24%  Similarity=0.396  Sum_probs=38.4

Q ss_pred             CCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccc----ccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeec
Q 044309           86 EVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSEL----SRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV  161 (259)
Q Consensus        86 ~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEl----s~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~  161 (259)
                      ++|++|.|+|+++++||+||+|.  ++++||||+|++    +|+++.++++.+++||.|+|+|+++|+ +++|+||+|++
T Consensus       666 ~vG~i~~G~V~~i~~fGaFV~l~--~g~eGLvHiSel~~~~s~~rv~~~~~~~~vGd~V~VkVi~vd~-~grI~LS~k~~  742 (757)
T 1e3p_A          666 EVGERILGSVVKTTTFGAFVSLL--PGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDS-RGKLSLIPVIE  742 (757)
T ss_dssp             -------CBEEECC-CSCEECCC-----CCCCC-------------------CCSSCBCCCCCCCCCS-SCC--------
T ss_pred             ccccEEEEEEEEccccEEEEEEc--CCcEEEEEhHHhccccCCCcccCcccccCCCCEEEEEEEEECC-CCCEEEEEecC
Confidence            39999999999999999999997  689999999999    999999999999999999999999998 89999999999


Q ss_pred             chhhHHHHHHhcc
Q 044309          162 SEEDIQACEERYN  174 (259)
Q Consensus       162 ~~~~~~~~~~~~~  174 (259)
                      .++||....++|.
T Consensus       743 ~~~pw~~~~~~~~  755 (757)
T 1e3p_A          743 GEEAASDEKKDDA  755 (757)
T ss_dssp             -------------
T ss_pred             CCCchhhhhhccc
Confidence            9999998766554

>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A

Probab=99.45  E-value=2.7e-13  Score=115.38  Aligned_cols=89  Identities=13%  Similarity=0.184  Sum_probs=78.6

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEEccC--------CCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeE
Q 044309           83 RYPEVDMAVMIQVKNIADMGAYVSLLEY--------NNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYI  154 (259)
Q Consensus        83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey--------~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI  154 (259)
                      ..|+ |++|.|+|++|.++||||+|..+        .+.+|+||+||+++.++.++++.|++||.|.|+|++     +++
T Consensus        54 y~p~-GdiV~G~V~~V~~~ga~V~I~~v~~~~~~~~~~~~Gll~isei~~~~~~~~~~~~~~GD~V~akVi~-----~~i  127 (179)
T 3m7n_A           54 EIVK-GDVVLGRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEISEAVGYLDILKARVIG-----DNL  127 (179)
T ss_dssp             CCCT-TCEEEEEEEEECSSEEEEEEEEETTCCSCCTTCEEEEEEGGGTTSSCCSSGGGTCCTTCEEEEEEEE-----TTT
T ss_pred             ccCC-CCEEEEEEEEEeCCcEEEEEccccCcccccccCeeEEEEHHHcCcchhhCHhhcCCCCCEEEEEEEC-----CeE
Confidence            4687 99999999999999999999721        079999999999999999999999999999999997     789


Q ss_pred             EEEEeecchhhHHHHHHhccccceEEEEEEecccccCCch
Q 044309          155 DLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDL  194 (259)
Q Consensus       155 ~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fv  194 (259)
                      .||+|+...                 |+|...+.++|..|
T Consensus       128 ~LS~k~~~l-----------------Gvv~a~~~~~g~~m  150 (179)
T 3m7n_A          128 RLSTKEEEM-----------------GVLRALCSNCKTEM  150 (179)
T ss_dssp             EEECCSTTC-----------------EEEECBCTTTCCBC
T ss_pred             EEEEecCCC-----------------CEEEecccccCCce
Confidence            999997543                 88888886688765

>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: b.40.4.5 d.230.1.1

Probab=99.45  E-value=4e-13  Score=114.40  Aligned_cols=81  Identities=16%  Similarity=0.315  Sum_probs=69.9

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccccccccc-----------CccccccCCCeEEEEEEEEeCCCC-
Q 044309           85 PEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIR-----------SVSSLIKVGRIEPVMVLRVDKEKG-  152 (259)
Q Consensus        85 ~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~-----------~~~~~~kvGd~V~vkVi~vD~~~g-  152 (259)
                      |.+|+++.|+|+++++||+||+|.   +.+||+|+|++++.++.           ++++.+++||.|.|+|+++|.+++ 
T Consensus        79 ~~~Gev~~G~V~~v~~~G~fV~l~---~~eglvhis~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~  155 (187)
T 1go3_E           79 PEMYELIEGEVVDVVEFGSFVRLG---PLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAER  155 (187)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEECS---SSEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEEECCC--
T ss_pred             cCCCCEEEEEEEEEeCcEEEEEEc---CccEEEEhHHhCCCcceECCccceEEecCCCeEEcCCCEEEEEEEEEEcccCC
Confidence            448999999999999999999995   59999999999987765           788999999999999999998644 


Q ss_pred             ----eEEEEEeecc--hhhHHH
Q 044309          153 ----YIDLSKRRVS--EEDIQA  168 (259)
Q Consensus       153 ----kI~LSlK~~~--~~~~~~  168 (259)
                          +|.||+++..  ..+|-+
T Consensus       156 p~~~~I~lS~k~~~LG~~~w~~  177 (187)
T 1go3_E          156 KRGSKIALTMRQPYLGKLEWIE  177 (187)
T ss_dssp             ---CEEEEECCSTTCEEHHHHH
T ss_pred             CCccEEEEEEcCCCCCcHHHHh
Confidence                9999999854  445543

>1wi5_A RRP5 protein homolog; S1 domain, OB-fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: b.40.4.5

Probab=99.44  E-value=2e-13  Score=108.56  Aligned_cols=78  Identities=18%  Similarity=0.221  Sum_probs=65.7

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccc-ccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeec
Q 044309           83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSEL-SRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV  161 (259)
Q Consensus        83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEl-s~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~  161 (259)
                      .+. +|+++.|+|++|++||+||+|.. ++.+|++|.++. +|.++.++++.|++||.|.|+|+++|.++++|.||+++.
T Consensus        18 ~l~-~G~i~~G~V~~v~~fG~fV~l~~-~~~~~l~~~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~i~Lslk~~   95 (119)
T 1wi5_A           18 ALK-PGMLLTGTVSSLEDHGYLVDIGV-DGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSVGHS   95 (119)
T ss_dssp             TCC-TTCEEEEEEEEECSSEEEEECCC-SSCEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCTTSCEEEEECCCC
T ss_pred             cCC-CCCEEEEEEEEEeCceEEEEECC-CCeEEEEEEecccccccccCccCEeCCCCEEEEEEEEEeCCCCEEEEEEchh
Confidence            455 99999999999999999999962 367777666664 345566788999999999999999999889999999976


Q ss_pred             c
Q 044309          162 S  162 (259)
Q Consensus       162 ~  162 (259)
                      .
T Consensus        96 ~   96 (119)
T 1wi5_A           96 E   96 (119)
T ss_dssp             C
T ss_pred             h
Confidence            4

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=99.44  E-value=9.1e-15  Score=147.46  Aligned_cols=85  Identities=31%  Similarity=0.514  Sum_probs=0.0

Q ss_pred             hcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeec
Q 044309           82 ARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV  161 (259)
Q Consensus        82 ~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~  161 (259)
                      ..+. +|++|.|+|+++.+||+||+|.  ++.+||||+|+++++++.++++.+++||.|+|+|+++|+ +++|+||+|++
T Consensus       623 ~~~~-vG~i~~G~V~~i~~fGaFVel~--~g~eGLvHiSel~~~~v~~~~~~~~vGd~V~VkVi~vd~-~grI~LS~k~~  698 (723)
T 3cdi_A          623 AEIE-VGRVYTGKVTRIVDFGAFVAIG--GGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDR-QGRIRLSIKEA  698 (723)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hhhh-cCcEEEEEEEEEecceEEEEeC--CCceEEEEHHHcCCccccCcccccCCCCEEEEEEEEECC-CCcEEEEEEec
Confidence            3444 9999999999999999999997  589999999999999999999999999999999999998 89999999999


Q ss_pred             chhhHHHHH
Q 044309          162 SEEDIQACE  170 (259)
Q Consensus       162 ~~~~~~~~~  170 (259)
                      .++++....
T Consensus       699 ~~~~g~~~~  707 (723)
T 3cdi_A          699 TEQSQPAAA  707 (723)
T ss_dssp             ---------
T ss_pred             cCCCCcccC
Confidence            888887653

>2nn6_I 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2

Probab=99.40  E-value=7.8e-13  Score=115.24  Aligned_cols=93  Identities=19%  Similarity=0.244  Sum_probs=79.4

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEEccC------CCEEEEEEcccccccccc--CccccccCCCeEEEEEEEEeCCCCeEE
Q 044309           84 YPEVDMAVMIQVKNIADMGAYVSLLEY------NNIEGMILFSELSRRRIR--SVSSLIKVGRIEPVMVLRVDKEKGYID  155 (259)
Q Consensus        84 ~~~~G~iv~G~V~~I~~~GafV~L~ey------~~~eGllhisEls~~~v~--~~~~~~kvGd~V~vkVi~vD~~~gkI~  155 (259)
                      .|++||+|.|+|++++++||||+|..+      .+.+|+||+||+++.++.  ++++.|++||.|.|+|++++..++++.
T Consensus        78 ~p~vGDvV~G~V~~v~~~~a~V~I~~v~~~~L~~~~~GlIhisei~~~~~~~~~~~~~l~~GD~V~akVisi~~~~~~i~  157 (209)
T 2nn6_I           78 LPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSNYL  157 (209)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEETTTTEEE
T ss_pred             CCCCCCEEEEEEEEEECceEEEEECccccccccCCceeEEEHHHcccccccccchhhhcCCCCEEEEEEEEEeCCCCeEE
Confidence            466999999999999999999998421      367999999999998888  899999999999999999998777999


Q ss_pred             EEEeecchhhHHHHHHhccccceEEEEEEecccccCCch
Q 044309          156 LSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDL  194 (259)
Q Consensus       156 LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fv  194 (259)
                      ||+|+...                 |+|...++. |..|
T Consensus       158 LS~k~~~l-----------------GVv~A~c~~-g~~m  178 (209)
T 2nn6_I          158 LTTAENEL-----------------GVVVAHSES-GIQM  178 (209)
T ss_dssp             EECCSSSC-----------------EECCCBCSS-SCBC
T ss_pred             EEEecCCC-----------------cEEEEEcCC-CCEE
Confidence            99998654                 777777764 5544

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

Probab=99.37  E-value=1.8e-12  Score=109.80  Aligned_cols=80  Identities=20%  Similarity=0.300  Sum_probs=67.3

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc-----------cCccccccCCCeEEEEEEEEeCC---
Q 044309           85 PEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI-----------RSVSSLIKVGRIEPVMVLRVDKE---  150 (259)
Q Consensus        85 ~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v-----------~~~~~~~kvGd~V~vkVi~vD~~---  150 (259)
                      |.+|+++.|+|+++++||+||++.   ..+||+|+|+++++++           ++..+.+++||.|+|||+++|.+   
T Consensus        79 p~~Gev~~G~V~~v~~~G~fv~l~---~~~glvh~s~l~~d~~~~d~~~~~~~g~~~~~~~~~Gd~VrvkV~~v~~~~~~  155 (180)
T 4ayb_E           79 PVVQEVVEGEVLQVDNYGVFVNLG---PMDGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISVASTVTG  155 (180)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEECS---SSEEEEEGGGSCSSCEEECSSSCCEEETTTCCCCCTTCEEEEEEEEECC----
T ss_pred             ccCCCEEEEEEeeeccceEEEEEC---CccceEEeeecCCCccccchhcceEEEeccCeEECCCCEEEEEEEEEeCCCCc
Confidence            348999999999999999999995   6899999999998766           56788999999999999999863   


Q ss_pred             -CCeEEEEEeecc--hhhHH
Q 044309          151 -KGYIDLSKRRVS--EEDIQ  167 (259)
Q Consensus       151 -~gkI~LSlK~~~--~~~~~  167 (259)
                       .++|.||+|+..  ..+|-
T Consensus       156 ~~~rI~ls~k~~gLG~~~W~  175 (180)
T 4ayb_E          156 RLPRIALTMRQPYLGKLEWI  175 (180)
T ss_dssp             ---CEEEECCSTTCEEHHHH
T ss_pred             ccCcEEEEcCCCCCCCChhH
Confidence             468999999843  44554

>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae}

Probab=99.35  E-value=1e-12  Score=138.45  Aligned_cols=77  Identities=10%  Similarity=0.134  Sum_probs=72.2

Q ss_pred             hcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccccccc-ccCccccccCCCeEEEEEEEEeCCCCeEEEEEee
Q 044309           82 ARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRR-IRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRR  160 (259)
Q Consensus        82 ~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~-v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~  160 (259)
                      +.+. +|++|.|+|++|++|||||+|+  +|++||||+|++++.+ +.++.+.|++||.|.|+|++||.++++|.||+|.
T Consensus       898 ~~l~-~G~iv~G~V~~V~~fGaFV~L~--~gveGLVHiSelsd~~~v~~p~~v~kvGd~V~vkVl~VD~~~~rI~LSlk~  974 (1219)
T 3psi_A          898 KTFF-KGSIIPVRVERFWHNDIICTTN--SEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAEVSLLD  974 (1219)
T ss_dssp             TTSC-TTCEEEEEEEEECSSCEEEECT--TSCEEEECTTSSSSTTSCSCSTTTSCTTCEEEEEEEEEEGGGTEEEEECCH
T ss_pred             hhCC-CCCEEEEEEEEEecceEEEEeC--CCceEEEEHHHcCCCcccCCHHHcCCCCCEEEEEEEEEECCCCEEEEEecH
Confidence            4566 8999999999999999999997  6899999999999998 8999999999999999999999999999999986


Q ss_pred             c
Q 044309          161 V  161 (259)
Q Consensus       161 ~  161 (259)
                      .
T Consensus       975 ~  975 (1219)
T 3psi_A          975 H  975 (1219)
T ss_dssp             H
T ss_pred             H
Confidence            4

>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} SCOP: a.60.2.6 a.60.2.6 a.294.1.1 b.40.4.5 c.55.3.13 PDB: 3bzk_A 2oce_A

Probab=99.32  E-value=6e-13  Score=135.16  Aligned_cols=77  Identities=26%  Similarity=0.396  Sum_probs=72.0

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecc
Q 044309           83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVS  162 (259)
Q Consensus        83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~  162 (259)
                      .+. +|++|.|+|++|++||+||+|+  .+.+||||+|++++.++.++.+.|++||.|.|+|+++|.++++|+||+|...
T Consensus       651 ~l~-vG~iv~G~V~~V~~fGaFV~l~--~~~eGLVhiS~Lsd~~v~d~~~~~~vGd~V~VkVi~VD~~~~rI~LSlk~~~  727 (785)
T 3bzc_A          651 DLK-PGMVLEGVVTNVTNFGAFVDIG--VHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGLSMRMSD  727 (785)
T ss_dssp             TCC-TTCBCCCEEEEEETTEEEEECS--SSSEEEEETTTSCSSCCSCHHHHCCTTCCCCCBEEEEETTTTEEEECCSSCC
T ss_pred             hcC-CCCEEEEEEEEEecCCeEEEeC--CCcEEEEEHHHcCccccCChhheeCCCCEEEEEEEEEECCCCEEEEEEecCC
Confidence            355 8999999999999999999997  5899999999999999999999999999999999999999999999999643

>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=99.31  E-value=3.4e-12  Score=111.71  Aligned_cols=89  Identities=13%  Similarity=0.025  Sum_probs=64.9

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCc----------cccccCCCeEEEEEEEEeCCCC--
Q 044309           85 PEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSV----------SSLIKVGRIEPVMVLRVDKEKG--  152 (259)
Q Consensus        85 ~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~----------~~~~kvGd~V~vkVi~vD~~~g--  152 (259)
                      |.+|+++.|+|+++++||+||+|+  + .+||||+|+|++.+.-++          ++.+++||.|+|+|+++|.+++  
T Consensus        81 p~vGev~~G~V~~vt~fG~FVelg--~-~dGlVhiS~l~d~~~~d~~~~~w~~~~~~~~~~~Gd~VrVkV~~vd~~~~~i  157 (215)
T 2b8k_G           81 PFKGEVVDGTVVSCSQHGFEVQVG--P-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSI  157 (215)
T ss_dssp             CCTTEEEEEEEEEEETTEEEEECT--T-SEEEEEGGGSCSSCCCBSSCSSCEEECSSCEEETTCEEEEEEEEEEEETTEE
T ss_pred             cCCCCEEEEEEEEEecceEEEEec--C-cEEEEEHHHCCccceeccccccceeeccccEECCCCEEEEEEEEEEcCCCcc
Confidence            348999999999999999999996  4 999999999986433222          2679999999999999998764  


Q ss_pred             -eEEEEEeecchhhHHHHHHhccccc
Q 044309          153 -YIDLSKRRVSEEDIQACEERYNKSK  177 (259)
Q Consensus       153 -kI~LSlK~~~~~~~~~~~~~~~~g~  177 (259)
                       +|. |+++....++.....+|+.+-
T Consensus       158 ~~Ig-Smk~~~LG~~~~~~~~~~~~~  182 (215)
T 2b8k_G          158 HAIG-SIKEDYLGAISHEKRRWKKNF  182 (215)
T ss_dssp             EEEE-ECCSTTCEEC-----------
T ss_pred             EEEE-EcCCCCCCCcchhhHHHHhhh
Confidence             677 898876666766555665443

>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae}

Probab=99.26  E-value=4.7e-13  Score=139.15  Aligned_cols=78  Identities=10%  Similarity=0.135  Sum_probs=0.0

Q ss_pred             hcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccccccc-ccCccccccCCCeEEEEEEEEeCCCCeEEEEEee
Q 044309           82 ARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRR-IRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRR  160 (259)
Q Consensus        82 ~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~-v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~  160 (259)
                      +.+. +|++|.|+|++|++|||||+|+  +|++||||+|++++.+ +.++.+.|++||.|.|+|++||.++++|.||+|.
T Consensus       901 ~~l~-~G~iv~G~V~~V~~fGaFV~L~--~gveGLVHiSelsd~~~v~~~~~v~kvGd~V~vkVl~VD~~~~rI~LSlk~  977 (1030)
T 3psf_A          901 KTFF-KGSIIPVRVERFWHNDIICTTN--SEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAEVSLLD  977 (1030)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHhc-CCCEEEEEEEEEccCeEEEEeC--CCcEEEEEHHHcCCCcccCCHHHcCCCCCEEEEEEEEEECCCCEEEEEech
Confidence            4555 8999999999999999999997  6899999999999988 8999999999999999999999989999999996


Q ss_pred             cc
Q 044309          161 VS  162 (259)
Q Consensus       161 ~~  162 (259)
                      ..
T Consensus       978 ~d  979 (1030)
T 3psf_A          978 HD  979 (1030)
T ss_dssp             --
T ss_pred             HH
Confidence            43

>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=99.23  E-value=2.5e-11  Score=102.15  Aligned_cols=65  Identities=11%  Similarity=-0.006  Sum_probs=54.0

