Citrus Sinensis ID: 005707

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-
Protein Sequence
MTPVIPCSISSISSIPVTAFTIKKNNCLTRYNSTRKSTKQTISSQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASPTLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQVTLTMKKEDDVGSNLQLTQGVIHAATNPFVLAFRSNKDISSFLDERDKSATAAKKSEKPTPIEIGGEVSQMEAGSSIPKVQDQPTSSDDGMASVPSAVGETVEDHEAPSKEKGELADIANRNDDPQNVMSGSSETLDGALQTIEKETEETTLNQTIEETPSTDVSGELAEQALSTDGPKAGEFTESQTEDTIAKDEVQILTPATEEKETKDTTEALAPEGSVSTEKQIIGEAASTNLSGEIAEQVSVSDSPKDEEVVQNQTDDVIAKDEEQIQTPTTESEIPSAGSLKEKESGPIPDKNGSITSSGEEPDVSSSQKTKGFKLGFLFFQSFSFNSCFYNFCLRNLYFSVQNVNLKP
Secondary Structure (PSIPRED)
ccccccccccccEEEccccEEEEccEEEEEEEccccccccEEEEEcccccccHHHHHHHHHcccccEEEEEEEEEEcEEEEEEEEEEcccccccccccccccccccccccEEEccccccccccHHccccHHccccccccccccccccccEEEEEEEEEEccEEEEEcccccccEEEEcccccccccccccccccccEEEEEEEEEEccccEEEEEEEccccHHHHHHcccccccccccccccccccccccccccccccccccccEEEEEEEEEEcccEEEEcccccccEEEccccccccccccccccccccccEEEEEEEEEcccEEEEccccccccccccccccccEEEEEccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccccHHHHHHcccccccccccccccccccHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHccccccccccHHHccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEEEcccccHHHHHHHccEEEEEEEccccc
Secondary Structure Prediction (SSPRO)
ccccEcccccccccEcccHcEcEEEEEEEEEEEccccccEEEEcHHHHHHHHHHHHHHHHHccccEEEEEEEEEEEcEEEEEEEEEEcccccccccccccccccccccEEEcEEEEEEEEEccHHHHHHHHHHHHHcHHHHHHHcccccEEEEEEEEEccccEEEEccccccEEEEEcHccccccccccHEEEcccEEEEEEEEEcccccEEEEEHHccccccHHHHHHHHcccccccccccccccccccHHHHHHHHHcccccEEEEEEEEEccccEEEEEcccccEEEEEccccccccccccccHEEEcccEEEEEEEEEcccEEEEcHHccccccHHHHHHHccccccccEEEEEEEEcccccEEEEEccccHccccccccccEEEEccccEEEEEEcccHHccccccHHHccccccccccccEEEcccccccccccEEEcccccccccHEEccccccEEEEEEEHHHHccccEEEEEEEcccHHHHHHHHHHHHHccccccHHHHHHHccccccccccEEEEcccccccccccccccccccccccHHHHcHHcccccccccccEEEccccccHHHHHHHHcccHHHHHHHHHHHccccHHccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEccccHHHHHHHHHEEEEEEcccccc
Coil and Loop (DISEMBL)
mtpvipcsississipvtaftikknncltrynstrkstkqtissqrfllplpssvrffsqfqsgsalqHKSALHIISATGInvaveesdspaadddsagasdipsdvetsesssikseasptlaESRRSrtarksemppvknedlipgatftgkvrsiqpfgafidfgaftdgLVHVSRLSdnfvkdvgsIVSVGQEVKVRLIEANAETGRISLTMRESDDISKlqqqkdatasgdkvrttrrstskpgqkrdemkttkfvkgqdlegtvknltrsgafislpegeegflptseesddgfanmmggsslqvgQEVSVRVLRISRGQvtltmkkeddvgsnlqltqgvihaatnpfvlafrsnkdissFLDERDKSAtaakksekptpieiggevsqmeagssipkvqdqptssddgmasvpsavgetvedheapskekgeladianrnddpqnvmsgsseTLDGALQTIEKETEEttlnqtieetpstdvsgeLAEQalstdgpkageftesqtedtiaKDEVqiltpateeketkdttealapegsvsteKQIIGEAastnlsgeiaeqvsvsdspkdeevVQNQTDdviakdeeqiqtptteseipsagslkekesgpipdkngsitssgeepdvsssqktkgfklGFLFFQSFSFNSCFYNFCLRNLYFSvqnvnlkp
Flexible Loop (DISEMBL)
mtpvipcsississipvtaftikknncltrynstrkstkqtissqRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPsdvetsesssikseasptlaesrrsrtarksemppvknedlipgATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSivsvgqevkVRLIeanaetgrisltmresddisklqqqkdatasgdkvrttrrstskpgqkrdemkttkfvkgqdlegtvknlTRSGAfislpegeegflpTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGqvtltmkkeddvgsNLQLTQGVIHAATNPFVLAFRSNKDISSFLDERDKsataakksekptpieiggevsqmeagssipKVQDQPTSSDDGMASVPSAVgetvedheapskekgeladianrnddpqnvmsGSSETLDGALQTIEKEteettlnqtieetpstdvsgELAEQALstdgpkageftesqtedtiakdevqiltpateeketkdttealapegsvstekQIIGEaastnlsgeiaeqvsvsdspkdeevVQNQTddviakdeeqiqtptteseipsagslkekesgpipdkngsitssgeepdvssSQKTKGFKLGFLFFQSFSFNSCFYNFCLRNLYFSvqnvnlkp
Low Complexity Region (SEG)
MTPVIPCsississiPVTAFTIKKNNCLTRYNSTRKSTKQTISSQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEEsdspaadddsagasdipsdvetsesssikseasPTLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQVTLTMKKEDDVGSNLQLTQGVIHAATNPFVLAFRSNKDISSFLDERDKSATAAKKSEKPTPIEIGGEVSQMEAGSSIPKVQDQPTSSDDGMASVPSAVGETVEDHEAPSKEKGELADIANRNDDPQNVMSGSSETLDGALQTIEKETEETTLNQTIEETPSTDVSGELAEQALSTDGPKAGEFTESQTEDTIAKDEVQILTPAteeketkdtteALAPEGSVSTEKQIIGEAASTNLSGEIAEQVSVSDSPKDEEVVQNQTDDVIAKDEEQIQTPTTESEIPSAGSLKEKESGPIPDKNGSITSSGEEPDVSSSQKTkgfklgflffqsfsfnscfynfclRNLYFSVQNVNLKP
Disordered region (IsUnstruct)
****IPCSISSISSIPVTAFTIKKNNCLTRYN*************RFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVA************************************************************LIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA**********************************************************************************************************EVSVRVLRISRGQVTLTMKKEDDVGSNLQLTQGVIHAATNPFVLAFRS*******************************************************************************************************************************************************************************************************************************************************************************************GFKLGFLFFQSFSFNSCFYNFCLRNLYFSVQNV****
Disordered Region (DISOPRED)
*TP*IPCSISSISSIPVTAFTIKKNNCL***********************PSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDS***SDI**DVETSES********************************LIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRIS***************************************************DLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQVTLTMK******************ATNPFVLAFRSNKDISSFLDERD**********************************************************************************************************************************************************************************************************************************************************************************LGFLFFQSFSFNSCFYNFCLRNLYFSVQNVNL**
Disordered Region (DISEMBL)
MTPVIPCSISSISSIPVTAFTIKKNNCLTRYN***********SQRFLLPLPSSVRFFSQF********KSALHIISATGINVAVE****************************************************PVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR**************************************KTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQVTLTMKKEDDVGSNLQLTQGVIHAATNPFVLAFRSNKDISSFLDER*************TPIEIGGEVSQ*****************************************KGELADIANRNDDPQNVMSGSSETLDGALQTIEKETEETTLNQTIEETPSTDVSGELAEQALSTDGPKAGEFTESQTEDTIAKDEVQILTPATE*****************STEKQIIGEAASTNLSGEI*****************NQTDDVIAKDEE************************IPDKNG***************KTKGFKLGFLFFQSFSFNSCFYNFCLRNLYFSVQNVNLKP
Disordered Region (DISPRO)
**PVIPCSISSISSIPVTAFTIKKNNCLTRYNSTRKSTKQTISSQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASPTLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDISKLQQQKDATA***************GQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQVTLTMKKEDDVGSNLQLTQGVIHAATNPFVLAFRSNKDISSFLDERDKSATAAKKSEKPTPIEIGGEVSQMEAGSSIPKVQDQPTSSDDGMASVP**VGETVEDHEAPSKEKGELADIANRNDDPQNVMSGSSETLDGALQTIEKETEETTLNQTIEETPSTDVSGELAEQALST******E****Q*******DE*******************************************EI*E**************QNQ***VIAKDE*************************************************GFKLGFLFFQSFSFNSCFYNFCLRNLYFSVQNVNL**
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTPVIPCSISSISSIPVTAFTIKKNNCLTRYNSTRKSTKQTISSQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASPTLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQVTLTMKKEDDVGSNLQLTQGVIHAATNPFVLAFRSNKDISSFLDERDKSATAAKKSEKPTPIEIGGEVSQMEAGSSIPKVQDQPTSSDDGMASVPSAVGETVEDHEAPSKEKGELADIANRNDDPQNVMSGSSETLDGALQTIEKETEETTLNQTIEETPSTDVSGELAEQALSTDGPKAGEFTESQTEDTIAKDEVQILTPATEEKETKDTTEALAPEGSVSTEKQIIGEAASTNLSGEIAEQVSVSDSPKDEEVVQNQTDDVIAKDEEQIQTPTTESEIPSAGSLKEKESGPIPDKNGSITSSGEEPDVSSSQKTKGFKLGFLFFQSFSFNSCFYNFCLRNLYFSVQNVNLKP
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	681	2.2.26 [Sep-21-2011]
Q8CWR9	400	30S Ribosomal protein S1	yes	no	0.229	0.39	0.352	5e-16
Q9JZ44	561	30S ribosomal protein S1	yes	no	0.234	0.285	0.321	2e-14
Q45388	791	Protein tex OS=Bordetella	yes	no	0.091	0.078	0.467	4e-14
Q6GGT5	391	30S ribosomal protein S1	yes	no	0.295	0.514	0.297	2e-13
P38494	382	30S ribosomal protein S1	yes	no	0.224	0.400	0.315	3e-13
P46837	773	Protein YhgF OS=Escherich	N/A	no	0.086	0.076	0.472	4e-13
Q1RJH1	572	30S ribosomal protein S1	yes	no	0.254	0.302	0.309	4e-13
P14129	568	30S ribosomal protein S1	yes	no	0.193	0.232	0.323	1e-12
P71353	762	Uncharacterized protein H	yes	no	0.148	0.132	0.409	1e-12
P57072	757	Uncharacterized protein N	no	no	0.092	0.083	0.461	2e-12

>sp|Q8CWR9|RS1_STRR6 30S Ribosomal protein S1 OS=Streptococcus pneumoniae (strain ATCC BAA-255 / R6) GN=rpsA PE=1 SV=1

 Score = 87.0 bits (214), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 67/190 (35%), Positives = 99/190 (52%), Gaps = 34/190 (17%)

Query: 145 LIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIE 204
           L  G   TGKV  I  FGAFID G   DGLVH++ LS        S+V+VG+E++V++++
Sbjct: 191 LAVGDVVTGKVARITSFGAFIDLGG-VDGLVHLTELSHERNVSPKSVVTVGEEIEVKILD 249

Query: 205 ANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQ 264
            N E GR+SL+++             AT  G            P    ++    K  KG 
Sbjct: 250 LNEEEGRVSLSLK-------------ATVPG------------PWDGVEQ----KLAKGD 280

Query: 265 DLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR 324
            +EGTVK LT  GAF+ +  G +G +  S+ S     N     +L+VGQEV V+VL ++ 
Sbjct: 281 VVEGTVKRLTDFGAFVEVLPGIDGLVHVSQISHKRIENPK--EALKVGQEVQVKVLEVNA 338

Query: 325 G--QVTLTMK 332
              +V+L++K
Sbjct: 339 DAERVSLSIK 348

Binds mRNA; thus facilitating recognition of the initiation point. It is needed to translate mRNA with a short Shine-Dalgarno (SD) purine-rich sequence (By similarity).
Streptococcus pneumoniae (strain ATCC BAA-255 / R6) (taxid: 171101)

>sp|Q9JZ44|RS1_NEIMB 30S ribosomal protein S1 OS=Neisseria meningitidis serogroup B (strain MC58) GN=rpsA PE=1 SV=1

 Score = 81.6 bits (200), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 62/193 (32%), Positives = 97/193 (50%), Gaps = 33/193 (17%)

Query: 143 EDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRL 202
           E+L  G+   G V++I  +GAF+D G   DGL+H++ L+   VK    ++ VGQEV+ ++
Sbjct: 188 ENLQEGSVIKGIVKNITDYGAFVDLGGI-DGLLHITDLAWRRVKHPSEVLEVGQEVEAKV 246

Query: 203 IEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVK 262
           ++ + E  R+SL M+         Q  +   SG     TRR                + +
Sbjct: 247 LKFDQEKQRVSLGMK---------QLGEDPWSG----LTRR----------------YPQ 277

Query: 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI 322
           G  L G V NLT  GAF+ + +G EG +  S E D    N+     +Q+G EV V +L I
Sbjct: 278 GTRLFGKVSNLTDYGAFVEIEQGIEGLVHVS-EMDWTNKNVHPSKVVQLGDEVEVMILEI 336

Query: 323 SRG--QVTLTMKK 333
             G  +++L MK+
Sbjct: 337 DEGRRRISLGMKQ 349

Binds mRNA; thus facilitating recognition of the initiation point. It is needed to translate mRNA with a short Shine-Dalgarno (SD) purine-rich sequence.

Neisseria meningitidis serogroup B (strain MC58) (taxid: 122586)

>sp|Q45388|TEX_BORPE Protein tex OS=Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251) GN=tex PE=4 SV=2

 Score = 80.5 bits (197), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 36/77 (46%), Positives = 50/77 (64%)

Query: 144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLI 203
           DL PG    G V ++  FGAF+D G   DGLVH+S L++ FVKD   +V VGQ V V+++
Sbjct: 666 DLFPGMVLEGVVTNVANFGAFVDIGVHQDGLVHISALAEKFVKDPRDVVRVGQTVTVKVL 725

Query: 204 EANAETGRISLTMRESD 220
           E +    R++LTMR +D
Sbjct: 726 EVDVARKRVALTMRLND 742

Transcription accessory protein. Exact function not known.

Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251) (taxid: 257313)

>sp|Q6GGT5|RS1_STAAR 30S ribosomal protein S1 OS=Staphylococcus aureus (strain MRSA252) GN=rpsA PE=3 SV=1

 Score = 78.6 bits (192), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 72/242 (29%), Positives = 112/242 (46%), Gaps = 41/242 (16%)

Query: 100 ASDIPSDVETSESSSIKSEASPTLAESRR---SRTARKSEMPPVKNEDLI----PGATFT 152
           ++D   D    +  +I+ +      E+ R   SR A + E    K + L+     G    
Sbjct: 139 STDFIEDFSVFDGQTIRIKVEELDPENNRVILSRKAVEQEENDAKKDQLLQSLNEGDVID 198

Query: 153 GKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRI 212
           GKV  +  FGAFID G   DGLVHVS LS   V+    +VS+GQ+VKV++   + +T RI
Sbjct: 199 GKVARLTQFGAFIDIGG-VDGLVHVSELSHEHVQTPEEVVSIGQDVKVKIKSIDRDTERI 257

Query: 213 SLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKN 272
           SL+++                  D + T   +    GQ         F +  D+EG V  
Sbjct: 258 SLSIK------------------DTLPTPFENIK--GQ---------FHENDDIEGVVVR 288

Query: 273 LTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLT 330
           L   GAF+ +  G +G +  SE +         G  L+ GQ+V+V++L I     +V+L+
Sbjct: 289 LANFGAFVEIAPGVQGLVHISEIAHKHIGT--PGEVLEPGQQVNVKILGIDEENERVSLS 346

Query: 331 MK 332
           +K
Sbjct: 347 IK 348

Binds mRNA; thus facilitating recognition of the initiation point. It is needed to translate mRNA with a short Shine-Dalgarno (SD) purine-rich sequence.

Staphylococcus aureus (strain MRSA252) (taxid: 282458)

>sp|P38494|RS1H_BACSU 30S ribosomal protein S1 homolog OS=Bacillus subtilis (strain 168) GN=ypfD PE=1 SV=1

 Score = 77.4 bits (189), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 59/187 (31%), Positives = 94/187 (50%), Gaps = 34/187 (18%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
           G+   GKV+ +  FGAF+D G   DGLVH+S+LS + V+    +V  GQEVKV+++  + 
Sbjct: 188 GSVLDGKVQRLTDFGAFVDIGGI-DGLVHISQLSHSHVEKPSDVVEEGQEVKVKVLSVDR 246

Query: 208 ETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLE 267
           +  RISL+++++               G+KV        KPG                LE
Sbjct: 247 DNERISLSIKDT-------LPGPWNQIGEKV--------KPGDV--------------LE 277

Query: 268 GTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQ- 326
           GTV+ L   GAF+ +  G EG +  S+ S+           L+ GQ V V+VL ++  + 
Sbjct: 278 GTVQRLVSFGAFVEILPGVEGLVHISQISNKHIGT--PHEVLEEGQTVKVKVLDVNENEE 335

Query: 327 -VTLTMK 332
            ++L+M+
Sbjct: 336 RISLSMR 342

Plays a role in sporulation.

Bacillus subtilis (strain 168) (taxid: 224308)

>sp|P46837|YHGF_ECOLI Protein YhgF OS=Escherichia coli (strain K12) GN=yhgF PE=1 SV=3

 Score = 77.4 bits (189), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 35/74 (47%), Positives = 49/74 (66%)

Query: 144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLI 203
           DL PG    G V ++  FGAF+D G   DGLVH+S LS+ FV+D  ++V  G  VKV+++
Sbjct: 647 DLQPGMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVL 706

Query: 204 EANAETGRISLTMR 217
           E + +  RI+LTMR
Sbjct: 707 EVDLQRKRIALTMR 720

Escherichia coli (strain K12) (taxid: 83333)

>sp|Q1RJH1|RS1_RICBR 30S ribosomal protein S1 OS=Rickettsia bellii (strain RML369-C) GN=rpsA PE=3 SV=1

 Score = 77.0 bits (188), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 66/213 (30%), Positives = 100/213 (46%), Gaps = 40/213 (18%)

Query: 123 LAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSD 182
           L ESR    AR   +  +K      G    G V++I  +GAFID G+  DGL+H++ +S 
Sbjct: 190 LEESRSE--ARDEMLSKIKE-----GMILEGTVKNITDYGAFIDLGS-VDGLLHLTDISW 241

Query: 183 NFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTR 242
             V     ++   Q+VKV +I+ N ET RISL M++ D                      
Sbjct: 242 ARVNHPSEVLEFNQKVKVMVIKFNEETKRISLGMKQLD---------------------- 279

Query: 243 RSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFAN 302
                P +K  E    +F  G+ + G V N    G FI L +G EG + +SE S    +N
Sbjct: 280 ---YNPWEKIKE----EFPVGKKMTGKVTNFADYGVFIELKDGLEGLVHSSEISWLK-SN 331

Query: 303 MMGGSSLQVGQEVSVRVLRI--SRGQVTLTMKK 333
                +L +GQEV   VL +   + +V+L++K+
Sbjct: 332 QNPRKTLTIGQEVEFMVLEVDTEKHRVSLSIKQ 364

Binds mRNA; thus facilitating recognition of the initiation point. It is needed to translate mRNA with a short Shine-Dalgarno (SD) purine-rich sequence.

Rickettsia bellii (strain RML369-C) (taxid: 336407)

>sp|P14129|RS1_RHIME 30S ribosomal protein S1 OS=Rhizobium meliloti (strain 1021) GN=rpsA PE=3 SV=2

 Score = 75.9 bits (185), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 55/170 (32%), Positives = 82/170 (48%), Gaps = 38/170 (22%)

Query: 129 SRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDV 188
           SR  ++SE+     ++L  G    G V++I  +GAF+D G   DGL+HV+ ++   V   
Sbjct: 183 SRAEQRSEIV----QNLEEGQVVEGVVKNITDYGAFVDLGGI-DGLLHVTDMAWRRVNHP 237

Query: 189 GSIVSVGQEVKVRLIEANAETGRISLTMR--ESDDISKLQQQKDATASGDKVRTTRRSTS 246
             I+++GQ+VKV++I  N ET RISL M+  ESD    +                     
Sbjct: 238 SEILNIGQQVKVQIIRINQETHRISLGMKQLESDPWDGI--------------------- 276

Query: 247 KPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEES 296
                       K+  G+ + GTV N+T  GAF+ L  G EG +  SE S
Sbjct: 277 ----------GAKYPVGKKISGTVTNITDYGAFVELEPGIEGLIHISEMS 316

Binds mRNA; thus facilitating recognition of the initiation point. It is needed to translate mRNA with a short Shine-Dalgarno (SD) purine-rich sequence.

Rhizobium meliloti (strain 1021) (taxid: 266834)

>sp|P71353|Y568_HAEIN Uncharacterized protein HI_0568 OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) GN=HI_0568 PE=4 SV=1

 Score = 75.5 bits (184), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 43/105 (40%), Positives = 57/105 (54%), Gaps = 4/105 (3%)

Query: 144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLI 203
           DL  G    G V ++  FGAF+D G   DGLVH+S LSD FV+D   +V  G  VKV+++
Sbjct: 647 DLKSGMILEGTVTNVTNFGAFVDIGVHQDGLVHISSLSDKFVEDPHQVVKTGNIVKVKVL 706

Query: 204 EANAETGRISLTMRESDDISKLQQQKDATAS----GDKVRTTRRS 244
           E +    RI+LTMR  +   K   + D T S    G+  R  R S
Sbjct: 707 EVDVPRKRIALTMRLDESAVKNDSKSDRTLSTRPRGNMQREARNS 751

Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (taxid: 71421)

>sp|P57072|YHGF_NEIMA Uncharacterized protein NMA0194 OS=Neisseria meningitidis serogroup A / serotype 4A (strain Z2491) GN=NMA0194 PE=4 SV=1

 Score = 75.1 bits (183), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 36/78 (46%), Positives = 49/78 (62%)

Query: 144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLI 203
           DL  G    G V ++  FGAF+D G   DGLVH+S LS+ FV+D   +V  G  VKV+++
Sbjct: 636 DLQVGMILEGVVSNVANFGAFVDIGVHQDGLVHISALSNKFVQDPREVVKAGDVVKVKVL 695

Query: 204 EANAETGRISLTMRESDD 221
           E +A   RI+LTMR  D+
Sbjct: 696 EVDAARKRIALTMRLDDE 713

Neisseria meningitidis serogroup A / serotype 4A (strain Z2491) (taxid: 122587)

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	681
225445166	1135	PREDICTED: uncharacterized protein LOC10	0.922	0.553	0.561	1e-179
255546407	972	elongation factor ts, putative [Ricinus	0.775	0.543	0.583	1e-166
224143592	976	predicted protein [Populus trichocarpa]	0.760	0.530	0.595	1e-159
449465685	1122	PREDICTED: uncharacterized protein LOC10	0.883	0.536	0.467	1e-130
356495216	1133	PREDICTED: uncharacterized protein LOC10	0.767	0.461	0.515	1e-129
356531295	1135	PREDICTED: uncharacterized protein LOC10	0.885	0.531	0.467	1e-129
449525214	1106	PREDICTED: LOW QUALITY PROTEIN: uncharac	0.869	0.535	0.463	1e-126
297738788	917	unnamed protein product [Vitis vinifera]	0.707	0.525	0.437	1e-108
357500731	1054	Elongation factor Ts [Medicago truncatul	0.537	0.347	0.557	1e-108
110741951	631	hypothetical protein [Arabidopsis thalia	0.541	0.584	0.544	1e-104

>gi|225445166|ref|XP_002280712.1| PREDICTED: uncharacterized protein LOC100262932 [Vitis vinifera]

 Score =  634 bits (1636), Expect = e-179,   Method: Compositional matrix adjust.
 Identities = 381/679 (56%), Positives = 482/679 (70%), Gaps = 51/679 (7%)

Query: 1   MTPVIPCSISSISSIPVTAFTIKKNNCLTRYNSTRKSTKQTISSQRFLLPLPSSVRFFSQ 60
           MTPVIP SIS+IS I  TAFT  KNNCLTR     KSTKQT+S QRFLLPL +SVR F Q
Sbjct: 1   MTPVIPSSISNISLISGTAFTSNKNNCLTRCYLLGKSTKQTLSPQRFLLPLSTSVRLFPQ 60

Query: 61  FQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSD-VETSESSSIKSEA 119
           ++SG  L  KS  HI+SATG +VAVE+SDSPA +D S+GA ++PSD  E SE  SIKS+ 
Sbjct: 61  YRSGCTLHRKSRTHILSATGTDVAVEQSDSPATED-SSGAPEVPSDSAEASEEPSIKSDG 119

Query: 120 SPTLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSR 179
             T ++ +R+R  RKSEMPPVKNE+L+PGATFTGKV+SIQPFGAFIDFGAFTDGLVHVSR
Sbjct: 120 GVTSSQPKRAR-PRKSEMPPVKNEELVPGATFTGKVKSIQPFGAFIDFGAFTDGLVHVSR 178

Query: 180 LSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVR 239
           LSD++VKDVG+IVS+GQEVKVRL+EAN ETGRISLTMR+SDD +K QQQKDA +S DK R
Sbjct: 179 LSDSYVKDVGNIVSIGQEVKVRLVEANTETGRISLTMRDSDDPTKPQQQKDAASSSDKPR 238

Query: 240 TTRRSTSKPGQKRDEM-KTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDD 298
            +RR+T +  Q+RDE+ KT+KFVKGQDLEGTVKNL R+GAFISLPEGEEGFLPTSEE+D+
Sbjct: 239 PSRRNTQRSNQRRDEVKKTSKFVKGQDLEGTVKNLNRAGAFISLPEGEEGFLPTSEEADE 298

Query: 299 GFANMMGGSSLQVGQEVSVRVLRISRGQVTLTMKKEDDVGS-NLQLTQGVIHAATNPFVL 357
           GF N+MGGSSLQVGQEVSVRVLRISRGQVTLTMKKE+D    +L+L +GV+H ATNPFVL
Sbjct: 299 GFGNLMGGSSLQVGQEVSVRVLRISRGQVTLTMKKEEDAEKLDLKLGEGVVHTATNPFVL 358

Query: 358 AFRSNKDISSFLDERDKSATAAKKSEKP-TPIEIGGEVSQMEAGSSIPKVQDQPTSSDDG 416
           AFR NK+I++FLDER+K+   A+    P T  EI G+V+Q E  + I +VQDQP SSD+ 
Sbjct: 359 AFRKNKEIATFLDEREKTVEPAEIPAIPKTSEEIEGKVNQAETVTDILEVQDQPASSDEK 418

Query: 417 MASVPSAVGETVEDHEAPSKE--------KGELADIANRNDDPQNVMSGSSETLDGALQT 468
             SVPSAV E VE  E PS+E           L ++A+ ++D ++V+S S ++ D A+QT
Sbjct: 419 SVSVPSAVDEKVEGDETPSEELDVGASAVDDALNEMASNSEDSESVISNSLQSGD-AVQT 477

Query: 469 IEK-----------ETEETTLNQTIEETPST---------DVSGELAEQALSTDGPKAGE 508
           IE+           E   +T +Q IEE  +T         D S  +A+Q LS++     E
Sbjct: 478 IEEKAVVSSEVLASERSISTASQIIEEASATHEVGSDAKSDPSTAIADQILSSESLVGKE 537

Query: 509 FTESQTEDTIAKDEVQILTP----ATEEKETKDTTEALAPEGSVSTEKQIIGEAASTNL- 563
             ESQ++DTIAK EVQI TP      EE++   T E      S + +  +     S N  
Sbjct: 538 VEESQSDDTIAKVEVQIETPPIVEPVEEEKVDPTPEKNGSVTSSNGQTDVPSSQESMNTD 597

Query: 564 ----------SGEIAE-QVSVSDSPKDEEVVQNQTDDVIAKDEEQIQTPTTESEIPSAGS 612
                     SGE+ E Q+  S+S   E+VV+NQ +D+++K+E QIQTP  E+EIPSA  
Sbjct: 598 GSEDGGKPAPSGELVESQILSSESQDSEKVVENQANDILSKEEVQIQTPAAENEIPSATP 657

Query: 613 LKEKESGPIPDKNGSITSS 631
           +++++   +  KN +I++S
Sbjct: 658 VEDEKVETVTAKNNNISNS 676

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255546407|ref|XP_002514263.1| elongation factor ts, putative [Ricinus communis] gi|223546719|gb|EEF48217.1| elongation factor ts, putative [Ricinus communis]

 Score =  592 bits (1527), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 325/557 (58%), Positives = 403/557 (72%), Gaps = 29/557 (5%)

Query: 1   MTPVIPCSISSISSIPVTAFTIKKNNCLTRYNSTRKSTKQTISSQRFLLPLPSSVRFFSQ 60
           MT V+PCS SSIS IP T F +KKNN LTR N  RKS+K  ISSQR +LPL +SV  F  
Sbjct: 1   MTTVVPCSTSSISLIPGTPFRLKKNNNLTRCNLLRKSSKHVISSQRHVLPLLTSVGLFPH 60

Query: 61  FQSGSALQHKSALHIISATGIN--VAVEESDSPAADDDSAGASDIPSDV-ETSESSSIKS 117
           ++      H+S ++ +SATG +  V +EE +SP  D++S GASDIP+D  ETSE+SSIKS
Sbjct: 61  YRRDCNWLHRSIVYGVSATGTDTDVVIEEPESPVTDENSGGASDIPADAAETSENSSIKS 120

Query: 118 EASPTLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHV 177
           +++   A+++RSR  RKSEMPPV NE+LIPGATFTGKVRSIQPFGAF+DFGAFTDGLVHV
Sbjct: 121 DSNRAPAQTKRSRPGRKSEMPPVTNEELIPGATFTGKVRSIQPFGAFVDFGAFTDGLVHV 180

Query: 178 SRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDISKLQQQKDA--TASG 235
           SRLSDNFVKDVG++VSVGQEV VRL+EAN ETGRISLTMRESDD +K QQQ+DA  TAS 
Sbjct: 181 SRLSDNFVKDVGNVVSVGQEVTVRLVEANTETGRISLTMRESDDTNKSQQQRDAPATASS 240

Query: 236 DKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEE 295
            K R  RR+  K GQ+R++ K +KFVKGQ+LEGTVKNLTRSG FISLPEGEEGFLPTSEE
Sbjct: 241 GKPRPGRRNAPKSGQRREDNKISKFVKGQELEGTVKNLTRSGTFISLPEGEEGFLPTSEE 300

Query: 296 SDDGFANMMGGSSLQVGQEVSVRVLRISRGQVTLTMKKEDDVGSNLQLTQGVIHAATNPF 355
           SD G  +MMGGSSL+VGQEVSVRVLRISRGQVTLTMKKE+D   N +L QGV+HAATNPF
Sbjct: 301 SDGGLESMMGGSSLEVGQEVSVRVLRISRGQVTLTMKKEEDNKLNTELLQGVVHAATNPF 360

Query: 356 VLAFRSNKDISSFLDERDKSATAAKKSEKP-TPIEIGGEVSQMEAGSSIPKVQDQPTSSD 414
           VLAFR N+DISSFL+ER+K    A +  +P  P+E+G +  Q E  S I +VQ QP+SS+
Sbjct: 361 VLAFRKNRDISSFLEEREKMEKVANQPVEPKIPVEVGEQEKQTETVSDILEVQGQPSSSN 420

Query: 415 DGMASVPSAVGETVEDHEAPSKEKGELADIANRNDDPQNVMSGSSETLDGALQTIEKETE 474
           +G  SV S V ET+ D  +P KE  E   IA  ++ P ++ S S ++++ A+QT+EKE E
Sbjct: 421 EGSDSVTSTVAETLVDETSP-KEVAEEPSIAGDDEVPGSIESSSPQSVEAAVQTVEKEAE 479

Query: 475 E-----------TTLNQTIEETPSTD---------VSGELAEQALSTDGPKAGEFTESQT 514
           E           +T +   E+TP TD           GE++ +  +   P A E  E+Q 
Sbjct: 480 ESSGTPDPIGSVSTADNITEQTPLTDEMGSDGKSGPYGEISSEVSTPVSPAAEEVVENQL 539

Query: 515 EDTIAKDEVQILTPATE 531
            ++I  +E+Q  TP  E
Sbjct: 540 GESITNEELQ--TPIAE 554

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224143592|ref|XP_002325009.1| predicted protein [Populus trichocarpa] gi|222866443|gb|EEF03574.1| predicted protein [Populus trichocarpa]

 Score =  567 bits (1462), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 316/531 (59%), Positives = 386/531 (72%), Gaps = 13/531 (2%)

Query: 1   MTPVIPCSISSISSIPVTAFTIKKNNCLTRYNSTRKSTKQTISSQRFLLPLPSSVRFFSQ 60
           MTPV+PCS S+I  IP TAF+I KNN L   + +RKSTK   SSQR +LPLP  V+ F Q
Sbjct: 1   MTPVLPCSTSNICLIPGTAFSINKNNSLKNGSLSRKSTKYASSSQRLVLPLPGFVKLFPQ 60

Query: 61  FQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEAS 120
           +    A+ H+S  H +SATG +VAVEE DSP  D DS G S+IP+D   +  SS K+ +S
Sbjct: 61  YHRDCAMVHRSVAHAVSATGTDVAVEEPDSPVVDKDSDGVSEIPADAVETIDSSTKAGSS 120

Query: 121 PTLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRL 180
           P  A+S RS+ +RKSEMPPVKNEDL+PGATFTGKVRSIQPFGAF+DFGAFTDGLVHVS+L
Sbjct: 121 PAPAQSSRSKGSRKSEMPPVKNEDLVPGATFTGKVRSIQPFGAFVDFGAFTDGLVHVSKL 180

Query: 181 SDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVR- 239
           SD+FVKDVGS+VSVGQEVKVRL+EAN ETGRISLTMRE+DD SK QQ+ D+ A+G   R 
Sbjct: 181 SDSFVKDVGSVVSVGQEVKVRLVEANTETGRISLTMRENDDTSKFQQRNDSPATGSSNRQ 240

Query: 240 TTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDG 299
             RR+TSKP Q++DE+K++KFVKGQ+LEGTVKNLTRSGAFISLPEGEEGFLP SEESDD 
Sbjct: 241 AARRNTSKPNQRKDEVKSSKFVKGQNLEGTVKNLTRSGAFISLPEGEEGFLPRSEESDDV 300

Query: 300 FANMMGGSSLQVGQEVSVRVLRISRGQVTLTMKKEDDVGSNLQLTQGVIHAATNPFVLAF 359
           FA MMG SSLQ+GQEVSVRVLRI+RGQVTLTMKKED    + +L QG++H ATNPF+LAF
Sbjct: 301 FAGMMGDSSLQIGQEVSVRVLRITRGQVTLTMKKEDADKRDTELIQGIVHTATNPFMLAF 360

Query: 360 RSNKDISSFLDERDKSATAAKKSEKPTPIEIGGEVSQMEAGSSIPKVQDQPTSSDDGMAS 419
           R NKDI++FLDER+    A ++ EKP P    GE +Q E   +I +VQDQP S+D+  + 
Sbjct: 361 RKNKDIAAFLDERE---IATEQPEKPIPSVQIGEKNQAEPLPNIAEVQDQPVSNDEVSSG 417

Query: 420 VPSAVGETVEDHEAPSKEKGELADIANRNDDPQNVMSGSSETLDGALQTIEKETEETTLN 479
           +PS V E+VE  E   KE    A++A+    P+ V S    ++D  LQT+EKE E T   
Sbjct: 418 IPSMVDESVEGDETSLKEVVVGANVASDEKQPETVES----SVDSTLQTVEKEAEVTGYK 473

Query: 480 --QTIE-ETP-STDVSGELAEQALSTDGPKAGEFTESQTEDTIAKDEVQIL 526
             ++IE  TP + D + +  E+    D  K  E  ES T    A D VQ L
Sbjct: 474 EPESIESSTPQNVDDTVQTLEKKAVADDDKEPESMESSTSQN-ADDTVQAL 523

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449465685|ref|XP_004150558.1| PREDICTED: uncharacterized protein LOC101216355 [Cucumis sativus]

 Score =  471 bits (1211), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 305/653 (46%), Positives = 413/653 (63%), Gaps = 51/653 (7%)

Query: 1   MTPVIPCSISSISSIPVTAFTIKKNNCLTRYNSTRKSTKQTISSQRFLLPLPSSVRFFSQ 60
           M+ + P SIS++S +P+   T  K N  TR++ +RK TK T  +QRFLLPL +SVR F  
Sbjct: 1   MSVISPSSISNVSLVPIANHT-GKTNSSTRFSFSRKPTKHTFHNQRFLLPLSTSVRLFPN 59

Query: 61  FQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSD-VETSESSSIKSEA 119
                   H   + I SATG +VAVEESDSP + ++S   S++ S  + T+E + +KS+ 
Sbjct: 60  CTKNLFCSHGRRIRIFSATGTDVAVEESDSPVSGEESTQNSELTSGAISTNEETPVKSDV 119

Query: 120 SPTLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSR 179
           +PT  +++RSR  RKSEMP V NE+LIPGATFTGKVRSIQPFGAF+DFGAFTDGLVHVSR
Sbjct: 120 APT--QTKRSRPVRKSEMPAVNNEELIPGATFTGKVRSIQPFGAFVDFGAFTDGLVHVSR 177

Query: 180 LSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVR 239
           LSD++VKDV S+VSVGQEVKVRLIEANAE GRISL+MRE+D      ++K++ AS DK  
Sbjct: 178 LSDSYVKDVASVVSVGQEVKVRLIEANAEAGRISLSMREND------ERKESPASNDKPG 231

Query: 240 TTRRSTSKP-GQKRDEM-KTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESD 297
           ++R+S  K  G +RDE+ K++ FVKGQDL+GTVKN+TRSGAFISLPEGEEGFLP+SEE+ 
Sbjct: 232 SSRKSAPKARGPRRDEVKKSSNFVKGQDLQGTVKNITRSGAFISLPEGEEGFLPSSEETF 291

Query: 298 DGFANMMGGSSLQVGQEVSVRVLRISRGQVTLTMKK-EDDVGSNLQLTQGVIHAATNPFV 356
           +GF N+MGGS+L++GQEV+VRVLRI+RG+VTLTMKK ED+  S+ Q  QG ++AATNPF+
Sbjct: 292 EGFGNLMGGSTLEIGQEVNVRVLRIARGRVTLTMKKDEDNDKSDSQFIQGKVYAATNPFL 351

Query: 357 LAFRSNKDISSFLDERDKSATAAKKS--EKPTPIEIG-GEVSQMEAGSSIPKVQDQPTSS 413
           LAFR N DI++FLDER+    AA KS  +K T I  G  +  Q+EA   + K        
Sbjct: 352 LAFRKNNDIATFLDERESIEEAANKSVVQKVTEIVEGIVDADQIEADDKVEK-------- 403

Query: 414 DDGMASVPSAVGETV-EDHEAPSKEKGELADIANRNDDPQNVMSGSSETLDGALQTIEKE 472
                SVP AV E V ED    S +   +A      DD ++++S S   +DG    ++ E
Sbjct: 404 -----SVPPAVDEAVKEDEPERSADSSAVA-----QDDSKSILSTSEGVVDG---VVDAE 450

Query: 473 TEETTLNQTIEETPSTDVSGELA--EQALSTDGPKAGEFTESQTEDTIA-KDEVQILTPA 529
            +E   N  I+ +    +  +LA  +  +  D       T+ + E T++  D +      
Sbjct: 451 NKEAEGNSEIKASDDNQLPNDLAVDKSEVLDDSSSDVLVTQDEGESTLSTSDNIVDAVTD 510

Query: 530 TEEKETKDTTEALAPEGSVSTEKQIIGEAASTNLSGEIAEQVSVSDSPKDEEVVQNQT-- 587
           T EK+  +++E    E   S E +++ EAA      E   QV+V D   ++ V    +  
Sbjct: 511 TTEKKAGESSEVKQSEDEQSEEVRVV-EAAQPIDGPETDGQVAVPDDEANKLVSSESSVS 569

Query: 588 -------DDVIAKDEEQIQTPTTESEIPSAGSLKEKESGPIPDKNGSITSSGE 633
                  D V A+ E +      E+EI SA S +++E  P  D NGSITS G+
Sbjct: 570 EELVAGEDSVAAEKESEQSRKDLENEIVSASSSEKEEDKPESDSNGSITSLGQ 622

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356495216|ref|XP_003516475.1| PREDICTED: uncharacterized protein LOC100797166 [Glycine max]

 Score =  470 bits (1209), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 287/557 (51%), Positives = 358/557 (64%), Gaps = 34/557 (6%)

Query: 1   MTPVIPCSISSISSIPVTAFTIKKNNCLTRYNSTRKSTKQTISSQRFLLPLPSSVRFFSQ 60
           M PVIPCSI ++S IPV  ++ +KNN LTR+N +R + K   SS RFLLP   +   F Q
Sbjct: 1   MNPVIPCSIGNVSIIPVFIYSTRKNNTLTRFNLSRSTVKPGSSSWRFLLPSFVASGAFPQ 60

Query: 61  FQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEAS 120
            +   +   KS+  I SAT  +V VEE  SP AD+DS   +   ++V  SE SS KS+A+
Sbjct: 61  NKGIRSFHKKSSTSI-SATETDVTVEEP-SPVADEDSGEITS--NEVGISEDSSSKSDAN 116

Query: 121 PTLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRL 180
           P  A+ RRSR ARKSEMPPVKNEDLIPGATFTGKV+S+QPFGAF+D GAFTDGLVH+S L
Sbjct: 117 PDPAKGRRSRPARKSEMPPVKNEDLIPGATFTGKVKSVQPFGAFVDIGAFTDGLVHISML 176

Query: 181 SDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRT 240
           SD++VKDV S+VSVGQEVKV+LIE N ET RISL+MRE+ D  K  Q+KDA    +K   
Sbjct: 177 SDSYVKDVTSVVSVGQEVKVKLIEVNTETQRISLSMRENADTGK--QRKDAPVKTEKAGP 234

Query: 241 TRRSTSKPGQKRDEM-KTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDG 299
            +R++SKP  K+D + K+TKF  GQ L G+VKNL RSGAFISLPEGEEGFLP SEE DDG
Sbjct: 235 GKRNSSKPSSKKDNVTKSTKFAIGQQLVGSVKNLARSGAFISLPEGEEGFLPVSEEPDDG 294

Query: 300 FANMMGGSSLQVGQEVSVRVLRISRGQVTLTMKKEDD-VGSNLQLTQGVIHAATNPFVLA 358
           F N+MG ++L+VGQEV+VRVLRI+RGQVTLTMKKE+D  G +     GV+H ATNPFVLA
Sbjct: 295 FDNVMGNTTLEVGQEVNVRVLRITRGQVTLTMKKEEDTAGLDSTFNHGVVHVATNPFVLA 354

Query: 359 FRSNKDISSFLDERDKSATAAKK-SEKPTPIEIGGEVSQMEAGSSIPKVQDQPTSSDDGM 417
           FR NKDI+SFLDER+K+    +K +   T  EI G V+Q E    +P VQ +P SS    
Sbjct: 355 FRKNKDIASFLDEREKTQNEVQKPTTASTSEEIKGTVNQGETVLDVPDVQGEPESSKLTD 414

Query: 418 ASVPSAVGETVEDHEAPSKEKGELADIANRNDDPQNVMSGSSETLDGALQTIEKETEE-- 475
             VPSA  + + ++   S   G    I    DD  N++S  S    G    IEKE E   
Sbjct: 415 DDVPSA-EDDISENVGTSATNGSSTAIV---DDESNLVSNVSSPTTGIDSAIEKEEEVAS 470

Query: 476 ---------TTLNQTIEETPSTDVSGELAEQALSTDGPKAGEFTESQTEDTIAKDEVQIL 526
                    +T+N  IEE   TDV+ +     L TD P      E   E+ I     QI+
Sbjct: 471 GSLIPEEDLSTVNPIIEEVTQTDVTND-----LKTDTP-----VEIANENVIETGVDQIV 520

Query: 527 TPATEEKETKDTTEALA 543
           T   ++ +T D  E  A
Sbjct: 521 TEDEKQSQTPDAIEEFA 537

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356531295|ref|XP_003534213.1| PREDICTED: uncharacterized protein LOC100804285 [Glycine max]

 Score =  468 bits (1205), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 327/699 (46%), Positives = 417/699 (59%), Gaps = 96/699 (13%)

Query: 1   MTPVIPCSISSISSIPVTAFTIKKNNCLTRYNSTRKSTKQTISSQRFLLP-------LPS 53
           M PVIPCSI ++S IP   ++ +KNN LTR N +R + K   SS RFLLP        P 
Sbjct: 1   MNPVIPCSIGNVSIIPGFTYSTRKNNTLTRLNLSRSTVKPGSSSWRFLLPSFVASGAFPQ 60

Query: 54  SVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSD-VETSES 112
           + R  S F       HK +   ISAT  +VAVEE   P AD+DS    ++PS+ V  SE 
Sbjct: 61  NKRILS-F-------HKKSRTSISATETDVAVEEP-GPVADEDSG---ELPSNEVGVSED 108

Query: 113 SSIKSEASPTLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTD 172
           S  KS+A+P  A++RRSR ARKSEMPPVKNEDL+PGATFTGKV+S+QPFGAF+D GAFTD
Sbjct: 109 SFTKSDANPDPAKARRSRPARKSEMPPVKNEDLLPGATFTGKVKSVQPFGAFVDIGAFTD 168

Query: 173 GLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDISKLQQQKDAT 232
           GLVH+S LSD++VKDV S+VSVGQEVKV+LIE N ET RISL+MRE+ D  K  Q+KDA 
Sbjct: 169 GLVHISMLSDSYVKDVASVVSVGQEVKVKLIEVNTETQRISLSMRENVDTGK--QRKDAP 226

Query: 233 ASGDKVRTTRRSTSKPGQKRDEM-KTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLP 291
              +K    +R+ SKP  K+D + K+TKF  GQ L G+VKNL RSGAFISLPEGEEGFLP
Sbjct: 227 TKTEKAGPGKRNNSKPSPKKDNVTKSTKFAIGQQLVGSVKNLARSGAFISLPEGEEGFLP 286

Query: 292 TSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQVTLTMKKEDD-VGSNLQLTQGVIHA 350
            SEE DDGF N+MG ++L+VGQEV+VRVLRI+RGQVTLTMKKE+D  G +    QGV+H 
Sbjct: 287 VSEEPDDGFDNVMGNTTLEVGQEVNVRVLRITRGQVTLTMKKEEDTAGLDSTFNQGVVHV 346

Query: 351 ATNPFVLAFRSNKDISSFLDERDKSAT-AAKKSEKPTPIEIGGEVSQMEAGSSIPKVQDQ 409
           ATNPFV+AFR NKDI+SFLD+R+K+ T   K S   T  EI G V+Q E    +P VQ +
Sbjct: 347 ATNPFVVAFRKNKDIASFLDDREKTQTEVLKPSTASTLEEIKGTVNQGETVLDVPDVQGE 406

Query: 410 PTSS---DDGMASVPSAVGETVEDHEAPSKEKGELADIANRNDDPQNVMSGSSETLDGAL 466
           P SS   DD    VPSA  + + ++   S   G    I    DD  N++S  S    G  
Sbjct: 407 PESSKLTDD----VPSA-EDDISENVGTSATNGSSTAIV---DDESNLVSNVSSPKTGID 458

Query: 467 QTIEKETEE-----------TTLNQTIEETPSTDVSGELAEQALSTDGPK--AGE-FTES 512
             IEKE E            +T+N  IEE   TDV+       L TD P   A E   E+
Sbjct: 459 SAIEKEEEVAFGSLIPEEDLSTVNPIIEEATQTDVTT----IDLKTDAPVEIANENVIET 514

Query: 513 QTEDTIAKDEVQILTP-ATEE----------------------KETKDTTEALAPEGSVS 549
             +  +A+DE Q  TP A EE                       E+  T+ A AP+ S  
Sbjct: 515 GVDQIVAEDEKQSQTPNAMEEFAAAVLTDSDVVEPSPDKNDAITESDITSSAPAPQESAG 574

Query: 550 TEKQIIGEA--ASTNLSG---EIAEQVSVSDSPKDE------------EVVQNQTDDVIA 592
            +   I E   + T+LSG   E++ + S++    +E            EVV+   DD   
Sbjct: 575 DDVGAITENIDSDTSLSGQSDELSPEGSLTTDATEETDQVPSPESSATEVVKTSIDD--P 632

Query: 593 KDEEQIQTPTTESEIPSAGSLKEKESGPIPDKNGSITSS 631
           ++E + QTP TE+E      +++KE     DKN S+++S
Sbjct: 633 EEEAKKQTPATENENSFTSQVEDKEVAIASDKNSSLSNS 671

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449525214|ref|XP_004169613.1| PREDICTED: LOW QUALITY PROTEIN: uncharacterized LOC101216355 [Cucumis sativus]

 Score =  460 bits (1184), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 308/664 (46%), Positives = 418/664 (62%), Gaps = 72/664 (10%)

Query: 1   MTPVIPCSISSISSIPVTAFTIKKNNCLTRYNSTRKSTKQTISSQRFLLPLPSSVRFFSQ 60
           M+ + P SIS++S +P+   T K N+  TR++ +RK TK T  +QRFLLPL +SVR F  
Sbjct: 1   MSVISPSSISNVSLVPIANHTGKTNSS-TRFSFSRKPTKHTFHNQRFLLPLSTSVRLFPN 59

Query: 61  FQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSD-VETSESSSIKSEA 119
                   H   + I SATG +VAVEESDSP + ++S   S++ S  + T+E + +KS+ 
Sbjct: 60  -HXKPFCSHGRRIRIFSATGTDVAVEESDSPVSGEESTQNSELTSGAISTNEETPVKSDV 118

Query: 120 SPTLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSR 179
           +PT  +++RSR  RKSEMP V NE+LIPGATFTGKVRSIQPFGAF+DFGAFTDGLVHVSR
Sbjct: 119 APT--QTKRSRPVRKSEMPAVNNEELIPGATFTGKVRSIQPFGAFVDFGAFTDGLVHVSR 176

Query: 180 LSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVR 239
           LSD++VKDV S+VSVGQEVKVRLIEANAE GRISL+MRE+D      ++K++ AS DK  
Sbjct: 177 LSDSYVKDVASVVSVGQEVKVRLIEANAEAGRISLSMREND------ERKESPASNDKPG 230

Query: 240 TTRRSTSKP-GQKRDEM-KTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESD 297
           ++R+S  K  G +RDE+ K++ FVKGQDL+GTVKN+TRSGAFISLPEGEEGFLP+SEE+ 
Sbjct: 231 SSRKSAPKARGPRRDEVKKSSNFVKGQDLQGTVKNITRSGAFISLPEGEEGFLPSSEETF 290

Query: 298 DGFANMMGGSSLQVGQEVSVRVLRISRGQVTLTMKK-EDDVGSNLQLTQGVIHAATNPFV 356
           +GF N+MGGS+L++GQEV+VRVLRI+RG+VTLTMKK ED+  S+ Q  QG ++AATNPF+
Sbjct: 291 EGFGNLMGGSTLEIGQEVNVRVLRIARGRVTLTMKKDEDNDKSDSQFIQGKVYAATNPFL 350

Query: 357 LAFRSNKDISSFLDERDKSATAAKKS--EKPTPIEIG-GEVSQMEAGSSIPKVQDQPTSS 413
           LAFR N DI++FLDER+    AA KS  +K T I  G  +  Q+EA   + K        
Sbjct: 351 LAFRKNNDIATFLDERESIEEAANKSVVQKVTEIVEGIVDADQIEADDKVEK-------- 402

Query: 414 DDGMASVPSAVGETV-EDHEAPSKEKGELADIANRNDDPQNVMSGSSETLDGALQTIEKE 472
                SVP AV E V ED    S +   +A      DD ++++S S   +DG    ++ E
Sbjct: 403 -----SVPPAVDEAVKEDEPERSADSSAVA-----QDDSKSILSTSEGVVDG---VVDAE 449

Query: 473 TEETTLNQTIEETPSTDVSGELAEQALSTDGPKAGEFTESQTEDTIAKDEVQILTPATEE 532
            +E   N  I+ +    +  +LA               +S+  D  + D   +L    E 
Sbjct: 450 NKEAEGNSEIKASDDNQLPNDLA-------------VDKSEVLDDSSSD---VLVTQDEG 493

Query: 533 KETKDTTEALAPEGSVSTEKQ--IIGEAASTNLSG-EIAEQVSVSDSPKDEEVVQNQT-- 587
           + T  T++ +    + +TEK+   + + +S   +G E   QV+V D   ++ V    +  
Sbjct: 494 ESTLSTSDNIVDAVTDTTEKKQGKVLKLSSRKTNGPETDGQVAVPDDEANKLVSSESSVS 553

Query: 588 -------DDVIAKDEEQIQTPTTESEIPSAGSLKEKESGPIPDKNGSITS---SGEEPDV 637
                  D V A+ E +      E+EI SA S +++E  P  D NGSITS   SGEE  V
Sbjct: 554 EELVAGEDSVAAEKESEQSRKDLENEIVSASSSEKEEDKPESDSNGSITSLGQSGEE--V 611

Query: 638 SSSQ 641
           + SQ
Sbjct: 612 AESQ 615

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297738788|emb|CBI28033.3| unnamed protein product [Vitis vinifera]

 Score =  399 bits (1025), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 284/649 (43%), Positives = 354/649 (54%), Gaps = 167/649 (25%)

Query: 1   MTPVIPCSISSISSIPVTAFTIKKNNCLTRYNSTRKSTKQTISSQRFLLPLPSSVRFFSQ 60
           MTPVIP SIS+IS I  TAFT  KNNCLTR     KSTKQT+S QRFLLPL +SVR F Q
Sbjct: 1   MTPVIPSSISNISLISGTAFTSNKNNCLTRCYLLGKSTKQTLSPQRFLLPLSTSVRLFPQ 60

Query: 61  FQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEAS 120
           ++SG  L                                          SE  SIKS+  
Sbjct: 61  YRSGCTLH----------------------------------------PSEEPSIKSDGG 80

Query: 121 PTLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRL 180
            T ++ +R+R  RKSEMPPVKNE+L+PGATFTGKV+SIQPFGAFIDFGAFTDGLVHVSRL
Sbjct: 81  VTSSQPKRAR-PRKSEMPPVKNEELVPGATFTGKVKSIQPFGAFIDFGAFTDGLVHVSRL 139

Query: 181 SDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRT 240
           SD++VKDVG+IVS+GQEVKVRL+EAN ETGRISLTM E                      
Sbjct: 140 SDSYVKDVGNIVSIGQEVKVRLVEANTETGRISLTMHEVK-------------------- 179

Query: 241 TRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGF 300
                          KT+KFVKGQDLEGTVKNL R+GAFISLPEGEEGFLPTSEE+D+GF
Sbjct: 180 ---------------KTSKFVKGQDLEGTVKNLNRAGAFISLPEGEEGFLPTSEEADEGF 224

Query: 301 ANMMGGSSLQVGQEVSVRVLRISRGQVTLTMKKEDDVGSNLQLTQGVIHAATNPFVLAFR 360
            N+MGGSSLQV                                   V+H ATNPFVLAF 
Sbjct: 225 GNLMGGSSLQV-----------------------------------VVHTATNPFVLAFP 249

Query: 361 SNKDISSFLDERDKSATAAKKSEKPTPIEIGGEVSQMEAGSSIPKVQDQPTSSDDGMASV 420
               I              K SE     EI G+V+Q E  + I +VQDQP SSD+   SV
Sbjct: 250 EIPAI-------------PKTSE-----EIEGKVNQAETVTDILEVQDQPASSDEKSVSV 291

Query: 421 PSAVGETVEDHEAPSKEKGELADIANRNDDPQNVMSGSSETL--DGALQTIEKETEETTL 478
           PSA G+ V+  E    EK  +                SSE L  + ++ T  +  EE + 
Sbjct: 292 PSASGDAVQTIE----EKAVV----------------SSEVLASERSISTASQIIEEASA 331

Query: 479 NQTIEETPSTDVSGELAEQALSTDGPKAGEFTESQTEDTIAKDEVQILTP----ATEEKE 534
              +     +D S  +A+Q LS++     E  ESQ++DTIAK EVQI TP      EE++
Sbjct: 332 THEVGSDAKSDPSTAIADQILSSESLVGKEVEESQSDDTIAKVEVQIETPPIVEPVEEEK 391

Query: 535 TKDTTEALAPEGSVSTEKQIIGEAASTNL-----------SGEIAE-QVSVSDSPKDEEV 582
              T E      S + +  +     S N            SGE+ E Q+  S+S   E+V
Sbjct: 392 VDPTPEKNGSVTSSNGQTDVPSSQESMNTDGSEDGGKPAPSGELVESQILSSESQDSEKV 451

Query: 583 VQNQTDDVIAKDEEQIQTPTTESEIPSAGSLKEKESGPIPDKNGSITSS 631
           V+NQ +D+++K+E QIQTP  E+EIPSA  +++++   +  KN +I++S
Sbjct: 452 VENQANDILSKEEVQIQTPAAENEIPSATPVEDEKVETVTAKNNNISNS 500

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357500731|ref|XP_003620654.1| Elongation factor Ts [Medicago truncatula] gi|355495669|gb|AES76872.1| Elongation factor Ts [Medicago truncatula]

 Score =  399 bits (1024), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 218/391 (55%), Positives = 272/391 (69%), Gaps = 25/391 (6%)

Query: 1   MTPVIPCSISSISSIPVTAFTIKKNNCLTRYNSTRKSTKQTISSQRFLLP-------LPS 53
           M P+I CS+ + S IP  A+  +KNN LTR N +R S +   S++RFL P        P 
Sbjct: 1   MNPIISCSVGNSSVIPGVAYLTRKNNSLTRLNFSRSSLRHGSSTRRFLFPSFVVNGVFPQ 60

Query: 54  SVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSD-VETSES 112
           + R +S          K +   ISAT   V+VE  DSP AD+ S  +   PS+ V TS  
Sbjct: 61  NKRIYSY--------RKKSRTFISATETEVSVEVQDSPVADEVSGES---PSNEVGTSGD 109

Query: 113 SSIKSEASPTLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTD 172
           SS KS+A+   A+++RSR ARKSEMPPVKNEDL+PGA FTGKV+SIQPFGAF+DFGAFTD
Sbjct: 110 SSPKSDANTGSAKAKRSRRARKSEMPPVKNEDLVPGAAFTGKVKSIQPFGAFVDFGAFTD 169

Query: 173 GLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDISKLQQQKDAT 232
           GLVH+S LSD+FVKDV S+VS+GQEV V++IE NAET RISL+MRE+ D  K    ++A 
Sbjct: 170 GLVHISMLSDSFVKDVSSVVSLGQEVTVKVIEVNAETKRISLSMRENTDTGK----RNAP 225

Query: 233 ASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPT 292
            + +K    RR +SK G ++D MK TKFV GQ+L+GTVKN+TRSG FISLPEGEEGFLP 
Sbjct: 226 NNDEKSGYGRRDSSKSGPRKD-MKKTKFVVGQELQGTVKNMTRSGTFISLPEGEEGFLPL 284

Query: 293 SEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQVTLTMKKEDDVGS-NLQLTQGVIHAA 351
           +EE D GF  +MG SSL++G+EVSVRVLRI+RGQ TLTMKKE      ++   Q     A
Sbjct: 285 AEEDDGGFGKIMGKSSLEIGREVSVRVLRITRGQATLTMKKEGAAAELDIAYAQVGDDVA 344

Query: 352 TNPFVLAFRSNKDISSFLDERDKSATAAKKS 382
           TNPFVLAFR NKDI+ FLD+R+K  +  K S
Sbjct: 345 TNPFVLAFRRNKDIAKFLDQREKLQSEVKSS 375

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|110741951|dbj|BAE98916.1| hypothetical protein [Arabidopsis thaliana]

 Score =  384 bits (987), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 220/404 (54%), Positives = 280/404 (69%), Gaps = 35/404 (8%)

Query: 1   MTPVIPCSISSISSIPVTAFTIKKNNCLTRYNSTRKSTKQTISS-QRFLLPLPSSVRFFS 59
           M  + P SIS+   IP  +FT+KK++C  + + +RK+ KQ +SS QR +LPL +S+R F 
Sbjct: 1   MATITPSSISNAWLIPGASFTVKKSDCSIKCSFSRKAGKQILSSTQRLVLPLSTSLRLFP 60

Query: 60  QFQSGSALQ-HKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSE 118
                  L  H+ A    + T +  AVEE DS            +  D ET  S   KS+
Sbjct: 61  THGRQFVLHPHRRA----TGTDVVAAVEEQDSTPV---------VAEDKETVASE--KSD 105

Query: 119 ASPTLAESR-RSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHV 177
           A    ++SR  +R  RKSEMP VKNE+L+PGATFTGKVR+IQPFGAF+DFGAFTDGLVHV
Sbjct: 106 APAPTSQSRGTARPGRKSEMPAVKNEELVPGATFTGKVRAIQPFGAFVDFGAFTDGLVHV 165

Query: 178 SRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDISKLQQQKDATASGDK 237
           S+LSDNFVKDV S+V++GQEVKVRL+EA+ E+ RISLTMRE+DD  K Q     +   DK
Sbjct: 166 SQLSDNFVKDVSSVVTIGQEVKVRLVEADIESKRISLTMRENDDPPKRQ-----SGGSDK 220

Query: 238 VRT-TRRSTSK-PGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEE 295
            R+  +R  SK  GQ++ E   +KF KGQ L+G VKNLTRSGAFI++ EGEEGFLPT+EE
Sbjct: 221 PRSGGKRDGSKGGGQRKGEGFNSKFAKGQMLDGVVKNLTRSGAFITIGEGEEGFLPTAEE 280

Query: 296 SDDGFAN-MMGGSSLQVGQEVSVRVLRISRGQVTLTMKKEDDVGSNLQLTQGVIHAATNP 354
           +DDG  + MMGGSSLQ GQEV VRVLRI+RG+VTLTMK+EDD   +   TQGV+H ATNP
Sbjct: 281 ADDGIGSMMMGGSSLQAGQEVKVRVLRIARGRVTLTMKEEDDGKFDETTTQGVVHTATNP 340

Query: 355 FVLAFRSNKDISSFLDERDKSATAAKKSEKP---TPIEIGGEVS 395
           F+LAFR N++I++FLD+R++ A      EKP   TP+E   E S
Sbjct: 341 FMLAFRKNEEIAAFLDKREEEA------EKPPVETPVEPEAEAS 378

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	681
TAIR|locus:2119946	953	emb2726 "embryo defective 2726	0.744	0.532	0.424	6e-99
UNIPROTKB|Q5LKS3	765	Q5LKS3 "S1 RNA binding domain	0.143	0.128	0.434	1.1e-12
TIGR_CMR|SPO_A0306	765	SPO_A0306 "S1 RNA binding doma	0.143	0.128	0.434	1.1e-12
UNIPROTKB|Q71X59	117	LMOf2365_2340 "S1 RNA binding	0.132	0.769	0.377	1.1e-12
TIGR_CMR|CPS_4965	796	CPS_4965 "putative transcripti	0.168	0.144	0.376	1.5e-12
TIGR_CMR|CBU_0528	551	CBU_0528 "ribosomal protein S1	0.139	0.172	0.326	6.8e-12
UNIPROTKB|Q724J5	142	LMOf2365_0229 "RNA-binding pro	0.185	0.887	0.315	4.5e-11
UNIPROTKB|Q8E8N3	784	tex "Transcriptional accessory	0.187	0.163	0.340	4.9e-11
TIGR_CMR|SO_4629	784	SO_4629 "conserved hypothetica	0.187	0.163	0.340	4.9e-11
UNIPROTKB|Q60A39	735	MCA1032 "S1 RNA binding domain	0.170	0.157	0.358	7.3e-11

TAIR|locus:2119946 emb2726 "embryo defective 2726" [Arabidopsis thaliana (taxid:3702)]

 Score = 947 (338.4 bits), Expect = 6.0e-99, Sum P(2) = 6.0e-99
 Identities = 231/544 (42%), Positives = 314/544 (57%)

Query:     1 MTPVIPCXXXXXXXXPVTAFTIKKNNCLTRYNSTRKSTKQTISS-QRFLLPLPSSVRFFS 59
             M  + P         P  +FT+KK++C  + + +RK+ KQ +SS QR +LPL +S+R F 
Sbjct:     1 MATITPSSISNAWLIPGASFTVKKSDCSIKCSFSRKAGKQILSSTQRLVLPLSTSLRLFP 60

Query:    60 QFQSGSALQ-HKSALHIISATGINVAVEEXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 118
                    L  H+ A    + T +  AVEE                               
Sbjct:    61 THGRQFVLHPHRRA----TGTDVVAAVEEQDSTPVVAEDKETVASEKSDAPA-------- 108

Query:   119 XXPTLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVS 178
               PT      +R  RKSEMP VKNE+L+PGATFTGKVR+IQPFGAF+DFGAFTDGLVHVS
Sbjct:   109 --PTSQSRGTARPGRKSEMPAVKNEELVPGATFTGKVRAIQPFGAFVDFGAFTDGLVHVS 166

Query:   179 RLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDISKLQQQ-KDATASGDK 237
             +LSDNFVKDV S+V++GQEVKVRL+EA+ E+ RISLTMRE+DD  K Q    D   SG K
Sbjct:   167 QLSDNFVKDVSSVVTIGQEVKVRLVEADIESKRISLTMRENDDPPKRQSGGSDKPRSGGK 226

Query:   238 VRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESD 297
                 R  +   GQ++ E   +KF KGQ L+G VKNLTRSGAFI++ EGEEGFLPT+EE+D
Sbjct:   227 ----RDGSKGGGQRKGEGFNSKFAKGQMLDGVVKNLTRSGAFITIGEGEEGFLPTAEEAD 282

Query:   298 DGFANMM-GGSSLQVGQEVSVRVLRISRGQVTLTMKKEDDVGSNLQLTQGVIHAATNPFV 356
             DG  +MM GGSSLQ GQEV VRVLRI+RG+VTLTMK+EDD   +   TQGV+H ATNPF+
Sbjct:   283 DGIGSMMMGGSSLQAGQEVKVRVLRIARGRVTLTMKEEDDGKFDETTTQGVVHTATNPFM 342

Query:   357 LAFRSNKDISSFLDERDKSATAAKKSEKPTPIEIGGEVS----QMEAGSSIP-KVQDQPT 411
             LAFR N++I++FLD+R++ A   +K    TP+E   E S    ++E    +P +V  +  
Sbjct:   343 LAFRKNEEIAAFLDKREEEA---EKPPVETPVEPEAEASVTSAEVEESVCVPAEVTSEEV 399

Query:   412 SSDDGMASVPSAVGETVEDHEAPSKEKGE--LADIANRND--DPQNVMSGSSETLDGALQ 467
              S +    V   V  T  + ++P KE+    LA  A   +   P        E ++ ++ 
Sbjct:   400 PSSETPKVVEEEVIATKAEDDSPEKEEQTETLAAAAEAEEVVPPIPETKSEEEIVENSIP 459

Query:   468 TIEKETEETTLNQTI--EETPSTDVSGELAEQALSTDGPKAGEFTESQTEDTIAKDEVQI 525
                  T+E +  + +  EE     V  E     + T  P   E +  ++ +T   + ++ 
Sbjct:   460 P-NSATDEVSSPEALASEEVEKEQVVAETPVDEVKTPAPVVTEASSEESGNTATAESIKG 518

Query:   526 LTPA 529
             ++PA
Sbjct:   519 ISPA 522

GO:0003723 "RNA binding" evidence=IEA

GO:0003746 "translation elongation factor activity" evidence=IEA;ISS

GO:0006414 "translational elongation" evidence=IEA;ISS

GO:0009793 "embryo development ending in seed dormancy" evidence=NAS

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0009507 "chloroplast" evidence=IDA

GO:0046686 "response to cadmium ion" evidence=IEP;RCA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0016117 "carotenoid biosynthetic process" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

GO:0034660 "ncRNA metabolic process" evidence=RCA

GO:0042744 "hydrogen peroxide catabolic process" evidence=RCA

UNIPROTKB|Q5LKS3 Q5LKS3 "S1 RNA binding domain protein" [Ruegeria pomeroyi DSS-3 (taxid:246200)]

 Score = 203 (76.5 bits), Expect = 1.1e-12, P = 1.1e-12
 Identities = 43/99 (43%), Positives = 60/99 (60%)

Query:   144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLI 203
             DL PG    G V ++  FGAF+D G   DGLVHVS+L+D FVKD   +V  GQ +KV + 
Sbjct:   641 DLRPGMVLEGTVTNVAAFGAFVDIGVHQDGLVHVSQLADRFVKDPHEVVKTGQVIKVTVT 700

Query:   204 EANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTR 242
             E +    RI L+MR+ D  +  +Q+K A + G + R+ R
Sbjct:   701 EIDVPRKRIGLSMRK-DGGASARQEKPARSGGPRDRSPR 738

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|SPO_A0306 SPO_A0306 "S1 RNA binding domain protein" [Ruegeria pomeroyi DSS-3 (taxid:246200)]

 Score = 203 (76.5 bits), Expect = 1.1e-12, P = 1.1e-12
 Identities = 43/99 (43%), Positives = 60/99 (60%)