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc----cCc------cccccCCCeEEEEEEEEeCCCC
Q 044309           85 PEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI----RSV------SSLIKVGRIEPVMVLRVDKEKG  152 (259)
Q Consensus        85 ~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v----~~~------~~~~kvGd~V~vkVi~vD~~~g  152 (259)
                      |.+|+++.|+|+++++||+||+|.  + .+||+|+|++++.+.    .++      ++.+++||.|+|+|+++|.+++
T Consensus        81 ~~~Gev~~G~V~~v~~fG~FV~l~--~-~dglvhis~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~  155 (171)
T 1y14_B           81 PFKGEVVDGTVVSCSQHGFEVQVG--P-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVS  155 (171)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEET--T-EEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEEEETT
T ss_pred             CCCCCEEEEEEEEEecCEEEEEec--C-eEEEEEHHHCCCCceECcccCceEEeccceEECCCCEEEEEEEEEEcCCC
Confidence            338999999999999999999996  5 999999999975422    111      2679999999999999998654

>2je6_I RRP4, exosome complex RNA-binding protein 1; nuclease, hydrolase, exonuclease, phosphorolytic, exoribonuclease, RNA degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1 PDB: 2jea_I* 2jeb_I* 3l7z_C

Probab=99.22  E-value=1.9e-11  Score=109.20  Aligned_cols=75  Identities=20%  Similarity=0.220  Sum_probs=68.6

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc---cCccccccCCCeEEEEEEEEeCCCCeEEEEEee
Q 044309           84 YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI---RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRR  160 (259)
Q Consensus        84 ~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v---~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~  160 (259)
                      .|++||+|.|+|+++.++||||+|.  .+.+|+||+|++++.+.   .++++.|++||.|.|+|++++. ++++.||+|+
T Consensus        71 ~p~~GDiV~G~V~~v~~~ga~VdI~--~~~~GlL~isei~~~~~~~~~~~~~~l~vGD~V~arVi~v~~-~~~i~LS~r~  147 (251)
T 2je6_I           71 YPKINDIVIGLVEDVEIYGWVVDIK--APYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDR-SIDPVLSVKG  147 (251)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECS--SSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEET-TEEEEEECCS
T ss_pred             CCCCCCEEEEEEEEEeCceEEEEcC--CCeEEEEEHHHhcCCccccccchhhcCCCCCEEEEEEEEECC-CCcEEEEEcc
Confidence            5679999999999999999999997  47999999999998777   8889999999999999999997 5899999985


Q ss_pred             c
Q 044309          161 V  161 (259)
Q Consensus       161 ~  161 (259)
                      .
T Consensus       148 ~  148 (251)
T 2je6_I          148 K  148 (251)
T ss_dssp             T
T ss_pred             c
Confidence            4

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

Probab=99.22  E-value=3.3e-11  Score=101.40  Aligned_cols=72  Identities=13%  Similarity=0.098  Sum_probs=58.5

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc----c--------CccccccCCCeEEEEEEEEeCCCC
Q 044309           85 PEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI----R--------SVSSLIKVGRIEPVMVLRVDKEKG  152 (259)
Q Consensus        85 ~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v----~--------~~~~~~kvGd~V~vkVi~vD~~~g  152 (259)
                      |.+|+++.|+|+++++||+||+|.   ..+||||+|++++.+.    .        +.++.+++||.|+|+|+++|.+++
T Consensus        79 ~~~Gev~~G~V~~v~~fG~fV~l~---~~~glvhis~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~  155 (172)
T 2c35_B           79 PFKGEVVDAVVTQVNKVGLFTEIG---PMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKN  155 (172)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEET---TEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEETT
T ss_pred             CCCCCEEEEEEEEEeCCEEEEEEC---CEEEEEEHHHCCCCcEECCCCCccEEEeCCCCEEECCCCEEEEEEEEEEcCCC
Confidence            348999999999999999999995   5789999999985422    2        125679999999999999998655


Q ss_pred             ---eEEEEEee
Q 044309          153 ---YIDLSKRR  160 (259)
Q Consensus       153 ---kI~LSlK~  160 (259)
                         ++. |+++
T Consensus       156 ~~~~ig-sm~~  165 (172)
T 2c35_B          156 DIFAIG-SLMD  165 (172)
T ss_dssp             EEEEEE-ECCS
T ss_pred             CcEEEE-EecC
Confidence               444 6665

>2ba0_A Archeal exosome RNA binding protein RRP4; RNAse PH, RNA degradation, exoribonuclease, S1domain, KH domain, archaeal; 2.70A {Archaeoglobus fulgidus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1

Probab=99.18  E-value=6.2e-11  Score=104.54  Aligned_cols=75  Identities=19%  Similarity=0.243  Sum_probs=68.1

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccc-cccCccccccCCCeEEEEEEEEeCCCCeEEEEEeec
Q 044309           84 YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRR-RIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV  161 (259)
Q Consensus        84 ~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~-~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~  161 (259)
                      .|++||+|.|+|+++.++||||+|.  ...+|+||+|+++.. ...++++.|++||.|.|+|++++. ++++.||+|+.
T Consensus        54 ~p~~GDiV~G~V~~v~~~~a~V~I~--~~~~g~l~isev~~~~~~~~~~~~l~~GD~V~arVi~v~~-~~~i~LS~r~~  129 (229)
T 2ba0_A           54 TPSVGDVVIGIIREVAANGWAVDIY--SPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDP-KMKVTLTMKDR  129 (229)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECS--SSSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECT-TCCEEEECCSS
T ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeC--CCeEEEEEHHHccccccccchhcccCCCCEEEEEEEEECC-CCcEEEEEccc
Confidence            5679999999999999999999997  468999999999974 678899999999999999999997 58999999864

>2z0s_A Probable exosome complex RNA-binding protein 1; alpha/beta protein, cytoplasm, structural genomics, NPPSFA; 3.20A {Aeropyrum pernix} SCOP: b.40.4.5 d.51.1.1

Probab=99.14  E-value=7.2e-11  Score=104.37  Aligned_cols=75  Identities=19%  Similarity=0.242  Sum_probs=66.9

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccc----cccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309           84 YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRR----RIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR  159 (259)
Q Consensus        84 ~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~----~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK  159 (259)
                      .|++||+|.|+|+++.++||||+|.  .+.+|+||+|+++.+    ...++++.|++||.|.|+|++++. .+++.||+|
T Consensus        63 ~p~~GDiV~G~V~~v~~~~~~V~I~--~~~~g~l~isei~~~~~~~~~~~~~~~l~~GD~V~a~Vi~v~~-~~~i~LS~k  139 (235)
T 2z0s_A           63 VPQAGDVVIGLIQSVGIMNWFVDIN--SPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDK-TRSPLLTVQ  139 (235)
T ss_dssp             CCCTTCCEEEEEEEECSSEEEEECS--SSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECT-TSCEEEECC
T ss_pred             CCCCCCEEEEEEEEEeCCeEEEEeC--CCeEEEEEHHHhCCCccccchhhHhhcCCCCCEEEEEEEEECC-CCcEEEEEe
Confidence            5679999999999999999999997  479999999999873    457788999999999999999997 579999998


Q ss_pred             ec
Q 044309          160 RV  161 (259)
Q Consensus       160 ~~  161 (259)
                      +.
T Consensus       140 ~~  141 (235)
T 2z0s_A          140 GE  141 (235)
T ss_dssp             SS
T ss_pred             cc
Confidence            54

>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=99.09  E-value=4.8e-11  Score=100.74  Aligned_cols=72  Identities=11%  Similarity=0.125  Sum_probs=59.3

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc----------cCccccccCCCeEEEEEEEEeCCCC--
Q 044309           85 PEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI----------RSVSSLIKVGRIEPVMVLRVDKEKG--  152 (259)
Q Consensus        85 ~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v----------~~~~~~~kvGd~V~vkVi~vD~~~g--  152 (259)
                      |.+|+++.|+|+++++||+||+|+   ..+||+|+|++++.+.          ++..+.+++||.|+|||+++|.+.+  
T Consensus        82 p~~Gev~~G~V~~v~~fG~FV~l~---~~~glVh~s~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~vd~~~~~~  158 (172)
T 3h0g_G           82 PFRGEVVDAIVTTVNKMGFFANIG---PLNVFVSSHLVPPDMKFDPTANPPNYSGEDQVIEKGSNVRLKIVGTRTDATEI  158 (172)
T ss_dssp             CCTTCEEECCCCEEETTEEECCBT---TBCCEEEGGGSCTTCCCBSSSSSCBEESSSCEECSSCCEEEEEEEEEESSSCE
T ss_pred             cCCCCEEEEEEEEEEcceEEEEeC---CeEEEEEHHHCCCccccCcccccceEecCCcEECCCCEEEEEEEEEECCCCCc
Confidence            338999999999999999999995   5789999999976433          3345789999999999999998764  


Q ss_pred             -eEEEEEee
Q 044309          153 -YIDLSKRR  160 (259)
Q Consensus       153 -kI~LSlK~  160 (259)
                       +|. |+|+
T Consensus       159 ~~Ig-tm~~  166 (172)
T 3h0g_G          159 FAIA-TMKE  166 (172)
T ss_dssp             EEEE-ECCS
T ss_pred             eEEE-EcCC
Confidence             455 6654

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

Probab=98.96  E-value=2.1e-09  Score=107.32  Aligned_cols=81  Identities=19%  Similarity=0.176  Sum_probs=67.4

Q ss_pred             hhhhhhhhcCCCCCc--EEEEEEEEEeCceEEEEEccCCCEEEEEEcccccc--ccc----------cCccccccCCCeE
Q 044309           75 LECRMYEARYPEVDM--AVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSR--RRI----------RSVSSLIKVGRIE  140 (259)
Q Consensus        75 ~~~R~~~~~~~~~G~--iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~--~~v----------~~~~~~~kvGd~V  140 (259)
                      ..|+++...   +|+  ++.|+|++|++||+||+|.+ .|++||||+|+++.  ++.          .+....+++||.|
T Consensus       549 ~~~~~l~~~---vGe~~~f~g~V~~V~~~G~fV~L~~-~gieGlVhis~l~~~~d~~~~d~~~~~l~~~~~~~~~lGD~V  624 (644)
T 2id0_A          549 LYARFLKDK---AGTDTRFAAEIVDISRGGMRVRLVD-NGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVI  624 (644)
T ss_dssp             HHHHHHGGG---TTSCCCEEEEEEEEETTEEEEEETT-TCCEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEE
T ss_pred             HHHHHhhhc---cCCCceEEEEEEEEeCCceEEEEcC-CcEEEEEEchhccCcCceeEEcccccEEEecCCCEeCCCCEE
Confidence            356666654   799  99999999999999999976 58999999999973  221          1445779999999


Q ss_pred             EEEEEEEeCCCCeEEEEEe
Q 044309          141 PVMVLRVDKEKGYIDLSKR  159 (259)
Q Consensus       141 ~vkVi~vD~~~gkI~LSlK  159 (259)
                      +|+|.++|.++++|++++-
T Consensus       625 ~VkV~~vd~~~~~I~~~l~  643 (644)
T 2id0_A          625 DVTIAEVRMETRSIIARPV  643 (644)
T ss_dssp             EEEEEEEETTTTEEEEEEC
T ss_pred             EEEEEEEeCCCCEEEEEEc
Confidence            9999999999999999874

>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A

Probab=98.77  E-value=4.1e-08  Score=91.24  Aligned_cols=66  Identities=20%  Similarity=0.162  Sum_probs=57.8

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCC--eEEEEEeec
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKG--YIDLSKRRV  161 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~g--kI~LSlK~~  161 (259)
                      +|++++|+|.+++++|+||++   ++.+|+||.+|++      +++.|++||+|+|.|++++.+++  +|.||++..
T Consensus       134 ~GeIV~G~V~ri~~~~v~VDl---Gk~EgiLp~sE~i------p~E~~~vGD~Vkv~V~~V~~~~kg~~I~LSRt~p  201 (344)
T 1hh2_P          134 KGTVTTAEVIRVMGEWADIRI---GKLETRLPKKEWI------PGEEIKAGDLVKVYIIDVVKTTKGPKILVSRRVP  201 (344)
T ss_dssp             TTCEEEEEEEEECSSEEEEEE---TTEEEEEEGGGSC------TTCCCCTTCEEEEEEEEEEEETTEEEEEEESSSH
T ss_pred             CCCEEEEEEEEEecCcEEEEe---CCeEEEEeHHHcC------CCcCCCCCCEEEEEEEEEEcCCCCcEEEEEeecc
Confidence            799999999999999999999   4899999999997      56789999999999999997544  666666643

>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe}

Probab=98.71  E-value=2.3e-08  Score=86.47  Aligned_cols=62  Identities=6%  Similarity=0.063  Sum_probs=54.2

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc-------------------cCccccccCCCeEEEEEEEE
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI-------------------RSVSSLIKVGRIEPVMVLRV  147 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v-------------------~~~~~~~kvGd~V~vkVi~v  147 (259)
                      +|+++.|+|++++++|+||+|+   .++|++|++++.++..                   ++.+..+++||.|+|||.++
T Consensus        81 ~GEv~~G~Vs~vt~~GifV~lg---~~eglv~~~~l~~d~~~fd~~~~~~v~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v  157 (203)
T 3ayh_B           81 RGEVMLGKIKSCSEEGIRVTIS---FFDDIFIPKDMLFDPCVFRPDERAWVWKIEGEDGSEGTELYFDIDEEIRFQIESE  157 (203)
T ss_dssp             TTCEEEEEEEEEETTEEEEECS---SCCCEEEEGGGBCTTEEEEGGGTEEEEEECCCTTSCCEEEECCTTCEEEEEEEEE
T ss_pred             CCCEEEEEEEEEeccEEEEEEe---CceEEEEcHHhCCCCceECccCceEEeecccccccccCCcEEcCCCEEEEEEEEE
Confidence            7999999999999999999994   6899999999976543                   45567799999999999999


Q ss_pred             eCCC
Q 044309          148 DKEK  151 (259)
Q Consensus       148 D~~~  151 (259)
                      +..+
T Consensus       158 ~~~~  161 (203)
T 3ayh_B          158 DFVD  161 (203)
T ss_dssp             EECC
T ss_pred             Eccc
Confidence            8753

>2vnu_D Exosome complex exonuclease RRP44; hydrolase-RNA complex, RNA degradation, RNA-binding, RNA Pro; HET: 1PE; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16

Probab=98.68  E-value=3.1e-08  Score=100.60  Aligned_cols=79  Identities=16%  Similarity=0.069  Sum_probs=57.6

Q ss_pred             hhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccc--cccc-----------cC----ccccccCCC
Q 044309           76 ECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELS--RRRI-----------RS----VSSLIKVGR  138 (259)
Q Consensus        76 ~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls--~~~v-----------~~----~~~~~kvGd  138 (259)
                      .|+++...   + +.+.|+|++|+++|+||.|.+ .+++|+||+|+++  ..+.           .+    ....|++||
T Consensus       662 ~~~~l~~~---~-~~~~g~V~~V~~~G~fV~l~~-~giEGlVhis~L~~~~d~~~fd~~~~~l~g~~~~~~~~~~~~lGD  736 (760)
T 2vnu_D          662 VGQVMRNN---E-STETGYVIKVFNNGIVVLVPK-FGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFD  736 (760)
T ss_dssp             HHHHHHTC---C-SEEEEEEEEEETTEEEEEETT-TTEEEEEEHHHHCSCGGGCEEETTTTEEEECCTTCSSCEEEETTC
T ss_pred             HHHHhhcC---c-eEEEEEEEEEECCeEEEEEeC-CCcEEEEEeccccCCCceeEEcccccEEEEecCCCccCcEEecCC
Confidence            45555544   4 799999999999999999986 3799999999996  3321           22    257899999


Q ss_pred             eEEEEEEEEeCC---CCeEEEEEe
Q 044309          139 IEPVMVLRVDKE---KGYIDLSKR  159 (259)
Q Consensus       139 ~V~vkVi~vD~~---~gkI~LSlK  159 (259)
                      .|+|+|+++|.+   +++|+||+|
T Consensus       737 ~V~VkV~~vd~~~~~~~kI~lslk  760 (760)
T 2vnu_D          737 KVEVQVRSVMDPITSKRKAELLLK  760 (760)
T ss_dssp             EEEEEEC--------CCEEEC---
T ss_pred             EEEEEEEEEECccccCCcEEEEeC
Confidence            999999999987   699999986

>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae}

Probab=98.65  E-value=2.7e-08  Score=87.07  Aligned_cols=64  Identities=13%  Similarity=0.019  Sum_probs=54.1

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc--------------cCccccccCCCeEEEEEEEEeCCCC
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI--------------RSVSSLIKVGRIEPVMVLRVDKEKG  152 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v--------------~~~~~~~kvGd~V~vkVi~vD~~~g  152 (259)
                      +|+++.|+|++++++|+||+|.  +.++|++|++++..+..              ++.+..+++||.|+|||.++|..++
T Consensus        81 vGEv~~G~Is~Vt~fGifVeL~--g~~eglv~~s~l~~d~~~fd~~~~~~vg~~~e~t~~~~~~Gd~VrvrV~~v~~~~~  158 (218)
T 2ckz_B           81 LGEIVTGWISKCTAEGIKVSLL--GIFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYFDVNEKIRFRIEREVFVDV  158 (218)
T ss_dssp             TTCEEEEEEEEEETTEEEEECT--TSCCCEEEETTTSCTTCEEETTTTEEEEECC--CEEEECTTCEEEEEEEEEEECCC
T ss_pred             CCCEEEEEEEEEccCcEEEEcc--CccceEEEcHHHCCCCcEEcCcCceEEeeccccCCcEEcCCCEEEEEEEEEEcccC
Confidence            7999999999999999999996  45899999999975432              3346779999999999999998654

>1yz7_A Probable translation initiation factor 2 alpha subunit; helical domain, alpha-beta domain; 2.26A {Pyrococcus abyssi}

Probab=98.59  E-value=2.2e-09  Score=92.06  Aligned_cols=69  Identities=22%  Similarity=0.324  Sum_probs=62.3

Q ss_pred             HHHHHhccccceEEEEEEecccccCCchHHHHHhhchhhHHhhcCHHHHHHHHhcCcchhhccCCCcccc
Q 044309          167 QACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTREVKE  236 (259)
Q Consensus       167 ~~~~~~~~~g~~v~g~V~~i~~~~G~fve~~~~~~sw~l~~~~~~~~~~fk~a~~~~~~~l~~l~~~~~~  236 (259)
                      .+..+.|+..+.++.++..+++++|..++++|..++|||+++|||+|+||+.|+.+++++|.++ +++..
T Consensus         4 r~Ki~~wk~~qkv~sil~~vAek~~~~~Eely~~i~w~L~~kyG~~ydaFk~av~~~~~vl~~l-ip~~~   72 (188)
T 1yz7_A            4 KAKLQEFKRAQKAENLLKLAAEKLGKDFETAWREVWVPLEEEWGEVYAAFEDAAKDGIDVLKGH-VPDEW   72 (188)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHTHHHHHHHHSSHHHHHHHHHHHCGGGSBTT-BCTTH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhCcHHHHHHHHHhcChHHHHHh-CCHHH
Confidence            4566888999999999999999999999999999999999999999999999999777899999 86543

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

Probab=98.58  E-value=1.1e-07  Score=92.75  Aligned_cols=62  Identities=13%  Similarity=0.220  Sum_probs=55.2