Query:   144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLI 203
             DL PG    G V ++  FGAF+D G   DGLVHVS+L+D FVKD   +V  GQ +KV + 
Sbjct:   641 DLRPGMVLEGTVTNVAAFGAFVDIGVHQDGLVHVSQLADRFVKDPHEVVKTGQVIKVTVT 700

Query:   204 EANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTR 242
             E +    RI L+MR+ D  +  +Q+K A + G + R+ R
Sbjct:   701 EIDVPRKRIGLSMRK-DGGASARQEKPARSGGPRDRSPR 738

GO:0003723 "RNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q71X59 LMOf2365_2340 "S1 RNA binding domain protein" [Listeria monocytogenes serotype 4b str. F2365 (taxid:265669)]

 Score = 178 (67.7 bits), Expect = 1.1e-12, P = 1.1e-12
 Identities = 34/90 (37%), Positives = 55/90 (61%)

Query:   148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
             G   +GK+  IQ +GAF+     T GLVH+S ++  FVKD+   + VGQEVKV++++ + 
Sbjct:     7 GDVVSGKIAGIQSYGAFVALDNSTQGLVHISEITHGFVKDIHDFLEVGQEVKVKILDIDE 66

Query:   208 ETGRISLTMRESDDISKLQQQKDATASGDK 237
             E  +ISL++R +++  K Q  K    S  +
Sbjct:    67 EKNKISLSIRATEEAPKEQPTKKKQVSSSE 96

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|CPS_4965 CPS_4965 "putative transcription accessory protein" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 202 (76.2 bits), Expect = 1.5e-12, P = 1.5e-12
 Identities = 47/125 (37%), Positives = 69/125 (55%)

Query:   144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLI 203
             DL PG    G V ++  FGAF+D G   DGLVH+S +++ F+ D   IV  G+ VKV+++
Sbjct:   654 DLTPGMILEGVVSNVANFGAFVDIGVHQDGLVHISSITEKFISDPREIVKAGEVVKVKVV 713

Query:   204 EANAETGRISLTMRESDDISKLQQQKDATASGD------KVRTTRRSTS---KPGQKRDE 254
             E +    RISLTMR  + +S  Q  K A+A  D      K +    S++   KP  K ++
Sbjct:   714 EVDIARKRISLTMRLEEQVSA-QTSKPASAKSDGKHDSNKAKNHENSSNNKGKPAVKHNK 772

Query:   255 MKTTK 259
              K+ K
Sbjct:   773 SKSKK 777

GO:0003723 "RNA binding" evidence=ISS

TIGR_CMR|CBU_0528 CBU_0528 "ribosomal protein S1" [Coxiella burnetii RSA 493 (taxid:227377)]

 Score = 136 (52.9 bits), Expect = 6.8e-12, Sum P(3) = 6.8e-12
 Identities = 32/98 (32%), Positives = 58/98 (59%)

Query:   126 SRRS-RTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNF 184
             SRR+   A  S     + E+L  G    G +++I  +GAF+D G   DGL+H++ ++   
Sbjct:   165 SRRAVMEAETSAERQARLEELQEGQEIKGVIKNITDYGAFVDLGG-VDGLLHITDMAWGR 223

Query:   185 VKDVGSIVSVGQEVKVRLIEANAETGRISLTMRE-SDD 221
             VK    +++VG EV V++++ + +  R+SL M++ +DD
Sbjct:   224 VKHPSDLLNVGDEVHVKVLKFDRDKKRVSLGMKQLADD 261

GO:0003735 "structural constituent of ribosome" evidence=ISS

UNIPROTKB|Q724J5 LMOf2365_0229 "RNA-binding protein" [Listeria monocytogenes serotype 4b str. F2365 (taxid:265669)]

 Score = 163 (62.4 bits), Expect = 4.5e-11, P = 4.5e-11
 Identities = 41/130 (31%), Positives = 70/130 (53%)

Query:   148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
             G    GKV  I  FGAF++      GLVH+S ++DN+VKD+  I++VG EV V+++    
Sbjct:     6 GNKLQGKVTGITNFGAFVELEGGKTGLVHISEVADNYVKDINDILTVGDEVTVKVMNIG- 64

Query:   208 ETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLE 267
             + G+I L++R++ D    + +K         +    +  KP +  +++ + KF+K  D  
Sbjct:    65 DDGKIGLSIRKAVDRPD-RPEKSYDRKPKYSKKPAGNYVKPAESFEDIMS-KFLKDSDER 122

Query:   268 -GTVKNLTRS 276
               T+K  T S
Sbjct:   123 LTTIKRQTES 132

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q8E8N3 tex "Transcriptional accessory protein Tex" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 188 (71.2 bits), Expect = 4.9e-11, P = 4.9e-11
 Identities = 47/138 (34%), Positives = 71/138 (51%)

Query:   143 EDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRL 202
             +DL P     G V ++  FGAF+D G   DGLVH+S L+D F+ D  ++V  G  VKV++
Sbjct:   647 KDLKPEMILEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDKFITDPHTVVKAGDVVKVKV 706

Query:   203 IEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVK 262
             +E + E  RI L+MR  + I + + Q  A A G      +   +KP Q+    K+ +   
Sbjct:   707 MEVDVERRRIGLSMRLDEAIDQSKTQTRAPAQG------KHQANKPNQQH---KSAQHQS 757

Query:   263 GQDLEGTVK-NLTRSGAF 279
             G+    +V  N     AF
Sbjct:   758 GRPAPKSVPVNAAMGNAF 775

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|SO_4629 SO_4629 "conserved hypothetical protein" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 188 (71.2 bits), Expect = 4.9e-11, P = 4.9e-11
 Identities = 47/138 (34%), Positives = 71/138 (51%)

Query:   143 EDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRL 202
             +DL P     G V ++  FGAF+D G   DGLVH+S L+D F+ D  ++V  G  VKV++
Sbjct:   647 KDLKPEMILEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDKFITDPHTVVKAGDVVKVKV 706

Query:   203 IEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVK 262
             +E + E  RI L+MR  + I + + Q  A A G      +   +KP Q+    K+ +   
Sbjct:   707 MEVDVERRRIGLSMRLDEAIDQSKTQTRAPAQG------KHQANKPNQQH---KSAQHQS 757

Query:   263 GQDLEGTVK-NLTRSGAF 279
             G+    +V  N     AF
Sbjct:   758 GRPAPKSVPVNAAMGNAF 775

GO:0008150 "biological_process" evidence=ND

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

UNIPROTKB|Q60A39 MCA1032 "S1 RNA binding domain protein" [Methylococcus capsulatus str. Bath (taxid:243233)]

 Score = 186 (70.5 bits), Expect = 7.3e-11, P = 7.3e-11
 Identities = 43/120 (35%), Positives = 68/120 (56%)

Query:   130 RTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVG 189
             +TAR  E    + +DL PG    G V ++  FGAF+D G   DGLVH+S L+D FV+D  
Sbjct:   601 KTARFKE-GVTEPKDLEPGMRLEGVVTNVTNFGAFVDVGVHQDGLVHISHLADRFVRDPR 659

Query:   190 SIVSVGQEVKVRLIEANAETGRISLTMRESDDISKLQQQKDATASGDKV-RTTRRSTSKP 248
              +V  G  V+V+++E +    RI+L+MR   D +K + +     +G+   +  RR+  +P
Sbjct:   660 EVVKAGDVVQVKVLEVDIPRRRIALSMRS--DAAKGEAEPPRRETGETAGKPRRRAAPQP 717

GO:0008150 "biological_process" evidence=ND

---

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

Your Input: GSVIVG00016702001 SubName- Full=Chromosome chr11 scaffold_13, whole genome shotgun sequence; (553 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	681
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	3e-28
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	4e-24
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	1e-19
cd05685	68	cd05685, S1_Tex, S1_Tex: The C-terminal S1 domain	1e-19
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	2e-19
cd04472	68	cd04472, S1_PNPase, S1_PNPase: Polynucleotide phos	6e-19
COG2183	780	COG2183, Tex, Transcriptional accessory protein [T	7e-19
PRK08059	123	PRK08059, PRK08059, general stress protein 13; Val	9e-19
smart00316	72	smart00316, S1, Ribosomal protein S1-like RNA-bind	2e-18
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	9e-18
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	1e-17
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	1e-17
COG1098	129	COG1098, VacB, Predicted RNA binding protein (cont	3e-17
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	4e-17
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	6e-17
cd05688	68	cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: R	8e-17
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	9e-17
cd05692	69	cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: R	5e-16
pfam00575	74	pfam00575, S1, S1 RNA binding domain	9e-16
cd00164	65	cd00164, S1_like, S1_like: Ribosomal protein S1-li	9e-16
PRK08582	139	PRK08582, PRK08582, hypothetical protein; Provisio	2e-15
cd05684	79	cd05684, S1_DHX8_helicase, S1_DHX8_helicase: The N	3e-15
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	5e-15
COG1185	692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	6e-15
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	1e-14
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	2e-14
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	1e-13
cd05708	77	cd05708, S1_Rrp5_repeat_sc12, S1_Rrp5_repeat_sc12:	3e-13
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	8e-13
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	1e-12
smart00316	72	smart00316, S1, Ribosomal protein S1-like RNA-bind	5e-12
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	5e-12
PRK07899	486	PRK07899, rpsA, 30S ribosomal protein S1; Reviewed	2e-11
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	4e-11
cd04471	83	cd04471, S1_RNase_R, S1_RNase_R: RNase R C-termina	6e-11
PRK08563	187	PRK08563, PRK08563, DNA-directed RNA polymerase su	6e-11
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	8e-11
PRK07400	318	PRK07400, PRK07400, 30S ribosomal protein S1; Revi	1e-10
cd04461	83	cd04461, S1_Rrp5_repeat_hs8_sc7, S1_Rrp5_repeat_hs	2e-10
PRK07252	120	PRK07252, PRK07252, hypothetical protein; Provisio	3e-10
cd04460	99	cd04460, S1_RpoE, S1_RpoE: RpoE, S1-like RNA-bindi	3e-09
cd05692	69	cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: R	3e-08
cd00164	65	cd00164, S1_like, S1_like: Ribosomal protein S1-li	4e-08
PRK12269	863	PRK12269, PRK12269, bifunctional cytidylate kinase	6e-08
PRK05807	136	PRK05807, PRK05807, hypothetical protein; Provisio	7e-08
COG1185	692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	8e-08
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	1e-07
TIGR02063	709	TIGR02063, RNase_R, ribonuclease R	1e-07
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	2e-07
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	2e-07
pfam00575	74	pfam00575, S1, S1 RNA binding domain	2e-07
COG0557	706	COG0557, VacB, Exoribonuclease R [Transcription]	2e-07
cd05686	73	cd05686, S1_pNO40, S1_pNO40: pNO40 , S1-like RNA-b	2e-07
cd05690	69	cd05690, S1_RPS1_repeat_ec5, S1_RPS1_repeat_ec5: R	3e-07
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	4e-07
cd05698	70	cd05698, S1_Rrp5_repeat_hs6_sc5, S1_Rrp5_repeat_hs	5e-07
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	2e-06
PLN00207	891	PLN00207, PLN00207, polyribonucleotide nucleotidyl	2e-06
cd04452	76	cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha sub	2e-06
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	3e-06
COG1093	269	COG1093, SUI2, Translation initiation factor 2, al	3e-06
cd05707	68	cd05707, S1_Rrp5_repeat_sc11, S1_Rrp5_repeat_sc11:	3e-06
PRK08582	139	PRK08582, PRK08582, hypothetical protein; Provisio	7e-06
cd05689	72	cd05689, S1_RPS1_repeat_ec4, S1_RPS1_repeat_ec4: R	7e-06
cd04472	68	cd04472, S1_PNPase, S1_PNPase: Polynucleotide phos	1e-05
COG1098	129	COG1098, VacB, Predicted RNA binding protein (cont	1e-05
cd04452	76	cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha sub	1e-05
cd04473	77	cd04473, S1_RecJ_like, S1_RecJ_like: The S1 domain	1e-05
cd05685	68	cd05685, S1_Tex, S1_Tex: The C-terminal S1 domain	2e-05
COG2183	780	COG2183, Tex, Transcriptional accessory protein [T	2e-05
cd05688	68	cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: R	3e-05
cd05691	73	cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: R	3e-05
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	5e-05
COG1093	269	COG1093, SUI2, Translation initiation factor 2, al	5e-05
COG2996	287	COG2996, COG2996, Predicted RNA-bindining protein	8e-05
cd05697	69	cd05697, S1_Rrp5_repeat_hs5, S1_Rrp5_repeat_hs5: R	8e-05
PRK12269	863	PRK12269, PRK12269, bifunctional cytidylate kinase	1e-04
cd05687	70	cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec	1e-04
PRK03987	262	PRK03987, PRK03987, translation initiation factor	2e-04
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	3e-04
COG1095	183	COG1095, RPB7, DNA-directed RNA polymerase, subuni	3e-04
cd04471	83	cd04471, S1_RNase_R, S1_RNase_R: RNase R C-termina	6e-04
TIGR02696	719	TIGR02696, pppGpp_PNP, guanosine pentaphosphate sy	6e-04
cd05689	72	cd05689, S1_RPS1_repeat_ec4, S1_RPS1_repeat_ec4: R	0.001
TIGR00448	179	TIGR00448, rpoE, DNA-directed RNA polymerase (rpoE	0.001
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	0.002
cd05684	79	cd05684, S1_DHX8_helicase, S1_DHX8_helicase: The N	0.002
PRK07400	318	PRK07400, PRK07400, 30S ribosomal protein S1; Revi	0.002
PRK12269	863	PRK12269, PRK12269, bifunctional cytidylate kinase	0.003
TIGR00358	654	TIGR00358, 3_prime_RNase, VacB and RNase II family	0.003
cd05691	73	cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: R	0.004
PRK03987	262	PRK03987, PRK03987, translation initiation factor	0.004

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

 Score =  119 bits (300), Expect = 3e-28
 Identities = 65/209 (31%), Positives = 95/209 (45%), Gaps = 34/209 (16%)

Query: 127 RRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVK 186
           R      +SE        L  G    G V++I  +GAF+D G   DGL+H+S +S   V 
Sbjct: 172 RAVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGAFVDIGGV-DGLLHISEISWKRVD 230

Query: 187 DVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTS 246
               +V VG EVKV++I  + E GR+SL++++                            
Sbjct: 231 HPSEVVKVGDEVKVKVISLDEERGRVSLSLKQ-------------------------LEE 265

Query: 247 KPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGG 306
            P     E    K+  G  +EG V NLT  GAF+ + EG EG +  SE S          
Sbjct: 266 DPW----EGIEKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKNVP--S 319

Query: 307 SSLQVGQEVSVRVLRI--SRGQVTLTMKK 333
             ++VGQEV V+VL I   R +++L +K+
Sbjct: 320 EVVKVGQEVEVKVLDIDPERRRISLGLKQ 348

Length = 541

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

 Score =  104 bits (262), Expect = 4e-24
 Identities = 62/183 (33%), Positives = 85/183 (46%), Gaps = 34/183 (18%)

Query: 143 EDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRL 202
             L  G    G V  +  FGAF+D G   DGLVH+S LS   V+    +VSVGQEV+V++
Sbjct: 188 SSLKEGDVVEGTVARLTDFGAFVDIGGV-DGLVHISELSHERVEKPSEVVSVGQEVEVKV 246

Query: 203 IEANAETGRISLTMRESDDISKLQQQKDATASG-DKVRTTRRSTSKPGQKRDEMKTTKFV 261
           +  + ET RISL++            KD      + V                    K  
Sbjct: 247 LSIDWETERISLSL------------KDTLPGPWEGV------------------EEKLP 276

Query: 262 KGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLR 321
           +G  +EGTVK LT  GAF+ +  G EG +  S+ S    A       L+ GQEV V+VL 
Sbjct: 277 EGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIAT--PSEVLEEGQEVKVKVLE 334

Query: 322 ISR 324
           ++ 
Sbjct: 335 VNE 337

Length = 390

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

 Score = 92.5 bits (230), Expect = 1e-19
 Identities = 66/211 (31%), Positives = 100/211 (47%), Gaps = 39/211 (18%)

Query: 125 ESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNF 184
           E  RS+   + E+     E+L  G    G V++I  FGAF+D G   DGL+H++ +S   
Sbjct: 171 EEERSQ--AREEL----LENLKEGDVVKGVVKNITDFGAFVDLGGV-DGLLHITDMSWKR 223

Query: 185 VKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRS 244
           VK     V VGQEVKV++I+ + E GRISL++++                          
Sbjct: 224 VKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQLG------------------------ 259

Query: 245 TSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMM 304
              P +  ++    KF  G  + G V NLT  G F+ + EG EG +  SE S     N  
Sbjct: 260 -EDPWEAIEK----KFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVK-KNSH 313

Query: 305 GGSSLQVGQEVSVRVLRI--SRGQVTLTMKK 333
               ++ G EV V +L I   R +++L +K+
Sbjct: 314 PSKVVKKGDEVEVMILDIDPERRRLSLGLKQ 344

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 = 82.7 bits (205), Expect = 1e-19
 Identities = 30/68 (44%), Positives = 44/68 (64%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
           G    G V ++  FGAF+D G   DGL+H+S+++D FV     +VSVG  V+V++I  + 
Sbjct: 1   GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDE 60

Query: 208 ETGRISLT 215
           E GRISL+
Sbjct: 61  ERGRISLS 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|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

 Score = 92.4 bits (230), Expect = 2e-19
 Identities = 43/152 (28%), Positives = 68/152 (44%), Gaps = 29/152 (19%)

Query: 147 PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEAN 206
            G    GKV ++  +GAF++     +GLVHVS +S         +V VGQEV+V++++ +
Sbjct: 277 VGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDID 336

Query: 207 AETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDL 266
            E  RISL +++  +                                E    K   G  +
Sbjct: 337 PERRRISLGLKQLKE-----------------------------NPWEEFADKHPVGDVV 367

Query: 267 EGTVKNLTRSGAFISLPEGEEGFLPTSEESDD 298
           EG VK++T  GAF+ L  G +G +  S+ S D
Sbjct: 368 EGKVKSITDFGAFVELEGGIDGLVHLSDLSWD 399

Length = 541

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

 Score = 81.0 bits (201), Expect = 6e-19
 Identities = 33/69 (47%), Positives = 46/69 (66%), Gaps = 1/69 (1%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
           G  + GKV  I+ FGAF++     DGLVH+S LSD  V+ V  ++ VG EVKV++IE + 
Sbjct: 1   GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVD- 59

Query: 208 ETGRISLTM 216
           + GRISL+ 
Sbjct: 60  DRGRISLSR 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|225094 COG2183, Tex, Transcriptional accessory protein [Transcription]

 Score = 90.8 bits (226), Expect = 7e-19
 Identities = 42/103 (40%), Positives = 57/103 (55%), Gaps = 2/103 (1%)

Query: 143 EDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRL 202
            DL PG    G VR++  FGAF+D G   DGLVH+S+LSD FVKD   +V VG  VKV++
Sbjct: 654 TDLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKV 713

Query: 203 IEANAETGRISLTMRESDDISKLQQQKD--ATASGDKVRTTRR 243
           IE +    RI+L+MR  ++  KL   +         + R    
Sbjct: 714 IEVDTARKRIALSMRLDEEEGKLNSGRGFCRERGLCRPRRAPV 756

Length = 780

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

 Score = 82.0 bits (203), Expect = 9e-19
 Identities = 35/82 (42%), Positives = 57/82 (69%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
           G+  TGKV  IQP+GAF+     T GLVH+S ++  FVKD+   +SVG EVKV+++  + 
Sbjct: 8   GSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDE 67

Query: 208 ETGRISLTMRESDDISKLQQQK 229
           E G+ISL++R +++  + +++K
Sbjct: 68  EKGKISLSIRATEEAPEAKRKK 89

Length = 123

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

 Score = 80.0 bits (198), Expect = 2e-18
 Identities = 30/71 (42%), Positives = 43/71 (60%)

Query: 147 PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEAN 206
            G    G V  I P GAF+D G   +GL+ +S LSD  VKD   ++ VG EVKV+++  +
Sbjct: 2   VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVD 61

Query: 207 AETGRISLTMR 217
            E GRI L+++
Sbjct: 62  EEKGRIILSLK 72

Length = 72

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

 Score = 86.8 bits (216), Expect = 9e-18
 Identities = 54/178 (30%), Positives = 82/178 (46%), Gaps = 33/178 (18%)

Query: 147 PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLS-DNFVKDVGSIVSVGQEVKVRLIEA 205
            G+   GKV +I  +GAF++     +GLVHVS +S     K    +VSVGQEV+V ++E 
Sbjct: 286 VGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLEI 345

Query: 206 NAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQD 265
           + E  RISL +                         ++    P ++  E    K+  G  
Sbjct: 346 DEEKRRISLGL-------------------------KQCKENPWEEFAE----KYPVGDV 376

Query: 266 LEGTVKNLTRSGAFISLPEGEEGFLPTSEES-DDGFANMMGGSSLQVGQEVSVRVLRI 322
           +EG VKN+T  GAF+ L  G +G +  S+ S D      +     + G EV   VL++
Sbjct: 377 VEGKVKNITDFGAFVGLEGGIDGLVHLSDISWDKKGEEAV--ELYKKGDEVEAVVLKV 432

Length = 565

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

 Score = 86.4 bits (215), Expect = 1e-17
 Identities = 65/219 (29%), Positives = 98/219 (44%), Gaps = 52/219 (23%)

Query: 126 SRR-----SRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRL 180
           SRR      R   + E+     E+L  G    G V++I  +GAF+D G   DGL+H++ +
Sbjct: 179 SRRAVLEEERAEEREEL----LENLEEGQVVEGVVKNITDYGAFVDLG-GVDGLLHITDI 233

Query: 181 SDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR--ESD---DISKLQQQKDATASG 235
           S   V     +V+VG EVKV++++ + E  R+SL ++    D    I K           
Sbjct: 234 SWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEK----------- 282

Query: 236 DKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEE 295
                                  K+  G  ++G V N+T  GAF+ L EG EG +  SE 
Sbjct: 283 -----------------------KYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEM 319

Query: 296 SDDGFANMMGGSSLQVGQEVSVRVLRI--SRGQVTLTMK 332
           S     N      + VGQEV V VL I   + +++L +K
Sbjct: 320 SWTK-KNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLK 357

Length = 565

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

 Score = 86.6 bits (216), Expect = 1e-17
 Identities = 28/71 (39%), Positives = 44/71 (61%), Gaps = 1/71 (1%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
           G  + GKV  I  FGAF++     DGLVH+S ++D  V+ V  ++  G EVKV+++E + 
Sbjct: 622 GEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEID- 680

Query: 208 ETGRISLTMRE 218
           + GRI L+ + 
Sbjct: 681 KRGRIRLSRKA 691

Length = 693

>gnl|CDD|224023 COG1098, VacB, Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]

 Score = 78.1 bits (193), Expect = 3e-17
 Identities = 33/82 (40%), Positives = 55/82 (67%), Gaps = 1/82 (1%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
           G+   GK+  I P+GAF++      GLVH+S ++D FVKD+   + VGQEVKV++++   
Sbjct: 6   GSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDI-D 64

Query: 208 ETGRISLTMRESDDISKLQQQK 229
           E G+ISL++R+ ++  + Q +K
Sbjct: 65  ENGKISLSIRKLEEEPEKQHRK 86

Length = 129

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

 Score = 84.4 bits (210), Expect = 4e-17
 Identities = 52/181 (28%), Positives = 78/181 (43%), Gaps = 36/181 (19%)

Query: 147 PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLS-DNFVKDVGSIVSVGQEVKVRLIEA 205
            G    GKV++I  FGAF+      DGLVH+S +S D   ++   +   G EV+  +++ 
Sbjct: 373 VGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKV 432

Query: 206 NAETGRISLTMR--ESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKG 263
           + E  RISL ++  E D   +  +                               K  KG
Sbjct: 433 DVEKERISLGIKQLEEDPFEEFAK-------------------------------KHKKG 461

Query: 264 QDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS 323
             + GTV  +   GAF+ L +G EG +  SE S D   +      L+VG EV  +V+ I 
Sbjct: 462 SIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDA--TEVLKVGDEVEAKVINID 519

Query: 324 R 324
           R
Sbjct: 520 R 520

Length = 565

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

 Score = 84.2 bits (209), Expect = 6e-17
 Identities = 47/180 (26%), Positives = 78/180 (43%), Gaps = 32/180 (17%)

Query: 143 EDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRL 202
             L  G    G+V+ +  FGAF+D G   DGL+HVS +S   V+    ++ VG E+KV +
Sbjct: 473 NSLEEGDVVEGEVKRLTDFGAFVDIGGV-DGLLHVSEISWGRVEKPSDVLKVGDEIKVYI 531

Query: 203 IEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVK 262
           ++ + E  ++SL+      + KL                      P +  +E    K+  
Sbjct: 532 LDIDKENKKLSLS------LKKL-------------------LPDPWENVEE----KYPV 562

Query: 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI 322
           G  + G V  +   GAF+ L  G +G +  S+ S            L  G+EV  ++L +
Sbjct: 563 GSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPE--DVLSEGEEVKAKILEV 620

Length = 647

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

 Score = 75.0 bits (185), Expect = 8e-17
 Identities = 30/68 (44%), Positives = 43/68 (63%), Gaps = 1/68 (1%)

Query: 147 PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEAN 206
            G    G V+SI  FGAF+D G   DGL+H+S +S   VK    +V+VG EV+V++++ +
Sbjct: 1   EGDVVEGTVKSITDFGAFVDLGGV-DGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKID 59

Query: 207 AETGRISL 214
            E  RISL
Sbjct: 60  KERKRISL 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 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|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

 Score = 83.5 bits (207), Expect = 9e-17
 Identities = 54/191 (28%), Positives = 83/191 (43%), Gaps = 40/191 (20%)

Query: 147 PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEAN 206
            G    GKV+SI  FGAF++     DGLVH+S LS +   +       G EV+ +++  +
Sbjct: 363 VGDVVEGKVKSITDFGAFVELEGGIDGLVHLSDLSWDRPGEEAEKYKKGDEVEAKVLAVD 422

Query: 207 AETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDL 266
            E  RISL           Q ++                  P ++  E     + KG  +
Sbjct: 423 KEKERISL--------GIKQLEES-----------------PWEEFSEK----YKKGSVV 453

Query: 267 EGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQ 326
           +G VK++   GAF+ L  G EG +  SE S D          L+VG EV   V+ I +  
Sbjct: 454 KGKVKSVKDKGAFVELGGGVEGLIRLSELSRD---------VLKVGDEVEAVVVSIDKKN 504

Query: 327 --VTLTMKKED 335
             + L++K  +
Sbjct: 505 RKILLSIKALE 515

Length = 541

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

 Score = 72.7 bits (179), Expect = 5e-16
 Identities = 27/70 (38%), Positives = 46/70 (65%), Gaps = 1/70 (1%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
           G+   G V  ++PFGAF++ G    GLVH+S+++   VKDV  ++  G +VKV+++ +  
Sbjct: 1   GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVL-SID 59

Query: 208 ETGRISLTMR 217
             GRISL+++
Sbjct: 60  ARGRISLSIK 69

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|216000 pfam00575, S1, S1 RNA binding domain

 Score = 71.9 bits (177), Expect = 9e-16
 Identities = 25/74 (33%), Positives = 43/74 (58%)

Query: 144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLI 203
               G    G V  +   GAF+D G   +G + +S +SD+ V+D   ++ VG EV+V+++
Sbjct: 1   KPEEGDVVKGTVTRVTKGGAFVDLGNGVEGFIPISEISDDRVEDPDEVLKVGDEVEVKVL 60

Query: 204 EANAETGRISLTMR 217
           + + E GRI L++R
Sbjct: 61  KVDKERGRIILSIR 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|238094 cd00164, S1_like, S1_like: Ribosomal protein S1-like RNA-binding domain

 Score = 71.6 bits (176), Expect = 9e-16
 Identities = 33/65 (50%), Positives = 44/65 (67%)

Query: 151 FTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETG 210
            TGKV SI  FG F++     +GLVH+S LSD FVKD   +  VG EV+V+++E + E G
Sbjct: 1   VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKG 60

Query: 211 RISLT 215
           RISL+
Sbjct: 61  RISLS 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|236305 PRK08582, PRK08582, hypothetical protein; Provisional

 Score = 73.1 bits (180), Expect = 2e-15
 Identities = 34/115 (29%), Positives = 59/115 (51%), Gaps = 6/115 (5%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
           G+   GKV  I  FGAF++      GLVH+S ++DN+VKD+   + VG EV+V+++    
Sbjct: 6   GSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNV-E 64

Query: 208 ETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVK 262
           + G+I L+++++ D  K Q  +                     +  E K ++F+K
Sbjct: 65  DDGKIGLSIKKAKDRPKRQHDRPRHEDNRGGGNDVAPK-----EDFEQKMSRFLK 114

Length = 139

>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 = 70.3 bits (173), Expect = 3e-15
 Identities = 30/80 (37%), Positives = 48/80 (60%), Gaps = 6/80 (7%)

Query: 148 GATFTGKVRSIQPFGAFI---DFGAFTDGLVHVSRLS-DNFVKDVGSIVSVGQEVKVRLI 203
           G  + GKV SI  FG F+         +GLVH+S+LS +  V +   +V  GQ+VKV++I
Sbjct: 1   GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVI 60

Query: 204 EANAETGRISLTMRESDDIS 223
             + + G+ISL+M++ D  +
Sbjct: 61  --SIQNGKISLSMKDVDQDT 78

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|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase

 Score = 78.3 bits (194), Expect = 5e-15
 Identities = 27/67 (40%), Positives = 42/67 (62%), Gaps = 1/67 (1%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
           G  + GKV  I  FGAF++     DGLVH+S +++  V+ V  ++  G EVKV+++E + 
Sbjct: 619 GKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEID- 677

Query: 208 ETGRISL 214
           + GRI L
Sbjct: 678 KQGRIKL 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|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]

 Score = 78.0 bits (193), Expect = 6e-15
 Identities = 28/74 (37%), Positives = 45/74 (60%), Gaps = 1/74 (1%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
           G  + G V  I  FGAF++     DGLVH+S+L+   V+ V  ++  G EVKV++IE + 
Sbjct: 620 GEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEID- 678

Query: 208 ETGRISLTMRESDD 221
           + GRI L+++   +
Sbjct: 679 KQGRIRLSIKAVLE 692

Length = 692

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

 Score = 76.7 bits (189), Expect = 1e-14
 Identities = 50/188 (26%), Positives = 87/188 (46%), Gaps = 34/188 (18%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLS-DNFVKDVGSIVSVGQEVKVRLIEAN 206
           G   TGK++ I  FGAF++     DGL+H+S +S D   ++   +   G E++  ++  +
Sbjct: 360 GDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAVD 419

Query: 207 AETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDL 266
            E  RISL +++                          T  P +K       K+  G  +
Sbjct: 420 KEKKRISLGVKQL-------------------------TENPWEKFAA----KYKVGSVV 450

Query: 267 EGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR-- 324
           +G V  +   GAF+ LP G EG +  SE S++   +      ++VG EV  +V+ I +  
Sbjct: 451 KGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKT--DEIKVGDEVEAKVVDIDKKN 508

Query: 325 GQVTLTMK 332
            +V+L++K
Sbjct: 509 RKVSLSVK 516

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

 Score = 76.3 bits (188), Expect = 2e-14
 Identities = 55/203 (27%), Positives = 87/203 (42%), Gaps = 38/203 (18%)

Query: 143 EDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDV---GSIVSVGQEVK 199
           + L  G   TGKV  + PFGAF++     +GLVHVS +S  + + V     +V+ G  V 
Sbjct: 288 DRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMS--WTRRVNKPEDVVAPGDAVA 345

Query: 200 VRLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTK 259
           V++ + +    RISL++R+              A GD           P     E    +
Sbjct: 346 VKIKDIDPAKRRISLSLRD--------------AEGD-----------PWADVAE----R 376

Query: 260 FVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRV 319
           F  G  + GTV+   + G F++L  G  G LP S  S  G         L+ G  V++ V
Sbjct: 377 FAPGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGKPATY--EKLKPGDSVTLVV 434

Query: 320 LRIS--RGQVTLTMKKEDDVGSN 340
             I   + +++L        G++
Sbjct: 435 EEIDTAKRKISLAPAGAAGSGAD 457

Length = 491

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

 Score = 73.8 bits (182), Expect = 1e-13
 Identities = 28/75 (37%), Positives = 47/75 (62%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
           G+   GKV  I PFGAF++     DGLVH+S++S   +     ++S G+EVK +++E + 
Sbjct: 563 GSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDP 622

Query: 208 ETGRISLTMRESDDI 222
           E  RI L+++E ++ 
Sbjct: 623 EEKRIRLSIKEVEEE 637

Length = 647

>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 = 65.0 bits (159), Expect = 3e-13
 Identities = 28/73 (38%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 148 GATFTGKVRSIQPFGAFIDF-GAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEAN 206
           G    G VR ++ +G FID  G    GL H S +SDN V D   +  VG +V+ ++++ +
Sbjct: 3   GQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKID 62

Query: 207 AETGRISLTMRES 219
           AE  RISL ++ S
Sbjct: 63  AEKKRISLGLKAS 75

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|233102 TIGR00717, rpsA, ribosomal protein S1

 Score = 70.9 bits (174), Expect = 8e-13
 Identities = 49/212 (23%), Positives = 85/212 (40%), Gaps = 49/212 (23%)

Query: 147 PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLS-DNFVKDVGSIVSVGQEVKVRLIEA 205
            G   TG+V ++  +G F++     +GLVHVS +S          +V  G EV+V +++ 
Sbjct: 272 VGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDI 331

Query: 206 NAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQD 265
           + E  R+SL +                         ++  + P ++ +E    K   G  
Sbjct: 332 DPERRRLSLGL-------------------------KQCKANPWEQFEE----KHPVGDR 362

Query: 266 LEGTVKNLTRSGAFISLPEGEEGFLPTSEES--DDGFANMMGGSSLQVGQEVSVRVLRIS 323
           + G +K +T  GAF+ L  G +G +  S+ S   DG          + G E+   VL + 
Sbjct: 363 VTGKIKKITDFGAFVELEGGIDGLIHLSDISWDKDGREAD---HLYKKGDEIEAVVLAVD 419

Query: 324 RGQVTLTMKKEDDVGSNLQLTQGVIHAATNPF 355
                    KE       +++ GV     NP+
Sbjct: 420 ---------KEKK-----RISLGVKQLTENPW 437

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

 Score = 70.8 bits (174), Expect = 1e-12
 Identities = 42/188 (22%), Positives = 82/188 (43%), Gaps = 33/188 (17%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
           G    GK+      G  +D        +  S +    V+D+  ++  G+E++ +++E + 
Sbjct: 106 GEIVEGKITGKVKGGLTVDIEGV-RAFLPGSLVDVRPVRDLDPLI--GKELEFKILELDK 162

Query: 208 ETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLE 267
           +   + L+ R   +  + +Q           R    +  + G+               +E
Sbjct: 163 KRNNVVLSRRAVLEEERSEQ-----------REELLNKLEVGEV--------------VE 197

Query: 268 GTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI--SRG 325
           G VKN+T  GAF+ +  G +G L  SE S     +      ++VG EV V+V+ +   RG
Sbjct: 198 GVVKNITDYGAFVDI-GGVDGLLHISEISWKRVDHP--SEVVKVGDEVKVKVISLDEERG 254

Query: 326 QVTLTMKK 333
           +V+L++K+
Sbjct: 255 RVSLSLKQ 262

Length = 541

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

 Score = 61.5 bits (150), Expect = 5e-12
 Identities = 29/73 (39%), Positives = 42/73 (57%), Gaps = 4/73 (5%)

Query: 262 KGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLR 321
            G  +EGTV  +T  GAF+ L  G EG +P SE SD    +      L+VG EV V+VL 
Sbjct: 2   VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDP--EEVLKVGDEVKVKVLS 59

Query: 322 I--SRGQVTLTMK 332
           +   +G++ L++K
Sbjct: 60  VDEEKGRIILSLK 72

Length = 72

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

 Score = 68.6 bits (168), Expect = 5e-12
 Identities = 50/196 (25%), Positives = 85/196 (43%), Gaps = 36/196 (18%)

Query: 143 EDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRL 202
           E +  G    G V  + PFGAF++     +G+VH+S LS + V+     VSVG  V+V++
Sbjct: 198 ETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKV 257

Query: 203 --IEANAETG--RISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTT 258
             IE   +    RISL++++              A GD   T                  
Sbjct: 258 LGIERAKKGKGLRISLSIKQ--------------AGGDPWDTV---------------GD 288

Query: 259 KFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVR 318
           +   G  + G V  L   GAF+ +  G EG +  SE S     N      +  G  V+V+
Sbjct: 289 RLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVN-KPEDVVAPGDAVAVK 347

Query: 319 V--LRISRGQVTLTMK 332
           +  +  ++ +++L+++
Sbjct: 348 IKDIDPAKRRISLSLR 363

Length = 491

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

 Score = 66.2 bits (162), Expect = 2e-11
 Identities = 60/186 (32%), Positives = 91/186 (48%), Gaps = 34/186 (18%)

Query: 153 GKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRI 212
           G V SI  FGAF+D G   DGLVHVS LS   +     +V VGQEV V +++ + +  R+
Sbjct: 214 GVVSSIVNFGAFVDLGG-VDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERV 272

Query: 213 SLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKN 272
           SL+++             AT   D  +   R T   GQ          V G+     V  
Sbjct: 273 SLSLK-------------ATQE-DPWQQFAR-THAIGQ---------IVPGK-----VTK 303

Query: 273 LTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI--SRGQVTLT 330
           L   GAF+ + EG EG +  SE ++      +    +QVG EV V+V+ I   R +++L+
Sbjct: 304 LVPFGAFVRVEEGIEGLVHISELAERHVE--VPEQVVQVGDEVFVKVIDIDLERRRISLS 361

Query: 331 MKKEDD 336
           +K+ ++
Sbjct: 362 LKQANE 367

Length = 486

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

 Score = 64.9 bits (159), Expect = 4e-11
 Identities = 31/102 (30%), Positives = 50/102 (49%), Gaps = 9/102 (8%)

Query: 143 EDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRL 202
           E L  G    G V+ +  FGAF++     +GLVH+S++S   +     ++  GQEVKV++
Sbjct: 273 EKLPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKV 332

Query: 203 IEANAETGRISLTMR---------ESDDISKLQQQKDATASG 235
           +E N E  RISL+++         E       Q +     +G
Sbjct: 333 LEVNEEEKRISLSIKALEEAPAEEEDRREEYRQYELPEEETG 374

Length = 390

>gnl|CDD|239917 cd04471, S1_RNase_R, S1_RNase_R: RNase R C-terminal S1 domain

 Score = 58.6 bits (143), Expect = 6e-11
 Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 16/83 (19%)

Query: 148 GATFTGKVRSIQPFGAFI---DFGAFTDGLVHVSRLSD---NFVKDVGSIV--------S 193
           G  F G +  +  FG F+   +     +GLVHVS L D    F ++  ++V         
Sbjct: 2   GEEFDGVISGVTSFGLFVELDNLTV--EGLVHVSTLGDDYYEFDEENHALVGERTGKVFR 59

Query: 194 VGQEVKVRLIEANAETGRISLTM 216
           +G +VKVR++  + +  +I   +
Sbjct: 60  LGDKVKVRVVRVDLDRRKIDFEL 82

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. Length = 83

>gnl|CDD|236289 PRK08563, PRK08563, DNA-directed RNA polymerase subunit E'; Provisional

 Score = 61.4 bits (150), Expect = 6e-11
 Identities = 24/81 (29%), Positives = 41/81 (50%), Gaps = 17/81 (20%)

Query: 153 GKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFV-----------KDVGSIVSVGQEVKVR 201
           G+V  +  FGAF+  G   DGL+H+S++ D+++           K+   ++ VG  V+ R
Sbjct: 87  GEVVEVVEFGAFVRIGPV-DGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRAR 145

Query: 202 LI-----EANAETGRISLTMR 217
           ++     E      +I LTMR
Sbjct: 146 IVAVSLKERRPRGSKIGLTMR 166

Length = 187

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

 Score = 64.8 bits (159), Expect = 8e-11
 Identities = 28/96 (29%), Positives = 52/96 (54%), Gaps = 7/96 (7%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
           G+  TG V  ++  GAF++     +GL+  S LS + V+D   ++ VG EV+ ++I  + 
Sbjct: 461 GSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDR 520

Query: 208 ETGRISLTMR------ESDDISKLQQQKDATAS-GD 236
           +  RISL+++      E + I++     D+  + GD
Sbjct: 521 KNRRISLSIKALDEAEEKEAIAEYNSASDSKTTLGD 556

Length = 565

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

 Score = 63.3 bits (154), Expect = 1e-10
 Identities = 30/71 (42%), Positives = 47/71 (66%), Gaps = 1/71 (1%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
           G    G VR I+P+GAFID G  + GL+H+S +S   ++   S+ +V  E+KV +I+ +A
Sbjct: 197 GEVVVGTVRGIKPYGAFIDIGGVS-GLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDA 255

Query: 208 ETGRISLTMRE 218
           E GRISL+ ++
Sbjct: 256 ERGRISLSTKQ 266

Length = 318

>gnl|CDD|239908 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

 Score = 56.8 bits (138), Expect = 2e-10
 Identities = 27/78 (34%), Positives = 37/78 (47%)

Query: 139 PVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEV 198
           P    DL PG    G VR+I P+G F++F     GL   S +SD FV D       GQ V
Sbjct: 6   PTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSV 65

Query: 199 KVRLIEANAETGRISLTM 216
             ++   + E  R  L++
Sbjct: 66  TAKVTSVDEEKQRFLLSL 83

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. Length = 83

>gnl|CDD|180908 PRK07252, PRK07252, hypothetical protein; Provisional

 Score = 57.8 bits (140), Expect = 3e-10
 Identities = 23/70 (32%), Positives = 44/70 (62%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
           G    G +  I+P+GAF+     T GL+H+S +   F+ ++  ++ VG+EV V++++ + 
Sbjct: 4   GDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDE 63

Query: 208 ETGRISLTMR 217
            TG+ SL++R
Sbjct: 64  YTGKASLSLR 73

Length = 120

>gnl|CDD|239907 cd04460, S1_RpoE, S1_RpoE: RpoE, S1-like RNA-binding domain

 Score = 54.2 bits (131), Expect = 3e-09
 Identities = 23/82 (28%), Positives = 42/82 (51%), Gaps = 17/82 (20%)

Query: 153 GKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFV-----------KDVGSIVSVGQEVKVR 201
           G+V  +  FGAF+  G   DGL+H+S++ D+++           ++   ++ VG  V+ R
Sbjct: 5   GEVVEVVDFGAFVRIGPV-DGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRAR 63

Query: 202 LI-----EANAETGRISLTMRE 218
           ++     E      +I LTMR+
Sbjct: 64  IVAVSLKERRPRESKIGLTMRQ 85

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. Length = 99

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

 Score = 50.4 bits (121), Expect = 3e-08
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 3/71 (4%)

Query: 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI 322
           G  +EGTV  L   GAF+ L  G  G +  S+ +     ++     L+ G +V V+VL I
Sbjct: 1   GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDV--KDVLKEGDKVKVKVLSI 58

Query: 323 -SRGQVTLTMK 332
            +RG+++L++K
Sbjct: 59  DARGRISLSIK 69

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

 Score = 50.1 bits (120), Expect = 4e-08
 Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 2/61 (3%)

Query: 266 LEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRG 325
           + G V ++T+ G F+ L +G EG +  SE SD    +       +VG EV V+VL +   
Sbjct: 1   VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSE--VFKVGDEVEVKVLEVDPE 58

Query: 326 Q 326
           +
Sbjct: 59  K 59

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

 Score = 55.9 bits (134), Expect = 6e-08
 Identities = 59/210 (28%), Positives = 91/210 (43%), Gaps = 42/210 (20%)

Query: 128 RSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKD 187
           R+R AR+     V  ED     + +G V+S   FGAFID G F DGL+HV+ +S   V  
Sbjct: 479 RARQAREEFFNSVHIED-----SVSGVVKSFTSFGAFIDLGGF-DGLLHVNDMSWGHVAR 532

Query: 188 VGSIVSVGQEVKVRLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSK 247
               V  GQ +++++I  +    RI+L+++       L+ +                   
Sbjct: 533 PREFVKKGQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFE------------------- 573

Query: 248 PGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGS 307
                      KF     ++G V  +   GAFI L EG EG    SE S   +       
Sbjct: 574 ----------NKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFS---WVKKTSKP 620

Query: 308 S--LQVGQEVSVRVL--RISRGQVTLTMKK 333
           S  +++G EV   +L   I  G+V+L +K+
Sbjct: 621 SDMVKIGDEVECMILGYDIQAGRVSLGLKQ 650

Length = 863

>gnl|CDD|235614 PRK05807, PRK05807, hypothetical protein; Provisional

 Score = 51.3 bits (123), Expect = 7e-08
 Identities = 32/118 (27%), Positives = 62/118 (52%), Gaps = 10/118 (8%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
           G+   G V +I  FGAF++    T GLVH+S ++D +VKD+   +    +VKV++I  + 
Sbjct: 6   GSILEGTVVNITNFGAFVEVEGKT-GLVHISEVADTYVKDIREHLKEQDKVKVKVISID- 63

Query: 208 ETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQD 265
           + G+ISL+++++    K  +  +     +K +    +         E + +KF+K  +
Sbjct: 64  DNGKISLSIKQAMKQKKSVKPAEIDWQKEKNKNNNGNF--------EDRLSKFLKDSE 113

Length = 136

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

 Score = 55.3 bits (134), Expect = 8e-08
 Identities = 22/75 (29%), Positives = 41/75 (54%), Gaps = 3/75 (4%)

Query: 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI 322
           G+  EGTV  +   GAF+ L  G++G +  S+ + +    +     L+ G EV V+V+ I
Sbjct: 620 GEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVEKV--EDVLKEGDEVKVKVIEI 677

Query: 323 -SRGQVTLTMKKEDD 336
             +G++ L++K   +
Sbjct: 678 DKQGRIRLSIKAVLE 692

Length = 692

>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 = 1e-07
 Identities = 42/193 (21%), Positives = 83/193 (43%), Gaps = 36/193 (18%)

Query: 144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLI 203
            +  G    G V S+     F+D G  ++G++ +  L+ + +  +   V VG E++V+++
Sbjct: 299 QIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVL 358

Query: 204 EANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKG 263
           +   E G + L+ +E+D     ++ ++A                            F  G
Sbjct: 359 KLEDEDGYVVLSKKEADREKAWKELEEA----------------------------FENG 390

Query: 264 QDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVL--- 320
           + ++G VK + + G  +    G   FLP S   + G+   +   S   GQE+ V+++   
Sbjct: 391 EPVKGKVKEVVK-GGLLVDYGGVRAFLPAS-HVELGYVEDL---SEYKGQELEVKIIEFN 445

Query: 321 RISRGQVTLTMKK 333
           R  R +V L+ K 
Sbjct: 446 RKRRKKVVLSRKA 458

Length = 647

>gnl|CDD|233703 TIGR02063, RNase_R, ribonuclease R

 Score = 54.6 bits (132), Expect = 1e-07
 Identities = 24/81 (29%), Positives = 42/81 (51%), Gaps = 12/81 (14%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFT-DGLVHVSRLSDNFV-----------KDVGSIVSVG 195
           G  F G +  +  FG F++    T +GLVH+S L D++            +  G +  +G
Sbjct: 628 GEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLG 687

Query: 196 QEVKVRLIEANAETGRISLTM 216
             VKVR+++A+ +TG+I   +
Sbjct: 688 DRVKVRVVKADLDTGKIDFEL 708

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 [Transcription, Degradation of RNA]. Length = 709

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

 Score = 53.5 bits (129), Expect = 2e-07
 Identities = 39/182 (21%), Positives = 77/182 (42%), Gaps = 36/182 (19%)

Query: 143 EDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRL 202
           E+  PG    G V SI+  G  +D G  ++G++ +S  S+   + V  +V VG EV+V +
Sbjct: 17  EEFEPGDVVKGTVVSIEKDGVLVDIGGKSEGVIPISEFSN---EPVEDVVQVGDEVEVLV 73

Query: 203 IEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVK 262
           +      G + L+ R      K ++++    + +K+                     F  
Sbjct: 74  LRVEDGEGELVLSRR------KAERER----AWEKLE------------------EAFEN 105

Query: 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI 322
           G+ +EG +    + G  + + EG   FLP S        ++       +G+E+  ++L +
Sbjct: 106 GEIVEGKITGKVKGGLTVDI-EGVRAFLPGSLVDVRPVRDL----DPLIGKELEFKILEL 160

Query: 323 SR 324
            +
Sbjct: 161 DK 162

Length = 541

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

 Score = 53.3 bits (129), Expect = 2e-07
 Identities = 47/187 (25%), Positives = 79/187 (42%), Gaps = 33/187 (17%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
           G     KV  +   G  +D      G +  S +S  FV+D       G+ ++V++IE + 
Sbjct: 106 GEVVEVKVTEVVKGGLVVDVEG-VRGFIPASLISTRFVEDFSDFK--GKTLEVKIIELDP 162

Query: 208 ETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLE 267
           E  R+ L+ R   +  +  ++++             S+ K G                 E
Sbjct: 163 EKNRVILSRRAVVEEERAAKKEEL-----------LSSLKEGDVV--------------E 197

Query: 268 GTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI--SRG 325
           GTV  LT  GAF+ +  G +G +  SE S +          + VGQEV V+VL I     
Sbjct: 198 GTVARLTDFGAFVDI-GGVDGLVHISELSHERVEKP--SEVVSVGQEVEVKVLSIDWETE 254

Query: 326 QVTLTMK 332
           +++L++K
Sbjct: 255 RISLSLK 261

Length = 390

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

 Score = 48.4 bits (116), Expect = 2e-07
 Identities = 31/76 (40%), Positives = 48/76 (63%), Gaps = 4/76 (5%)

Query: 259 KFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVR 318
           K  +G  ++GTV  +T+ GAF+ L  G EGF+P SE SDD   +      L+VG EV V+
Sbjct: 1   KPEEGDVVKGTVTRVTKGGAFVDLGNGVEGFIPISEISDDRVED--PDEVLKVGDEVEVK 58

Query: 319 VLRI--SRGQVTLTMK 332
           VL++   RG++ L+++
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|223631 COG0557, VacB, Exoribonuclease R [Transcription]

 Score = 54.3 bits (131), Expect = 2e-07
 Identities = 24/87 (27%), Positives = 40/87 (45%), Gaps = 16/87 (18%)

Query: 147 PGATFTGKVRSIQPFGAFI---DFGAFTDGLVHVSRLSDNFV-----------KDVGSIV 192
            G  F G V  +  FG F+   + G   +GLVH+S L D++            +  G + 
Sbjct: 622 VGEEFDGVVTGVTSFGFFVELPELGL--EGLVHISSLPDDYYHFDERGQALVGEKSGKVY 679

Query: 193 SVGQEVKVRLIEANAETGRISLTMRES 219
            +G EVKV++   + +  +I   + ES
Sbjct: 680 RLGDEVKVKVTSVDLDERKIDFELVES 706

Length = 706

>gnl|CDD|240191 cd05686, S1_pNO40, S1_pNO40: pNO40 , S1-like RNA-binding domain

 Score = 48.6 bits (116), Expect = 2e-07
 Identities = 23/67 (34%), Positives = 37/67 (55%), Gaps = 2/67 (2%)

Query: 151 FTGKVRSIQPFGAFIDF-GAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAET 209
           F G+V S+  +GAF+   G    GLVH S +S   V D   +V VG++V V++I      
Sbjct: 7   FKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVI-GREMK 65

Query: 210 GRISLTM 216
            ++ L++
Sbjct: 66  DKMKLSL 72

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. Length = 73

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

 Score = 47.5 bits (113), Expect = 3e-07
 Identities = 26/68 (38%), Positives = 37/68 (54%), Gaps = 1/68 (1%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLS-DNFVKDVGSIVSVGQEVKVRLIEAN 206
           G   +GK++SI  FG F+      DGLVH+S +S    V+    I   GQEV+  ++  +
Sbjct: 1   GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNID 60

Query: 207 AETGRISL 214
            E  RISL
Sbjct: 61  VERERISL 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|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional

 Score = 53.1 bits (129), Expect = 4e-07
 Identities = 25/77 (32%), Positives = 41/77 (53%), Gaps = 3/77 (3%)

Query: 257 TTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVS 316
           T +   G+  EG V  +   GAF+ +  G++G +  SE +D+    +     L+ G EV 
Sbjct: 616 TAEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKV--EDVLKEGDEVK 673

Query: 317 VRVLRI-SRGQVTLTMK 332
           V+VL I  RG++ L+ K
Sbjct: 674 VKVLEIDKRGRIRLSRK 690

Length = 693

>gnl|CDD|240203 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

 Score = 47.2 bits (113), Expect = 5e-07
 Identities = 20/65 (30%), Positives = 34/65 (52%)

Query: 153 GKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRI 212
           G +  ++P G  + F     G +  S LS+ F+KD      VGQ VKV+++  + E  R+
Sbjct: 6   GTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRL 65

Query: 213 SLTMR 217
            L+ +
Sbjct: 66  LLSCK 70

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. Length = 70

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

 Score = 50.3 bits (121), Expect = 2e-06
 Identities = 48/189 (25%), Positives = 84/189 (44%), Gaps = 34/189 (17%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEAN- 206
           G    GKV+ +   G  +D+G      +  S +   +V+D+      GQE++V++IE N 
Sbjct: 390 GEPVKGKVKEVVKGGLLVDYGGVR-AFLPASHVELGYVEDLSEYK--GQELEVKIIEFNR 446

Query: 207 AETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDL 266
               ++ L+ +       L+++K                    +K+ E       +G  +
Sbjct: 447 KRRKKVVLSRKAI-----LEEEK--------------------EKKKEETWNSLEEGDVV 481

Query: 267 EGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR-- 324
           EG VK LT  GAF+ +  G +G L  SE S            L+VG E+ V +L I +  
Sbjct: 482 EGEVKRLTDFGAFVDI-GGVDGLLHVSEISWGRVEKPS--DVLKVGDEIKVYILDIDKEN 538

Query: 325 GQVTLTMKK 333
            +++L++KK
Sbjct: 539 KKLSLSLKK 547

Length = 647

>gnl|CDD|215104 PLN00207, PLN00207, polyribonucleotide nucleotidyltransferase; Provisional

 Score = 51.0 bits (122), Expect = 2e-06
 Identities = 34/125 (27%), Positives = 58/125 (46%), Gaps = 10/125 (8%)

Query: 155 VRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISL 214
           ++SI P+GAF++     +GL H+S LS N++        VG  + V+LIE N + G++ L
Sbjct: 762 IKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVN-DKGQLRL 820

Query: 215 TMR------ESDDISKLQQQ---KDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQD 265
           + R       S+  S+ QQ    KD       V T+ R       +++  +     K +D
Sbjct: 821 SRRALLPEANSEKSSQKQQGGSTKDKAPQKKYVNTSSRPRRAAQAEKNSAENAAVPKKKD 880

Query: 266 LEGTV 270
            +   
Sbjct: 881 YKRAT 885

Length = 891

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

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 18/67 (26%), Positives = 37/67 (55%), Gaps = 2/67 (2%)

Query: 153 GKVRSIQPFGAFIDFGAFTD--GLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETG 210
             V+SI   GA++    + +  G++ +S LS   ++ +  +V VG++  V++I  + E G
Sbjct: 9   VTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKG 68

Query: 211 RISLTMR 217
            I L+ +
Sbjct: 69  YIDLSKK 75

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

 Score = 50.0 bits (120), Expect = 3e-06
 Identities = 24/93 (25%), Positives = 51/93 (54%), Gaps = 11/93 (11%)

Query: 142 NEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVR 201
           +E    G+   GKV+S++  GAF++ G   +GL+ +S LS +       ++ VG EV+  
Sbjct: 444 SEKYKKGSVVKGKVKSVKDKGAFVELGGGVEGLIRLSELSRD-------VLKVGDEVEAV 496

Query: 202 LIEANAETGRISLTMRESDDISKLQQQKDATAS 234
           ++  + +  +I L+++  +     +++K+A  S
Sbjct: 497 VVSIDKKNRKILLSIKALER----KEEKEALES 525

Length = 541

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

 Score = 49.2 bits (118), Expect = 3e-06
 Identities = 20/82 (24%), Positives = 45/82 (54%), Gaps = 5/82 (6%)

Query: 153 GKVRSIQPFGAFIDFGAFTD--GLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETG 210
           G V+ +  +GA+++   +    G +H+S ++  +VK++   V  GQ+V  +++  + + G
Sbjct: 17  GTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRG 76

Query: 211 RISLTMR---ESDDISKLQQQK 229
            I L+++   E     K+Q+ K
Sbjct: 77  HIDLSLKRVTEHQRRKKIQEWK 98

Length = 269

>gnl|CDD|240212 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

 Score = 44.6 bits (106), Expect = 3e-06
 Identities = 24/63 (38%), Positives = 36/63 (57%)

Query: 153 GKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRI 212
           G V++I   G F+  G   D  V VS LSD+++KD      VGQ VK +++  + + GRI
Sbjct: 6   GFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRI 65

Query: 213 SLT 215
            +T
Sbjct: 66  EMT 68

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. Length = 68

>gnl|CDD|236305 PRK08582, PRK08582, hypothetical protein; Provisional

 Score = 45.8 bits (109), Expect = 7e-06
 Identities = 29/75 (38%), Positives = 45/75 (60%), Gaps = 3/75 (4%)

Query: 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI 322
           G  L+G V  +T  GAF+ LPEG+ G +  SE +D+   ++     L+VG EV V+VL +
Sbjct: 6   GSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDI--NDHLKVGDEVEVKVLNV 63

Query: 323 SR-GQVTLTMKKEDD 336
              G++ L++KK  D
Sbjct: 64  EDDGKIGLSIKKAKD 78

Length = 139

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

 Score = 43.7 bits (103), Expect = 7e-06
 Identities = 25/69 (36%), Positives = 41/69 (59%), Gaps = 3/69 (4%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDV--GSIVSVGQEVKVRLIEA 205
           G    GKV ++  +G F++     +GLVHVS + D   K++    +VS+G EV+V +++ 
Sbjct: 4   GTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEM-DWTNKNIHPSKVVSLGDEVEVMVLDI 62

Query: 206 NAETGRISL 214
           + E  RISL
Sbjct: 63  DEERRRISL 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|239918 cd04472, S1_PNPase, S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain

 Score = 42.9 bits (102), Expect = 1e-05
 Identities = 23/70 (32%), Positives = 40/70 (57%), Gaps = 3/70 (4%)

Query: 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI 322
           G+  EG V  +   GAF+ +  G++G +  SE SD+    +     L+VG EV V+V+ +
Sbjct: 1   GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKV--EDVLKVGDEVKVKVIEV 58

Query: 323 -SRGQVTLTM 331
             RG+++L+ 
Sbjct: 59  DDRGRISLSR 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|224023 COG1098, VacB, Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]

 Score = 45.0 bits (107), Expect = 1e-05
 Identities = 26/75 (34%), Positives = 45/75 (60%), Gaps = 3/75 (4%)

Query: 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI 322
           G  L+G +  +T  GAF+ L  G+ G +  SE +D    ++     L+VGQEV V+VL I
Sbjct: 6   GSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDI--HDHLKVGQEVKVKVLDI 63

Query: 323 -SRGQVTLTMKKEDD 336
              G+++L+++K ++
Sbjct: 64  DENGKISLSIRKLEE 78

Length = 129

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

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 21/70 (30%), Positives = 39/70 (55%), Gaps = 6/70 (8%)

Query: 268 GTVKNLTRSGAFISLPE--GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI--S 323
            TVK++   GA++SL E    EG +  SE S     ++     ++VG++  V+V+R+   
Sbjct: 9   VTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSI--RKLVKVGRKEVVKVIRVDKE 66

Query: 324 RGQVTLTMKK 333
           +G + L+ K+
Sbjct: 67  KGYIDLSKKR 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|239919 cd04473, S1_RecJ_like, S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 20/62 (32%), Positives = 30/62 (48%), Gaps = 8/62 (12%)

Query: 143 EDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRL 202
           EDL  G  + GKV  +  +G F+D      GL+H S L  ++         VG EV V++
Sbjct: 12  EDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLRDY--------EVGDEVIVQV 63

Query: 203 IE 204
            +
Sbjct: 64  TD 65

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. Length = 77

>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 = 42.2 bits (100), Expect = 2e-05
 Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 4/70 (5%)

Query: 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI 322
           G  LEG V N+T  GAF+ +   ++G +  S+ +D   ++      + VG  V V+V+ I
Sbjct: 1   GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDV--VSVGDIVEVKVISI 58

Query: 323 --SRGQVTLT 330
              RG+++L+
Sbjct: 59  DEERGRISLS 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|225094 COG2183, Tex, Transcriptional accessory protein [Transcription]

 Score = 47.3 bits (113), Expect = 2e-05
 Identities = 35/136 (25%), Positives = 62/136 (45%), Gaps = 18/136 (13%)

Query: 217 RESDDISKLQQQKDATASGDKVRTTR---RSTSKPGQK-RDEMKT----------TKFVK 262
           RE   +  L  ++ A      + T         KPG+  RDE  T          T    
Sbjct: 599 RERAKLKSLNLEEFADELDFGLPTLEDIILELEKPGRDPRDEFHTPTLDEGVESITDLKP 658

Query: 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI 322
           G  LEGTV+N+   GAF+ +   ++G +  S+ SD    +      ++VG  V V+V+ +
Sbjct: 659 GMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPN--EVVKVGDIVKVKVIEV 716

Query: 323 --SRGQVTLTMKKEDD 336
             +R ++ L+M+ +++
Sbjct: 717 DTARKRIALSMRLDEE 732

Length = 780

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

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 24/63 (38%), Positives = 36/63 (57%), Gaps = 3/63 (4%)

Query: 262 KGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLR 321
           +G  +EGTVK++T  GAF+ L  G +G L  S+ S     +      + VG EV V+VL+
Sbjct: 1   EGDVVEGTVKSITDFGAFVDL-GGVDGLLHISDMSWGRVKH--PSEVVNVGDEVEVKVLK 57

Query: 322 ISR 324
           I +
Sbjct: 58  IDK 60

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

 Score = 42.3 bits (100), Expect = 3e-05
 Identities = 20/70 (28%), Positives = 37/70 (52%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
           G+  TGKV  +   GA +  G   +G +  + LS + V+D      VG EV+ ++   + 
Sbjct: 1   GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDR 60

Query: 208 ETGRISLTMR 217
           +  +ISL+++
Sbjct: 61  KNRKISLSIK 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 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|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase

 Score = 46.0 bits (110), Expect = 5e-05
 Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 3/68 (4%)

Query: 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI 322
           G+  EG V  +   GAF+ +  G++G +  SE +++    +     L+ G EV V+VL I
Sbjct: 619 GKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVEKV--EDVLKEGDEVKVKVLEI 676

Query: 323 SR-GQVTL 329
            + G++ L
Sbjct: 677 DKQGRIKL 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|224018 COG1093, SUI2, Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]

 Score = 45.0 bits (107), Expect = 5e-05
 Identities = 25/70 (35%), Positives = 41/70 (58%), Gaps = 6/70 (8%)

Query: 268 GTVKNLTRSGAFISLPE--GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI--S 323
           GTVK +   GA++ L E  G+EGF+  SE +     N+     ++ GQ+V  +VLR+   
Sbjct: 17  GTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIR--DYVKEGQKVVAKVLRVDPK 74

Query: 324 RGQVTLTMKK 333
           RG + L++K+
Sbjct: 75  RGHIDLSLKR 84

Length = 269

>gnl|CDD|225543 COG2996, COG2996, Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]

 Score = 44.6 bits (106), Expect = 8e-05
 Identities = 39/183 (21%), Positives = 65/183 (35%), Gaps = 46/183 (25%)

Query: 153 GKVRSIQP-FGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGR 211
            KV  +    GAF+D+G   D LV +  L              G ++ V L       GR
Sbjct: 79  LKVVEVNKDLGAFLDWGLPKDLLVPLDELP----TLKSLWPQKGDKLLVYLYVDK--KGR 132

Query: 212 ISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVK 271
           I  T+     +  L                                   +K Q+++ TV 
Sbjct: 133 IWGTLAIEKILENL----------------------------ATPAYNNLKNQEVDATVY 164

Query: 272 NLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR-GQVTLT 330
            L  SG F+    G  GF+  SE     FA        ++G+ ++ RV+ +   G++ L+
Sbjct: 165 RLLESGTFVITENGYLGFIHKSER----FA------EPRLGERLTARVIGVREDGKLNLS 214

Query: 331 MKK 333
           ++ 
Sbjct: 215 LRP 217

Length = 287

>gnl|CDD|240202 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

 Score = 40.7 bits (96), Expect = 8e-05
 Identities = 20/68 (29%), Positives = 30/68 (44%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
           G    G +R ++P G F+       GLV    L+D  +K        G +VK R++    
Sbjct: 1   GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEP 60

Query: 208 ETGRISLT 215
           E  R+ LT
Sbjct: 61  ERKRLVLT 68

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. Length = 69

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

 Score = 45.1 bits (106), Expect = 1e-04
 Identities = 37/147 (25%), Positives = 65/147 (44%), Gaps = 34/147 (23%)

Query: 153 GKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGS---IVSVGQEVKVRLIEANAET 209
           G+V  I  FGAFI+     +GL H+S  S  +VK       +V +G EV+  ++  + + 
Sbjct: 584 GRVTKIADFGAFIELAEGIEGLAHISEFS--WVKKTSKPSDMVKIGDEVECMILGYDIQA 641

Query: 210 GRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGT 269
           GR+SL +++                          T+ P ++ +     ++  G      
Sbjct: 642 GRVSLGLKQV-------------------------TANPWEEIE----ARYPVGARFTRR 672

Query: 270 VKNLTRSGAFISLPEGEEGFLPTSEES 296
           +  +T +GAFI + EG +GFL   + S
Sbjct: 673 IVKVTNAGAFIEMEEGIDGFLHVDDLS 699

Length = 863

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

 Score = 40.6 bits (96), Expect = 1e-04
 Identities = 20/70 (28%), Positives = 36/70 (51%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
           G    G V S+      +D G  ++G++ +S  SD+ +++    V VG EV+V ++    
Sbjct: 1   GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVED 60

Query: 208 ETGRISLTMR 217
           E G + L+ R
Sbjct: 61  EEGNVVLSKR 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|235188 PRK03987, PRK03987, translation initiation factor IF-2 subunit alpha; Validated

 Score = 43.3 bits (103), Expect = 2e-04
 Identities = 24/70 (34%), Positives = 42/70 (60%), Gaps = 6/70 (8%)

Query: 268 GTVKNLTRSGAFISLPE--GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI--S 323
           GTVK +   GAF++L E  G+EGF+  SE +     N+     ++ GQ+V  +V+R+   
Sbjct: 14  GTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIR--DHVKEGQKVVCKVIRVDPR 71

Query: 324 RGQVTLTMKK 333
           +G + L++K+
Sbjct: 72  KGHIDLSLKR 81

Length = 262

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

 Score = 43.6 bits (104), Expect = 3e-04
 Identities = 36/153 (23%), Positives = 68/153 (44%), Gaps = 38/153 (24%)

Query: 185 VKDVGSIVSVGQEVKVRLIEANAETGRISLTMR---ESDDISKLQQQKDATASGDKVRTT 241
           V+D   +   G+E++ ++I+ + +   I ++ R   E +                     
Sbjct: 151 VRDTDPLE--GKELEFKVIKLDKKRNNIVVSRRAVLEEER-------------------- 188

Query: 242 RRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFA 301
                   ++R+E+      +GQ +EG VKN+T  GAF+ L  G +G L  ++ S     
Sbjct: 189 -------AEEREELLE-NLEEGQVVEGVVKNITDYGAFVDL-GGVDGLLHITDISWKRVN 239

Query: 302 NMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMK 332
           +      + VG EV V+VL+    + +V+L +K
Sbjct: 240 HP--SEVVNVGDEVKVKVLKFDKEKKRVSLGLK 270

Length = 565

>gnl|CDD|224020 COG1095, RPB7, DNA-directed RNA polymerase, subunit E' [Transcription]

 Score = 41.9 bits (99), Expect = 3e-04
 Identities = 24/83 (28%), Positives = 42/83 (50%), Gaps = 17/83 (20%)

Query: 152 TGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFV-----------KDVGSIVSVGQEVKV 200
            G+V  +  FGAF+  G   DGLVHVS++ D+++           ++   ++ VG +V+ 
Sbjct: 86  EGEVVEVVEFGAFVRIGPL-DGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRA 144

Query: 201 RLI-----EANAETGRISLTMRE 218
           R++            +I LTMR+
Sbjct: 145 RIVGVSLKSRRPRESKIGLTMRQ 167

Length = 183

>gnl|CDD|239917 cd04471, S1_RNase_R, S1_RNase_R: RNase R C-terminal S1 domain

 Score = 38.5 bits (91), Expect = 6e-04
 Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 12/81 (14%)

Query: 263 GQDLEGTVKNLTRSGAFISLPE-GEEGFLPTSEESDDGF----ANMM-----GGSSLQVG 312
           G++ +G +  +T  G F+ L     EG +  S   DD +     N        G   ++G
Sbjct: 2   GEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLG 61

Query: 313 QEVSVRVLRIS--RGQVTLTM 331
            +V VRV+R+   R ++   +
Sbjct: 62  DKVKVRVVRVDLDRRKIDFEL 82

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. Length = 83

>gnl|CDD|131743 TIGR02696, pppGpp_PNP, guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