Q ss_pred             CCcEEEEEEEEEeCc--eEEEEEccCCCEEEEEEccccccccc---------cCccccccCCCeEEEEEEEEeCC
Q 044309           87 VDMAVMIQVKNIADM--GAYVSLLEYNNIEGMILFSELSRRRI---------RSVSSLIKVGRIEPVMVLRVDKE  150 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~--GafV~L~ey~~~eGllhisEls~~~v---------~~~~~~~kvGd~V~vkVi~vD~~  150 (259)
                      +|++|.|+|++|.++  ||||+++  .+..||||+||+++.++         .++.+.+++||.|.|+|++....
T Consensus        45 vGnIY~GkV~rv~p~~~aAFVdiG--~gk~gfLhisei~~~~~~~~~~~~~~~~i~d~lk~Gq~VlVQV~Ke~~g  117 (517)
T 2bx2_L           45 KANIYKGKITRIEPSLEAAFVDYG--AERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERG  117 (517)
T ss_dssp             TTCEEEEEEEEEETTTTEEEEESS--SSSCEEEEGGGSCGGGCC-------CCCGGGTCCTTCEEEEEEEECCCT
T ss_pred             CCCEEEEEEEEeccCCceEEEEeC--CCcEEEEEHHHcChhhhccccccccccchhhhccCCCEEEEEEEeeccc
Confidence            899999999999999  9999998  58999999999987663         35678899999999999997654

>2nn6_H Exosome complex exonuclease RRP4; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1

Probab=98.55  E-value=7.1e-08  Score=88.45  Aligned_cols=74  Identities=19%  Similarity=0.267  Sum_probs=61.9

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccc----ccc------CccccccCCCeEEEEEEEEeCCCCe
Q 044309           84 YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRR----RIR------SVSSLIKVGRIEPVMVLRVDKEKGY  153 (259)
Q Consensus        84 ~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~----~v~------~~~~~~kvGd~V~vkVi~vD~~~gk  153 (259)
                      .|++||+|.|+|+++.++|+||+|.  ....|++|+|+++..    |.+      ++++.|++||.|.|+|++++. ++.
T Consensus        92 ~P~vGDvViG~Vt~V~~~~a~VdI~--s~~~~~l~iS~v~f~gg~iR~~~~~D~~~m~~~l~vGDlV~ArVisv~~-~~~  168 (308)
T 2nn6_H           92 IGEVGDIVVGRITEVQQKRWKVETN--SRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFS-DGA  168 (308)
T ss_dssp             CCCSSBCCCEEEEEEETTEEEEECS--SSSCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEET-TTE
T ss_pred             CCCCCCEEEEEEEEEeCceEEEEEC--CCcCCceechhhccccceeecccchhhhhhhccCCCCCEEEEEEEEcCC-CCC
Confidence            6789999999999999999999996  358999999998752    222      345789999999999999996 689


Q ss_pred             EEEEEee
Q 044309          154 IDLSKRR  160 (259)
Q Consensus       154 I~LSlK~  160 (259)
                      +.||.|+
T Consensus       169 i~LStr~  175 (308)
T 2nn6_H          169 VSLHTRS  175 (308)
T ss_dssp             EEEECCS
T ss_pred             EEEEecC
Confidence            9999985

>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae}

Probab=98.53  E-value=1.1e-07  Score=98.97  Aligned_cols=79  Identities=16%  Similarity=0.088  Sum_probs=63.8

Q ss_pred             hhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccc--cccc-----------cC----ccccccCCC
Q 044309           76 ECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELS--RRRI-----------RS----VSSLIKVGR  138 (259)
Q Consensus        76 ~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls--~~~v-----------~~----~~~~~kvGd  138 (259)
                      .|+++...    |+++.|+|++|+++|+||.|.+ .|++|+||+|+++  .++.           ++    ....|++||
T Consensus       879 ~~~~l~~~----ge~~~g~V~~V~~~G~fV~L~~-~giEGlVhis~L~~~~d~y~fde~~~~L~g~~~~g~~~~~~~lGD  953 (977)
T 2wp8_J          879 VGQVMRNN----ESTETGYVIKVFNNGIVVLVPK-FGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFD  953 (977)
T ss_dssp             HHHHHHHT----TCEEEEEEEEECSSEEEEECTT-TCCEEEEEGGGTCSCGGGCEEETTTTEEEECCTTCCSCEEEETTC
T ss_pred             Hhhhhccc----ceEEEEEEEEEcCCeEEEEEcC-CCeEEEEEeccccCCCceeEEcccccEEEeecCCCccCcEEccCC
Confidence            45555432    8899999999999999999986 3799999999997  3321           22    357899999


Q ss_pred             eEEEEEEEEeCC---CCeEEEEEe
Q 044309          139 IEPVMVLRVDKE---KGYIDLSKR  159 (259)
Q Consensus       139 ~V~vkVi~vD~~---~gkI~LSlK  159 (259)
                      .|+|+|..+|.+   +++|.||+|
T Consensus       954 ~V~VkV~~vd~~~~~~~kI~Lslk  977 (977)
T 2wp8_J          954 KVEVQVRSVMDPITSKRKAELLLK  977 (977)
T ss_dssp             EEEEEECCCCCSSSCCCCCCEEEC
T ss_pred             EEEEEEEEEcCcccCCCceEEEeC
Confidence            999999999873   389999986

>2ja9_A Exosome complex exonuclease RRP40; RNA-binding protein, RNA, S1 domain, KH domain, hydrolase, RNA-binding, nuclear protein; 2.20A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.51.1.1

Probab=98.52  E-value=2.3e-07  Score=78.62  Aligned_cols=71  Identities=15%  Similarity=0.115  Sum_probs=62.7

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEEccCC-CEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEE
Q 044309           84 YPEVDMAVMIQVKNIADMGAYVSLLEYN-NIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSK  158 (259)
Q Consensus        84 ~~~~G~iv~G~V~~I~~~GafV~L~ey~-~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSl  158 (259)
                      .|++||+|.|.|+++..++++|+|.  + ...|+||++++. ...++.+..|++||.|.|+|..++. ++.+.||.
T Consensus         4 ~P~~gDvViG~V~~v~~~~~~VdI~--~~~~~a~L~~s~~~-g~~k~~r~~l~~GDlV~ArV~~~~~-~~~~~Ltc   75 (175)
T 2ja9_A            4 IPSVNDFVIGVIIGTFSDSYKVSLQ--NFSSSVSLSYMAFP-NASKKNRPTLQVGDLVYARVCTAEK-ELEAEIEC   75 (175)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEESS--TTSCCEEEETTSST-TCCSSSCCCCCTTCEEEEEEEECCT-TSCCEEES
T ss_pred             cCCCcCEEEEEEEEEECcEEEEEEC--CCCccEEEEHHHCC-chhhhhhccCCCCCEEEEEEEEecC-CCceEEEe
Confidence            5669999999999999999999997  5 599999999986 4456778899999999999999987 57899994

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1

Probab=98.45  E-value=6.4e-07  Score=83.74  Aligned_cols=78  Identities=14%  Similarity=-0.008  Sum_probs=63.5

Q ss_pred             CCCCcEEEEEEEE----EeCceEEEEEccCC---CEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEE
Q 044309           85 PEVDMAVMIQVKN----IADMGAYVSLLEYN---NIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLS  157 (259)
Q Consensus        85 ~~~G~iv~G~V~~----I~~~GafV~L~ey~---~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LS  157 (259)
                      ..+|++|+|+|.+    +.+.++||+|+  .   +.+|+||.+|+.      |++.|++||.|+|.|++|+.+.+...++
T Consensus       128 ~r~GeIVtG~V~r~~~~v~~~~v~VdLG--~~~~k~EgiLP~~Eqi------P~E~~~~GDrVkvyV~~V~~~~kgpqI~  199 (366)
T 1k0r_A          128 TREGEIVAGVIQRDSRANARGLVVVRIG--TETKASEGVIPAAEQV------PGESYEHGNRLRCYVVGVTRGAREPLIT  199 (366)
T ss_dssp             CCTTCEEEEEEECCHHHHHTTCEEEEEC--CSSSCEEEEECGGGSC------TTCCCCTTCEEEEEEEEEECCSSSCEEE
T ss_pred             hcCCCEEEEEEEEccccccCCeEEEEeC--CCccceEEEEcHHHcC------CCccCCCCCEEEEEEEEEecCCCccEEE
Confidence            3489999999999    99999999995  2   399999999987      4689999999999999999875555555


Q ss_pred             EeecchhhHHHHH
Q 044309          158 KRRVSEEDIQACE  170 (259)
Q Consensus       158 lK~~~~~~~~~~~  170 (259)
                      +.+..++...++.
T Consensus       200 LSRT~p~lv~~Lf  212 (366)
T 1k0r_A          200 LSRTHPNLVRKLF  212 (366)
T ss_dssp             EESSCHHHHHHHH
T ss_pred             EEeCChHHHHHHH
Confidence            5555666555543

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

Probab=98.39  E-value=2e-07  Score=72.03  Aligned_cols=42  Identities=24%  Similarity=0.409  Sum_probs=38.0

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc
Q 044309           83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI  127 (259)
Q Consensus        83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v  127 (259)
                      .+. +|+.|.++|+++++||+||+|.  ++++||||+|+++|.++
T Consensus        58 ~l~-~Ge~V~g~V~~i~~fG~fv~l~--~~~eGlvhis~i~~~~~   99 (101)
T 2bh8_A           58 NPQ-QGDRVEGKIKSITDFGIFIGLD--GGIDGLVHLSDISWAQA   99 (101)
T ss_dssp             CCC-TTCEEEEEEEECCSEEEEECTT--SCEEEEEEEEEEEECCC
T ss_pred             CCC-CCCEEEEEEEEeCCcEEEEEcC--CCceEEEEHHHCccCcC
Confidence            344 9999999999999999999997  58999999999999765

>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A

Probab=98.27  E-value=2e-06  Score=76.54  Aligned_cols=68  Identities=19%  Similarity=0.083  Sum_probs=59.9

Q ss_pred             CCcEEEEEEEE----EeCceEEEEEccCC---CEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCC--CeEEEE
Q 044309           87 VDMAVMIQVKN----IADMGAYVSLLEYN---NIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEK--GYIDLS  157 (259)
Q Consensus        87 ~G~iv~G~V~~----I~~~GafV~L~ey~---~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~--gkI~LS  157 (259)
                      +|++|+|+|.+    +.+..+||+|+  .   +.+|+||.+|+.      +++.|++||.++|.|++++...  ++|.||
T Consensus         7 ~GeIVtG~V~r~~~~v~~~~ViVdlG--~~~~k~EgiLP~~Eqi------p~E~~~~GDrIkayV~~V~~~~~gpqIiLS   78 (251)
T 2asb_A            7 EGEIVAGVIQRDSRANARGLVVVRIG--TETKASEGVIPAAEQV------PGESYEHGNRLRCYVVGVTRGAREPLITLS   78 (251)
T ss_dssp             TTCEEEEEEECCHHHHHTTCEEEEEC--SSSSCEEEEECGGGSC------TTCCCCTTCEEEEEEEEEECCSSSCEEEEE
T ss_pred             CCCEEEEEEEEccccccCCeEEEEeC--CCCcceEEEEcHHHcC------CCccCCCCCEEEEEEEEEEcCCCCCEEEEE
Confidence            89999999999    88889999995  2   499999999987      5688999999999999999864  689999


Q ss_pred             Eeecc
Q 044309          158 KRRVS  162 (259)
Q Consensus       158 lK~~~  162 (259)
                      +....
T Consensus        79 Rt~p~   83 (251)
T 2asb_A           79 RTHPN   83 (251)
T ss_dssp             SSCHH
T ss_pred             eccHH
Confidence            88653

>2nn6_G Exosome complex exonuclease RRP40; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1

Probab=97.90  E-value=1.9e-05  Score=71.79  Aligned_cols=74  Identities=9%  Similarity=-0.041  Sum_probs=64.0

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEee
Q 044309           83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRR  160 (259)
Q Consensus        83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~  160 (259)
                      ..|++||+|.|+|+++....+.|+|.  ....|+||.+++. ...+..+..|++||.|.|+|++++. .+.+.||...
T Consensus       123 YiP~vGDiVIG~Vt~v~~~~~~VdI~--s~~~a~L~~~~f~-Gatk~~r~~f~~GDlV~ArV~s~~~-~~~~eLsc~~  196 (289)
T 2nn6_G          123 YVPVKGDHVIGIVTAKSGDIFKVDVG--GSEPASLSYLSFE-GATKRNRPNVQVGDLIYGQFVVANK-DMEPEMVCID  196 (289)
T ss_dssp             CCCCSSEEEEEEEEEEETTEEEEECS--SSSCCCEESCSSS-CCSSCSSSSSCTTCEEEEEEEECCT-TSCCEEECSB
T ss_pred             CCCCCCCEEEEEEEEEeCcEEEEEEC--CCceeEEehhhcC-cchhhhhhhcCCCCEEEEEEEEcCC-CCceEEEecc
Confidence            35789999999999999999999997  5688999999876 3456788899999999999999986 5778998843

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

Probab=97.13  E-value=0.001  Score=51.00  Aligned_cols=57  Identities=14%  Similarity=0.074  Sum_probs=38.1

Q ss_pred             CCcEEEEEEEEE---eCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEE
Q 044309           87 VDMAVMIQVKNI---ADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRV  147 (259)
Q Consensus        87 ~G~iv~G~V~~I---~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~v  147 (259)
                      .++.++|+|+..   +.|| |+.-++ ++.++|+|+|++.+...  ....+++||.+.+.|.++
T Consensus        13 ~~~~~~G~Vk~fn~~kGfG-FI~~~~-gg~dvfvH~s~l~~~~~--~~~~l~~Ge~V~g~V~~i   72 (101)
T 2bh8_A           13 QSGKMTGIVKWFNADKGFG-FITPDD-GSKDVFVHFSAGSSGAA--VRGNPQQGDRVEGKIKSI   72 (101)
T ss_dssp             ---CEEEEEEEEEGGGTEE-EEEESS-SSCEEEEECCCSCSSSC--CCCCCCTTCEEEEEEEEC
T ss_pred             ccccceeEEEEEECCCCCE-EEEeCC-CCcEEEEEEEEEecCCc--cccCCCCCCEEEEEEEEe
Confidence            688899999988   6789 888764 56999999999997543  112244555555555444

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

Probab=96.63  E-value=0.00062  Score=52.53  Aligned_cols=49  Identities=10%  Similarity=0.002  Sum_probs=33.2

Q ss_pred             EEEEeecchhhHHHHHHhccccceEEEEEEecccccCCchH------HH--HHhhchh
Q 044309          155 DLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLE------EL--YVNIGWP  204 (259)
Q Consensus       155 ~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fve------~~--~~~~sw~  204 (259)
                      +-|+|++.++||+.....++.|+++.|+|+++.+ +|+|++      ++  .++++|.
T Consensus        11 ~~~iKq~~~~p~~~~~~~~~~G~iv~G~V~~v~~-~G~fV~l~~~~~Gll~~sel~~~   67 (109)
T 2khj_A           11 SSGLVPRGSHMFNNWVALNKKGAIVTGKVTAVDA-KGATVELADGVEGYLRASEASRD   67 (109)
T ss_dssp             ----------CHHHHTTTCCSSSEEEEEEEEECS-SCEEEECSTTCBCCBCTTCCCSS
T ss_pred             ccchhhcccCHHHHHhhcCCCCCEEEEEEEEEEC-CeEEEEECCCCEEEEEHHHcCcc
Confidence            4589999999999999999999999999999976 999983      33  6666663

>1jjg_A M156R; beta barrel, S1 motif, OB fold, MYXV156R, NESG project, structural genomics, EIF-2A homolog, PSI, protein structure initiative; NMR {Myxoma virus} SCOP: b.40.4.5

Probab=96.60  E-value=0.0093  Score=45.13  Aligned_cols=69  Identities=25%  Similarity=0.256  Sum_probs=52.9

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcc-ccccccccCccccccCCCeEEEEEEEEeCCCCeEEE
Q 044309           83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFS-ELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDL  156 (259)
Q Consensus        83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhis-Els~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~L  156 (259)
                      .+. .|++.+|.|+ +.+.-++|.|.+|+|.+|+|--. ++..++..+.++.+ +|..|+|+|+++|.-  .|++
T Consensus        29 ~~~-~g~VtkGiVy-~kd~~fyV~L~dY~glEaii~dYvnv~~dr~~klkkkL-VGKtIkVqVIRvD~l--YIDV   98 (102)
T 1jjg_A           29 DLS-PGSVHEGIVY-FKDGIFKVRLLGYEGHECILLDYLNYRQDTLDRLKERL-VGRVIKTRVVRADGL--YVDL   98 (102)
T ss_dssp             CCC-SSCEEEEEEE-EETTEEEEECTTTSSCEEEECTTCCSSCCCCCHHHHHH-TTCEEEEEEEEECSS--EEEE
T ss_pred             ccC-CCceEeeEEE-EeCCEEEEEecCCCCceeeeehhhhhhHHHHHHHHHHh-cCceEEEEEEEeccE--EEEE
Confidence            344 6999999997 57888999999998999997432 23334555555555 899999999999974  6665

>2r7d_A Ribonuclease II family protein; structural genomics, PSI-2, structure initiative, northeast structural genomics consort NESG; 1.80A {Deinococcus radiodurans R1} SCOP: b.40.4.5 b.40.4.16 PDB: 2r7f_A

Probab=96.46  E-value=0.0065  Score=58.37  Aligned_cols=67  Identities=13%  Similarity=0.106  Sum_probs=49.6

Q ss_pred             hhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEE
Q 044309           76 ECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYID  155 (259)
Q Consensus        76 ~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~  155 (259)
                      .|+++.+.   +|+.+.|.|++         +.   +.+|++|++++... . .....+++||.|.|+|.++|..+++|+
T Consensus       395 ~~~~l~~~---~g~~f~g~vv~---------l~---~~~glV~v~~l~~d-~-~~~~~~~lGd~V~V~v~~vd~~~~~i~  457 (469)
T 2r7d_A          395 TLRFIAAQ---PERVWDAVVVD---------RR---GAQATLLIPDLAFD-V-QVNTPAAPGTALQVQFADIDLPQMRVR  457 (469)
T ss_dssp             HHHHHHTC---TTCCEEEEEEE---------EE---TTEEEEEEGGGTEE-E-EEECCCCTTCEEEEEEEEEETTTTEEE
T ss_pred             HHHHHHhC---CCCEEEEEEEE---------Ee---CcEEEEEECCCCeE-E-ecCCcCCCCCEEEEEEEEEccCCCEEE
Confidence            45666553   79999988754         43   34788888887654 1 223579999999999999999999998


Q ss_pred             EEEe
Q 044309          156 LSKR  159 (259)
Q Consensus       156 LSlK  159 (259)
                      +...
T Consensus       458 f~~~  461 (469)
T 2r7d_A          458 ARSV  461 (469)
T ss_dssp             EEEC
T ss_pred             EEEE
Confidence            8653

>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=96.37  E-value=8.8e-07  Score=75.41  Aligned_cols=67  Identities=9%  Similarity=0.217  Sum_probs=56.5

Q ss_pred             Cccccchhhhh----hhhcccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeC-ceEEEEEccCCCEEEEEEcccc
Q 044309           48 TPFEFSRENAK----AKKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIAD-MGAYVSLLEYNNIEGMILFSEL  122 (259)
Q Consensus        48 ~~~eid~e~~r----iK~l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~-~GafV~L~ey~~~eGllhisEl  122 (259)
                      .++++|++++|    +|++.++||..          ..++|+ .|+.+.|+|+++++ ||  |+|.  ++++||+|+|++
T Consensus        71 kVl~vD~~~~rI~LSlk~~~~~p~~~----------~~~~~~-~g~~v~g~v~~i~~~~g--v~l~--~giegl~h~s~~  135 (182)
T 1kl9_A           71 VVIRVDKEKGYIDLSKRRVSPEEAIK----------CEDKFT-KSKTVYSILRHVAEVLE--YTKD--EQLESLFQRTAW  135 (182)
T ss_dssp             EEEEEETTTTEEEEESTTCCHHHHHH----------HHHHHH-HHHHHHHHHHHHHHHTT--CCSH--HHHHHHHHHTHH
T ss_pred             EEEEEECCCCEEEEEEeecCcChHHH----------HHHhcc-CCCEEEEEEEEchhhcC--Cccc--CChhheEEeeec
Confidence            34578999988    48999999987          777888 99999999999998 99  8887  489999999998


Q ss_pred             ccc-cccC
Q 044309          123 SRR-RIRS  129 (259)
Q Consensus       123 s~~-~v~~  129 (259)
                      +|. ++.+
T Consensus       136 ~~~~~~~~  143 (182)
T 1kl9_A          136 VFDDKYKR  143 (182)
T ss_dssp             HHHHHHTC
T ss_pred             chhhhcCC
Confidence            874 3444

>3d0f_A Penicillin-binding 1 transmembrane protein MRCA; BIG_1156.2, STR genomics, PSI-2, protein structure initiative; 1.64A {Nitrosomonas europaea atcc 19718}

Probab=95.43  E-value=0.055  Score=41.24  Aligned_cols=59  Identities=14%  Similarity=-0.080  Sum_probs=49.4

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc-----cC-ccccccCCCeEEEE
Q 044309           83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI-----RS-VSSLIKVGRIEPVM  143 (259)
Q Consensus        83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v-----~~-~~~~~kvGd~V~vk  143 (259)
                      .++..|+.+-|.|+++.+.++-|.+.  ++..+.|+.+.+.|.+-     +. +.+.+++||.|.|+
T Consensus        29 ~~~~~~~~~~AvV~~v~~~~~~v~~~--~g~~~~l~~~~~~WA~~~~~~~~~~~~~~l~~GdvI~V~   93 (106)
T 3d0f_A           29 DIGNSDDILAAVVLSATPGAVEAFRK--NGETIRITGDGLKAAHRFLSNDPKIGEKRIRPGALIRVK   93 (106)
T ss_dssp             TSCTTTTCEEEEEEEEETTEEEEEET--TSCEEEECGGGGSTTGGGTTTCTTTGGGSCCTTEEEEEE
T ss_pred             ccCccCCeEEEEEEEeCCCeEEEEEc--CCCeEEEcHHHChhhhhcccccccchhccCCCCCEEEEE
Confidence            34557999999999999999999997  46788899999999642     34 66789999999988

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A

Probab=95.41  E-value=0.0013  Score=66.65  Aligned_cols=105  Identities=12%  Similarity=0.180  Sum_probs=35.3

Q ss_pred             CCcEE--EEEEEE--EeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecc
Q 044309           87 VDMAV--MIQVKN--IADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVS  162 (259)
Q Consensus        87 ~G~iv--~G~V~~--I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~  162 (259)
                      .|+++  .|++.+  +.++|+||+++   . +|.+|++..++.......+.                    +.    .+.
T Consensus       609 i~~vIG~gGk~Ik~I~~~~G~~IdI~---~-dG~v~Is~~~~~~~~~a~~~--------------------i~----~i~  660 (757)
T 1e3p_A          609 IGEVIGPKRQMINQIQEDTGAEITIE---D-DGTIYIGAADGPAAEAARAT--------------------IN----GIA  660 (757)
T ss_dssp             ------------CTTCCCCCSCC------------CCCBSSHHHHCC---------------------------------
T ss_pred             eehcccccceeeehhhHhhCCEEEec---C-CceEEEecCCHHHHHHHHHH--------------------HH----Hhc
Confidence            56665  366666  57999999995   3 89999999887554332111                    10    011


Q ss_pred             hhhHHHHHHhccccceEEEEEEecccccCCch------HHH--HHhh----chhhHHhhcCHHHHHHHHhcCcchh-hcc
Q 044309          163 EEDIQACEERYNKSKLVHSIMRHVAETLGIDL------EEL--YVNI----GWPLYWKYGHAFEAFKIIVTDPDSV-LNS  229 (259)
Q Consensus       163 ~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fv------e~~--~~~~----sw~l~~~~~~~~~~fk~a~~~~~~~-l~~  229 (259)
                       +|     ..++.|+++.|+|+++.+ ||+||      ++|  .+++    +|.   ++.++.+.|    .-|+.+ .+-
T Consensus       661 -~p-----~~~~vG~i~~G~V~~i~~-fGaFV~l~~g~eGLvHiSel~~~~s~~---rv~~~~~~~----~vGd~V~VkV  726 (757)
T 1e3p_A          661 -NP-----TSPEVGERILGSVVKTTT-FGAFVSLLPGKDGLLHISQIRKLAGGK---RVENVEDVL----GVGQKVQVEI  726 (757)
T ss_dssp             ------------------CBEEECC--CSCEECCC---CCCCC----------------------C----CSSCBCCCCC
T ss_pred             -ch-----hhcccccEEEEEEEEccc-cEEEEEEcCCcEEEEEhHHhccccCCC---cccCccccc----CCCCEEEEEE
Confidence             12     467899999999999977 99998      344  8888    884   455555544    555544 333


Q ss_pred             CCCc
Q 044309          230 LTRE  233 (259)
Q Consensus       230 l~~~  233 (259)
                      ++++
T Consensus       727 i~vd  730 (757)
T 1e3p_A          727 AEID  730 (757)
T ss_dssp             CCCC
T ss_pred             EEEC
Confidence            3433

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

Probab=95.18  E-value=0.0017  Score=50.58  Aligned_cols=47  Identities=17%  Similarity=0.253  Sum_probs=31.7

Q ss_pred             EEEeecchhhHHHHHHhccccceEEEEEEecccccCCchH------HH--HHhhch
Q 044309          156 LSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLE------EL--YVNIGW  203 (259)
Q Consensus       156 LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fve------~~--~~~~sw  203 (259)
                      -|+|++..+||......++.|+++.|+|+.+.+ +|+|++      ++  .++++|
T Consensus        11 ~~~k~~~~~p~~~~~~~~~~G~~~~G~V~~v~~-~G~FV~l~~~~~Glvhisel~~   65 (115)
T 2khi_A           11 SSGLVPRGSHWVAIAKRYPEGTKLTGRVTNLTD-YGCFVEIEEGVEGLVHVSEMDW   65 (115)
T ss_dssp             ----------CCCSSCSSCSSCEEEEEEEEEET-TEEEEECSTTCEEEEETTSSSC
T ss_pred             cchhhcccCCHHHHhhcCCCCCEEEEEEEEEEC-CEEEEEECCCCEEEEEHHHCCc
Confidence            478999999999988899999999999999977 999983      33  677777

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=94.27  E-value=0.0078  Score=60.80  Aligned_cols=90  Identities=8%  Similarity=0.175  Sum_probs=0.0

Q ss_pred             CCcEEE--E-EEEEE-eCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecc
Q 044309           87 VDMAVM--I-QVKNI-ADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVS  162 (259)
Q Consensus        87 ~G~iv~--G-~V~~I-~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~  162 (259)
                      .|+++-  | +|.+| .++|+||+++    -+|.++++..++.......+                              
T Consensus       571 i~~~ig~gGk~I~~I~~~~G~~IdI~----~dg~v~I~~~~~~~~~~a~~------------------------------  616 (723)
T 3cdi_A          571 IKDVIGKGGSVIRALTEETGTTIEIE----DDGTVKIAATDGEKAKHAIR------------------------------  616 (723)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hcccccccceeeeeeehhhCceEEec----CCccEEEecCCHHHHHHHHH------------------------------
Confidence            455542  3 46666 5789999995    37899888766543322211                              


Q ss_pred             hhhHHHHHHhccccceEEEEEEecccccCCch------HHH--HHhhchhhHHhhcCHHHHH
Q 044309          163 EEDIQACEERYNKSKLVHSIMRHVAETLGIDL------EEL--YVNIGWPLYWKYGHAFEAF  216 (259)
Q Consensus       163 ~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fv------e~~--~~~~sw~l~~~~~~~~~~f  216 (259)
                        -++.....++.|+++.|+|+++.+ ||+|+      ++|  .++++|.   ++.++.+.|
T Consensus       617 --~i~~i~~~~~vG~i~~G~V~~i~~-fGaFVel~~g~eGLvHiSel~~~---~v~~~~~~~  672 (723)
T 3cdi_A          617 --RIEEITAEIEVGRVYTGKVTRIVD-FGAFVAIGGGKEGLVHISQIADK---RVEKVTDYL  672 (723)
T ss_dssp             --------------------------------------------------------------
T ss_pred             --HHHHHhhhhhcCcEEEEEEEEEec-ceEEEEeCCCceEEEEHHHcCCc---cccCccccc
Confidence              012223567899999999999977 99998      345  8888884   455555555

>2rf4_A DNA-directed RNA polymerase I subunit RPA4; transferase DNA/RNA, DNA-binding, phosphorylation, POL I, POLI, rpoli, nuclear protein; 3.10A {Saccharomyces cerevisiae}

Probab=94.05  E-value=0.2  Score=43.15  Aligned_cols=66  Identities=9%  Similarity=-0.085  Sum_probs=46.8

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCc------------cccccCCCeEEEEEEEEeCCCC
Q 044309           85 PEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSV------------SSLIKVGRIEPVMVLRVDKEKG  152 (259)
Q Consensus        85 ~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~------------~~~~kvGd~V~vkVi~vD~~~g  152 (259)
                      |.+|+++.|+|+.+++.|+.+-+.  +-...+||...|...+.-++            .+--++|+.|+++|.+++...+
T Consensus       127 Pf~GevL~G~V~~~s~~~Ig~~~~--G~Fn~~Ip~~~ip~~~~f~~~~~~~~~~~wv~~~~~~ig~~IRFrV~~~~~~~~  204 (214)
T 2rf4_A          127 PQVGDVLEGYIFIQSASHIGLLIH--DAFNASIKKNNIPVDWTFVHNDGNRSLGHWVDSNGEPIDGKLRFTVRNVHTTGR  204 (214)
T ss_dssp             CCTTCEEEEEECCCCSSCEEEEET--TTEEEEECSTTSCSSCBCCCCSCC-CCCCCBCSSCCBCCSEEEEEEEEEECCSS
T ss_pred             cCCCCEEEEEEEEECCCcEEEEEe--CCEEEEEcHHHCCCcccccccccccCCCceEcCCCCCCCCEEEEEEEEEEecCC
Confidence            448999999999999977766543  45788999998853321111            0112469999999999997433

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

Probab=90.68  E-value=0.015  Score=45.65  Aligned_cols=53  Identities=9%  Similarity=0.063  Sum_probs=39.3

Q ss_pred             ecchhhHHHHHHhccccceEEEEEEecccccCCchH-------HH--HHhhchhhHHhhcCHHHHH
Q 044309          160 RVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLE-------EL--YVNIGWPLYWKYGHAFEAF  216 (259)
Q Consensus       160 ~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fve-------~~--~~~~sw~l~~~~~~~~~~f  216 (259)
                      ++.+++|+.....++.|+++.|+|+++.+ ||+|++       +|  .++++|.   .+.++.+.|
T Consensus         7 ~~~~~~~~~~~~~~~vG~iv~G~V~~I~~-fGaFV~l~g~~~~Glvhisel~~~---~~~~~~~~~   68 (119)
T 2cqo_A            7 GMNSGRPETMENLPALYTIFQGEVAMVTD-YGAFIKIPGCRKQGLVHRTHMSSC---RVDKPSEIV   68 (119)
T ss_dssp             CSCCCCCCCSCCSCCTTCEEEEEEEEEET-TEEEEECTTCSSCEEEEHHHHCSS---CCSCHHHHC
T ss_pred             cccccchhhhhcccCCCCEEEEEEEEEeC-ceEEEEECCCcEEEEEEHHHCCcc---cccChhhcC
Confidence            34556677777788999999999999976 999972       23  7888884   455665555

>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=89.83  E-value=1.9  Score=31.11  Aligned_cols=63  Identities=16%  Similarity=0.155  Sum_probs=42.3

Q ss_pred             CcEEEEEEEEEe-CceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCe
Q 044309           88 DMAVMIQVKNIA-DMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGY  153 (259)
Q Consensus        88 G~iv~G~V~~I~-~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gk  153 (259)
                      .....|+|+... +.|. |+.-++ ++-+-|+|+|.+....-+.--..++.||.|.+.+..-  .+|.
T Consensus         6 ~~~~~G~Vkwfn~~kGfGFI~~~~-gg~DvFvH~s~i~~~~~~~g~~~l~~G~~V~f~~~~~--~kG~   70 (79)
T 1h95_A            6 ATKVLGTVKWFNVRNGYGFINRND-TKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEG--EKGA   70 (79)
T ss_dssp             EEEEEEEEEEEETTTTEEEEEEGG-GTEEEEEEGGGBCSCCCSCCSCSCCSSCEEEEEEEEC--SSSE
T ss_pred             ccccceEEEEEECCCCcEEEecCC-CCccEEEEhHHccccccccccccCCCCCEEEEEEEEC--CCCc
Confidence            557889999985 3343 555543 4799999999997531111124578999999987642  3454

>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=89.05  E-value=2.1  Score=31.71  Aligned_cols=53  Identities=11%  Similarity=0.060  Sum_probs=41.0

Q ss_pred             CCcEEEEEEEEEeCceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEE
Q 044309           87 VDMAVMIQVKNIADMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLR  146 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~  146 (259)
                      ......|+|+... .|. |+.-++ ++-+-|+|+|.+...     ...++.||.|.+.+..
T Consensus        15 ~~~~~~G~Vkwf~-KGfGFI~~dd-gg~DVFvH~s~i~~~-----~~~L~~G~~V~F~v~~   68 (89)
T 1wfq_A           15 AALRETGVIEKLL-TSYGFIQCSE-RQARLFFHCSQYNGN-----LQDLKVGDDVEFEVSS   68 (89)
T ss_dssp             CCCEEEEEEEEEC-SSEEEEEETT-TTEEEEEETTTCSSC-----TTTCCTTCCEEEEEEE
T ss_pred             cccccceEEEEEe-CCeeEEecCC-CCccEEEEhHHhhCc-----cCCCCCCCEEEEEEEE
Confidence            4568899999985 555 676664 459999999999743     2568899999999764

>3h8z_A FragIle X mental retardation syndrome-related Pro; tudor domains, FXR2, structura genomics, structural genomics consortium, SGC; 1.92A {Homo sapiens} PDB: 3o8v_A 3kuf_A 2bkd_N*

Probab=87.82  E-value=1.7  Score=34.63  Aligned_cols=58  Identities=14%  Similarity=0.003  Sum_probs=41.1

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEE
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMV  144 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkV  144 (259)
                      .|..+.|+|+.+.+.+++|....--..+--+|++++..-.-......|.+||+|+|-.
T Consensus        14 ~G~~y~a~V~~v~~d~~~V~f~n~w~~~~~vp~~~vRlpP~~~~~~~f~~gd~VEV~~   71 (128)
T 3h8z_A           14 NGAFYKGFVKDVHEDSVTIFFENNWQSERQIPFGDVRLPPPADYNKEITEGDEVEVYS   71 (128)
T ss_dssp             TSCEEEEEEEEECSSEEEEEETTCTTCCEEEEGGGEECCCCC----CCCTTCEEEEEE
T ss_pred             CCCEEEEEEEEEeCCcEEEEEccccCcceEechhhEEcCCCcccccCCCCCCEEEEEe
Confidence            5999999999999999999996201225677888876533333345689999999853

>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=86.97  E-value=1.2  Score=33.05  Aligned_cols=52  Identities=12%  Similarity=0.157  Sum_probs=40.4

Q ss_pred             CCcEEEEEEEEEeCceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEE
Q 044309           87 VDMAVMIQVKNIADMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVL  145 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi  145 (259)
                      .+....|+|+... .|. |+.-++ ++-+-|+|+|.+...     .+.++.||.|.+.+.
T Consensus        15 ~~~~~~G~Vk~f~-kGfGFI~~dd-gg~DvFvH~S~i~~~-----~~~L~~G~~V~F~~~   67 (88)
T 2yty_A           15 NSKRLLGYVATLK-DNFGFIETAN-HDKEIFFHYSEFSGD-----VDSLELGDMVEYSLS   67 (88)
T ss_dssp             SCCCEEEEEEEEC-SSEEEEECSS-SSCEEEEETTTCCSC-----TTTCCTTCEEEECCC
T ss_pred             CCCceeEEEEEEE-CCccEEecCC-CCceEEEEEhhhccc-----cCcCCCCCEEEEEEE
Confidence            4778999999986 355 666653 468999999999743     256889999998874

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

Probab=85.31  E-value=8.1  Score=27.46  Aligned_cols=59  Identities=12%  Similarity=0.111  Sum_probs=39.5

Q ss_pred             EEEEEEEEe-CceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309           91 VMIQVKNIA-DMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR  159 (259)
Q Consensus        91 v~G~V~~I~-~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK  159 (259)
                      ..|+|+... ..|. |+.-++ ++-+ |+|+|.+....      .++.||.|.+.+.. + .+|.-...++
T Consensus         3 ~~G~Vkwfn~~KGfGFI~~~d-g~~d-FvH~s~i~~~g------~l~~G~~V~F~~~~-g-~kG~~A~~V~   63 (74)
T 2k5n_A            3 MNGTITTWFKDKGFGFIKDEN-GDNR-YFHVIKVANPD------LIKKDAAVTFEPTT-N-NKGLSAYAVK   63 (74)
T ss_dssp             EEEEEEEEETTTTEEEEEESS-SCEE-EEEGGGBSSGG------GCCTTCEEEEEEEE-C-SSSEEEEEEE
T ss_pred             cceEEEEEECCCCeEEEecCC-CCce-EEEHhHcccCC------CCCCCCEEEEEEEe-C-CCCceeEEEE
Confidence            579999884 3343 555553 4566 99999997432      68999999999764 2 3564333333

>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=84.78  E-value=3.7  Score=28.89  Aligned_cols=52  Identities=12%  Similarity=0.170  Sum_probs=37.7

Q ss_pred             EEEEEEEEEe---CceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEE
Q 044309           90 AVMIQVKNIA---DMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRV  147 (259)
Q Consensus        90 iv~G~V~~I~---~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~v  147 (259)
                      ...|+|+...   .|| |+.-++ ++-+-|+|+|.+....    .+.++.||.|.+.+..-
T Consensus         5 ~~~G~Vk~fn~~kGfG-FI~~~~-g~~dvFvH~s~i~~~g----~~~l~~G~~V~f~~~~~   59 (71)
T 3i2z_B            5 KIKGNVKWFNESKGFG-FITPED-GSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNG   59 (71)
T ss_dssp             CEEEEEEEEETTTTEE-EEEETT-CCCCEEEEGGGBCCSS----CCCCCTTCEEEEEEEEE
T ss_pred             cccEEEEEEECCCCcE-EEecCC-CCccEEEEhHHccccc----CcCCCCCCEEEEEEEEC
Confidence            4679999885   345 566553 4589999999997432    23578999999987653