 Score = 42.9 bits (101), Expect = 6e-04
 Identities = 40/147 (27%), Positives = 67/147 (45%), Gaps = 39/147 (26%)

Query: 75  IISATGINVAVEESDS---PAADDDSAGASDIPSDVETSESSSIKSEASPTLAESRRSRT 131
           I   TG  +++E+  +    AAD  SA A+           + I + A+PT         
Sbjct: 603 IQDETGAEISIEDDGTVYIGAADGPSAEAA----------RAMINAIANPT--------- 643

Query: 132 ARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSD----NFVKD 187
                MP V       G  F G V     FGAF+      DGL+H+S++        V++
Sbjct: 644 -----MPEV-------GERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVEN 691

Query: 188 VGSIVSVGQEVKVRLIEANAETGRISL 214
           V  ++SVGQ+++V + + + + G++SL
Sbjct: 692 VEDVLSVGQKIQVEIADID-DRGKLSL 717

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. Length = 719

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

 Score = 37.9 bits (88), Expect = 0.001
 Identities = 25/60 (41%), Positives = 30/60 (50%), Gaps = 1/60 (1%)

Query: 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI 322
           G  L G V NLT  G F+ L EG EG +  S E D    N+     + +G EV V VL I
Sbjct: 4   GTRLFGKVTNLTDYGCFVELEEGVEGLVHVS-EMDWTNKNIHPSKVVSLGDEVEVMVLDI 62

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|129540 TIGR00448, rpoE, DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form

 Score = 39.8 bits (93), Expect = 0.001
 Identities = 27/83 (32%), Positives = 42/83 (50%), Gaps = 17/83 (20%)

Query: 152 TGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFV-----------KDVGSIVSVGQEVKV 200
            G+V  I  FGAF+  G F DGL HVS+++D++            K+   ++  G +V+ 
Sbjct: 86  EGEVIEIVEFGAFVSLGPF-DGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRA 144

Query: 201 R-----LIEANAETGRISLTMRE 218
           R     L +   E  +I LTMR+
Sbjct: 145 RIVALSLKDRRPEGSKIGLTMRQ 167

This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE [Transcription, DNA-dependent RNA polymerase]. Length = 179

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

 Score = 40.6 bits (96), Expect = 0.002
 Identities = 37/183 (20%), Positives = 78/183 (42%), Gaps = 34/183 (18%)

Query: 143 EDLIPGATFTGKVRSIQPFGAFID-FGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVR 201
           +++  G   TG+V  ++    F++  G   +G++ +S LS++ ++D+  +V VG E++V 
Sbjct: 13  KEVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDINDVVKVGDELEVY 72

Query: 202 LIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFV 261
           +++     G + L+ R  +      + ++    G+ V               E+K T+ V
Sbjct: 73  VLKVEDGEGNLLLSKRRLEAEKAWDKLEEKFEEGEVV---------------EVKVTEVV 117

Query: 262 KGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLR 321
           K              G  +   EG  GF+P S  S     +     S   G+ + V+++ 
Sbjct: 118 K--------------GGLVVDVEGVRGFIPASLISTRFVED----FSDFKGKTLEVKIIE 159

Query: 322 ISR 324
           +  
Sbjct: 160 LDP 162

Length = 390

>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 = 37.2 bits (87), Expect = 0.002
 Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 4/72 (5%)

Query: 267 EGTVKNLTRSGAFISL---PEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS 323
           +G V ++   G F+ L      +EG +  S+ S +G         ++ GQ+V V+V+ I 
Sbjct: 5   KGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPS-DVVKRGQKVKVKVISIQ 63

Query: 324 RGQVTLTMKKED 335
            G+++L+MK  D
Sbjct: 64  NGKISLSMKDVD 75

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|180960 PRK07400, PRK07400, 30S ribosomal protein S1; Reviewed

 Score = 40.2 bits (94), Expect = 0.002
 Identities = 64/261 (24%), Positives = 103/261 (39%), Gaps = 62/261 (23%)

Query: 147 PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEAN 206
           PG    G V S++P GA ID GA T   + +  +S N V+    ++   +  +  ++   
Sbjct: 31  PGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDE 90

Query: 207 AETGRISLT------MRESDDISKLQQQKDATASGDKVRTTRR----------------- 243
            E G+++L+      MR  + + +LQ++ DAT   +   T R                  
Sbjct: 91  NEDGQLTLSIRRIEYMRAWERVRQLQKE-DATVRSEVFATNRGGALVRIEGLRGFIPGSH 149

Query: 244 -STSKPGQKRD-----------------------------EMKTTKFVKGQDLEGTVKNL 273
            ST KP  K +                             E K  +   G+ + GTV+ +
Sbjct: 150 ISTRKP--KEELVGEELPLKFLEVDEERNRLVLSHRRALVERKMNRLEVGEVVVGTVRGI 207

Query: 274 TRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRV--LRISRGQVTLTM 331
              GAFI +  G  G L  SE S +        S   V  E+ V +  L   RG+++L+ 
Sbjct: 208 KPYGAFIDI-GGVSGLLHISEISHEHIETPH--SVFNVNDEMKVMIIDLDAERGRISLST 264

Query: 332 KK-EDDVGSNLQLTQGVIHAA 351
           K+ E + G  L+  Q V   A
Sbjct: 265 KQLEPEPGDMLKDPQKVFDKA 285

Length = 318

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

 Score = 40.5 bits (94), Expect = 0.003
 Identities = 36/144 (25%), Positives = 60/144 (41%), Gaps = 30/144 (20%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLS-DNFVKDVGSIVSVGQEVKVRLIEAN 206
           GA FT ++  +   GAFI+     DG +HV  LS     +     + VG+E++  +IE +
Sbjct: 666 GARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWVKRTRPADHELEVGKEIECMVIECD 725

Query: 207 AETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDL 266
            +  RI L +++  D                          P Q    +    +  G  +
Sbjct: 726 PQARRIRLGVKQLSD-------------------------NPWQ----VFANAYGVGSTV 756

Query: 267 EGTVKNLTRSGAFISLPEGEEGFL 290
           EG V ++T  G F+ +P G EG +
Sbjct: 757 EGEVSSVTDFGIFVRVPGGVEGLV 780

Length = 863

>gnl|CDD|232937 TIGR00358, 3_prime_RNase, VacB and RNase II family 3'-5' exoribonucleases

 Score = 40.5 bits (95), Expect = 0.003
 Identities = 24/81 (29%), Positives = 38/81 (46%), Gaps = 12/81 (14%)

Query: 148 GATFTGKVRSIQPFGAFIDF-GAFTDGLVHVSRLSDNFV-----------KDVGSIVSVG 195
           G  F+G++ S+  FG F+       DGL+H+S L +++            K  G +  +G
Sbjct: 573 GTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIG 632

Query: 196 QEVKVRLIEANAETGRISLTM 216
             V V+L E N ET  I   +
Sbjct: 633 DRVTVKLTEVNMETRSIIFEL 653

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 [Transcription, Degradation of RNA]. Length = 654

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

 Score = 36.1 bits (84), Expect = 0.004
 Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 2/62 (3%)

Query: 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI 322
           G  + G V  +   GA + L +G EGFL  +E S D   +       +VG EV  ++  +
Sbjct: 1   GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDA--TERFKVGDEVEAKITNV 58

Query: 323 SR 324
            R
Sbjct: 59  DR 60

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

 Score = 39.4 bits (93), Expect = 0.004
 Identities = 23/82 (28%), Positives = 44/82 (53%), Gaps = 5/82 (6%)

Query: 153 GKVRSIQPFGAFIDFGAFTD--GLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETG 210
           G V+ ++ FGAF+    +    G +H+S ++  +VK++   V  GQ+V  ++I  +   G
Sbjct: 14  GTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKG 73

Query: 211 RISLTMR---ESDDISKLQQQK 229
            I L+++   E     K+Q+ K
Sbjct: 74  HIDLSLKRVNEHQRREKIQEWK 95

Length = 262

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	681
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	100.0
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	100.0
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	100.0
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	100.0
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	100.0
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	100.0
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	100.0
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	100.0
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	100.0
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	100.0
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	100.0
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	100.0
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	100.0
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	100.0
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	99.97
PRK07400	318	30S ribosomal protein S1; Reviewed	99.97
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	99.97
PRK07400	318	30S ribosomal protein S1; Reviewed	99.96
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	99.69
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.69
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.62
COG1098	129	VacB Predicted RNA binding protein (contains ribos	99.56
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	99.52
COG1098	129	VacB Predicted RNA binding protein (contains ribos	99.5
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	99.45
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	99.44
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	99.43
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	99.4
PRK08582	139	hypothetical protein; Provisional	99.39
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	99.38
PRK08582	139	hypothetical protein; Provisional	99.36
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	99.36
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	99.35
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	99.35
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	99.34
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	99.34
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	99.34
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	99.34
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	99.32
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	99.32
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	99.31
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	99.31
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	99.3
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	99.29
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	99.29
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	99.29
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	99.28
PRK07252	120	hypothetical protein; Provisional	99.27
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	99.26
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	99.25
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	99.23
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	99.23
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	99.23
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	99.21
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	99.2
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	99.2
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	99.2
PRK05807	136	hypothetical protein; Provisional	99.2
PRK08059	123	general stress protein 13; Validated	99.19
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	99.19
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	99.18
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	99.17
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	99.17
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	99.17
PRK07252	120	hypothetical protein; Provisional	99.16
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	99.15
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	99.15
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	99.15
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	99.15
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	99.14
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	99.13
PRK05807	136	hypothetical protein; Provisional	99.13
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	99.12
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	99.12
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	99.11
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	99.11
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	99.11
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	99.11
PRK11642	813	exoribonuclease R; Provisional	99.11
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	99.11
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	99.1
PRK08059	123	general stress protein 13; Validated	99.1
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	99.1
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	99.09
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	99.09
PHA02945	88	interferon resistance protein; Provisional	99.07
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	99.07
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	99.06
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	99.03
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	99.02
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	98.99
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	98.98
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	98.97
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	98.97
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	98.96
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	98.95
PRK03987	262	translation initiation factor IF-2 subunit alpha;	98.95
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	98.93
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	98.93
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	98.91
COG2183	780	Tex Transcriptional accessory protein [Transcripti	98.9
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	98.88
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	98.88
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	98.88
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	98.87
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	98.86
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.85
PHA02945	88	interferon resistance protein; Provisional	98.84
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	98.84
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	98.84
PRK03987	262	translation initiation factor IF-2 subunit alpha;	98.82
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	98.81
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	98.81
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	98.79
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.79
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	98.76
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	98.76
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	98.75
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	98.66
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	98.66
PRK09202	470	nusA transcription elongation factor NusA; Validat	98.63
PRK05054	644	exoribonuclease II; Provisional	98.63
COG2183	780	Tex Transcriptional accessory protein [Transcripti	98.62
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	98.61
COG0557	706	VacB Exoribonuclease R [Transcription]	98.61
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	98.61
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	98.6
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	98.57
PRK09202	470	nusA transcription elongation factor NusA; Validat	98.54
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	98.53
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	98.52
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	98.5
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	98.47
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	98.45
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	98.43
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	98.4
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	98.38
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	98.31
PRK12327	362	nusA transcription elongation factor NusA; Provisi	98.2
TIGR01953	341	NusA transcription termination factor NusA. This m	98.2
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	98.16
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	98.14
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	98.1
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	98.06
PRK11642	813	exoribonuclease R; Provisional	98.05
TIGR01953	341	NusA transcription termination factor NusA. This m	98.05
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	98.05
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	98.04
PRK12327	362	nusA transcription elongation factor NusA; Provisi	98.01
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	97.99
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	97.91
PHA02858	86	EIF2a-like PKR inhibitor; Provisional	97.87
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	97.83
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	97.78
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	97.74
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	97.65
KOG2916	304	consensus Translation initiation factor 2, alpha s	97.52
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	97.48
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	97.36
PHA02858	86	EIF2a-like PKR inhibitor; Provisional	97.33
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	97.32
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	97.32
PRK12328	374	nusA transcription elongation factor NusA; Provisi	97.23
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	97.18
COG1107	715	Archaea-specific RecJ-like exonuclease, contains D	97.18
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	97.15
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	97.11
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	97.1
PRK05054	644	exoribonuclease II; Provisional	97.04
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	96.99
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	96.94
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	96.85
PRK12329	449	nusA transcription elongation factor NusA; Provisi	96.5
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	96.47
COG1107	715	Archaea-specific RecJ-like exonuclease, contains D	96.43
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	96.43
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	96.3
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	96.3
KOG1856	1299	consensus Transcription elongation factor SPT6 [RN	96.21
PRK12328	374	nusA transcription elongation factor NusA; Provisi	96.14
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	96.01
KOG2916	304	consensus Translation initiation factor 2, alpha s	95.96
PRK10811	1068	rne ribonuclease E; Reviewed	95.8
PRK12329	449	nusA transcription elongation factor NusA; Provisi	95.72
PRK10811	1068	rne ribonuclease E; Reviewed	95.7
COG0557	706	VacB Exoribonuclease R [Transcription]	95.58
PRK11712	489	ribonuclease G; Provisional	95.17
PRK11712	489	ribonuclease G; Provisional	94.93
KOG1856	1299	consensus Transcription elongation factor SPT6 [RN	94.89
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	94.66
KOG3298	170	consensus DNA-directed RNA polymerase subunit E' [	93.57
PF08292	122	RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I	93.4
COG1530	487	CafA Ribonucleases G and E [Translation, ribosomal	91.41
KOG3298	170	consensus DNA-directed RNA polymerase subunit E' [	91.14
COG1530	487	CafA Ribonucleases G and E [Translation, ribosomal	90.56
PF10246	104	MRP-S35: Mitochondrial ribosomal protein MRP-S35;	89.16
PRK12442	87	translation initiation factor IF-1; Reviewed	88.9
TIGR00008	68	infA translation initiation factor IF-1. This fami	88.49
PF10246	104	MRP-S35: Mitochondrial ribosomal protein MRP-S35;	86.95
KOG3409	193	consensus Exosomal 3'-5' exoribonuclease complex,	86.9
PF08292	122	RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I	84.45
PF00313	66	CSD: 'Cold-shock' DNA-binding domain; InterPro: IP	83.88
KOG3409	193	consensus Exosomal 3'-5' exoribonuclease complex,	83.27
cd05700	65	S1_Rrp5_repeat_hs9 S1_Rrp5_repeat_hs9: Rrp5 is a t	81.88
cd04458	65	CSP_CDS Cold-Shock Protein (CSP) contains an S1-li	81.17

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

Probab=100.00  E-value=3.8e-47  Score=420.91  Aligned_cols=274  Identities=26%  Similarity=0.359  Sum_probs=244.7

Q ss_pred             ceeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCChhh
Q 005707           44 SQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASPTL  123 (681)
Q Consensus        44 ~~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~~da  123 (681)
                      ..|+++|++|+|||+|+|+++..  +-.++..|+|+++.++|+++|++++   ++++|+|               +.-++
T Consensus       118 KGG~~Vdi~gvr~FlP~S~v~~r--~v~d~~~~~Gk~~~~kiie~d~~~n---~vv~SrR---------------~~~e~  177 (541)
T COG0539         118 KGGLTVDIEGVRAFLPGSLVDVR--PVRDLDPLIGKELEFKILELDKKRN---NVVLSRR---------------AVLEE  177 (541)
T ss_pred             cCcEEEEECCEEEeccHHHhccc--ccccccccCCceEEEEEEEEccccC---cEEEEhH---------------HHhhH
Confidence            47899999999999999999976  2234667899999999999999999   9999998               11111


Q ss_pred             HHhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEE
Q 005707          124 AESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLI  203 (681)
Q Consensus       124 ek~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl  203 (681)
                      ++    .+.+..     .+..|++|+++.|+|+++++||+||+|+| ++||||+++|+|.++.+|.+.|++||.|+|+|+
T Consensus       178 ~~----~~~r~e-----~~~~l~~G~vV~G~V~~It~~GafVdigG-vdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi  247 (541)
T COG0539         178 ER----SEQREE-----LLNKLEVGEVVEGVVKNITDYGAFVDIGG-VDGLLHISEISWKRVDHPSEVVKVGDEVKVKVI  247 (541)
T ss_pred             HH----HHHHHH-----HHhcCCCCceEEEEEEEeecCcEEEEecC-eeeEEehhhccccccCCHHHhcccCCEEEEEEE
Confidence            11    111112     26789999999999999999999999999 999999999999999999999999999999999


Q ss_pred             EEeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEEEeC
Q 005707          204 EANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLP  283 (681)
Q Consensus       204 ~VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFVeIg  283 (681)
                      ++|.+++||.||+|++.++||.                             ....+|++|+.+.|+|+++++|||||++.
T Consensus       248 ~~D~e~~RVsLSlK~l~~dPw~-----------------------------~i~~~~~~g~~v~G~Vt~i~~~GafVei~  298 (541)
T COG0539         248 SLDEERGRVSLSLKQLEEDPWE-----------------------------GIEKKYPVGDKVEGKVTNLTDYGAFVEIE  298 (541)
T ss_pred             EEccCCCeEEEEehhcccCcHH-----------------------------HHhhhcCCCCEEEEEEEEeecCcEEEEec
Confidence            9999999999999999999994                             56788999999999999999999999999


Q ss_pred             CCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCcCCc--------ceeeeEEEEeec
Q 005707          284 EGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVGSNL--------QLTQGVIHAATN  353 (681)
Q Consensus       284 ~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP~e~--------~lv~G~V~~~i~  353 (681)
                      +|++||+|.||++|.+...  |.+.+++||.|.|+||.||  ++||.|+||+...|||..        ..+.|.|. +++
T Consensus       299 ~GvEGlvhvSEisw~~~~~--P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~~~~~~~g~~v~g~v~-~~t  375 (541)
T COG0539         299 EGVEGLVHVSEISWTKKNV--PSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFADKHPVGDVVEGKVK-SIT  375 (541)
T ss_pred             CCccceeechhhcccccCC--HHHhcccCCEEEEEEEeeCchhceEEeeehhhhcChhhhhhhhcCCCCeEEEEEe-eec
Confidence            9999999999999998643  8999999999999999997  699999999999999882        34688888 899


Q ss_pred             ccEEEEEEcCCeEEEeeCCccccccc
Q 005707          354 PFVLAFRSNKDISSFLDERDKSATAA  379 (681)
Q Consensus       354 ~fGlfV~l~~gI~GfIp~~els~~~~  379 (681)
                      +||+|+.+.+|+.||+|.++++|...
T Consensus       376 ~~g~fv~le~gidG~vh~~d~sw~~~  401 (541)
T COG0539         376 DFGAFVELEGGIDGLVHLSDLSWDRP  401 (541)
T ss_pred             ccceEEccCCCccceEEHHhcCcccc
Confidence            99999999999999999999998644

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=100.00  E-value=2.3e-40  Score=367.78  Aligned_cols=274  Identities=20%  Similarity=0.254  Sum_probs=234.9

Q ss_pred             ceeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCChhh
Q 005707           44 SQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASPTL  123 (681)
Q Consensus        44 ~~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~~da  123 (681)
                      ..++++++.|++||+|.+++++...  ..+..++|+.+.|+|+++|++++   +++||+|              ......
T Consensus       128 ~~G~~V~i~g~~~flP~s~~~~~~~--~~~~~~vG~~i~~~V~~id~~~~---~v~lSrk--------------~~~~~~  188 (491)
T PRK13806        128 KGGFNVEVLGRRAFCPVSQIDLRYV--EDPESYVGQTFQFLITRVEENGR---NIVVSRR--------------ALLERE  188 (491)
T ss_pred             cCCEEEEECCEEEEEEHHHhccccC--CChHHcCCCeEEEEEEEEECCCC---eEEEEee--------------hhhhhh
Confidence            4678899999999999999997622  23445799999999999999888   8999987              110000


Q ss_pred             HHhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEE
Q 005707          124 AESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLI  203 (681)
Q Consensus       124 ek~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl  203 (681)
                      ..    . ....     -+..+++|+++.|+|+++.++|+||+|++++.||||+++++|.++.++.+.|++||.|+|+|+
T Consensus       189 ~~----~-~~~~-----~~~~l~~G~iv~G~V~~v~~~G~fV~l~~gv~g~v~~sels~~~~~~~~~~~~vGd~i~vkVl  258 (491)
T PRK13806        189 QK----E-ALEA-----FMETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVL  258 (491)
T ss_pred             hH----H-HHHH-----HHhhCCCCCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCCccccChhHhcCCCCEEEEEEE
Confidence            00    0 0000     034689999999999999999999999877999999999999999999999999999999999


Q ss_pred             EEeccC----CceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEE
Q 005707          204 EANAET----GRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAF  279 (681)
Q Consensus       204 ~VD~ek----grI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaF  279 (681)
                      ++|.++    +||.||+|++..+||.                             ....+|++|+++.|+|+++.++|+|
T Consensus       259 ~id~~~~~~~~ri~lS~K~~~~~p~~-----------------------------~~~~~~~~G~~v~G~V~~v~~~G~f  309 (491)
T PRK13806        259 GIERAKKGKGLRISLSIKQAGGDPWD-----------------------------TVGDRLKAGDKVTGKVVRLAPFGAF  309 (491)
T ss_pred             EEecccCCcceEEEEEehhhhcccch-----------------------------hhhccCCCCCEEEEEEEEEeCceEE
Confidence            999876    4799999999988882                             4577899999999999999999999


Q ss_pred             EEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCcCC--------cceeeeEEE
Q 005707          280 ISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVGSN--------LQLTQGVIH  349 (681)
Q Consensus       280 VeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP~e--------~~lv~G~V~  349 (681)
                      |++++|++||+|.++++|... ..++...|++||.|+|+|+++|  ++|+.||+|++..|||.        ++.+.|+|+
T Consensus       310 V~l~~gv~Glvh~sels~~~~-~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~~~p~~~~~~~~~vG~~v~G~V~  388 (491)
T PRK13806        310 VEILPGIEGLVHVSEMSWTRR-VNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAERFAPGTTVTGTVE  388 (491)
T ss_pred             EEeCCCcEEEEEHHHcCcccc-cCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEeecccChhHHhhhhCCCCCEEEEEEE
Confidence            999999999999999998431 2356788999999999999997  58999999999999987        356799999


Q ss_pred             EeecccEEEEEEcCCeEEEeeCCccccc
Q 005707          350 AATNPFVLAFRSNKDISSFLDERDKSAT  377 (681)
Q Consensus       350 ~~i~~fGlfV~l~~gI~GfIp~~els~~  377 (681)
                       .+.+||+||++.+|+.||||.+++++.
T Consensus       389 -~i~~~G~FV~l~~gv~Gli~~se~s~~  415 (491)
T PRK13806        389 -KRAQFGLFVNLAPGVTGLLPASVISRA  415 (491)
T ss_pred             -EEecCceEEEcCCCcEEEEEHHHcCcc
Confidence             899999999999999999999999986

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=100.00  E-value=6e-39  Score=374.25  Aligned_cols=270  Identities=19%  Similarity=0.268  Sum_probs=234.2

Q ss_pred             ceeEEeccCCceeEEeCcccCccc-ccccchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCChh
Q 005707           44 SQRFLLPLPSSVRFFSQFQSGSAL-QHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASPT  122 (681)
Q Consensus        44 ~~~l~~dl~glrGfIP~sq~~~~~-~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~~d  122 (681)
                      ..++.++++|++||+|.++++|.. .+...+. .+|+.+.|+|+++|++++   +++||.|              .... 
T Consensus       506 ~~G~fVdl~Gv~Gfvp~SeiS~~~v~~~~~~~-kvGq~v~vkVi~iD~e~~---rI~LSlK--------------~l~~-  566 (863)
T PRK12269        506 SFGAFIDLGGFDGLLHVNDMSWGHVARPREFV-KKGQTIELKVIRLDQAEK---RINLSLK--------------HFQP-  566 (863)
T ss_pred             CCcEEEEECCEEEEEEchhccccccCCHHHhc-cCCCEEEEEEEEEecCCC---eEEEEEe--------------cccc-
Confidence            578999999999999999999862 2222223 379999999999999988   9999987              0000 


Q ss_pred             hHHhhhchhhhhcCCCCCC-cCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCC-ccccCcccccccCCEEEE
Q 005707          123 LAESRRSRTARKSEMPPVK-NEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSD-NFVKDVGSIVSVGQEVKV  200 (681)
Q Consensus       123 aek~~~kr~~rk~e~~~lt-~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~-~~v~d~~e~fkVGd~VkV  200 (681)
                                    .+... .+.+++|+++.|+|+++.+||+||+|+.+++||+|+++++| .++.+|.+.|++||.|+|
T Consensus       567 --------------~p~~~~~~~~~vG~iV~G~V~~I~~fG~fVeL~~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~v  632 (863)
T PRK12269        567 --------------DPWLEFENKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVEC  632 (863)
T ss_pred             --------------chhhhhhccCCCCCEEEEEEEEEeCCeEEEEecCCceeeeEHHHhcCccccCCHHHcCCCCCEEEE
Confidence                          01111 34689999999999999999999999877999999999999 578899999999999999


Q ss_pred             EEEEEeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEE
Q 005707          201 RLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFI  280 (681)
Q Consensus       201 kVl~VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFV  280 (681)
                      +|+++|+++++|.||+|++..+||.                             ....+|++|+++.|+|+++++||+||
T Consensus       633 kVl~iD~e~~rIsLS~K~l~~~Pw~-----------------------------~~~~~~~vG~~v~G~V~~i~~~G~fV  683 (863)
T PRK12269        633 MILGYDIQAGRVSLGLKQVTANPWE-----------------------------EIEARYPVGARFTRRIVKVTNAGAFI  683 (863)
T ss_pred             EEEEEecccCceEEEehhcccCchH-----------------------------HHHHhCCCCCEEEEEEEEEecceEEE
Confidence            9999999999999999999999993                             34678999999999999999999999


Q ss_pred             EeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCcCC--------cceeeeEEEE
Q 005707          281 SLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVGSN--------LQLTQGVIHA  350 (681)
Q Consensus       281 eIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP~e--------~~lv~G~V~~  350 (681)
                      +|++|++||||.++++|.+.. .++...|++||.|+|+|+++|  ++||.||+|++..|||+        ++.+.|+|. 
T Consensus       684 ~l~~gV~GlIh~sels~~~~~-~~~~~~~kvGq~VkvkVl~ID~e~rrI~LS~K~l~~dpw~~~~~~~~vG~iV~GkV~-  761 (863)
T PRK12269        684 EMEEGIDGFLHVDDLSWVKRT-RPADHELEVGKEIECMVIECDPQARRIRLGVKQLSDNPWQVFANAYGVGSTVEGEVS-  761 (863)
T ss_pred             EeCCCcEEEEEhHHhhccccc-cchhhccCCCCEEEEEEEEEeccCCEEEEEecccccChHHHHHhhCCCCCEEEEEEE-
Confidence            999999999999999997631 234568999999999999997  59999999999999988        245788998 


Q ss_pred             eecccEEEEEEcCCeEEEeeCCccccc
Q 005707          351 ATNPFVLAFRSNKDISSFLDERDKSAT  377 (681)
Q Consensus       351 ~i~~fGlfV~l~~gI~GfIp~~els~~  377 (681)
                      .+.+||+||++.+|+.||+|.+++++.
T Consensus       762 ~v~~~GvFVeL~~gVeGlI~~s~lsdd  788 (863)
T PRK12269        762 SVTDFGIFVRVPGGVEGLVRKQHLVEN  788 (863)
T ss_pred             EEecCeEEEEcCCCeEEEEEHHHcCCc
Confidence            799999999999999999999999986

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=100.00  E-value=1.4e-38  Score=371.09  Aligned_cols=274  Identities=24%  Similarity=0.268  Sum_probs=233.6

Q ss_pred             eeEEeccC-CceeEEeCcccCcccccccchhhcccceeEEEEEecCCCC--CCCCcceecCCCCCcccccccccccCCCh
Q 005707           45 QRFLLPLP-SSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPA--ADDDSAGASDIPSDVETSESSSIKSEASP  121 (681)
Q Consensus        45 ~~l~~dl~-glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~--~~~~~lvlSer~s~v~~ae~ss~~sea~~  121 (681)
                      .++++|++ |++||||.+|++..  ....+..++|+.+.|+|+++|...  .+..++++|+|              .+..
T Consensus       414 gG~~Vdig~~~~gfiP~se~~~~--~~~~~~~~vG~~ie~~V~~~~~~~~~~~~~~iVlSrr--------------~~l~  477 (863)
T PRK12269        414 SGFEVDLGAGMMAFLPISQSDCQ--KVDAPESLIGLTSKFYIERISQSKQHRGNDNIVINRR--------------RYLE  477 (863)
T ss_pred             CEEEEEECCCcEEEEEHHHhccc--cccchHHhCCCeEEEEEEEEecccccCCCCeEEEEHH--------------HHHH
Confidence            47889995 89999999999865  333466789999999999998632  22337999987              1111


Q ss_pred             hhHHhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEE
Q 005707          122 TLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVR  201 (681)
Q Consensus       122 daek~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVk  201 (681)
                      +..+     ..+..     .+..+++|++|.|+|+++.++|+||+++| ++||||+++++|.++.++.+.|++||.|+|+
T Consensus       478 e~~~-----~~~ee-----~~~~l~~G~~V~G~Vk~i~~~G~fVdl~G-v~Gfvp~SeiS~~~v~~~~~~~kvGq~v~vk  546 (863)
T PRK12269        478 ERAR-----QAREE-----FFNSVHIEDSVSGVVKSFTSFGAFIDLGG-FDGLLHVNDMSWGHVARPREFVKKGQTIELK  546 (863)
T ss_pred             HHHH-----HHHHH-----HHhcCCCCCEEEEEEEEEeCCcEEEEECC-EEEEEEchhccccccCCHHHhccCCCEEEEE
Confidence            1111     11111     15679999999999999999999999965 9999999999999999999999999999999


Q ss_pred             EEEEeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEEE
Q 005707          202 LIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFIS  281 (681)
Q Consensus       202 Vl~VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFVe  281 (681)
                      |+++|+++++|.||+|.+..+||.                             ....+|++|+++.|+|+++.+||+||+
T Consensus       547 Vi~iD~e~~rI~LSlK~l~~~p~~-----------------------------~~~~~~~vG~iV~G~V~~I~~fG~fVe  597 (863)
T PRK12269        547 VIRLDQAEKRINLSLKHFQPDPWL-----------------------------EFENKFGVNDVVKGRVTKIADFGAFIE  597 (863)
T ss_pred             EEEEecCCCeEEEEEeccccchhh-----------------------------hhhccCCCCCEEEEEEEEEeCCeEEEE
Confidence            999999999999999999888883                             346679999999999999999999999


Q ss_pred             eCCCeEEEEeCCCCCcc-cccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCcCCc--------ceeeeEEEE
Q 005707          282 LPEGEEGFLPTSEESDD-GFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVGSNL--------QLTQGVIHA  350 (681)
Q Consensus       282 Ig~GIeGLLpiSELSd~-~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP~e~--------~lv~G~V~~  350 (681)
                      |++|++||+|+++++|. +.  .+|...|++||+|+|+|+++|  ++|+.||+|++..|||+.        +.+.|+|. 
T Consensus       598 L~~gveGLvhiSEls~~~~~--~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw~~~~~~~~vG~~v~G~V~-  674 (863)
T PRK12269        598 LAEGIEGLAHISEFSWVKKT--SKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIEARYPVGARFTRRIV-  674 (863)
T ss_pred             ecCCceeeeEHHHhcCcccc--CCHHHcCCCCCEEEEEEEEEecccCceEEEehhcccCchHHHHHhCCCCCEEEEEEE-
Confidence            99999999999999994 42  356788999999999999998  589999999999999972        45788998 


Q ss_pred             eecccEEEEEEcCCeEEEeeCCccccc
Q 005707          351 ATNPFVLAFRSNKDISSFLDERDKSAT  377 (681)
Q Consensus       351 ~i~~fGlfV~l~~gI~GfIp~~els~~  377 (681)
                      .+.+||+||.+.+|+.||||.+++++.
T Consensus       675 ~i~~~G~fV~l~~gV~GlIh~sels~~  701 (863)
T PRK12269        675 KVTNAGAFIEMEEGIDGFLHVDDLSWV  701 (863)
T ss_pred             EEecceEEEEeCCCcEEEEEhHHhhcc
Confidence            899999999999999999999999875

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

Probab=100.00  E-value=8.9e-39  Score=354.46  Aligned_cols=268  Identities=22%  Similarity=0.294  Sum_probs=240.0

Q ss_pred             ceeEEeccCCceeEEeCcccCcc-cccccchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCChh
Q 005707           44 SQRFLLPLPSSVRFFSQFQSGSA-LQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASPT  122 (681)
Q Consensus        44 ~~~l~~dl~glrGfIP~sq~~~~-~~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~~d  122 (681)
                      +.++.+|++|+.||+|.++++|. ..+...... +|+.|.|+|+.+|++++   |+.||=+                   
T Consensus       205 ~~GafVdigGvdGLlHiseiS~~rv~~P~~vvk-vGd~VkvkVi~~D~e~~---RVsLSlK-------------------  261 (541)
T COG0539         205 DYGAFVDIGGVDGLLHISEISWKRVDHPSEVVK-VGDEVKVKVISLDEERG---RVSLSLK-------------------  261 (541)
T ss_pred             cCcEEEEecCeeeEEehhhccccccCCHHHhcc-cCCEEEEEEEEEccCCC---eEEEEeh-------------------
Confidence            68899999999999999999998 444455566 89999999999999999   8888765                   


Q ss_pred             hHHhhhchhhhhcCCCCCC--cCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEE
Q 005707          123 LAESRRSRTARKSEMPPVK--NEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKV  200 (681)
Q Consensus       123 aek~~~kr~~rk~e~~~lt--~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkV  200 (681)
                                 +....||.  ...+.+|+.+.|+|+++++||+||++..+++||+|+|||+|.+...|.+++++||.|.|
T Consensus       262 -----------~l~~dPw~~i~~~~~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V  330 (541)
T COG0539         262 -----------QLEEDPWEGIEKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEV  330 (541)
T ss_pred             -----------hcccCcHHHHhhhcCCCCEEEEEEEEeecCcEEEEecCCccceeechhhcccccCCHHHhcccCCEEEE
Confidence                       22334554  46899999999999999999999999999999999999999999889999999999999


Q ss_pred             EEEEEeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEE
Q 005707          201 RLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFI  280 (681)
Q Consensus       201 kVl~VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFV  280 (681)
                      +|+++|++++||.|++|++..+||+                             .....|++|.++.|+|++++++|+||
T Consensus       331 ~Vl~id~e~rRIsL~iKq~~~~pw~-----------------------------~~~~~~~~g~~v~g~v~~~t~~g~fv  381 (541)
T COG0539         331 KVLDIDPERRRISLGLKQLKENPWE-----------------------------EFADKHPVGDVVEGKVKSITDFGAFV  381 (541)
T ss_pred             EEEeeCchhceEEeeehhhhcChhh-----------------------------hhhhhcCCCCeEEEEEeeecccceEE
Confidence            9999999999999999999999993                             34566999999999999999999999


Q ss_pred             EeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCcCCc--------ceeeeEEEE
Q 005707          281 SLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVGSNL--------QLTQGVIHA  350 (681)
Q Consensus       281 eIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP~e~--------~lv~G~V~~  350 (681)
                      .+++|++||+|.++++|....  .+...|+.|+.++++||.+|  ++|+.|++|++..+||..        ..++|.|. 
T Consensus       382 ~le~gidG~vh~~d~sw~~~~--~~~~~~k~Gd~v~~~vl~vd~~~~~isLgiKql~~~p~~~~~~~~~~~~~v~~~v~-  458 (541)
T COG0539         382 ELEGGIDGLVHLSDLSWDRPG--EEAEKYKKGDEVEAKVLAVDKEKERISLGIKQLEESPWEEFSEKYKKGSVVKGKVK-  458 (541)
T ss_pred             ccCCCccceEEHHhcCccccC--cHHHhhccCcEEEEEEEEEecccceeeeehhhhccCchhhhHhhccCCCeEEEEEE-
Confidence            999999999999999998743  23449999999999999998  479999999999999983        45688888 


Q ss_pred             eecccEEEEEEcCCeEEEeeCCccccc
Q 005707          351 ATNPFVLAFRSNKDISSFLDERDKSAT  377 (681)
Q Consensus       351 ~i~~fGlfV~l~~gI~GfIp~~els~~  377 (681)
                      .+.++|+|+++.+++.||++.++++..
T Consensus       459 ~i~~~G~~v~l~~~v~G~i~~~~~~~~  485 (541)
T COG0539         459 SVKDKGAFVELGGGVEGLIRLSELSRD  485 (541)
T ss_pred             EEccCceEEEecCceeeeeecchhhhh
Confidence            899999999999999999999999985

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=2.3e-37  Score=347.87  Aligned_cols=273  Identities=26%  Similarity=0.336  Sum_probs=234.6

Q ss_pred             ceeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCChhh
Q 005707           44 SQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASPTL  123 (681)
Q Consensus        44 ~~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~~da  123 (681)
                      ..+++++++|++||+|.+++++..  ...+..++|+.+.|+|+++|.+++   +++||+|              .+....
T Consensus       127 ~~G~~V~~~g~~gfip~s~~~~~~--~~~~~~~vG~~i~~~V~~~d~~~~---~i~lS~k--------------~~~~~~  187 (565)
T PRK06299        127 KGGFTVDLNGVEAFLPGSQVDVRP--VRDTDPLEGKELEFKVIKLDKKRN---NIVVSRR--------------AVLEEE  187 (565)
T ss_pred             CCEEEEEECCEEEEEEHHHccCcC--CCChHHhCCCEEEEEEEEEECCCC---EEEEEhH--------------Hhhhhh
Confidence            468899999999999999999863  223456799999999999999998   9999998              111010


Q ss_pred             HHhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEE
Q 005707          124 AESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLI  203 (681)
Q Consensus       124 ek~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl  203 (681)
                      +...     +..     .+.++++|+++.|+|+.+.++|+||+++ ++.||||+++++|.++.++.+.|++||.|+|+|+
T Consensus       188 ~~~~-----~~~-----~~~~l~~G~iv~g~V~~v~~~G~~V~i~-g~~glv~~se~s~~~~~~~~~~~kvG~~v~v~V~  256 (565)
T PRK06299        188 RAEE-----REE-----LLENLEEGQVVEGVVKNITDYGAFVDLG-GVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVL  256 (565)
T ss_pred             hhhH-----HHH-----HHhcCCCCCEEEEEEEEEeCCeEEEEEC-CEEEEEEHHHhcccccCCHhhcCCCCCEEEEEEE
Confidence            0000     001     1567999999999999999999999998 5999999999999999999999999999999999


Q ss_pred             EEeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEEEeC
Q 005707          204 EANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLP  283 (681)
Q Consensus       204 ~VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFVeIg  283 (681)
                      .+|+++++|.||+|.+..+||.                             ....+|++|+++.|+|+++.++|+||+|+
T Consensus       257 ~~d~~~~~i~lS~k~~~~~p~~-----------------------------~~~~~~~~G~~v~g~V~~i~~~G~fV~l~  307 (565)
T PRK06299        257 KFDKEKKRVSLGLKQLGEDPWE-----------------------------AIEKKYPVGSKVKGKVTNITDYGAFVELE  307 (565)
T ss_pred             EEeCCCCeEEEEEEecccChhH-----------------------------HHHhhCCCCCEEEEEEEEEeCCeEEEEeC
Confidence            9999999999999999989983                             34567999999999999999999999999


Q ss_pred             CCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCcCC--------cceeeeEEEEeec
Q 005707          284 EGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVGSN--------LQLTQGVIHAATN  353 (681)
Q Consensus       284 ~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP~e--------~~lv~G~V~~~i~  353 (681)
                      +|++||+|.++++|.+. ..+|...|++||.|.|+|+.+|  ++++.||+|+...+||.        ++.+.|.|. .++
T Consensus       308 ~~v~Glv~~sel~~~~~-~~~~~~~~~~G~~v~v~V~~id~~~~~i~ls~k~~~~~p~~~~~~~~~~G~~v~g~V~-~v~  385 (565)
T PRK06299        308 EGIEGLVHVSEMSWTKK-NKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCKENPWEEFAEKYPVGDVVEGKVK-NIT  385 (565)
T ss_pred             CCCEEEEEHHHcCcccc-ccCHHHhcCCCCEEEEEEEEEcCCCCEEEEehHHhccchhhhHHHhCCCCCEEEEEEE-EEe
Confidence            99999999999998642 2345567999999999999997  48999999999999986        356789998 799


Q ss_pred             ccEEEEEEcCCeEEEeeCCccccc
Q 005707          354 PFVLAFRSNKDISSFLDERDKSAT  377 (681)
Q Consensus       354 ~fGlfV~l~~gI~GfIp~~els~~  377 (681)
                      ++|+||++.+++.||+|.+++++.
T Consensus       386 ~~G~fV~l~~~v~g~i~~s~l~~~  409 (565)
T PRK06299        386 DFGAFVGLEGGIDGLVHLSDISWD  409 (565)
T ss_pred             cceEEEECCCCCEEEEEHHHcCcc
Confidence            999999998899999999999864

>TIGR00717 rpsA ribosomal protein S1

Probab=100.00  E-value=5.8e-36  Score=332.54  Aligned_cols=272  Identities=28%  Similarity=0.356  Sum_probs=231.7

Q ss_pred             eeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCChhhH
Q 005707           45 QRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASPTLA  124 (681)
Q Consensus        45 ~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~~dae  124 (681)
                      .+++++++|++||+|.++++....+  ....++|+.+.|+|+++|...+   ++++|+|              ......+
T Consensus       114 ~g~~V~i~g~~~flP~s~~~~~~~~--~~~~~vG~~i~~~v~~~~~~~~---~iv~Srk--------------~~l~~~~  174 (516)
T TIGR00717       114 GGFIVDLNGVEAFLPGSQVDVKPIK--DLDSLIGKTLKFKIIKLDQKRN---NIVVSRR--------------AYLEEER  174 (516)
T ss_pred             CEEEEEECCEEEEEeHHHhcCcccC--chhhhCCCEEEEEEEEEECCCC---cEEEEHH--------------HHHHHHH
Confidence            6788999999999999998764211  2345799999999999999877   8999987              1111111


Q ss_pred             HhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEE
Q 005707          125 ESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIE  204 (681)
Q Consensus       125 k~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~  204 (681)
                      +    . .+..     .+..+++|++++|+|+++.++|+||+++| ++||||.++++|.+..++.+.|++|+.|+|+|+.
T Consensus       175 ~----~-~~~~-----~~~~l~~G~~v~g~V~~i~~~G~~V~l~g-~~g~lp~~e~s~~~~~~~~~~~~vG~~v~v~Vl~  243 (516)
T TIGR00717       175 S----Q-AREE-----LLENLKEGDVVKGVVKNITDFGAFVDLGG-VDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIK  243 (516)
T ss_pred             H----H-HHHH-----HHHhccCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHcCCCCCCCHHHhccCCCEEEEEEEE
Confidence            0    0 0111     14579999999999999999999999976 9999999999999999999999999999999999


Q ss_pred             EeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEEEeCC
Q 005707          205 ANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPE  284 (681)
Q Consensus       205 VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFVeIg~  284 (681)
                      +|++++++.||+|.+..+||.                             ....++++|+++.|+|+++.++|+||++++
T Consensus       244 ~d~~~~~i~lS~k~~~~~p~~-----------------------------~~~~~~~~G~i~~g~V~~v~~~G~fV~l~~  294 (516)
T TIGR00717       244 FDKEKGRISLSLKQLGEDPWE-----------------------------AIEKKFPVGDKITGRVTNLTDYGVFVEIEE  294 (516)
T ss_pred             EECCCCcEEEEEEecchhHHH-----------------------------HHHhhccCCCEEEEEEEEeeCCcEEEEeCC
Confidence            999999999999999888883                             345679999999999999999999999999


Q ss_pred             CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCcCC--------cceeeeEEEEeecc
Q 005707          285 GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVGSN--------LQLTQGVIHAATNP  354 (681)
Q Consensus       285 GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP~e--------~~lv~G~V~~~i~~  354 (681)
                      |+.||||.++++|.+. ..++...|++||.|.|+|+.+|  ++++.||+|+...+||.        ++.+.|+|. .+.+
T Consensus       295 ~v~g~v~~sels~~~~-~~~~~~~~~vG~~v~v~V~~id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~-~v~~  372 (516)
T TIGR00717       295 GIEGLVHVSEMSWVKK-NSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEKHPVGDRVTGKIK-KITD  372 (516)
T ss_pred             CCEEEEEHHHcCCccc-cCCHHHhccCCCEEEEEEEEEcCCCCEEEEEehhcccCcHHHHHHhCCCCCEEEEEEE-EEec
Confidence            9999999999998632 2234567999999999999997  58999999999999984        467789999 7999


Q ss_pred             cEEEEEEcCCeEEEeeCCccccc
Q 005707          355 FVLAFRSNKDISSFLDERDKSAT  377 (681)
Q Consensus       355 fGlfV~l~~gI~GfIp~~els~~  377 (681)
                      +|+||.+.+|+.||+|.+++++.
T Consensus       373 ~G~fV~l~~~v~glv~~s~ls~~  395 (516)
T TIGR00717       373 FGAFVELEGGIDGLIHLSDISWD  395 (516)
T ss_pred             ceEEEECCCCCEEEEEHHHCcCc
Confidence            99999999999999999999975

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=100.00  E-value=3.8e-35  Score=326.02  Aligned_cols=272  Identities=19%  Similarity=0.239  Sum_probs=230.1

Q ss_pred             ceeEEeccCCceeEEeCcccCcccccc-cchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCChh
Q 005707           44 SQRFLLPLPSSVRFFSQFQSGSALQHK-SALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASPT  122 (681)
Q Consensus        44 ~~~l~~dl~glrGfIP~sq~~~~~~~~-~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~~d  122 (681)
                      +.++.++++|+.||+|.+++++...+. ..+.. +|+.+.|+|+.+|.+++   ++.+|.+              .+...
T Consensus       200 ~~G~~V~l~g~~g~lp~~e~s~~~~~~~~~~~~-vG~~v~v~Vl~~d~~~~---~i~lS~k--------------~~~~~  261 (516)
T TIGR00717       200 DFGAFVDLGGVDGLLHITDMSWKRVKHPSEYVK-VGQEVKVKVIKFDKEKG---RISLSLK--------------QLGED  261 (516)
T ss_pred             CCeEEEEECCEEEEEEHHHcCCCCCCCHHHhcc-CCCEEEEEEEEEECCCC---cEEEEEE--------------ecchh
Confidence            467888999999999999998763222 22233 89999999999999888   8899877              11000


Q ss_pred             hHHhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCc-cccCcccccccCCEEEEE
Q 005707          123 LAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDN-FVKDVGSIVSVGQEVKVR  201 (681)
Q Consensus       123 aek~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~-~v~d~~e~fkVGd~VkVk  201 (681)
                      +.   .      .     ....+++|+++.|+|+++.++|+||+++.++.||||+++++|+ ...++...|++||.|+|+
T Consensus       262 p~---~------~-----~~~~~~~G~i~~g~V~~v~~~G~fV~l~~~v~g~v~~sels~~~~~~~~~~~~~vG~~v~v~  327 (516)
T TIGR00717       262 PW---E------A-----IEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVM  327 (516)
T ss_pred             HH---H------H-----HHhhccCCCEEEEEEEEeeCCcEEEEeCCCCEEEEEHHHcCCccccCCHHHhccCCCEEEEE
Confidence            00   0      0     0246889999999999999999999998889999999999986 456677789999999999


Q ss_pred             EEEEeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEEE
Q 005707          202 LIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFIS  281 (681)
Q Consensus       202 Vl~VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFVe  281 (681)
                      |+.+|++++++.||+|.+..+||.                             ....++++|+++.|+|++++++|+||+
T Consensus       328 V~~id~~~~~i~lS~k~~~~~p~~-----------------------------~~~~~~~~G~~v~g~V~~v~~~G~fV~  378 (516)
T TIGR00717       328 ILDIDPERRRLSLGLKQCKANPWE-----------------------------QFEEKHPVGDRVTGKIKKITDFGAFVE  378 (516)
T ss_pred             EEEEcCCCCEEEEEehhcccCcHH-----------------------------HHHHhCCCCCEEEEEEEEEecceEEEE
Confidence            999999999999999998888883                             345678999999999999999999999


Q ss_pred             eCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCcCC--------cceeeeEEEEe
Q 005707          282 LPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVGSN--------LQLTQGVIHAA  351 (681)
Q Consensus       282 Ig~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP~e--------~~lv~G~V~~~  351 (681)
                      +++|++||+|.++++|.+. ..++...|++||.|.|+|+.+|  ++||.||+|++..|||.        ++.+.|.|. .
T Consensus       379 l~~~v~glv~~s~ls~~~~-~~~~~~~~~~G~~V~~~Vl~vd~~~~~i~ls~K~~~~~p~~~~~~~~~~G~~v~g~V~-~  456 (516)
T TIGR00717       379 LEGGIDGLIHLSDISWDKD-GREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQLTENPWEKFAAKYKVGSVVKGKVT-E  456 (516)
T ss_pred             CCCCCEEEEEHHHCcCccc-CCCHhHccCCCCEEEEEEEEEeCcCCEEEEeeccccCCchhhhhhccCcceEEEEEEE-E
Confidence            9999999999999999753 1234678999999999999997  58999999999999985        245788888 7


Q ss_pred             ecccEEEEEEcCCeEEEeeCCcccccc
Q 005707          352 TNPFVLAFRSNKDISSFLDERDKSATA  378 (681)
Q Consensus       352 i~~fGlfV~l~~gI~GfIp~~els~~~  378 (681)
                      +.++|+||++.+++.||+|.+++++..
T Consensus       457 v~~~G~fV~l~~~~~Glv~~s~l~~~~  483 (516)
T TIGR00717       457 IKDFGAFVELPGGVEGLIRNSELSENR  483 (516)
T ss_pred             EecceEEEEcCCCeEEEEEHHHcCccc
Confidence            999999999999999999999999863

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=100.00  E-value=2.7e-34  Score=323.09  Aligned_cols=269  Identities=23%  Similarity=0.296  Sum_probs=231.0

Q ss_pred             ceeEEeccCCceeEEeCcccCccc-ccccchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCChh
Q 005707           44 SQRFLLPLPSSVRFFSQFQSGSAL-QHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASPT  122 (681)
Q Consensus        44 ~~~l~~dl~glrGfIP~sq~~~~~-~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~~d  122 (681)
                      +.++.++++|+.||+|.++++|.. .+...+.. +|+.+.|+|+.+|.+++   ++.||.+              ...  
T Consensus       214 ~~G~~V~i~g~~glv~~se~s~~~~~~~~~~~k-vG~~v~v~V~~~d~~~~---~i~lS~k--------------~~~--  273 (565)
T PRK06299        214 DYGAFVDLGGVDGLLHITDISWKRVNHPSEVVN-VGDEVKVKVLKFDKEKK---RVSLGLK--------------QLG--  273 (565)
T ss_pred             CCeEEEEECCEEEEEEHHHhcccccCCHhhcCC-CCCEEEEEEEEEeCCCC---eEEEEEE--------------ecc--
Confidence            467888999999999999998862 22222333 79999999999999888   8899876              000  


Q ss_pred             hHHhhhchhhhhcCCCCCC--cCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCc-cccCcccccccCCEEE
Q 005707          123 LAESRRSRTARKSEMPPVK--NEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDN-FVKDVGSIVSVGQEVK  199 (681)
Q Consensus       123 aek~~~kr~~rk~e~~~lt--~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~-~v~d~~e~fkVGd~Vk  199 (681)
                                    ..+|.  ...+++|+++.|+|+++.++|+||+|+.++.||+|+++++|. +..++...|++||.|+
T Consensus       274 --------------~~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~~v~Glv~~sel~~~~~~~~~~~~~~~G~~v~  339 (565)
T PRK06299        274 --------------EDPWEAIEKKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSWTKKNKHPSKVVSVGQEVE  339 (565)
T ss_pred             --------------cChhHHHHhhCCCCCEEEEEEEEEeCCeEEEEeCCCCEEEEEHHHcCccccccCHHHhcCCCCEEE
Confidence                          01111  246889999999999999999999998789999999999986 4577778899999999


Q ss_pred             EEEEEEeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEE
Q 005707          200 VRLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAF  279 (681)
Q Consensus       200 VkVl~VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaF  279 (681)
                      |+|+++|+++++|.||+|.+..+||.                             ....+|++|+++.|+|+++.++|+|
T Consensus       340 v~V~~id~~~~~i~ls~k~~~~~p~~-----------------------------~~~~~~~~G~~v~g~V~~v~~~G~f  390 (565)
T PRK06299        340 VMVLEIDEEKRRISLGLKQCKENPWE-----------------------------EFAEKYPVGDVVEGKVKNITDFGAF  390 (565)
T ss_pred             EEEEEEcCCCCEEEEehHHhccchhh-----------------------------hHHHhCCCCCEEEEEEEEEecceEE
Confidence            99999999999999999999888882                             3456789999999999999999999


Q ss_pred             EEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCcCC--------cceeeeEEE
Q 005707          280 ISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVGSN--------LQLTQGVIH  349 (681)
Q Consensus       280 VeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP~e--------~~lv~G~V~  349 (681)
                      |+|+++++||+|.++++|.+. ...+...|++||.|+|+|+++|  +++|.||+|+...|||.        ++.+.|+|.
T Consensus       391 V~l~~~v~g~i~~s~l~~~~~-~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~k~~~~~p~~~~~~~~~~G~vV~G~V~  469 (565)
T PRK06299        391 VGLEGGIDGLVHLSDISWDKK-GEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQLEEDPFEEFAKKHKKGSIVTGTVT  469 (565)
T ss_pred             EECCCCCEEEEEHHHcCcccc-ccChHhhCCCCCEEEEEEEEEeCCCCEEEEEEehhhcCchhHHHhhcCCCCEEEEEEE
Confidence            999999999999999998763 1345789999999999999997  58999999999999985        357899998


Q ss_pred             EeecccEEEEEEcCCeEEEeeCCccccc
Q 005707          350 AATNPFVLAFRSNKDISSFLDERDKSAT  377 (681)
Q Consensus       350 ~~i~~fGlfV~l~~gI~GfIp~~els~~  377 (681)
                       .+.++|+||.+.+|+.||||.+++++.
T Consensus       470 -~v~~~G~fV~l~~gi~g~i~~se~s~~  496 (565)
T PRK06299        470 -EVKDKGAFVELEDGVEGLIRASELSRD  496 (565)
T ss_pred             -EEecCceEEecCCCcEEEEEHHHhcch
Confidence             899999999999999999999999876

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=1.8e-34  Score=319.83  Aligned_cols=269  Identities=21%  Similarity=0.255  Sum_probs=220.8

Q ss_pred             ceeEEeccC-CceeEEeCcccCcccc-cccchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCCh
Q 005707           44 SQRFLLPLP-SSVRFFSQFQSGSALQ-HKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASP  121 (681)
Q Consensus        44 ~~~l~~dl~-glrGfIP~sq~~~~~~-~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~~  121 (681)
                      ..++++|+. +++||||.+++++... +...... +|+.|.++|+.+|....   +++||.|              .+  
T Consensus        48 ~~gv~VdIg~k~eG~Ip~~Els~~~~~~~~~~~~-vGd~Ie~~V~~~~~~~g---~liLS~k--------------~~--  107 (486)
T PRK07899         48 RDEVLLDIGYKTEGVIPSRELSIKHDVDPNEVVE-VGDEVEALVLQKEDKEG---RLILSKK--------------RA--  107 (486)
T ss_pred             CCcEEEEECCCcEEEEEHHHhcccccCChhhcCC-CCCEEEEEEEEEECCCC---eEEEEeh--------------hh--
Confidence            467889987 7899999999987521 1122233 89999999999988777   7999987              00  


Q ss_pred             hhHHhhhchhhhhcCCCCCCcC-CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEE
Q 005707          122 TLAESRRSRTARKSEMPPVKNE-DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKV  200 (681)
Q Consensus       122 daek~~~kr~~rk~e~~~lt~~-~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkV  200 (681)
                        .   .       ....-.+. .++.|++++|+|+++.++|+||+| | ++||||.+++++.++.++..  .+|+.|+|
T Consensus       108 --~---~-------~~~w~~ie~~~e~g~~V~G~V~~v~k~G~~Vdl-G-i~gflP~Sel~~~~~~~~~~--~vGq~V~v  171 (486)
T PRK07899        108 --Q---Y-------ERAWGTIEKIKEKDGVVTGTVIEVVKGGLILDI-G-LRGFLPASLVEMRRVRDLQP--YIGQEIEA  171 (486)
T ss_pred             --c---c-------cchHHHHHHHhcCCCEEEEEEEEEECCeEEEEE-C-CEEEEEhhHhcccccCChhh--cCCCEEEE
Confidence              0   0       00000122 245799999999999999999999 4 89999999999988887765  39999999


Q ss_pred             EEEEEeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEE
Q 005707          201 RLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFI  280 (681)
Q Consensus       201 kVl~VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFV  280 (681)
                      +|+.+|+++++|.||+|.+....+.               ..|          ...+.++++|+++.|+|++++++|+||
T Consensus       172 kVleid~~~~~ivLSrr~~l~~~~~---------------~~~----------~~~~~~lk~G~iv~G~V~~i~~~G~FV  226 (486)
T PRK07899        172 KIIELDKNRNNVVLSRRAWLEQTQS---------------EVR----------SEFLNQLQKGQVRKGVVSSIVNFGAFV  226 (486)
T ss_pred             EEEEEECCCCEEEEEhHHHHHhhhH---------------HHH----------HHHHHhccCCCEEEEEEEEEECCeEEE
Confidence            9999999999999999976443221               001          245788999999999999999999999


Q ss_pred             EeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCcCCc--------ceeeeEEEE
Q 005707          281 SLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVGSNL--------QLTQGVIHA  350 (681)
Q Consensus       281 eIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP~e~--------~lv~G~V~~  350 (681)
                      +|+ |++||||.++++|.++.  ++...|++||.|+|+|+++|  ++||.||+|++..|||..        +.+.|+|. 
T Consensus       227 dlg-gv~Glv~~Sels~~~v~--~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~~~~~~vG~vv~G~V~-  302 (486)
T PRK07899        227 DLG-GVDGLVHVSELSWKHID--HPSEVVEVGQEVTVEVLDVDMDRERVSLSLKATQEDPWQQFARTHAIGQIVPGKVT-  302 (486)
T ss_pred             EEC-CEEEEEEHHHCCCcccC--CHHHhcCCCCEEEEEEEEEECCCCEEEEEEeeccccchhhhHHhcCCCCEEEEEEE-
Confidence            996 89999999999998854  45788999999999999997  589999999999999872        45789999 


Q ss_pred             eecccEEEEEEcCCeEEEeeCCccccc
Q 005707          351 ATNPFVLAFRSNKDISSFLDERDKSAT  377 (681)
Q Consensus       351 ~i~~fGlfV~l~~gI~GfIp~~els~~  377 (681)
                      .+.+||+||++.+|+.||+|.+++++.
T Consensus       303 ~I~~fGvFVeL~~gieGLvh~SeLs~~  329 (486)
T PRK07899        303 KLVPFGAFVRVEEGIEGLVHISELAER  329 (486)
T ss_pred             EEeccEEEEEeCCCcEEEEEHHHcCcc
Confidence            899999999999999999999999875

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=1.2e-33  Score=313.28  Aligned_cols=232  Identities=28%  Similarity=0.383  Sum_probs=198.6

Q ss_pred             eeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCChhhH
Q 005707           45 QRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASPTLA  124 (681)
Q Consensus        45 ~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~~dae  124 (681)
                      .++++++ |++||+|.+++++..  ...+..++|+.+.|+|+++|.+++   +++||+|      +        ......
T Consensus       136 ~G~~Vdl-Gi~gflP~Sel~~~~--~~~~~~~vGq~V~vkVleid~~~~---~ivLSrr------~--------~l~~~~  195 (486)
T PRK07899        136 GGLILDI-GLRGFLPASLVEMRR--VRDLQPYIGQEIEAKIIELDKNRN---NVVLSRR------A--------WLEQTQ  195 (486)
T ss_pred             CeEEEEE-CCEEEEEhhHhcccc--cCChhhcCCCEEEEEEEEEECCCC---EEEEEhH------H--------HHHhhh
Confidence            5788899 899999999999863  223456799999999999999988   8999987      0        000000


Q ss_pred             HhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEE
Q 005707          125 ESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIE  204 (681)
Q Consensus       125 k~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~  204 (681)
                          . ..+..     .+..+++|+++.|+|+++.++|+||+|+| ++||||+++|+|.++.++.+.|++||.|+|+|+.
T Consensus       196 ----~-~~~~~-----~~~~lk~G~iv~G~V~~i~~~G~FVdlgg-v~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~  264 (486)
T PRK07899        196 ----S-EVRSE-----FLNQLQKGQVRKGVVSSIVNFGAFVDLGG-VDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLD  264 (486)
T ss_pred             ----H-HHHHH-----HHHhccCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEE
Confidence                0 00111     14578999999999999999999999976 9999999999999999999999999999999999


Q ss_pred             EeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEEEeCC
Q 005707          205 ANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPE  284 (681)
Q Consensus       205 VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFVeIg~  284 (681)
                      +|+++++|.||+|++..+||.                             ....++++|+++.|+|+++.++|+||+|.+
T Consensus       265 iD~e~~rI~LSlK~~~~dPw~-----------------------------~~~~~~~vG~vv~G~V~~I~~fGvFVeL~~  315 (486)
T PRK07899        265 VDMDRERVSLSLKATQEDPWQ-----------------------------QFARTHAIGQIVPGKVTKLVPFGAFVRVEE  315 (486)
T ss_pred             EECCCCEEEEEEeeccccchh-----------------------------hhHHhcCCCCEEEEEEEEEeccEEEEEeCC
Confidence            999999999999999999982                             345668899999999999999999999999


Q ss_pred             CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCc
Q 005707          285 GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVG  338 (681)
Q Consensus       285 GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP  338 (681)
                      |++||||++++++.++.  .+...|++||.|+|+|+++|  ++||.||+|+...+-
T Consensus       316 gieGLvh~SeLs~~~v~--~~~~~~kvGd~V~VkIi~ID~e~rrI~LSlK~~~~~~  369 (486)
T PRK07899        316 GIEGLVHISELAERHVE--VPEQVVQVGDEVFVKVIDIDLERRRISLSLKQANEGV  369 (486)
T ss_pred             CcEEEEEHHHcCccccc--CccceeCCCCEEEEEEEEEECCCCEEEEEEEEcccCC
Confidence            99999999999998764  35788999999999999997  699999999986553

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=4.1e-32  Score=292.66  Aligned_cols=271  Identities=20%  Similarity=0.272  Sum_probs=221.0

Q ss_pred             ceeEEecc-C-CceeEEeCcccCccc-ccccchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCC
Q 005707           44 SQRFLLPL-P-SSVRFFSQFQSGSAL-QHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEAS  120 (681)
Q Consensus        44 ~~~l~~dl-~-glrGfIP~sq~~~~~-~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~  120 (681)
                      +.++++++ . ++.||+|.+++.+.. ........ +|+.+.|.|+.+|.+.+   +++||.++.              .
T Consensus        30 ~~g~~V~i~~~~~~g~lp~~e~~~~~~~~~~~~~~-vGd~v~~~V~~v~~~~~---~i~lS~k~~--------------~   91 (390)
T PRK06676         30 DKQVFVNIEGYKVEGVIPISELSNDHIEDINDVVK-VGDELEVYVLKVEDGEG---NLLLSKRRL--------------E   91 (390)
T ss_pred             CCeEEEEEecCCcEEEEEHHHhccccccCcccccC-CCCEEEEEEEEEECCCC---CEEEEHHHh--------------h
Confidence            36789998 4 899999999987641 11111233 89999999999999888   899988610              0


Q ss_pred             hhhHHhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEE
Q 005707          121 PTLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKV  200 (681)
Q Consensus       121 ~daek~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkV  200 (681)
                        ..     +.....      ...++.|+++.|+|+++.++|+||+++| +.||||++++++.+..++...  +|+.++|
T Consensus        92 --~~-----~~~~~~------~~~~~~G~~v~g~V~~v~~~G~~V~~~G-~~gflp~~el~~~~~~~~~~~--vG~~v~~  155 (390)
T PRK06676         92 --AE-----KAWDKL------EEKFEEGEVVEVKVTEVVKGGLVVDVEG-VRGFIPASLISTRFVEDFSDF--KGKTLEV  155 (390)
T ss_pred             --hh-----hhHHHH------HHhccCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHcCCccCCChHHc--CCCEEEE
Confidence              00     000000      2356899999999999999999999976 799999999999888887653  9999999


Q ss_pred             EEEEEeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEE
Q 005707          201 RLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFI  280 (681)
Q Consensus       201 kVl~VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFV  280 (681)
                      +|+.+|++++++.||+|.+....+.                         ..+...+.++++|+++.|+|+++.++|+||
T Consensus       156 ~Vl~~d~~~~~i~lS~k~~~~~~~~-------------------------~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV  210 (390)
T PRK06676        156 KIIELDPEKNRVILSRRAVVEEERA-------------------------AKKEELLSSLKEGDVVEGTVARLTDFGAFV  210 (390)
T ss_pred             EEEEEECCCCEEEEEeHHHhhhhhh-------------------------hHHHHHHhhCCCCCEEEEEEEEEecceEEE
Confidence            9999999999999999976553320                         001134677899999999999999999999


Q ss_pred             EeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCcCCc--------ceeeeEEEE
Q 005707          281 SLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVGSNL--------QLTQGVIHA  350 (681)
Q Consensus       281 eIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP~e~--------~lv~G~V~~  350 (681)
                      +++ |++||||.++++|.++.  ++...|++||.|+|+|+++|  ++++.||+|+...+||..        ..+.|+|. 
T Consensus       211 ~l~-~v~g~v~~sels~~~~~--~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~~~~G~~v~g~V~-  286 (390)
T PRK06676        211 DIG-GVDGLVHISELSHERVE--KPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEEKLPEGDVIEGTVK-  286 (390)
T ss_pred             EeC-CeEEEEEHHHcCccccC--CHHHhcCCCCEEEEEEEEEeCCCCEEEEEEeecccCccccchhhhcCCcEEEEEEE-
Confidence            996 89999999999998753  45778999999999999997  489999999999999862        45788998 


Q ss_pred             eecccEEEEEEcCCeEEEeeCCccccc
Q 005707          351 ATNPFVLAFRSNKDISSFLDERDKSAT  377 (681)
Q Consensus       351 ~i~~fGlfV~l~~gI~GfIp~~els~~  377 (681)
                      .+.++|+||++.+|+.||+|.+++++.
T Consensus       287 ~i~~~G~fV~l~~gi~Glv~~se~~~~  313 (390)
T PRK06676        287 RLTDFGAFVEVLPGVEGLVHISQISHK  313 (390)
T ss_pred             EEeCceEEEEECCCCeEEEEhHHcCcc
Confidence            799999999999999999999999875

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=1.1e-31  Score=289.30  Aligned_cols=237  Identities=28%  Similarity=0.388  Sum_probs=202.5

Q ss_pred             ceeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCChhh
Q 005707           44 SQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASPTL  123 (681)
Q Consensus        44 ~~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~~da  123 (681)
                      ..+++++++|++||+|.+++++....  ....++|+.+.|+|+++|++.+   +++||.|              .+....
T Consensus       118 ~~G~~V~~~G~~gflp~~el~~~~~~--~~~~~vG~~v~~~Vl~~d~~~~---~i~lS~k--------------~~~~~~  178 (390)
T PRK06676        118 KGGLVVDVEGVRGFIPASLISTRFVE--DFSDFKGKTLEVKIIELDPEKN---RVILSRR--------------AVVEEE  178 (390)
T ss_pred             CCeEEEEECCEEEEEEHHHcCCccCC--ChHHcCCCEEEEEEEEEECCCC---EEEEEeH--------------HHhhhh
Confidence            46889999999999999999876322  2345699999999999999888   8999987              000000


Q ss_pred             HHhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEE
Q 005707          124 AESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLI  203 (681)
Q Consensus       124 ek~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl  203 (681)
                      .    ..... .     .+..+++|+++.|+|+++.++|+||++++ ++||||+++++|.++.++.+.|++||.|+|+|+
T Consensus       179 ~----~~~~~-~-----~~~~~~~G~~v~g~V~~v~~~G~fV~l~~-v~g~v~~sels~~~~~~~~~~~~vGd~i~~~Vl  247 (390)
T PRK06676        179 R----AAKKE-E-----LLSSLKEGDVVEGTVARLTDFGAFVDIGG-VDGLVHISELSHERVEKPSEVVSVGQEVEVKVL  247 (390)
T ss_pred             h----hhHHH-H-----HHhhCCCCCEEEEEEEEEecceEEEEeCC-eEEEEEHHHcCccccCCHHHhcCCCCEEEEEEE
Confidence            0    00000 0     14568899999999999999999999976 999999999999999999999999999999999


Q ss_pred             EEeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEEEeC
Q 005707          204 EANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLP  283 (681)
Q Consensus       204 ~VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFVeIg  283 (681)
                      .+|+++++|.||+|.+..+||.                             ....++++|+++.|+|+++.++|+||++.
T Consensus       248 ~vd~~~~~i~lS~k~~~~~~~~-----------------------------~~~~~~~~G~~v~g~V~~i~~~G~fV~l~  298 (390)
T PRK06676        248 SIDWETERISLSLKDTLPGPWE-----------------------------GVEEKLPEGDVIEGTVKRLTDFGAFVEVL  298 (390)
T ss_pred             EEeCCCCEEEEEEeecccCccc-----------------------------cchhhhcCCcEEEEEEEEEeCceEEEEEC
Confidence            9999999999999998888872                             34678999999999999999999999999


Q ss_pred             CCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCcCCc
Q 005707          284 EGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVGSNL  341 (681)
Q Consensus       284 ~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP~e~  341 (681)
                      +|+.||+|.++++|.++.  ++...|++||.|.|+|+++|  ++++.|++|+...+||..
T Consensus       299 ~gi~Glv~~se~~~~~~~--~~~~~~~~Gd~v~v~V~~id~e~~~i~ls~k~~~~~~~~~  356 (390)
T PRK06676        299 PGVEGLVHISQISHKHIA--TPSEVLEEGQEVKVKVLEVNEEEKRISLSIKALEEAPAEE  356 (390)
T ss_pred             CCCeEEEEhHHcCccccC--ChhhccCCCCEEEEEEEEEECCCCEEEEEEEecccChhhh
Confidence            999999999999988753  45778999999999999998  699999999999999974

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=100.00  E-value=7.3e-32  Score=299.95  Aligned_cols=236  Identities=25%  Similarity=0.315  Sum_probs=198.7

Q ss_pred             ceeEEecc-CCceeEEeCcccCcccccc-cchhhcccceeEEEEEecCCCCCC-CCcceecCCCCCcccccccccccCCC
Q 005707           44 SQRFLLPL-PSSVRFFSQFQSGSALQHK-SALHIISATGINVAVEESDSPAAD-DDSAGASDIPSDVETSESSSIKSEAS  120 (681)
Q Consensus        44 ~~~l~~dl-~glrGfIP~sq~~~~~~~~-~~~~~lvG~~i~VkVievD~~~~~-~~~lvlSer~s~v~~ae~ss~~sea~  120 (681)
                      ..++.+++ .|+.||||.+++++..... ..+.. +|+.+.|+|+++|.+.+. -.++.||.|              .+ 
T Consensus       215 ~~G~fV~l~~gv~g~v~~sels~~~~~~~~~~~~-vGd~i~vkVl~id~~~~~~~~ri~lS~K--------------~~-  278 (491)
T PRK13806        215 PFGAFVELAPGVEGMVHISELSWSRVQKADEAVS-VGDTVRVKVLGIERAKKGKGLRISLSIK--------------QA-  278 (491)
T ss_pred             CCeEEEEcCCCcEEEEEHHHCCCccccChhHhcC-CCCEEEEEEEEEecccCCcceEEEEEeh--------------hh-
Confidence            46889998 5899999999999862211 22233 899999999999997631 016888876              00 


Q ss_pred             hhhHHhhhchhhhhcCCCCCC--cCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCC-ccccCcccccccCCE
Q 005707          121 PTLAESRRSRTARKSEMPPVK--NEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSD-NFVKDVGSIVSVGQE  197 (681)
Q Consensus       121 ~daek~~~kr~~rk~e~~~lt--~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~-~~v~d~~e~fkVGd~  197 (681)
                                     ...+|.  ...+++|+++.|+|+++.++|+||+++.+++||||+++++| .++.++.+.|++||.
T Consensus       279 ---------------~~~p~~~~~~~~~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~  343 (491)
T PRK13806        279 ---------------GGDPWDTVGDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDA  343 (491)
T ss_pred             ---------------hcccchhhhccCCCCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCE
Confidence                           011222  45789999999999999999999999877999999999998 567888999999999


Q ss_pred             EEEEEEEEeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecce
Q 005707          198 VKVRLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSG  277 (681)
Q Consensus       198 VkVkVl~VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~G  277 (681)
                      |+|+|+.+|+++++|.||+|++..+||.                             ....+|++|+++.|+|+++++||
T Consensus       344 v~vkVl~iD~e~~ri~Ls~K~~~~~p~~-----------------------------~~~~~~~vG~~v~G~V~~i~~~G  394 (491)
T PRK13806        344 VAVKIKDIDPAKRRISLSLRDAEGDPWA-----------------------------DVAERFAPGTTVTGTVEKRAQFG  394 (491)
T ss_pred             EEEEEEEEEccCCEEEEEEeecccChhH-----------------------------HhhhhCCCCCEEEEEEEEEecCc
Confidence            9999999999999999999999999993                             45678999999999999999999


Q ss_pred             EEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccC-----CCcCCc
Q 005707          278 AFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKED-----DVGSNL  341 (681)
Q Consensus       278 aFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~-----~DP~e~  341 (681)
                      +||++.+|++||||+++++|.+.  .++...|++||.|+|+|+.+|  ++||.||+|...     .+||..
T Consensus       395 ~FV~l~~gv~Gli~~se~s~~~~--~~~~~~~~~Gd~v~~~V~~id~e~~ri~Ls~~~~~~~~~~~~~~~~  463 (491)
T PRK13806        395 LFVNLAPGVTGLLPASVISRAGK--PATYEKLKPGDSVTLVVEEIDTAKRKISLAPAGAAGSGADDDDWKQ  463 (491)
T ss_pred             eEEEcCCCcEEEEEHHHcCcccc--cchhhcCCCCCEEEEEEEEEeCCCCEEEEEeehhhhhhhhhhHHHh
Confidence            99999999999999999999875  345789999999999999997  589999999762     366763

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

Probab=99.97  E-value=7.6e-30  Score=292.04  Aligned_cols=270  Identities=21%  Similarity=0.269  Sum_probs=220.4

Q ss_pred             eeEEeccC-CceeEEeCcccCccccc-ccchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCChh
Q 005707           45 QRFLLPLP-SSVRFFSQFQSGSALQH-KSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASPT  122 (681)
Q Consensus        45 ~~l~~dl~-glrGfIP~sq~~~~~~~-~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~~d  122 (681)
                      .+++++++ ++.||+|.+++.+.... ...... +|+.+.|.|+.+|.+.+   +++||.++.            ..  .
T Consensus       316 ~gv~Vdig~~~~G~lp~~els~~~~~~~~~~~~-vGd~V~v~V~~vd~~~g---~i~LS~k~~------------~~--~  377 (647)
T PRK00087        316 NEVFVDVGYKSEGVIPLRELTLDEISSLKESVK-VGDEIEVKVLKLEDEDG---YVVLSKKEA------------DR--E  377 (647)
T ss_pred             CEEEEEECCCeEEEEEHHHhcccccCChhhccC-CCCEEEEEEEEEECCCC---cEEEEeehh------------cc--h
Confidence            56788885 67899999998865211 122233 89999999999998877   899998711            00  0


Q ss_pred             hHHhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEE
Q 005707          123 LAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRL  202 (681)
Q Consensus       123 aek~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkV  202 (681)
                      ..+    ..+         ...++.|+++.|+|+++.++|+||++++ ++||||.+++++.+..++...  +|+.++|+|
T Consensus       378 ~~~----~~l---------~~~~~~G~iv~g~V~~v~~~G~~V~lgg-i~gfiP~sel~~~~~~d~~~~--vG~~v~v~V  441 (647)
T PRK00087        378 KAW----KEL---------EEAFENGEPVKGKVKEVVKGGLLVDYGG-VRAFLPASHVELGYVEDLSEY--KGQELEVKI  441 (647)
T ss_pred             hHH----HHH---------HHHhhCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHhCccccCCHHHh--CCCEEEEEE
Confidence            011    001         1246899999999999999999999998 999999999999988887653  899999999


Q ss_pred             EEEeccCCc-eEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEEE
Q 005707          203 IEANAETGR-ISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFIS  281 (681)
Q Consensus       203 l~VD~ekgr-I~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFVe  281 (681)
                      +.+|+++++ +.+|+|........                         ......+.++++|+++.|+|+++.++|+||+
T Consensus       442 l~vd~e~~~~l~lS~k~~~~~~~~-------------------------~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~  496 (647)
T PRK00087        442 IEFNRKRRKKVVLSRKAILEEEKE-------------------------KKKEETWNSLEEGDVVEGEVKRLTDFGAFVD  496 (647)
T ss_pred             EEEEcCCCcEEEEEeHHHhhhhhh-------------------------hHHHHHHHhCCCCCEEEEEEEEEeCCcEEEE
Confidence            999999998 99999976431110                         0112456778999999999999999999999


Q ss_pred             eCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCcCCc--------ceeeeEEEEe
Q 005707          282 LPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVGSNL--------QLTQGVIHAA  351 (681)
Q Consensus       282 Ig~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP~e~--------~lv~G~V~~~  351 (681)
                      + +|++||||.++++|.++.  ++...|++||.|.|+|+++|  ++++.||+|+...+||..        +.+.|+|. .
T Consensus       497 l-~gv~Gll~~sels~~~~~--~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~~~~~~~G~~v~g~V~-~  572 (647)
T PRK00087        497 I-GGVDGLLHVSEISWGRVE--KPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEKYPVGSIVLGKVV-R  572 (647)
T ss_pred             E-CCEEEEEEHHHcCccccC--CHHHhcCCCCEEEEEEEEEECCCCEEEEEeeccccChhhhhhhhccCCeEEEEEEE-E
Confidence            9 699999999999998754  45788999999999999997  499999999999999873        45688888 7


Q ss_pred             ecccEEEEEEcCCeEEEeeCCccccc
Q 005707          352 TNPFVLAFRSNKDISSFLDERDKSAT  377 (681)
Q Consensus       352 i~~fGlfV~l~~gI~GfIp~~els~~  377 (681)
                      +.+||+||++.+++.||+|.+++++.
T Consensus       573 i~~~G~fV~l~~~i~Gli~~sel~~~  598 (647)
T PRK00087        573 IAPFGAFVELEPGVDGLVHISQISWK  598 (647)
T ss_pred             EECCeEEEEECCCCEEEEEhhhcCcc
Confidence            99999999999999999999999875

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=99.97  E-value=2.6e-29  Score=266.11  Aligned_cols=224  Identities=19%  Similarity=0.248  Sum_probs=184.9

Q ss_pred             ceeEEeccCC-ceeEEeCcccCcccc-cccchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCCh
Q 005707           44 SQRFLLPLPS-SVRFFSQFQSGSALQ-HKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASP  121 (681)
Q Consensus        44 ~~~l~~dl~g-lrGfIP~sq~~~~~~-~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~~  121 (681)
                      ..++++|+++ .+||+|.+++++... ....+.. +|+.++|+|+++|.+..   +++||.|+.                
T Consensus        44 ~~g~~Vdig~k~~g~lp~sEis~~~~~~~~~~~~-~G~~v~~~Vi~~~~~~~---~i~lS~k~~----------------  103 (318)
T PRK07400         44 PRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQ-PNETREFFILSDENEDG---QLTLSIRRI----------------  103 (318)
T ss_pred             CCEEEEEECCCeEEEEEHHHhccccccCHHHccC-CCCEEEEEEEEEeCCCC---eEEEehhhh----------------
Confidence            4689999965 799999999987631 1222333 69999999999998877   899998810                


Q ss_pred             hhHHhhhchhhhhcCCCCCC-c-CCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEE
Q 005707          122 TLAESRRSRTARKSEMPPVK-N-EDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVK  199 (681)
Q Consensus       122 daek~~~kr~~rk~e~~~lt-~-~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~Vk  199 (681)
                        ...           ..|. + ...+.|+++.|+|+++.++|+||+++| ++||||+++++|.+..   ..+ +|+.|.
T Consensus       104 --~~~-----------~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V~l~G-v~gfip~s~ls~~~~~---~~~-vG~~i~  165 (318)
T PRK07400        104 --EYM-----------RAWERVRQLQKEDATVRSEVFATNRGGALVRIEG-LRGFIPGSHISTRKPK---EEL-VGEELP  165 (318)
T ss_pred             --hhh-----------hHHHHHHHhccCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHcCccCCc---ccc-CCCEEE
Confidence              000           0011 1 134569999999999999999999975 9999999999986433   334 999999


Q ss_pred             EEEEEEeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEE
Q 005707          200 VRLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAF  279 (681)
Q Consensus       200 VkVl~VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaF  279 (681)
                      |+|+.+|+++++|.||+|.+....                                .+.++++|+++.|+|++|++||+|
T Consensus       166 ~kVl~id~~~~~i~lS~K~~~~~~--------------------------------~~~~~k~G~vv~G~V~~I~~~G~f  213 (318)
T PRK07400        166 LKFLEVDEERNRLVLSHRRALVER--------------------------------KMNRLEVGEVVVGTVRGIKPYGAF  213 (318)
T ss_pred             EEEEEEEcccCEEEEEhhHhhhhh--------------------------------hhccCCCCCEEEEEEEEEECCeEE
Confidence            999999999999999999654322                                266799999999999999999999


Q ss_pred             EEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCcCC
Q 005707          280 ISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVGSN  340 (681)
Q Consensus       280 VeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP~e  340 (681)
                      |+++ |+.||||+++++|.+..  ++...|++||.|+|+|+++|  ++++.||+|++..|||+
T Consensus       214 V~i~-gv~Gllhisels~~~~~--~~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K~l~~~P~~  273 (318)
T PRK07400        214 IDIG-GVSGLLHISEISHEHIE--TPHSVFNVNDEMKVMIIDLDAERGRISLSTKQLEPEPGD  273 (318)
T ss_pred             EEEC-CEEEEEEHHHccccccc--ChhhccCCCCEEEEEEEEEeCCCCEEEEEEeccccChhh
Confidence            9996 89999999999999854  45889999999999999998  59999999999999997

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

Probab=99.97  E-value=2.5e-29  Score=287.78  Aligned_cols=234  Identities=22%  Similarity=0.318  Sum_probs=200.3

Q ss_pred             ceeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCc-ceecCCCCCcccccccccccCCChh
Q 005707           44 SQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDS-AGASDIPSDVETSESSSIKSEASPT  122 (681)
Q Consensus        44 ~~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~-lvlSer~s~v~~ae~ss~~sea~~d  122 (681)
                      ..+++++++|++||+|.+++++...  .++..++|+.+.|+|+++|++++   + +++|.|              .....
T Consensus       402 ~~G~~V~lggi~gfiP~sel~~~~~--~d~~~~vG~~v~v~Vl~vd~e~~---~~l~lS~k--------------~~~~~  462 (647)
T PRK00087        402 KGGLLVDYGGVRAFLPASHVELGYV--EDLSEYKGQELEVKIIEFNRKRR---KKVVLSRK--------------AILEE  462 (647)
T ss_pred             CCeEEEEECCEEEEEEHHHhCcccc--CCHHHhCCCEEEEEEEEEEcCCC---cEEEEEeH--------------HHhhh
Confidence            3578999999999999999987632  23345699999999999999988   7 999987              00000


Q ss_pred             hHHhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEE
Q 005707          123 LAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRL  202 (681)
Q Consensus       123 aek~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkV  202 (681)
                       .     +.....    ..+.++++|+++.|+|+++.++|+||++ ++++||||+++++|.++.++.+.|++||.|+|+|
T Consensus       463 -~-----~~~~~~----~~~~~l~~G~iV~g~V~~v~~~G~fV~l-~gv~Gll~~sels~~~~~~~~~~~~vGd~V~vkV  531 (647)
T PRK00087        463 -E-----KEKKKE----ETWNSLEEGDVVEGEVKRLTDFGAFVDI-GGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYI  531 (647)
T ss_pred             -h-----hhhHHH----HHHHhCCCCCEEEEEEEEEeCCcEEEEE-CCEEEEEEHHHcCccccCCHHHhcCCCCEEEEEE
Confidence             0     000000    1255789999999999999999999999 5699999999999999999999999999999999


Q ss_pred             EEEeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEEEe
Q 005707          203 IEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISL  282 (681)
Q Consensus       203 l~VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFVeI  282 (681)
                      +++|+++++|.||+|++..+||.                             ....+|++|+++.|+|+++.++|+||+|
T Consensus       532 ~~id~~~~~I~lS~K~~~~~p~~-----------------------------~~~~~~~~G~~v~g~V~~i~~~G~fV~l  582 (647)
T PRK00087        532 LDIDKENKKLSLSLKKLLPDPWE-----------------------------NVEEKYPVGSIVLGKVVRIAPFGAFVEL  582 (647)
T ss_pred             EEEECCCCEEEEEeeccccChhh-----------------------------hhhhhccCCeEEEEEEEEEECCeEEEEE
Confidence            99999999999999999998882                             3456789999999999999999999999


Q ss_pred             CCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCc
Q 005707          283 PEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVG  338 (681)
Q Consensus       283 g~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP  338 (681)
                      .+|+.||+|.++++|.++.  ++...|++||.|+|+|+++|  ++|+.|++|...++|
T Consensus       583 ~~~i~Gli~~sel~~~~~~--~~~~~~kvGd~V~vkV~~id~e~~rI~lslk~~~~~~  638 (647)
T PRK00087        583 EPGVDGLVHISQISWKRID--KPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEEEP  638 (647)
T ss_pred             CCCCEEEEEhhhcCccccC--CHhhcCCCCCEEEEEEEEEeCCCCEEEEEEeecccCc
Confidence            9999999999999998753  45788999999999999997  599999999999888

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=99.96  E-value=1e-27  Score=254.00  Aligned_cols=197  Identities=21%  Similarity=0.336  Sum_probs=172.8

Q ss_pred             CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccch-h
Q 005707          144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDD-I  222 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~-d  222 (681)
                      .++.|+++.|+|.++.++|+||+||++.+||||+++++|+++.++.+.|++||.|+|+|+++|.+++++.||+|.+.. .
T Consensus        28 ~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i~lS~k~~~~~~  107 (318)
T PRK07400         28 HFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQLTLSIRRIEYMR  107 (318)
T ss_pred             hcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccccccCHHHccCCCCEEEEEEEEEeCCCCeEEEehhhhhhhh
Confidence            589999999999999999999999998999999999999999999999999999999999999999999999998753 5


Q ss_pred             hHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccc
Q 005707          223 SKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFAN  302 (681)
Q Consensus       223 p~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~  302 (681)
                      +|.                             .....+..|+++.|+|+++.++|+||+++ |+.||||.++++|...  
T Consensus       108 ~w~-----------------------------~l~~~~~~~~~V~g~V~~~~~~G~~V~l~-Gv~gfip~s~ls~~~~--  155 (318)
T PRK07400        108 AWE-----------------------------RVRQLQKEDATVRSEVFATNRGGALVRIE-GLRGFIPGSHISTRKP--  155 (318)
T ss_pred             HHH-----------------------------HHHHhccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHcCccCC--
Confidence            552                             23344567999999999999999999995 9999999999998542  


Q ss_pred             cCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCc-CC----cceeeeEEEEeecccEEEEEEcCCeEEEeeCCccc
Q 005707          303 MMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVG-SN----LQLTQGVIHAATNPFVLAFRSNKDISSFLDERDKS  375 (681)
Q Consensus       303 ~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP-~e----~~lv~G~V~~~i~~fGlfV~l~~gI~GfIp~~els  375 (681)
                         ... .+|+.|.|+|+++|  ++|+.||+|+...+. +.    ++++.|+|. .+.+||+||.+ .|+.||+|.++++
T Consensus       156 ---~~~-~vG~~i~~kVl~id~~~~~i~lS~K~~~~~~~~~~~k~G~vv~G~V~-~I~~~G~fV~i-~gv~Gllhisels  229 (318)
T PRK07400        156 ---KEE-LVGEELPLKFLEVDEERNRLVLSHRRALVERKMNRLEVGEVVVGTVR-GIKPYGAFIDI-GGVSGLLHISEIS  229 (318)
T ss_pred             ---ccc-cCCCEEEEEEEEEEcccCEEEEEhhHhhhhhhhccCCCCCEEEEEEE-EEECCeEEEEE-CCEEEEEEHHHcc
Confidence               233 49999999999997  489999999765443 22    477899999 89999999998 6899999999999


Q ss_pred             ccc
Q 005707          376 ATA  378 (681)
Q Consensus       376 ~~~  378 (681)
                      +..
T Consensus       230 ~~~  232 (318)
T PRK07400        230 HEH  232 (318)
T ss_pred             ccc
Confidence            874

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=99.69  E-value=1.3e-18  Score=184.32  Aligned_cols=149  Identities=15%  Similarity=0.267  Sum_probs=127.6

Q ss_pred             CCCC-CCcEEEEEEEEEecCeeEEEEC--CCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEecc
Q 005707          143 EDLI-PGATFTGKVRSIQPFGAFIDFG--AFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRES  219 (681)
Q Consensus       143 ~~Lk-vGdIVeGkV~sV~d~GaFVdLg--ggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l  219 (681)
                      ..+. +|++|.|+|++|.+||+||+|.  ++++||||+++|+|.++.++.+++++||.|.|+|+.+|+++++|.||+|++
T Consensus        12 ~~~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~v   91 (319)
T PTZ00248         12 QKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKKRV   91 (319)
T ss_pred             hhCCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEeeec
Confidence            3454 7999999999999999999995  569999999999999999999999999999999999999999999999999


Q ss_pred             chhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEe-cceEEEE------eCCCeEEEEeC
Q 005707          220 DDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLT-RSGAFIS------LPEGEEGFLPT  292 (681)
Q Consensus       220 ~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt-~~GaFVe------Ig~GIeGLLpi  292 (681)
                      ..+||.                             ....+|+.|++++|+|+++. ++|+|++      ..++..+|.|.
T Consensus        92 ~~~pw~-----------------------------~~~e~~~~g~~v~~~V~~ia~~~g~~~eely~~i~~pl~~~~gh~  142 (319)
T PTZ00248         92 SPEDIE-----------------------------ACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYGHA  142 (319)
T ss_pred             ccchHH-----------------------------HHHHhCcCCCEEEEEEEEchhhcCCCHHHHHHHHHHHHHHhcCCH
Confidence            999993                             56788999999999999995 5999998      55688999998


Q ss_pred             CCCCcccccccCCCCccc---CCCEEEEEEEEE
Q 005707          293 SEESDDGFANMMGGSSLQ---VGQEVSVRVLRI  322 (681)
Q Consensus       293 SELSd~~ie~~~p~~~fk---VGqkVkVrVL~I  322 (681)
                      .++....+.  .+...|.   +++.+...++.+
T Consensus       143 y~af~~~v~--~~~evl~~l~i~~ev~~~l~~~  173 (319)
T PTZ00248        143 LDALKEALT--NPDNVFEGLDIPEEVKESLLQD  173 (319)
T ss_pred             HHHHHHHhc--CchhhhccCCCCHHHHHHHHHH
Confidence            877655432  2333444   777777666655

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

Probab=99.69  E-value=1.8e-15  Score=178.90  Aligned_cols=293  Identities=20%  Similarity=0.205  Sum_probs=225.6

Q ss_pred             CCceeEEeCcccCccc---ccccchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCChhhHHhhh
Q 005707           52 PSSVRFFSQFQSGSAL---QHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASPTLAESRR  128 (681)
Q Consensus        52 ~glrGfIP~sq~~~~~---~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~~daek~~~  128 (681)
                      .-++|=||.-.+++..   +....++. +|+.++..|...|....     +. .-                         
T Consensus      1009 p~v~~RIplld~s~~~~~le~~e~~F~-~g~al~~~V~~~~~~~t-----v~-~i------------------------- 1056 (1710)
T KOG1070|consen 1009 PFVDGRIPLLDTSLDLHVLELPESLFP-LGKALDEYVVRNDKSKT-----VR-AI------------------------- 1056 (1710)
T ss_pred             ccccceeeeeeccchhhhhhCchhhcc-cccceeeEEecccceeE-----EE-ec-------------------------
Confidence            5667778887777542   22233444 89999999999983322     21 10                         


Q ss_pred             chhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEec-cccCCccccCcccccccCCEEEEEEEEEec
Q 005707          129 SRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHV-SRLSDNFVKDVGSIVSVGQEVKVRLIEANA  207 (681)
Q Consensus       129 kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPi-SELS~~~v~d~~e~fkVGd~VkVkVl~VD~  207 (681)
                      .  .-+.      .....+|++.-|+|..+.+.++.++++.++.|-++. .++++++..+|...|..++.+.+.++.++.
T Consensus      1057 G--~~~~------~k~~s~G~~l~Grv~kv~~~~~~l~~~~~~~G~~~~i~~~~d~~~~~P~~~f~~~~~v~~~~L~vs~ 1128 (1710)
T KOG1070|consen 1057 G--FSKS------DKNPSPGDILFGRVSKVLPGYLILQLPFKVFGRVSFIEDMSDSYSMTPVEHFTKIQIVYVCVLSVSA 1128 (1710)
T ss_pred             c--cccC------CCCCCcchhhcceeeeeccceeEEecCCccccceEEeeehhccccCChHHhcccccEEEEEEEEEec
Confidence            0  0000      112338999999999999999999999989995554 499999999999999999999999999999


Q ss_pred             cCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEEEeCCCeE
Q 005707          208 ETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEE  287 (681)
Q Consensus       208 ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFVeIg~GIe  287 (681)
                      .++.+.||++......-     +                -.+.+...+...+++.|+++.|+|+++.+.|+||.+..+++
T Consensus      1129 ~n~~leLslr~sr~~~t-----~----------------~~~kd~~iks~eDlk~g~iv~G~V~nv~~~glfi~ls~~v~ 1187 (1710)
T KOG1070|consen 1129 LNKGLELSLRESRTKIT-----P----------------VDSKDGSIKSIEDLKIGDIVRGFVKNVETKGLFIALSRKVE 1187 (1710)
T ss_pred             ccccceeecccccccCc-----c----------------ccccCCcccchhhcccCceeEEEEEEecCCcEEEEEccceE
Confidence            88889999986554111     0                01222334678999999999999999999999999999999


Q ss_pred             EEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccC-CCcCC----------cceeeeEEEEeecc
Q 005707          288 GFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKED-DVGSN----------LQLTQGVIHAATNP  354 (681)
Q Consensus       288 GLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~-~DP~e----------~~lv~G~V~~~i~~  354 (681)
                      +|++++++++...  ..+...|.+|+.|.++|++++  .+|+.|+||... .|+..          ++-..|+|. ...+
T Consensus      1188 a~v~is~~~ds~~--k~w~k~~~~gklv~~rv~~ve~~s~riel~Lk~s~~~d~~~~~~~~~~l~~gd~~~g~v~-~~~~ 1264 (1710)
T KOG1070|consen 1188 AFVPISGLSDSFE--KEWEKHLPVGKLVTGRVLSVEEDSKRIELSLKNSDIKDTVKLLKDSKDLKKGDREDGTVE-VVDP 1264 (1710)
T ss_pred             EEEEccccccchh--hhhhccCCccceeeeEEEEeeccCceEEEEEeccccCCchhhhhhhhhhhccccccceEE-EecC
Confidence            9999999998773  456899999999999999996  589999999874 22322          234578888 8999


Q ss_pred             cEEEEEEcCCe--EEEeeCCccccccc------------cCCCCCCCccccceeeccccccCCCCCCC
Q 005707          355 FVLAFRSNKDI--SSFLDERDKSATAA------------KKSEKPTPIEIGGEVSQMEAGSSIPKVQD  408 (681)
Q Consensus       355 fGlfV~l~~gI--~GfIp~~els~~~~------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  408 (681)
                      ||+|+++..++  .|++|..+..+...            +.+.......+..+|+.+++-+++..+..
T Consensus      1265 ~G~fi~l~~tv~~~g~~~~~e~~d~~~e~it~~~~~~~~V~a~~lk~~~ek~rIsl~~k~s~~~~~dd 1332 (1710)
T KOG1070|consen 1265 FGLFIKLDVTVNMVGLCHISEEADDRGENITALYYAGDRVKACVLKEDSEKKRISLGLKSSYLSSEDD 1332 (1710)
T ss_pred             CceEEEecCcceecccccceeecchhhhhcccceeccceeeeEeeeccchhhhhhhhhhhhccCChhh
Confidence            99999998765  99999998887554            56667777788888887777777765543

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

Probab=99.62  E-value=2.7e-15  Score=177.58  Aligned_cols=169  Identities=24%  Similarity=0.388  Sum_probs=148.6

Q ss_pred             CCcCCCCCCcEEEEEEEEEecCeeEEEEC-CCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEec
Q 005707          140 VKNEDLIPGATFTGKVRSIQPFGAFIDFG-AFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRE  218 (681)
Q Consensus       140 lt~~~LkvGdIVeGkV~sV~d~GaFVdLg-ggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~  218 (681)
                      ++..++++|++|.|+|..+.+.|+.|.+. +.+.|+||.+++++-...-+...|.+|..+++||+.++.+.+++.|++|.
T Consensus       502 ~~~nDI~iG~~V~~~I~~vt~~Gv~v~v~~~ni~g~lp~~hlsd~~~~~p~~~f~v~~~~k~RVl~~~~~~~~v~l~~K~  581 (1710)
T KOG1070|consen  502 LRVNDIEIGQLVPGVIRKVTPQGVEVLVTFGNIKGVLPKEHLSDHPLQPPLRDFKVGSGVKLRVLSVNRDRNRVALTLKK  581 (1710)
T ss_pred             cccccccccceeeeEEEEecCCcEEEEEecCceeeecChHhhhhcccccccceeeeccccEEEEEEEEccCCeeEEEech
Confidence            34677999999999999999999999884 44999999999999988888888999999999999999999999999997


Q ss_pred             cchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcc
Q 005707          219 SDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDD  298 (681)
Q Consensus       219 l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~  298 (681)
                      .+.+-..            |              .-..+.+..+|.++.|+|.++.++||||.|.+|+.||+|.+++++.
T Consensus       582 slv~~~~------------p--------------lp~d~~~~~pg~~~~G~l~~~~~~g~~V~F~g~lsGf~p~s~~sd~  635 (1710)
T KOG1070|consen  582 SLVNTQL------------P--------------LPSDFEQAIPGKITKGTLCAIKENGAFVTFTGGLSGFAPVSEMSDD  635 (1710)
T ss_pred             hhhcccC------------C--------------CccchhhcCCCceEEEEEeeeccCCeEEEecCccccccchhhhhhh
Confidence            7654421            0              1134777889999999999999999999999999999999999999


Q ss_pred             cccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCC
Q 005707          299 GFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDD  336 (681)
Q Consensus       299 ~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~  336 (681)
                      ++.  .+.+.|.+||+|.++|+++|  ++|+.|++|....
T Consensus       636 ~v~--~~~ehf~vGqTv~~~i~nvd~ek~rm~l~~r~s~~  673 (1710)
T KOG1070|consen  636 FVL--SDSEHFPVGQTVRAKIVNVDDEKRRMPLGLRASSC  673 (1710)
T ss_pred             hhc--ChhhhcccccEEEEEEEecCchhceeehhhhhhhh
Confidence            864  45899999999999999997  6899999998753

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

Probab=99.56  E-value=3.2e-15  Score=138.44  Aligned_cols=80  Identities=38%  Similarity=0.759  Sum_probs=76.9

Q ss_pred             CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccchhh
Q 005707          144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDIS  223 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~dp  223 (681)
                      .+++|++++|+|++|++||+||+|.++-+||||+|+++++|+.++.+++++||.|+|+|+++|. +++|.||+|.+...|
T Consensus         2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide-~GKisLSIr~~~e~p   80 (129)
T COG1098           2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDE-NGKISLSIRKLEEEP   80 (129)
T ss_pred             CccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeecc-CCCcceehHHhhhCc
Confidence            5789999999999999999999999999999999999999999999999999999999999997 999999999998877


Q ss_pred             H
Q 005707          224 K  224 (681)
Q Consensus       224 ~  224 (681)
                      .
T Consensus        81 e   81 (129)
T COG1098          81 E   81 (129)
T ss_pred             c
Confidence            5

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=99.52  E-value=8.3e-15  Score=155.54  Aligned_cols=120  Identities=19%  Similarity=0.224  Sum_probs=102.7

Q ss_pred             cccCCc-cCcEEEEEEEEEecceEEEEeC--CCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEE
Q 005707          256 KTTKFV-KGQDLEGTVKNLTRSGAFISLP--EGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLT  330 (681)
Q Consensus       256 ~~sklk-vGdIV~G~VknVt~~GaFVeIg--~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LS  330 (681)
                      ...+|+ +|++|.|+|++|.+||+||+|.  +|++||||++|++|.++.  ++...|++||.|.|+||++|  +++|.||
T Consensus        10 ~~~~~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~--~i~d~vkvGd~v~vkVl~VD~ekg~IdLS   87 (319)
T PTZ00248         10 YEQKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIR--SINKLIRVGRHEVVVVLRVDKEKGYIDLS   87 (319)
T ss_pred             hhhhCCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccC--CHHHhcCCCCEEEEEEEEEeCCCCEEEEE
Confidence            456787 7999999999999999999996  699999999999999864  45899999999999999997  6999999


Q ss_pred             EeccCCCcCCc--------ceeeeEEEEeecccEEEEE------EcCCeEEEeeCCccccc
Q 005707          331 MKKEDDVGSNL--------QLTQGVIHAATNPFVLAFR------SNKDISSFLDERDKSAT  377 (681)
Q Consensus       331 LK~~~~DP~e~--------~lv~G~V~~~i~~fGlfV~------l~~gI~GfIp~~els~~  377 (681)
                      +|++..+||..        +.+.|+|......||++++      ..+.+.+|.|..+..+.
T Consensus        88 ~K~v~~~pw~~~~e~~~~g~~v~~~V~~ia~~~g~~~eely~~i~~pl~~~~gh~y~af~~  148 (319)
T PTZ00248         88 KKRVSPEDIEACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYGHALDALKE  148 (319)
T ss_pred             eeecccchHHHHHHhCcCCCEEEEEEEEchhhcCCCHHHHHHHHHHHHHHhcCCHHHHHHH
Confidence            99999999872        5578888843367999997      57788888887666554

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

Probab=99.50  E-value=1.3e-14  Score=134.36  Aligned_cols=79  Identities=33%  Similarity=0.584  Sum_probs=74.3

Q ss_pred             CCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe-CCeEEEEEeccCCC
Q 005707          259 KFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS-RGQVTLTMKKEDDV  337 (681)
Q Consensus       259 klkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID-kgKI~LSLK~~~~D  337 (681)
                      .+++|+++.|+|+.|++||+||+|++|-.||+|+||+.+.++.++  .+.+++||.|.|+||.+| +||+.||||.+.+.
T Consensus         2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI--~d~L~vG~eV~vKVl~ide~GKisLSIr~~~e~   79 (129)
T COG1098           2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDI--HDHLKVGQEVKVKVLDIDENGKISLSIRKLEEE   79 (129)
T ss_pred             CccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhH--HHHhcCCCEEEEEEEeeccCCCcceehHHhhhC
Confidence            478999999999999999999999999999999999999998877  799999999999999997 79999999999877


Q ss_pred             cC
Q 005707          338 GS  339 (681)
Q Consensus       338 P~  339 (681)
                      |-
T Consensus        80 pe   81 (129)
T COG1098          80 PE   81 (129)
T ss_pred             cc
Confidence            64

>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=99.45  E-value=2.2e-13  Score=116.07  Aligned_cols=71  Identities=21%  Similarity=0.383  Sum_probs=66.3

Q ss_pred             CCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCc---ccccccCCEEEEEEEEEeccCCceEEE
Q 005707          145 LIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDV---GSIVSVGQEVKVRLIEANAETGRISLT  215 (681)
Q Consensus       145 LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~---~e~fkVGd~VkVkVl~VD~ekgrI~LS  215 (681)
                      +++|+++.|+|++++++|+||+|+.+++||||+++++|+++.++   .+.|++||.|+|+|+++|+++++|.||
T Consensus         1 ~k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~LS   74 (74)
T cd05705           1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS   74 (74)
T ss_pred             CCCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence            57899999999999999999999988999999999999987765   578999999999999999999999885

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.

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

Probab=99.44  E-value=6e-13  Score=111.20  Aligned_cols=73  Identities=37%  Similarity=0.725  Sum_probs=70.5

Q ss_pred             CCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707          145 LIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR  217 (681)
Q Consensus       145 LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK  217 (681)
                      +++|+++.|+|.++.++|+||+|+++++||||++++++.+..++...|++||.++|+|+++|.+++++.||+|
T Consensus         2 ~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS~k   74 (74)
T PF00575_consen    2 LKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK   74 (74)
T ss_dssp             SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred             CCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence            6889999999999999999999998899999999999999999999999999999999999999999999986

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....

>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains

Probab=99.43  E-value=4e-13  Score=115.66  Aligned_cols=75  Identities=35%  Similarity=0.540  Sum_probs=72.2

Q ss_pred             cCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEE
Q 005707          142 NEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTM  216 (681)
Q Consensus       142 ~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSl  216 (681)
                      +.++++|+++.|+|+++.++|+||++++++.||+|+++++++++.++...|++||.|+|+|+.+|.++++|.||+
T Consensus         9 ~~~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i~lsl   83 (83)
T cd04461           9 FSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL   83 (83)
T ss_pred             HHhCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEeC
Confidence            678999999999999999999999998889999999999999999999999999999999999999999999985

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.

>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=99.40  E-value=6.5e-13  Score=113.22  Aligned_cols=71  Identities=23%  Similarity=0.303  Sum_probs=62.9

Q ss_pred             CccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccC-CCCcccCCCEEEEEEEEEe--CCeEEEE
Q 005707          260 FVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMM-GGSSLQVGQEVSVRVLRIS--RGQVTLT  330 (681)
Q Consensus       260 lkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~-p~~~fkVGqkVkVrVL~ID--kgKI~LS  330 (681)
                      |++|+++.|+|++++++|+||+|+++++||+|+++++|.++.+.. +...|++||.|+|+|+++|  +++|.||
T Consensus         1 ~k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~LS   74 (74)
T cd05705           1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS   74 (74)
T ss_pred             CCCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence            579999999999999999999999999999999999998865432 4589999999999999997  4777764

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.

>PRK08582 hypothetical protein; Provisional

Probab=99.39  E-value=1.9e-12  Score=123.17  Aligned_cols=81  Identities=36%  Similarity=0.694  Sum_probs=76.5

Q ss_pred             CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccchhh
Q 005707          144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDIS  223 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~dp  223 (681)
                      .+++|++|.|+|+.|+++|+||+|++++.||||+++++|+++.++...|++||.|+|+|+.+|. .++|.||++++..+|
T Consensus         2 ~~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~-~gkI~LSlk~~~~~~   80 (139)
T PRK08582          2 SIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVED-DGKIGLSIKKAKDRP   80 (139)
T ss_pred             CCcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECC-CCcEEEEEEecccCc
Confidence            4789999999999999999999999889999999999999999999999999999999999997 499999999998888


Q ss_pred             Hh
Q 005707          224 KL  225 (681)
Q Consensus       224 ~e  225 (681)
                      |.
T Consensus        81 ~~   82 (139)
T PRK08582         81 KR   82 (139)
T ss_pred             hh
Confidence            83

>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=99.38  E-value=1.6e-12  Score=107.73  Aligned_cols=70  Identities=30%  Similarity=0.527  Sum_probs=67.3

Q ss_pred             CcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707          148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR  217 (681)
Q Consensus       148 GdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK  217 (681)
                      |+++.|+|+++.++|+||+|++++.||+|++++++++..++.+.|++||.++|+|+++|++++++.||+|
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 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK   70 (70)
T ss_pred             CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence            7899999999999999999988899999999999998999999999999999999999999999999985

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.

>PRK08582 hypothetical protein; Provisional

Probab=99.36  E-value=3.2e-12  Score=121.60  Aligned_cols=81  Identities=36%  Similarity=0.602  Sum_probs=74.5

Q ss_pred             CCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe-CCeEEEEEeccCCC
Q 005707          259 KFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS-RGQVTLTMKKEDDV  337 (681)
Q Consensus       259 klkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID-kgKI~LSLK~~~~D  337 (681)
                      .+++|++|.|+|++|+++|+||+|+++++||||+++++|.++.+  +...|++||.|+|+|+++| .++|.||+|++..+
T Consensus         2 ~~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~--~~~~l~vGD~VkvkV~~id~~gkI~LSlk~~~~~   79 (139)
T PRK08582          2 SIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKD--INDHLKVGDEVEVKVLNVEDDGKIGLSIKKAKDR   79 (139)
T ss_pred             CCcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccccc--cccccCCCCEEEEEEEEECCCCcEEEEEEecccC
Confidence            37899999999999999999999999999999999999988643  4688999999999999998 59999999999999


Q ss_pred             cCCc
Q 005707          338 GSNL  341 (681)
Q Consensus       338 P~e~  341 (681)
                      ||..
T Consensus        80 ~~~~   83 (139)
T PRK08582         80 PKRQ   83 (139)
T ss_pred             chhh
Confidence            9874

>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=99.36  E-value=4e-12  Score=108.56  Aligned_cols=71  Identities=25%  Similarity=0.371  Sum_probs=65.6

Q ss_pred             CCCCCcEEEEEEEEEecCeeEEEEC-CCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccc
Q 005707          144 DLIPGATFTGKVRSIQPFGAFIDFG-AFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESD  220 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~GaFVdLg-ggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~  220 (681)
                      +|+.|+++.|+|++|.++|+||+++ ++++||||.++++|.      ..|++||.+.|+|+++|++++++.||+|+..
T Consensus         1 dl~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~------~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~~~   72 (74)
T cd05694           1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSK   72 (74)
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc------cccCCCCEEEEEEEEEECCCCEEEEEEeecc
Confidence            4789999999999999999999997 569999999999986      5689999999999999999999999999654

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.

>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=99.35  E-value=3.1e-12  Score=108.58  Aligned_cols=70  Identities=20%  Similarity=0.340  Sum_probs=66.6

Q ss_pred             CcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCcc--ccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707          148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNF--VKDVGSIVSVGQEVKVRLIEANAETGRISLTMR  217 (681)
Q Consensus       148 GdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~--v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK  217 (681)
                      |+++.|+|+++.++|+||.|+.+++|+||.++++|..  ..++.+.|++||.|+|+|+.+|+++++|.||++
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 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR   72 (73)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence            7899999999999999999988899999999999864  788999999999999999999999999999986

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.

>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=99.35  E-value=5.6e-12  Score=105.41  Aligned_cols=73  Identities=15%  Similarity=0.311  Sum_probs=69.1

Q ss_pred             CCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707          145 LIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR  217 (681)
Q Consensus       145 LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK  217 (681)
                      +++|+++.|+|+++.++|+||+|+.+++|++|.+++++++..++...|++||.|+|+|+++|..++++.||++
T Consensus         1 ~~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls~~   73 (73)
T cd05706           1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR   73 (73)
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence            4789999999999999999999998899999999999998888888999999999999999999999999975

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.

>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=99.34  E-value=3.8e-12  Score=105.67  Aligned_cols=69  Identities=29%  Similarity=0.504  Sum_probs=66.0

Q ss_pred             CcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEE
Q 005707          148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTM  216 (681)
Q Consensus       148 GdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSl  216 (681)
                      |+++.|+|+++.++|+||+|+++++||+|.+++++.+..++...|++||.++|+|+++|++++++.||+
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 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL   69 (69)
T ss_pred             CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence            789999999999999999998889999999999999988999999999999999999999999999985

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.

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

Probab=99.34  E-value=4.4e-12  Score=105.98  Aligned_cols=72  Identities=36%  Similarity=0.660  Sum_probs=65.4

Q ss_pred             CCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEe
Q 005707          259 KFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMK  332 (681)
Q Consensus       259 klkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK  332 (681)
                      ++++|+++.|+|+++.++|+||+|+++++||||.+++++.+.  ..+...|++||.|.|+|+++|  ++++.||+|
T Consensus         1 k~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~~~--~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS~k   74 (74)
T PF00575_consen    1 KLKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRI--DDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK   74 (74)
T ss_dssp             -SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEE--SSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred             CCCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCccc--cccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence            478999999999999999999999999999999999999753  345789999999999999998  588999986

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 ....

>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=99.34  E-value=3.5e-12  Score=107.78  Aligned_cols=71  Identities=25%  Similarity=0.381  Sum_probs=66.6

Q ss_pred             CCCCcEEEEEEEEEec-CeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707          145 LIPGATFTGKVRSIQP-FGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR  217 (681)
Q Consensus       145 LkvGdIVeGkV~sV~d-~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK  217 (681)
                      |++|++|.|+|+++.+ +|+||+|+.+.+|++|+++++|++..++.+.|++||.|+|+|+++|.  +++.||++
T Consensus         1 l~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~--~~i~LSl~   72 (72)
T cd05704           1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD--GKYQLSLR   72 (72)
T ss_pred             CCCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecC--CEEEEEeC
Confidence            5789999999999986 89999999889999999999999999999999999999999999975  89999985

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.

>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=99.34  E-value=5.6e-12  Score=107.63  Aligned_cols=70  Identities=27%  Similarity=0.446  Sum_probs=63.3

Q ss_pred             CCccCcEEEEEEEEEecceEEEEeC-CCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccC
Q 005707          259 KFVKGQDLEGTVKNLTRSGAFISLP-EGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKED  335 (681)
Q Consensus       259 klkvGdIV~G~VknVt~~GaFVeIg-~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~  335 (681)
                      +++.|+++.|+|++|.++|+||+++ +|+.||+|.++++|.        ..|++||.+.|+|+++|  ++++.||+|+..
T Consensus         1 dl~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~--------~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~~~   72 (74)
T cd05694           1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF--------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSK   72 (74)
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc--------cccCCCCEEEEEEEEEECCCCEEEEEEeecc
Confidence            4789999999999999999999997 699999999999875        46899999999999997  588999999874


Q ss_pred             C
Q 005707          336 D  336 (681)
Q Consensus       336 ~  336 (681)
                      .
T Consensus        73 ~   73 (74)
T cd05694          73 V   73 (74)
T ss_pred             c
Confidence            3

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.

>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=99.32  E-value=4.1e-12  Score=107.39  Aligned_cols=71  Identities=23%  Similarity=0.305  Sum_probs=65.1

Q ss_pred             CccCcEEEEEEEEEec-ceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCeEEEEEe
Q 005707          260 FVKGQDLEGTVKNLTR-SGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQVTLTMK  332 (681)
Q Consensus       260 lkvGdIV~G~VknVt~-~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgKI~LSLK  332 (681)
                      +++|+++.|+|+++.+ +|+||++++|.+|++|+++++|.+..  ++...|++||.|+|+|++++++|+.||+|
T Consensus         1 l~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~--~~~~~~~~Gd~v~~kV~~~~~~~i~LSl~   72 (72)
T cd05704           1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTE--NPLEGFKPGKIVRCCILSKKDGKYQLSLR   72 (72)
T ss_pred             CCCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccC--CHHHhCCCCCEEEEEEEEecCCEEEEEeC
Confidence            4689999999999986 89999999999999999999999854  44678999999999999999999999986

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.

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

Probab=99.32  E-value=8.9e-12  Score=105.22  Aligned_cols=70  Identities=31%  Similarity=0.531  Sum_probs=65.2

Q ss_pred             CCCcEEEEEEEEEecCeeEEEECC-CeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEE
Q 005707          146 IPGATFTGKVRSIQPFGAFIDFGA-FTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTM  216 (681)
Q Consensus       146 kvGdIVeGkV~sV~d~GaFVdLgg-gV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSl  216 (681)
                      +.|+++.|+|+++.+||+||++.+ +.+||+|+++++|.++.++.+.|++||.|+|+|+++|.++ ++.||+
T Consensus         2 ~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~-ki~ls~   72 (73)
T cd05686           2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKD-KMKLSL   72 (73)
T ss_pred             cCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCC-cEEEEe
Confidence            579999999999999999999965 3799999999999999999999999999999999999876 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.

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

Probab=99.31  E-value=1.3e-10  Score=120.30  Aligned_cols=178  Identities=20%  Similarity=0.162  Sum_probs=147.4

Q ss_pred             CCCCCcEEEEEEEEEecCeeEEEECCC-eEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccchh
Q 005707          144 DLIPGATFTGKVRSIQPFGAFIDFGAF-TDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDI  222 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~GaFVdLggg-V~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~d  222 (681)
                      .+.+|++..+.|....++|+|++=+.+ ..-++|.++...+       .+.+||.|.|.|+-  ...+++.++++     
T Consensus         2 ~~~iG~~~~l~V~~~~~~g~fL~~~~~~~~ilL~k~~~~~~-------e~evGdev~vFiY~--D~~~rl~aTt~-----   67 (287)
T COG2996           2 MIKIGQINSLEVVEFSDFGYFLDAGEDGTTILLPKSEPEED-------ELEVGDEVTVFIYV--DSEDRLIATTR-----   67 (287)
T ss_pred             cccccceEEEEEEEeeceeEEEecCCCceEEeccccCCcCC-------ccccCcEEEEEEEE--CCCCceeheee-----
Confidence            467899999999999999999998764 3788888766433       26799999999986  45678888887     


Q ss_pred             hHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEe-cceEEEEeCCCeEEEEeCCCCCccccc
Q 005707          223 SKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLT-RSGAFISLPEGEEGFLPTSEESDDGFA  301 (681)
Q Consensus       223 p~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt-~~GaFVeIg~GIeGLLpiSELSd~~ie  301 (681)
                                                        ...+.+|+.-.++|+.+. +-|+||+.+-.-+-|+|.+++...+  
T Consensus        68 ----------------------------------~p~~tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp~~~--  111 (287)
T COG2996          68 ----------------------------------EPKATVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDELPTLK--  111 (287)
T ss_pred             ----------------------------------cceEeecceeEEEEEEEcCCcceEEecCCCcceeeehhhccccc--
Confidence                                              334778999999999998 8899999998899999999987543  


Q ss_pred             ccCCCCcccCCCEEEEEEEEEe-CCeEEEEEecc-----CCCc----CCcceeeeEEEEeecccEEEEEEcCCeEEEeeC
Q 005707          302 NMMGGSSLQVGQEVSVRVLRIS-RGQVTLTMKKE-----DDVG----SNLQLTQGVIHAATNPFVLAFRSNKDISSFLDE  371 (681)
Q Consensus       302 ~~~p~~~fkVGqkVkVrVL~ID-kgKI~LSLK~~-----~~DP----~e~~lv~G~V~~~i~~fGlfV~l~~gI~GfIp~  371 (681)
                          +-++++||++-|+ |.+| ++||.-+++.-     ..+|    +.++.+.|+|+ .....|.|+-+++++-||||+
T Consensus       112 ----~~wpq~Gd~l~v~-l~~Dkk~Ri~g~~a~~~~l~~l~~~~~~~l~nq~v~~tVY-r~~~~G~fv~~e~~~~GfIh~  185 (287)
T COG2996         112 ----SLWPQKGDKLLVY-LYVDKKGRIWGTLAIEKILENLATPAYNNLKNQEVDATVY-RLLESGTFVITENGYLGFIHK  185 (287)
T ss_pred             ----ccCCCCCCEEEEE-EEEccCCcEEEEecchhHHHhcCCccchhhhcCeeeeEEE-EEeccceEEEEcCCeEEEEcc
Confidence                4579999999999 5666 69999888654     1223    23677899999 789999999999999999999


Q ss_pred             Cccccc
Q 005707          372 RDKSAT  377 (681)
Q Consensus       372 ~els~~  377 (681)
                      +|.-..
T Consensus       186 sEr~~~  191 (287)
T COG2996         186 SERFAE  191 (287)
T ss_pred             hhhccc
Confidence            998877

>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=99.31  E-value=5.4e-12  Score=108.60  Aligned_cols=75  Identities=24%  Similarity=0.386  Sum_probs=68.5

Q ss_pred             ccccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEE
Q 005707          255 MKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTM  331 (681)
Q Consensus       255 ~~~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSL  331 (681)
                      ..+.++++|+++.|+|+++.++|+||++++|++||+|.+++++.++.  ++...|++||.|+|+|+++|  ++++.|||
T Consensus         7 ~~~~~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~--~~~~~~~~Gd~v~vkV~~id~~~~~i~lsl   83 (83)
T cd04461           7 TNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVT--DPSFGFKKGQSVTAKVTSVDEEKQRFLLSL   83 (83)
T ss_pred             hhHHhCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCccccc--CHHHhcCCCCEEEEEEEEEcCCCCEEEEeC
Confidence            45778999999999999999999999999999999999999998754  45789999999999999997  58999986

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.

>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=99.30  E-value=7.7e-12  Score=103.55  Aligned_cols=68  Identities=37%  Similarity=0.576  Sum_probs=65.3

Q ss_pred             CcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEE
Q 005707          148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLT  215 (681)
Q Consensus       148 GdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LS  215 (681)
                      |+++.|+|+++.++|+||+|++++.||+|.+++++++..++...|++||.|+|+|+++|+++++|.||
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 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT   68 (68)
T ss_pred             CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence            78999999999999999999988999999999999999999999999999999999999999999875

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.

>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=99.29  E-value=9.9e-12  Score=104.76  Aligned_cols=69  Identities=29%  Similarity=0.396  Sum_probs=65.4

Q ss_pred             CcEEE-EEEEEE-ecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEE
Q 005707          148 GATFT-GKVRSI-QPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTM  216 (681)
Q Consensus       148 GdIVe-GkV~sV-~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSl  216 (681)
                      |++|+ |+|+++ .++|+||+|.++++||||++++++.+..++...|++||.++|+|+++|+.+++|.||+
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 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL   71 (71)
T ss_pred             CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence            78999 999999 6999999998779999999999999999899999999999999999999999999985

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.

>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=99.29  E-value=7.7e-12  Score=106.19  Aligned_cols=70  Identities=20%  Similarity=0.374  Sum_probs=62.0

Q ss_pred             CcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEe
Q 005707          263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMK  332 (681)
Q Consensus       263 GdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK  332 (681)
                      |+++.|+|+++.++|+||+|+++++|+||.++++|..-...++...|++||.|+|+|+++|  ++||.||+|
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 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR   72 (73)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence            7899999999999999999999999999999999863112245788999999999999998  488999986

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.

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

Probab=99.29  E-value=1.8e-11  Score=102.65  Aligned_cols=74  Identities=26%  Similarity=0.453  Sum_probs=68.9

Q ss_pred             CCCCcEEEEEEEEEecCeeEEEECC--CeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEec
Q 005707          145 LIPGATFTGKVRSIQPFGAFIDFGA--FTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRE  218 (681)
Q Consensus       145 LkvGdIVeGkV~sV~d~GaFVdLgg--gV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~  218 (681)
                      ++.|+++.|+|+++.++|+||+|.+  +++||||+++++++++.++...|++||.|+|+|+++|..++++.||+|+
T Consensus         1 ~~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls~k~   76 (76)
T cd04452           1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR   76 (76)
T ss_pred             CCCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence            3579999999999999999999963  4999999999999999999999999999999999999999999999873

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

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

Probab=99.28  E-value=1.7e-11  Score=101.71  Aligned_cols=72  Identities=28%  Similarity=0.515  Sum_probs=68.8

Q ss_pred             CcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEecc
Q 005707          148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRES  219 (681)
Q Consensus       148 GdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l  219 (681)
                      |+++.|+|+++.++|+||+|+++++|++|.++++++++.++.+.|++||.++|+|+.+|.+++++.||++.+
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 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAK   72 (73)
T ss_pred             CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEc
Confidence            789999999999999999998889999999999999999999999999999999999999999999999864

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>PRK07252 hypothetical protein; Provisional

Probab=99.27  E-value=2e-11  Score=113.66  Aligned_cols=78  Identities=29%  Similarity=0.642  Sum_probs=73.7

Q ss_pred             CCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccchhh
Q 005707          146 IPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDIS  223 (681)
Q Consensus       146 kvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~dp  223 (681)
                      ++|+++.|+|++|.++|+||+|.+++.||||+++++++++.++...|++||.|+|+|+++|.+++++.||++.+..+.
T Consensus         2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~~~~   79 (120)
T PRK07252          2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLEEEK   79 (120)
T ss_pred             CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeecccCc
Confidence            579999999999999999999988899999999999999999989999999999999999999999999999887644

>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=99.26  E-value=3.1e-11  Score=100.93  Aligned_cols=74  Identities=36%  Similarity=0.641  Sum_probs=69.2

Q ss_pred             CCCcEEEEEEEEEecCeeEEEECC-CeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEecc
Q 005707          146 IPGATFTGKVRSIQPFGAFIDFGA-FTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRES  219 (681)
Q Consensus       146 kvGdIVeGkV~sV~d~GaFVdLgg-gV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l  219 (681)
                      ++|+++.|+|+++.++|+||+|.+ +..|++|++++++++..++...|++||.|+|+|+++|.+++++.|++|..
T Consensus         1 ~~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k~~   75 (77)
T cd05708           1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS   75 (77)
T ss_pred             CCCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence            369999999999999999999974 69999999999999888889999999999999999999999999999854

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.

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

Probab=99.25  E-value=2.9e-11  Score=100.37  Aligned_cols=70  Identities=29%  Similarity=0.507  Sum_probs=67.0

Q ss_pred             CcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707          148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR  217 (681)
Q Consensus       148 GdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK  217 (681)
                      |+++.|+|.++.++|+||+|+++.+|+||.+++++.+..++.+.|++||.++|+|+++|++++++.||++
T Consensus         1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~   70 (70)
T cd05687           1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR   70 (70)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence            7899999999999999999988899999999999999999999999999999999999988899999985

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.

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

Probab=99.23  E-value=2.4e-11  Score=100.05  Aligned_cols=68  Identities=38%  Similarity=0.600  Sum_probs=63.2

Q ss_pred             CcEEEEEEEEEecCeeEEEECCCeEEEEeccccCC-ccccCcccccccCCEEEEEEEEEeccCCceEEE
Q 005707          148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSD-NFVKDVGSIVSVGQEVKVRLIEANAETGRISLT  215 (681)
Q Consensus       148 GdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~-~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LS  215 (681)
                      |+++.|+|+++.++|+||+|.++++||+|+++++| .+..++...|++||.|+|+|+++|.++++|.|+
T Consensus         1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~~~~i~l~   69 (69)
T cd05690           1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISLG   69 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCcCEEeCC
Confidence            78999999999999999999888999999999997 567788889999999999999999999998874

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.

>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=99.23  E-value=2.4e-11  Score=100.67  Aligned_cols=68  Identities=31%  Similarity=0.452  Sum_probs=62.0

Q ss_pred             CcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC--CeEEEEEe
Q 005707          263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR--GQVTLTMK  332 (681)
Q Consensus       263 GdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk--gKI~LSLK  332 (681)
                      |+++.|+|+++.++|+||+|+++++||+|.+++++.+..  ++...|++||.++|+|+++|+  +++.||+|
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 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIK--DPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK   70 (70)
T ss_pred             CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhcC--CHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence            789999999999999999999999999999999988743  457889999999999999974  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 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.23  E-value=5.7e-11  Score=99.37  Aligned_cols=71  Identities=17%  Similarity=0.179  Sum_probs=64.1

Q ss_pred             CccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC--CeEEEEEe
Q 005707          260 FVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR--GQVTLTMK  332 (681)
Q Consensus       260 lkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk--gKI~LSLK  332 (681)
                      +++|+++.|+|+++.++|+||+++++++|++|.++++|++..  ++...|++||.|+|+|+++|.  +++.||+|
T Consensus         1 ~~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~~~~--~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls~~   73 (73)
T cd05706           1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSE--ALPYKFKKNDIVRACVLSVDVPNKKIALSLR   73 (73)
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCcccc--ccccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence            468999999999999999999999999999999999987632  447889999999999999984  89999985

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.

>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=99.21  E-value=4.1e-11  Score=99.47  Aligned_cols=67  Identities=30%  Similarity=0.536  Sum_probs=60.5

Q ss_pred             CcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEE
Q 005707          263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTM  331 (681)
Q Consensus       263 GdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSL  331 (681)
                      |+++.|+|++|.++|+||+|++|++||+|.++++|.++.  ++...|++||.++|+|+++|  ++++.|+|
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 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLK--HPEKKFKPGLKVKCRVLSVEPERKRLVLTL   69 (69)
T ss_pred             CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCcccc--CHHHcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence            789999999999999999999999999999999988753  34678999999999999997  48898875

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.

>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=99.20  E-value=8.1e-11  Score=100.30  Aligned_cols=73  Identities=32%  Similarity=0.506  Sum_probs=66.0

Q ss_pred             CcEEEEEEEEEecceEEEEeC---CCeEEEEeCCCCCcccc-cccCCCCcccCCCEEEEEEEEEeCCeEEEEEeccCCC
Q 005707          263 GQDLEGTVKNLTRSGAFISLP---EGEEGFLPTSEESDDGF-ANMMGGSSLQVGQEVSVRVLRISRGQVTLTMKKEDDV  337 (681)
Q Consensus       263 GdIV~G~VknVt~~GaFVeIg---~GIeGLLpiSELSd~~i-e~~~p~~~fkVGqkVkVrVL~IDkgKI~LSLK~~~~D  337 (681)
                      |+++.|+|+++.+||+||+|+   ++++||+|.++++|.++ .  ++...|++||.|+|+|+++|++++.|++|.+.++
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 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVA--NPSDVVKRGQKVKVKVISIQNGKISLSMKDVDQD   77 (79)
T ss_pred             CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcC--ChhheeCCCCEEEEEEEEEeCCEEEEEEEecccC
Confidence            789999999999999999998   47999999999999874 3  4477899999999999999999999999998654

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.

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

Probab=99.20  E-value=7.5e-11  Score=95.68  Aligned_cols=69  Identities=41%  Similarity=0.801  Sum_probs=65.6

Q ss_pred             CcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707          148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR  217 (681)
Q Consensus       148 GdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK  217 (681)
                      |+++.|+|+++.++|+||+++.+..||+|.++++++++.++...|++||.|+|+|+.+|. ++++.||+|
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 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA-RGRISLSIK   69 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECC-CCcEEEEEC
Confidence            789999999999999999999889999999999999988998999999999999999998 899999985

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.

>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=99.20  E-value=7.8e-11  Score=100.41  Aligned_cols=72  Identities=40%  Similarity=0.682  Sum_probs=66.6

Q ss_pred             CcEEEEEEEEEecCeeEEEEC---CCeEEEEeccccCCccc-cCcccccccCCEEEEEEEEEeccCCceEEEEeccch
Q 005707          148 GATFTGKVRSIQPFGAFIDFG---AFTDGLVHVSRLSDNFV-KDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDD  221 (681)
Q Consensus       148 GdIVeGkV~sV~d~GaFVdLg---ggV~GLVPiSELS~~~v-~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~  221 (681)
                      |+++.|+|+++.++|+||+|+   .+..||+|+++++|.+. .++...|++||.|+|+|+++|  ++++.+|+|.+.+
T Consensus         1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd--~~~i~~s~k~~~~   76 (79)
T cd05684           1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ--NGKISLSMKDVDQ   76 (79)
T ss_pred             CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe--CCEEEEEEEeccc
Confidence            789999999999999999998   35999999999999986 888899999999999999999  8999999997654

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.

>PRK05807 hypothetical protein; Provisional

Probab=99.20  E-value=9.3e-11  Score=111.26  Aligned_cols=75  Identities=35%  Similarity=0.640  Sum_probs=70.5

Q ss_pred             CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccc
Q 005707          144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESD  220 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~  220 (681)
                      .+++|++|.|+|+.+.++|+||+|. +..||||++++++.++.++...|++||.|+|+|+.+|. .++|.||++.+.
T Consensus         2 ~~~vG~vv~G~Vt~i~~~GafV~L~-~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~-~gkI~LSlk~~~   76 (136)
T PRK05807          2 TLKAGSILEGTVVNITNFGAFVEVE-GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD-NGKISLSIKQAM   76 (136)
T ss_pred             CccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECC-CCcEEEEEEecc
Confidence            4778999999999999999999995 48999999999999999999999999999999999998 799999999875

>PRK08059 general stress protein 13; Validated

Probab=99.19  E-value=8.1e-11  Score=109.49  Aligned_cols=82  Identities=41%  Similarity=0.760  Sum_probs=76.5

Q ss_pred             cCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccch
Q 005707          142 NEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDD  221 (681)
Q Consensus       142 ~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~  221 (681)
                      +..+++|++|.|+|.++.++|+||+|+.++.|++|+++++++++.++...|++||.|+|+|+++|.+++++.||++.+..
T Consensus         2 ~~~~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk~~~~   81 (123)
T PRK08059          2 MSQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEE   81 (123)
T ss_pred             cccCCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEEccc
Confidence            34688999999999999999999999988999999999999999888889999999999999999999999999998876


Q ss_pred             hh
Q 005707          222 IS  223 (681)
Q Consensus       222 dp  223 (681)
                      ++
T Consensus        82 ~~   83 (123)
T PRK08059         82 AP   83 (123)
T ss_pred             Cc
Confidence            55

>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=99.19  E-value=6e-11  Score=100.01  Aligned_cols=67  Identities=25%  Similarity=0.414  Sum_probs=60.2

Q ss_pred             CcEEE-EEEEEE-ecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEE
Q 005707          263 GQDLE-GTVKNL-TRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTM  331 (681)
Q Consensus       263 GdIV~-G~VknV-t~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSL  331 (681)
                      |+++. |+|+++ .++|+||++.+|++||+|.+++++.+..  .+...|++||.+.|+|+.+|  ++++.||+
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 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVP--SDTGPFKAGTTHKARIIGYSPMDGLLQLSL   71 (71)
T ss_pred             CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcchhc--CcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence            78899 999999 6999999999999999999999988754  34788999999999999998  47899885

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

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

Probab=99.18  E-value=1.1e-10  Score=98.69  Aligned_cols=69  Identities=25%  Similarity=0.378  Sum_probs=60.8

Q ss_pred             ccCcEEEEEEEEEecceEEEEeCC-CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC-CeEEEEE
Q 005707          261 VKGQDLEGTVKNLTRSGAFISLPE-GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR-GQVTLTM  331 (681)
Q Consensus       261 kvGdIV~G~VknVt~~GaFVeIg~-GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk-gKI~LSL  331 (681)
                      ..|+++.|+|+++.+||+||++.+ +.+||+|+++++|.++.  ++...|++||.|+|+|+++|. +|+.|||
T Consensus         2 ~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~~--~~~~~~~~Gd~v~vkv~~vd~~~ki~ls~   72 (73)
T cd05686           2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVD--DPSEVVDVGEKVWVKVIGREMKDKMKLSL   72 (73)
T ss_pred             cCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCccc--CHhhEECCCCEEEEEEEEECCCCcEEEEe
Confidence            589999999999999999999953 37999999999998764  457889999999999999984 5888886

pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.

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

Probab=99.17  E-value=1.1e-10  Score=97.42  Aligned_cols=71  Identities=32%  Similarity=0.528  Sum_probs=64.0

Q ss_pred             CCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCc-cccCcccccccCCEEEEEEEEEeccCCceEEE
Q 005707          145 LIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDN-FVKDVGSIVSVGQEVKVRLIEANAETGRISLT  215 (681)
Q Consensus       145 LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~-~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LS  215 (681)
                      +.+|+++.|+|+++.++|+||+|.++++||+|.+++.|. +..++...|++||.|+|+|+++|.+++++.|+
T Consensus         1 ~~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~~   72 (72)
T cd05689           1 YPEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISLG   72 (72)
T ss_pred             CcCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCcCEEeCC
Confidence            468999999999999999999998789999999999875 44577788999999999999999999988764

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.

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=99.17  E-value=4.1e-11  Score=141.14  Aligned_cols=84  Identities=23%  Similarity=0.357  Sum_probs=76.1

Q ss_pred             cccCCccCcEEE-EEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe-CCeEEEEEec
Q 005707          256 KTTKFVKGQDLE-GTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS-RGQVTLTMKK  333 (681)
Q Consensus       256 ~~sklkvGdIV~-G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID-kgKI~LSLK~  333 (681)
                      .+.+.++|++|. |+|++|.+||+||+|.+|++||||+++++|.++.  ++...|++||.|+|+|+++| ++||.|++|.
T Consensus       747 l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv~--~~~dv~kvGD~V~VkVi~ID~~grI~LSlK~  824 (891)
T PLN00207        747 LTMVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLA--KPEDAFKVGDRIDVKLIEVNDKGQLRLSRRA  824 (891)
T ss_pred             HhcCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCcccc--CHHHhcCCCCEEEEEEEEECCCCcEEEEEec
Confidence            345678999995 6999999999999999999999999999999865  44788999999999999998 5899999999


Q ss_pred             cCCCcCCc
Q 005707          334 EDDVGSNL  341 (681)
Q Consensus       334 ~~~DP~e~  341 (681)
                      +..|||+.
T Consensus       825 l~~~Pw~~  832 (891)
T PLN00207        825 LLPEANSE  832 (891)
T ss_pred             cccCchhh
Confidence            99999994

>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=99.17  E-value=5.1e-11  Score=107.40  Aligned_cols=76  Identities=25%  Similarity=0.430  Sum_probs=68.7

Q ss_pred             CCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccc-------------------cCcccccccCCEEEEEEEEE
Q 005707          145 LIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFV-------------------KDVGSIVSVGQEVKVRLIEA  205 (681)
Q Consensus       145 LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v-------------------~d~~e~fkVGd~VkVkVl~V  205 (681)
                      |++|++|.|+|+++.++|+||.|++++.|++|+++++|++.                   .++.+.|++||.|+|+|+++
T Consensus         1 L~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~   80 (100)
T cd05693           1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSL   80 (100)
T ss_pred             CCCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEc
Confidence            57899999999999999999999988999999999999763                   34678899999999999999


Q ss_pred             ecc---CCceEEEEeccc
Q 005707          206 NAE---TGRISLTMRESD  220 (681)
Q Consensus       206 D~e---kgrI~LSlK~l~  220 (681)
                      |+.   +++|.||+++..
T Consensus        81 d~~~~~~~~i~LSlr~~~   98 (100)
T cd05693          81 DKSKSGKKRIELSLEPEL   98 (100)
T ss_pred             cCCcCCCcEEEEEecHHH
Confidence            997   789999999643

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.