>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=84.42  E-value=3.8  Score=28.53  Aligned_cols=52  Identities=17%  Similarity=0.105  Sum_probs=37.1

Q ss_pred             EEEEEEEEe-CceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEE
Q 044309           91 VMIQVKNIA-DMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRV  147 (259)
Q Consensus        91 v~G~V~~I~-~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~v  147 (259)
                      ..|+|+... +.|. |+.-++ ++-+-|+|+|.+...-.    ..++.||.|...+..-
T Consensus         2 ~~G~Vk~fn~~kGfGFI~~~~-gg~dvFvH~s~i~~~g~----~~l~~G~~V~f~~~~~   55 (67)
T 3cam_A            2 ATGIVKWFNDAKGFGFITPDE-GGEDLFAHFSAINMEGF----KTLKEGQRVSFDVTTG   55 (67)
T ss_dssp             EEEEEEEEETTTTEEEEEETT-SCCCEEEEGGGBCGGGG----SSCCTTCEEEEEEEEE
T ss_pred             CCEEEEEEECCCCeEEEecCC-CCccEEEEHHHccccCC----CCCCCCCEEEEEEEEC
Confidence            368999884 3344 555553 46899999999974322    4578999999997653

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

Probab=83.23  E-value=4.1  Score=33.06  Aligned_cols=54  Identities=7%  Similarity=0.044  Sum_probs=40.8

Q ss_pred             CCcEEEEEEEEEe-CceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEE
Q 044309           87 VDMAVMIQVKNIA-DMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRV  147 (259)
Q Consensus        87 ~G~iv~G~V~~I~-~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~v  147 (259)
                      .|....|+|+-.. +.|. |+.-++ ++-+-|+|+|.+...      ..+..||.|.+.+...
T Consensus        59 ~g~m~~GtVKwFn~~KGfGFI~~dd-Gg~DVFVH~Sai~~~------~~L~eGq~V~Fev~~~  114 (147)
T 3aqq_A           59 QGPVYKGVCKCFCRSKGHGFITPAD-GGPDIFLHISDVEGE------YVPVEGDEVTYKMCSI  114 (147)
T ss_dssp             HSCCEEEEEEEEETTTTEEEEEESS-SCSCEEEEGGGEESS------BCCCTTCEEEEEEEEC
T ss_pred             cCCccceEEEEEeCCCCeEEeccCC-CCccEEEEeeeecCC------CcCCCCCEEEEEEEec
Confidence            5788999999984 3344 555553 458999999999632      2689999999998653

>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=83.09  E-value=1.4  Score=33.09  Aligned_cols=51  Identities=10%  Similarity=0.012  Sum_probs=39.7

Q ss_pred             CcEEEEEEEEEeCceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEE
Q 044309           88 DMAVMIQVKNIADMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVL  145 (259)
Q Consensus        88 G~iv~G~V~~I~~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi  145 (259)
                      .....|+|+.. ..|. |+.-++ ++-+-|+|+|.+...     ...++.||.|.+.+.
T Consensus        16 ~~~~~G~Vkwf-~KGfGFI~~dd-g~~DvFvH~s~i~~~-----~~~L~~G~~V~F~v~   67 (97)
T 2ytx_A           16 QARCQGVVCAM-KEAFGFIERGD-VVKEIFFHYSEFKGD-----LETLQPGDDVEFTIK   67 (97)
T ss_dssp             CCCEEEEECCC-CSSEEEEECSS-SCCCEEEETTTCCSC-----TTSCCSCCEEEEEEC
T ss_pred             CcceeEEEEEE-eCCceEEecCC-CCceEEEEehHhccc-----cCCCCCCCEEEEEEE
Confidence            56789999988 5565 666653 458999999999753     256889999999884

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

Probab=82.49  E-value=0.29  Score=35.09  Aligned_cols=32  Identities=9%  Similarity=0.122  Sum_probs=25.5

Q ss_pred             hccccceEEEEEEecccccCCchH------HH--HHhhchh
Q 044309          172 RYNKSKLVHSIMRHVAETLGIDLE------EL--YVNIGWP  204 (259)
Q Consensus       172 ~~~~g~~v~g~V~~i~~~~G~fve------~~--~~~~sw~  204 (259)
                      .++.|+++.|+|+++.+ +|+|++      ++  .++++|.
T Consensus         2 ~~~~G~iv~G~V~~v~~-~G~fV~l~~~~~Gllh~sel~~~   41 (80)
T 2k52_A            2 DVEPGKFYKGVVTRIEK-YGAFINLNEQVRGLLRPRDMISL   41 (80)
T ss_dssp             CCCTTCEEEEEEEEEET-TEEEEEEETTEEEEECGGGCSSC
T ss_pred             CCCCCCEEEEEEEEEeC-CEEEEEECCCCEEEEEHHHCCcc
Confidence            46889999999999976 999983      33  7777774

>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=82.45  E-value=6.7  Score=27.02  Aligned_cols=51  Identities=10%  Similarity=0.165  Sum_probs=36.8

Q ss_pred             EEEEEEEEe-CceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEE
Q 044309           91 VMIQVKNIA-DMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRV  147 (259)
Q Consensus        91 v~G~V~~I~-~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~v  147 (259)
                      ..|+|+... +.|. |+.-+  ++-+-|+|+|.+....    ...+..||.|...+..-
T Consensus         2 ~~G~Vk~fn~~kGfGFI~~~--~g~dvFvH~s~i~~~g----~~~l~~G~~V~f~~~~~   54 (66)
T 1c9o_A            2 QRGKVKWFNNEKGYGFIEVE--GGSDVFVHFTAIQGEG----FKTLEEGQEVSFEIVQG   54 (66)
T ss_dssp             EEEEEEEEETTTTEEEEEET--TEEEEEEEGGGBCSSS----CCCCCTTCEEEEEEEEE
T ss_pred             CceEEEEEECCCCeEEEecC--CCccEEEEHHHccccC----CCCCCCCCEEEEEEEEC
Confidence            479999885 3344 66665  3589999999997532    23478999999987643

>1luz_A Protein K3, protein K2; stranded anti-parallel beta barrel, viral protein; 1.80A {Vaccinia virus} SCOP: b.40.4.5

Probab=82.14  E-value=0.36  Score=35.60  Aligned_cols=39  Identities=5%  Similarity=0.099  Sum_probs=28.6

Q ss_pred             ccccceEEEEEEecccccCCchH--------HH--HH-hhchhhHHhhcCHHHHH
Q 044309          173 YNKSKLVHSIMRHVAETLGIDLE--------EL--YV-NIGWPLYWKYGHAFEAF  216 (259)
Q Consensus       173 ~~~g~~v~g~V~~i~~~~G~fve--------~~--~~-~~sw~l~~~~~~~~~~f  216 (259)
                      .+.|+++.|+|+ +.+ ||+|++        ++  .+ +++|.   .+.++.+.|
T Consensus         9 ~~vG~~~~G~V~-v~~-fG~FVel~~~~~~eGLvhis~el~~~---~~~~~~~~~   58 (88)
T 1luz_A            9 PNAGDVIKGRVY-EKD-YALYIYLFDYPHFEAILAESVKMHMD---RYVEYRDKL   58 (88)
T ss_dssp             CCTTCEEEEEEE-EET-TEEEEEETTCTTSEEEEGGGSSCCHH---HHHHHHHHH
T ss_pred             CCCCCEEEEEEE-EEc-cEEEEEECCCCCeEEEEEeeHHhCcc---cccCHhHEe
Confidence            468999999999 976 999872        23  67 88884   455555555

>3i4o_A Translation initiation factor IF-1; cytoplasm, protein biosynthesis; 1.47A {Mycobacterium tuberculosis} SCOP: b.40.4.5

Probab=80.43  E-value=2.9  Score=30.42  Aligned_cols=62  Identities=19%  Similarity=0.038  Sum_probs=43.0

Q ss_pred             cEEEEEEEEEeCceE-EEEEccCCCEEEEEEcccccc-ccccCccccccCCCeEEEEEEEEeCCCCeEEEE
Q 044309           89 MAVMIQVKNIADMGA-YVSLLEYNNIEGMILFSELSR-RRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLS  157 (259)
Q Consensus        89 ~iv~G~V~~I~~~Ga-fV~L~ey~~~eGllhisEls~-~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LS  157 (259)
                      -.+.|+|+...+.|. +|.++  +|..-++|++=--. .++     .+-+||.|.+.+...|..+|+|..-
T Consensus        14 ie~~G~Vik~l~n~~f~V~l~--nG~~~~c~i~GK~Rk~~I-----~Il~GD~V~ve~~~yd~~kgrIi~R   77 (79)
T 3i4o_A           14 IEVEGRVVEPLPNAMFRIELE--NGHKVLAHISGKMRQHYI-----RILPEDRVVVELSPYDLSRGRIVYR   77 (79)
T ss_dssp             SEEEEEEEEEETTTEEEEEET--TSCEEEEEECHHHHHTTC-----CCCTTCEEEEEEETTEEEEEEEEEE
T ss_pred             EEEEEEEEEEcCCCEEEEEeC--CCCEEEEEeCcceecCCc-----cCCCCCEEEEEECccCCCcEEEEEE
Confidence            357999999986665 58886  57677777764221 122     2679999999887666666777643

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

Probab=80.02  E-value=5.9  Score=27.95  Aligned_cols=51  Identities=12%  Similarity=0.170  Sum_probs=36.7

Q ss_pred             EEEEEEEEe-CceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEE
Q 044309           91 VMIQVKNIA-DMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRV  147 (259)
Q Consensus        91 v~G~V~~I~-~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~v  147 (259)
                      .+|+|+... ..|. |+.-+  ++-+-|+|+|.+...-.    ..+..||.|.+.+..-
T Consensus         2 ~~G~Vk~fn~~kGfGFI~~~--~g~dvFvH~s~i~~~g~----~~l~~G~~V~f~~~~~   54 (73)
T 3a0j_A            2 QKGRVKWFNAEKGYGFIERE--GDTDVFVHYTAINAKGF----RTLNEGDIVTFDVEPG   54 (73)
T ss_dssp             EEEEEEEEETTTTEEEEECT--TSCCEEEEGGGBCSSSC----SSCCTTCEEEEEEECC
T ss_pred             CCEEEEEEECCCCEEEEecC--CCCcEEEEhhhccccCC----CCCCCCCEEEEEEEEC
Confidence            479999885 3344 66655  36899999999974322    3578999999987643

---

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	259
d1q46a1	87	a.60.14.1 (A:89-175) Eukaryotic initiation factor	6e-35
d1kl9a1	94	a.60.14.1 (A:89-182) Eukaryotic initiation factor	4e-31
d2ahob1	91	a.60.14.1 (B:85-175) Eukaryotic initiation factor	1e-22
d1kl9a2	86	b.40.4.5 (A:3-88) Eukaryotic initiation factor 2al	3e-20
d2ahob2	84	b.40.4.5 (B:1-84) Eukaryotic initiation factor 2al	2e-14
d1e3pa2	62	b.40.4.5 (A:656-717) S1 RNA-binding domain of poly	2e-07
d1sroa_	76	b.40.4.5 (A:) S1 RNA-binding domain of polyribonuc	2e-07
d3bzka4	94	b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas ae	1e-06
d2z0sa1	88	b.40.4.5 (A:60-147) S1-domain of exosome complex R	3e-06
d1go3e1	106	b.40.4.5 (E:79-184) C-terminal domain of RNA polym	4e-06
d1luza_	85	b.40.4.5 (A:) Viral structural mimic of eIF2alpha	1e-04
d2nn6h1	95	b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-pro	3e-04
d2je6i1	87	b.40.4.5 (I:66-152) S1-domain of exosome complex R	0.001
d2ba0a1	83	b.40.4.5 (A:53-135) S1-domain of exosome complex R	0.003
d2ix0a3	87	b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Esche	0.004

>d1q46a1 a.60.14.1 (A:89-175) Eukaryotic initiation factor 2alpha, eIF2alpha, domain 2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 87

class: All alpha proteins
fold: SAM domain-like
superfamily: eIF2alpha middle domain-like
family: eIF2alpha middle domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, domain 2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  118 bits (297), Expect = 6e-35
 Identities = 40/77 (51%), Positives = 50/77 (64%), Gaps = 1/77 (1%)

Query: 161 VSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIV 220
           VS EDI  CEE+Y KSK VHSI+R+ AE   I LEELY  I WPL  K+GHA+EAFK+ +
Sbjct: 1   VSSEDIIKCEEKYQKSKTVHSILRYCAEKFQIPLEELYKTIAWPLSRKFGHAYEAFKLSI 60

Query: 221 TDPDSVLNSLTREVKEI 237
            D   V   +    K++
Sbjct: 61  IDET-VWEGIEPPSKDV 76

>d1kl9a1 a.60.14.1 (A:89-182) Eukaryotic initiation factor 2alpha, eIF2alpha, domain 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 94

class: All alpha proteins
fold: SAM domain-like
superfamily: eIF2alpha middle domain-like
family: eIF2alpha middle domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, domain 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  108 bits (272), Expect = 4e-31
 Identities = 35/86 (40%), Positives = 49/86 (56%), Gaps = 11/86 (12%)

Query: 161 VSEEDIQACEERYNKSKLVHSIMRHVAETL----GIDLEELYVNIGWPLYWKYGH----A 212
           VS E+   CE+++ KSK V+SI+RHVAE L       LE L+    W    KY      A
Sbjct: 1   VSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLFQRTAWVFDDKYKRPGYGA 60

Query: 213 FEAFKIIVTDPDSVLNSL--TREVKE 236
           ++AFK  V+DP S+L+SL    + +E
Sbjct: 61  YDAFKHAVSDP-SILDSLDLNEDERE 85

>d2ahob1 a.60.14.1 (B:85-175) Eukaryotic initiation factor 2alpha, eIF2alpha, domain 2 {Sulfolobus solfataricus [TaxId: 2287]} Length = 91

class: All alpha proteins
fold: SAM domain-like
superfamily: eIF2alpha middle domain-like
family: eIF2alpha middle domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, domain 2
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 87.0 bits (216), Expect = 1e-22
 Identities = 13/70 (18%), Positives = 34/70 (48%)

Query: 161 VSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIV 220
           V++++ +    ++ K + +  I+  V++ L +  ++ +  + W L  KYG    A +  V
Sbjct: 1   VTDDERRKKNLQWKKIQRLDKILELVSQKLKLSEKDAWEQVAWKLEAKYGDPITAIEKAV 60

Query: 221 TDPDSVLNSL 230
            + + +L   
Sbjct: 61  KEGEKILIDA 70

>d1kl9a2 b.40.4.5 (A:3-88) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 86

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]

 Score = 80.4 bits (198), Expect = 3e-20
 Identities = 62/86 (72%), Positives = 76/86 (88%)

Query: 75  LECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLI 134
           L CR Y+ ++PEV+  VM+ V++IA+MGAYVSLLEYNNIEGMIL SELSRRRIRS++ LI
Sbjct: 1   LSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLI 60

Query: 135 KVGRIEPVMVLRVDKEKGYIDLSKRR 160
           ++GR E V+V+RVDKEKGYIDLSKRR
Sbjct: 61  RIGRNECVVVIRVDKEKGYIDLSKRR 86

>d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]} Length = 84

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]

 Score = 64.7 bits (157), Expect = 2e-14
 Identities = 25/81 (30%), Positives = 49/81 (60%)

Query: 80  YEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRI 139
             ++ P     ++  VK + D G+YVSL EY  ++  + +SE+S + ++++  ++K  R 
Sbjct: 4   SRSKLPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRK 63

Query: 140 EPVMVLRVDKEKGYIDLSKRR 160
             V V+RVD+ KG +D+S ++
Sbjct: 64  VIVKVIRVDRRKGTVDVSLKK 84

>d1e3pa2 b.40.4.5 (A:656-717) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Streptomyces antibioticus [TaxId: 1890]} Length = 62

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: Streptomyces antibioticus [TaxId: 1890]

 Score = 45.1 bits (107), Expect = 2e-07
 Identities = 14/61 (22%), Positives = 29/61 (47%), Gaps = 6/61 (9%)

Query: 95  VKNIADMGAYVSLLEYNNIEGMILFSELSR----RRIRSVSSLIKVGRIEPVMVLRVDKE 150
           V      GA+VSL      +G++  S++ +    +R+ +V  ++ VG+   V +  +D  
Sbjct: 3   VVKTTTFGAFVSL--LPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSR 60

Query: 151 K 151
            
Sbjct: 61  G 61

>d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Escherichia coli [TaxId: 562]} Length = 76

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]

 Score = 45.1 bits (107), Expect = 2e-07
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 3/75 (4%)

Query: 85  PEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMV 144
            EV      +V  I D GA+V        EG++  S+++ +R+  V+  +++G+  PV V
Sbjct: 3   IEVGRVYTGKVTRIVDFGAFV--AIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKV 60

Query: 145 LRVDKEKGYIDLSKR 159
           L VD++ G I LS +
Sbjct: 61  LEVDRQ-GRIRLSIK 74

>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]} Length = 94

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]

 Score = 43.7 bits (103), Expect = 1e-06
 Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 2/78 (2%)

Query: 86  EVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVL 145
           +  M +   V N+ + GA+V +    + +G++  S LS + ++    ++K G I  V V+
Sbjct: 17  KPGMVLEGVVTNVTNFGAFVDI--GVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVM 74

Query: 146 RVDKEKGYIDLSKRRVSE 163
            VD  +  + LS R    
Sbjct: 75  EVDIPRNRVGLSMRMSDT 92

>d2z0sa1 b.40.4.5 (A:60-147) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Length = 88

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]

 Score = 42.6 bits (100), Expect = 3e-06
 Identities = 14/80 (17%), Positives = 31/80 (38%), Gaps = 7/80 (8%)

Query: 84  YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRS----VSSLIKVGRI 139
            P+    V+  ++++  M  +V +   +    ++   +   R        + SL+KVG  
Sbjct: 4   VPQAGDVVIGLIQSVGIMNWFVDI--NSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDY 61

Query: 140 EPVMVLRVDKEKGYIDLSKR 159
               V+  DK      L+ +
Sbjct: 62  IKAKVVAFDKT-RSPLLTVQ 80

>d1go3e1 b.40.4.5 (E:79-184) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 106

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]

 Score = 42.3 bits (99), Expect = 4e-06
 Identities = 15/109 (13%), Positives = 39/109 (35%), Gaps = 19/109 (17%)

Query: 85  PEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEP--- 141
           PE+   +  +V ++ + G++V       ++G+I  S++    +        +   E    
Sbjct: 1   PEMYELIEGEVVDVVEFGSFV---RLGPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKV 57

Query: 142 --------VMVLRVDKEK-----GYIDLSKRRVSEEDIQACEERYNKSK 177
                     ++ +  +        I L+ R+     ++  EE   K +
Sbjct: 58  LEIGDYVRARIVAISLKAERKRGSKIALTMRQPYLGKLEWIEEEKAKKQ 106