>PRK07252 hypothetical protein; Provisional

Probab=99.16  E-value=1.6e-10  Score=107.61  Aligned_cols=76  Identities=29%  Similarity=0.489  Sum_probs=68.8

Q ss_pred             ccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCc
Q 005707          261 VKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVG  338 (681)
Q Consensus       261 kvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP  338 (681)
                      ++|+++.|+|++|.++|+||+|++++.||+|.+++++.++.+  +...|++||.|.|+|+++|  ++++.|++|....+.
T Consensus         2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~--~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~~~~   79 (120)
T PRK07252          2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDN--IHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLEEEK   79 (120)
T ss_pred             CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccC--hhhccCCCCEEEEEEEEEeCCCCEEEEEEeecccCc
Confidence            579999999999999999999999999999999999988643  4788999999999999998  599999999996643

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

Probab=99.15  E-value=1.7e-10  Score=96.70  Aligned_cols=71  Identities=31%  Similarity=0.446  Sum_probs=63.5

Q ss_pred             ccCcEEEEEEEEEecceEEEEeCC--CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC--CeEEEEEec
Q 005707          261 VKGQDLEGTVKNLTRSGAFISLPE--GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR--GQVTLTMKK  333 (681)
Q Consensus       261 kvGdIV~G~VknVt~~GaFVeIg~--GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk--gKI~LSLK~  333 (681)
                      ++|+++.|+|+++.++|+||+|.+  |++||||.+++++.++.  ++...|++||.|+|+|+++|.  +++.|++|+
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 EEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIR--SIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR   76 (76)
T ss_pred             CCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccC--CHHHeeCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence            579999999999999999999974  69999999999998754  347789999999999999984  889999974

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

>TIGR02063 RNase_R ribonuclease R

Probab=99.15  E-value=1.6e-11  Score=143.09  Aligned_cols=158  Identities=21%  Similarity=0.315  Sum_probs=106.8

Q ss_pred             ccccceeeecccccccccceeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCcceecCCCC
Q 005707           26 NCLTRYNSTRKSTKQTISSQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPS  105 (681)
Q Consensus        26 ~~~~~~~~~r~~~~~~~s~~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s  105 (681)
                      .+.+||||+-.+|.|||||.|++.||-.+|-+. ....+.......   .    .         .+..   .-.+.    
T Consensus       539 ~~~~HfgL~~~~YthfTSPIRRY~DLivHr~L~-~~l~~~~~~~~~---~----~---------~~~~---~~~l~----  594 (709)
T TIGR02063       539 ENIGHFGLALEYYTHFTSPIRRYPDLIVHRLIK-KALFGGENTTTE---K----E---------REYL---EAKLE----  594 (709)
T ss_pred             CCCCccccccccccccCCccccchHHHHHHHHH-HHHcCCCCCCcc---c----c---------chhh---HHHHH----
Confidence            467999999999999999999999987764221 111110000000   0    0         0000   00011    


Q ss_pred             CcccccccccccCCChhhHHhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECC-CeEEEEeccccCCcc
Q 005707          106 DVETSESSSIKSEASPTLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGA-FTDGLVHVSRLSDNF  184 (681)
Q Consensus       106 ~v~~ae~ss~~sea~~daek~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgg-gV~GLVPiSELS~~~  184 (681)
                        ..+.+.+.+.+.+..+++.....  ...     .|..-++|+++.|+|++|+++|+||+|.+ +++||||++++.+++
T Consensus       595 --~~~~~~~~~er~a~~aer~~~~~--~~~-----~yl~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~  665 (709)
T TIGR02063       595 --EIAEHSSKTERRADEAERDVNDW--KKA-----EYMSEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDY  665 (709)
T ss_pred             --HHHHHHHHHHHHHHHHHHHHHHH--HHH-----HhhhccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCc
Confidence              11344555555655555544431  222     14456789999999999999999999976 699999999998765


Q ss_pred             c-----------cCcccccccCCEEEEEEEEEeccCCceEEEE
Q 005707          185 V-----------KDVGSIVSVGQEVKVRLIEANAETGRISLTM  216 (681)
Q Consensus       185 v-----------~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSl  216 (681)
                      +           .+....|++||.|+|+|+++|..+++|.|++
T Consensus       666 ~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~~~~~I~~~l  708 (709)
T TIGR02063       666 YVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTGKIDFEL  708 (709)
T ss_pred             EEEcccceEEEeccCCcEECCCCEEEEEEEEEecccCeEEEEE
Confidence            3           2345679999999999999999999999986

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.

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

Probab=99.15  E-value=3.3e-09  Score=110.10  Aligned_cols=145  Identities=26%  Similarity=0.350  Sum_probs=117.3

Q ss_pred             CCCCCcEEEEEEEEEe-cCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccchh
Q 005707          144 DLIPGATFTGKVRSIQ-PFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDI  222 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~-d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~d  222 (681)
                      .+.+|+--.++|+.+. +-|+||++|-.-+.+||.+++....    .-.+++||.+-|.+.- |+ ++||...++.-..-
T Consensus        70 ~~tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp~~~----~~wpq~Gd~l~v~l~~-Dk-k~Ri~g~~a~~~~l  143 (287)
T COG2996          70 KATVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDELPTLK----SLWPQKGDKLLVYLYV-DK-KGRIWGTLAIEKIL  143 (287)
T ss_pred             eEeecceeEEEEEEEcCCcceEEecCCCcceeeehhhccccc----ccCCCCCCEEEEEEEE-cc-CCcEEEEecchhHH
Confidence            5677999999999999 8899999998899999999986531    2347899999999874 54 55888887732211


Q ss_pred             hHhhhhccccccCCccccccccCCCCCCccccccccCCc---cCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCccc
Q 005707          223 SKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFV---KGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDG  299 (681)
Q Consensus       223 p~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklk---vGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~  299 (681)
                      .                               .....+-   .++.++|+|.++...|.||-+.++.-||||.+|..   
T Consensus       144 ~-------------------------------~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr~---  189 (287)
T COG2996         144 E-------------------------------NLATPAYNNLKNQEVDATVYRLLESGTFVITENGYLGFIHKSERF---  189 (287)
T ss_pred             H-------------------------------hcCCccchhhhcCeeeeEEEEEeccceEEEEcCCeEEEEcchhhc---
Confidence            1                               1222233   49999999999999999999999999999999865   


Q ss_pred             ccccCCCCcccCCCEEEEEEEEE-eCCeEEEEEeccC
Q 005707          300 FANMMGGSSLQVGQEVSVRVLRI-SRGQVTLTMKKED  335 (681)
Q Consensus       300 ie~~~p~~~fkVGqkVkVrVL~I-DkgKI~LSLK~~~  335 (681)
                             ..++.|+.+++||+.+ ++|+|.||+++..
T Consensus       190 -------~~prlG~~l~~rVi~~reDg~lnLSl~p~~  219 (287)
T COG2996         190 -------AEPRLGERLTARVIGVREDGKLNLSLRPRA  219 (287)
T ss_pred             -------ccccCCceEEEEEEEEccCCeeeccccccc
Confidence                   3568999999999999 5799999999873

>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=99.15  E-value=1.1e-10  Score=94.57  Aligned_cols=68  Identities=44%  Similarity=0.819  Sum_probs=64.3

Q ss_pred             CcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEE
Q 005707          148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLT  215 (681)
Q Consensus       148 GdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LS  215 (681)
                      |+++.|+|+++.++|+||+++.+..||+|.+++++.++.++...|++||.++|+|+++|.+++++.||
T Consensus         1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls   68 (68)
T cd05685           1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS   68 (68)
T ss_pred             CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence            78999999999999999999988999999999999988889889999999999999999999998875

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.

>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=99.14  E-value=1.6e-10  Score=96.19  Aligned_cols=66  Identities=23%  Similarity=0.341  Sum_probs=60.0

Q ss_pred             CcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEE
Q 005707          148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLT  215 (681)
Q Consensus       148 GdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LS  215 (681)
                      |++++|+|+++.++|+||+|.++++||+|.++++..+..  ...|++|+.++|+|+.+|+++++|.||
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 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSS--KSTYKEGQKVRARILYVDPSTKVVGLS   66 (66)
T ss_pred             CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCccCc--ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence            789999999999999999997779999999999865544  677999999999999999999998876

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.

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=99.13  E-value=1e-10  Score=137.83  Aligned_cols=83  Identities=29%  Similarity=0.518  Sum_probs=77.7

Q ss_pred             CCCCCCcEEE-EEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccch
Q 005707          143 EDLIPGATFT-GKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDD  221 (681)
Q Consensus       143 ~~LkvGdIVe-GkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~  221 (681)
                      ...++|++|. |+|++|.+||+||+|.++++||||+++|+|+++.++.+.|++||.|+|+|+++|. +++|.||+|.+..
T Consensus       749 ~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~ID~-~grI~LSlK~l~~  827 (891)
T PLN00207        749 MVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVND-KGQLRLSRRALLP  827 (891)
T ss_pred             cCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEECC-CCcEEEEEecccc
Confidence            4578999996 6999999999999998779999999999999999999999999999999999997 7999999999999


Q ss_pred             hhHhh
Q 005707          222 ISKLQ  226 (681)
Q Consensus       222 dp~ek  226 (681)
                      +||..
T Consensus       828 ~Pw~~  832 (891)
T PLN00207        828 EANSE  832 (891)
T ss_pred             Cchhh
Confidence            99953

>PRK05807 hypothetical protein; Provisional

Probab=99.13  E-value=3e-10  Score=107.83  Aligned_cols=74  Identities=34%  Similarity=0.535  Sum_probs=67.5

Q ss_pred             CCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe-CCeEEEEEeccC
Q 005707          259 KFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS-RGQVTLTMKKED  335 (681)
Q Consensus       259 klkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID-kgKI~LSLK~~~  335 (681)
                      .+++|++|.|+|+.|+++|+||+| ++..||||++++++.++.+  +...|++||.|+|+|+++| .++|.||||.+.
T Consensus         2 ~~~vG~vv~G~Vt~i~~~GafV~L-~~~~Glvhiseis~~~v~~--~~~~~kvGd~V~VkV~~id~~gkI~LSlk~~~   76 (136)
T PRK05807          2 TLKAGSILEGTVVNITNFGAFVEV-EGKTGLVHISEVADTYVKD--IREHLKEQDKVKVKVISIDDNGKISLSIKQAM   76 (136)
T ss_pred             CccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEhhhcccccccC--ccccCCCCCEEEEEEEEECCCCcEEEEEEecc
Confidence            478999999999999999999999 6899999999999988654  3688999999999999998 589999999985

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

Probab=99.12  E-value=2.8e-10  Score=94.38  Aligned_cols=70  Identities=30%  Similarity=0.542  Sum_probs=63.7

Q ss_pred             CcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC--CeEEEEEecc
Q 005707          263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR--GQVTLTMKKE  334 (681)
Q Consensus       263 GdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk--gKI~LSLK~~  334 (681)
                      |+++.|+|+++.++|+||++.++++|++|.+++++.++.  ++...|++||.++|+|+++|.  +++.|++|..
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 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVE--DATERFKVGDEVEAKITNVDRKNRKISLSIKAK   72 (73)
T ss_pred             CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCcccc--CHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEc
Confidence            789999999999999999999999999999999988754  357889999999999999984  7899999875

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.

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

Probab=99.12  E-value=2.7e-10  Score=95.03  Aligned_cols=69  Identities=36%  Similarity=0.540  Sum_probs=59.6

Q ss_pred             CccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC--CeEEE
Q 005707          260 FVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR--GQVTL  329 (681)
Q Consensus       260 lkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk--gKI~L  329 (681)
                      |++|+++.|+|+++.++|+||+|.++++||+|.+++.|... ..++...|++||.|+|+|+++|.  +++.|
T Consensus         1 ~~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~~-~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~   71 (72)
T cd05689           1 YPEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNK-NIHPSKVVSLGDEVEVMVLDIDEERRRISL   71 (72)
T ss_pred             CcCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCccc-ccCcccEeCCCCEEEEEEEEeeCCcCEEeC
Confidence            57899999999999999999999999999999999987521 23456789999999999999974  66655

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.

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

Probab=99.11  E-value=3.1e-10  Score=93.87  Aligned_cols=67  Identities=28%  Similarity=0.402  Sum_probs=61.3

Q ss_pred             CcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707          148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR  217 (681)
Q Consensus       148 GdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK  217 (681)
                      |+++.|+|+.+.++|+||++ ++++||||.+++++.+..++..  .+|+.++|+|+++|+++++|.||+|
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-EGVRAFLPASQVDLRPVEDLDE--YVGKELKFKIIEIDRERNNIVLSRR   67 (67)
T ss_pred             CCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHCCCcccCChHH--hCCCEEEEEEEEEeCCCCEEEEEcC
Confidence            78999999999999999999 5699999999999988777765  3899999999999999999999975

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.

>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=99.11  E-value=1.6e-10  Score=95.61  Aligned_cols=66  Identities=30%  Similarity=0.480  Sum_probs=59.6

Q ss_pred             CcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEE
Q 005707          263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLT  330 (681)
Q Consensus       263 GdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LS  330 (681)
                      |+++.|+|+++.++|+||+|+++++||+|.+++++.+..  ++...|++||.|+|+|+++|  ++++.||
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 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLK--DWKKRFKVGQLVKGKIVSIDPDNGRIEMT   68 (68)
T ss_pred             CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchhhc--CHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence            789999999999999999999999999999999988754  45788999999999999998  4777764

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.

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

Probab=99.11  E-value=3.6e-10  Score=91.13  Aligned_cols=72  Identities=43%  Similarity=0.756  Sum_probs=67.2

Q ss_pred             CCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707          146 IPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR  217 (681)
Q Consensus       146 kvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK  217 (681)
                      ++|+++.|+|.++.++|+||++++++.|++|.+++.+.+..++...|++||.+.|+|+.+|..++++.||++
T Consensus         1 ~~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~~   72 (72)
T smart00316        1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK   72 (72)
T ss_pred             CCCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence            369999999999999999999997799999999999988788888899999999999999998899999875

>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=99.11  E-value=3.1e-10  Score=94.89  Aligned_cols=72  Identities=31%  Similarity=0.526  Sum_probs=64.6

Q ss_pred             ccCcEEEEEEEEEecceEEEEeCC-CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEecc
Q 005707          261 VKGQDLEGTVKNLTRSGAFISLPE-GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKE  334 (681)
Q Consensus       261 kvGdIV~G~VknVt~~GaFVeIg~-GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~  334 (681)
                      ++|+++.|+|+++.++|+||+|.+ +++|++|.++++|.+..  .+...|++||.|+|+|+++|  ++++.|++|+.
T Consensus         1 ~~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~~~--~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k~~   75 (77)
T cd05708           1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVA--DASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS   75 (77)
T ss_pred             CCCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCccC--CHhHeecCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence            369999999999999999999985 89999999999998743  35688999999999999998  58999999875

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.

>PRK11642 exoribonuclease R; Provisional

Probab=99.11  E-value=5.7e-11  Score=140.20  Aligned_cols=164  Identities=19%  Similarity=0.244  Sum_probs=111.3

Q ss_pred             ccccceeeecccccccccceeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCcceecCCCC
Q 005707           26 NCLTRYNSTRKSTKQTISSQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPS  105 (681)
Q Consensus        26 ~~~~~~~~~r~~~~~~~s~~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s  105 (681)
                      .+.+||||+..+|.||+||+|+|.||-.+|-+.- ...+... ....+..    .....   .  ...   .  +     
T Consensus       551 ~~~gHfGLa~~~YtHFTSPIRRY~DLivHR~Lk~-~L~~~~~-~~~~~~~----~~~~~---~--~~~---~--l-----  609 (813)
T PRK11642        551 ENRGHFGLALQSYAHFTSPIRRYPDLSLHRAIKY-LLAKEQG-HKGNTTE----TGGYH---Y--SME---E--M-----  609 (813)
T ss_pred             CCCCccccccccccccCchhhhhHHHHHHHHHHH-HHhCCCC-ccccccc----ccccc---c--CHH---H--H-----
Confidence            5789999999999999999999999877753321 1000000 0000000    00000   0  000   0  0     


Q ss_pred             CcccccccccccCCChhhHHhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECC-CeEEEEeccccCCcc
Q 005707          106 DVETSESSSIKSEASPTLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGA-FTDGLVHVSRLSDNF  184 (681)
Q Consensus       106 ~v~~ae~ss~~sea~~daek~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgg-gV~GLVPiSELS~~~  184 (681)
                       ...++++|.+++.+.++++......  +..     +..-++|+++.|+|++|+++|+||+|.. +++||||+++|.++|
T Consensus       610 -~~~~~~~s~~er~A~~aeR~~~~~~--~~~-----~m~~~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~  681 (813)
T PRK11642        610 -LQLGQHCSMTERRADEATRDVADWL--KCD-----FMLDQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDY  681 (813)
T ss_pred             -HHHHHHHHHHHHHHHHHHHHHHHHH--HHh-----hhhccCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcc
Confidence             1225567777777777776555422  221     3344689999999999999999999975 499999999999874


Q ss_pred             cc-----------CcccccccCCEEEEEEEEEeccCCceEEEEec
Q 005707          185 VK-----------DVGSIVSVGQEVKVRLIEANAETGRISLTMRE  218 (681)
Q Consensus       185 v~-----------d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~  218 (681)
                      +.           +....|++||.|+|+|+.+|..+++|.|++..
T Consensus       682 y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~~~rkI~f~l~~  726 (813)
T PRK11642        682 YRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKIDFSLIS  726 (813)
T ss_pred             eEecchheEEecccCCcEECCCCEEEEEEEEeecCCCeEEEEEec
Confidence            32           23467999999999999999999999999863

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

Probab=99.11  E-value=3e-10  Score=92.58  Aligned_cols=68  Identities=49%  Similarity=0.780  Sum_probs=64.3

Q ss_pred             CcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEE
Q 005707          148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTM  216 (681)
Q Consensus       148 GdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSl  216 (681)
                      |+++.|+|..+.++|+||+|+.+..||+|.+++++.++.++...|++||.|+|+|+++|. ++++.||+
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 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD-RGRISLSR   68 (68)
T ss_pred             CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECC-CCcEEeeC
Confidence            789999999999999999998889999999999999888888899999999999999998 89999885

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.

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

Probab=99.10  E-value=2.9e-10  Score=92.24  Aligned_cols=68  Identities=34%  Similarity=0.526  Sum_probs=61.6

Q ss_pred             CcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC-CeEEEEEe
Q 005707          263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR-GQVTLTMK  332 (681)
Q Consensus       263 GdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk-gKI~LSLK  332 (681)
                      |+++.|+|+++.++|+||+++++..||+|.+++++.++.  ++...|++||.|.|+|+++|. +++.||+|
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 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVK--DVKDVLKEGDKVKVKVLSIDARGRISLSIK   69 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCcccC--CHHHccCCCCEEEEEEEEECCCCcEEEEEC
Confidence            789999999999999999999999999999999987743  346789999999999999985 89999986

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.

>PRK08059 general stress protein 13; Validated

Probab=99.10  E-value=3.8e-10  Score=105.03  Aligned_cols=80  Identities=26%  Similarity=0.475  Sum_probs=72.0

Q ss_pred             ccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEecc
Q 005707          257 TTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKE  334 (681)
Q Consensus       257 ~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~  334 (681)
                      +.++++|+++.|+|.++.++|+||++.++++||+|.+++++.++.  ++...|++||.|.|+|+++|  ++++.|++|..
T Consensus         2 ~~~~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~--~~~~~~~vGD~I~vkI~~id~~~~~i~lslk~~   79 (123)
T PRK08059          2 MSQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVK--DIHDFLSVGDEVKVKVLSVDEEKGKISLSIRAT   79 (123)
T ss_pred             cccCCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCccccc--CHHHcCCCCCEEEEEEEEEECCCCeEEEEEEEc
Confidence            346899999999999999999999999999999999999988753  34678999999999999997  48999999999


Q ss_pred             CCCc
Q 005707          335 DDVG  338 (681)
Q Consensus       335 ~~DP  338 (681)
                      ..+|
T Consensus        80 ~~~~   83 (123)
T PRK08059         80 EEAP   83 (123)
T ss_pred             ccCc
Confidence            8777

>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=99.10  E-value=7.9e-11  Score=106.18  Aligned_cols=77  Identities=27%  Similarity=0.395  Sum_probs=66.4

Q ss_pred             CccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccc-----------------cCCCCcccCCCEEEEEEEEE
Q 005707          260 FVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFAN-----------------MMGGSSLQVGQEVSVRVLRI  322 (681)
Q Consensus       260 lkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~-----------------~~p~~~fkVGqkVkVrVL~I  322 (681)
                      +++|++|.|+|++|.++|+||.|++|+.|++|+++++|.+...                 ..+...|++||.|.|+|+++
T Consensus         1 L~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~   80 (100)
T cd05693           1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSL   80 (100)
T ss_pred             CCCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEc
Confidence            5789999999999999999999999999999999999864211                 12467899999999999999


Q ss_pred             eC-----CeEEEEEeccCC
Q 005707          323 SR-----GQVTLTMKKEDD  336 (681)
Q Consensus       323 Dk-----gKI~LSLK~~~~  336 (681)
                      |+     ++|.||+|+...
T Consensus        81 d~~~~~~~~i~LSlr~~~v   99 (100)
T cd05693          81 DKSKSGKKRIELSLEPELV   99 (100)
T ss_pred             cCCcCCCcEEEEEecHHHC
Confidence            74     589999998654

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.

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

Probab=99.09  E-value=3.4e-10  Score=92.11  Aligned_cols=68  Identities=44%  Similarity=0.737  Sum_probs=63.9

Q ss_pred             CCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEE
Q 005707          147 PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLT  215 (681)
Q Consensus       147 vGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LS  215 (681)
                      +|+++.|+|.++.++|+||++++ +.|++|.+++++.+..++.+.|++||.|+|+|+++|.+++++.||
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 EGDVVEGTVKSITDFGAFVDLGG-VDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG   68 (68)
T ss_pred             CCCEEEEEEEEEEeeeEEEEECC-eEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECCCCEEecC
Confidence            48999999999999999999985 999999999999888888899999999999999999999998875

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.

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

Probab=99.09  E-value=2.5e-10  Score=93.98  Aligned_cols=67  Identities=30%  Similarity=0.411  Sum_probs=57.3

Q ss_pred             CcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEE
Q 005707          263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLT  330 (681)
Q Consensus       263 GdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LS  330 (681)
                      |+++.|+|+++.++|+||+|.++++||+|.++++|... ..++...|++||.|+|+|+++|  ++|+.|+
T Consensus         1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~~-~~~~~~~~~~G~~v~v~v~~id~~~~~i~l~   69 (69)
T cd05690           1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQR-VRHPSEIYKKGQEVEAVVLNIDVERERISLG   69 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCccc-cCChhhEECCCCEEEEEEEEEECCcCEEeCC
Confidence            78999999999999999999999999999999997321 2245678999999999999998  4677653

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.

>PHA02945 interferon resistance protein; Provisional

Probab=99.07  E-value=6.2e-10  Score=98.12  Aligned_cols=77  Identities=21%  Similarity=0.324  Sum_probs=70.0

Q ss_pred             cCCCCCCcEEEEEEEEEecCeeEEEE--CCCeEEEEecccc--CCccccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707          142 NEDLIPGATFTGKVRSIQPFGAFIDF--GAFTDGLVHVSRL--SDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR  217 (681)
Q Consensus       142 ~~~LkvGdIVeGkV~sV~d~GaFVdL--gggV~GLVPiSEL--S~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK  217 (681)
                      |.-.++|+++.|+|.. .++|+||.|  .++.+||||++++  +.+|+++ ++.+ +||++.|+|+.+|+.++.|.||+|
T Consensus         6 y~~P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~-rd~l-~GqkvV~KVirVd~~kg~IDlSlK   82 (88)
T PHA02945          6 YSLPNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY-RDKL-VGKTVKVKVIRVDYTKGYIDVNYK   82 (88)
T ss_pred             ecCCCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEee-eeEe-cCCEEEEEEEEECCCCCEEEeEee
Confidence            5567899999999999 999999999  4579999999955  9999999 8888 999999999999999999999999


Q ss_pred             ccch
Q 005707          218 ESDD  221 (681)
Q Consensus       218 ~l~~  221 (681)
                      +...
T Consensus        83 ~V~~   86 (88)
T PHA02945         83 RMCR   86 (88)
T ss_pred             Eccc
Confidence            7643

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

Probab=99.07  E-value=6.1e-11  Score=137.26  Aligned_cols=155  Identities=20%  Similarity=0.271  Sum_probs=107.8

Q ss_pred             ccccceeeecccccccccceeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCcceecCCCC
Q 005707           26 NCLTRYNSTRKSTKQTISSQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPS  105 (681)
Q Consensus        26 ~~~~~~~~~r~~~~~~~s~~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s  105 (681)
                      .+.+||||+-.+|.|||||.|++.||-.+|-+ -+...              |....- ....+       .--+     
T Consensus       487 ~~~~HfgL~~~~YthfTSPIRRY~DLivHr~L-~a~l~--------------~~~~~~-~~~~~-------~~~l-----  538 (654)
T TIGR00358       487 EPLGHFGLGLEHYAHFTSPIRRYPDLTNHRLI-KAVLA--------------KEQTDT-ERYQP-------QDEL-----  538 (654)
T ss_pred             CCCCccccccccccccCCccccchHHHHHHHH-HHHHc--------------CCCCcc-cchhh-------HHHH-----
Confidence            57899999999999999999999998766422 11111              110000 00000       0001     


Q ss_pred             CcccccccccccCCChhhHHhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEEC-CCeEEEEeccccCCcc
Q 005707          106 DVETSESSSIKSEASPTLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFG-AFTDGLVHVSRLSDNF  184 (681)
Q Consensus       106 ~v~~ae~ss~~sea~~daek~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLg-ggV~GLVPiSELS~~~  184 (681)
                       ...+++++.+++.+.++++...+.  ....     |..-++|++++|+|++++++|+||+|. .+++||||++++.+++
T Consensus       539 -~~~~~~~~~~er~a~~aer~~~~~--~~~~-----yl~~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~  610 (654)
T TIGR00358       539 -LQIAEHCSDTERRARDAERDVADW--LKCR-----YLLDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDY  610 (654)
T ss_pred             -HHHHHHHHHHHHHHHHHHHHHHHH--HHHH-----hhhhCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcc
Confidence             112445666666666666555432  1121     344467999999999999999999997 6799999999999874


Q ss_pred             c-----------cCcccccccCCEEEEEEEEEeccCCceEEEE
Q 005707          185 V-----------KDVGSIVSVGQEVKVRLIEANAETGRISLTM  216 (681)
Q Consensus       185 v-----------~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSl  216 (681)
                      +           .+....|++||.|+|+|+++|..+++|.+++
T Consensus       611 y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~~~~I~f~l  653 (654)
T TIGR00358       611 YVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMETRSIIFEL  653 (654)
T ss_pred             eEEeccccEEEeccCCcEECCCCEEEEEEEEEecccCeEEEEE
Confidence            2           2334679999999999999999999999975

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.

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

Probab=99.06  E-value=5.9e-10  Score=96.31  Aligned_cols=74  Identities=16%  Similarity=0.190  Sum_probs=67.1

Q ss_pred             CCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCC----ccccCcccccccCCEEEEEEEEEeccCCceEEEEecc
Q 005707          145 LIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSD----NFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRES  219 (681)
Q Consensus       145 LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~----~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l  219 (681)
                      +++|++|.|+|+++.++|++|+++++.+|+||++++++    .+..++.+.+++||.++|+|+++|++ +++.||++..
T Consensus         4 p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~-~~i~LS~~~~   81 (86)
T cd05789           4 PEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSD-GSVSLHTRSL   81 (86)
T ss_pred             CCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCC-CCEEEEeCcc
Confidence            57899999999999999999999988999999999986    45567778899999999999999876 9999999854

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".

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

Probab=99.03  E-value=8.9e-10  Score=91.42  Aligned_cols=68  Identities=35%  Similarity=0.573  Sum_probs=61.8

Q ss_pred             CcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC--CeEEEEEe
Q 005707          263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR--GQVTLTMK  332 (681)
Q Consensus       263 GdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk--gKI~LSLK  332 (681)
                      |+++.|+|.++.++|+||+|+.+.+|++|.+++++.+..  ++...|++||.++|+|+++++  +++.||+|
T Consensus         1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~~~~--~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~   70 (70)
T cd05687           1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIE--NGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR   70 (70)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCccccC--CHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence            789999999999999999999999999999999988754  457889999999999999973  78999986

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.

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

Probab=99.02  E-value=4.5e-10  Score=115.91  Aligned_cols=81  Identities=21%  Similarity=0.520  Sum_probs=76.2

Q ss_pred             CCCCCcEEEEEEEEEecCeeEEEE--CCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccch
Q 005707          144 DLIPGATFTGKVRSIQPFGAFIDF--GAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDD  221 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~GaFVdL--gggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~  221 (681)
                      -..+|++|-|+|+.|.+||+||.|  .++++||+|+||++.+|++++++++++||.+-|+|+.||+.++.|.||+|....
T Consensus         8 ~PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkrV~~   87 (269)
T COG1093           8 YPEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKRVTE   87 (269)
T ss_pred             CCCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehhhCCH
Confidence            467899999999999999999999  467999999999999999999999999999999999999999999999999887


Q ss_pred             hhH
Q 005707          222 ISK  224 (681)
Q Consensus       222 dp~  224 (681)
                      +..
T Consensus        88 ~q~   90 (269)
T COG1093          88 HQR   90 (269)
T ss_pred             HHH
Confidence            664

>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=98.99  E-value=1.3e-09  Score=90.74  Aligned_cols=64  Identities=20%  Similarity=0.261  Sum_probs=56.0

Q ss_pred             CcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEE
Q 005707          263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLT  330 (681)
Q Consensus       263 GdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LS  330 (681)
                      |+++.|+|+++.++|+||+|.++++||+|.++++..+.   . ...|++|++|.|+|+.+|  +++|.||
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 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKS---S-KSTYKEGQKVRARILYVDPSTKVVGLS   66 (66)
T ss_pred             CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCccC---c-ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence            78999999999999999999889999999999976542   1 678999999999999998  4677764

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.

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

Probab=98.98  E-value=2.3e-09  Score=94.55  Aligned_cols=74  Identities=28%  Similarity=0.477  Sum_probs=66.3

Q ss_pred             CCCCCcEEEEEEEEEecC--eeEEEECCCeEEEEeccccCC---ccccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707          144 DLIPGATFTGKVRSIQPF--GAFIDFGAFTDGLVHVSRLSD---NFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR  217 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~--GaFVdLgggV~GLVPiSELS~---~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK  217 (681)
                      .+++|++|.|+|+++.++  |+||+|+++.+||||+++++|   .++.++.+.+++||.|.|+|+......+...|+.+
T Consensus         4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~lt~~   82 (88)
T cd04453           4 EPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLTTN   82 (88)
T ss_pred             cCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCceEEEE
Confidence            467899999999999997  999999988999999999999   66788888999999999999998777777777765

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=98.97  E-value=3e-09  Score=90.32  Aligned_cols=70  Identities=30%  Similarity=0.701  Sum_probs=61.9

Q ss_pred             CCcEEEEEEEEEecCeeEEEECC-CeEEEEeccccCCcccc-----------CcccccccCCEEEEEEEEEeccCCceEE
Q 005707          147 PGATFTGKVRSIQPFGAFIDFGA-FTDGLVHVSRLSDNFVK-----------DVGSIVSVGQEVKVRLIEANAETGRISL  214 (681)
Q Consensus       147 vGdIVeGkV~sV~d~GaFVdLgg-gV~GLVPiSELS~~~v~-----------d~~e~fkVGd~VkVkVl~VD~ekgrI~L  214 (681)
                      +|+++.|+|+++.++|+||+|+. +++|++|.++++++++.           +....|++||.|+|+|+.+|.+++++.+
T Consensus         1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~~i~~   80 (83)
T cd04471           1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF   80 (83)
T ss_pred             CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccCEEEE
Confidence            48999999999999999999986 69999999999876432           3457799999999999999999999998


Q ss_pred             EE
Q 005707          215 TM  216 (681)
Q Consensus       215 Sl  216 (681)
                      ++
T Consensus        81 ~l   82 (83)
T cd04471          81 EL   82 (83)
T ss_pred             EE
Confidence            85

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.

>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=98.97  E-value=1.4e-09  Score=88.22  Aligned_cols=66  Identities=32%  Similarity=0.537  Sum_probs=58.7

Q ss_pred             CcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC--CeEEEE
Q 005707          263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR--GQVTLT  330 (681)
Q Consensus       263 GdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk--gKI~LS  330 (681)
                      |+++.|+|++++++|+||+++++.+||+|.+++.+.++.  ++...|++||.|.|+|+++|.  +++.||
T Consensus         1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~~~~--~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls   68 (68)
T cd05685           1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVS--HPSDVVSVGDIVEVKVISIDEERGRISLS   68 (68)
T ss_pred             CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCcccc--CHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence            789999999999999999999999999999999988754  346779999999999999984  777764

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=98.96  E-value=2e-09  Score=93.05  Aligned_cols=75  Identities=19%  Similarity=0.161  Sum_probs=64.1

Q ss_pred             CccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCccccc--ccCCCCcccCCCEEEEEEEEEeC-CeEEEEEecc
Q 005707          260 FVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFA--NMMGGSSLQVGQEVSVRVLRISR-GQVTLTMKKE  334 (681)
Q Consensus       260 lkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie--~~~p~~~fkVGqkVkVrVL~IDk-gKI~LSLK~~  334 (681)
                      .++|++|.|+|+.+.++|+||+++.+.+|+||.+++++.+++  .......|++||.+.|+|+++++ +++.||+|..
T Consensus         4 p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~~~i~LS~~~~   81 (86)
T cd05789           4 PEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSDGSVSLHTRSL   81 (86)
T ss_pred             CCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCCCCEEEEeCcc
Confidence            469999999999999999999999999999999999863221  11235679999999999999975 8999999875

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".

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

Probab=98.95  E-value=3.6e-09  Score=90.92  Aligned_cols=73  Identities=14%  Similarity=0.098  Sum_probs=68.7

Q ss_pred             CCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEec
Q 005707          145 LIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRE  218 (681)
Q Consensus       145 LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~  218 (681)
                      .++|++|.|+|+++.+.|++|+++++.+|++|.++++..+..++...|++||.+.|+|+.+|.+ +++.||++.
T Consensus         4 p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~-~~i~LS~~~   76 (82)
T cd04454           4 PDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVLLTTAD   76 (82)
T ss_pred             CCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC-CCEEEEECC
Confidence            4789999999999999999999998899999999999888888889999999999999999986 899999985

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".

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

Probab=98.95  E-value=2.7e-09  Score=111.42  Aligned_cols=80  Identities=25%  Similarity=0.535  Sum_probs=73.8

Q ss_pred             CCCCCcEEEEEEEEEecCeeEEEECC--CeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccch
Q 005707          144 DLIPGATFTGKVRSIQPFGAFIDFGA--FTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDD  221 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~GaFVdLgg--gV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~  221 (681)
                      -+++|++|.|+|+++.++|+||+|..  ++.||||+++++++++.++.+.|++||.|.|+|+.+|.++++|.||+|....
T Consensus         5 ~P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~v~~   84 (262)
T PRK03987          5 WPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKRVNE   84 (262)
T ss_pred             CCCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEEeccc
Confidence            35789999999999999999999963  6999999999999999999999999999999999999999999999997765


Q ss_pred             hh
Q 005707          222 IS  223 (681)
Q Consensus       222 dp  223 (681)
                      +.
T Consensus        85 ~e   86 (262)
T PRK03987         85 HQ   86 (262)
T ss_pred             ch
Confidence            44

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

Probab=98.93  E-value=3.4e-09  Score=86.37  Aligned_cols=67  Identities=34%  Similarity=0.608  Sum_probs=59.9

Q ss_pred             CcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe-CCeEEEEE
Q 005707          263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS-RGQVTLTM  331 (681)
Q Consensus       263 GdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID-kgKI~LSL  331 (681)
                      |+++.|+|.++.++|+||+++++..||+|.+++.+.++.  ++...|++||.|.|+|+++| .+++.||+
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 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVE--KVEDVLKVGDEVKVKVIEVDDRGRISLSR   68 (68)
T ss_pred             CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCcccc--CHHHccCCCCEEEEEEEEECCCCcEEeeC
Confidence            789999999999999999999999999999999988743  34678999999999999998 47888875

PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.

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

Probab=98.93  E-value=3.5e-09  Score=85.35  Aligned_cols=70  Identities=41%  Similarity=0.648  Sum_probs=61.8

Q ss_pred             ccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC--CeEEEEEe
Q 005707          261 VKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR--GQVTLTMK  332 (681)
Q Consensus       261 kvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk--gKI~LSLK  332 (681)
                      ++|+++.|+|.++.++|+||++++++.|++|.+++.+.+.  .++...|++||.|.|+|++++.  +++.|+++
T Consensus         1 ~~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~--~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~~   72 (72)
T smart00316        1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRV--KDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK   72 (72)
T ss_pred             CCCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCcccc--CCHHHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence            3699999999999999999999999999999999998752  2335679999999999999974  88999875

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

Probab=98.91  E-value=4.9e-09  Score=86.68  Aligned_cols=65  Identities=26%  Similarity=0.549  Sum_probs=56.2

Q ss_pred             CcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEe
Q 005707          263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMK  332 (681)
Q Consensus       263 GdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK  332 (681)
                      |+++.|+|+++.++|+||++ +|++||||.+++++.+..+.    ...+||.+.|+|+++|  ++++.||+|
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-EGVRAFLPASQVDLRPVEDL----DEYVGKELKFKIIEIDRERNNIVLSRR   67 (67)
T ss_pred             CCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHCCCcccCCh----HHhCCCEEEEEEEEEeCCCCEEEEEcC
Confidence            78999999999999999999 69999999999998764322    2248999999999998  488999975

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.

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=98.90  E-value=1.7e-09  Score=124.99  Aligned_cols=82  Identities=48%  Similarity=0.804  Sum_probs=77.6

Q ss_pred             CCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEecc
Q 005707          140 VKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRES  219 (681)
Q Consensus       140 lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l  219 (681)
                      ..+.+|++|++++|+|++|.++|+||+||-+.+|+||++++++.++.+|.+++++||.|+|+|+++|..++||.|||+..
T Consensus       651 ~~i~dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~  730 (780)
T COG2183         651 ESITDLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMRLD  730 (780)
T ss_pred             hhHhhccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEeecc
Confidence            34679999999999999999999999999999999999999999999999999999999999999999999999999965


Q ss_pred             ch
Q 005707          220 DD  221 (681)
Q Consensus       220 ~~  221 (681)
                      ..
T Consensus       731 ~~  732 (780)
T COG2183         731 EE  732 (780)
T ss_pred             CC
Confidence            44

>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=98.88  E-value=6.4e-09  Score=86.94  Aligned_cols=63  Identities=27%  Similarity=0.421  Sum_probs=58.6

Q ss_pred             CcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCcc--ccCcccccccCCEEEEEEEEEeccCC
Q 005707          148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNF--VKDVGSIVSVGQEVKVRLIEANAETG  210 (681)
Q Consensus       148 GdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~--v~d~~e~fkVGd~VkVkVl~VD~ekg  210 (681)
                      |+++.|+|+++.++|+||+++++++|++|++++++++  ..++.+.|++||.|+|+|+++|.++.
T Consensus         1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~~   65 (70)
T cd05702           1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKT   65 (70)
T ss_pred             CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCccc
Confidence            7899999999999999999998899999999999885  78888899999999999999987654

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.

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

Probab=98.88  E-value=6e-09  Score=91.95  Aligned_cols=74  Identities=27%  Similarity=0.343  Sum_probs=59.4

Q ss_pred             CCccCcEEEEEEEEEecc--eEEEEeCCCeEEEEeCCCCCccccc-ccCCCCcccCCCEEEEEEEEEe--CCeEEEEEe
Q 005707          259 KFVKGQDLEGTVKNLTRS--GAFISLPEGEEGFLPTSEESDDGFA-NMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMK  332 (681)
Q Consensus       259 klkvGdIV~G~VknVt~~--GaFVeIg~GIeGLLpiSELSd~~ie-~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK  332 (681)
                      ++++|+++.|+|+++.++  |+||+|++|.+||||.++++|.+.. ..++...|++||.|.|+|++..  .+.-.||.+
T Consensus         4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~lt~~   82 (88)
T cd04453           4 EPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLTTN   82 (88)
T ss_pred             cCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCceEEEE
Confidence            578999999999999997  9999999999999999999983211 1234678999999999999984  233444443

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

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=98.88  E-value=6e-09  Score=121.63  Aligned_cols=76  Identities=37%  Similarity=0.625  Sum_probs=72.2

Q ss_pred             CCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEecc
Q 005707          143 EDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRES  219 (681)
Q Consensus       143 ~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l  219 (681)
                      ..+++|++|.|+|+++.+||+||+|.++.+||||+++++|.++.++.+.|++||.|+|+|+++|.+ ++|.||+|.+
T Consensus       617 ~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD~~-grI~LS~k~~  692 (693)
T PRK11824        617 AEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKR-GRIRLSRKAV  692 (693)
T ss_pred             ccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCccccCccceeCCCCEEEEEEEEECCC-CcEEEEEEec
Confidence            468899999999999999999999988899999999999999999999999999999999999987 9999999865

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

Probab=98.87  E-value=1.2e-08  Score=86.58  Aligned_cols=70  Identities=27%  Similarity=0.550  Sum_probs=59.6

Q ss_pred             cCcEEEEEEEEEecceEEEEeCC-CeEEEEeCCCCCcccccc---------cCCCCcccCCCEEEEEEEEEe--CCeEEE
Q 005707          262 KGQDLEGTVKNLTRSGAFISLPE-GEEGFLPTSEESDDGFAN---------MMGGSSLQVGQEVSVRVLRIS--RGQVTL  329 (681)
Q Consensus       262 vGdIV~G~VknVt~~GaFVeIg~-GIeGLLpiSELSd~~ie~---------~~p~~~fkVGqkVkVrVL~ID--kgKI~L  329 (681)
                      +|+++.|+|++++++|+||++++ |++|++|.+++.++++..         ......|++||.|+|+|..+|  ++++.|
T Consensus         1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~~i~~   80 (83)
T cd04471           1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF   80 (83)
T ss_pred             CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccCEEEE
Confidence            48999999999999999999998 899999999998764321         123578999999999999997  588888


Q ss_pred             EE
Q 005707          330 TM  331 (681)
Q Consensus       330 SL  331 (681)
                      ++
T Consensus        81 ~l   82 (83)
T cd04471          81 EL   82 (83)
T ss_pred             EE
Confidence            76

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.

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

Probab=98.86  E-value=5.6e-09  Score=82.76  Aligned_cols=65  Identities=51%  Similarity=0.845  Sum_probs=60.2

Q ss_pred             EEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEE
Q 005707          151 FTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLT  215 (681)
Q Consensus       151 VeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LS  215 (681)
                      +.|+|+++.++|+||+++.+..|++|.+++++.+..++...|++||.|+|+|+++|.+++++.||
T Consensus         1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~~~~i~ls   65 (65)
T cd00164           1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS   65 (65)
T ss_pred             CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence            47999999999999999977999999999999888888889999999999999999988888775

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.

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=98.85  E-value=6.1e-09  Score=120.87  Aligned_cols=71  Identities=32%  Similarity=0.578  Sum_probs=65.5

Q ss_pred             CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccC----CccccCcccccccCCEEEEEEEEEeccCCceEEE
Q 005707          144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLS----DNFVKDVGSIVSVGQEVKVRLIEANAETGRISLT  215 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS----~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LS  215 (681)
                      .+++|++|.|+|+++.+||+||+|.++++||||+++|+    |.++.++.+.|++||.|+|+|+++|. ++||.|+
T Consensus       644 ~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID~-~gKI~L~  718 (719)
T TIGR02696       644 MPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDD-RGKLSLV  718 (719)
T ss_pred             cCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEECC-CCCeeec
Confidence            47899999999999999999999987799999999996    46889999999999999999999995 7888875

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.

>PHA02945 interferon resistance protein; Provisional

Probab=98.84  E-value=1.3e-08  Score=89.93  Aligned_cols=73  Identities=26%  Similarity=0.378  Sum_probs=63.9

Q ss_pred             CccCcEEEEEEEEEecceEEEEeCC--CeEEEEeCCCC--CcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEec
Q 005707          260 FVKGQDLEGTVKNLTRSGAFISLPE--GEEGFLPTSEE--SDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKK  333 (681)
Q Consensus       260 lkvGdIV~G~VknVt~~GaFVeIg~--GIeGLLpiSEL--Sd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~  333 (681)
                      -.+|+++.|+|+. .++|+||.|.+  |.+||+|.++.  +..++.+   ++.+ .||+|.|+|+++|  +|.|.||||.
T Consensus         9 P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~---rd~l-~GqkvV~KVirVd~~kg~IDlSlK~   83 (88)
T PHA02945          9 PNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY---RDKL-VGKTVKVKVIRVDYTKGYIDVNYKR   83 (88)
T ss_pred             CCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEee---eeEe-cCCEEEEEEEEECCCCCEEEeEeeE
Confidence            4689999999999 99999999975  99999999955  8887643   6778 9999999999998  5889999998


Q ss_pred             cCCC
Q 005707          334 EDDV  337 (681)
Q Consensus       334 ~~~D  337 (681)
                      ...+
T Consensus        84 V~~~   87 (88)
T PHA02945         84 MCRH   87 (88)
T ss_pred             cccC
Confidence            7543

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

Probab=98.84  E-value=1.1e-08  Score=83.30  Aligned_cols=66  Identities=38%  Similarity=0.595  Sum_probs=57.8

Q ss_pred             cCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC--CeEEEE
Q 005707          262 KGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR--GQVTLT  330 (681)
Q Consensus       262 vGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk--gKI~LS  330 (681)
                      +|+++.|+|.++.++|+||+++ +++|++|.+++++.+..  .+...|++||.|+|+|+++|.  +++.||
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-GVDGLLHISDMSWGRVK--HPSEVVNVGDEVEVKVLKIDKERKRISLG   68 (68)
T ss_pred             CCCEEEEEEEEEEeeeEEEEEC-CeEEEEEhHHCCCcccc--CHhHEECCCCEEEEEEEEEECCCCEEecC
Confidence            4899999999999999999997 79999999999987643  346789999999999999984  777764

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.

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

Probab=98.84  E-value=2.4e-08  Score=85.41  Aligned_cols=68  Identities=35%  Similarity=0.579  Sum_probs=61.5

Q ss_pred             CCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEE
Q 005707          140 VKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTM  216 (681)
Q Consensus       140 lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSl  216 (681)
                      +.+.+++.|+++.|+|.+++++|+||++.++..||+|.+++.        ..|++||.++|+|.++ .+++++.+++
T Consensus         9 ~~~~~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~~--------~~~~iGd~v~v~I~~i-~e~~~i~l~~   76 (77)
T cd04473           9 CTMEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLL--------RDYEVGDEVIVQVTDI-PENGNIDLIP   76 (77)
T ss_pred             cchhhCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhcc--------CcCCCCCEEEEEEEEE-CCCCcEEEEE
Confidence            346789999999999999999999999988899999999873        3489999999999999 8889999986

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.

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

Probab=98.82  E-value=1e-08  Score=107.14  Aligned_cols=76  Identities=33%  Similarity=0.566  Sum_probs=68.0

Q ss_pred             CccCcEEEEEEEEEecceEEEEeCC--CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccC
Q 005707          260 FVKGQDLEGTVKNLTRSGAFISLPE--GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKED  335 (681)
Q Consensus       260 lkvGdIV~G~VknVt~~GaFVeIg~--GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~  335 (681)
                      .++|+++.|+|++|.++|+||+|.+  |++||||.+++++.++.+  +...|++||.|.|+|+++|  ++++.||+|...
T Consensus         6 P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~--i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~v~   83 (262)
T PRK03987          6 PEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKN--IRDHVKEGQKVVCKVIRVDPRKGHIDLSLKRVN   83 (262)
T ss_pred             CCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccC--HHHhCCCCCEEEEEEEEEecccCeEEEEEEecc
Confidence            4689999999999999999999985  899999999999988654  3788999999999999998  488999999876


Q ss_pred             CC
Q 005707          336 DV  337 (681)
Q Consensus       336 ~D  337 (681)
                      .+
T Consensus        84 ~~   85 (262)
T PRK03987         84 EH   85 (262)
T ss_pred             cc
Confidence            54

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

Probab=98.81  E-value=2.8e-08  Score=85.03  Aligned_cols=66  Identities=26%  Similarity=0.442  Sum_probs=59.1

Q ss_pred             cccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEE-eCCeEEEEE
Q 005707          256 KTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI-SRGQVTLTM  331 (681)
Q Consensus       256 ~~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~I-DkgKI~LSL  331 (681)
                      .+.+++.|+.+.|+|++++++|+||++.++++||+|.+++.          ..|++||.++++|.++ +++++.|++
T Consensus        10 ~~~~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~~----------~~~~iGd~v~v~I~~i~e~~~i~l~~   76 (77)
T cd04473          10 TMEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLL----------RDYEVGDEVIVQVTDIPENGNIDLIP   76 (77)
T ss_pred             chhhCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhcc----------CcCCCCCEEEEEEEEECCCCcEEEEE
Confidence            36679999999999999999999999999999999999853          4689999999999999 458888876

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=98.81  E-value=1.4e-08  Score=84.94  Aligned_cols=64  Identities=20%  Similarity=0.246  Sum_probs=55.9

Q ss_pred             CcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCe
Q 005707          263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQ  326 (681)
Q Consensus       263 GdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgK  326 (681)
                      |+++.|+|+++.++|+||++++|++|++|.+++++.+.....+.+.|++||.|.|+|+++|..+
T Consensus         1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~   64 (70)
T cd05702           1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAK   64 (70)
T ss_pred             CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCcc
Confidence            7899999999999999999999999999999998874222345788999999999999998644

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.

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=98.79  E-value=1.5e-08  Score=118.32  Aligned_cols=76  Identities=32%  Similarity=0.490  Sum_probs=69.7

Q ss_pred             ccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC-CeEEEEEecc
Q 005707          257 TTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR-GQVTLTMKKE  334 (681)
Q Consensus       257 ~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk-gKI~LSLK~~  334 (681)
                      ..++++|+++.|+|++|.+||+||+|.+|.+||+|+++++|.++.  ++...|++||.|+|+|+++|. +|+.||+|.+
T Consensus       616 ~~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~~v~--~~~~v~kvGD~V~VkV~~iD~~grI~LS~k~~  692 (693)
T PRK11824        616 TAEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVE--KVEDVLKEGDEVKVKVLEIDKRGRIRLSRKAV  692 (693)
T ss_pred             cccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCcccc--CccceeCCCCEEEEEEEEECCCCcEEEEEEec
Confidence            356899999999999999999999999999999999999999865  457899999999999999974 9999999975

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=98.79  E-value=9.9e-09  Score=119.16  Aligned_cols=70  Identities=33%  Similarity=0.463  Sum_probs=62.2

Q ss_pred             CCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCC---c-ccccccCCCCcccCCCEEEEEEEEEe-CCeEEEE
Q 005707          259 KFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEES---D-DGFANMMGGSSLQVGQEVSVRVLRIS-RGQVTLT  330 (681)
Q Consensus       259 klkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELS---d-~~ie~~~p~~~fkVGqkVkVrVL~ID-kgKI~LS  330 (681)
                      .+++|++|.|+|++|.+||+||+|.+|++||||+++++   | .++.  ++.+.|++||.|+|+|+++| ++|+.|+
T Consensus       644 ~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~~~rv~--~~~dv~kvGd~V~VKVl~ID~~gKI~L~  718 (719)
T TIGR02696       644 MPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVE--NVEDVLSVGQKIQVEIADIDDRGKLSLV  718 (719)
T ss_pred             cCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccccccCcC--CHHHcCCCCCEEEEEEEEECCCCCeeec
Confidence            47899999999999999999999999999999999986   4 4543  45889999999999999998 5888875

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.

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=98.76  E-value=5.3e-08  Score=96.78  Aligned_cols=75  Identities=17%  Similarity=0.295  Sum_probs=66.1

Q ss_pred             ccCCccCcEEEEEEEEEecceEEEEeC----------CCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCe
Q 005707          257 TTKFVKGQDLEGTVKNLTRSGAFISLP----------EGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQ  326 (681)
Q Consensus       257 ~sklkvGdIV~G~VknVt~~GaFVeIg----------~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgK  326 (681)
                      ...+++|++|.|+|+++.++|+||+|.          .++.|++|.+++++....+  +...|++||.|.|+|++++ ++
T Consensus        59 ~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~--~~~~~~~GD~V~akV~~i~-~~  135 (189)
T PRK09521         59 PPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVES--LTDAFKIGDIVRAKVISYT-DP  135 (189)
T ss_pred             CCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhh--HHhccCCCCEEEEEEEecC-Cc
Confidence            456789999999999999999999985          4789999999999876543  4788999999999999999 89


Q ss_pred             EEEEEecc
Q 005707          327 VTLTMKKE  334 (681)
Q Consensus       327 I~LSLK~~  334 (681)
                      +.||+|..
T Consensus       136 i~LS~k~~  143 (189)
T PRK09521        136 LQLSTKGK  143 (189)
T ss_pred             EEEEEecC
Confidence            99999853

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

Probab=98.76  E-value=5.2e-09  Score=108.16  Aligned_cols=76  Identities=34%  Similarity=0.598  Sum_probs=69.5

Q ss_pred             ccCcEEEEEEEEEecceEEEEeCC--CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCC
Q 005707          261 VKGQDLEGTVKNLTRSGAFISLPE--GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDD  336 (681)
Q Consensus       261 kvGdIV~G~VknVt~~GaFVeIg~--GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~  336 (681)
                      .+|++|-|+|++|.+||+||.|.+  |++||+|+||++..++.++  ++.+++||++-|+||++|  +|.|.||||...+
T Consensus        10 eeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknI--rd~vkegqkvV~kVlrVd~~rg~IDLSlkrV~~   87 (269)
T COG1093          10 EEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNI--RDYVKEGQKVVAKVLRVDPKRGHIDLSLKRVTE   87 (269)
T ss_pred             CCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHH--HHHhhcCCeEEEEEEEEcCCCCeEeeehhhCCH
Confidence            479999999999999999999974  9999999999999998776  899999999999999998  5889999999876


Q ss_pred             Cc
Q 005707          337 VG  338 (681)
Q Consensus       337 DP  338 (681)
                      +-
T Consensus        88 ~q   89 (269)
T COG1093          88 HQ   89 (269)
T ss_pred             HH
Confidence            53

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

Probab=98.75  E-value=3.4e-08  Score=84.87  Aligned_cols=72  Identities=18%  Similarity=0.134  Sum_probs=64.2

Q ss_pred             ccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC-CeEEEEEecc
Q 005707          261 VKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR-GQVTLTMKKE  334 (681)
Q Consensus       261 kvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk-gKI~LSLK~~  334 (681)
                      ++|++|.|+|+++.+.|++|+++.+.+|++|.++++.....  .....|++||.+.|+|+++++ +++.||++..
T Consensus         5 ~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~--~~~~~~~~GD~i~~~V~~~~~~~~i~LS~~~~   77 (82)
T cd04454           5 DVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKK--EIRKSLQPGDLILAKVISLGDDMNVLLTTADN   77 (82)
T ss_pred             CCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchH--HHHhcCCCCCEEEEEEEEeCCCCCEEEEECCC
Confidence            68999999999999999999999999999999999876533  336789999999999999986 7899999763

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".

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

Probab=98.66  E-value=4.1e-08  Score=112.44  Aligned_cols=79  Identities=29%  Similarity=0.492  Sum_probs=72.9

Q ss_pred             ccccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC-CeEEEEEec
Q 005707          255 MKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR-GQVTLTMKK  333 (681)
Q Consensus       255 ~~~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk-gKI~LSLK~  333 (681)
                      ....++++|+++.|+|+++.+||+||.|.+|-+||||++++++.+++..  ...+++||.|.|+|+.+|+ ||+.|++|.
T Consensus       612 ~i~~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~rv~kv--~dvlk~Gd~v~Vkv~~iD~~Gri~ls~~~  689 (692)
T COG1185         612 AITREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVEKV--EDVLKEGDEVKVKVIEIDKQGRIRLSIKA  689 (692)
T ss_pred             HHHhhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhhhhhcc--cceeecCceEEEEEeeecccCCccceehh
Confidence            4568899999999999999999999999999999999999999987655  7999999999999999985 999999987


Q ss_pred             cC
Q 005707          334 ED  335 (681)
Q Consensus       334 ~~  335 (681)
                      ..
T Consensus       690 ~~  691 (692)
T COG1185         690 VL  691 (692)
T ss_pred             cc
Confidence            53

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

Probab=98.66  E-value=1.1e-07  Score=79.37  Aligned_cols=64  Identities=19%  Similarity=0.329  Sum_probs=55.4

Q ss_pred             CCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccC--CceEEEE
Q 005707          146 IPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAET--GRISLTM  216 (681)
Q Consensus       146 kvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ek--grI~LSl  216 (681)
                      ..|++++|+|.++.++|+||++++ .+|+||.++++.      .+.|++|+.|+|.|++++.++  ..|.||+
T Consensus         2 ~~g~iV~G~V~~~~~~~~~vdig~-~eg~lp~~e~~~------~~~~~~Gd~v~v~v~~v~~~~~~~~i~lSr   67 (67)
T cd04455           2 REGEIVTGIVKRVDRGNVIVDLGK-VEAILPKKEQIP------GESYRPGDRIKAYVLEVRKTSKGPQIILSR   67 (67)
T ss_pred             CCCCEEEEEEEEEcCCCEEEEcCC-eEEEeeHHHCCC------CCcCCCCCEEEEEEEEEecCCCCCEEEEeC
Confidence            469999999999999999999987 999999999963      345899999999999999755  4677774

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.

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=98.63  E-value=4.7e-08  Score=109.53  Aligned_cols=71  Identities=18%  Similarity=0.282  Sum_probs=64.1

Q ss_pred             cCCCC--CCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCC--ceEEEEe
Q 005707          142 NEDLI--PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETG--RISLTMR  217 (681)
Q Consensus       142 ~~~Lk--vGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekg--rI~LSlK  217 (681)
                      +..++  .|+++.|+|+++.++|+||+|++ +.||||.+++.      |.+.|++|+.|+|+|+.++++++  +|.||++
T Consensus       127 ~~eyk~~~GeIV~G~V~ri~~~giiVDLgg-vea~LP~sE~i------p~E~~~~GdrIka~I~~Vd~~~kg~qIilSRt  199 (470)
T PRK09202        127 YEEYKDRVGEIITGVVKRVERGNIIVDLGR-AEAILPRKEQI------PRENFRPGDRVRAYVYEVRKEARGPQIILSRT  199 (470)
T ss_pred             HHHHHhhcCCEEEEEEEEEecCCEEEEECC-eEEEecHHHcC------CCccCCCCCEEEEEEEEEecCCCCCeEEEEeC
Confidence            66676  89999999999999999999976 99999999985      67789999999999999999877  8999998


Q ss_pred             cc
Q 005707          218 ES  219 (681)
Q Consensus       218 ~l  219 (681)
                      ..
T Consensus       200 ~p  201 (470)
T PRK09202        200 HP  201 (470)
T ss_pred             cH
Confidence            54

>PRK05054 exoribonuclease II; Provisional

Probab=98.63  E-value=1.7e-08  Score=116.93  Aligned_cols=148  Identities=11%  Similarity=0.018  Sum_probs=98.3

Q ss_pred             ccccceeeecccccccccceeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCcceecCCCC
Q 005707           26 NCLTRYNSTRKSTKQTISSQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPS  105 (681)
Q Consensus        26 ~~~~~~~~~r~~~~~~~s~~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s  105 (681)
                      .+.+||||+-.+|.|||||.|++.||-.+|-+. +.              |.|....        ...   .        
T Consensus       481 ~~~gHfgL~~~~YthfTSPIRRY~DLivHR~L~-a~--------------l~~~~~~--------~~~---~--------  526 (644)
T PRK05054        481 EPGPHFGLGLEAYATWTSPIRKYGDMINHRLLK-AV--------------IKGETAE--------RPQ---D--------  526 (644)
T ss_pred             CCcCccccccccccccCChhhhhHHHHHHHHHH-HH--------------HcCCCCC--------ccH---H--------
Confidence            567999999999999999999999987764221 11              1111000        000   0        


Q ss_pred             CcccccccccccCCChhhHHhhhchhhhhcCCCCCCcCCCCCC--cEEEEEEEEEecCeeEEEEC-CCeEEEEeccccCC
Q 005707          106 DVETSESSSIKSEASPTLAESRRSRTARKSEMPPVKNEDLIPG--ATFTGKVRSIQPFGAFIDFG-AFTDGLVHVSRLSD  182 (681)
Q Consensus       106 ~v~~ae~ss~~sea~~daek~~~kr~~rk~e~~~lt~~~LkvG--dIVeGkV~sV~d~GaFVdLg-ggV~GLVPiSELS~  182 (681)
                        ..+++.+.++..+..+++...+..  +..     |..=.+|  +.+.|.|++|+.+|+||+|. .++.||||.+.|.+
T Consensus       527 --~~~~~~s~~er~a~~aer~~~~~~--~~~-----y~~~~~G~~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~~  597 (644)
T PRK05054        527 --EITVQLAERRRLNRMAERDVGDWL--YAR-----YLKDKAGTDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHA  597 (644)
T ss_pred             --HHHHHHHHHHHHHHHHHHHHHHHH--HHH-----HHhhccCCCeEEEEEEEeeecCcEEEEEeCCceEEEEEccccCC
Confidence              012234444445555554333311  111     2233455  59999999999999999994 55999999999975


Q ss_pred             c--cc-c--C-------cccccccCCEEEEEEEEEeccCCceEEEE
Q 005707          183 N--FV-K--D-------VGSIVSVGQEVKVRLIEANAETGRISLTM  216 (681)
Q Consensus       183 ~--~v-~--d-------~~e~fkVGd~VkVkVl~VD~ekgrI~LSl  216 (681)
                      +  ++ .  +       -...|++||.|+|+|..+|..+++|.+..
T Consensus       598 ~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~~~~~i~~~~  643 (644)
T PRK05054        598 VRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETRSIIARP  643 (644)
T ss_pred             CccceEEccccceEEEeCCEEEcCCCEEEEEEEEEccccCeEEEEE
Confidence            3  11 1  1       12469999999999999999999998864

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=98.62  E-value=4.3e-08  Score=113.72  Aligned_cols=79  Identities=29%  Similarity=0.473  Sum_probs=72.7

Q ss_pred             ccccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEe
Q 005707          255 MKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMK  332 (681)
Q Consensus       255 ~~~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK  332 (681)
                      ..+.+|++|+++.|+|+|+.+||+||+|+-+.+|++|++.+++.++.  +|.+.+++||.|+|+|+.+|  ++||.|||+
T Consensus       651 ~~i~dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~--~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr  728 (780)
T COG2183         651 ESITDLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVK--DPNEVVKVGDIVKVKVIEVDTARKRIALSMR  728 (780)
T ss_pred             hhHhhccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcC--ChHHhcccCCEEEEEEEEEecccCeeeeEee
Confidence            45679999999999999999999999999999999999999999864  46899999999999999998  699999998


Q ss_pred             ccC
Q 005707          333 KED  335 (681)
Q Consensus       333 ~~~  335 (681)
                      ...
T Consensus       729 ~~~  731 (780)
T COG2183         729 LDE  731 (780)
T ss_pred             ccC
Confidence            763

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

Probab=98.61  E-value=8.7e-08  Score=75.91  Aligned_cols=63  Identities=35%  Similarity=0.616  Sum_probs=54.7

Q ss_pred             EEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEE
Q 005707          266 LEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLT  330 (681)
Q Consensus       266 V~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LS  330 (681)
                      +.|+|+++.++|+||+++.++.|++|.+++++.++.  ++...|++||.|.|+|+++|  ++++.||
T Consensus         1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~~~~--~~~~~~~~G~~v~~~v~~~d~~~~~i~ls   65 (65)
T cd00164           1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVK--DPSEVFKVGDEVEVKVLEVDPEKGRISLS   65 (65)
T ss_pred             CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCcccc--CHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence            479999999999999999999999999999987643  34678999999999999997  4667654

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.

>COG0557 VacB Exoribonuclease R [Transcription]

Probab=98.61  E-value=1.8e-08  Score=117.96  Aligned_cols=160  Identities=19%  Similarity=0.306  Sum_probs=109.9

Q ss_pred             eeeeeeccccccceeeecccccccccceeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCc
Q 005707           18 TAFTIKKNNCLTRYNSTRKSTKQTISSQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDS   97 (681)
Q Consensus        18 ~~~~~~~~~~~~~~~~~r~~~~~~~s~~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~   97 (681)
                      ..|.+.   +.+||||+-.+|.|||||.|++.|+=.+|.+.- ...+........                +       .
T Consensus       533 a~Ys~~---~~~HfgL~~~~YtHFTSPIRRY~DLivHR~L~~-~l~~~~~~~~~~----------------~-------~  585 (706)
T COG0557         533 AEYSPD---NVGHFGLALDYYTHFTSPIRRYPDLIVHRQLKA-LLSGEPIPEKKT----------------S-------E  585 (706)
T ss_pred             CeecCC---CCCceeccccchhccCCchhhchHHHHHHHHHH-HhcCCCCCccch----------------h-------H
Confidence            344444   789999999999999999999999876643321 111100000000                0       0


Q ss_pred             ceecCCCCCcccccccccccCCChhhHHhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECCC-eEEEEe
Q 005707           98 AGASDIPSDVETSESSSIKSEASPTLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAF-TDGLVH  176 (681)
Q Consensus        98 lvlSer~s~v~~ae~ss~~sea~~daek~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLggg-V~GLVP  176 (681)
                      ..+      ...+.+++-+++++.++++....  ....     .+..-.+|+.+.|.|.+|..+|+||.|.+. ++|+||
T Consensus       586 ~~l------~~i~~~~s~~er~a~~aer~~~~--~~~~-----~~m~~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~  652 (706)
T COG0557         586 EEL------DELAAHISSAERRAQEAERDVID--LLKA-----EYMKKRVGEEFDGVVTGVTSFGFFVELPELGLEGLVH  652 (706)
T ss_pred             HHH------HHHHHHhCHHHHHHHHHHHHHHH--HHHH-----HHHHHhcCCEEEEEEEEEEeccEEEEecccccccceE
Confidence            001      11134456666666666665433  1222     256677899999999999999999999654 999999


Q ss_pred             ccccCCccc-----------cCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707          177 VSRLSDNFV-----------KDVGSIVSVGQEVKVRLIEANAETGRISLTMR  217 (681)
Q Consensus       177 iSELS~~~v-----------~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK  217 (681)
                      ++.+..+++           ......|+.|+.|+|+|+.+|...++|.+++.
T Consensus       653 ~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~~~~i~~~~v  704 (706)
T COG0557         653 ISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDLDERKIDFELV  704 (706)
T ss_pred             cccCCCceeeeccccceeeccccccccccCCEEEEEEEEEcccccceEEEec
Confidence            999996543           22334699999999999999999999998764

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=98.61  E-value=6.9e-08  Score=112.73  Aligned_cols=70  Identities=39%  Similarity=0.659  Sum_probs=65.5

Q ss_pred             CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEE
Q 005707          144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISL  214 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~L  214 (681)
                      .+++|++|.|+|+++.+||+||+|.++.+||||+++++|.++.++.+.|++||.|+|+|+++|. +++|.|
T Consensus       615 ~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id~-~gki~L  684 (684)
T TIGR03591       615 EPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDK-QGRIKL  684 (684)
T ss_pred             ccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEECC-CCCccC
Confidence            5789999999999999999999998889999999999999999999999999999999999997 677654

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).

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

Probab=98.60  E-value=1.8e-07  Score=83.48  Aligned_cols=75  Identities=29%  Similarity=0.591  Sum_probs=64.9

Q ss_pred             cEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccC-----------cccccccCCEEEEEEEEEeccC-----Cce
Q 005707          149 ATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKD-----------VGSIVSVGQEVKVRLIEANAET-----GRI  212 (681)
Q Consensus       149 dIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d-----------~~e~fkVGd~VkVkVl~VD~ek-----grI  212 (681)
                      +++.|+|+++.++|+||+|.+ +.||+|+++++++++..           ....|++||.|+|+|.++|.+.     +++
T Consensus         1 ~vv~g~V~~i~~~GifV~l~~-v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i   79 (99)
T cd04460           1 EVVEGEVVEVVDFGAFVRIGP-VDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKI   79 (99)
T ss_pred             CEEEEEEEEEEeccEEEEEcC-eEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCceE
Confidence            479999999999999999986 99999999999876643           3477999999999999999764     589


Q ss_pred             EEEEeccchhhH
Q 005707          213 SLTMRESDDISK  224 (681)
Q Consensus       213 ~LSlK~l~~dp~  224 (681)
                      .||++.....++
T Consensus        80 ~ls~k~~~~g~~   91 (99)
T cd04460          80 GLTMRQPGLGKL   91 (99)
T ss_pred             EEEEecCCCCcH
Confidence            999998776665

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.