>d1luza_ b.40.4.5 (A:) Viral structural mimic of eIF2alpha {Vaccinia virus [TaxId: 10245]} Length = 85

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Viral structural mimic of eIF2alpha
species: Vaccinia virus [TaxId: 10245]

 Score = 37.8 bits (88), Expect = 1e-04
 Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 2/59 (3%)

Query: 104 YVSLLEYNNIEGMIL-FSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV 161
           Y+ L +Y + E ++    ++   R       + VG+   V V+RVD  KGYID++ +R+
Sbjct: 24  YIYLFDYPHFEAILAESVKMHMDRYVEYRDKL-VGKTVKVKVIRVDYTKGYIDVNYKRM 81

>d2nn6h1 b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of Ribosomal RNA-processing protein 4, RRP4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.8 bits (85), Expect = 3e-04
 Identities = 14/89 (15%), Positives = 31/89 (34%), Gaps = 14/89 (15%)

Query: 82  ARY-PEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELS----------RRRIRSV 130
            RY  EV   V+ ++  +      V     + ++ ++L S ++               ++
Sbjct: 2   TRYIGEVGDIVVGRITEVQQKRWKVETN--SRLDSVLLLSSMNLPGGELRRRSAEDELAM 59

Query: 131 SSLIKVGRIEPVMVLRVDKEKGYIDLSKR 159
              ++ G +    V  V    G + L  R
Sbjct: 60  RGFLQEGDLISAEVQAVFS-DGAVSLHTR 87

>d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 87

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]

 Score = 35.0 bits (80), Expect = 0.001
 Identities = 14/79 (17%), Positives = 29/79 (36%), Gaps = 6/79 (7%)

Query: 84  YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEP-- 141
           YP+++  V+  V+++   G  V +      +  +  S L  R I     L +   +    
Sbjct: 4   YPKINDIVIGLVEDVEIYGWVVDI--KAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYV 61

Query: 142 -VMVLRVDKEKGYIDLSKR 159
              +   D+      LS +
Sbjct: 62  IARIENFDRSID-PVLSVK 79

>d2ba0a1 b.40.4.5 (A:53-135) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 83

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]

 Score = 33.8 bits (77), Expect = 0.003
 Identities = 14/77 (18%), Positives = 31/77 (40%), Gaps = 4/77 (5%)

Query: 84  YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRR-RIRSVSSLIKVGRIEPV 142
            P V   V+  ++ +A  G  V    Y+  +  +  SE       +  + ++ +G     
Sbjct: 2   TPSVGDVVIGIIREVAANGWAVD--IYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIA 59

Query: 143 MVLRVDKEKGYIDLSKR 159
            VL +D +   + L+ +
Sbjct: 60  KVLNIDPK-MKVTLTMK 75

>d2ix0a3 b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]} Length = 87

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]

 Score = 33.2 bits (76), Expect = 0.004
 Identities = 14/74 (18%), Positives = 23/74 (31%), Gaps = 13/74 (17%)

Query: 95  VKNIADMGAYVSLLEYNNIEGMILFSELSRRR------------IRSVSSLIKVGRIEPV 142
           + +I+  G  V L++ N     I    L   R                 ++ KV  +  V
Sbjct: 11  IVDISRGGMRVRLVD-NGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDV 69

Query: 143 MVLRVDKEKGYIDL 156
            +  V  E   I  
Sbjct: 70  TIAEVRMETRSIIA 83

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	259
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.9
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.84
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	99.77
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	99.73
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	99.72
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	99.7
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	99.66
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	99.65
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	99.54
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	99.5
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	99.44
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	99.38
d1q46a1	87	Eukaryotic initiation factor 2alpha, eIF2alpha, do	99.25
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	99.22
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	99.21
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	99.12
d1kl9a1	94	Eukaryotic initiation factor 2alpha, eIF2alpha, do	99.1
d2ahob1	91	Eukaryotic initiation factor 2alpha, eIF2alpha, do	99.07
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	99.05
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	98.74
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	98.67
d1luza_	85	Viral structural mimic of eIF2alpha {Vaccinia viru	98.31
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	98.18
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	97.77
d1jjga_	102	Viral structural mimic of eIF2alpha {Myxoma virus,	97.09
d1wfqa_	89	Cold shock domain protein E1 (UNR) {Human (Homo sa	93.55
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	93.46
d1h95a_	79	Y-box protein 1 cold shock domain (YB1-CSD) {Human	92.63
d1k3ra1	71	Hypothetical protein MTH1 (MT0001), insert domain	92.17
d1c9oa_	66	Major cold shock protein {Bacillus caldolyticus [T	90.96
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	90.76
d1mjca_	69	Major cold shock protein {Escherichia coli [TaxId:	90.65
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	89.2
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	85.37
d2vnud2	88	Exosome complex exonuclease RRP44 {Saccharomyces c	85.14
d1e1oa1	143	Lysyl-tRNA synthetase (LysRS) {Escherichia coli, g	83.91

>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=99.90  E-value=4.8e-24  Score=159.58  Aligned_cols=86  Identities=72%  Similarity=1.171  Sum_probs=70.7

Q ss_pred             hhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeE
Q 044309           75 LECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYI  154 (259)
Q Consensus        75 ~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI  154 (259)
                      +.||||.+++|++|+++.|+|++++++|+||+|.+|++++||||+||++|.++.++.+.|++||.|.|+|+++|+++++|
T Consensus         1 ~~cr~~~~~~p~~G~iv~G~V~~i~~~G~fV~l~~~~~i~G~i~~sels~~~~~~~~~~~~~Gd~v~~kV~~vd~~~~ki   80 (86)
T d1kl9a2           1 LSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYI   80 (86)
T ss_dssp             CCCCSSSSSSCCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC------------CTTCEEEEEEEEEETTTTEE
T ss_pred             CeeeehhhcCCCCCCEEEEEEEEEeCCeEEEEEecCCCEEEEEEeeeccccccccceEEeecccEEEEEEEEEECCCCEE
Confidence            47999999999999999999999999999999987678999999999999999999999999999999999999999999


Q ss_pred             EEEEee
Q 044309          155 DLSKRR  160 (259)
Q Consensus       155 ~LSlK~  160 (259)
                      .||+|+
T Consensus        81 ~LS~Kq   86 (86)
T d1kl9a2          81 DLSKRR   86 (86)
T ss_dssp             EEESTT
T ss_pred             EEEeeC
Confidence            999985

>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=99.84  E-value=2.4e-21  Score=143.90  Aligned_cols=81  Identities=31%  Similarity=0.568  Sum_probs=71.8

Q ss_pred             hhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309           80 YEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR  159 (259)
Q Consensus        80 ~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK  159 (259)
                      +..++|++|+++.|+|++++++|+||+|.+|+|++||||.||++|.++.++.+.|++||.+.|+|+++|+++++|.||+|
T Consensus         4 ~~~~~p~~G~iv~G~V~~v~~~G~fV~l~~~~gi~Gli~~sels~~~~~~~~~~~~~G~~v~~kV~~vd~~~~~i~LS~K   83 (84)
T d2ahob2           4 SRSKLPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDVSLK   83 (84)
T ss_dssp             CSSSSCCTTCCCEEEEEEEETTEEEEEETTTTTEEEEECGGGCC-----CHHHHTCSSCEEECEEEEEETTTTEEEEESS
T ss_pred             ccccCCCCCCEEEEEEEEEECCEEEEEECCcCCEEEEEEccccccccccccceEeecccEEEEEEEEEECCCCEEEEEEc
Confidence            45578889999999999999999999998777899999999999999999999999999999999999999999999998


Q ss_pred             e
Q 044309          160 R  160 (259)
Q Consensus       160 ~  160 (259)
                      +
T Consensus        84 q   84 (84)
T d2ahob2          84 K   84 (84)
T ss_dssp             S
T ss_pred             C
Confidence            5

>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=99.77  E-value=1.4e-19  Score=132.13  Aligned_cols=72  Identities=32%  Similarity=0.561  Sum_probs=68.8

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeec
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV  161 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~  161 (259)
                      +|+++.|+|+++++||+||+|.  ++++||||+||++|.++.++++.|++||.+.|+|+++|+ ++||.||+|+.
T Consensus         5 vG~iv~G~V~~v~~~G~fV~l~--~~~~Glv~~sels~~~~~~~~~~~~~G~~v~v~Vi~id~-~~ri~LS~k~a   76 (76)
T d1sroa_           5 VGRVYTGKVTRIVDFGAFVAIG--GGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDR-QGRIRLSIKEA   76 (76)
T ss_dssp             TTSEEEEEEEEEETTEEEEECS--SSCCCBCCTTSSCSSCCSCHHHHCCTTCEEEEEEEECCT-TCCCEEEECCC
T ss_pred             CCCEEEEEEEEEeCcEEEEEeC--CCCEEEEEhHHhCccccCCHHHccCCCCEEEEEEEEECC-CCCEEEEEEcC
Confidence            8999999999999999999997  589999999999999999999999999999999999997 58999999973

>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=99.73  E-value=5.2e-18  Score=131.30  Aligned_cols=87  Identities=17%  Similarity=0.323  Sum_probs=76.3

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc-----------cCccccccCCCeEEEEEEEEeCCCCe
Q 044309           85 PEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI-----------RSVSSLIKVGRIEPVMVLRVDKEKGY  153 (259)
Q Consensus        85 ~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v-----------~~~~~~~kvGd~V~vkVi~vD~~~gk  153 (259)
                      |++|+++.|+|++|++||+||+|+   +++||||+|+|++.++           +++.+.|++||.|.|+|++||.++++
T Consensus         1 p~~gei~~g~V~~v~~~G~FVel~---~ieGlv~~s~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkV~~vd~~~~~   77 (106)
T d1go3e1           1 PEMYELIEGEVVDVVEFGSFVRLG---PLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAER   77 (106)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEECS---SSEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEEECCC--
T ss_pred             CCCCCEEEEEEEEEeeeEEEEEee---CeEEEEEeecccCceeeeccceeEEeecccccceeecceEEEEEEEEchhhcc
Confidence            468999999999999999999994   7999999999999776           47889999999999999999987765


Q ss_pred             -----EEEEEeecchhhHHHHHHhcc
Q 044309          154 -----IDLSKRRVSEEDIQACEERYN  174 (259)
Q Consensus       154 -----I~LSlK~~~~~~~~~~~~~~~  174 (259)
                           |.||+|+...+||+...+++.
T Consensus        78 ~~~~~i~ls~K~~~~~~~e~~~~~~~  103 (106)
T d1go3e1          78 KRGSKIALTMRQPYLGKLEWIEEEKA  103 (106)
T ss_dssp             ---CEEEEECCSTTCEEHHHHHHHHH
T ss_pred             ccCceeecccccCCCCcchhhhhHhh
Confidence                 889999999899988776543

>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=99.72  E-value=8.3e-18  Score=127.28  Aligned_cols=76  Identities=26%  Similarity=0.399  Sum_probs=72.7

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeec
Q 044309           83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV  161 (259)
Q Consensus        83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~  161 (259)
                      .+. +|+++.|+|+++.++|+||+|.  ++++||||.+++++.++.++++.|++||.|.|+|+++|+++++|.||+|+.
T Consensus        15 ~~k-~G~iv~g~V~~v~~~G~~V~l~--~~i~G~i~~~~ls~~~~~~~~~~~~vGq~v~~~V~~id~~~~~i~LS~K~~   90 (94)
T d3bzka4          15 DLK-PGMVLEGVVTNVTNFGAFVDIG--VHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGLSMRMS   90 (94)
T ss_dssp             GCC-TTCEEEEEEEEEETTEEEEECS--SSSCEEEEGGGGCSSCCSCHHHHCCTTCEEEEEEEEEETTTTEEEEESCTT
T ss_pred             cCC-CCCEEEEEEEEEECcEEEEEeC--CCceEEeehhhhhcccccChhhhhccCcEEEEEEEEEECCCCEEEEEEecc
Confidence            566 8999999999999999999997  689999999999999999999999999999999999999999999999975

>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=99.70  E-value=1.5e-17  Score=122.76  Aligned_cols=77  Identities=18%  Similarity=0.232  Sum_probs=70.4

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccccccc-ccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecc
Q 044309           84 YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRR-IRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVS  162 (259)
Q Consensus        84 ~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~-v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~  162 (259)
                      .|++|++|.|+|++++++|+||+|.  ++++||||+||+++.+ ..++++.|++||.|.|+|+++|+ +++|.||+|+..
T Consensus         2 ~Pk~Gd~V~G~V~~v~~~g~~V~i~--~~~~g~l~~se~s~~~~~~~~~~~~~vGd~V~~kV~~vd~-~~~i~LS~k~~~   78 (83)
T d2ba0a1           2 TPSVGDVVIGIIREVAANGWAVDIY--SPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDP-KMKVTLTMKDRI   78 (83)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECS--SSSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECT-TCCEEEECCSSS
T ss_pred             cCCCCCEEEEEEEEEECCEEEEecC--CCeeEEEecccccccccccChhhhcccccEEEEEEEEECC-CCCEEEEecCCC
Confidence            4679999999999999999999997  6899999999999865 67899999999999999999996 589999999875


Q ss_pred             h
Q 044309          163 E  163 (259)
Q Consensus       163 ~  163 (259)
                      .
T Consensus        79 ~   79 (83)
T d2ba0a1          79 C   79 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.66  E-value=1e-16  Score=119.45  Aligned_cols=75  Identities=20%  Similarity=0.219  Sum_probs=68.0

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccccccccc---CccccccCCCeEEEEEEEEeCCCCeEEEEEee
Q 044309           84 YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIR---SVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRR  160 (259)
Q Consensus        84 ~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~---~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~  160 (259)
                      .|++|++|.|+|++++++|+||+|.  ++++||||+|++++.++.   ++++.|++||.|.|+|+++|+ ++++.||+|+
T Consensus         4 ~Pk~Gdiv~G~V~~i~~~g~fV~i~--~~~~gll~~s~~~~~~~~~~~~~~~~~~~Gd~v~~kV~~vd~-~~~i~LS~k~   80 (87)
T d2je6i1           4 YPKINDIVIGLVEDVEIYGWVVDIK--APYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDR-SIDPVLSVKG   80 (87)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECS--SSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEET-TEEEEEECCS
T ss_pred             cCCCCCEEEEEEEEEECCEEEEEeC--CCEEEEEehHHhCCceeccccccchhhcccceEEEEEEEECC-CCCEEEEEec
Confidence            4679999999999999999999997  589999999999997664   577899999999999999997 5899999996


Q ss_pred             c
Q 044309          161 V  161 (259)
Q Consensus       161 ~  161 (259)
                      .
T Consensus        81 ~   81 (87)
T d2je6i1          81 K   81 (87)
T ss_dssp             T
T ss_pred             C
Confidence            5

>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=99.65  E-value=1.2e-16  Score=119.13  Aligned_cols=75  Identities=19%  Similarity=0.234  Sum_probs=68.3

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccccccccc----CccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309           84 YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIR----SVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR  159 (259)
Q Consensus        84 ~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~----~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK  159 (259)
                      .|++||+|.|+|++++++|+||+|.  ++.+||||.||+++.+++    ++++.|++||.|.|+|+++|+ ++++.||+|
T Consensus         4 ~Pk~GdvV~G~V~~v~~~g~fV~i~--~~~~g~l~~se~~~~~~~~~~~~~~~~~~vGd~V~~kV~~vd~-~~~i~Ls~k   80 (88)
T d2z0sa1           4 VPQAGDVVIGLIQSVGIMNWFVDIN--SPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDK-TRSPLLTVQ   80 (88)
T ss_dssp             CCCTTCCEEEEEEEECSSEEEEECS--SSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECT-TSCEEEECC
T ss_pred             CCCCCCEEEEEEEEEECCeEEEEeC--CCeEEEEehHHhCcccccccccchhhhcccCcEEEEEEEEECC-CCCEEEEEe
Confidence            5679999999999999999999997  589999999999997764    678899999999999999996 589999999


Q ss_pred             ec
Q 044309          160 RV  161 (259)
Q Consensus       160 ~~  161 (259)
                      +.
T Consensus        81 ~~   82 (88)
T d2z0sa1          81 GE   82 (88)
T ss_dssp             SS
T ss_pred             cC
Confidence            75

>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=99.54  E-value=5e-15  Score=116.41  Aligned_cols=80  Identities=18%  Similarity=0.222  Sum_probs=72.2

Q ss_pred             hcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccc-cccCccccccCCCeEEEEEEEEeCCCCeEEEEEee
Q 044309           82 ARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRR-RIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRR  160 (259)
Q Consensus        82 ~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~-~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~  160 (259)
                      +.+. +|+++.|+|++|+++|+||+|. +++++||||++++++. +..++.+.|++||.|.|+|+++|+.+++|.||+|+
T Consensus        17 ~~l~-~G~iv~G~V~~i~~~G~~V~lg-~~~~~G~l~~~els~~~~~~~~~~~~~vGq~v~~~V~~vd~~~~~i~LS~k~   94 (119)
T d1wi5a_          17 EALK-PGMLLTGTVSSLEDHGYLVDIG-VDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSVGH   94 (119)
T ss_dssp             TTCC-TTCEEEEEEEEECSSEEEEECC-CSSCEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCTTSCEEEEECCC
T ss_pred             hhcC-CCCEEEEEEEEEeccEEEEEEe-ccccceEEeHHHhccccccCCHHHhcccceEEEEEEEEEeCCCCEEEEEecH
Confidence            4566 8999999999999999999994 2589999999999986 47889999999999999999999999999999998


Q ss_pred             cch
Q 044309          161 VSE  163 (259)
Q Consensus       161 ~~~  163 (259)
                      ...
T Consensus        95 ~~~   97 (119)
T d1wi5a_          95 SEV   97 (119)
T ss_dssp             CCS
T ss_pred             HHh
Confidence            754

>d2nn6h1 b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-processing protein 4, RRP4 {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 Ribosomal RNA-processing protein 4, RRP4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.50  E-value=7.5e-15  Score=111.11  Aligned_cols=75  Identities=16%  Similarity=0.217  Sum_probs=65.2

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccc----------cccCccccccCCCeEEEEEEEEeCCCCe
Q 044309           84 YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRR----------RIRSVSSLIKVGRIEPVMVLRVDKEKGY  153 (259)
Q Consensus        84 ~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~----------~v~~~~~~~kvGd~V~vkVi~vD~~~gk  153 (259)
                      .|++|++|.|+|+++.++|+||+|.  +..+|+||+|+++|.          ++.++++.|++||.|.|+|+++|. +++
T Consensus         5 ~P~vGdiV~G~V~~v~~~g~~V~I~--~~~~g~l~is~i~~~~~~~rr~~~~~~~~~~~~~~~Gd~V~~kV~~v~~-dg~   81 (95)
T d2nn6h1           5 IGEVGDIVVGRITEVQQKRWKVETN--SRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFS-DGA   81 (95)
T ss_dssp             CCCSSBCCCEEEEEEETTEEEEECS--SSSCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEET-TTE
T ss_pred             cCCCCCEEEEEEEEEecCcEEEEeC--CCceEEEEHHHccccccccccccchhhhhhhhhcccccEEEEEEEEECC-CCC
Confidence            5779999999999999999999997  578999999999763          234567889999999999999998 699


Q ss_pred             EEEEEeec
Q 044309          154 IDLSKRRV  161 (259)
Q Consensus       154 I~LSlK~~  161 (259)
                      +.||+|..
T Consensus        82 i~Ls~r~~   89 (95)
T d2nn6h1          82 VSLHTRSL   89 (95)
T ss_dssp             EEEECCSS
T ss_pred             EEEEeccc
Confidence            99999864

>d1e3pa2 b.40.4.5 (A:656-717) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Streptomyces antibioticus [TaxId: 1890]}

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: Streptomyces antibioticus [TaxId: 1890]

Probab=99.44  E-value=8.3e-16  Score=107.95  Aligned_cols=56  Identities=27%  Similarity=0.517  Sum_probs=35.4

Q ss_pred             EEEEEEeCceEEEEEccCCCEEEEEEcccccc----ccccCccccccCCCeEEEEEEEEeCC
Q 044309           93 IQVKNIADMGAYVSLLEYNNIEGMILFSELSR----RRIRSVSSLIKVGRIEPVMVLRVDKE  150 (259)
Q Consensus        93 G~V~~I~~~GafV~L~ey~~~eGllhisEls~----~~v~~~~~~~kvGd~V~vkVi~vD~~  150 (259)
                      |+|++|++|||||+|.  ++++||||+|||++    .++.++++.|++||+|+|+|+++|++
T Consensus         1 G~V~~i~~fG~FV~l~--~g~~Glihiseis~~~~~~~v~~~~~~~~~G~~V~vkV~~iD~~   60 (62)
T d1e3pa2           1 GSVVKTTTFGAFVSLL--PGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSR   60 (62)
T ss_dssp             CBEEECC-CSCEECCC-----CCCCC-------------------CCSSCBCCCCCCCCCSS
T ss_pred             CEEEEEEeceEEEEec--CCceEEEEHHHcccccccccccCHHHhcCCCCEEEEEEEEEcCC
Confidence            7899999999999997  68999999999986    47889999999999999999999974

>d2ix0a3 b.40.4.5 (A:558-644) 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=99.38  E-value=9.4e-13  Score=98.06  Aligned_cols=69  Identities=22%  Similarity=0.166  Sum_probs=60.7

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc------------cCccccccCCCeEEEEEEEEeCCCCeE
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI------------RSVSSLIKVGRIEPVMVLRVDKEKGYI  154 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v------------~~~~~~~kvGd~V~vkVi~vD~~~gkI  154 (259)
                      .|+.+.|+|++|+++|+||+|.+ .+.+||||+|+|++++.            ++....|++||+|+|+|+++|+++++|
T Consensus         3 ~~~~F~g~Is~v~~~GifV~L~e-~~~eGlI~~s~L~~d~y~~d~~~~~l~~~~~~~~~~~~Gd~V~V~v~~vd~~~r~I   81 (87)
T d2ix0a3           3 TDTRFAAEIVDISRGGMRVRLVD-NGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETRSI   81 (87)
T ss_dssp             SCCCEEEEEEEEETTEEEEEETT-TCCEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEEEEEETTTTEE
T ss_pred             CCCEEEEEEEEEEcCeEEEEEec-CCcEEEEEehhCCCceEEEeccceEEEEEEcccEEEECCCEEEEEEEEEecccCeE
Confidence            57899999999999999999986 67999999999998643            223567999999999999999999999


Q ss_pred             EE
Q 044309          155 DL  156 (259)
Q Consensus       155 ~L  156 (259)
                      .+
T Consensus        82 ~~   83 (87)
T d2ix0a3          82 IA   83 (87)
T ss_dssp             EE
T ss_pred             EE
Confidence            75

>d1q46a1 a.60.14.1 (A:89-175) Eukaryotic initiation factor 2alpha, eIF2alpha, domain 2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: SAM domain-like
superfamily: eIF2alpha middle domain-like
family: eIF2alpha middle domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, domain 2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.25  E-value=2.6e-13  Score=100.77  Aligned_cols=70  Identities=56%  Similarity=0.913  Sum_probs=64.9

Q ss_pred             cchhhHHHHHHhccccceEEEEEEecccccCCchHHHHHhhchhhHHhhcCHHHHHHHHhcCcchhhccCC
Q 044309          161 VSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLT  231 (259)
Q Consensus       161 ~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fve~~~~~~sw~l~~~~~~~~~~fk~a~~~~~~~l~~l~  231 (259)
                      +.+++..+|.++|..++.|+.+++++++++|..++++|..++|||.++||++|+|||.|+.+|+ +|.+++
T Consensus         1 VS~edi~kCeery~K~K~V~sIlrhvAekl~~~lEeLy~~iaWpL~~kyG~aydaFk~av~dp~-vl~~l~   70 (87)
T d1q46a1           1 VSSEDIIKCEEKYQKSKTVHSILRYCAEKFQIPLEELYKTIAWPLSRKFGHAYEAFKLSIIDET-VWEGIE   70 (87)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHTHHHHHHHHSSHHHHHHHHHHCGG-GGTTCC
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHhhhhHhhcchHHHHHHHHhcCHH-HHccCc
Confidence            3567888999999999999999999999999999999999999999999999999999999965 888775

>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=99.22  E-value=4.1e-11  Score=89.05  Aligned_cols=67  Identities=12%  Similarity=0.002  Sum_probs=59.4

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc----------cCccccccCCCeEEEEEEEEeCCCCeEEE
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI----------RSVSSLIKVGRIEPVMVLRVDKEKGYIDL  156 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v----------~~~~~~~kvGd~V~vkVi~vD~~~gkI~L  156 (259)
                      +|+++.|+|++++++|+||+++   ..+||||.++|.+.+.          ++..+.++.||.|+|||+++|.++++|..
T Consensus         3 ~Gev~~g~I~~v~~~G~fv~lg---~~eg~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~~i~~   79 (91)
T d1y14b1           3 KGEVVDGTVVSCSQHGFEVQVG---PMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHA   79 (91)
T ss_dssp             TTCEEEEEEEEEETTEEEEEET---TEEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEEEETTEEEE
T ss_pred             CCCEEEEEEEEEEeeEEEEEEc---CeEEEEEhhhcCcceEEccccceeEecccCeEEeCCCEEEEEEEEEecccCccEE
Confidence            6999999999999999999995   6899999999987543          44567899999999999999998888865

>d2nn6g1 b.40.4.5 (G:107-194) S1-domain of exosome component 3 (RRP40) {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 exosome component 3 (RRP40)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.21  E-value=1.2e-11  Score=92.17  Aligned_cols=74  Identities=9%  Similarity=-0.037  Sum_probs=67.3

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeec
Q 044309           84 YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV  161 (259)
Q Consensus        84 ~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~  161 (259)
                      .|++||+|.|+|++++.+|+||+|.  +..+|+||++++. ..+++.+..+++||.|.|+|.++|. .+++.||....
T Consensus         3 ~P~~GD~ViG~V~~~~~~~~~VdI~--s~~~a~L~~~~f~-g~~k~~r~~l~~GD~V~arV~~v~~-~~~~~Lscvd~   76 (88)
T d2nn6g1           3 VPVKGDHVIGIVTAKSGDIFKVDVG--GSEPASLSYLSFE-GATKRNRPNVQVGDLIYGQFVVANK-DMEPEMVCIDS   76 (88)
T ss_dssp             CCCSSEEEEEEEEEEETTEEEEECS--SSSCCCEESCSSS-CCSSCSSSSSCTTCEEEEEEEECCT-TSCCEEECSBT
T ss_pred             cCCCCCEEEEEEEEEeCCeEEEEcC--CCeeEEEeHHHcC-ccccccCcccCCCCEEEEEEEEeCC-CCCEEEEEEcc
Confidence            5679999999999999999999998  5799999999996 5788889999999999999999997 68999998764

>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=99.12  E-value=1.4e-10  Score=86.72  Aligned_cols=67  Identities=10%  Similarity=0.057  Sum_probs=58.9

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc------------cCccccccCCCeEEEEEEEEeCCCCeE
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI------------RSVSSLIKVGRIEPVMVLRVDKEKGYI  154 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v------------~~~~~~~kvGd~V~vkVi~vD~~~gkI  154 (259)
                      .|+++.|+|++++++|+||+++   ..+||+|.+++.++..            ++....++.||.|++||++++.+.++|
T Consensus         4 ~Gev~~g~V~~v~~~G~fv~lg---~~~~~v~~~~l~~d~~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~~I   80 (94)
T d2c35b1           4 KGEVVDAVVTQVNKVGLFTEIG---PMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDI   80 (94)
T ss_dssp             TTCEEEEEEEEEETTEEEEEET---TEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEETTEE
T ss_pred             CCCEEEEEEEEEEeeEEEEEec---CceEEEEhhhcCcceeecccccceEEEcccceEEEeCCCEEEEEEEEEecCcCcc
Confidence            5999999999999999999994   6899999999998642            345567999999999999999988888


Q ss_pred             EE
Q 044309          155 DL  156 (259)
Q Consensus       155 ~L  156 (259)
                      ..
T Consensus        81 ~~   82 (94)
T d2c35b1          81 FA   82 (94)
T ss_dssp             EE
T ss_pred             eE
Confidence            63

>d1kl9a1 a.60.14.1 (A:89-182) Eukaryotic initiation factor 2alpha, eIF2alpha, domain 2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: eIF2alpha middle domain-like
family: eIF2alpha middle domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, domain 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.10  E-value=3.3e-12  Score=95.74  Aligned_cols=71  Identities=46%  Similarity=0.741  Sum_probs=63.8

Q ss_pred             cchhhHHHHHHhccccceEEEEEEecccccCCc----hHHHHHhhchhhHHhhcC----HHHHHHHHhcCcchhhccCCC
Q 044309          161 VSEEDIQACEERYNKSKLVHSIMRHVAETLGID----LEELYVNIGWPLYWKYGH----AFEAFKIIVTDPDSVLNSLTR  232 (259)
Q Consensus       161 ~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~f----ve~~~~~~sw~l~~~~~~----~~~~fk~a~~~~~~~l~~l~~  232 (259)
                      +.+++..+|.++|.+++.|+.+++++++.+|..    +|+||..++|||.++||+    +|+|||.|+.+|+ +|.+|++
T Consensus         1 VSpEdi~kCEery~KsK~VhSIlRhVAe~~~~~~~~~lE~LY~~iaWpl~~ky~~~g~~aydaFK~av~dp~-il~~l~l   79 (94)
T d1kl9a1           1 VSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDPS-ILDSLDL   79 (94)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSHHHHHHHHHHTHHHHHHHHTCTTHHHHHHHHHHHHCGG-GGTTSSC
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCccccHHHHHHHhhcccHHHhCCCCccHHHHHHHHhcCcc-ccccCCC
Confidence            356788899999999999999999999987764    799999999999999987    8999999999975 9999984

>d2ahob1 a.60.14.1 (B:85-175) Eukaryotic initiation factor 2alpha, eIF2alpha, domain 2 {Sulfolobus solfataricus [TaxId: 2287]}

class: All alpha proteins
fold: SAM domain-like
superfamily: eIF2alpha middle domain-like
family: eIF2alpha middle domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, domain 2
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.07  E-value=1.7e-12  Score=97.36  Aligned_cols=82  Identities=17%  Similarity=0.306  Sum_probs=75.1

Q ss_pred             cchhhHHHHHHhccccceEEEEEEecccccCCchHHHHHhhchhhHHhhcCHHHHHHHHhcCcchhhccCCCccccCCCC
Q 044309          161 VSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTREVKEIGPD  240 (259)
Q Consensus       161 ~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fve~~~~~~sw~l~~~~~~~~~~fk~a~~~~~~~l~~l~~~~~~~~~~  240 (259)
                      +.+++..++.+.|+..+.++.++..++++.|..++++|.+++|+|.++||++|+||+.|+.+|+++|.++++++...+|.
T Consensus         1 Vs~~qrr~k~~~~k~~qka~~il~~vAek~g~~~eely~~i~~~L~~kyg~lY~AFe~a~~~g~~~l~~~~i~~~~~~~l   80 (91)
T d2ahob1           1 VTDDERRKKNLQWKKIQRLDKILELVSQKLKLSEKDAWEQVAWKLEAKYGDPITAIEKAVKEGEKILIDAGVPEIWVKPL   80 (91)
T ss_dssp             CCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHTTHHHHTTTTSCHHHHHHHHHHSCTHHHHTTTCCTTTHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHCcHHHHHHHHHhcChhhHhhCCCCHHHHHHH
Confidence            35678889999999999999999999999999999999999999999999999999999999999999999998877665


Q ss_pred             Cc
Q 044309          241 GQ  242 (259)
Q Consensus       241 ~~  242 (259)
                      ..
T Consensus        81 ~e   82 (91)
T d2ahob1          81 LE   82 (91)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>d2ja9a1 b.40.4.5 (A:62-151) S1-domain of exosome component 3 (RRP40) {Saccharomyces cerevisiae [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome component 3 (RRP40)
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=99.05  E-value=1.5e-10  Score=86.31  Aligned_cols=75  Identities=16%  Similarity=0.030  Sum_probs=68.2

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeec
Q 044309           84 YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV  161 (259)
Q Consensus        84 ~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~  161 (259)
                      .|++||+|.|+|+++...|+||+|.  +...|++|.++...+..++.+..+++||.|.|+|.++|+ ++.+.||.+..
T Consensus         4 ~P~~gD~ViG~V~~~~~~~~~vdI~--~~~~~~L~~~~~f~g~~k~~r~~l~~GDlV~arV~~v~~-~~~~~Lsc~~~   78 (90)
T d2ja9a1           4 IPSVNDFVIGVIIGTFSDSYKVSLQ--NFSSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAEK-ELEAEIECFDS   78 (90)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEESS--TTSCCEEEETTSSTTCCSSSCCCCCTTCEEEEEEEECCT-TSCCEEESSCT
T ss_pred             cCCCCCEEEEEEEEEeCCcEEEEcC--CcchhhhhhhhccCccccccCCccCCCCEEEEEEEEECC-CCCEEEEEecc
Confidence            4679999999999999999999997  468999999988888889999999999999999999997 68999998754

>d1hh2p1 b.40.4.5 (P:127-198) S1 domain of NusA {Thermotoga maritima [TaxId: 2336]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 domain of NusA
species: Thermotoga maritima [TaxId: 2336]

Probab=98.74  E-value=3.2e-08  Score=70.59  Aligned_cols=62  Identities=19%  Similarity=0.153  Sum_probs=54.8

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCC--eEEEE
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKG--YIDLS  157 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~g--kI~LS  157 (259)
                      +|+++.|+|.++.+.+++|+|   ++.+|+||.+|..      |++.|++||.|+|-|.+|+...+  +|.||
T Consensus         8 ~geiv~G~V~r~~~~~~~Vdl---g~~eaiLp~~eqi------p~E~~~~Gdrik~~i~~V~~~~kgpqI~lS   71 (72)
T d1hh2p1           8 KGTVTTAEVIRVMGEWADIRI---GKLETRLPKKEWI------PGEEIKAGDLVKVYIIDVVKTTKGPKILVS   71 (72)
T ss_dssp             TTCEEEEEEEEECSSEEEEEE---TTEEEEEEGGGSC------TTCCCCTTCEEEEEEEEEEEETTEEEEEEE
T ss_pred             cCcEEEEEEEEEcCCCEEEEE---CCcEEECCHHHcC------CCCCCCCCCEEEEEEEEEEEcCCCCeEEEe
Confidence            899999999999999999999   4899999999976      56899999999999999986432  56666

>d2nn6i1 b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {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: Exosome component 1, EXOSC1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.67  E-value=4e-08  Score=77.09  Aligned_cols=93  Identities=19%  Similarity=0.219  Sum_probs=74.0

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEEccC------CCEEEEEEcccccc--ccccCccccccCCCeEEEEEEEEeCCCCeE
Q 044309           83 RYPEVDMAVMIQVKNIADMGAYVSLLEY------NNIEGMILFSELSR--RRIRSVSSLIKVGRIEPVMVLRVDKEKGYI  154 (259)
Q Consensus        83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey------~~~eGllhisEls~--~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI  154 (259)
                      -.|++||+|.|+|+++.+..|+|++.--      ....|++|.+++..  ....++.+.|++||.|.|+|+++...+..+
T Consensus         3 ~vP~vGDiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~g~i~~~dvr~te~d~~~m~~~fr~GDiV~A~Vis~~~~~~~~   82 (125)
T d2nn6i1           3 LLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSNY   82 (125)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEETTTTEE
T ss_pred             cCCCCCCEEEEEEEEecCCEEEEEEeEecCcccccCccccccHHHcccchhhhhhHHHhcCCCCEEEEEEEEccCCCccE
Confidence            3678999999999999999999999410      14779999999853  344568899999999999999998766679


Q ss_pred             EEEEeecchhhHHHHHHhccccceEEEEEEecccccCCc
Q 044309          155 DLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGID  193 (259)
Q Consensus       155 ~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~f  193 (259)
                      .||.++-.                 -|.|...++ .|..
T Consensus        83 ~Lst~~~~-----------------LGVv~A~c~-~g~~  103 (125)
T d2nn6i1          83 LLTTAENE-----------------LGVVVAHSE-SGIQ  103 (125)
T ss_dssp             EEECCSSS-----------------CEECCCBCS-SSCB
T ss_pred             EEEecCCC-----------------cEEEEEECC-CCCE
Confidence            99988643                 277777776 4543

>d1luza_ b.40.4.5 (A:) Viral structural mimic of eIF2alpha {Vaccinia virus [TaxId: 10245]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Viral structural mimic of eIF2alpha
species: Vaccinia virus [TaxId: 10245]

Probab=98.31  E-value=1.2e-06  Score=63.09  Aligned_cols=78  Identities=28%  Similarity=0.462  Sum_probs=63.6

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcc-ccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeec
Q 044309           83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFS-ELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV  161 (259)
Q Consensus        83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhis-Els~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~  161 (259)
                      .+|.+|++.+|.|+ +.+.-++|.|.+|++.+|+|--+ ++..++..+.++.+ +|..|+|+|+++|.-+|.|+++.|+.
T Consensus         4 ~lPnigdVtkGiVy-~kd~~fyV~L~dY~g~ea~l~dy~~~~~d~~~klk~kL-VGKtIkvqVIR~d~lKGYIDVr~~~~   81 (85)
T d1luza_           4 SLPNAGDVIKGRVY-EKDYALYIYLFDYPHFEAILAESVKMHMDRYVEYRDKL-VGKTVKVKVIRVDYTKGYIDVNYKRM   81 (85)
T ss_dssp             CCCCTTCEEEEEEE-EETTEEEEEETTCTTSEEEEGGGSSCCHHHHHHHHHHH-TTCEEEEEEEEEETTTTEEEEEEEEE
T ss_pred             ccCCCCceeeeEEE-EeCCEEEEEecCCCCceEEeeehhhhhhHHHHHHHHHh-cCceEEEEEEEEcceeeEEEehhhhh
Confidence            37889999999997 47888999999998999997433 33334555555555 89999999999999999999999986


Q ss_pred             c
Q 044309          162 S  162 (259)
Q Consensus       162 ~  162 (259)
                      .
T Consensus        82 ~   82 (85)
T d1luza_          82 C   82 (85)
T ss_dssp             C
T ss_pred             h
Confidence            4