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

Probab=98.57  E-value=2.7e-07  Score=82.37  Aligned_cols=76  Identities=26%  Similarity=0.346  Sum_probs=64.0

Q ss_pred             cEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCccccccc---------CCCCcccCCCEEEEEEEEEeC-------CeE
Q 005707          264 QDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANM---------MGGSSLQVGQEVSVRVLRISR-------GQV  327 (681)
Q Consensus       264 dIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~---------~p~~~fkVGqkVkVrVL~IDk-------gKI  327 (681)
                      +++.|+|+.+.++|+||++. +++||+|.+++.+.++...         .....|++||.|.|+|.++|.       +++
T Consensus         1 ~vv~g~V~~i~~~GifV~l~-~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i   79 (99)
T cd04460           1 EVVEGEVVEVVDFGAFVRIG-PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKI   79 (99)
T ss_pred             CEEEEEEEEEEeccEEEEEc-CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCceE
Confidence            47899999999999999998 6999999999987765322         124789999999999999973       589


Q ss_pred             EEEEeccCCCcCC
Q 005707          328 TLTMKKEDDVGSN  340 (681)
Q Consensus       328 ~LSLK~~~~DP~e  340 (681)
                      .||+|.....||+
T Consensus        80 ~ls~k~~~~g~~~   92 (99)
T cd04460          80 GLTMRQPGLGKLE   92 (99)
T ss_pred             EEEEecCCCCcHH
Confidence            9999998777754

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.

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=98.54  E-value=5.2e-08  Score=109.20  Aligned_cols=123  Identities=17%  Similarity=0.273  Sum_probs=90.1

Q ss_pred             EEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEE-EeccchhhHhhhhccccccCCccccccccCCCCCC
Q 005707          172 DGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLT-MRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQ  250 (681)
Q Consensus       172 ~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LS-lK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~  250 (681)
                      .+.++.++...     ....+.+|+.+.+.|...+  -+|+.++ .|+.....|.                        .
T Consensus        72 ~~eI~L~eAk~-----~~~~~~vGD~ie~~I~~~~--fgRia~q~aKq~i~Qkir------------------------e  120 (470)
T PRK09202         72 TKEISLEEARK-----IDPDAEVGDYIEEEIESVD--FGRIAAQTAKQVIVQKIR------------------------E  120 (470)
T ss_pred             cceeeHHHHhh-----hCccccCCCeEEEEEcccc--CChHHHHHHHHHHHHHHH------------------------H
Confidence            35566555422     2233789999999998876  3444333 3333333331                        1


Q ss_pred             ccccccccCCc--cCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC--C-
Q 005707          251 KRDEMKTTKFV--KGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR--G-  325 (681)
Q Consensus       251 ~k~~~~~sklk--vGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk--g-  325 (681)
                      ..+...+..|+  .|+++.|+|+++.++|+||+++ |++||||.+++.        |...|++||.|+|+|+++++  + 
T Consensus       121 ~ere~i~~eyk~~~GeIV~G~V~ri~~~giiVDLg-gvea~LP~sE~i--------p~E~~~~GdrIka~I~~Vd~~~kg  191 (470)
T PRK09202        121 AERERVYEEYKDRVGEIITGVVKRVERGNIIVDLG-RAEAILPRKEQI--------PRENFRPGDRVRAYVYEVRKEARG  191 (470)
T ss_pred             HHHHHHHHHHHhhcCCEEEEEEEEEecCCEEEEEC-CeEEEecHHHcC--------CCccCCCCCEEEEEEEEEecCCCC
Confidence            12235678887  9999999999999999999996 999999999874        46789999999999999974  3 


Q ss_pred             -eEEEEEecc
Q 005707          326 -QVTLTMKKE  334 (681)
Q Consensus       326 -KI~LSLK~~  334 (681)
                       +|.||.+..
T Consensus       192 ~qIilSRt~p  201 (470)
T PRK09202        192 PQIILSRTHP  201 (470)
T ss_pred             CeEEEEeCcH
Confidence             799999654

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

Probab=98.53  E-value=1.2e-07  Score=108.59  Aligned_cols=77  Identities=36%  Similarity=0.645  Sum_probs=72.4

Q ss_pred             cCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEecc
Q 005707          142 NEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRES  219 (681)
Q Consensus       142 ~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l  219 (681)
                      ...+++|+++.|+|+++.+||+||.|.++-+|++|++++++.++....+.+++||.|+|+|+.+|+ ++++.||++..
T Consensus       614 ~~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD~-~Gri~ls~~~~  690 (692)
T COG1185         614 TREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEIDK-QGRIRLSIKAV  690 (692)
T ss_pred             HhhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhhhhhcccceeecCceEEEEEeeecc-cCCccceehhc
Confidence            478999999999999999999999998889999999999999999999999999999999999985 78999999854

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=98.52  E-value=2.4e-07  Score=92.19  Aligned_cols=73  Identities=19%  Similarity=0.358  Sum_probs=66.7

Q ss_pred             CCCCCCcEEEEEEEEEecCeeEEEECC----------CeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCce
Q 005707          143 EDLIPGATFTGKVRSIQPFGAFIDFGA----------FTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRI  212 (681)
Q Consensus       143 ~~LkvGdIVeGkV~sV~d~GaFVdLgg----------gV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI  212 (681)
                      ..+++|++|.|+|+++.++|+||+|++          +..|++|.+++++.+..++.+.|++||.|+|+|+.++   +++
T Consensus        60 ~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~---~~i  136 (189)
T PRK09521         60 PLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT---DPL  136 (189)
T ss_pred             CCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC---CcE
Confidence            467899999999999999999999952          4789999999999888888999999999999999997   789


Q ss_pred             EEEEec
Q 005707          213 SLTMRE  218 (681)
Q Consensus       213 ~LSlK~  218 (681)
                      .||++.
T Consensus       137 ~LS~k~  142 (189)
T PRK09521        137 QLSTKG  142 (189)
T ss_pred             EEEEec
Confidence            999984

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=98.50  E-value=1.7e-07  Score=109.55  Aligned_cols=72  Identities=31%  Similarity=0.491  Sum_probs=64.0

Q ss_pred             cccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC-CeEEE
Q 005707          256 KTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR-GQVTL  329 (681)
Q Consensus       256 ~~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk-gKI~L  329 (681)
                      ....+++|+++.|+|++|.+||+||+|.+|++||||+++++|.++.  ++...|++||.|+|+|+++|. +|+.|
T Consensus       612 ~~~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~~v~--~~~~~~kvGD~V~VkVi~id~~gki~L  684 (684)
T TIGR03591       612 ITAEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVE--KVEDVLKEGDEVKVKVLEIDKQGRIKL  684 (684)
T ss_pred             hhcccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCCccc--ChhhccCCCCEEEEEEEEECCCCCccC
Confidence            3456789999999999999999999999999999999999998865  347889999999999999984 77654

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).

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=98.47  E-value=4.7e-07  Score=93.19  Aligned_cols=73  Identities=18%  Similarity=0.240  Sum_probs=66.8

Q ss_pred             CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccc----cCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707          144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFV----KDVGSIVSVGQEVKVRLIEANAETGRISLTMR  217 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v----~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK  217 (681)
                      ..++|++|.|+|+++.++|+||+|+....|+||++++++.++    .++...|++||.|+|+|+++++++ .+.||++
T Consensus        60 ~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~-~~~LS~k  136 (235)
T PRK04163         60 IPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTR-DVVLTLK  136 (235)
T ss_pred             cCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCCC-cEEEEEc
Confidence            458899999999999999999999988999999999999887    788889999999999999998654 5999997

>TIGR02062 RNase_B exoribonuclease II

Probab=98.45  E-value=8.4e-08  Score=111.24  Aligned_cols=147  Identities=10%  Similarity=0.019  Sum_probs=96.5

Q ss_pred             ccccceeeecccccccccceeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCcceecCCCC
Q 005707           26 NCLTRYNSTRKSTKQTISSQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPS  105 (681)
Q Consensus        26 ~~~~~~~~~r~~~~~~~s~~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s  105 (681)
                      .+.+||||+-.+|.|||||.|++.||-.+|-+. ..              |.|+....         .      +     
T Consensus       477 ~~~~HfgL~~~~YthfTSPIRRY~DLivHR~L~-~~--------------l~~~~~~~---------~------~-----  521 (639)
T TIGR02062       477 EPGPHFGLGLEAYATWTSPIRKYGDMINHRLLK-AV--------------IKGETATR---------P------Q-----  521 (639)
T ss_pred             CCcCcchhccccccccCChhhhhHHHHHHHHHH-HH--------------HcCCCCCC---------C------H-----
Confidence            467999999999999999999999987764221 11              11110000         0      0     


Q ss_pred             CcccccccccccCCChhhHHhhhchhhhhcCCCCCCcCCCCC--CcEEEEEEEEEecCeeEEEE-CCCeEEEEeccccCC
Q 005707          106 DVETSESSSIKSEASPTLAESRRSRTARKSEMPPVKNEDLIP--GATFTGKVRSIQPFGAFIDF-GAFTDGLVHVSRLSD  182 (681)
Q Consensus       106 ~v~~ae~ss~~sea~~daek~~~kr~~rk~e~~~lt~~~Lkv--GdIVeGkV~sV~d~GaFVdL-gggV~GLVPiSELS~  182 (681)
                       ...+++.+.++..+..+++...+..  ...     |..-++  |+.+.|.|.++..+|+||+| ..++.||||.+.+.+
T Consensus       522 -~~~~~~~s~~er~a~~aeR~~~~~~--~~~-----yl~~~~g~~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~  593 (639)
T TIGR02062       522 -EDITVQLAERRRLNRIAERDVADWL--YAR-----FLADKAAKNTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHA  593 (639)
T ss_pred             -HHHHHHHHHHHHHHHHHHHHHHHHH--HHH-----HHhhccCCCcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCC
Confidence             0012233444444445554333211  111     223345  45999999999999999999 566999999999965


Q ss_pred             --ccc-cC-------c--ccccccCCEEEEEEEEEeccCCceEEE
Q 005707          183 --NFV-KD-------V--GSIVSVGQEVKVRLIEANAETGRISLT  215 (681)
Q Consensus       183 --~~v-~d-------~--~e~fkVGd~VkVkVl~VD~ekgrI~LS  215 (681)
                        +++ -+       +  ...|+.||.|+|+|..+|..+++|.+.
T Consensus       594 ~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd~~~~~i~~~  638 (639)
T TIGR02062       594 NREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMETRSIIAR  638 (639)
T ss_pred             CCcceEEcccccEEEEeccEEEecCCEEEEEEEEeccccCcEeee
Confidence              222 11       1  126999999999999999999998874

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.

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

Probab=98.43  E-value=9e-07  Score=73.81  Aligned_cols=61  Identities=28%  Similarity=0.493  Sum_probs=52.9

Q ss_pred             ccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC----CeEEEE
Q 005707          261 VKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR----GQVTLT  330 (681)
Q Consensus       261 kvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk----gKI~LS  330 (681)
                      +.|+++.|+|.++.++|+||+++ +.+|+||.+++..        ...|++||.|+++|+++++    ++|.||
T Consensus         2 ~~g~iV~G~V~~~~~~~~~vdig-~~eg~lp~~e~~~--------~~~~~~Gd~v~v~v~~v~~~~~~~~i~lS   66 (67)
T cd04455           2 REGEIVTGIVKRVDRGNVIVDLG-KVEAILPKKEQIP--------GESYRPGDRIKAYVLEVRKTSKGPQIILS   66 (67)
T ss_pred             CCCCEEEEEEEEEcCCCEEEEcC-CeEEEeeHHHCCC--------CCcCCCCCEEEEEEEEEecCCCCCEEEEe
Confidence            47999999999999999999997 5999999998863        3468999999999999963    457776

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.

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=98.40  E-value=2.3e-06  Score=88.19  Aligned_cols=75  Identities=24%  Similarity=0.276  Sum_probs=65.6

Q ss_pred             CccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccc--cccCCCCcccCCCEEEEEEEEEeC-CeEEEEEecc
Q 005707          260 FVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGF--ANMMGGSSLQVGQEVSVRVLRISR-GQVTLTMKKE  334 (681)
Q Consensus       260 lkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~i--e~~~p~~~fkVGqkVkVrVL~IDk-gKI~LSLK~~  334 (681)
                      .++||+|.|+|+++.++|+||+|+.+..|+||.++++|.++  +..++...|++||.|.|+|+++++ +++.||+|..
T Consensus        61 P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~~~~LS~k~~  138 (235)
T PRK04163         61 PKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKGK  138 (235)
T ss_pred             CCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCCCcEEEEEcCC
Confidence            47999999999999999999999999999999999998764  223457789999999999999975 5799999864

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

Probab=98.38  E-value=4.3e-07  Score=101.80  Aligned_cols=83  Identities=27%  Similarity=0.452  Sum_probs=73.9

Q ss_pred             CcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccc
Q 005707          141 KNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESD  220 (681)
Q Consensus       141 t~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~  220 (681)
                      ...+|+.|.+++|+|+.+.++|+||.|.++..||+|+++|+..++.+|.+.+.+||.|.|+.+..|+. +.+.++.+.++
T Consensus       662 ~~~~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  662 QVQDLEFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDPR-GGIMLSSRALL  740 (760)
T ss_pred             cccceEeeeEEEEEEeeecccceEEEecCCchhhccchhcccccccChHHHHhhcceeEEEEEeecCc-cceeehhhhhc
Confidence            36689999999999999999999999998899999999999999999999999999999999999974 55566666666


Q ss_pred             hhhH
Q 005707          221 DISK  224 (681)
Q Consensus       221 ~dp~  224 (681)
                      ++|.
T Consensus       741 p~p~  744 (760)
T KOG1067|consen  741 PDPA  744 (760)
T ss_pred             CCcc
Confidence            6664

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

Probab=98.31  E-value=2.5e-06  Score=84.23  Aligned_cols=79  Identities=32%  Similarity=0.554  Sum_probs=66.0

Q ss_pred             CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCcccc-----------CcccccccCCEEEEEEEEEe-----c
Q 005707          144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVK-----------DVGSIVSVGQEVKVRLIEAN-----A  207 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~-----------d~~e~fkVGd~VkVkVl~VD-----~  207 (681)
                      ....|++++|+|++++++|+||+++. ++|++|.+++.+++..           +....|++|+.|+++|.++|     +
T Consensus        78 ~p~~gEvv~G~V~~v~~~GifV~lg~-~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~  156 (179)
T TIGR00448        78 KPELGEIVEGEVIEIVEFGAFVSLGP-FDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRP  156 (179)
T ss_pred             eccCCCEEEEEEEEEEeeEEEEEeCC-ceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCC
Confidence            45679999999999999999999965 9999999999865432           23467999999999999998     5


Q ss_pred             cCCceEEEEeccchhh
Q 005707          208 ETGRISLTMRESDDIS  223 (681)
Q Consensus       208 ekgrI~LSlK~l~~dp  223 (681)
                      +..+|.+|+|+.-.-+
T Consensus       157 ~~~~I~lt~k~~~LG~  172 (179)
T TIGR00448       157 EGSKIGLTMRQPLLGK  172 (179)
T ss_pred             CcceEEEEeccCcCCc
Confidence            6678999999754433

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

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=98.20  E-value=2.2e-06  Score=93.51  Aligned_cols=70  Identities=16%  Similarity=0.284  Sum_probs=60.6

Q ss_pred             cCCC--CCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCC--ceEEEEe
Q 005707          142 NEDL--IPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETG--RISLTMR  217 (681)
Q Consensus       142 ~~~L--kvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekg--rI~LSlK  217 (681)
                      |..+  +.|+++.|+|.++.++|+||++|+ ++|+||.+++..      .+.|++||.++|.|++++..++  .|.||+.
T Consensus       127 ~~ef~~k~GeiV~G~V~~~~~~~~~Vdlg~-vEa~LP~~E~ip------~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt  199 (362)
T PRK12327        127 YNEFSEREGDIVTGVVQRRDNRFVYVNLGK-IEAVLPPAEQIP------GETYKHGDRIKVYVVKVEKTTKGPQIFVSRT  199 (362)
T ss_pred             HHHHHHhcCCEEEEEEEEEeCCcEEEEeCC-eEEEecHHHcCC------CCCCCCCCEEEEEEEEEecCCCCCeEEEEeC
Confidence            6677  899999999999999999999987 999999877743      5669999999999999997654  5888887


Q ss_pred             c
Q 005707          218 E  218 (681)
Q Consensus       218 ~  218 (681)
                      .
T Consensus       200 ~  200 (362)
T PRK12327        200 H  200 (362)
T ss_pred             C
Confidence            4

>TIGR01953 NusA transcription termination factor NusA

Probab=98.20  E-value=2.4e-06  Score=92.56  Aligned_cols=72  Identities=18%  Similarity=0.433  Sum_probs=60.5

Q ss_pred             cCCC--CCCcEEEEEEEEEecCe-eEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccC--CceEEEE
Q 005707          142 NEDL--IPGATFTGKVRSIQPFG-AFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAET--GRISLTM  216 (681)
Q Consensus       142 ~~~L--kvGdIVeGkV~sV~d~G-aFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ek--grI~LSl  216 (681)
                      +..+  +.|+++.|+|.++.+.| +||+||+ ++|+||.+++..      .+.|++||.++|.|+.++...  ..|.||+
T Consensus       124 ~~ey~~k~GeiV~G~V~~v~~~g~v~VdiG~-~ea~LP~~E~ip------~E~~~~Gd~ik~~V~~V~~~~kg~qIivSR  196 (341)
T TIGR01953       124 YDEFSSKEGEIISGTVKRVNRRGNLYVELGK-TEGILPKKEQIP------GEKFRIGDRIKAYVYEVRKTAKGPQIILSR  196 (341)
T ss_pred             HHHHHhhcCCEEEEEEEEEecCCcEEEEECC-eEEEecHHHcCC------CcCCCCCCEEEEEEEEEEcCCCCCeEEEEe
Confidence            4455  59999999999999988 6999965 999999999873      445999999999999999654  5799999


Q ss_pred             eccc
Q 005707          217 RESD  220 (681)
Q Consensus       217 K~l~  220 (681)
                      +...
T Consensus       197 t~~~  200 (341)
T TIGR01953       197 THPE  200 (341)
T ss_pred             CcHH
Confidence            8543

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.

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

Probab=98.16  E-value=9.2e-06  Score=80.25  Aligned_cols=78  Identities=27%  Similarity=0.312  Sum_probs=63.7

Q ss_pred             CccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccc-c--------CCCCcccCCCEEEEEEEEEe-------
Q 005707          260 FVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFAN-M--------MGGSSLQVGQEVSVRVLRIS-------  323 (681)
Q Consensus       260 lkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~-~--------~p~~~fkVGqkVkVrVL~ID-------  323 (681)
                      -.+|+++.|+|++++++|+||+++ .++|++|.+++.++.... .        .....|++||.|+++|++++       
T Consensus        79 p~~gEvv~G~V~~v~~~GifV~lg-~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~  157 (179)
T TIGR00448        79 PELGEIVEGEVIEIVEFGAFVSLG-PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRPE  157 (179)
T ss_pred             ccCCCEEEEEEEEEEeeEEEEEeC-CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCCC
Confidence            347999999999999999999996 699999999987654321 0        12467999999999999996       


Q ss_pred             CCeEEEEEeccCCCc
Q 005707          324 RGQVTLTMKKEDDVG  338 (681)
Q Consensus       324 kgKI~LSLK~~~~DP  338 (681)
                      ..++.||||+....+
T Consensus       158 ~~~I~lt~k~~~LG~  172 (179)
T TIGR00448       158 GSKIGLTMRQPLLGK  172 (179)
T ss_pred             cceEEEEeccCcCCc
Confidence            368999999875555

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

>TIGR02063 RNase_R ribonuclease R

Probab=98.14  E-value=7e-06  Score=96.43  Aligned_cols=74  Identities=26%  Similarity=0.471  Sum_probs=61.8

Q ss_pred             cCCccCcEEEEEEEEEecceEEEEeCC-CeEEEEeCCCCCcccccc---------cCCCCcccCCCEEEEEEEEEe--CC
Q 005707          258 TKFVKGQDLEGTVKNLTRSGAFISLPE-GEEGFLPTSEESDDGFAN---------MMGGSSLQVGQEVSVRVLRIS--RG  325 (681)
Q Consensus       258 sklkvGdIV~G~VknVt~~GaFVeIg~-GIeGLLpiSELSd~~ie~---------~~p~~~fkVGqkVkVrVL~ID--kg  325 (681)
                      .+-++|+++.|+|++|++||+||+|.+ |++||+|.+++.++++..         ......|++||.|+|+|.++|  ++
T Consensus       623 l~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~~~~  702 (709)
T TIGR02063       623 MSEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTG  702 (709)
T ss_pred             hhccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEecccC
Confidence            334679999999999999999999998 899999999998654311         122467999999999999998  58


Q ss_pred             eEEEEE
Q 005707          326 QVTLTM  331 (681)
Q Consensus       326 KI~LSL  331 (681)
                      +|.|++
T Consensus       703 ~I~~~l  708 (709)
T TIGR02063       703 KIDFEL  708 (709)
T ss_pred             eEEEEE
Confidence            898876

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.

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

Probab=98.10  E-value=2.8e-06  Score=95.46  Aligned_cols=83  Identities=19%  Similarity=0.310  Sum_probs=75.8

Q ss_pred             cccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe-CCeEEEEEecc
Q 005707          256 KTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS-RGQVTLTMKKE  334 (681)
Q Consensus       256 ~~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID-kgKI~LSLK~~  334 (681)
                      ...++..|-++.|+|+.+.++|+||+|+++..||||.++|+..++  .+|...|++||.|.++.+..| ++.+.|+.|.+
T Consensus       662 ~~~~l~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e~i--akpsd~levGq~I~vk~ie~d~~g~~~ls~ral  739 (760)
T KOG1067|consen  662 QVQDLEFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQEKI--AKPSDLLEVGQEIQVKYIERDPRGGIMLSSRAL  739 (760)
T ss_pred             cccceEeeeEEEEEEeeecccceEEEecCCchhhccchhcccccc--cChHHHHhhcceeEEEEEeecCccceeehhhhh
Confidence            355788999999999999999999999999999999999999885  577899999999999999998 68899999999


Q ss_pred             CCCcCC
Q 005707          335 DDVGSN  340 (681)
Q Consensus       335 ~~DP~e  340 (681)
                      +++|.-
T Consensus       740 Lp~p~~  745 (760)
T KOG1067|consen  740 LPDPAT  745 (760)
T ss_pred             cCCccc
Confidence            998854

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

Probab=98.06  E-value=1e-05  Score=80.57  Aligned_cols=77  Identities=32%  Similarity=0.673  Sum_probs=64.1

Q ss_pred             CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccc-----------cCcccccccCCEEEEEEEEEeccC---
Q 005707          144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFV-----------KDVGSIVSVGQEVKVRLIEANAET---  209 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v-----------~d~~e~fkVGd~VkVkVl~VD~ek---  209 (681)
                      ....|++|.|.|+.+.++|+||.||. .+||+|.+++.++++           +.....+++|+.|+++|+.+....   
T Consensus        78 kP~~gEVV~GeVv~~~~~G~fV~igp-~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~~  156 (183)
T COG1095          78 KPFRGEVVEGEVVEVVEFGAFVRIGP-LDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRRP  156 (183)
T ss_pred             EeccccEEEEEEEEEeecceEEEecc-ccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCcc
Confidence            34579999999999999999999997 999999999998844           123347899999999999987655   


Q ss_pred             --CceEEEEeccch
Q 005707          210 --GRISLTMRESDD  221 (681)
Q Consensus       210 --grI~LSlK~l~~  221 (681)
                        .+|.++|++.-.
T Consensus       157 ~~~~I~lTmrq~~L  170 (183)
T COG1095         157 RESKIGLTMRQPGL  170 (183)
T ss_pred             ccceEEEEeccccC
Confidence              478899986544

>PRK11642 exoribonuclease R; Provisional

Probab=98.05  E-value=1.2e-05  Score=95.92  Aligned_cols=72  Identities=21%  Similarity=0.392  Sum_probs=61.1

Q ss_pred             ccCcEEEEEEEEEecceEEEEeCCC-eEEEEeCCCCCccccccc---------CCCCcccCCCEEEEEEEEEe--CCeEE
Q 005707          261 VKGQDLEGTVKNLTRSGAFISLPEG-EEGFLPTSEESDDGFANM---------MGGSSLQVGQEVSVRVLRIS--RGQVT  328 (681)
Q Consensus       261 kvGdIV~G~VknVt~~GaFVeIg~G-IeGLLpiSELSd~~ie~~---------~p~~~fkVGqkVkVrVL~ID--kgKI~  328 (681)
                      ++|+++.|+|++|++||+||+|.++ ++||||.+++.++++...         .....|++||.|+|+|+.+|  +++|.
T Consensus       642 ~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~~~rkI~  721 (813)
T PRK11642        642 QVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKID  721 (813)
T ss_pred             cCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEeecCCCeEE
Confidence            6899999999999999999999874 999999999987643211         12467999999999999997  68899


Q ss_pred             EEEe
Q 005707          329 LTMK  332 (681)
Q Consensus       329 LSLK  332 (681)
                      |++-
T Consensus       722 f~l~  725 (813)
T PRK11642        722 FSLI  725 (813)
T ss_pred             EEEe
Confidence            9884

>TIGR01953 NusA transcription termination factor NusA

Probab=98.05  E-value=3e-06  Score=91.86  Aligned_cols=114  Identities=26%  Similarity=0.465  Sum_probs=80.6

Q ss_pred             cCcccccccCCEEEEEEEEEeccCCceEEE-EeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCc--c
Q 005707          186 KDVGSIVSVGQEVKVRLIEANAETGRISLT-MRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFV--K  262 (681)
Q Consensus       186 ~d~~e~fkVGd~VkVkVl~VD~ekgrI~LS-lK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklk--v  262 (681)
                      ......+++||.|.+.|...+  -+|+.++ .|+...+..                  |      ...++..+..|+  .
T Consensus        78 ~~~d~~~~vGD~I~~~I~~~~--fgR~aaq~aKqvi~Qki------------------r------e~ere~i~~ey~~k~  131 (341)
T TIGR01953        78 REIDPDVQIGDEVKKEIPPEN--FGRIAAQTAKQVILQKI------------------R------EAERERVYDEFSSKE  131 (341)
T ss_pred             HhhccccccCCEEEEEecccC--CCHHHHHHHHHHHHHHH------------------H------HHHHHHHHHHHHhhc
Confidence            334455889999998885432  2443333 222111110                  0      112235677774  9


Q ss_pred             CcEEEEEEEEEecce-EEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC----CeEEEEEecc
Q 005707          263 GQDLEGTVKNLTRSG-AFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR----GQVTLTMKKE  334 (681)
Q Consensus       263 GdIV~G~VknVt~~G-aFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk----gKI~LSLK~~  334 (681)
                      |+++.|+|.++.+.| +||+++ +++|+||.+++.        |.+.|++||.++|+|+++++    .+|.||.+..
T Consensus       132 GeiV~G~V~~v~~~g~v~VdiG-~~ea~LP~~E~i--------p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~~  199 (341)
T TIGR01953       132 GEIISGTVKRVNRRGNLYVELG-KTEGILPKKEQI--------PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHP  199 (341)
T ss_pred             CCEEEEEEEEEecCCcEEEEEC-CeEEEecHHHcC--------CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCcH
Confidence            999999999999988 699996 999999998765        34669999999999999973    4699999764

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.

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

Probab=98.05  E-value=2e-05  Score=78.16  Aligned_cols=75  Identities=29%  Similarity=0.617  Sum_probs=63.7

Q ss_pred             CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCcccc-----------CcccccccCCEEEEEEEEEeccCC--
Q 005707          144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVK-----------DVGSIVSVGQEVKVRLIEANAETG--  210 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~-----------d~~e~fkVGd~VkVkVl~VD~ekg--  210 (681)
                      ....|+++.|+|+++.++|+||+++. .+|++|.+++.+++..           +....|++|+.|+++|++++...+  
T Consensus        78 ~P~~GEVv~g~V~~v~~~Gi~V~lg~-~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~  156 (187)
T PRK08563         78 KPELQEVVEGEVVEVVEFGAFVRIGP-VDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRP  156 (187)
T ss_pred             eccCCCEEEEEEEEEEccEEEEEEeC-ceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCCC
Confidence            46689999999999999999999986 9999999999876432           345678999999999999987653  


Q ss_pred             ---ceEEEEecc
Q 005707          211 ---RISLTMRES  219 (681)
Q Consensus       211 ---rI~LSlK~l  219 (681)
                         +|.+|++..
T Consensus       157 ~~~~I~ls~~~~  168 (187)
T PRK08563        157 RGSKIGLTMRQP  168 (187)
T ss_pred             CCCEEEEEecCC
Confidence               788899864

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

Probab=98.04  E-value=1.7e-05  Score=70.80  Aligned_cols=73  Identities=16%  Similarity=0.194  Sum_probs=64.2

Q ss_pred             CCCCcEEEEEEEEEecCeeEEEE--------CCCeEEEEeccccCCcccc--CcccccccCCEEEEEEEEEeccCCceEE
Q 005707          145 LIPGATFTGKVRSIQPFGAFIDF--------GAFTDGLVHVSRLSDNFVK--DVGSIVSVGQEVKVRLIEANAETGRISL  214 (681)
Q Consensus       145 LkvGdIVeGkV~sV~d~GaFVdL--------gggV~GLVPiSELS~~~v~--d~~e~fkVGd~VkVkVl~VD~ekgrI~L  214 (681)
                      .++|++|-|+|+++....++|+|        .....|++|.+++...+..  ++.+.|++||.|+|+|++++. .+.+.|
T Consensus         4 P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~-~~~~~L   82 (92)
T cd05791           4 PKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGD-ASSYYL   82 (92)
T ss_pred             CCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCC-CCCcEE
Confidence            47899999999999999999999        6778999999999877665  678899999999999999864 466889


Q ss_pred             EEec
Q 005707          215 TMRE  218 (681)
Q Consensus       215 SlK~  218 (681)
                      |++.
T Consensus        83 st~~   86 (92)
T cd05791          83 STAE   86 (92)
T ss_pred             EecC
Confidence            9874

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".

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=98.01  E-value=3.3e-06  Score=92.11  Aligned_cols=71  Identities=21%  Similarity=0.402  Sum_probs=60.4

Q ss_pred             cccccCC--ccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC----CeE
Q 005707          254 EMKTTKF--VKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR----GQV  327 (681)
Q Consensus       254 ~~~~skl--kvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk----gKI  327 (681)
                      ...+..|  +.|+++.|+|.++.++|+||+++ +++||||.+++.        |...|++||.++|+|+++++    -+|
T Consensus       124 e~v~~ef~~k~GeiV~G~V~~~~~~~~~Vdlg-~vEa~LP~~E~i--------p~e~~~~Gd~Ika~V~~V~~~~kgp~I  194 (362)
T PRK12327        124 EIIYNEFSEREGDIVTGVVQRRDNRFVYVNLG-KIEAVLPPAEQI--------PGETYKHGDRIKVYVVKVEKTTKGPQI  194 (362)
T ss_pred             HHHHHHHHHhcCCEEEEEEEEEeCCcEEEEeC-CeEEEecHHHcC--------CCCCCCCCCEEEEEEEEEecCCCCCeE
Confidence            3668888  89999999999999999999997 799999987653        36789999999999999973    258


Q ss_pred             EEEEec
Q 005707          328 TLTMKK  333 (681)
Q Consensus       328 ~LSLK~  333 (681)
                      .||...
T Consensus       195 ivSRt~  200 (362)
T PRK12327        195 FVSRTH  200 (362)
T ss_pred             EEEeCC
Confidence            888743

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

Probab=97.99  E-value=2e-05  Score=92.00  Aligned_cols=71  Identities=21%  Similarity=0.469  Sum_probs=60.0

Q ss_pred             ccCcEEEEEEEEEecceEEEEeC-CCeEEEEeCCCCCcccccc---------cCCCCcccCCCEEEEEEEEEe--CCeEE
Q 005707          261 VKGQDLEGTVKNLTRSGAFISLP-EGEEGFLPTSEESDDGFAN---------MMGGSSLQVGQEVSVRVLRIS--RGQVT  328 (681)
Q Consensus       261 kvGdIV~G~VknVt~~GaFVeIg-~GIeGLLpiSELSd~~ie~---------~~p~~~fkVGqkVkVrVL~ID--kgKI~  328 (681)
                      ++|+++.|+|++|+++|+||+|+ .+++||+|.+++.|+++..         ......|++||.|+|+|.++|  +++|.
T Consensus       571 ~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~~~~I~  650 (654)
T TIGR00358       571 KVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMETRSII  650 (654)
T ss_pred             CCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEecccCeEE
Confidence            57999999999999999999998 6899999999998864211         112467999999999999997  58888


Q ss_pred             EEE
Q 005707          329 LTM  331 (681)
Q Consensus       329 LSL  331 (681)
                      +++
T Consensus       651 f~l  653 (654)
T TIGR00358       651 FEL  653 (654)
T ss_pred             EEE
Confidence            875

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.

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

Probab=97.91  E-value=2.4e-05  Score=69.77  Aligned_cols=75  Identities=12%  Similarity=0.109  Sum_probs=64.2

Q ss_pred             CccCcEEEEEEEEEecceEEEEe--------CCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC-CeEEEE
Q 005707          260 FVKGQDLEGTVKNLTRSGAFISL--------PEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR-GQVTLT  330 (681)
Q Consensus       260 lkvGdIV~G~VknVt~~GaFVeI--------g~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk-gKI~LS  330 (681)
                      .++|++|-|+|+.+....++|+|        .....|++|.+++.....+.....+.|++||.|+++|+++++ ..+.||
T Consensus         4 P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~~~~~~Ls   83 (92)
T cd05791           4 PKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASSYYLS   83 (92)
T ss_pred             CCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCCCCCcEEE
Confidence            37899999999999999999999        778999999998876655433457889999999999999965 779999


Q ss_pred             Eecc
Q 005707          331 MKKE  334 (681)
Q Consensus       331 LK~~  334 (681)
                      ++..
T Consensus        84 t~~~   87 (92)
T cd05791          84 TAEN   87 (92)
T ss_pred             ecCC
Confidence            9753

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".

>PHA02858 EIF2a-like PKR inhibitor; Provisional

Probab=97.87  E-value=3.5e-05  Score=67.97  Aligned_cols=73  Identities=10%  Similarity=0.103  Sum_probs=66.8

Q ss_pred             cCCCCCCcEEEEEEEEEecCeeEEEE-CCCeEEEEe-ccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEE
Q 005707          142 NEDLIPGATFTGKVRSIQPFGAFIDF-GAFTDGLVH-VSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTM  216 (681)
Q Consensus       142 ~~~LkvGdIVeGkV~sV~d~GaFVdL-gggV~GLVP-iSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSl  216 (681)
                      +.-.++|+++. .|+.+.+.|+||.| +.+++|+|. .++++.++++.+.+.+ +|..+.|+|+.+|+++|-|.||.
T Consensus        11 y~~P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~KGYIDLs~   85 (86)
T PHA02858         11 YVFPNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKGYIDVRH   85 (86)
T ss_pred             EecCCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCCCEEEeEc
Confidence            56678999998 99999999999999 344999998 9999999999999999 99999999999999999999984

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

Probab=97.83  E-value=8.1e-05  Score=73.80  Aligned_cols=76  Identities=28%  Similarity=0.380  Sum_probs=62.0

Q ss_pred             CCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccc---------cCCCCcccCCCEEEEEEEEEeC-----
Q 005707          259 KFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFAN---------MMGGSSLQVGQEVSVRVLRISR-----  324 (681)
Q Consensus       259 klkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~---------~~p~~~fkVGqkVkVrVL~IDk-----  324 (681)
                      +..+|+++.|+|+++.++|+||+++ .++||+|.+++.+++...         ......+++||.|+++|++++.     
T Consensus        78 ~P~~GEVv~g~V~~v~~~Gi~V~lg-~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~  156 (187)
T PRK08563         78 KPELQEVVEGEVVEVVEFGAFVRIG-PVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRP  156 (187)
T ss_pred             eccCCCEEEEEEEEEEccEEEEEEe-CceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCCC
Confidence            4557999999999999999999998 699999999988764321         0124678999999999999962     


Q ss_pred             --CeEEEEEeccC
Q 005707          325 --GQVTLTMKKED  335 (681)
Q Consensus       325 --gKI~LSLK~~~  335 (681)
                        .++.||||..-
T Consensus       157 ~~~~I~ls~~~~~  169 (187)
T PRK08563        157 RGSKIGLTMRQPG  169 (187)
T ss_pred             CCCEEEEEecCCC
Confidence              37999998763

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

Probab=97.78  E-value=6.7e-05  Score=74.85  Aligned_cols=80  Identities=28%  Similarity=0.392  Sum_probs=64.4

Q ss_pred             ccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccC---------CCCcccCCCEEEEEEEEEe---C
Q 005707          257 TTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMM---------GGSSLQVGQEVSVRVLRIS---R  324 (681)
Q Consensus       257 ~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~---------p~~~fkVGqkVkVrVL~ID---k  324 (681)
                      .-+...|++|.|.|+++.++|+||.|+ -.+||+|.+.+.++++....         -...|++|+.|++||+.+.   +
T Consensus        76 ~fkP~~gEVV~GeVv~~~~~G~fV~ig-p~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~  154 (183)
T COG1095          76 VFKPFRGEVVEGEVVEVVEFGAFVRIG-PLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSR  154 (183)
T ss_pred             EEEeccccEEEEEEEEEeecceEEEec-cccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccC
Confidence            334558999999999999999999999 89999999999887432110         1237999999999999994   2


Q ss_pred             ----CeEEEEEeccCCC
Q 005707          325 ----GQVTLTMKKEDDV  337 (681)
Q Consensus       325 ----gKI~LSLK~~~~D  337 (681)
                          -++.||||+.-..
T Consensus       155 ~~~~~~I~lTmrq~~LG  171 (183)
T COG1095         155 RPRESKIGLTMRQPGLG  171 (183)
T ss_pred             ccccceEEEEeccccCC
Confidence                6799999987443

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=97.74  E-value=0.00013  Score=60.43  Aligned_cols=61  Identities=31%  Similarity=0.384  Sum_probs=38.1

Q ss_pred             CCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707          147 PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR  217 (681)
Q Consensus       147 vGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK  217 (681)
                      +|++...+|..+.++|+|++.+.+.+.|||.+++...        +++||.|.|.|+.  ...+|+.+|+|
T Consensus         1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~~~--------~~~Gd~v~VFvY~--D~~~rl~AT~k   61 (61)
T PF13509_consen    1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVPEP--------LKVGDEVEVFVYL--DKEGRLVATTK   61 (61)
T ss_dssp             --------EEEE-SSEEEEEETT-EEEEEEGGG--------------TTSEEEEEEEE---TTS-EEEE--
T ss_pred             CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcCCC--------CCCCCEEEEEEEE--CCCCCEEEecC
Confidence            5899999999999999999998889999999988543        7899999999997  34578888875

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

Probab=97.65  E-value=0.00028  Score=62.63  Aligned_cols=64  Identities=16%  Similarity=0.302  Sum_probs=52.9

Q ss_pred             CCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCc-----------ccccccCCEEEEEEEEEeccCCc
Q 005707          147 PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDV-----------GSIVSVGQEVKVRLIEANAETGR  211 (681)
Q Consensus       147 vGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~-----------~e~fkVGd~VkVkVl~VD~ekgr  211 (681)
                      .|+++.|+|+++.++|+||.+|. +++|+|...+..+...++           ...+.+|+.|++||+.+..+.+.
T Consensus         1 kgEVi~g~V~~v~~~G~~v~~Gp-l~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~   75 (88)
T cd04462           1 KGEVVDAIVTSVNKTGFFAEVGP-LSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVDATD   75 (88)
T ss_pred             CCcEEEEEEEEEeccEEEEEEcC-ceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEccCc
Confidence            48999999999999999999988 999999999976644333           23478999999999998765443

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.

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

Probab=97.52  E-value=7.2e-05  Score=77.98  Aligned_cols=81  Identities=23%  Similarity=0.363  Sum_probs=75.5

Q ss_pred             CCCCCcEEEEEEEEEecCeeEEEE--CCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccch
Q 005707          144 DLIPGATFTGKVRSIQPFGAFIDF--GAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDD  221 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~GaFVdL--gggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~  221 (681)
                      -..++++|-+.|+.|.+-|+||.|  .++++|+|-.++||..+++.+..+.++|..=-|.|+.||+++|.|.||.+...+
T Consensus        13 yPev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekGYIDLSkrrVs~   92 (304)
T KOG2916|consen   13 YPEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRRVSP   92 (304)
T ss_pred             CCCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCCCceechhccCCH
Confidence            456799999999999999999999  577999999999999999999999999999999999999999999999998877


Q ss_pred             hhH
Q 005707          222 ISK  224 (681)
Q Consensus       222 dp~  224 (681)
                      ...
T Consensus        93 ed~   95 (304)
T KOG2916|consen   93 EDK   95 (304)
T ss_pred             HHH
Confidence            654

>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=97.48  E-value=0.00025  Score=61.16  Aligned_cols=70  Identities=26%  Similarity=0.280  Sum_probs=57.3

Q ss_pred             CcEEEEEEEEEecceEEEEeCC-CeEEEEeCCCCCcccccccCCCCcccCCCEE-EEEEEEEeCCeEEEEEe
Q 005707          263 GQDLEGTVKNLTRSGAFISLPE-GEEGFLPTSEESDDGFANMMGGSSLQVGQEV-SVRVLRISRGQVTLTMK  332 (681)
Q Consensus       263 GdIV~G~VknVt~~GaFVeIg~-GIeGLLpiSELSd~~ie~~~p~~~fkVGqkV-kVrVL~IDkgKI~LSLK  332 (681)
                      |++|.|+|...++.+++|++.+ |+.|++|..+++|..-++...-.++++||++ .+.|++.-.+.+.||.|
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 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCLSNYKGRIILTKK   72 (72)
T ss_pred             CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCCchhhCHHHHhhhhcCCCccceEEEeccccEEEEecC
Confidence            7899999999999999999998 9999999999999322222235789999999 89999434577888765

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.

>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=97.36  E-value=0.00053  Score=59.21  Aligned_cols=68  Identities=18%  Similarity=0.189  Sum_probs=56.8

Q ss_pred             CcEEEEEEEEEecCeeEEEECC-CeEEEEeccccCCccccC--cccccccCCEE-EEEEEEEeccCCceEEEEe
Q 005707          148 GATFTGKVRSIQPFGAFIDFGA-FTDGLVHVSRLSDNFVKD--VGSIVSVGQEV-KVRLIEANAETGRISLTMR  217 (681)
Q Consensus       148 GdIVeGkV~sV~d~GaFVdLgg-gV~GLVPiSELS~~~v~d--~~e~fkVGd~V-kVkVl~VD~ekgrI~LSlK  217 (681)
                      |++|.|+|..-++.+++|++.+ ++.|+||..++++..-++  .-..+++||++ ++.|+  |...+.|.+|.|
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 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCL--SNYKGRIILTKK   72 (72)
T ss_pred             CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCCchhhCHHHHhhhhcCCCccceEEE--eccccEEEEecC
Confidence            7899999999999999999965 799999999999932222  23568999999 99999  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.

>PHA02858 EIF2a-like PKR inhibitor; Provisional

Probab=97.33  E-value=0.00045  Score=61.12  Aligned_cols=72  Identities=15%  Similarity=0.215  Sum_probs=61.0

Q ss_pred             cccCCccCcEEEEEEEEEecceEEEEeCC-CeEEEEe-CCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEE
Q 005707          256 KTTKFVKGQDLEGTVKNLTRSGAFISLPE-GEEGFLP-TSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTM  331 (681)
Q Consensus       256 ~~sklkvGdIV~G~VknVt~~GaFVeIg~-GIeGLLp-iSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSL  331 (681)
                      .+.--++|+++. .|+.+.+.|+||.|-+ |++|++. .+|++..++..+  .+.+ +|..+.|+|+++|  +|-|.||.
T Consensus        10 cy~~P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~rirsi--~kll-VGk~e~v~ViRVDk~KGYIDLs~   85 (86)
T PHA02858         10 CYVFPNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADRAEKL--KKKL-VGKTINVQVIRTDKLKGYIDVRH   85 (86)
T ss_pred             EEecCCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHHHHHhh--hhhh-cCCeeEEEEEEECCCCCEEEeEc
Confidence            445567899998 8999999999999865 8999998 999999887655  6677 9999999999998  47788774

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=97.32  E-value=0.00062  Score=75.89  Aligned_cols=74  Identities=26%  Similarity=0.489  Sum_probs=57.9

Q ss_pred             CCCCCcEEEEEEEEEecC--eeEEEECCCeEEEEeccccCCcc------------ccCcccccccCCEEEEEEEEEeccC
Q 005707          144 DLIPGATFTGKVRSIQPF--GAFIDFGAFTDGLVHVSRLSDNF------------VKDVGSIVSVGQEVKVRLIEANAET  209 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~--GaFVdLgggV~GLVPiSELS~~~------------v~d~~e~fkVGd~VkVkVl~VD~ek  209 (681)
                      ...+|.+|.|+|+++.++  |+||+||.+..||||++++.+.+            ..++.+.+++||.|-|.|+.--...
T Consensus        22 ~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke~~~~  101 (414)
T TIGR00757        22 RQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVKEPRGN  101 (414)
T ss_pred             cCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEeeCCcCC
Confidence            345799999999999998  99999999999999999997531            3345567999999999999833333


Q ss_pred             CceEEEEe
Q 005707          210 GRISLTMR  217 (681)
Q Consensus       210 grI~LSlK  217 (681)
                      +.-.||..
T Consensus       102 Kgp~lT~~  109 (414)
T TIGR00757       102 KGARLTTD  109 (414)
T ss_pred             CCCeEEEE
Confidence            44444443

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.

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=97.32  E-value=0.00072  Score=55.99  Aligned_cols=61  Identities=36%  Similarity=0.388  Sum_probs=37.9

Q ss_pred             cCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCeEEEEEe
Q 005707          262 KGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQVTLTMK  332 (681)
Q Consensus       262 vGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgKI~LSLK  332 (681)
                      +|++...+|..++++|+|++.+.+-+-|||.++..          ..+++||.|.|.|-.-..+|+..|+|
T Consensus         1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~----------~~~~~Gd~v~VFvY~D~~~rl~AT~k   61 (61)
T PF13509_consen    1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVP----------EPLKVGDEVEVFVYLDKEGRLVATTK   61 (61)
T ss_dssp             --------EEEE-SSEEEEEETT-EEEEEEGGG----------------TTSEEEEEEEE-TTS-EEEE--
T ss_pred             CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcC----------CCCCCCCEEEEEEEECCCCCEEEecC
Confidence            48899999999999999999998899999988764          34799999999977755789999886

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=97.23  E-value=0.00088  Score=73.58  Aligned_cols=68  Identities=19%  Similarity=0.243  Sum_probs=57.5

Q ss_pred             CCCCcEEEEEEEEEecC-eeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCC---ceEEEEecc
Q 005707          145 LIPGATFTGKVRSIQPF-GAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETG---RISLTMRES  219 (681)
Q Consensus       145 LkvGdIVeGkV~sV~d~-GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekg---rI~LSlK~l  219 (681)
                      -++|+++.|+|.++... ++||+||+ +.|+||..+..      +.+.|++||.++|.|.+|+...+   .|.||+...
T Consensus       136 ~~~Geiv~g~V~r~~~~~~i~vdlg~-~ea~LP~~eqi------p~E~~~~Gdrik~~i~~V~~~~k~gp~IilSRt~p  207 (374)
T PRK12328        136 KKVGKIVFGTVVRVDNEENTFIEIDE-IRAVLPMKNRI------KGEKFKVGDVVKAVLKRVKIDKNNGILIELSRTSP  207 (374)
T ss_pred             HhcCcEEEEEEEEEecCCCEEEEcCC-eEEEeCHHHcC------CCCcCCCCCEEEEEEEEEecCCCCCCEEEEEcCCH
Confidence            35899999999999974 58999986 99999987764      45679999999999999998765   788888743

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

Probab=97.18  E-value=0.0019  Score=64.32  Aligned_cols=74  Identities=19%  Similarity=0.262  Sum_probs=58.0

Q ss_pred             CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCcccc------------CcccccccCCEEEEEEEEEeccCC-
Q 005707          144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVK------------DVGSIVSVGQEVKVRLIEANAETG-  210 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~------------d~~e~fkVGd~VkVkVl~VD~ekg-  210 (681)
                      ....|++++|+|+++.++|+||.+|. .++|||.++|.++..-            +-...+..|+.|++||+.+..+.+ 
T Consensus        78 rPf~gEVv~g~V~~v~~~G~~v~~Gp-~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~  156 (176)
T PTZ00162         78 KPFKDEVLDAIVTDVNKLGFFAQAGP-LKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASN  156 (176)
T ss_pred             ecCCCCEEEEEEEEEecceEEEEeeC-eEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCC
Confidence            46689999999999999999999976 7899999999854221            123468999999999988765443 


Q ss_pred             -ceEEEEec
Q 005707          211 -RISLTMRE  218 (681)
Q Consensus       211 -rI~LSlK~  218 (681)
                       ++.+|||+
T Consensus       157 ~~~i~T~~~  165 (176)
T PTZ00162        157 LFAIATINS  165 (176)
T ss_pred             cEEEEEecC
Confidence             46667774

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

Probab=97.18  E-value=0.001  Score=75.91  Aligned_cols=163  Identities=21%  Similarity=0.395  Sum_probs=109.1

Q ss_pred             CCCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEec
Q 005707          139 PVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRE  218 (681)
Q Consensus       139 ~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~  218 (681)
                      .-++.+++.|..+.|+|.++..||+||+|..++.|++|.++++..      ..|.+|+.+-|.+..+-+.++.|.+....
T Consensus       114 ~c~~~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~------~~~~vgdeiiV~v~~vr~~~geidf~~~~  187 (715)
T COG1107         114 SCTMEDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGD------PDYAVGDEIIVQVSDVRPEKGEIDFEPVG  187 (715)
T ss_pred             ccchhhcccceeeeccccchhhhcceeecChhhhccccccccCCC------CCCCCCCeEEEEeeccCCCCCccceeecC
Confidence            345889999999999999999999999999999999999998762      13789999999999998888988887776


Q ss_pred             cchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcE--EEEEEEEEecc-eE-EEEeCCCeEEEEeCCC
Q 005707          219 SDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQD--LEGTVKNLTRS-GA-FISLPEGEEGFLPTSE  294 (681)
Q Consensus       219 l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdI--V~G~VknVt~~-Ga-FVeIg~GIeGLLpiSE  294 (681)
                      +......+        .++.          -.+....-+.+ ..|+.  +.|.|+.|... |= ...|- .-.|+++..-
T Consensus       188 ~~~Y~~~~--------~~ke----------~~r~~i~~id~-~ig~tV~I~GeV~qikqT~GPTVFtlt-Detg~i~aAA  247 (715)
T COG1107         188 LDRYREVQ--------VEKE----------LPRTLIDDLDE-MIGKTVRIEGEVTQIKQTSGPTVFTLT-DETGAIWAAA  247 (715)
T ss_pred             Cccchhhh--------hhhh----------cccccHHHHHh-hcCceEEEEEEEEEEEEcCCCEEEEEe-cCCCceehhh
Confidence            55222110        0000          00111122333 56776  58999998544 32 22343 4456777654


Q ss_pred             CCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEE
Q 005707          295 ESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTM  331 (681)
Q Consensus       295 LSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSL  331 (681)
                      +....+   ...-.+++|+.|.+. =.++  .|++.+-+
T Consensus       248 Fe~aGv---RAyP~IevGdiV~Vi-G~V~~r~g~lQiE~  282 (715)
T COG1107         248 FEEAGV---RAYPEIEVGDIVEVI-GEVTRRDGRLQIEI  282 (715)
T ss_pred             hccCCc---ccCCCCCCCceEEEE-EEEeecCCcEEEee
Confidence            443332   224568999998753 2233  47776643

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

Probab=97.15  E-value=0.0022  Score=66.53  Aligned_cols=73  Identities=23%  Similarity=0.383  Sum_probs=64.3

Q ss_pred             CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCcc----ccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707          144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNF----VKDVGSIVSVGQEVKVRLIEANAETGRISLTMR  217 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~----v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK  217 (681)
                      ..++||+|-|+|..+...+-.|||++...+++|.+++.+..    ..+++..|++||.|.|+|..+|+ .+.+.|++|
T Consensus        61 iP~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~-~~~~~L~~k  137 (239)
T COG1097          61 IPEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDR-DGEVELTLK  137 (239)
T ss_pred             cCCCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhcccccccccccccccccCCEEEEEEEEccC-CCceEEEee
Confidence            56789999999999999999999999999999999996544    35778899999999999999985 577788875

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

Probab=97.11  E-value=0.0027  Score=56.54  Aligned_cols=72  Identities=18%  Similarity=0.134  Sum_probs=61.1

Q ss_pred             CCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEec
Q 005707          145 LIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRE  218 (681)
Q Consensus       145 LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~  218 (681)
                      .++||+|-|+|+.+...+.+|+|+....|+||..++... .+..+..+++||.|.|+|..+|+. ....||+..
T Consensus         4 P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV~~~~~~-~~~eLtc~~   75 (86)
T cd05790           4 PAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGA-TKRNRPNLNVGDLVYARVVKANRD-MEPELSCVD   75 (86)
T ss_pred             CCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcccc-cccccccCCCCCEEEEEEEecCCC-CCeEEEEeC
Confidence            468999999999999999999999889999999887543 344566799999999999999865 457888874

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".

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=97.10  E-value=0.00086  Score=74.78  Aligned_cols=65  Identities=26%  Similarity=0.342  Sum_probs=52.3

Q ss_pred             cCCccCcEEEEEEEEEecc--eEEEEeCCCeEEEEeCCCCCccccc----------ccCCCCcccCCCEEEEEEEEE
Q 005707          258 TKFVKGQDLEGTVKNLTRS--GAFISLPEGEEGFLPTSEESDDGFA----------NMMGGSSLQVGQEVSVRVLRI  322 (681)
Q Consensus       258 sklkvGdIV~G~VknVt~~--GaFVeIg~GIeGLLpiSELSd~~ie----------~~~p~~~fkVGqkVkVrVL~I  322 (681)
                      ....+|+++.|+|++|.++  |+||+|+.+..||+|.+++.+....          ..+....+++||.|.|.|.+-
T Consensus        21 ~~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke   97 (414)
T TIGR00757        21 SRQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVKE   97 (414)
T ss_pred             CcCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEeeC
Confidence            3467999999999999999  9999999999999999998653100          011234699999999999884

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.

>PRK05054 exoribonuclease II; Provisional

Probab=97.04  E-value=0.0018  Score=75.84  Aligned_cols=69  Identities=16%  Similarity=0.297  Sum_probs=54.5

Q ss_pred             CcEEEEEEEEEecceEEEEeCC-CeEEEEeCCCCCccccc-----c-----cCCCCcccCCCEEEEEEEEEe--CCeEEE
Q 005707          263 GQDLEGTVKNLTRSGAFISLPE-GEEGFLPTSEESDDGFA-----N-----MMGGSSLQVGQEVSVRVLRIS--RGQVTL  329 (681)
Q Consensus       263 GdIV~G~VknVt~~GaFVeIg~-GIeGLLpiSELSd~~ie-----~-----~~p~~~fkVGqkVkVrVL~ID--kgKI~L  329 (681)
                      |+.+.|.|+.|+.+|+||+|.+ |++||||.+.|.+.+..     +     ......|+.||.|+|+|.++|  +++|.+
T Consensus       562 ~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~~~~~i~~  641 (644)
T PRK05054        562 DTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETRSIIA  641 (644)
T ss_pred             CeEEEEEEEeeecCcEEEEEeCCceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEccccCeEEE
Confidence            4599999999999999999965 79999999998653110     0     011357999999999999998  577776


Q ss_pred             EE
Q 005707          330 TM  331 (681)
Q Consensus       330 SL  331 (681)
                      .+
T Consensus       642 ~~  643 (644)
T PRK05054        642 RP  643 (644)
T ss_pred             EE
Confidence            54

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

Probab=96.99  E-value=0.012  Score=61.11  Aligned_cols=80  Identities=24%  Similarity=0.243  Sum_probs=68.0

Q ss_pred             ccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCccccc--ccCCCCcccCCCEEEEEEEEEeC-CeEEEEEeccCCC
Q 005707          261 VKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFA--NMMGGSSLQVGQEVSVRVLRISR-GQVTLTMKKEDDV  337 (681)
Q Consensus       261 kvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie--~~~p~~~fkVGqkVkVrVL~IDk-gKI~LSLK~~~~D  337 (681)
                      ++||+|-|+|..+...+-.|+|+.-..+++|.+++.+..++  ....+..|++||.|.++|..+|+ +.+.|++|....-
T Consensus        63 ~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~~~~G  142 (239)
T COG1097          63 EVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKDEGLG  142 (239)
T ss_pred             CCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhcccccccccccccccccCCEEEEEEEEccCCCceEEEeecCCCc
Confidence            57999999999999999999999889999999999766654  23467899999999999999985 8899999776444


Q ss_pred             cCC
Q 005707          338 GSN  340 (681)
Q Consensus       338 P~e  340 (681)
                      ++.
T Consensus       143 kL~  145 (239)
T COG1097         143 KLK  145 (239)
T ss_pred             ccc
Confidence            433

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

Probab=96.94  E-value=0.0036  Score=55.64  Aligned_cols=61  Identities=15%  Similarity=0.212  Sum_probs=47.6

Q ss_pred             cCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCccccccc---------CCCCcccCCCEEEEEEEEEe
Q 005707          262 KGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANM---------MGGSSLQVGQEVSVRVLRIS  323 (681)
Q Consensus       262 vGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~---------~p~~~fkVGqkVkVrVL~ID  323 (681)
                      +|+++.|+|++++++|+||.++ .+++|+|...+..+..-+.         .....+++|+.|++||+.+.
T Consensus         1 kgEVi~g~V~~v~~~G~~v~~G-pl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~   70 (88)
T cd04462           1 KGEVVDAIVTSVNKTGFFAEVG-PLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTR   70 (88)
T ss_pred             CCcEEEEEEEEEeccEEEEEEc-CceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEE
Confidence            5899999999999999999997 8889988877654321110         11356899999999999884

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.

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

Probab=96.85  E-value=0.004  Score=61.99  Aligned_cols=75  Identities=19%  Similarity=0.248  Sum_probs=57.0

Q ss_pred             CCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcc-cccc---------cCCCCcccCCCEEEEEEEEEe----C
Q 005707          259 KFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDD-GFAN---------MMGGSSLQVGQEVSVRVLRIS----R  324 (681)
Q Consensus       259 klkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~-~ie~---------~~p~~~fkVGqkVkVrVL~ID----k  324 (681)
                      +.-+|+++.|+|++++++|+||.++ -.++|+|.+.+.+. .++.         ......++.|+.|++||+.+.    .
T Consensus        78 rPf~gEVv~g~V~~v~~~G~~v~~G-p~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~  156 (176)
T PTZ00162         78 KPFKDEVLDAIVTDVNKLGFFAQAG-PLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASN  156 (176)
T ss_pred             ecCCCCEEEEEEEEEecceEEEEee-CeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCC
Confidence            3458999999999999999999997 66799999888643 1111         111356999999999999983    2


Q ss_pred             CeEEEEEecc
Q 005707          325 GQVTLTMKKE  334 (681)
Q Consensus       325 gKI~LSLK~~  334 (681)
                      .++.+|||+-
T Consensus       157 ~~~i~T~~~~  166 (176)
T PTZ00162        157 LFAIATINSD  166 (176)
T ss_pred             cEEEEEecCC
Confidence            4566688764

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=96.50  E-value=0.0085  Score=67.21  Aligned_cols=68  Identities=9%  Similarity=0.051  Sum_probs=56.3

Q ss_pred             CCCCcEEEEEEEEEecCeeEEEEC---C--CeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccC---CceEEEE
Q 005707          145 LIPGATFTGKVRSIQPFGAFIDFG---A--FTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAET---GRISLTM  216 (681)
Q Consensus       145 LkvGdIVeGkV~sV~d~GaFVdLg---g--gV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ek---grI~LSl  216 (681)
                      -++|+++.|+|.++...+++|+|+   |  ++.|+||..+..      +.+.|++|+.|+|.|..|....   -+|.||+
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            348999999999999999999994   3  389999987763      4566999999999999998753   2688888


Q ss_pred             ec
Q 005707          217 RE  218 (681)
Q Consensus       217 K~  218 (681)
                      ..
T Consensus       224 t~  225 (449)
T PRK12329        224 AN  225 (449)
T ss_pred             CC
Confidence            74

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

Probab=96.47  E-value=0.012  Score=59.17  Aligned_cols=73  Identities=21%  Similarity=0.346  Sum_probs=64.0

Q ss_pred             cCCCCCCcEEEEEEEEEecCeeEEEECC----------CeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCc
Q 005707          142 NEDLIPGATFTGKVRSIQPFGAFIDFGA----------FTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGR  211 (681)
Q Consensus       142 ~~~LkvGdIVeGkV~sV~d~GaFVdLgg----------gV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgr  211 (681)
                      ...++.|++|-|+|+++....+.|++.+          ...|-+|++++.+.++.+..+.|++||.|+++|++.-   ..
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            4568899999999999999999887731          2568899999999999999999999999999999962   67


Q ss_pred             eEEEEe
Q 005707          212 ISLTMR  217 (681)
Q Consensus       212 I~LSlK  217 (681)
                      +.||++
T Consensus       136 ~~Lst~  141 (188)
T COG1096         136 IQLSTK  141 (188)
T ss_pred             eEEEec
Confidence            888887

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

Probab=96.43  E-value=0.0063  Score=69.74  Aligned_cols=76  Identities=17%  Similarity=0.287  Sum_probs=61.7

Q ss_pred             ccccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCeEEEEEecc
Q 005707          255 MKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQVTLTMKKE  334 (681)
Q Consensus       255 ~~~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgKI~LSLK~~  334 (681)
                      -.+.++..|..++|+|.++.+||+||++...+.||+|.++++..        ..|.+|+.+-|.|..+..++-.++++..
T Consensus       115 c~~~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~--------~~~~vgdeiiV~v~~vr~~~geidf~~~  186 (715)
T COG1107         115 CTMEDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGD--------PDYAVGDEIIVQVSDVRPEKGEIDFEPV  186 (715)
T ss_pred             cchhhcccceeeeccccchhhhcceeecChhhhccccccccCCC--------CCCCCCCeEEEEeeccCCCCCccceeec
Confidence            45788999999999999999999999999999999999988752        4679999999999999644333444444


Q ss_pred             CCCc
Q 005707          335 DDVG  338 (681)
Q Consensus       335 ~~DP  338 (681)
                      ..++
T Consensus       187 ~~~~  190 (715)
T COG1107         187 GLDR  190 (715)
T ss_pred             CCcc
Confidence            3333

>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=96.43  E-value=0.0068  Score=53.61  Aligned_cols=60  Identities=15%  Similarity=0.197  Sum_probs=41.7

Q ss_pred             CCCcEEEEEEEEEecCeeEEEEC------------------CCeEEEEeccccCCcccc--CcccccccCCEEEEEEEEE
Q 005707          146 IPGATFTGKVRSIQPFGAFIDFG------------------AFTDGLVHVSRLSDNFVK--DVGSIVSVGQEVKVRLIEA  205 (681)
Q Consensus       146 kvGdIVeGkV~sV~d~GaFVdLg------------------ggV~GLVPiSELS~~~v~--d~~e~fkVGd~VkVkVl~V  205 (681)
                      ++|++|.|+|+++++.-++++|-                  ....|+|+.+++......  .+.+.|++||.|+|+|+++
T Consensus         3 ~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~ViSl   82 (82)
T PF10447_consen    3 KVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVISL   82 (82)
T ss_dssp             -TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEEEE
T ss_pred             CCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhccCCCCEEEEEEeeC
Confidence            67999999999999999887762                  246799999998765443  3578899999999999974

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.

>TIGR02062 RNase_B exoribonuclease II

Probab=96.30  E-value=0.009  Score=70.10  Aligned_cols=67  Identities=13%  Similarity=0.363  Sum_probs=51.8

Q ss_pred             CcEEEEEEEEEecceEEEEe-CCCeEEEEeCCCCCc--ccc--c------ccCCCCcccCCCEEEEEEEEEe--CCeEEE
Q 005707          263 GQDLEGTVKNLTRSGAFISL-PEGEEGFLPTSEESD--DGF--A------NMMGGSSLQVGQEVSVRVLRIS--RGQVTL  329 (681)
Q Consensus       263 GdIV~G~VknVt~~GaFVeI-g~GIeGLLpiSELSd--~~i--e------~~~p~~~fkVGqkVkVrVL~ID--kgKI~L  329 (681)
                      |+.+.|.|..++.+|+||+| ..|++||||.+.+.+  +.+  +      .+.....|+.||.|+|+|.++|  +++|.+
T Consensus       558 ~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd~~~~~i~~  637 (639)
T TIGR02062       558 NTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMETRSIIA  637 (639)
T ss_pred             CcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEEEeccccCcEee
Confidence            45899999999999999999 558999999998865  221  0      1111236999999999999998  455554

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.

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

Probab=96.30  E-value=0.021  Score=50.98  Aligned_cols=72  Identities=19%  Similarity=0.146  Sum_probs=59.6

Q ss_pred             CccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC-CeEEEEEecc
Q 005707          260 FVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR-GQVTLTMKKE  334 (681)
Q Consensus       260 lkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk-gKI~LSLK~~  334 (681)
                      -++||.|-|+|+.+...+.+|+|+.-..|++|...+....   .+.+..|++||.|-|+|..+++ ....|++...
T Consensus         4 P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~gat---k~~rp~L~~GDlV~ArV~~~~~~~~~eLtc~~~   76 (86)
T cd05790           4 PAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGAT---KRNRPNLNVGDLVYARVVKANRDMEPELSCVDS   76 (86)
T ss_pred             CCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHccccc---ccccccCCCCCEEEEEEEecCCCCCeEEEEeCC
Confidence            3589999999999999999999998899999997764332   1225789999999999999985 5688888653

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".

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

Probab=96.21  E-value=0.0052  Score=74.48  Aligned_cols=80  Identities=25%  Similarity=0.277  Sum_probs=70.7

Q ss_pred             CCCCCCcEEEEEEEEEecCe---eEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEecc
Q 005707          143 EDLIPGATFTGKVRSIQPFG---AFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRES  219 (681)
Q Consensus       143 ~~LkvGdIVeGkV~sV~d~G---aFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l  219 (681)
                      +.+..|.+|.++|++|...-   +-|.+.+|++|+||...+++..+.+|...+++|+.|.|+|+.+|.++=-+.||++..
T Consensus       981 et~~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~id~e~f~v~Ls~r~s 1060 (1299)
T KOG1856|consen  981 ETFYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVELSCRTS 1060 (1299)
T ss_pred             hHhccCceEEEeeeEEEecccceeEEEecCCCceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhhhhhhhhH
Confidence            35779999999999998554   457888889999999999999999999999999999999999999888889998876


Q ss_pred             chh
Q 005707          220 DDI  222 (681)
Q Consensus       220 ~~d  222 (681)
                      ...
T Consensus      1061 dlk 1063 (1299)
T KOG1856|consen 1061 DLK 1063 (1299)
T ss_pred             Hhh
Confidence            554

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=96.14  E-value=0.018  Score=63.63  Aligned_cols=69  Identities=22%  Similarity=0.337  Sum_probs=56.1

Q ss_pred             cccCC--ccCcEEEEEEEEEecc-eEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC--C---eE
Q 005707          256 KTTKF--VKGQDLEGTVKNLTRS-GAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR--G---QV  327 (681)
Q Consensus       256 ~~skl--kvGdIV~G~VknVt~~-GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk--g---KI  327 (681)
                      .+..|  +.|+++.|+|.++... ++||+|+ +.+|+||..+..        |.+.|++||.++|.|.++++  +   +|
T Consensus       130 i~~ey~~~~Geiv~g~V~r~~~~~~i~vdlg-~~ea~LP~~eqi--------p~E~~~~Gdrik~~i~~V~~~~k~gp~I  200 (374)
T PRK12328        130 IFEKYKKKVGKIVFGTVVRVDNEENTFIEID-EIRAVLPMKNRI--------KGEKFKVGDVVKAVLKRVKIDKNNGILI  200 (374)
T ss_pred             HHHHHHHhcCcEEEEEEEEEecCCCEEEEcC-CeEEEeCHHHcC--------CCCcCCCCCEEEEEEEEEecCCCCCCEE
Confidence            44444  4899999999999864 6999997 899999987643        57889999999999999952  3   67


Q ss_pred             EEEEec
Q 005707          328 TLTMKK  333 (681)
Q Consensus       328 ~LSLK~  333 (681)
                      .||+..
T Consensus       201 ilSRt~  206 (374)
T PRK12328        201 ELSRTS  206 (374)
T ss_pred             EEEcCC
Confidence            788743

>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=96.01  E-value=0.012  Score=52.08  Aligned_cols=62  Identities=15%  Similarity=0.161  Sum_probs=41.3

Q ss_pred             ccCcEEEEEEEEEecceEEEEeC------------------CCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEE
Q 005707          261 VKGQDLEGTVKNLTRSGAFISLP------------------EGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI  322 (681)
Q Consensus       261 kvGdIV~G~VknVt~~GaFVeIg------------------~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~I  322 (681)
                      ++|++|.|+|+++++.-++++|-                  +...|+++.+++.....+.....+.|++||.|.++|++.
T Consensus         3 ~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~ViSl   82 (82)
T PF10447_consen    3 KVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVISL   82 (82)
T ss_dssp             -TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEEEE
T ss_pred             CCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhccCCCCEEEEEEeeC
Confidence            58999999999999998888752                  256789999887655444445578899999999999974

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.

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

Probab=95.96  E-value=0.0037  Score=65.61  Aligned_cols=75  Identities=23%  Similarity=0.363  Sum_probs=66.6

Q ss_pred             ccCcEEEEEEEEEecceEEEEeC--CCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCC
Q 005707          261 VKGQDLEGTVKNLTRSGAFISLP--EGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDD  336 (681)
Q Consensus       261 kvGdIV~G~VknVt~~GaFVeIg--~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~  336 (681)
                      .++++|-+.|+.|.+.|+||.|-  ++++|++-.+||+..++..+  ....++|..=.|.||++|  +|-|.||++...+
T Consensus        15 ev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI--~klirVGr~E~vvVlrVDkekGYIDLSkrrVs~   92 (304)
T KOG2916|consen   15 EVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSI--QKLIRVGRNEPVVVLRVDKEKGYIDLSKRRVSP   92 (304)
T ss_pred             CcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHHHHH--HHHHhcCCcceEEEEEEcCCCCceechhccCCH
Confidence            47999999999999999999985  59999999999999887655  788999999999999998  4779999988754


Q ss_pred             C
Q 005707          337 V  337 (681)
Q Consensus       337 D  337 (681)
                      +
T Consensus        93 e   93 (304)
T KOG2916|consen   93 E   93 (304)
T ss_pred             H
Confidence            4

>PRK10811 rne ribonuclease E; Reviewed

Probab=95.80  E-value=0.017  Score=69.79  Aligned_cols=63  Identities=27%  Similarity=0.369  Sum_probs=50.7

Q ss_pred             ccCcEEEEEEEEEecc--eEEEEeCCCeEEEEeCCCCCccccccc-------CCCCcccCCCEEEEEEEEEe
Q 005707          261 VKGQDLEGTVKNLTRS--GAFISLPEGEEGFLPTSEESDDGFANM-------MGGSSLQVGQEVSVRVLRIS  323 (681)
Q Consensus       261 kvGdIV~G~VknVt~~--GaFVeIg~GIeGLLpiSELSd~~ie~~-------~p~~~fkVGqkVkVrVL~ID  323 (681)
                      .+|.||.|+|.+|.+.  ++||+|+.|..||||+++.....+.+.       +....++.||.|.|.|.+-.
T Consensus        37 ~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa  108 (1068)
T PRK10811         37 KKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEE  108 (1068)
T ss_pred             CccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeecc
Confidence            4899999999999877  999999999999999998854332111       12346899999999999863

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=95.72  E-value=0.033  Score=62.62  Aligned_cols=70  Identities=17%  Similarity=0.306  Sum_probs=56.4

Q ss_pred             cccCC--ccCcEEEEEEEEEecceEEEEeC----C-CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCC---
Q 005707          256 KTTKF--VKGQDLEGTVKNLTRSGAFISLP----E-GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRG---  325 (681)
Q Consensus       256 ~~skl--kvGdIV~G~VknVt~~GaFVeIg----~-GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkg---  325 (681)
                      .+.+|  ++|+++.|+|.++.+.+++|+++    . +++|+||.++.        .|.+.|++|+.|+|.|.+|.++   
T Consensus       144 i~~ef~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eq--------ip~E~y~~Gdrika~i~~V~~~~~k  215 (449)
T PRK12329        144 IQEEFQDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQ--------LPNDNYRANATFKVFLKEVSEGPRR  215 (449)
T ss_pred             HHHHHHHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHc--------CCCCcCCCCCEEEEEEEEeecCCCC
Confidence            34444  48999999999999999999993    2 49999998764        3578899999999999999532   


Q ss_pred             --eEEEEEec
Q 005707          326 --QVTLTMKK  333 (681)
Q Consensus       326 --KI~LSLK~  333 (681)
                        +|.||...
T Consensus       216 GpqIilSRt~  225 (449)
T PRK12329        216 GPQLFVSRAN  225 (449)
T ss_pred             CCEEEEEcCC
Confidence              58888743

>PRK10811 rne ribonuclease E; Reviewed

Probab=95.70  E-value=0.025  Score=68.44  Aligned_cols=60  Identities=25%  Similarity=0.560  Sum_probs=49.5

Q ss_pred             CCCcEEEEEEEEEecC--eeEEEECCCeEEEEeccccCCcccc---------CcccccccCCEEEEEEEEE
Q 005707          146 IPGATFTGKVRSIQPF--GAFIDFGAFTDGLVHVSRLSDNFVK---------DVGSIVSVGQEVKVRLIEA  205 (681)
Q Consensus       146 kvGdIVeGkV~sV~d~--GaFVdLgggV~GLVPiSELS~~~v~---------d~~e~fkVGd~VkVkVl~V  205 (681)
                      .+|.||.|+|.+|.+.  ++||+||.+..||||+.++...++.         .....+++||.|-|.|..-
T Consensus        37 ~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KE  107 (1068)
T PRK10811         37 KKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKE  107 (1068)
T ss_pred             CccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeec
Confidence            4799999999999974  8999999999999999999644322         2244688999999999874

>COG0557 VacB Exoribonuclease R [Transcription]

Probab=95.58  E-value=0.033  Score=66.14  Aligned_cols=75  Identities=29%  Similarity=0.506  Sum_probs=59.6

Q ss_pred             ccCCccCcEEEEEEEEEecceEEEEeCC-CeEEEEeCCCCCccccccc---------CCCCcccCCCEEEEEEEEEe--C
Q 005707          257 TTKFVKGQDLEGTVKNLTRSGAFISLPE-GEEGFLPTSEESDDGFANM---------MGGSSLQVGQEVSVRVLRIS--R  324 (681)
Q Consensus       257 ~sklkvGdIV~G~VknVt~~GaFVeIg~-GIeGLLpiSELSd~~ie~~---------~p~~~fkVGqkVkVrVL~ID--k  324 (681)
                      +.+-.+|+.+.|+|.+++.+|+||.|.+ +++|++|.+.+...++...         .-...|+.||.|+++|..++  .
T Consensus       617 ~m~~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~~  696 (706)
T COG0557         617 YMKKRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDLDE  696 (706)
T ss_pred             HHHHhcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEcccc
Confidence            3445689999999999999999999987 5999999999985332111         11346999999999999996  5


Q ss_pred             CeEEEEE
Q 005707          325 GQVTLTM  331 (681)
Q Consensus       325 gKI~LSL  331 (681)
                      +++.+++
T Consensus       697 ~~i~~~~  703 (706)
T COG0557         697 RKIDFEL  703 (706)
T ss_pred             cceEEEe
Confidence            7777765

>PRK11712 ribonuclease G; Provisional

Probab=95.17  E-value=0.05  Score=62.17  Aligned_cols=73  Identities=27%  Similarity=0.478  Sum_probs=54.6

Q ss_pred             CCCCcEEEEEEEEEecC--eeEEEECCCeEEEEeccccCCc------------cccCcccccccCCEEEEEEEEEeccCC
Q 005707          145 LIPGATFTGKVRSIQPF--GAFIDFGAFTDGLVHVSRLSDN------------FVKDVGSIVSVGQEVKVRLIEANAETG  210 (681)
Q Consensus       145 LkvGdIVeGkV~sV~d~--GaFVdLgggV~GLVPiSELS~~------------~v~d~~e~fkVGd~VkVkVl~VD~ekg  210 (681)
                      ..+|.||.|+|.+|.+.  ++||+||.+..||+|..++...            ....+...+++||.|-|.|+.--...+
T Consensus        36 ~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke~~~~K  115 (489)
T PRK11712         36 GIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKDPLGTK  115 (489)
T ss_pred             cccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeCCcCCC
Confidence            45799999999999984  8999999999999999998321            011234558999999999998543444


Q ss_pred             ceEEEEe
Q 005707          211 RISLTMR  217 (681)
Q Consensus       211 rI~LSlK  217 (681)
                      .-.||..
T Consensus       116 G~~lT~~  122 (489)
T PRK11712        116 GARLTTD  122 (489)
T ss_pred             CCeEEEE
Confidence            4444443

>PRK11712 ribonuclease G; Provisional

Probab=94.93  E-value=0.041  Score=62.83  Aligned_cols=64  Identities=19%  Similarity=0.239  Sum_probs=49.1

Q ss_pred             CCccCcEEEEEEEEEecc--eEEEEeCCCeEEEEeCCCCCcccc----------cccCCCCcccCCCEEEEEEEEE
Q 005707          259 KFVKGQDLEGTVKNLTRS--GAFISLPEGEEGFLPTSEESDDGF----------ANMMGGSSLQVGQEVSVRVLRI  322 (681)
Q Consensus       259 klkvGdIV~G~VknVt~~--GaFVeIg~GIeGLLpiSELSd~~i----------e~~~p~~~fkVGqkVkVrVL~I  322 (681)
                      ...+|.++.|+|.+|.+.  +|||+|+.+..||+|.+++.....          ........++.||.|-|.|.+-
T Consensus        35 ~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke  110 (489)
T PRK11712         35 RGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKD  110 (489)
T ss_pred             ccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeC
Confidence            456899999999999887  899999999999999998731100          0001134589999999998885

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

Probab=94.89  E-value=0.03  Score=68.31  Aligned_cols=77  Identities=23%  Similarity=0.357  Sum_probs=62.6

Q ss_pred             cccCCccCcEEEEEEEEEecce---EEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCeE--EEE
Q 005707          256 KTTKFVKGQDLEGTVKNLTRSG---AFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQV--TLT  330 (681)
Q Consensus       256 ~~sklkvGdIV~G~VknVt~~G---aFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgKI--~LS  330 (681)
                      ..+.+.+|.+|.++|++|+..-   +-|.+..|+.|+|+..++++..+  .+|..++++||.|.|+|+++|..++  .||
T Consensus       979 t~et~~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~Sd~~v--~~p~~~v~vgq~v~~kvi~id~e~f~v~Ls 1056 (1299)
T KOG1856|consen  979 TPETFYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDV--RRPENRVKVGQTVYCKVIKIDKERFSVELS 1056 (1299)
T ss_pred             ChhHhccCceEEEeeeEEEecccceeEEEecCCCceeeeccccChhhc--cCHHHhhccCceEEEEeeeeeHhhhhhhhh
Confidence            3455789999999999997553   46789999999999999999654  3578999999999999999997664  456


Q ss_pred             Eecc
Q 005707          331 MKKE  334 (681)
Q Consensus       331 LK~~  334 (681)
                      +|..
T Consensus      1057 ~r~s 1060 (1299)
T KOG1856|consen 1057 CRTS 1060 (1299)
T ss_pred             hhhH
Confidence            5544

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

Probab=94.66  E-value=0.2  Score=50.68  Aligned_cols=106  Identities=16%  Similarity=0.182  Sum_probs=73.0

Q ss_pred             ccCCccCcEEEEEEEEEecceEEEEeCC----------CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCe
Q 005707          257 TTKFVKGQDLEGTVKNLTRSGAFISLPE----------GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQ  326 (681)
Q Consensus       257 ~sklkvGdIV~G~VknVt~~GaFVeIg~----------GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgK  326 (681)
                      ..-.++|++|-|.|+.+....+.|++-.          -..|-+|++...+.+.++.  .+.|++||.|+++|++.- --
T Consensus        59 ~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~--~d~f~~GDivrA~Vis~~-~~  135 (188)
T COG1096          59 PPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKL--SDAFRIGDIVRARVISTG-DP  135 (188)
T ss_pred             CCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEeccccccccc--ccccccccEEEEEEEecC-CC
Confidence            4457889999999999999999998752          1456789999998887655  799999999999999985 45


Q ss_pred             EEEEEeccCCCcCCcceeeeEEEEeecccEEEEEEcCCeEEEeeCCccc
Q 005707          327 VTLTMKKEDDVGSNLQLTQGVIHAATNPFVLAFRSNKDISSFLDERDKS  375 (681)
Q Consensus       327 I~LSLK~~~~DP~e~~lv~G~V~~~i~~fGlfV~l~~gI~GfIp~~els  375 (681)
                      +.||.+.-         --|.|...-..-|..+.. .|..=.+|.....
T Consensus       136 ~~Lst~~~---------dlGVI~A~CsrC~~~L~~-~~~~l~Cp~Cg~t  174 (188)
T COG1096         136 IQLSTKGN---------DLGVIYARCSRCRAPLVK-KGNMLKCPNCGNT  174 (188)
T ss_pred             eEEEecCC---------cceEEEEEccCCCcceEE-cCcEEECCCCCCE
Confidence            66666432         126666322222333333 5555555554443

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

Probab=93.57  E-value=0.32  Score=48.21  Aligned_cols=65  Identities=18%  Similarity=0.342  Sum_probs=48.1

Q ss_pred             CCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCc-----------ccccccCCEEEEEEEEEeccCC
Q 005707          145 LIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDV-----------GSIVSVGQEVKVRLIEANAETG  210 (681)
Q Consensus       145 LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~-----------~e~fkVGd~VkVkVl~VD~ekg  210 (681)
                      .--|++++|.|+.|...|+|+++|. ++.++-...+..++--+|           ....++|..|+++|+..-.+..
T Consensus        79 pfKGEVvdgvV~~Vnk~G~F~~~GP-l~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr~~~~  154 (170)
T KOG3298|consen   79 PFKGEVVDGVVTKVNKMGVFARSGP-LEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTRVDET  154 (170)
T ss_pred             ecCCcEEEEEEEEEeeeeEEEeccc-eEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEEEeee
Confidence            3469999999999999999999998 888876555543222111           2268899999999998654443

>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=93.40  E-value=0.42  Score=45.26  Aligned_cols=61  Identities=23%  Similarity=0.361  Sum_probs=46.4

Q ss_pred             CCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccc-------------cCcccccccCCEEEEEEEEEec
Q 005707          147 PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFV-------------KDVGSIVSVGQEVKVRLIEANA  207 (681)
Q Consensus       147 vGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v-------------~d~~e~fkVGd~VkVkVl~VD~  207 (681)
                      +|+++.|+|++....|+.|.|+-.-+.+||...|.....             ..-.-.|..|+.|++||.++.-
T Consensus         3 ~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~f   76 (122)
T PF08292_consen    3 VGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEIF   76 (122)
T ss_dssp             TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEEE
T ss_pred             CCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEEE
Confidence            699999999999999999999888899999999974322             1223346899999999998753

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=91.41  E-value=0.31  Score=55.84  Aligned_cols=75  Identities=27%  Similarity=0.455  Sum_probs=60.4

Q ss_pred             CCCCCcEEEEEEEEEecC--eeEEEECCCeEEEEeccccCCccccCc-----ccccccCCEEEEEEEEEeccCCceEEEE
Q 005707          144 DLIPGATFTGKVRSIQPF--GAFIDFGAFTDGLVHVSRLSDNFVKDV-----GSIVSVGQEVKVRLIEANAETGRISLTM  216 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~--GaFVdLgggV~GLVPiSELS~~~v~d~-----~e~fkVGd~VkVkVl~VD~ekgrI~LSl  216 (681)
                      ...+|.+|.|+|++|.+.  .+|||+|..-.||+|.+++.+ +...+     ...++.||.+-|.|+.-...++--.||.
T Consensus        34 ~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv~ke~~G~Kga~lT~  112 (487)
T COG1530          34 EQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQVVKEPRGTKGARLTT  112 (487)
T ss_pred             EeeecCceEEEecccCccchhheeeccCCccceEEecccch-hhhhcccccceeeecCCceEEEEEEeecCcccccccee
Confidence            455799999999999986  789999999999999999998 44433     3478999999999998766666556665


Q ss_pred             ecc
Q 005707          217 RES  219 (681)
Q Consensus       217 K~l  219 (681)
                      .-.
T Consensus       113 ~Is  115 (487)
T COG1530         113 DIS  115 (487)
T ss_pred             EEe
Confidence            543

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

Probab=91.14  E-value=0.98  Score=44.93  Aligned_cols=63  Identities=24%  Similarity=0.287  Sum_probs=43.0

Q ss_pred             CccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCC----ccccccc-----CCCCcccCCCEEEEEEEEEe
Q 005707          260 FVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEES----DDGFANM-----MGGSSLQVGQEVSVRVLRIS  323 (681)
Q Consensus       260 lkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELS----d~~ie~~-----~p~~~fkVGqkVkVrVL~ID  323 (681)
                      .=+|++++|+|+.++..|+|++++ -+.-|+...-..    ...-++.     .-.++.++|..|+++|+...
T Consensus        79 pfKGEVvdgvV~~Vnk~G~F~~~G-Pl~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr  150 (170)
T KOG3298|consen   79 PFKGEVVDGVVTKVNKMGVFARSG-PLEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTR  150 (170)
T ss_pred             ecCCcEEEEEEEEEeeeeEEEecc-ceEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEE
Confidence            347999999999999999999998 455554432222    1111110     00236899999999999883

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

Probab=90.56  E-value=0.32  Score=55.75  Aligned_cols=67  Identities=27%  Similarity=0.371  Sum_probs=55.2

Q ss_pred             ccCCccCcEEEEEEEEEecc--eEEEEeCCCeEEEEeCCCCCcccccccCC---CCcccCCCEEEEEEEEEeC
Q 005707          257 TTKFVKGQDLEGTVKNLTRS--GAFISLPEGEEGFLPTSEESDDGFANMMG---GSSLQVGQEVSVRVLRISR  324 (681)
Q Consensus       257 ~sklkvGdIV~G~VknVt~~--GaFVeIg~GIeGLLpiSELSd~~ie~~~p---~~~fkVGqkVkVrVL~IDk  324 (681)
                      .....+|.++.|+|++|.+.  .+||+++.+-.||+|.+++.+ ++.....   ...++.||.+-|.|+.-..
T Consensus        32 ~~~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv~ke~~  103 (487)
T COG1530          32 AKEQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQVVKEPR  103 (487)
T ss_pred             CcEeeecCceEEEecccCccchhheeeccCCccceEEecccch-hhhhcccccceeeecCCceEEEEEEeecC
Confidence            45567899999999999887  899999999999999999988 3322211   3589999999999988753

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

Probab=89.16  E-value=1.6  Score=40.50  Aligned_cols=58  Identities=21%  Similarity=0.295  Sum_probs=47.6

Q ss_pred             CcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEe
Q 005707          141 KNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEAN  206 (681)
Q Consensus       141 t~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD  206 (681)
                      .+.+ ..|.+|.|+|..+.+.-+|+|+|+...+.++......       +.|..|..|.+++.+..
T Consensus        18 ~lG~-~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~~~~-------~~y~~G~rV~lrLkdlE   75 (104)
T PF10246_consen   18 QLGD-PEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPAVNG-------EKYVRGSRVRLRLKDLE   75 (104)
T ss_pred             hcCC-ccCCEEEEEEEEEecCceEEEeCCceeEEEecccccc-------cccccCCEEEEEECCHh
Confidence            3445 4799999999999999999999999999999765533       34889999998887753

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 [].

>PRK12442 translation initiation factor IF-1; Reviewed

Probab=88.90  E-value=1.9  Score=38.89  Aligned_cols=65  Identities=17%  Similarity=0.237  Sum_probs=51.3

Q ss_pred             EEEEEEEEEecCeeE-EEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEec
Q 005707          150 TFTGKVRSIQPFGAF-IDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRE  218 (681)
Q Consensus       150 IVeGkV~sV~d~GaF-VdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~  218 (681)
                      .++|+|+.+.+.+.| |.|.++...+.|++=    ..+.-.-.+.+||.|.|.+...|..+++|..-.+.
T Consensus         8 e~~G~V~e~Lp~~~frV~LenG~~vla~isG----KmR~~rIrIl~GD~V~VE~spYDltkGRIiyR~~~   73 (87)
T PRK12442          8 ELDGIVDEVLPDSRFRVTLENGVEVGAYASG----RMRKHRIRILAGDRVTLELSPYDLTKGRINFRHKD   73 (87)
T ss_pred             EEEEEEEEECCCCEEEEEeCCCCEEEEEecc----ceeeeeEEecCCCEEEEEECcccCCceeEEEEecC
Confidence            589999999999887 688877777777642    22222334679999999999999999999998873

>TIGR00008 infA translation initiation factor IF-1

Probab=88.49  E-value=2  Score=37.06  Aligned_cols=61  Identities=26%  Similarity=0.341  Sum_probs=47.5

Q ss_pred             EEEEEEEEEecCeeE-EEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEE
Q 005707          150 TFTGKVRSIQPFGAF-IDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISL  214 (681)
Q Consensus       150 IVeGkV~sV~d~GaF-VdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~L  214 (681)
                      .+.|+|+...+.+.| |.+.++..-+.|++=    ..+.-.-...+||.|.|.+...|..+++|..
T Consensus         6 e~~G~V~e~L~~~~f~V~l~ng~~vla~i~G----Kmr~~rI~I~~GD~V~Ve~spyd~tkgrIi~   67 (68)
T TIGR00008         6 EMEGKVTESLPNAMFRVELENGHEVLAHISG----KIRMHYIRILPGDKVKVELSPYDLTRGRITY   67 (68)
T ss_pred             EEEEEEEEECCCCEEEEEECCCCEEEEEecC----cchhccEEECCCCEEEEEECcccCCcEeEEe
Confidence            489999999999987 688877887777642    2232234478999999999999998888864

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).

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

Probab=86.95  E-value=2.2  Score=39.54  Aligned_cols=54  Identities=13%  Similarity=0.211  Sum_probs=46.3

Q ss_pred             ccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe
Q 005707          261 VKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS  323 (681)
Q Consensus       261 kvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID  323 (681)
                      ..|.+|.|+|..|.+.-+||++|....+.|++....         .+.|..|.+|.+++...+
T Consensus        22 ~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~~~---------~~~y~~G~rV~lrLkdlE   75 (104)
T PF10246_consen   22 PEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPAVN---------GEKYVRGSRVRLRLKDLE   75 (104)
T ss_pred             ccCCEEEEEEEEEecCceEEEeCCceeEEEeccccc---------ccccccCCEEEEEECCHh
Confidence            489999999999999999999999999999976543         356889999999877664

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 [].

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

Probab=86.90  E-value=2.1  Score=43.12  Aligned_cols=74  Identities=20%  Similarity=0.094  Sum_probs=55.2

Q ss_pred             CCCCCCcEEEEEEEEEecCeeEEEEC--------CCeEEEEeccccCCc--cccCcccccccCCEEEEEEEEEeccCCce
Q 005707          143 EDLIPGATFTGKVRSIQPFGAFIDFG--------AFTDGLVHVSRLSDN--FVKDVGSIVSVGQEVKVRLIEANAETGRI  212 (681)
Q Consensus       143 ~~LkvGdIVeGkV~sV~d~GaFVdLg--------ggV~GLVPiSELS~~--~v~d~~e~fkVGd~VkVkVl~VD~ekgrI  212 (681)
                      --...|+||.++|.++...-+-|+|-        ...+|+||..++..-  ..-++-+-|++||.|.++|++.+ .+...
T Consensus        64 ~LP~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~-~~~~y  142 (193)
T KOG3409|consen   64 LLPFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLG-DGSNY  142 (193)
T ss_pred             cCCccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecC-CCCcE
Confidence            34567999999999999877766652        357899999888632  12344566999999999999965 35566


Q ss_pred             EEEEe
Q 005707          213 SLTMR  217 (681)
Q Consensus       213 ~LSlK  217 (681)
                      .|+..
T Consensus       143 ~LTtA  147 (193)
T KOG3409|consen  143 LLTTA  147 (193)
T ss_pred             EEEEe
Confidence            77765

>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=84.45  E-value=3.4  Score=39.20  Aligned_cols=62  Identities=26%  Similarity=0.311  Sum_probs=44.4

Q ss_pred             cCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcc-ccccc----------CCCCcccCCCEEEEEEEEEe
Q 005707          262 KGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDD-GFANM----------MGGSSLQVGQEVSVRVLRIS  323 (681)
Q Consensus       262 vGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~-~ie~~----------~p~~~fkVGqkVkVrVL~ID  323 (681)
                      +|+++.|+|++-++.|+.|.|+---+-+||.+.|... .++..          .-.-.|..|+.|++||.++.
T Consensus         3 ~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~   75 (122)
T PF08292_consen    3 VGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEI   75 (122)
T ss_dssp             TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEE
T ss_pred             CCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEE
Confidence            6999999999999999999998777889999887632 11100          01235689999999999984

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

>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []

Probab=83.88  E-value=9.3  Score=31.54  Aligned_cols=50  Identities=26%  Similarity=0.286  Sum_probs=38.1

Q ss_pred             EEEEEEEEec---CeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEE
Q 005707          151 FTGKVRSIQP---FGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIE  204 (681)
Q Consensus       151 VeGkV~sV~d---~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~  204 (681)
                      +.|+|+...+   ||++..-++.-+.|+|.+++....    ...++.|+.|.+.+..
T Consensus         1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~~----~~~l~~G~~V~F~~~~   53 (66)
T PF00313_consen    1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGNG----FRSLKEGDRVEFEVEE   53 (66)
T ss_dssp             EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSSS----STS--TTSEEEEEEEE
T ss_pred             CeEEEEEEECCCCceEEEEcccceeEEeccccccccc----cccCCCCCEEEEEEEE
Confidence            4799999985   566666666669999999998764    2347799999999988

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 ....

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

Probab=83.27  E-value=4  Score=41.23  Aligned_cols=71  Identities=14%  Similarity=0.149  Sum_probs=54.1

Q ss_pred             ccCcEEEEEEEEEecceEEEEe--------CCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEE-eCCeEEEEE
Q 005707          261 VKGQDLEGTVKNLTRSGAFISL--------PEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI-SRGQVTLTM  331 (681)
Q Consensus       261 kvGdIV~G~VknVt~~GaFVeI--------g~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~I-DkgKI~LSL  331 (681)
                      ..|++|.++|..++..-+-|+|        .....|+||..++-..-.+..++-+.|++||.|.++|++. +.....||.
T Consensus        67 ~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~~~~y~LTt  146 (193)
T KOG3409|consen   67 FVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGDGSNYLLTT  146 (193)
T ss_pred             ccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCCCCcEEEEE
Confidence            4899999999999877666654        3477899999877543333345567899999999999997 456677776

>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=81.88  E-value=4  Score=34.67  Aligned_cols=63  Identities=17%  Similarity=0.355  Sum_probs=43.1

Q ss_pred             CcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEE
Q 005707          263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTM  331 (681)
Q Consensus       263 GdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSL  331 (681)
                      |+.+.-.|-.++..|--+--++.+.|+.-..    .+..  .....+.+||++++.||+||  +-++.+||
T Consensus         1 G~~L~LvV~~~~edgsv~fs~g~v~g~tv~A----tryH--~~g~nl~pGqK~kaviLhvD~l~~~VhVSl   65 (65)
T cd05700           1 GDQLKLVVQDVTEDGSVMFSGGQVSGLTVLA----SRYH--KEGVNVTPGCKLKAVILHVDFVKSQVHVSL   65 (65)
T ss_pred             CceEEEEEeeeccCCcEEEecCCcCCcEEEE----EEEE--ecceecCCCceeEEEEEEEeeEEeEEEEeC
Confidence            6778888999888876665666666653221    1110  12567899999999999999  56666654

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.

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

Probab=81.17  E-value=6.9  Score=32.22  Aligned_cols=57  Identities=32%  Similarity=0.445  Sum_probs=42.0

Q ss_pred             EEEEEEEec---ceEEEEeCC-CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCeEEEE
Q 005707          267 EGTVKNLTR---SGAFISLPE-GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQVTLT  330 (681)
Q Consensus       267 ~G~VknVt~---~GaFVeIg~-GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgKI~LS  330 (681)
                      .|+|+...+   || ||...+ |-+-|+|.+++....      ...+++|+.|.+.+..-+++.....
T Consensus         2 ~G~Vk~~~~~kGfG-FI~~~~~g~diffh~~~~~~~~------~~~~~~G~~V~f~~~~~~~g~~A~~   62 (65)
T cd04458           2 TGTVKWFDDEKGFG-FITPDDGGEDVFVHISALEGDG------FRSLEEGDRVEFELEEGDKGPQAVN   62 (65)
T ss_pred             cEEEEEEECCCCeE-EEecCCCCcCEEEEhhHhhccC------CCcCCCCCEEEEEEEECCCCCeEEE
Confidence            478888755   45 777666 899999999887542      2578999999998777655544433

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	681
2oce_A	780	Crystal Structure Of Tex Family Protein Pa5201 From		4e-14
3bzc_A	785	Crystal Structure Of The Tex Protein From Pseudomon		5e-14
2k4k_A	130	Solution Structure Of Gsp13 From Bacillus Subtilis		4e-13
3cdi_A	723	Crystal Structure Of E. Coli Pnpase Length = 723		8e-10
3cdi_A	723	Crystal Structure Of E. Coli Pnpase Length = 723		3e-04
1sro_A	76	S1 Rna Binding Domain, Nmr, 20 Structures Length =		7e-09
4aim_A	726	Crystal Structure Of C. Crescentus Pnpase Bound To		9e-07
4aid_A	726	Crystal Structure Of C. Crescentus Pnpase Bound To		9e-07
4am3_A	717	Crystal Structure Of C. Crescentus Pnpase Bound To		9e-07
1q8k_A	308	Solution Structure Of Alpha Subunit Of Human Eif2 L		5e-05
2eqs_A	103	Solution Structure Of The S1 Rna Binding Domain Of		8e-05
3aev_A	275	Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex		3e-04
1yz6_A	274	Crystal Structure Of Intact Alpha Subunit Of Aif2 F		7e-04
1go3_E	187	Structure Of An Archeal Homolog Of The Eukaryotic R		9e-04

>pdb|2OCE|A Chain A, Crystal Structure Of Tex Family Protein Pa5201 From Pseudomonas Aeruginosa Length = 780

Iteration: 1
 Score = 76.6 bits (187), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 36/78 (46%), Positives = 49/78 (62%)
Query: 143 EDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRL 202
           +DL PG    G V ++  FGAF+D G   DGLVH+S LS+ FVKD   +V  G  VKV++
Sbjct: 651 KDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKV 710
Query: 203 IEANAETGRISLTMRESD 220
           +E +    R+ L+MR SD
Sbjct: 711 MEVDIPRNRVGLSMRMSD 728

>pdb|3BZC|A Chain A, Crystal Structure Of The Tex Protein From Pseudomonas Aeruginosa, Crystal Form I Length = 785

Iteration: 1
 Score = 76.6 bits (187), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 36/78 (46%), Positives = 49/78 (62%)
Query: 143 EDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRL 202
           +DL PG    G V ++  FGAF+D G   DGLVH+S LS+ FVKD   +V  G  VKV++
Sbjct: 650 KDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKV 709
Query: 203 IEANAETGRISLTMRESD 220
           +E +    R+ L+MR SD
Sbjct: 710 MEVDIPRNRVGLSMRMSD 727

>pdb|2K4K|A Chain A, Solution Structure Of Gsp13 From Bacillus Subtilis Length = 130

Iteration: 1
 Score = 73.2 bits (178), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 31/70 (44%), Positives = 49/70 (70%)
Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
           G+ +TGKV  +Q +GAF+     T GLVH+S ++  FVKD+   +SVG EV+V+++  + 
Sbjct: 8   GSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQVKVLAVDE 67
Query: 208 ETGRISLTMR 217
           E G+ISL++R
Sbjct: 68  EKGKISLSIR 77

>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase Length = 723

Iteration: 1
 Score = 62.4 bits (150), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 30/72 (41%), Positives = 49/72 (68%), Gaps = 1/72 (1%)
Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
           G  +TGKV  I  FGAF+  G   +GLVH+S+++D  V+ V   + +GQEV V+++E + 
Sbjct: 628 GRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDR 687
Query: 208 ETGRISLTMRES 219
           + GRI L+++E+
Sbjct: 688 Q-GRIRLSIKEA 698

>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase Length = 723

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 30/98 (30%), Positives = 52/98 (53%), Gaps = 3/98 (3%)
Query: 237 KVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEES 296
           K+  T    +K   +R E  T +   G+   G V  +   GAF+++  G+EG +  S+ +
Sbjct: 602 KIAATDGEKAKHAIRRIEEITAEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIA 661
Query: 297 DDGFANMMGGSSLQVGQEVSVRVLRISR-GQVTLTMKK 333
           D     +     LQ+GQEV V+VL + R G++ L++K+
Sbjct: 662 DKRVEKVT--DYLQMGQEVPVKVLEVDRQGRIRLSIKE 697

>pdb|1SRO|A Chain A, S1 Rna Binding Domain, Nmr, 20 Structures Length = 76

Iteration: 1
 Score = 59.3 bits (142), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 30/72 (41%), Positives = 49/72 (68%), Gaps = 1/72 (1%)
Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
           G  +TGKV  I  FGAF+  G   +GLVH+S+++D  V+ V   + +GQEV V+++E + 
Sbjct: 6   GRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDR 65
Query: 208 ETGRISLTMRES 219
           + GRI L+++E+
Sbjct: 66  Q-GRIRLSIKEA 76

>pdb|4AIM|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E Recognition Peptide Length = 726

Iteration: 1
 Score = 52.4 bits (124), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 31/82 (37%), Positives = 48/82 (58%), Gaps = 6/82 (7%)
Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
           G  + GKV  +  FGAF++F    DGLVHVS++S+  V     ++  GQ VKV+L+  + 
Sbjct: 638 GKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFD- 696
Query: 208 ETGRISLTMRESD-----DISK 224
           + G+  L+M+  D     D+SK
Sbjct: 697 DRGKTKLSMKVVDQETGEDLSK 718

>pdb|4AID|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E Recognition Peptide Length = 726

Iteration: 1
 Score = 52.4 bits (124), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 31/82 (37%), Positives = 48/82 (58%), Gaps = 6/82 (7%)
Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
           G  + GKV  +  FGAF++F    DGLVHVS++S+  V     ++  GQ VKV+L+  + 
Sbjct: 638 GKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFD- 696
Query: 208 ETGRISLTMRESD-----DISK 224
           + G+  L+M+  D     D+SK
Sbjct: 697 DRGKTKLSMKVVDQETGEDLSK 718

>pdb|4AM3|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rna Length = 717

Iteration: 1
 Score = 52.4 bits (124), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 31/82 (37%), Positives = 48/82 (58%), Gaps = 6/82 (7%)
Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
           G  + GKV  +  FGAF++F    DGLVHVS++S+  V     ++  GQ VKV+L+  + 
Sbjct: 629 GKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFD- 687
Query: 208 ETGRISLTMRESD-----DISK 224
           + G+  L+M+  D     D+SK
Sbjct: 688 DRGKTKLSMKVVDQETGEDLSK 709

>pdb|1Q8K|A Chain A, Solution Structure Of Alpha Subunit Of Human Eif2 Length = 308

Iteration: 1
 Score = 46.6 bits (109), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 38/65 (58%), Gaps = 2/65 (3%)
Query: 155 VRSIQPFGAFIDFGAFTD--GLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRI 212
           VRSIQ  GA++    + +  G++H+S LS   ++ +  ++ +G+   V++I  + E G I
Sbjct: 21  VRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNECVKVIRVDKEKGYI 80
Query: 213 SLTMR 217
            L+ R
Sbjct: 81  DLSKR 85

>pdb|2EQS|A Chain A, Solution Structure Of The S1 Rna Binding Domain Of Human Atp-Dependent Rna Helicase Dhx8 Length = 103

Iteration: 1
 Score = 45.8 bits (107), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 28/77 (36%), Positives = 42/77 (54%), Gaps = 6/77 (7%)
Query: 148 GATFTGKVRSIQPFGAFIDFGAF---TDGLVHVSRL-SDNFVKDVGSIVSVGQEVKVRLI 203
           G  + GKV SI  FG F+         +GLVH+S L  +  V +V  +VS GQ VKV+++
Sbjct: 13  GDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVL 72
Query: 204 EANAETGRISLTMRESD 220
                  + SL+M++ D
Sbjct: 73  SFTGT--KTSLSMKDVD 87

>pdb|3AEV|A Chain A, Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex From Pyrococcus Horikoshii Ot3 Length = 275

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/97 (23%), Positives = 50/97 (51%), Gaps = 5/97 (5%)
Query: 148 GATFTGKVRSIQPFGAFIDFGAF--TDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEA 205
           G      V+ I  +GAF++   +   +  +H+S ++  +V+++   +  GQ+V  ++I  
Sbjct: 12  GEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRV 71
Query: 206 NAETGRISLTMR---ESDDISKLQQQKDATASGDKVR 239
           +   G I L++R   +    +KLQ+ K A  + + +R
Sbjct: 72  DPRKGHIDLSLRRVTQQQRKAKLQEFKRAQKAENLLR 108

>pdb|1YZ6|A Chain A, Crystal Structure Of Intact Alpha Subunit Of Aif2 From Pyrococcus Abyssi Length = 274

Iteration: 1
 Score = 42.7 bits (99), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 22/89 (24%), Positives = 46/89 (51%), Gaps = 5/89 (5%)
Query: 148 GATFTGKVRSIQPFGAFIDFGAF--TDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEA 205
           G      V+ I  +GAF++   +   +  +H+S ++  +V+++   +  GQ+V  ++I  
Sbjct: 11  GEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRV 70
Query: 206 NAETGRISLTMR---ESDDISKLQQQKDA 231
           +   G I L++R   +    +KLQ+ K A
Sbjct: 71  DPRKGHIDLSLRRVTQQQRKAKLQEFKRA 99

>pdb|1GO3|E Chain E, Structure Of An Archeal Homolog Of The Eukaryotic Rna Polymerase Ii Rpb4RPB7 COMPLEX Length = 187

Iteration: 1
 Score = 42.4 bits (98), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 25/82 (30%), Positives = 45/82 (54%), Gaps = 17/82 (20%)
Query: 153 GKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFV-----------KDVGSIVSVGQEVKVR 201
           G+V  +  FG+F+  G   DGL+HVS++ D++V           K+ G ++ +G  V+ R
Sbjct: 87  GEVVDVVEFGSFVRLGPL-DGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRAR 145
Query: 202 LIEANAETGR-----ISLTMRE 218
           ++  + +  R     I+LTMR+
Sbjct: 146 IVAISLKAERKRGSKIALTMRQ 167

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	681
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	1e-27
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	1e-09
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	9e-26
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	6e-07
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	3e-21
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	9e-10
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	2e-20
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	6e-06
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	6e-19
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	2e-09
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	9e-19
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	2e-09
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	4e-18
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	3e-05
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	5e-18
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	9e-06
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	1e-17
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	1e-04
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	1e-16
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	1e-08
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	4e-16
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	3e-05
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	6e-15
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	3e-06
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	8e-15
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	1e-08
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	1e-14
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	1e-08
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	2e-14
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	2e-06
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	8e-13
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	5e-07
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	1e-12
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	3e-07
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	8e-11
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	1e-05
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	2e-09
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	2e-09
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	5e-08
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	4e-07
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	8e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-06
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	1e-05
2r7d_A	469	Ribonuclease II family protein; structural genomic	2e-04

>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis} Length = 130

 Score =  107 bits (269), Expect = 1e-27
 Identities = 37/155 (23%), Positives = 66/155 (42%), Gaps = 31/155 (20%)

Query: 143 EDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRL 202
                G+ +TGKV  +Q +GAF+     T GLVH+S ++  FVKD+   +SVG EV+V++
Sbjct: 3   AKFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQVKV 62

Query: 203 IEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVK 262
           +  + E G+ISL++R +    + ++ K                                +
Sbjct: 63  LAVDEEKGKISLSIRATQAAPEKKESKP-------------------------------R 91

Query: 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESD 297
                   +  +    F +L +  E ++  S   D
Sbjct: 92  KPKAAQVSEEASTPQGFNTLKDKLEEWIEMSNRKD 126

>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis} Length = 130

 Score = 55.5 bits (134), Expect = 1e-09
 Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 4/82 (4%)

Query: 257 TTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVS 316
             KF  G    G V  L   GAF++L E  +G +  SE +     ++     L VG EV 
Sbjct: 2   AAKFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDI--NEHLSVGDEVQ 59

Query: 317 VRVLRI--SRGQVTLTMKKEDD 336
           V+VL +   +G+++L+++    
Sbjct: 60  VKVLAVDEEKGKISLSIRATQA 81

>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 =  111 bits (281), Expect = 9e-26
 Identities = 38/110 (34%), Positives = 57/110 (51%)

Query: 143 EDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRL 202
           +DL PG    G V ++  FGAF+D G   DGLVH+S LS+ FVKD   +V  G  VKV++
Sbjct: 650 KDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKV 709

Query: 203 IEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKR 252
           +E +    R+ L+MR SD   +  + +         +  +   +  GQ  
Sbjct: 710 MEVDIPRNRVGLSMRMSDTPGEKVEGQRGGRPTGSGQPRQERGAPRGQSA 759

>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 = 51.8 bits (125), Expect = 6e-07
 Identities = 31/105 (29%), Positives = 50/105 (47%), Gaps = 15/105 (14%)

Query: 247 KPGQK-RDEMKTTKFVK----------GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEE 295
           KPG+  R E KT +F +          G  LEG V N+T  GAF+ +   ++G +  S  
Sbjct: 628 KPGRDPRPEFKTAEFQEGVESLKDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISAL 687

Query: 296 SDDGFANMMGGSSLQVGQEVSVRVLRI--SRGQVTLTMKKEDDVG 338
           S+    +      ++ G  V V+V+ +   R +V L+M+  D  G
Sbjct: 688 SEKFVKDPY--EVVKAGDIVKVKVMEVDIPRNRVGLSMRMSDTPG 730

>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii} Length = 80

 Score = 87.3 bits (217), Expect = 3e-21
 Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 4/75 (5%)

Query: 144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLI 203
           D+ PG  + G V  I+ +GAFI+      GL+    +    +++    ++VG E+ V+ I
Sbjct: 2   DVEPGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDMISLRLEN----LNVGDEIIVQAI 57

Query: 204 EANAETGRISLTMRE 218
           +   E   I      
Sbjct: 58  DVRPEKREIDFKYIP 72

>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii} Length = 80

 Score = 54.6 bits (132), Expect = 9e-10
 Identities = 17/76 (22%), Positives = 31/76 (40%), Gaps = 8/76 (10%)

Query: 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI 322
           G+  +G V  + + GAFI+L E   G L   +       N      L VG E+ V+ + +
Sbjct: 6   GKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDMISLRLEN------LNVGDEIIVQAIDV 59

Query: 323 --SRGQVTLTMKKEDD 336
              + ++       + 
Sbjct: 60  RPEKREIDFKYIPLEH 75

>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 = 85.9 bits (213), Expect = 2e-20
 Identities = 28/98 (28%), Positives = 42/98 (42%), Gaps = 3/98 (3%)

Query: 127 RRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDF-GAFTDGLVHVSRLSDNFV 185
               +   S  P            F G+V  +  +GAFI   G    GLVH + +S   V
Sbjct: 2   SSGSSGMNSGRPETMENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRV 61

Query: 186 KDVGSIVSVGQEVKVRLI--EANAETGRISLTMRESDD 221
                IV VG +V V+LI  E   +  ++SL+M+  + 
Sbjct: 62  DKPSEIVDVGDKVWVKLIGREMKNDRIKVSLSMKVVNQ 99

>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 = 44.7 bits (106), Expect = 6e-06
 Identities = 21/92 (22%), Positives = 37/92 (40%), Gaps = 7/92 (7%)

Query: 250 QKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLP-EGEEGFLPTSEESDDGFANMMGGSS 308
             R E            +G V  +T  GAFI +P   ++G +  +  S            
Sbjct: 10  SGRPETMENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKP--SEI 67

Query: 309 LQVGQEVSVRVLRIS----RGQVTLTMKKEDD 336
           + VG +V V+++       R +V+L+MK  + 
Sbjct: 68  VDVGDKVWVKLIGREMKNDRIKVSLSMKVVNQ 99

>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae} Length = 1219

 Score = 90.7 bits (225), Expect = 6e-19
 Identities = 14/148 (9%), Positives = 38/148 (25%), Gaps = 2/148 (1%)

Query: 143  EDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKD-VGSIVSVGQEVKVR 201
            +    G+    +V             +  + +V+  R +   ++     I  +G+    +
Sbjct: 898  KTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAK 957

Query: 202  LIEANAETGRISLTMRESDDISKLQQQK-DATASGDKVRTTRRSTSKPGQKRDEMKTTKF 260
            +I  +       +++ + D   +          S   ++       +  +        K 
Sbjct: 958  VIYIDYANITAEVSLLDHDVKQQYVPISYSKDPSIWDLKQELEDAEEERKLMMAEARAKR 1017

Query: 261  VKGQDLEGTVKNLTRSGAFISLPEGEEG 288
                             A   L   E G
Sbjct: 1018 THRVINHPYYFPFNGRQAEDYLRSKERG 1045

>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae} Length = 1219

 Score = 60.3 bits (146), Expect = 2e-09
 Identities = 9/78 (11%), Positives = 24/78 (30%), Gaps = 3/78 (3%)

Query: 260 FVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRV 319
           F KG  +   V+    +    +     E  +     +             ++G+    +V
Sbjct: 900 FFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPA-NEIYEIGKTYPAKV 958

Query: 320 LRI--SRGQVTLTMKKED 335
           + I  +     +++   D
Sbjct: 959 IYIDYANITAEVSLLDHD 976

>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae} Length = 1030

 Score = 89.9 bits (223), Expect = 9e-19
 Identities = 8/79 (10%), Positives = 27/79 (34%), Gaps = 1/79 (1%)

Query: 143 EDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKD-VGSIVSVGQEVKVR 201
           +    G+    +V             +  + +V+  R +   ++     I  +G+    +
Sbjct: 901 KTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAK 960

Query: 202 LIEANAETGRISLTMRESD 220
           +I  +       +++ + D
Sbjct: 961 VIYIDYANITAEVSLLDHD 979

>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae} Length = 1030

 Score = 59.9 bits (145), Expect = 2e-09
 Identities = 9/78 (11%), Positives = 24/78 (30%), Gaps = 3/78 (3%)

Query: 260 FVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRV 319
           F KG  +   V+    +    +     E  +     +             ++G+    +V
Sbjct: 903 FFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPA-NEIYEIGKTYPAKV 961

Query: 320 LRI--SRGQVTLTMKKED 335
           + I  +     +++   D
Sbjct: 962 IYIDYANITAEVSLLDHD 979

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A Length = 723

 Score = 87.6 bits (218), Expect = 4e-18
 Identities = 33/97 (34%), Positives = 55/97 (56%), Gaps = 1/97 (1%)

Query: 147 PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEAN 206
            G  +TGKV  I  FGAF+  G   +GLVH+S+++D  V+ V   + +GQEV V+++E +
Sbjct: 627 VGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVD 686

Query: 207 AETGRISLTMRESDDISKLQQQKDATASGDKVRTTRR 243
              GRI L+++E+ + S+     +A A+         
Sbjct: 687 -RQGRIRLSIKEATEQSQPAAAPEAPAAEQGEHHHHH 722

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A Length = 723

 Score = 46.3 bits (111), Expect = 3e-05
 Identities = 23/71 (32%), Positives = 41/71 (57%), Gaps = 3/71 (4%)

Query: 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI 322
           G+   G V  +   GAF+++  G+EG +  S+ +D     +     LQ+GQEV V+VL +
Sbjct: 628 GRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKV--TDYLQMGQEVPVKVLEV 685

Query: 323 -SRGQVTLTMK 332
             +G++ L++K
Sbjct: 686 DRQGRIRLSIK 696

>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 = 78.9 bits (195), Expect = 5e-18
 Identities = 29/82 (35%), Positives = 44/82 (53%), Gaps = 6/82 (7%)

Query: 143 EDLIPGATFTGKVRSIQPFGAFIDFGAF---TDGLVHVSRLS-DNFVKDVGSIVSVGQEV 198
           E+   G  + GKV SI  FG F+         +GLVH+S L  +  V +V  +VS GQ V
Sbjct: 8   EEPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRV 67

Query: 199 KVRLIEANAETGRISLTMRESD 220
           KV+++       + SL+M++ D
Sbjct: 68  KVKVLS--FTGTKTSLSMKDVD 87

>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 = 43.8 bits (104), Expect = 9e-06
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 4/73 (5%)

Query: 263 GQDLEGTVKNLTRSGAFISLP---EGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRV 319
           G    G V ++ + G F+ L    +  EG +  SE   +G    +    +  GQ V V+V
Sbjct: 13  GDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVA-DVVSKGQRVKVKV 71

Query: 320 LRISRGQVTLTMK 332
           L  +  + +L+MK
Sbjct: 72  LSFTGTKTSLSMK 84

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A Length = 726

 Score = 86.4 bits (215), Expect = 1e-17
 Identities = 30/90 (33%), Positives = 49/90 (54%), Gaps = 1/90 (1%)

Query: 147 PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEAN 206
            G  + GKV  +  FGAF++F    DGLVHVS++S+  V     ++  GQ VKV+L+  +
Sbjct: 637 VGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFD 696

Query: 207 AETGRISLTMRESDDISKLQQQKDATASGD 236
            + G+  L+M+  D  +     K   A+ +
Sbjct: 697 -DRGKTKLSMKVVDQETGEDLSKKEAAAEE 725

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A Length = 726

 Score = 44.4 bits (106), Expect = 1e-04
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 3/71 (4%)

Query: 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI 322
           G+  +G V  +   GAF++    ++G +  S+ S++  A       L+ GQ V V++L  
Sbjct: 638 GKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKP--SDVLKEGQMVKVKLLGF 695

Query: 323 -SRGQVTLTMK 332
             RG+  L+MK
Sbjct: 696 DDRGKTKLSMK 706

>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 = 77.5 bits (191), Expect = 1e-16
 Identities = 27/156 (17%), Positives = 55/156 (35%), Gaps = 31/156 (19%)

Query: 147 PGATFTGKVRSIQPFGAFIDFGAF--TDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIE 204
                   VRSI   GA++    +   +G++ +S LS   ++ +  ++ +G+   V +I 
Sbjct: 15  VEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIR 74

Query: 205 ANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQ 264
            + E G I L+ R                              P +        KF K +
Sbjct: 75  VDKEKGYIDLSKRRV---------------------------SPEEAIK--CEDKFTKSK 105

Query: 265 DLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGF 300
            +   ++++     +    + E  F  T+   DD +
Sbjct: 106 TVYSILRHVAEVLEYTKDEQLESLFQRTAWVFDDKY 141

>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 = 54.0 bits (130), Expect = 1e-08
 Identities = 17/75 (22%), Positives = 37/75 (49%), Gaps = 6/75 (8%)

Query: 263 GQDLEGTVKNLTRSGAFISLPE--GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVL 320
              +   V+++   GA++SL E    EG +  SE S     ++     +++G+   V V+
Sbjct: 16  EDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSI--NKLIRIGRNECVVVI 73

Query: 321 RI--SRGQVTLTMKK 333
           R+   +G + L+ ++
Sbjct: 74  RVDKEKGYIDLSKRR 88

>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 = 81.5 bits (202), Expect = 4e-16
 Identities = 25/88 (28%), Positives = 44/88 (50%), Gaps = 5/88 (5%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNF----VKDVGSIVSVGQEVKVRLI 203
           G    G V     FGAF+      DGL+H+S++        V++V  ++ VGQ+V+V + 
Sbjct: 668 GERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIA 727

Query: 204 EANAETGRISLTMRESDDISKLQQQKDA 231
           E +   G++SL      + +   ++KD 
Sbjct: 728 EID-SRGKLSLIPVIEGEEAASDEKKDD 754

>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 = 46.0 bits (110), Expect = 3e-05
 Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 3/77 (3%)

Query: 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSS--LQVGQEVSVRVL 320
           G+ + G+V   T  GAF+SL  G++G L  S+         +      L VGQ+V V + 
Sbjct: 668 GERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIA 727

Query: 321 RI-SRGQVTLTMKKEDD 336
            I SRG+++L    E +
Sbjct: 728 EIDSRGKLSLIPVIEGE 744

>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 115

 Score = 70.4 bits (173), Expect = 6e-15
 Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 147 PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLS-DNFVKDVGSIVSVGQEVKVRLIEA 205
            G   TG+V ++  +G F++     +GLVHVS +   N       +V+VG  V+V +++ 
Sbjct: 30  EGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDWTNKNIHPSKVVNVGDVVEVMVLDI 89

Query: 206 NAETGRISLTMRE 218
           + E  RISL +++
Sbjct: 90  DEERRRISLGLKQ 102

>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 115

 Score = 45.7 bits (109), Expect = 3e-06
 Identities = 26/78 (33%), Positives = 38/78 (48%), Gaps = 3/78 (3%)

Query: 257 TTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVS 316
             ++ +G  L G V NLT  G F+ + EG EG +  SE       N+     + VG  V 
Sbjct: 25  AKRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDWTN-KNIHPSKVVNVGDVVE 83

Query: 317 VRVLRI--SRGQVTLTMK 332
           V VL I   R +++L +K
Sbjct: 84  VMVLDIDEERRRISLGLK 101

>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 109

 Score = 69.9 bits (172), Expect = 8e-15
 Identities = 23/74 (31%), Positives = 40/74 (54%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
           GA  TGKV ++   GA ++     +G +  S  S + V+D   ++SVG EV+ +    + 
Sbjct: 32  GAIVTGKVTAVDAKGATVELADGVEGYLRASEASRDRVEDATLVLSVGDEVEAKFTGVDR 91

Query: 208 ETGRISLTMRESDD 221
           +   ISL++R  D+
Sbjct: 92  KNRAISLSVRAKDE 105

>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 109

 Score = 52.2 bits (126), Expect = 1e-08
 Identities = 23/82 (28%), Positives = 38/82 (46%), Gaps = 4/82 (4%)

Query: 257 TTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVS 316
                KG  + G V  +   GA + L +G EG+L  SE S D   +      L VG EV 
Sbjct: 26  VALNKKGAIVTGKVTAVDAKGATVELADGVEGYLRASEASRDRVEDA--TLVLSVGDEVE 83

Query: 317 VRVLRISRGQ--VTLTMKKEDD 336
            +   + R    ++L+++ +D+
Sbjct: 84  AKFTGVDRKNRAISLSVRAKDE 105

>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 = 71.7 bits (176), Expect = 1e-14
 Identities = 29/178 (16%), Positives = 59/178 (33%), Gaps = 37/178 (20%)

Query: 147 PGATFTGKVRSIQPFGAFIDFGAF--TDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIE 204
                   V+ I   GA++    +   +G++ +S LS   ++ +  ++ VG+     ++ 
Sbjct: 15  IDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLR 74

Query: 205 ANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQ 264
            + E G I L+                          RR +S+   K +E    K+ K +
Sbjct: 75  VDKEKGYIDLSK-------------------------RRVSSEDIIKCEE----KYQKSK 105

Query: 265 DLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI 322
               TV ++ R  A       EE +   +      F +       ++          I
Sbjct: 106 ----TVHSILRYCAEKFQIPLEELYKTIAWPLSRKFGHAYEA--FKLSIIDETVWEGI 157

>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 = 54.0 bits (130), Expect = 1e-08
 Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 6/75 (8%)

Query: 263 GQDLEGTVKNLTRSGAFISLPE--GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVL 320
              +   V+ +   GA++ L E    EG +  SE S     ++     ++VG+     VL
Sbjct: 16  DDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSI--QKLIRVGKNDVAVVL 73

Query: 321 RI--SRGQVTLTMKK 333
           R+   +G + L+ ++
Sbjct: 74  RVDKEKGYIDLSKRR 88

>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 = 73.1 bits (179), Expect = 2e-14
 Identities = 27/144 (18%), Positives = 59/144 (40%), Gaps = 2/144 (1%)

Query: 137 MPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAF--TDGLVHVSRLSDNFVKDVGSIVSV 194
           MP    E    G      V+ I  +GAF++   +   +  +H+S ++  +V+++   +  
Sbjct: 1   MPRKAREYPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKE 60

Query: 195 GQEVKVRLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDE 254
           GQ+V  ++I  +   G I L++R      +  + ++   +       R +  K G+  + 
Sbjct: 61  GQKVVAKVIRVDPRKGHIDLSLRRVTQQQRKAKLQEFKRAQKAENLLRLAAEKLGKDFEA 120

Query: 255 MKTTKFVKGQDLEGTVKNLTRSGA 278
                +V  ++  G V       A
Sbjct: 121 AWREVWVPLEEEWGEVYAAFEDAA 144

>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 = 49.2 bits (117), Expect = 2e-06
 Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 6/75 (8%)

Query: 263 GQDLEGTVKNLTRSGAFISLPE--GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVL 320
           G+ +  TVK +   GAF+ L E  G+E F+  SE +     N+     L+ GQ+V  +V+
Sbjct: 12  GEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNI--RDYLKEGQKVVAKVI 69

Query: 321 RI--SRGQVTLTMKK 333
           R+   +G + L++++
Sbjct: 70  RVDPRKGHIDLSLRR 84

>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 = 68.1 bits (166), Expect = 8e-13
 Identities = 14/109 (12%), Positives = 43/109 (39%), Gaps = 5/109 (4%)

Query: 147 PGATFTGKVRSIQPFGAFIDFGAF--TDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIE 204
            G      V+ +  +G+++    +      +  S +S  +VK++  ++   ++V V++I 
Sbjct: 11  EGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIR 70

Query: 205 ANAETGRISLTMR---ESDDISKLQQQKDATASGDKVRTTRRSTSKPGQ 250
            +   G + ++++   + +   K  Q K        +    +      +
Sbjct: 71  VDRRKGTVDVSLKKVTDDERRKKNLQWKKIQRLDKILELVSQKLKLSEK 119

>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 = 50.8 bits (121), Expect = 5e-07
 Identities = 26/75 (34%), Positives = 43/75 (57%), Gaps = 6/75 (8%)

Query: 263 GQDLEGTVKNLTRSGAFISLPE--GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVL 320
           G+ L  TVK +   G+++SL E  G + FLP SE S     N+     L+  ++V V+V+
Sbjct: 12  GEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNI--RDVLKENRKVIVKVI 69

Query: 321 RI--SRGQVTLTMKK 333
           R+   +G V +++KK
Sbjct: 70  RVDRRKGTVDVSLKK 84

>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 = 68.1 bits (166), Expect = 1e-12
 Identities = 29/162 (17%), Positives = 59/162 (36%), Gaps = 31/162 (19%)

Query: 147 PGATFTGKVRSIQPFGAFIDFGAF--TDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIE 204
                   VRSIQ  GA++    +   +G++H+S LS   ++ +  ++ +G+   V++I 
Sbjct: 13  VEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNECVKVIR 72

Query: 205 ANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQ 264
            + E G I L+ R                             +   +       KF K +
Sbjct: 73  VDKEKGYIDLSKR-----------------------------RVSPEEAIKCEDKFTKSK 103

Query: 265 DLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGG 306
            +   ++++     +    + E  F  T+   DD +     G
Sbjct: 104 TVYSILRHVAEVLEYTKDEQLESLFQRTAWVFDDKYKRPGYG 145

>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 = 51.9 bits (124), Expect = 3e-07
 Identities = 17/75 (22%), Positives = 38/75 (50%), Gaps = 6/75 (8%)

Query: 263 GQDLEGTVKNLTRSGAFISLPE--GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVL 320
              +   V+++   GA++SL E    EG +  SE S     ++     +++G+   V+V+
Sbjct: 14  EDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSI--NKLIRIGRNECVKVI 71

Query: 321 RI--SRGQVTLTMKK 333
           R+   +G + L+ ++
Sbjct: 72  RVDKEKGYIDLSKRR 86

>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 = 58.9 bits (142), Expect = 8e-11
 Identities = 21/95 (22%), Positives = 41/95 (43%), Gaps = 2/95 (2%)

Query: 140 VKNEDLIPGATFTGKVRSIQPFGAFIDFGA--FTDGLVHVSRLSDNFVKDVGSIVSVGQE 197
           +  E L PG   TG V S++  G  +D G       L  +        K+ G+ + VGQ 
Sbjct: 14  LSAEALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQY 73

Query: 198 VKVRLIEANAETGRISLTMRESDDISKLQQQKDAT 232
           +   + +     G +SL++  S+  + +  ++ + 
Sbjct: 74  LNCIVEKVKGNGGVVSLSVGHSEVSTAIATEQQSW 108

>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 = 44.2 bits (104), Expect = 1e-05
 Identities = 22/95 (23%), Positives = 40/95 (42%), Gaps = 4/95 (4%)

Query: 244 STSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISL-PEGEEGFLPTSEESDDGFAN 302
           S S        +       G  L GTV +L   G  + +  +G   FLP  +  +     
Sbjct: 3   SGSSGKNVNRVLSAEALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQK 62

Query: 303 MMGGSSLQVGQEVSVRVLRI--SRGQVTLTMKKED 335
             G + L+VGQ ++  V ++  + G V+L++   +
Sbjct: 63  NKG-AKLKVGQYLNCIVEKVKGNGGVVSLSVGHSE 96

>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 Length = 180

 Score = 56.4 bits (136), Expect = 2e-09
 Identities = 25/113 (22%), Positives = 45/113 (39%), Gaps = 22/113 (19%)

Query: 121 PTLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRL 180
                +            PV  E         G+V  +  +G F++ G   DGLVH+S++
Sbjct: 61  FGDGATYHEVEFDMITYVPVVQE------VVEGEVLQVDNYGVFVNLG-PMDGLVHISQI 113

Query: 181 SDNFV-----------KDVGSIVSVGQEVKVRLI----EANAETGRISLTMRE 218
           +D+ +           +    ++  G +V+ R+I           RI+LTMR+
Sbjct: 114 TDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISVASTVTGRLPRIALTMRQ 166

>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 = 58.0 bits (140), Expect = 2e-09
 Identities = 34/203 (16%), Positives = 64/203 (31%), Gaps = 54/203 (26%)

Query: 136 EMPPVKNEDLIPGATFTGKVRSIQP-FGAFIDFGAFT-DGLVHVSRLSDNFVKDVGSIVS 193
                  +         G+V  ++   G F+D G    + +V +  L +           
Sbjct: 63  LEVTATQDQFG-----WGRVTEVRKDLGVFVDTGLPDKEIVVSLDILPELKELWP----K 113

Query: 194 VGQEVKVRLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRD 253
            G ++ +RL     +  RI   +   +D  +L +                          
Sbjct: 114 KGDQLYIRLEVD--KKDRIWGLLAYQEDFQRLAR-------------------------- 145

Query: 254 EMKTTKFVKGQDLEGTVKNLTRSGAFISLPEGE-EGFLPTSEESDDGFANMMGGSSLQVG 312
                  ++ Q+    V  L  SG F+ LPE    GF+  SE   +           ++G
Sbjct: 146 --PAYNNMQNQNWPAIVYRLKLSGTFVYLPENNMLGFIHPSERYAE----------PRLG 193

Query: 313 QEVSVRVLRI--SRGQVTLTMKK 333
           Q +  RV+        + L++K 
Sbjct: 194 QVLDARVIGFREVDRTLNLSLKP 216

>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 172

 Score = 52.3 bits (125), Expect = 5e-08
 Identities = 12/84 (14%), Positives = 27/84 (32%), Gaps = 13/84 (15%)

Query: 147 PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFV----------KDVGSIVSVGQ 196
            G      V ++   G F + G   +  V    +  +                 ++  G 
Sbjct: 84  RGEVVDAIVTTVNKMGFFANIG-PLNVFVSSHLVPPDMKFDPTANPPNYSGEDQVIEKGS 142

Query: 197 EVKVRLIEANAETGRIS--LTMRE 218
            V+++++    +   I    TM+E
Sbjct: 143 NVRLKIVGTRTDATEIFAIATMKE 166

>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: b.40.4.5 d.230.1.1 Length = 187

 Score = 49.9 bits (119), Expect = 4e-07
 Identities = 26/114 (22%), Positives = 48/114 (42%), Gaps = 23/114 (20%)

Query: 121 PTLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRL 180
                +            P   E         G+V  +  FG+F+  G   DGL+HVS++
Sbjct: 61  HGDGSAYHPVVFETLVYIPEMYE------LIEGEVVDVVEFGSFVRLG-PLDGLIHVSQI 113

Query: 181 SDNFV-----------KDVGSIVSVGQEVKVRLIEANAET-----GRISLTMRE 218
            D++V           K+ G ++ +G  V+ R++  + +       +I+LTMR+
Sbjct: 114 MDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAERKRGSKIALTMRQ 167

>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 Length = 172

 Score = 48.8 bits (116), Expect = 8e-07
 Identities = 8/86 (9%), Positives = 24/86 (27%), Gaps = 15/86 (17%)

Query: 147 PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFV------------KDVGSIVSV 194
            G      V  +   G F + G      +    +                  D   ++  
Sbjct: 81  KGEVVDAVVTQVNKVGLFTEIG-PMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQ 139

Query: 195 GQEVKVRLIEANAETGRISL--TMRE 218
             E++++++    +   I    ++ +
Sbjct: 140 DDEIRLKIVGTRVDKNDIFAIGSLMD 165

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 49.9 bits (118), Expect = 2e-06
 Identities = 73/505 (14%), Positives = 142/505 (28%), Gaps = 189/505 (37%)

Query: 174 LVHVSRLSDNFVKDVG---------SIVSVGQEVKVRLIEANAETG--RISLTMRESDDI 222
           ++ V    D FV +           SI+S  +E+   ++  +A +G  R+  T+    + 
Sbjct: 21  ILSV--FEDAFVDNFDCKDVQDMPKSILS-KEEIDHIIMSKDAVSGTLRLFWTLLSKQE- 76

Query: 223 SKLQQ------QKDATASGDKVRTTRRSTSKPG----QKRDEMKTT--KFVKGQ------ 264
             +Q+      + +       ++T +R  S       ++RD +      F K        
Sbjct: 77  EMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQP 136

Query: 265 --DLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGG---SSLQVGQEV--SV 317
              L   +  L R    + +    +G               + G   + + +  +V  S 
Sbjct: 137 YLKLRQALLEL-RPAKNVLI----DG---------------VLGSGKTWVAL--DVCLSY 174

Query: 318 RVLRISRGQVT-LTMKKEDDVGSNLQLTQGVIHAATNPFVLAFRSNKDISSFLDERDKSA 376
           +V      ++  L +K  +   + L++ Q           L ++ + + +S  D      
Sbjct: 175 KVQCKMDFKIFWLNLKNCNSPETVLEMLQK----------LLYQIDPNWTSRSD------ 218

Query: 377 TAAKKSEKPTPIEIGGEVSQMEAGSSIPKVQDQPTS---SDDGMASVPSAVGETVEDHEA 433
                      + I    S       + K +          +            V++   
Sbjct: 219 -----HSSNIKLRIH---SIQAELRRLLKSKPYENCLLVLLN------------VQN--- 255

Query: 434 PSKEKGELADIANRNDDPQNVMSGSSETLDGALQTIEKETEETTLNQTIEETPSTDVSGE 493
                   A   N         + S + L      +      TT  + +     TD    
Sbjct: 256 --------AKAWN-------AFNLSCKIL------L------TTRFKQV-----TDFLSA 283

Query: 494 LAEQALSTDGPKAGEFTESQTEDTIAKDEVQILTPATEEKETKDTTEALAPEGSVSTEKQ 553
                +S D       T  + +  + K     L     +   +D    L P         
Sbjct: 284 ATTTHISLDHHSMT-LTPDEVKSLLLK----YL-----DCRPQD----L-PR-------- 320

Query: 554 IIGEAASTN---LSGEIAEQVSVSDSPK--D--EEVVQNQTDDVIAKDEEQIQTPTTESE 606
              E  +TN   LS  IAE  S+ D     D  + V  ++   +I         P    +
Sbjct: 321 ---EVLTTNPRRLSI-IAE--SIRDGLATWDNWKHVNCDKLTTIIESSLNV-LEPAEYRK 373

Query: 607 -------IPSAGSLKEKESGPIPDK 624
                   P         S  IP  
Sbjct: 374 MFDRLSVFP--------PSAHIPTI 390

>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 Length = 644

 Score = 47.2 bits (113), Expect = 1e-05
 Identities = 14/78 (17%), Positives = 22/78 (28%), Gaps = 17/78 (21%)

Query: 150 TFTGKVRSIQPFGAFI---DFGAFTDGLVHVSRLSDN---FVKDV---------GSIVSV 194
            F  ++  I   G  +   D GA     +    L       V             ++  V
Sbjct: 563 RFAAEIVDISRGGMRVRLVDNGA--IAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKV 620

Query: 195 GQEVKVRLIEANAETGRI 212
              + V + E   ET  I
Sbjct: 621 TDVIDVTIAEVRMETRSI 638

>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 Length = 469

 Score = 43.8 bits (104), Expect = 2e-04
 Identities = 9/71 (12%), Positives = 20/71 (28%), Gaps = 18/71 (25%)

Query: 147 PGATFTGKVRSIQPFGAFI---DFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLI 203
           P   +   V   +   A +   D     D  V+                + G  ++V+  
Sbjct: 403 PERVWDAVVVDRRGAQATLLIPDLAF--DVQVNTP-------------AAPGTALQVQFA 447