>d2asba1 b.40.4.5 (A:108-183) S1 domain of NusA {Mycobacterium tuberculosis [TaxId: 1773]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 domain of NusA
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=98.18  E-value=2.6e-06  Score=60.99  Aligned_cols=65  Identities=18%  Similarity=0.094  Sum_probs=52.9

Q ss_pred             CCcEEEEEEEEEeCce----EEEEEcc-CCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCC--CeEEEE
Q 044309           87 VDMAVMIQVKNIADMG----AYVSLLE-YNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEK--GYIDLS  157 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~G----afV~L~e-y~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~--gkI~LS  157 (259)
                      +|+++.|+|.++....    ++|+|+. -++.+|+||.+|.-      |.+.|++||.++|.|.+|+...  -+|.||
T Consensus         4 ~geiv~G~V~r~~~~~~~~~v~vdlG~~~~~~EaiLp~~eqi------p~E~y~~Gdrik~~i~~V~~~~kGp~IilS   75 (76)
T d2asba1           4 EGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV------PGESYEHGNRLRCYVVGVTRGAREPLITLS   75 (76)
T ss_dssp             TTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSC------TTCCCCTTCEEEEEEEEEECCSSSCEEEEE
T ss_pred             cceEEEEEEEEEecCCCceEEEEECCCCCCCEEEECCHHHcC------CCcccCCCCEEEEEEEEEEecCCCCEEEEe
Confidence            8999999999986432    8999951 12599999999976      5689999999999999998753  266666

>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=97.77  E-value=3.1e-05  Score=56.55  Aligned_cols=57  Identities=14%  Similarity=0.220  Sum_probs=47.1

Q ss_pred             cEEEEEEEEEeC--ceEEEEEccCCCEEEEEEccccccccc---------cCccccccCCCeEEEEEEEE
Q 044309           89 MAVMIQVKNIAD--MGAYVSLLEYNNIEGMILFSELSRRRI---------RSVSSLIKVGRIEPVMVLRV  147 (259)
Q Consensus        89 ~iv~G~V~~I~~--~GafV~L~ey~~~eGllhisEls~~~v---------~~~~~~~kvGd~V~vkVi~v  147 (259)
                      ++|.|+|++|.+  .+|||+++  .+..||||++++.....         .++.+.+++||.|-|.|.+-
T Consensus         2 NIY~G~V~~V~pgl~AAFVDiG--~~k~gFL~~~di~~~~~~~~~~~~~~~~i~~~l~~G~~ilVQV~Ke   69 (87)
T d1smxa_           2 NIYKGKITRIEPSLEAAFVDYG--AERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKE   69 (87)
T ss_dssp             CCEEEEEEEEEGGGTEEEEESS--SSSCEEEEGGGSCGGGCSSCCCSSSCCCGGGTCCTTCEEEEEEEEC
T ss_pred             CcEEEEEEEecCCceEEEEEeC--CCccceeEecccceeeeccccccccccchhhhccCCCeEEEEEeec
Confidence            589999999975  47999998  58999999999876432         34677899999999999864

>d1jjga_ b.40.4.5 (A:) Viral structural mimic of eIF2alpha {Myxoma virus, m156r [TaxId: 10273]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Viral structural mimic of eIF2alpha
species: Myxoma virus, m156r [TaxId: 10273]

Probab=97.09  E-value=0.00072  Score=49.40  Aligned_cols=66  Identities=26%  Similarity=0.259  Sum_probs=52.2

Q ss_pred             CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcc-ccccccccCccccccCCCeEEEEEEEEeCCCCeEEE
Q 044309           87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFS-ELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDL  156 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhis-Els~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~L  156 (259)
                      +|++.+|.|+ +.++-++|.|.+|++.+|+|--+ ++..++..+.++.+ +|..|+|+|+++|.  +.|++
T Consensus        32 ~G~V~kGiVy-~rd~~fyV~L~dY~g~eail~dY~n~~~dr~~klkkkL-VGKTIkVqVIRvDk--lYIDV   98 (102)
T d1jjga_          32 PGSVHEGIVY-FKDGIFKVRLLGYEGHECILLDYLNYRQDTLDRLKERL-VGRVIKTRVVRADG--LYVDL   98 (102)
T ss_dssp             SSCEEEEEEE-EETTEEEEECTTTSSCEEEECTTCCSSCCCCCHHHHHH-TTCEEEEEEEEECS--SEEEE
T ss_pred             CCcEeeeEEE-EeCCEEEEEecCCCCceeeeeehhhhhHHHHHHHHHHh-cCceEEEEEEEecc--EEEEE
Confidence            6999999997 57888999999998999996422 34445555566665 89999999999984  57776

>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=93.55  E-value=0.39  Score=33.93  Aligned_cols=68  Identities=10%  Similarity=0.057  Sum_probs=46.4

Q ss_pred             CCcEEEEEEEEEeCceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeec
Q 044309           87 VDMAVMIQVKNIADMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV  161 (259)
Q Consensus        87 ~G~iv~G~V~~I~~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~  161 (259)
                      .+...+|+|....+ |. ||.-++ .+.+-|+|+|++...     ...+++||.|.+.|..-++......+.++.+
T Consensus        15 ~~~r~~G~I~~~~~-gfGFI~~~~-~~~dvF~H~s~~~~~-----~~~l~~G~~VeF~v~~~~kg~k~~Av~V~~~   83 (89)
T d1wfqa_          15 AALRETGVIEKLLT-SYGFIQCSE-RQARLFFHCSQYNGN-----LQDLKVGDDVEFEVSSDRRTGKPIAVKLVKI   83 (89)
T ss_dssp             CCCEEEEEEEEECS-SEEEEEETT-TTEEEEEETTTCSSC-----TTTCCTTCCEEEEEEECSSSCCEEEEEEEES
T ss_pred             ccceEEEEEEEecC-ccceEEeCC-CCceEEEEeehhhcc-----CCcccCCCEEEEEEEECCCCCceEEEEEEEC
Confidence            57778999999964 44 666654 468999999999532     2458899999999765332222344445444

>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=93.46  E-value=0.0041  Score=43.22  Aligned_cols=42  Identities=10%  Similarity=0.173  Sum_probs=33.9

Q ss_pred             hccccceEEEEEEecccccCCch------HHH--HHhhchhhHHhhcCHHHHHH
Q 044309          172 RYNKSKLVHSIMRHVAETLGIDL------EEL--YVNIGWPLYWKYGHAFEAFK  217 (259)
Q Consensus       172 ~~~~g~~v~g~V~~i~~~~G~fv------e~~--~~~~sw~l~~~~~~~~~~fk  217 (259)
                      .+++|+++.|+|.++.+ ||+|+      +++  .++++|.   +..++.+.|+
T Consensus         2 d~kvG~iv~G~V~~v~~-~G~fV~l~~~~~Glv~~sels~~---~~~~~~~~~~   51 (76)
T d1sroa_           2 EIEVGRVYTGKVTRIVD-FGAFVAIGGGKEGLVHISQIADK---RVEKVTDYLQ   51 (76)
T ss_dssp             CCCTTSEEEEEEEEEET-TEEEEECSSSCCCBCCTTSSCSS---CCSCHHHHCC
T ss_pred             CCCCCCEEEEEEEEEeC-cEEEEEeCCCCEEEEEhHHhCcc---ccCCHHHccC
Confidence            46899999999999976 99998      344  8999994   6677777763

>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=92.63  E-value=0.32  Score=33.70  Aligned_cols=59  Identities=12%  Similarity=0.138  Sum_probs=41.8

Q ss_pred             CCcEEEEEEEEEe-CceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEE
Q 044309           87 VDMAVMIQVKNIA-DMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLR  146 (259)
Q Consensus        87 ~G~iv~G~V~~I~-~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~  146 (259)
                      ....+.|+|+-.. ..|. ||.-++ ++-+-|+|.|.+...-....-..+..||.|.+.+..
T Consensus         5 ~~~r~~G~VKwfn~~KGfGFI~~dd-g~~DvFvH~s~i~~~g~~~~~~~L~~G~~V~f~~~~   65 (79)
T d1h95a_           5 IATKVLGTVKWFNVRNGYGFINRND-TKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVE   65 (79)
T ss_dssp             CEEEEEEEEEEEETTTTEEEEEEGG-GTEEEEEEGGGBCSCCCSCCSCSCCSSCEEEEEEEE
T ss_pred             hcCcccEEEEEEcCCCCeEEEEECC-CCccEEEEhhHcccCCCcceeeecCCCCEEEEEEEe
Confidence            3457899999874 3454 666654 568999999999754322233457899999998764

>d1k3ra1 b.40.4.10 (A:93-163) Hypothetical protein MTH1 (MT0001), insert domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Hypothetical protein MTH1 (MT0001), insert domain
domain: Hypothetical protein MTH1 (MT0001), insert domain
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=92.17  E-value=0.14  Score=35.06  Aligned_cols=48  Identities=21%  Similarity=0.204  Sum_probs=38.9

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEE
Q 044309           85 PEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRV  147 (259)
Q Consensus        85 ~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~v  147 (259)
                      |++|++-.|.+.+-...|+||+++    ++-+..+.+           .|..|+.+.++|.++
T Consensus         8 p~vGEiReG~~~rr~~~g~~vDiG----lD~la~~k~-----------~~~~~~r~tfrIvs~   55 (71)
T d1k3ra1           8 PVTGEYRQGLTVKRVKKGTLVDIG----ADKLALCRE-----------KLTVNRIMSFRVVRL   55 (71)
T ss_dssp             CCTTCEEEEEEEEECSSSEEEESS----SSCEEECSS-----------CCCSSCEEEEEEEEC
T ss_pred             CcccceeeEEEEEecCCcEEEEec----CCceeeeec-----------ccccCcEEEEEEEEc
Confidence            559999999999999999999994    444444332           367999999999997

>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=90.96  E-value=1.1  Score=29.64  Aligned_cols=50  Identities=10%  Similarity=0.203  Sum_probs=36.3

Q ss_pred             EEEEEEEe-CceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEE
Q 044309           92 MIQVKNIA-DMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRV  147 (259)
Q Consensus        92 ~G~V~~I~-~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~v  147 (259)
                      +|+|+-.. +.|. ||..+  ++-+-|+|+|.+.....    ..+..||.|.+.+..-
T Consensus         3 ~G~Vk~fn~~kGfGFI~~d--~g~DiF~H~s~l~~~~~----~~L~~G~~V~f~~~~~   54 (66)
T d1c9oa_           3 RGKVKWFNNEKGYGFIEVE--GGSDVFVHFTAIQGEGF----KTLEEGQEVSFEIVQG   54 (66)
T ss_dssp             EEEEEEEETTTTEEEEEET--TEEEEEEEGGGBCSSSC----CCCCTTCEEEEEEEEE
T ss_pred             CeEEEEEECCCCEEEEEec--CCceEEEEehhcccccC----CcCCCCCEEEEEEEEC
Confidence            68888874 3444 56665  57899999999974322    3478999999987653

>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=90.76  E-value=0.02  Score=40.29  Aligned_cols=41  Identities=12%  Similarity=0.256  Sum_probs=22.7

Q ss_pred             hc-cccceEEEEEEecccccCCchH--------HH--HHhhchhhHHhhcCHHHHH
Q 044309          172 RY-NKSKLVHSIMRHVAETLGIDLE--------EL--YVNIGWPLYWKYGHAFEAF  216 (259)
Q Consensus       172 ~~-~~g~~v~g~V~~i~~~~G~fve--------~~--~~~~sw~l~~~~~~~~~~f  216 (259)
                      +| +.|+++.|+|.++.+ +|+|++        ++  .++++|.   ...++.+.|
T Consensus         9 ~~p~~G~iv~G~V~~i~~-~G~fV~l~~~~~i~G~i~~sels~~---~~~~~~~~~   60 (86)
T d1kl9a2           9 KFPEVEDVVMVNVRSIAE-MGAYVSLLEYNNIEGMILLSELSRR---RIRSINKLI   60 (86)
T ss_dssp             SSCCTTCEEEEEEEEECS-SEEEEEETTTTTEEEEEEGGGC---------------
T ss_pred             cCCCCCCEEEEEEEEEeC-CeEEEEEecCCCEEEEEEeeecccc---ccccceEEe
Confidence            45 479999999999976 899862        23  8899984   556666666

>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=90.65  E-value=0.49  Score=31.73  Aligned_cols=52  Identities=13%  Similarity=0.175  Sum_probs=37.5

Q ss_pred             EEEEEEEEEe-CceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEE
Q 044309           90 AVMIQVKNIA-DMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLR  146 (259)
Q Consensus        90 iv~G~V~~I~-~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~  146 (259)
                      .++|+|+-.. ..|. |+.-++ ++-+-|+|+|.+.....    ..+++||.|.+.+..
T Consensus         3 r~~G~Vk~f~~~kGfGFI~~d~-g~~diFvH~s~l~~~~~----~~L~~G~~V~f~~~~   56 (69)
T d1mjca_           3 KMTGIVKWFNADKGFGFITPDD-GSKDVFVHFSAIQNDGY----KSLDEGQKVSFTIES   56 (69)
T ss_dssp             CEEEEEEEEETTTTEEEEEETT-SCCCEEEEGGGBCCTTT----CCCCTTCEEEEEEEC
T ss_pred             CEEEEEEEEeCCCCEEEEEEcC-CCccEEEEhHHhcccCC----CcCCCCCEEEEEEEe
Confidence            3789999874 4455 666653 45899999999975322    347899999998653

>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=89.20  E-value=0.038  Score=39.53  Aligned_cols=43  Identities=9%  Similarity=0.186  Sum_probs=34.1

Q ss_pred             HHhccccceEEEEEEecccccCCch------HHH--HHhhchhhHHhhcCHHHHH
Q 044309          170 EERYNKSKLVHSIMRHVAETLGIDL------EEL--YVNIGWPLYWKYGHAFEAF  216 (259)
Q Consensus       170 ~~~~~~g~~v~g~V~~i~~~~G~fv------e~~--~~~~sw~l~~~~~~~~~~f  216 (259)
                      .+.+++|+++.|+|.++.+ +|+|+      +++  .++++|.   ...++.+.|
T Consensus        13 ~~~~k~G~iv~g~V~~v~~-~G~~V~l~~~i~G~i~~~~ls~~---~~~~~~~~~   63 (94)
T d3bzka4          13 LKDLKPGMVLEGVVTNVTN-FGAFVDIGVHQDGLVHISALSEK---FVKDPYEVV   63 (94)
T ss_dssp             GGGCCTTCEEEEEEEEEET-TEEEEECSSSSCEEEEGGGGCSS---CCSCHHHHC
T ss_pred             HhcCCCCCEEEEEEEEEEC-cEEEEEeCCCceEEeehhhhhcc---cccChhhhh
Confidence            4678999999999999976 89987      333  8999984   566777766

>d1e3pa2 b.40.4.5 (A:656-717) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Streptomyces antibioticus [TaxId: 1890]}

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: Streptomyces antibioticus [TaxId: 1890]

Probab=85.37  E-value=0.064  Score=35.57  Aligned_cols=48  Identities=8%  Similarity=-0.023  Sum_probs=18.0

Q ss_pred             EEEEecccccCCch------HHH--HHhhchh-hHHhhcCHHHHHHHHhcCcchh-hccCCCc
Q 044309          181 SIMRHVAETLGIDL------EEL--YVNIGWP-LYWKYGHAFEAFKIIVTDPDSV-LNSLTRE  233 (259)
Q Consensus       181 g~V~~i~~~~G~fv------e~~--~~~~sw~-l~~~~~~~~~~fk~a~~~~~~~-l~~l~~~  233 (259)
                      |+|+++.+ ||+|+      ++|  .+++||. -.++..++.+.|    ..|+++ ..-+.++
T Consensus         1 G~V~~i~~-fG~FV~l~~g~~Glihiseis~~~~~~~v~~~~~~~----~~G~~V~vkV~~iD   58 (62)
T d1e3pa2           1 GSVVKTTT-FGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVL----GVGQKVQVEIAEID   58 (62)
T ss_dssp             CBEEECC--CSCEECCC---CCCCC-------------------C----CSSCBCCCCCCCCC
T ss_pred             CEEEEEEe-ceEEEEecCCceEEEEHHHcccccccccccCHHHhc----CCCCEEEEEEEEEc
Confidence            67899987 99998      344  8888874 123455666655    445544 3444433

>d2vnud2 b.40.4.5 (D:911-998) Exosome complex exonuclease RRP44 {Saccharomyces cerevisiae [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exosome complex exonuclease RRP44
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=85.14  E-value=1.5  Score=30.88  Aligned_cols=56  Identities=20%  Similarity=0.141  Sum_probs=38.9

Q ss_pred             EEEEEEEEeCceEEEEEccCCCEEEEEEccccccc-----ccc----------C--ccccccCCCeEEEEEEEE
Q 044309           91 VMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRR-----RIR----------S--VSSLIKVGRIEPVMVLRV  147 (259)
Q Consensus        91 v~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~-----~v~----------~--~~~~~kvGd~V~vkVi~v  147 (259)
                      =.|.|.+|...|+-|-++.| |++|.+.+.+....     +-.          +  -.-.+++=|.|+|+|-.+
T Consensus         4 EegyV~~Vr~NGivVfVPky-GiEG~v~l~~~~~~~~~~~~De~~~~l~~~~~~~~~~~~~~vFD~V~V~is~v   76 (88)
T d2vnud2           4 ETGYVIKVFNNGIVVLVPKF-GVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSV   76 (88)
T ss_dssp             EEEEEEEEETTEEEEEETTT-TEEEEEEHHHHCSCGGGCEEETTTTEEEECCTTCSSCEEEETTCEEEEEEC--
T ss_pred             eEEEEEEEecccEEEEEecc-ceeEEEEEeccCCCCcceEEcchheEEEEecccCCCcEEEEecceEEEEEEEE
Confidence            36999999999999999986 79999999765421     000          0  112355668888888766

>d1e1oa1 b.40.4.1 (A:11-153) Lysyl-tRNA synthetase (LysRS) {Escherichia coli, gene lysU [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Anticodon-binding domain
domain: Lysyl-tRNA synthetase (LysRS)
species: Escherichia coli, gene lysU [TaxId: 562]

Probab=83.91  E-value=2.6  Score=31.85  Aligned_cols=70  Identities=13%  Similarity=0.092  Sum_probs=48.3

Q ss_pred             EEEEEEEEEeCc--eEEEEEccCC-CEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309           90 AVMIQVKNIADM--GAYVSLLEYN-NIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR  159 (259)
Q Consensus        90 iv~G~V~~I~~~--GafV~L~ey~-~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK  159 (259)
                      .+-|+|..+..+  .+|++|.+.+ .++.++...++.........+.+.+||.|-|+=.=....+|.++|-..
T Consensus        58 ~vaGRI~~~R~~Gk~~F~~i~D~~g~iQi~~~~~~~~~~~~~~~~k~ld~GDiIgv~G~~~~TktGElsi~~~  130 (143)
T d1e1oa1          58 SVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQTGELSIHCT  130 (143)
T ss_dssp             EEEEEEEEEEEETTEEEEEEEETTEEEEEEEETTTSSTTHHHHTGGGCCTTCEEEEEEEEEECTTCCEEEEEE
T ss_pred             EEEEEEEEEcccCCeeEEEEEeCCceEEEEEccccchhhhHHHHHhcCCcccEEEeecccEECCCCcEEEEee
Confidence            488999988654  5899998643 488899888887655544557789999997642222334677665444