Query: 204 EANAETGRISL 214
           + +    R+  
Sbjct: 448 DIDLPQMRVRA 458

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	681
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	99.95
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	99.92
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	99.76
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	99.61
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	99.61
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	99.59
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	99.57
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	99.5
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	99.5
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	99.49
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	99.49
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	99.49
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	99.48
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	99.46
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	99.45
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	99.45
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	99.44
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	99.43
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	99.42
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	99.4
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	99.4
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	99.39
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	99.34
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	99.26
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	99.21
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	99.2
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	99.18
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	99.13
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	99.12
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	99.07
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	99.05
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	99.03
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	99.01
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	99.01
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	98.99
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	98.99
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	98.97
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	98.95
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	98.95
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	98.94
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	98.89
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	98.88
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	98.88
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	98.83
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	98.83
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	98.82
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	98.82
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	98.81
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	98.8
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	98.79
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	98.79
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	98.77
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	98.77
2bh8_A	101	1B11; transcription, molecular evolution, unique a	98.77
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	98.71
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	98.69
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	98.67
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	98.67
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	98.64
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	98.63
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	98.6
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	98.6
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	98.59
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	98.56
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	98.56
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	98.51
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	98.37
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	98.34
2bh8_A	101	1B11; transcription, molecular evolution, unique a	98.19
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	98.12
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	98.1
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	98.04
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	98.04
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	97.96
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	97.86
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	97.8
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	97.78
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	97.75
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	97.71
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	97.71
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	97.66
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	97.58
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	97.54
2r7d_A	469	Ribonuclease II family protein; structural genomic	97.5
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	97.46
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	97.39
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	97.3
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	96.34
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	94.97
2rf4_A	214	DNA-directed RNA polymerase I subunit RPA4; transf	91.89
1wfq_A	89	UNR protein; beta-barrel, translational regulation	87.51
3d0f_A	106	Penicillin-binding 1 transmembrane protein MRCA; B	87.41
2yty_A	88	Cold shock domain-containing protein E1; cell-free	85.87
3d0f_A	106	Penicillin-binding 1 transmembrane protein MRCA; B	84.15
2rf4_A	214	DNA-directed RNA polymerase I subunit RPA4; transf	83.17
1c9o_A	66	CSPB, cold-shock protein; beta barrel, homodimer,	82.52
2ytx_A	97	Cold shock domain-containing protein E1; cell-free	81.26
2r7d_A	469	Ribonuclease II family protein; structural genomic	80.61

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

Probab=99.95  E-value=1.4e-26  Score=240.63  Aligned_cols=199  Identities=16%  Similarity=0.167  Sum_probs=168.8

Q ss_pred             ceeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCChhh
Q 005707           44 SQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASPTL  123 (681)
Q Consensus        44 ~~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~~da  123 (681)
                      ..+++++++|..||+|.+++..          -+|+++.|.|. .|++.+    ++++.+                    
T Consensus        19 ~~G~fv~~~g~egllp~se~~~----------~vGdevev~v~-~d~~~r----~iat~~--------------------   63 (285)
T 3go5_A           19 DRFYFVQKDGQTYALAKEEGQH----------TVGDTVKGFAY-TDMKQK----LRLTTL--------------------   63 (285)
T ss_dssp             SSEEEEEETTEEEEEEGGGCCC----------CTTSEEEEEEE-ECTTSC----EEEECS--------------------
T ss_pred             CCEEEEEcCCeEEEEEHHHCcc----------ccCCEEEEEEE-ECCCCC----EEEecc--------------------
Confidence            4788999999999999999842          39999999998 465544    666543                    


Q ss_pred             HHhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEe-cCeeEEEECC-CeEEEEeccccCCccccCcccccccCCEEEEE
Q 005707          124 AESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQ-PFGAFIDFGA-FTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVR  201 (681)
Q Consensus       124 ek~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~-d~GaFVdLgg-gV~GLVPiSELS~~~v~d~~e~fkVGd~VkVk  201 (681)
                                        ...+++|+++.|+|++++ ++|+||++|. +.+||||+++++|.+.    ..+++||.+.|+
T Consensus        64 ------------------~p~~~~G~~~~g~V~~v~~~~GaFVdiG~~~~d~lvp~sel~~~~~----~~~~~Gd~v~v~  121 (285)
T 3go5_A           64 ------------------EVTATQDQFGWGRVTEVRKDLGVFVDTGLPDKEIVVSLDILPELKE----LWPKKGDQLYIR  121 (285)
T ss_dssp             ------------------CCCSCSSSCEEEEEEEEETTTEEEEECSCTTCCEEEEGGGSCSSGG----GSCCTTCEEEEE
T ss_pred             ------------------cccccCCCEEEEEEEEEccCceEEEEECCCCcEEEEEHHHCCcccc----cccCCCCEEEEE
Confidence                              124689999999999999 7999999997 6999999999998643    246899999766


Q ss_pred             EEEEeccCCceEEEEecc-chhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEE
Q 005707          202 LIEANAETGRISLTMRES-DDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFI  280 (681)
Q Consensus       202 Vl~VD~ekgrI~LSlK~l-~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFV  280 (681)
                       +.+|+ ++||.+|+|+. ..++|.                             ....+|++|++|.|+|++++++|+||
T Consensus       122 -l~iD~-~~Ri~ls~k~~~~~~~~~-----------------------------~~~~~~~~G~~V~g~V~~i~~~G~fV  170 (285)
T 3go5_A          122 -LEVDK-KDRIWGLLAYQEDFQRLA-----------------------------RPAYNNMQNQNWPAIVYRLKLSGTFV  170 (285)
T ss_dssp             -EEECT-TSCEEEEECCHHHHHHHC-----------------------------CCCCSCCTTCEEEEEEEEEETTEEEE
T ss_pred             -EEECC-CCcEEEEehhhhhcchhh-----------------------------hhhhhCCCCCEEEEEEEEEeCCcEEE
Confidence             58998 78999999976 456772                             34678999999999999999999999


Q ss_pred             -EeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCcCC
Q 005707          281 -SLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVGSN  340 (681)
Q Consensus       281 -eIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP~e  340 (681)
                       .+++|++||||.+|+++          .|++||.|+|+|++|+  ++||.||||+....+++
T Consensus       171 ~~i~~g~~Glih~SEl~~----------~l~~Gd~v~~~V~~id~~d~kI~LSlk~~~~~~~~  223 (285)
T 3go5_A          171 YLPENNMLGFIHPSERYA----------EPRLGQVLDARVIGFREVDRTLNLSLKPRSFEMLE  223 (285)
T ss_dssp             EETTTTEEEEECGGGCSS----------CCCTTCEEEEEEEEEETTTTEEEEECSCCCCCCCC
T ss_pred             EEeCCCeEEEEEHHHccc----------cCCCCCEEEEEEEEEECCCCeEEEEeChhhhhccc
Confidence             99999999999999873          4799999999999997  59999999998766655

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

Probab=99.92  E-value=1.2e-24  Score=226.26  Aligned_cols=172  Identities=12%  Similarity=0.029  Sum_probs=147.9

Q ss_pred             CCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccchhhHh
Q 005707          146 IPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDISKL  225 (681)
Q Consensus       146 kvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~dp~e  225 (681)
                      .+|++++|+|+++.++|+||+++ +.+||||.++++.          ++||.|+|+|+. |. .+|+.+|++    .|  
T Consensus         5 ~~G~~v~g~V~~~~~~G~fv~~~-g~egllp~se~~~----------~vGdevev~v~~-d~-~~r~iat~~----~p--   65 (285)
T 3go5_A            5 NLASFIVGLIIDENDRFYFVQKD-GQTYALAKEEGQH----------TVGDTVKGFAYT-DM-KQKLRLTTL----EV--   65 (285)
T ss_dssp             TTTEEEEEEEEEECSSEEEEEET-TEEEEEEGGGCCC----------CTTSEEEEEEEE-CT-TSCEEEECS----CC--
T ss_pred             cCCCEEEEEEEEEECCEEEEEcC-CeEEEEEHHHCcc----------ccCCEEEEEEEE-CC-CCCEEEecc----cc--
Confidence            47999999999999999999997 5999999999943          799999999984 54 567777764    22  


Q ss_pred             hhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEe-cceEEEEeCC-CeEEEEeCCCCCccccccc
Q 005707          226 QQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLT-RSGAFISLPE-GEEGFLPTSEESDDGFANM  303 (681)
Q Consensus       226 k~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt-~~GaFVeIg~-GIeGLLpiSELSd~~ie~~  303 (681)
                                                       .+++|+++.|+|++++ ++|+||+++. +++||||.++++|.+.   
T Consensus        66 ---------------------------------~~~~G~~~~g~V~~v~~~~GaFVdiG~~~~d~lvp~sel~~~~~---  109 (285)
T 3go5_A           66 ---------------------------------TATQDQFGWGRVTEVRKDLGVFVDTGLPDKEIVVSLDILPELKE---  109 (285)
T ss_dssp             ---------------------------------CSCSSSCEEEEEEEEETTTEEEEECSCTTCCEEEEGGGSCSSGG---
T ss_pred             ---------------------------------cccCCCEEEEEEEEEccCceEEEEECCCCcEEEEEHHHCCcccc---
Confidence                                             3789999999999999 7999999997 7999999999999752   


Q ss_pred             CCCCcccCCCEEEEEEEEEe-CCeEEEEEecc-CCCcCC--------cceeeeEEEEeecccEEEE-EEcCCeEEEeeCC
Q 005707          304 MGGSSLQVGQEVSVRVLRIS-RGQVTLTMKKE-DDVGSN--------LQLTQGVIHAATNPFVLAF-RSNKDISSFLDER  372 (681)
Q Consensus       304 ~p~~~fkVGqkVkVrVL~ID-kgKI~LSLK~~-~~DP~e--------~~lv~G~V~~~i~~fGlfV-~l~~gI~GfIp~~  372 (681)
                         ..+++||.|.|+ +.+| ++||.||+|+. ..+||.        ++.+.|+|. ++.+||+|| .+++++.||||.+
T Consensus       110 ---~~~~~Gd~v~v~-l~iD~~~Ri~ls~k~~~~~~~~~~~~~~~~~G~~V~g~V~-~i~~~G~fV~~i~~g~~Glih~S  184 (285)
T 3go5_A          110 ---LWPKKGDQLYIR-LEVDKKDRIWGLLAYQEDFQRLARPAYNNMQNQNWPAIVY-RLKLSGTFVYLPENNMLGFIHPS  184 (285)
T ss_dssp             ---GSCCTTCEEEEE-EEECTTSCEEEEECCHHHHHHHCCCCCSCCTTCEEEEEEE-EEETTEEEEEETTTTEEEEECGG
T ss_pred             ---cccCCCCEEEEE-EEECCCCcEEEEehhhhhcchhhhhhhhCCCCCEEEEEEE-EEeCCcEEEEEeCCCeEEEEEHH
Confidence               467999999766 6898 58999999875 345654        366899999 899999999 9999999999999


Q ss_pred             ccccc
Q 005707          373 DKSAT  377 (681)
Q Consensus       373 els~~  377 (681)
                      |+++.
T Consensus       185 El~~~  189 (285)
T 3go5_A          185 ERYAE  189 (285)
T ss_dssp             GCSSC
T ss_pred             Hcccc
Confidence            99975

>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=99.76  E-value=4.7e-21  Score=187.65  Aligned_cols=124  Identities=19%  Similarity=0.291  Sum_probs=104.0

Q ss_pred             CCCCcEEEEEEEEEecCeeEEEE--CCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccchh
Q 005707          145 LIPGATFTGKVRSIQPFGAFIDF--GAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDI  222 (681)
Q Consensus       145 LkvGdIVeGkV~sV~d~GaFVdL--gggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~d  222 (681)
                      +++|+++.|+|++|++||+||+|  .++++||||+++|+|+++.++.+.|++||.|+|+|+++|.++++|.||+|++..+
T Consensus        13 p~~G~iv~G~V~~I~~fGaFV~L~e~~g~eGLvhiSels~~~v~~~~~~~~vGd~V~VkVl~vD~~~~rI~LSlk~~~~~   92 (182)
T 1kl9_A           13 PEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVSPE   92 (182)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC------------CTTCEEEEEEEEEETTTTEEEEESTTCCHH
T ss_pred             CCCCCEEEEEEEEEeccEEEEEEccCCCcEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeecCcC
Confidence            58999999999999999999999  5679999999999999999999999999999999999999999999999999999


Q ss_pred             hHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEec-ceEEEEeCCCeEEEEeCCCCCccc
Q 005707          223 SKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTR-SGAFISLPEGEEGFLPTSEESDDG  299 (681)
Q Consensus       223 p~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~-~GaFVeIg~GIeGLLpiSELSd~~  299 (681)
                      ||.                             ....+|+.|+.+.|+|+++++ +|  |.|.+|++||+|.++++|.+
T Consensus        93 p~~-----------------------------~~~~~~~~g~~v~g~v~~i~~~~g--v~l~~giegl~h~s~~~~~~  139 (182)
T 1kl9_A           93 EAI-----------------------------KCEDKFTKSKTVYSILRHVAEVLE--YTKDEQLESLFQRTAWVFDD  139 (182)
T ss_dssp             HHH-----------------------------HHHHHHHHHHHHHHHHHHHHHHTT--CCSHHHHHHHHHHTHHHHHH
T ss_pred             hHH-----------------------------HHHHhccCCCEEEEEEEEchhhcC--CcccCChhheEEeeecchhh
Confidence            983                             456789999999999999998 99  89999999999999887753

>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=99.61  E-value=1.1e-17  Score=163.94  Aligned_cols=113  Identities=15%  Similarity=0.241  Sum_probs=89.3

Q ss_pred             CccCcEEEEEEEEEecceEEEEe--CCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccC
Q 005707          260 FVKGQDLEGTVKNLTRSGAFISL--PEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKED  335 (681)
Q Consensus       260 lkvGdIV~G~VknVt~~GaFVeI--g~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~  335 (681)
                      +++|+++.|+|++|++||+||+|  .+|++||||+++++|.++.  ++...|++||.|.|+|+++|  ++||.||||+..
T Consensus        13 p~~G~iv~G~V~~I~~fGaFV~L~e~~g~eGLvhiSels~~~v~--~~~~~~~vGd~V~VkVl~vD~~~~rI~LSlk~~~   90 (182)
T 1kl9_A           13 PEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIR--SINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVS   90 (182)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC--------------CTTCEEEEEEEEEETTTTEEEEESTTCC
T ss_pred             CCCCCEEEEEEEEEeccEEEEEEccCCCcEEEEEHHHCCCcccC--CHHHhcCCCCEEEEEEEEEECCCCEEEEEEeecC
Confidence            37999999999999999999999  5799999999999999864  45899999999999999998  589999999999


Q ss_pred             CCcCCc---c-----eeeeEEEEeecc-cEEEEEEcCCeEEEeeCCccccc
Q 005707          336 DVGSNL---Q-----LTQGVIHAATNP-FVLAFRSNKDISSFLDERDKSAT  377 (681)
Q Consensus       336 ~DP~e~---~-----lv~G~V~~~i~~-fGlfV~l~~gI~GfIp~~els~~  377 (681)
                      .+||..   +     .+.|+|. .+.+ ||  +.+.+|++||+|.+++++.
T Consensus        91 ~~p~~~~~~~~~~g~~v~g~v~-~i~~~~g--v~l~~giegl~h~s~~~~~  138 (182)
T 1kl9_A           91 PEEAIKCEDKFTKSKTVYSILR-HVAEVLE--YTKDEQLESLFQRTAWVFD  138 (182)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH-HHHHHTT--CCSHHHHHHHHHHTHHHHH
T ss_pred             cChHHHHHHhccCCCEEEEEEE-EchhhcC--CcccCChhheEEeeecchh
Confidence            999873   2     3466766 5666 99  7888999999999988654

>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=99.61  E-value=1.2e-16  Score=155.65  Aligned_cols=104  Identities=16%  Similarity=0.293  Sum_probs=89.2

Q ss_pred             CCCcEEEEEEEEEecCeeEEEE--CCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccchhh
Q 005707          146 IPGATFTGKVRSIQPFGAFIDF--GAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDIS  223 (681)
Q Consensus       146 kvGdIVeGkV~sV~d~GaFVdL--gggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~dp  223 (681)
                      ++|+++.|+|+++.+||+||+|  +++++||||+++|+|+++.++.+.|++||.|+|+|+.+|+++++|.||+|.+..+|
T Consensus        14 ~~G~iv~G~V~~i~~fGaFV~L~e~~gveGLvhiSels~~~v~~~~~~~~vGd~V~vkVl~vd~~~~~I~LSlk~~~~~~   93 (175)
T 2a19_A           14 EIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKRRVSSED   93 (175)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEETTTTTCEEEEECC--------CCCCCCCTTSEEEEEEEEEETTTTEEEEESTTCCHHH
T ss_pred             CCCCEEEEEEEEEecceEEEEEcCCCCcEEEEEHHHcCCcccCCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEecCcCh
Confidence            4899999999999999999999  36699999999999999999999999999999999999999999999999999999


Q ss_pred             HhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEe-cceE
Q 005707          224 KLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLT-RSGA  278 (681)
Q Consensus       224 ~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt-~~Ga  278 (681)
                      |.                             ....+|+.|+.+.|+|++++ ++|+
T Consensus        94 ~~-----------------------------~~~~~~~~g~~v~g~V~~i~~~~G~  120 (175)
T 2a19_A           94 II-----------------------------KCEEKYQKSKTVHSILRYCAEKFQI  120 (175)
T ss_dssp             HH-----------------------------HHHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             HH-----------------------------HHHHhccCCCcceEEEEEchhhcCC
Confidence            83                             45778999999999999998 7886

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

Probab=99.59  E-value=5.5e-15  Score=134.00  Aligned_cols=85  Identities=29%  Similarity=0.420  Sum_probs=76.4

Q ss_pred             ccccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcc-cccccCCCCcccCCCEEEEEEEEEe--CCeEEEEE
Q 005707          255 MKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDD-GFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTM  331 (681)
Q Consensus       255 ~~~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~-~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSL  331 (681)
                      ....++++|+++.|+|++|.++|+||+|++|++||||+++++|. +.  .++...|++||.|.|+|+++|  ++||.|||
T Consensus        23 ~~~~~~~~G~~~~G~V~~v~~~G~FV~l~~~~~Glvhisel~~~~~~--~~~~~~~~vGd~V~vkV~~vd~~~~rI~lsl  100 (115)
T 2khi_A           23 AIAKRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDWTNKN--IHPSKVVNVGDVVEVMVLDIDEERRRISLGL  100 (115)
T ss_dssp             CSSCSSCSSCEEEEEEEEEETTEEEEECSTTCEEEEETTSSSCSSTT--CSSTTTCCTTCEEEEEEEEEETTTTEEEECC
T ss_pred             HHhhcCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCccccc--cCcccEECCCCEEEEEEEEEECCCCEEEEEE
Confidence            34578999999999999999999999999999999999999984 33  345789999999999999998  58999999


Q ss_pred             eccCCCcCCc
Q 005707          332 KKEDDVGSNL  341 (681)
Q Consensus       332 K~~~~DP~e~  341 (681)
                      |+..+|||+.
T Consensus       101 k~~~~~p~~~  110 (115)
T 2khi_A          101 KQCKANPWQQ  110 (115)
T ss_dssp             CCCCSSCCCC
T ss_pred             EecCcCHHHH
Confidence            9999999984

>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=99.57  E-value=2.3e-16  Score=165.71  Aligned_cols=111  Identities=21%  Similarity=0.340  Sum_probs=102.5

Q ss_pred             cCCCCCCcEEEEEEEEEecCeeEEEEC--CCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEecc
Q 005707          142 NEDLIPGATFTGKVRSIQPFGAFIDFG--AFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRES  219 (681)
Q Consensus       142 ~~~LkvGdIVeGkV~sV~d~GaFVdLg--ggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l  219 (681)
                      ...+++|++|.|+|++|.+||+||+|+  ++++||||+++++|+++.++.+.|++||.|+|+|+.+|+++++|.||+|.+
T Consensus         8 ~~~~~vG~iv~G~V~~I~~fGaFV~L~ey~gveGLvhiSels~~~i~~~~~~~kvGd~V~VkVl~vD~~~~rI~LSlK~~   87 (308)
T 1q8k_A            8 HKFPEVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNECVKVIRVDKEKGYIDLSKRRV   87 (308)
T ss_dssp             SCCCSSCCEEEEEEEEEETTEEEEESCTTTSCCEEECGGGTSCSSCSCCTTTCSSSCEEEEEEEEEETTTTEEEEECSSC
T ss_pred             hcCCCCCCEEEEEEEEEeCcEEEEEECCCCCeEEEEEhHHcCcccccCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEEec
Confidence            445679999999999999999999997  679999999999999999999999999999999999999999999999999


Q ss_pred             chhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEec-ceEEEE
Q 005707          220 DDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTR-SGAFIS  281 (681)
Q Consensus       220 ~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~-~GaFVe  281 (681)
                      ..+||.                             ....+|++|+++.|+|+++.+ ||+|++
T Consensus        88 ~~~p~~-----------------------------~~~~~~~~G~~v~G~V~~v~~~~G~fi~  121 (308)
T 1q8k_A           88 SPEEAI-----------------------------KCEDKFTKSKTVYSILRHVAEVLEYTKD  121 (308)
T ss_dssp             CHHHHH-----------------------------HHHHHHHHHHHHHHHHHHHHHHTTCCSS
T ss_pred             ccChHH-----------------------------HHHHHccCCCeeEEEEEEcccccCCccC
Confidence            999983                             456789999999999999998 599874

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

Probab=99.50  E-value=2.4e-14  Score=128.38  Aligned_cols=80  Identities=29%  Similarity=0.438  Sum_probs=71.8

Q ss_pred             ccccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC--CeEEEEEe
Q 005707          255 MKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR--GQVTLTMK  332 (681)
Q Consensus       255 ~~~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk--gKI~LSLK  332 (681)
                      ....++++|+++.|+|++|.++|+||+|++|++||||.+++++.++.  .+...|++||.|.|+|+++|.  ++|.||+|
T Consensus        24 ~~~~~~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gll~~sel~~~~~~--~~~~~~~vGd~V~v~V~~vd~~~~ki~LS~k  101 (109)
T 2khj_A           24 NWVALNKKGAIVTGKVTAVDAKGATVELADGVEGYLRASEASRDRVE--DATLVLSVGDEVEAKFTGVDRKNRAISLSVR  101 (109)
T ss_dssp             HHTTTCCSSSEEEEEEEEECSSCEEEECSTTCBCCBCTTCCCSSSSS--SGGGSCCTTCEEEEEEEEEETTTTEEEEETT
T ss_pred             HHhhcCCCCCEEEEEEEEEECCeEEEEECCCCEEEEEHHHcCccccc--ChhhccCCCCEEEEEEEEEECCCCEEEEEEe
Confidence            45678999999999999999999999999999999999999998754  347789999999999999984  68999999


Q ss_pred             ccCC
Q 005707          333 KEDD  336 (681)
Q Consensus       333 ~~~~  336 (681)
                      .+.+
T Consensus       102 ~~~~  105 (109)
T 2khj_A          102 AKDE  105 (109)
T ss_dssp             SSSS
T ss_pred             ecCh
Confidence            8754

>1luz_A Protein K3, protein K2; stranded anti-parallel beta barrel, viral protein; 1.80A {Vaccinia virus} SCOP: b.40.4.5

Probab=99.50  E-value=3.1e-14  Score=123.97  Aligned_cols=80  Identities=16%  Similarity=0.234  Sum_probs=74.1

Q ss_pred             CCcCCCCCCcEEEEEEEEEecCeeEEEEC--CCeEEEEecc-ccCCccccCcccccccCCEEEEEEEEEeccCCceEEEE
Q 005707          140 VKNEDLIPGATFTGKVRSIQPFGAFIDFG--AFTDGLVHVS-RLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTM  216 (681)
Q Consensus       140 lt~~~LkvGdIVeGkV~sV~d~GaFVdLg--ggV~GLVPiS-ELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSl  216 (681)
                      +.|...++|+++.|+|+ +++||+||+|.  ++++||||++ +++++++.++.+.+ +||.|+|+|+++|.++++|.||+
T Consensus         4 ~~y~~~~vG~~~~G~V~-v~~fG~FVel~~~~~~eGLvhis~el~~~~~~~~~~~~-~Gd~V~VkV~~vd~~~~kI~lsl   81 (88)
T 1luz_A            4 FCYSLPNAGDVIKGRVY-EKDYALYIYLFDYPHFEAILAESVKMHMDRYVEYRDKL-VGKTVKVKVIRVDYTKGYIDVNY   81 (88)
T ss_dssp             CCSCCCCTTCEEEEEEE-EETTEEEEEETTCTTSEEEEGGGSSCCHHHHHHHHHHH-TTCEEEEEEEEEETTTTEEEEEE
T ss_pred             EEecCCCCCCEEEEEEE-EEccEEEEEECCCCCeEEEEEeeHHhCcccccCHhHEe-CCCEEEEEEEEEECCCCEEEEEE
Confidence            45788899999999999 99999999996  3699999999 99999999999999 99999999999999999999999


Q ss_pred             eccch
Q 005707          217 RESDD  221 (681)
Q Consensus       217 K~l~~  221 (681)
                      |.+.+
T Consensus        82 k~~~~   86 (88)
T 1luz_A           82 KRMCR   86 (88)
T ss_dssp             EEECS
T ss_pred             eecCC
Confidence            97654

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

Probab=99.49  E-value=6.6e-14  Score=129.79  Aligned_cols=82  Identities=38%  Similarity=0.727  Sum_probs=77.8

Q ss_pred             CCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccchh
Q 005707          143 EDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDI  222 (681)
Q Consensus       143 ~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~d  222 (681)
                      ..+++|++|.|+|++|.++|+||+|+++++||||+++++++++.++...|++||.|+|+|+.+|.++++|.||++.+..+
T Consensus         3 ~~~~vG~iv~G~V~~i~~~G~FV~l~~~~~Glihisel~~~~~~~~~~~~~vGd~V~vkV~~vd~~~~kI~LSlk~~~~~   82 (130)
T 2k4k_A            3 AKFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQVKVLAVDEEKGKISLSIRATQAA   82 (130)
T ss_dssp             CCCCTTCEEEEEEEEEETTEEEEEEETTEEEEEEGGGTSSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEEESHHHHHS
T ss_pred             CcCCCCCEEEEEEEEEeCCeEEEEECCCcEEEEEHHHCCcccccCccccCCCCCEEEEEEEEEeCCCCEEEEEEeecccC
Confidence            46899999999999999999999998889999999999999999999999999999999999999999999999988877


Q ss_pred             hH
Q 005707          223 SK  224 (681)
Q Consensus       223 p~  224 (681)
                      |+
T Consensus        83 p~   84 (130)
T 2k4k_A           83 PE   84 (130)
T ss_dssp             CC
T ss_pred             cc
Confidence            75

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

Probab=99.49  E-value=8.2e-14  Score=126.31  Aligned_cols=83  Identities=27%  Similarity=0.454  Sum_probs=78.1

Q ss_pred             cCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCc-cccCcccccccCCEEEEEEEEEeccCCceEEEEeccc
Q 005707          142 NEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDN-FVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESD  220 (681)
Q Consensus       142 ~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~-~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~  220 (681)
                      ...+++|+++.|+|+++.++|+||+|+++++||||+++++++ +..++...|++||.|+|+|+.+|.++++|.||++.+.
T Consensus        25 ~~~~~~G~~~~G~V~~v~~~G~FV~l~~~~~Glvhisel~~~~~~~~~~~~~~vGd~V~vkV~~vd~~~~rI~lslk~~~  104 (115)
T 2khi_A           25 AKRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDWTNKNIHPSKVVNVGDVVEVMVLDIDEERRRISLGLKQCK  104 (115)
T ss_dssp             SCSSCSSCEEEEEEEEEETTEEEEECSTTCEEEEETTSSSCSSTTCSSTTTCCTTCEEEEEEEEEETTTTEEEECCCCCC
T ss_pred             hhcCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCccccccCcccEECCCCEEEEEEEEEECCCCEEEEEEEecC
Confidence            357899999999999999999999999889999999999984 7788899999999999999999999999999999999


Q ss_pred             hhhH
Q 005707          221 DISK  224 (681)
Q Consensus       221 ~dp~  224 (681)
                      .+||
T Consensus       105 ~~p~  108 (115)
T 2khi_A          105 ANPW  108 (115)
T ss_dssp             SSCC
T ss_pred             cCHH
Confidence            9998

>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=99.49  E-value=5.7e-14  Score=125.17  Aligned_cols=83  Identities=25%  Similarity=0.344  Sum_probs=74.4

Q ss_pred             cccCCccCcEEEEEEEEEecceEEEEeCC---CeEEEEeCCCC-CcccccccCCCCcccCCCEEEEEEEEEeCCeEEEEE
Q 005707          256 KTTKFVKGQDLEGTVKNLTRSGAFISLPE---GEEGFLPTSEE-SDDGFANMMGGSSLQVGQEVSVRVLRISRGQVTLTM  331 (681)
Q Consensus       256 ~~sklkvGdIV~G~VknVt~~GaFVeIg~---GIeGLLpiSEL-Sd~~ie~~~p~~~fkVGqkVkVrVL~IDkgKI~LSL  331 (681)
                      ...++++|+++.|+|++|.+||+||+|++   +++||||++++ ++.++.  ++...|++||.|+|+|+++|.+||.|||
T Consensus         6 ~~~~~~vG~i~~G~V~~v~~fG~FV~l~~~~~~~~Glvhisel~~~~~~~--~~~~~~~~Gd~V~VkV~~vd~~~i~LSl   83 (103)
T 2eqs_A            6 SGEEPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVA--NVADVVSKGQRVKVKVLSFTGTKTSLSM   83 (103)
T ss_dssp             CCSSCCTTCEEEEEEEEECSSCEEEEECSSSSCCEEEECGGGTSSSSCCC--CHHHHCCTTCEEEEEEEEEETTEEEEES
T ss_pred             ccccCCCCCEEEEEEEEEeccEEEEEEcCCCCCeEEEEEHHHCCCCcccC--CcccEeCCCCEEEEEEEEEECCeeEEEE
Confidence            46678999999999999999999999996   99999999999 555432  3467899999999999999999999999


Q ss_pred             eccCCCcCC
Q 005707          332 KKEDDVGSN  340 (681)
Q Consensus       332 K~~~~DP~e  340 (681)
                      |...++||.
T Consensus        84 k~~~~~~~~   92 (103)
T 2eqs_A           84 KDVDQETGE   92 (103)
T ss_dssp             TTBCTTTCC
T ss_pred             eecccCCch
Confidence            999999987

>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB: 1yz6_A

Probab=99.48  E-value=3.8e-15  Score=154.27  Aligned_cols=109  Identities=20%  Similarity=0.415  Sum_probs=99.9

Q ss_pred             CCCCCcEEEEEEEEEecCeeEEEEC--CCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccch
Q 005707          144 DLIPGATFTGKVRSIQPFGAFIDFG--AFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDD  221 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~GaFVdLg--ggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~  221 (681)
                      .+++|++|.|+|+++.+||+||+|+  ++++||||+++++++++.++.+.|++||.|.|+|+.+|+++++|.||++.+..
T Consensus         8 ~p~~Gdiv~G~V~~I~~fGaFV~L~e~~gieGlIhiSels~~~v~~~~~~~kvGd~V~vkVi~vD~~~~~I~LSlk~~~~   87 (275)
T 3aev_A            8 YPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVDPRKGHIDLSLRRVTQ   87 (275)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEETTSTTCEEEEEGGGSCSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEEESTTCCH
T ss_pred             CCCCCCEEEEEEEEEECcEEEEEECCCCCeEEEEEHHHcCcccccCHHhccCCCCEEEEEEEEEECCCCEEEEEEeecCc
Confidence            4568999999999999999999997  57999999999999999999999999999999999999999999999999998


Q ss_pred             hhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEe-cceEEEE
Q 005707          222 ISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLT-RSGAFIS  281 (681)
Q Consensus       222 dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt-~~GaFVe  281 (681)
                      ++|.                             ....+|+.|+.+.|.|+++. ++|++++
T Consensus        88 ~~~~-----------------------------~~~~~~~~g~~v~g~v~~v~~~~G~~~e  119 (275)
T 3aev_A           88 QQRK-----------------------------AKLQEFKRAQKAENLLRLAAEKLGKDFE  119 (275)
T ss_dssp             HHHH-----------------------------HHHHHHHHHHHHHHHHHHHHHHHTCCHH
T ss_pred             chhH-----------------------------HHHHhccCCCeEEEEEEEchhhcCCCHH
Confidence            8883                             34677899999999999998 8898655

>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=99.46  E-value=1.5e-13  Score=122.47  Aligned_cols=82  Identities=35%  Similarity=0.594  Sum_probs=75.6

Q ss_pred             CcCCCCCCcEEEEEEEEEecCeeEEEECC---CeEEEEecccc-CCccccCcccccccCCEEEEEEEEEeccCCceEEEE
Q 005707          141 KNEDLIPGATFTGKVRSIQPFGAFIDFGA---FTDGLVHVSRL-SDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTM  216 (681)
Q Consensus       141 t~~~LkvGdIVeGkV~sV~d~GaFVdLgg---gV~GLVPiSEL-S~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSl  216 (681)
                      ....+++|++|.|+|++|.+||+||+|++   +++||||++++ ++.++.++.+.|++||.|+|+|+.+|.  ++|.||+
T Consensus         6 ~~~~~~vG~i~~G~V~~v~~fG~FV~l~~~~~~~~Glvhisel~~~~~~~~~~~~~~~Gd~V~VkV~~vd~--~~i~LSl   83 (103)
T 2eqs_A            6 SGEEPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTG--TKTSLSM   83 (103)
T ss_dssp             CCSSCCTTCEEEEEEEEECSSCEEEEECSSSSCCEEEECGGGTSSSSCCCCHHHHCCTTCEEEEEEEEEET--TEEEEES
T ss_pred             ccccCCCCCEEEEEEEEEeccEEEEEEcCCCCCeEEEEEHHHCCCCcccCCcccEeCCCCEEEEEEEEEEC--CeeEEEE
Confidence            46678999999999999999999999985   79999999999 677788899999999999999999997  6999999


Q ss_pred             eccchhhH
Q 005707          217 RESDDISK  224 (681)
Q Consensus       217 K~l~~dp~  224 (681)
                      |.+.+++|
T Consensus        84 k~~~~~~~   91 (103)
T 2eqs_A           84 KDVDQETG   91 (103)
T ss_dssp             TTBCTTTC
T ss_pred             eecccCCc
Confidence            99988887

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

Probab=99.45  E-value=4e-13  Score=114.18  Aligned_cols=74  Identities=26%  Similarity=0.463  Sum_probs=68.3

Q ss_pred             CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccch
Q 005707          144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDD  221 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~  221 (681)
                      ++++|+++.|+|+++.++|+||+|+++++||||++++++.++    +.|++||.|+|+|+++|.++++|.||++++..
T Consensus         2 ~~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gllh~sel~~~~~----~~~~~Gd~V~v~V~~vd~~~~~i~lsl~~~~~   75 (80)
T 2k52_A            2 DVEPGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDMISLRL----ENLNVGDEIIVQAIDVRPEKREIDFKYIPLEH   75 (80)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEEETTEEEEECGGGCSSCCG----GGCCTTCEEEEEEEEEETTTTEEEEEECSCC-
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEECCCCEEEEEHHHCCcccc----eeeCCCCEEEEEEEEEECCCCEEEEEEeeccc
Confidence            578999999999999999999999978999999999998765    67999999999999999999999999997654

>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=99.45  E-value=6.7e-14  Score=128.11  Aligned_cols=83  Identities=29%  Similarity=0.406  Sum_probs=76.9

Q ss_pred             cCCCCCCcEEEEEEEEEecCeeEEEECC-CeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccC--CceEEEEec
Q 005707          142 NEDLIPGATFTGKVRSIQPFGAFIDFGA-FTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAET--GRISLTMRE  218 (681)
Q Consensus       142 ~~~LkvGdIVeGkV~sV~d~GaFVdLgg-gV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ek--grI~LSlK~  218 (681)
                      ...+++|++|.|+|++|.+||+||+|++ +.+||||+++++|+++.++.+.|++||.|+|+|+.+|.++  ++|.||+|.
T Consensus        17 ~~~~~vG~iv~G~V~~I~~fGaFV~l~g~~~~Glvhisel~~~~~~~~~~~~~~Gd~V~VkV~~vd~~~~~~~i~LSlk~   96 (119)
T 2cqo_A           17 ENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSLSMKV   96 (119)
T ss_dssp             CCSCCTTCEEEEEEEEEETTEEEEECTTCSSCEEEEHHHHCSSCCSCHHHHCCTTCEEEEEEEEEEECSSCEEEEEESTT
T ss_pred             hcccCCCCEEEEEEEEEeCceEEEEECCCcEEEEEEHHHCCcccccChhhcCCCCCEEEEEEEEEeccccCceEEEEEee
Confidence            4578899999999999999999999966 4799999999999999999999999999999999999864  699999999


Q ss_pred             cchhhH
Q 005707          219 SDDISK  224 (681)
Q Consensus       219 l~~dp~  224 (681)
                      +..++|
T Consensus        97 ~~~~~~  102 (119)
T 2cqo_A           97 VNQGTG  102 (119)
T ss_dssp             BCSSSC
T ss_pred             cccCCc
Confidence            988888

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

Probab=99.44  E-value=1.2e-13  Score=123.77  Aligned_cols=80  Identities=29%  Similarity=0.422  Sum_probs=75.3

Q ss_pred             cCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccch
Q 005707          142 NEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDD  221 (681)
Q Consensus       142 ~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~  221 (681)
                      ...+++|++|.|+|+++.++|+||+|+++++||||+++++++++.++.+.|++||.|+|+|+.+|.++++|.||++.+..
T Consensus        26 ~~~~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gll~~sel~~~~~~~~~~~~~vGd~V~v~V~~vd~~~~ki~LS~k~~~~  105 (109)
T 2khj_A           26 VALNKKGAIVTGKVTAVDAKGATVELADGVEGYLRASEASRDRVEDATLVLSVGDEVEAKFTGVDRKNRAISLSVRAKDE  105 (109)
T ss_dssp             TTTCCSSSEEEEEEEEECSSCEEEECSTTCBCCBCTTCCCSSSSSSGGGSCCTTCEEEEEEEEEETTTTEEEEETTSSSS
T ss_pred             hhcCCCCCEEEEEEEEEECCeEEEEECCCCEEEEEHHHcCcccccChhhccCCCCEEEEEEEEEECCCCEEEEEEeecCh
Confidence            46899999999999999999999999988999999999999999999999999999999999999999999999997643

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

Probab=99.43  E-value=2.1e-13  Score=126.45  Aligned_cols=82  Identities=29%  Similarity=0.491  Sum_probs=75.0

Q ss_pred             cCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccC
Q 005707          258 TKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKED  335 (681)
Q Consensus       258 sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~  335 (681)
                      .++++|++|.|+|++|++||+||+|++|++||||+++++|.++.+  +...|++||.|.|+|+++|  +++|.||||++.
T Consensus         3 ~~~~vG~iv~G~V~~i~~~G~FV~l~~~~~Glihisel~~~~~~~--~~~~~~vGd~V~vkV~~vd~~~~kI~LSlk~~~   80 (130)
T 2k4k_A            3 AKFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKD--INEHLSVGDEVQVKVLAVDEEKGKISLSIRATQ   80 (130)
T ss_dssp             CCCCTTCEEEEEEEEEETTEEEEEEETTEEEEEEGGGTSSSCCSC--GGGTCCTTCEEEEEEEEEETTTTEEEEESHHHH
T ss_pred             CcCCCCCEEEEEEEEEeCCeEEEEECCCcEEEEEHHHCCcccccC--ccccCCCCCEEEEEEEEEeCCCCEEEEEEeecc
Confidence            468999999999999999999999999999999999999988643  4788999999999999997  599999999999


Q ss_pred             CCcCCc
Q 005707          336 DVGSNL  341 (681)
Q Consensus       336 ~DP~e~  341 (681)
                      .+|+..
T Consensus        81 ~~p~~~   86 (130)
T 2k4k_A           81 AAPEKK   86 (130)
T ss_dssp             HSCCCC
T ss_pred             cCcccc
Confidence            999763

>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=99.42  E-value=1.5e-13  Score=125.76  Aligned_cols=85  Identities=21%  Similarity=0.239  Sum_probs=75.1

Q ss_pred             ccccCCccCcEEEEEEEEEecceEEEEeCC-CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC----CeEEE
Q 005707          255 MKTTKFVKGQDLEGTVKNLTRSGAFISLPE-GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR----GQVTL  329 (681)
Q Consensus       255 ~~~sklkvGdIV~G~VknVt~~GaFVeIg~-GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk----gKI~L  329 (681)
                      .....+++|++|.|+|++|.+||+||+|++ +++||||+++++|.++.+  +...|++||.|.|+|+++|.    +||.|
T Consensus        15 ~~~~~~~vG~iv~G~V~~I~~fGaFV~l~g~~~~Glvhisel~~~~~~~--~~~~~~~Gd~V~VkV~~vd~~~~~~~i~L   92 (119)
T 2cqo_A           15 TMENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDK--PSEIVDVGDKVWVKLIGREMKNDRIKVSL   92 (119)
T ss_dssp             CSCCSCCTTCEEEEEEEEEETTEEEEECTTCSSCEEEEHHHHCSSCCSC--HHHHCCTTCEEEEEEEEEEECSSCEEEEE
T ss_pred             hhhcccCCCCEEEEEEEEEeCceEEEEECCCcEEEEEEHHHCCcccccC--hhhcCCCCCEEEEEEEEEeccccCceEEE
Confidence            566789999999999999999999999965 479999999999987543  36789999999999999972    59999


Q ss_pred             EEeccCCCcCCc
Q 005707          330 TMKKEDDVGSNL  341 (681)
Q Consensus       330 SLK~~~~DP~e~  341 (681)
                      |||+...+||+.
T Consensus        93 Slk~~~~~~~~~  104 (119)
T 2cqo_A           93 SMKVVNQGTGKD  104 (119)
T ss_dssp             ESTTBCSSSCCB
T ss_pred             EEeecccCCccc
Confidence            999999999873

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

Probab=99.40  E-value=9e-13  Score=112.01  Aligned_cols=72  Identities=22%  Similarity=0.408  Sum_probs=65.6

Q ss_pred             CCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCC
Q 005707          259 KFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDD  336 (681)
Q Consensus       259 klkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~  336 (681)
                      ++++|+++.|+|+++.++|+||+|+++++||||.++++|.++      ..|++||.|+|+|+++|  ++|+.||+|+...
T Consensus         2 ~~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gllh~sel~~~~~------~~~~~Gd~V~v~V~~vd~~~~~i~lsl~~~~~   75 (80)
T 2k52_A            2 DVEPGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDMISLRL------ENLNVGDEIIVQAIDVRPEKREIDFKYIPLEH   75 (80)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEEETTEEEEECGGGCSSCCG------GGCCTTCEEEEEEEEEETTTTEEEEEECSCC-
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEECCCCEEEEEHHHCCcccc------eeeCCCCEEEEEEEEEECCCCEEEEEEeeccc
Confidence            578999999999999999999999999999999999998763      57999999999999997  4999999998753

>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=99.40  E-value=4.4e-13  Score=130.49  Aligned_cols=96  Identities=19%  Similarity=0.288  Sum_probs=75.3

Q ss_pred             CCc-cCcEEEEEEEEEecceEEEEeC--CCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEec
Q 005707          259 KFV-KGQDLEGTVKNLTRSGAFISLP--EGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKK  333 (681)
Q Consensus       259 klk-vGdIV~G~VknVt~~GaFVeIg--~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~  333 (681)
                      .|. +|+++.|+|++|++||+||+|.  +|++||||+++++|.++.  ++...|++||.|.|+|+++|  ++||.||||+
T Consensus        11 ~~p~~G~iv~G~V~~i~~fGaFV~L~e~~gveGLvhiSels~~~v~--~~~~~~~vGd~V~vkVl~vd~~~~~I~LSlk~   88 (175)
T 2a19_A           11 KYPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIR--SIQKLIRVGKNDVAVVLRVDKEKGYIDLSKRR   88 (175)
T ss_dssp             SSCCTTCEEEEEEEEEETTEEEEEETTTTTCEEEEECC----------CCCCCCCTTSEEEEEEEEEETTTTEEEEESTT
T ss_pred             cCCCCCCEEEEEEEEEecceEEEEEcCCCCcEEEEEHHHcCCcccC--CHHHcCCCCCEEEEEEEEEECCCCeEEEEEEe
Confidence            444 8999999999999999999994  799999999999998864  45899999999999999998  5899999999


Q ss_pred             cCCCcCCc--------ceeeeEEEEeec-ccEE
Q 005707          334 EDDVGSNL--------QLTQGVIHAATN-PFVL  357 (681)
Q Consensus       334 ~~~DP~e~--------~lv~G~V~~~i~-~fGl  357 (681)
                      ...+||..        +.+.|+|. .+. .||+
T Consensus        89 ~~~~~~~~~~~~~~~g~~v~g~V~-~i~~~~G~  120 (175)
T 2a19_A           89 VSSEDIIKCEEKYQKSKTVHSILR-YCAEKFQI  120 (175)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHH-HHHHHTTC
T ss_pred             cCcChHHHHHHhccCCCcceEEEE-EchhhcCC
Confidence            99999873        33466666 444 6776

>1luz_A Protein K3, protein K2; stranded anti-parallel beta barrel, viral protein; 1.80A {Vaccinia virus} SCOP: b.40.4.5

Probab=99.39  E-value=4.2e-13  Score=116.87  Aligned_cols=78  Identities=23%  Similarity=0.306  Sum_probs=68.8

Q ss_pred             cccCCccCcEEEEEEEEEecceEEEEeCC--CeEEEEeCC-CCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEE
Q 005707          256 KTTKFVKGQDLEGTVKNLTRSGAFISLPE--GEEGFLPTS-EESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLT  330 (681)
Q Consensus       256 ~~sklkvGdIV~G~VknVt~~GaFVeIg~--GIeGLLpiS-ELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LS  330 (681)
                      .+...++|+++.|+|+ |++||+||+|.+  |++||+|++ +++|+++.+.  ...| +||.|+|+|+++|  ++||.||
T Consensus         5 ~y~~~~vG~~~~G~V~-v~~fG~FVel~~~~~~eGLvhis~el~~~~~~~~--~~~~-~Gd~V~VkV~~vd~~~~kI~ls   80 (88)
T 1luz_A            5 CYSLPNAGDVIKGRVY-EKDYALYIYLFDYPHFEAILAESVKMHMDRYVEY--RDKL-VGKTVKVKVIRVDYTKGYIDVN   80 (88)
T ss_dssp             CSCCCCTTCEEEEEEE-EETTEEEEEETTCTTSEEEEGGGSSCCHHHHHHH--HHHH-TTCEEEEEEEEEETTTTEEEEE
T ss_pred             EecCCCCCCEEEEEEE-EEccEEEEEECCCCCeEEEEEeeHHhCcccccCH--hHEe-CCCEEEEEEEEEECCCCEEEEE
Confidence            4667789999999999 999999999974  899999999 9999886543  5678 9999999999998  5899999


Q ss_pred             EeccCCC
Q 005707          331 MKKEDDV  337 (681)
Q Consensus       331 LK~~~~D  337 (681)
                      ||+..+|
T Consensus        81 lk~~~~~   87 (88)
T 1luz_A           81 YKRMCRH   87 (88)
T ss_dssp             EEEECSC
T ss_pred             EeecCCC
Confidence            9998654

>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=99.34  E-value=1.4e-13  Score=144.52  Aligned_cols=97  Identities=16%  Similarity=0.249  Sum_probs=85.7

Q ss_pred             CccCcEEEEEEEEEecceEEEEeC--CCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccC
Q 005707          260 FVKGQDLEGTVKNLTRSGAFISLP--EGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKED  335 (681)
Q Consensus       260 lkvGdIV~G~VknVt~~GaFVeIg--~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~  335 (681)
                      +++|+++.|+|++|.+||+||+|+  +|++||||+++++|.++.  ++...|++||.|.|+|+++|  +++|.||+|+..
T Consensus        11 ~~vG~iv~G~V~~I~~fGaFV~L~ey~gveGLvhiSels~~~i~--~~~~~~kvGd~V~VkVl~vD~~~~rI~LSlK~~~   88 (308)
T 1q8k_A           11 PEVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIR--SINKLIRIGRNECVKVIRVDKEKGYIDLSKRRVS   88 (308)
T ss_dssp             CSSCCEEEEEEEEEETTEEEEESCTTTSCCEEECGGGTSCSSCS--CCTTTCSSSCEEEEEEEEEETTTTEEEEECSSCC
T ss_pred             CCCCCEEEEEEEEEeCcEEEEEECCCCCeEEEEEhHHcCccccc--CHHHhcCCCCEEEEEEEEEeCCCCEEEEEEEecc
Confidence            469999999999999999999998  699999999999998854  45899999999999999998  599999999999


Q ss_pred             CCcCCc--------ceeeeEEEEeecc-cEEEE
Q 005707          336 DVGSNL--------QLTQGVIHAATNP-FVLAF  359 (681)
Q Consensus       336 ~DP~e~--------~lv~G~V~~~i~~-fGlfV  359 (681)
                      .+||..        +.+.|+|. .+.+ ||+|+
T Consensus        89 ~~p~~~~~~~~~~G~~v~G~V~-~v~~~~G~fi  120 (308)
T 1q8k_A           89 PEEAIKCEDKFTKSKTVYSILR-HVAEVLEYTK  120 (308)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH-HHHHHTTCCS
T ss_pred             cChHHHHHHHccCCCeeEEEEE-EcccccCCcc
Confidence            999873        34567887 6777 59987

>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=99.26  E-value=3.9e-12  Score=131.12  Aligned_cols=85  Identities=14%  Similarity=0.373  Sum_probs=79.9

Q ss_pred             CcCCCCCCcEEEEEEEEEecCeeEEEEC--CCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEec
Q 005707          141 KNEDLIPGATFTGKVRSIQPFGAFIDFG--AFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRE  218 (681)
Q Consensus       141 t~~~LkvGdIVeGkV~sV~d~GaFVdLg--ggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~  218 (681)
                      ....+++|++|.|+|+++.++|+||+|+  +++.||||+++++|+++.++.+.|++||.|.|+|+.+|.++++|.||+|.
T Consensus         5 ~~~~~~vG~iv~G~V~~I~~~GaFV~l~e~~~~~GlihiSels~~~v~~~~~~~~vGd~V~VkVi~vd~~~g~I~LSlk~   84 (266)
T 3cw2_C            5 RSKLPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDVSLKK   84 (266)
T ss_dssp             SSSSCCTTCEEEEEEEECCSSSBEEEETTTTSEECBBCGGGSSCSSCCCHHHHSCTTCEEEEEECCCCSSSCCCBEESTT
T ss_pred             ccccCCCCCEEEEEEEEEeccEEEEEEcCCCCeEEEEEhHHcCcccccCHHHhCcCCCEEEEEEEEEeCCCCEEEEEEEe
Confidence            3457889999999999999999999997  77999999999999999999999999999999999999999999999999


Q ss_pred             cchhhHh
Q 005707          219 SDDISKL  225 (681)
Q Consensus       219 l~~dp~e  225 (681)
                      ...++|.
T Consensus        85 ~~~~~~~   91 (266)
T 3cw2_C           85 VTDDERR   91 (266)
T ss_dssp             SCTTHHH
T ss_pred             cchhhHH
Confidence            9999984

>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=99.21  E-value=3.5e-13  Score=155.91  Aligned_cols=134  Identities=24%  Similarity=0.284  Sum_probs=52.6

Q ss_pred             CCCCcEE--EEEEEE--EecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccc
Q 005707          145 LIPGATF--TGKVRS--IQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESD  220 (681)
Q Consensus       145 LkvGdIV--eGkV~s--V~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~  220 (681)
                      =++|+++  .|++.+  +.++|+||+|+.  +|.++++..++.......+                    +|.    .+ 
T Consensus       607 ~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~--dG~v~Is~~~~~~~~~a~~--------------------~i~----~i-  659 (757)
T 1e3p_A          607 DKIGEVIGPKRQMINQIQEDTGAEITIED--DGTIYIGAADGPAAEAARA--------------------TIN----GI-  659 (757)
T ss_dssp             --------------CTTCCCCCSCC----------CCCBSSHHHHCC---------------------------------
T ss_pred             HHeehcccccceeeehhhHhhCCEEEecC--CceEEEecCCHHHHHHHHH--------------------HHH----Hh-
Confidence            3456665  355665  468999999986  8999999887654322110                    000    00 


Q ss_pred             hhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCC----C
Q 005707          221 DISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEE----S  296 (681)
Q Consensus       221 ~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSEL----S  296 (681)
                      .+                                  ..++++|++|.|+|++|.+||+||+|.+|++||||++++    +
T Consensus       660 ~~----------------------------------p~~~~vG~i~~G~V~~i~~fGaFV~l~~g~eGLvHiSel~~~~s  705 (757)
T 1e3p_A          660 AN----------------------------------PTSPEVGERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAG  705 (757)
T ss_dssp             -----------------------------------------------CBEEECC-CSCEECCC---CCCCC---------
T ss_pred             cc----------------------------------hhhcccccEEEEEEEEccccEEEEEEcCCcEEEEEhHHhccccC
Confidence            00                                  145889999999999999999999999999999999999    9


Q ss_pred             cccccccCCCCcccCCCEEEEEEEEEe-CCeEEEEEeccCCCcCCc
Q 005707          297 DDGFANMMGGSSLQVGQEVSVRVLRIS-RGQVTLTMKKEDDVGSNL  341 (681)
Q Consensus       297 d~~ie~~~p~~~fkVGqkVkVrVL~ID-kgKI~LSLK~~~~DP~e~  341 (681)
                      |.+++  ++...|++||.|+|+|+++| ++||.||||+...+||..
T Consensus       706 ~~rv~--~~~~~~~vGd~V~VkVi~vd~~grI~LS~k~~~~~pw~~  749 (757)
T 1e3p_A          706 GKRVE--NVEDVLGVGQKVQVEIAEIDSRGKLSLIPVIEGEEAASD  749 (757)
T ss_dssp             ------------CCSSCBCCCCCCCCCSSCC---------------
T ss_pred             CCccc--CcccccCCCCEEEEEEEEECCCCCEEEEEecCCCCchhh
Confidence            98864  45889999999999999998 699999999999999973

>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB: 1yz6_A

Probab=99.20  E-value=2.1e-11  Score=126.29  Aligned_cols=96  Identities=25%  Similarity=0.421  Sum_probs=82.7

Q ss_pred             ccCcEEEEEEEEEecceEEEEeC--CCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCC
Q 005707          261 VKGQDLEGTVKNLTRSGAFISLP--EGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDD  336 (681)
Q Consensus       261 kvGdIV~G~VknVt~~GaFVeIg--~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~  336 (681)
                      ++|+++.|+|++|.+||+||+|+  +|++||||+++++|.++.+  +...|++||.|.|+|+++|  +++|.||||....
T Consensus        10 ~~Gdiv~G~V~~I~~fGaFV~L~e~~gieGlIhiSels~~~v~~--~~~~~kvGd~V~vkVi~vD~~~~~I~LSlk~~~~   87 (275)
T 3aev_A           10 EEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRN--IRDYLKEGQKVVAKVIRVDPRKGHIDLSLRRVTQ   87 (275)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEETTSTTCEEEEEGGGSCSSCCSC--GGGTCCTTCEEEEEEEEEETTTTEEEEESTTCCH
T ss_pred             CCCCEEEEEEEEEECcEEEEEECCCCCeEEEEEHHHcCcccccC--HHhccCCCCEEEEEEEEEECCCCEEEEEEeecCc
Confidence            48999999999999999999998  6999999999999988654  4789999999999999998  5999999999988


Q ss_pred             CcCCc--------ceeeeEEEEeec-ccEEEE
Q 005707          337 VGSNL--------QLTQGVIHAATN-PFVLAF  359 (681)
Q Consensus       337 DP~e~--------~lv~G~V~~~i~-~fGlfV  359 (681)
                      +||..        +.+.|+|. .+. .||+++
T Consensus        88 ~~~~~~~~~~~~g~~v~g~v~-~v~~~~G~~~  118 (275)
T 3aev_A           88 QQRKAKLQEFKRAQKAENLLR-LAAEKLGKDF  118 (275)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH-HHHHHHTCCH
T ss_pred             chhHHHHHhccCCCeEEEEEE-EchhhcCCCH
Confidence            99862        33466766 455 888744

>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=99.18  E-value=3.2e-11  Score=109.65  Aligned_cols=82  Identities=26%  Similarity=0.381  Sum_probs=69.3

Q ss_pred             CCcCCCCCCcEEEEEEEEEecCeeEEEEC-CCeEEEEecccc-CCccccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707          140 VKNEDLIPGATFTGKVRSIQPFGAFIDFG-AFTDGLVHVSRL-SDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR  217 (681)
Q Consensus       140 lt~~~LkvGdIVeGkV~sV~d~GaFVdLg-ggV~GLVPiSEL-S~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK  217 (681)
                      +.+.++++|++|.|+|++|.+||+||+|+ ++..|++|.++. .|.++.++.+.|++||.|+|+|+++|.++++|.||++
T Consensus        14 ~~~~~l~~G~i~~G~V~~v~~fG~fV~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~i~Lslk   93 (119)
T 1wi5_A           14 LSAEALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSVG   93 (119)
T ss_dssp             CCTTTCCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCTTSCEEEEECC
T ss_pred             ccHhcCCCCCEEEEEEEEEeCceEEEEECCCCeEEEEEEecccccccccCccCEeCCCCEEEEEEEEEeCCCCEEEEEEc
Confidence            34678999999999999999999999998 557777776664 2444557888999999999999999999999999999


Q ss_pred             ccch
Q 005707          218 ESDD  221 (681)
Q Consensus       218 ~l~~  221 (681)
                      +...
T Consensus        94 ~~~l   97 (119)
T 1wi5_A           94 HSEV   97 (119)
T ss_dssp             CCCS
T ss_pred             hhhc
Confidence            6544

>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=99.13  E-value=7.3e-11  Score=107.29  Aligned_cols=79  Identities=25%  Similarity=0.409  Sum_probs=65.7

Q ss_pred             ccccCCccCcEEEEEEEEEecceEEEEeC-CCeEEEEeCCCC-CcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEE
Q 005707          255 MKTTKFVKGQDLEGTVKNLTRSGAFISLP-EGEEGFLPTSEE-SDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLT  330 (681)
Q Consensus       255 ~~~sklkvGdIV~G~VknVt~~GaFVeIg-~GIeGLLpiSEL-Sd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LS  330 (681)
                      ..+.++++|+++.|+|++|.+||+||+|+ +++.||+|.++. .|.++  .++...|++||.|+|+|+++|  ++|+.|+
T Consensus        14 ~~~~~l~~G~i~~G~V~~v~~fG~fV~l~~~~~~~l~~~~~~~~~~~~--~~~~~~~~~Gd~V~vkV~~vd~~~~~i~Ls   91 (119)
T 1wi5_A           14 LSAEALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQ--KNKGAKLKVGQYLNCIVEKVKGNGGVVSLS   91 (119)
T ss_dssp             CCTTTCCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHHHHHH--HSSSCCCCTTCEEEEEEEECCTTSCEEEEE
T ss_pred             ccHhcCCCCCEEEEEEEEEeCceEEEEECCCCeEEEEEEecccccccc--cCccCEeCCCCEEEEEEEEEeCCCCEEEEE
Confidence            45788999999999999999999999999 578888776654 23222  245789999999999999997  4899999


Q ss_pred             EeccC
Q 005707          331 MKKED  335 (681)
Q Consensus       331 LK~~~  335 (681)
                      +|+..
T Consensus        92 lk~~~   96 (119)
T 1wi5_A           92 VGHSE   96 (119)
T ss_dssp             CCCCC
T ss_pred             Echhh
Confidence            99864

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=99.12  E-value=6e-12  Score=145.14  Aligned_cols=83  Identities=29%  Similarity=0.500  Sum_probs=0.0

Q ss_pred             ccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe-CCeEEEEEeccC
Q 005707          257 TTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS-RGQVTLTMKKED  335 (681)
Q Consensus       257 ~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID-kgKI~LSLK~~~  335 (681)
                      ..++++|++|.|+|++|.+||+||+|.+|++||||+++++|.++.  ++...|++||.|+|+|+++| ++||.||||...
T Consensus       622 ~~~~~vG~i~~G~V~~i~~fGaFVel~~g~eGLvHiSel~~~~v~--~~~~~~~vGd~V~VkVi~vd~~grI~LS~k~~~  699 (723)
T 3cdi_A          622 TAEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVE--KVTDYLQMGQEVPVKVLEVDRQGRIRLSIKEAT  699 (723)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hhhhhcCcEEEEEEEEEecceEEEEeCCCceEEEEHHHcCCcccc--CcccccCCCCEEEEEEEEECCCCcEEEEEEecc
Confidence            457889999999999999999999999999999999999998864  45889999999999999998 699999999998


Q ss_pred             CCcCCc
Q 005707          336 DVGSNL  341 (681)
Q Consensus       336 ~DP~e~  341 (681)
                      ++|+..
T Consensus       700 ~~~g~~  705 (723)
T 3cdi_A          700 EQSQPA  705 (723)
T ss_dssp             ------
T ss_pred             CCCCcc
Confidence            888764

>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=99.07  E-value=2.6e-11  Score=124.95  Aligned_cols=82  Identities=32%  Similarity=0.413  Sum_probs=74.2

Q ss_pred             cCCccCcEEEEEEEEEecceEEEEeC--CCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEec
Q 005707          258 TKFVKGQDLEGTVKNLTRSGAFISLP--EGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKK  333 (681)
Q Consensus       258 sklkvGdIV~G~VknVt~~GaFVeIg--~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~  333 (681)
                      ..+++|+++.|+|++|.+||+||+|+  +|++||||.++++|.++.+  +...|++||.|.|+|+++|  ++++.||+|.
T Consensus         7 ~~~~vG~iv~G~V~~I~~~GaFV~l~e~~~~~GlihiSels~~~v~~--~~~~~~vGd~V~VkVi~vd~~~g~I~LSlk~   84 (266)
T 3cw2_C            7 KLPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKN--IRDVLKENRKVIVKVIRVDRRKGTVDVSLKK   84 (266)
T ss_dssp             SSCCTTCEEEEEEEECCSSSBEEEETTTTSEECBBCGGGSSCSSCCC--HHHHSCTTCEEEEEECCCCSSSCCCBEESTT
T ss_pred             ccCCCCCEEEEEEEEEeccEEEEEEcCCCCeEEEEEhHHcCcccccC--HHHhCcCCCEEEEEEEEEeCCCCEEEEEEEe
Confidence            45689999999999999999999997  7999999999999988643  4678999999999999997  5999999999


Q ss_pred             cCCCcCCc
Q 005707          334 EDDVGSNL  341 (681)
Q Consensus       334 ~~~DP~e~  341 (681)
                      ...+||..
T Consensus        85 ~~~~~~~~   92 (266)
T 3cw2_C           85 VTDDERRK   92 (266)
T ss_dssp             SCTTHHHH
T ss_pred             cchhhHHH
Confidence            99999863

>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae}

Probab=99.05  E-value=2.7e-10  Score=137.34  Aligned_cols=81  Identities=10%  Similarity=0.145  Sum_probs=76.4

Q ss_pred             CcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCcc-ccCcccccccCCEEEEEEEEEeccCCceEEEEecc
Q 005707          141 KNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNF-VKDVGSIVSVGQEVKVRLIEANAETGRISLTMRES  219 (681)
Q Consensus       141 t~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~-v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l  219 (681)
                      +..++++|++|.|+|++|.+||+||+|+.+++||||+++|++++ +.++.+.|++||.|+|+|+.+|.++++|.||+|..
T Consensus       896 t~~~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSelsd~~~v~~p~~v~kvGd~V~vkVl~VD~~~~rI~LSlk~~  975 (1219)
T 3psi_A          896 SEKTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAEVSLLDH  975 (1219)
T ss_dssp             CTTTSCTTCEEEEEEEEECSSCEEEECTTSCEEEECTTSSSSTTSCSCSTTTSCTTCEEEEEEEEEEGGGTEEEEECCHH
T ss_pred             cHhhCCCCCEEEEEEEEEecceEEEEeCCCceEEEEHHHcCCCcccCCHHHcCCCCCEEEEEEEEEECCCCEEEEEecHH
Confidence            45899999999999999999999999998899999999999998 79999999999999999999999999999999965


Q ss_pred             ch
Q 005707          220 DD  221 (681)
Q Consensus       220 ~~  221 (681)
                      ..
T Consensus       976 dl  977 (1219)
T 3psi_A          976 DV  977 (1219)
T ss_dssp             HH
T ss_pred             Hh
Confidence            54

>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=99.03  E-value=6.5e-10  Score=108.07  Aligned_cols=79  Identities=29%  Similarity=0.543  Sum_probs=70.2

Q ss_pred             cCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCcccc-----------CcccccccCCEEEEEEEEEeccCC
Q 005707          142 NEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVK-----------DVGSIVSVGQEVKVRLIEANAETG  210 (681)
Q Consensus       142 ~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~-----------d~~e~fkVGd~VkVkVl~VD~ekg  210 (681)
                      +...++|+++.|+|+++.++|+||+|++ .+||||+++++++++.           ++...|++||.|+|+|+++|...+
T Consensus        76 ~~~~~~Gev~~G~V~~v~~~G~fV~l~~-~eglvhis~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~  154 (187)
T 1go3_E           76 VYIPEMYELIEGEVVDVVEFGSFVRLGP-LDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAE  154 (187)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEECSS-SEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEEECCC-
T ss_pred             EEccCCCCEEEEEEEEEeCcEEEEEEcC-ccEEEEhHHhCCCcceECCccceEEecCCCeEEcCCCEEEEEEEEEEcccC
Confidence            3568899999999999999999999977 9999999999988765           778899999999999999998755


Q ss_pred             -----ceEEEEeccch
Q 005707          211 -----RISLTMRESDD  221 (681)
Q Consensus       211 -----rI~LSlK~l~~  221 (681)
                           +|.||++....
T Consensus       155 ~p~~~~I~lS~k~~~L  170 (187)
T 1go3_E          155 RKRGSKIALTMRQPYL  170 (187)
T ss_dssp             ----CEEEEECCSTTC
T ss_pred             CCCccEEEEEEcCCCC
Confidence                 99999997443

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=99.01  E-value=3.1e-11  Score=139.00  Aligned_cols=84  Identities=27%  Similarity=0.398  Sum_probs=0.0

Q ss_pred             ccccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe-CCeEEEEEec
Q 005707          255 MKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS-RGQVTLTMKK  333 (681)
Q Consensus       255 ~~~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID-kgKI~LSLK~  333 (681)
                      ....++++|++|.|+|++|.+||+||+|.+|++||||+++++|.++.  ++...|++||.|+|+|+++| ++||.||||+
T Consensus       630 ~i~~~~~vG~v~~G~V~~I~~fGaFVel~~g~eGLvHiSels~~rv~--~~~d~~kvGD~V~VkVi~iD~~grI~LS~K~  707 (726)
T 4aid_A          630 SITDEAEVGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVA--KPSDVLKEGQMVKVKLLGFDDRGKTKLSMKV  707 (726)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHhhhhcCCcEEEEEEEEEeccEEEEEECCCcEEEEEHHHcCccccc--CccccCCCCCEEEEEEEEECCCCcEEEEEee
Confidence            45678999999999999999999999999999999999999999875  45889999999999999998 6999999999


Q ss_pred             cCCCcCC
Q 005707          334 EDDVGSN  340 (681)
Q Consensus       334 ~~~DP~e  340 (681)
                      ..++|+.
T Consensus       708 ~~~~~G~  714 (726)
T 4aid_A          708 VDQETGE  714 (726)
T ss_dssp             -------
T ss_pred             cccCcch
Confidence            9888865

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=99.01  E-value=3.5e-11  Score=138.65  Aligned_cols=82  Identities=34%  Similarity=0.574  Sum_probs=0.0

Q ss_pred             cCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccch
Q 005707          142 NEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDD  221 (681)
Q Consensus       142 ~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~  221 (681)
                      ...+++|++|.|+|++|.+||+||+|.++++||||+++++|+++.++.+.|++||.|+|+|+++|+ +++|.||+|.+.+
T Consensus       632 ~~~~~vG~v~~G~V~~I~~fGaFVel~~g~eGLvHiSels~~rv~~~~d~~kvGD~V~VkVi~iD~-~grI~LS~K~~~~  710 (726)
T 4aid_A          632 TDEAEVGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFDD-RGKTKLSMKVVDQ  710 (726)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hhhhcCCcEEEEEEEEEeccEEEEEECCCcEEEEEHHHcCcccccCccccCCCCCEEEEEEEEECC-CCcEEEEEeeccc
Confidence            468899999999999999999999998889999999999999999999999999999999999998 7999999999988


Q ss_pred             hhH
Q 005707          222 ISK  224 (681)
Q Consensus       222 dp~  224 (681)
                      +++
T Consensus       711 ~~G  713 (726)
T 4aid_A          711 ETG  713 (726)
T ss_dssp             ---
T ss_pred             Ccc
Confidence            877

>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=98.99  E-value=1.4e-10  Score=134.64  Aligned_cols=80  Identities=44%  Similarity=0.733  Sum_probs=75.8

Q ss_pred             CCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEecc
Q 005707          140 VKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRES  219 (681)
Q Consensus       140 lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l  219 (681)
                      .++.++++|++|.|+|++|.+||+||+|+.+++||||+++|+|.++.++.+.|++||.|+|+|+++|.++++|.||+|..
T Consensus       647 e~~~~l~vG~iv~G~V~~V~~fGaFV~l~~~~eGLVhiS~Lsd~~v~d~~~~~~vGd~V~VkVi~VD~~~~rI~LSlk~~  726 (785)
T 3bzc_A          647 ESLKDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGLSMRMS  726 (785)
T ss_dssp             CSSTTCCTTCBCCCEEEEEETTEEEEECSSSSEEEEETTTSCSSCCSCHHHHCCTTCCCCCBEEEEETTTTEEEECCSSC
T ss_pred             cchhhcCCCCEEEEEEEEEecCCeEEEeCCCcEEEEEHHHcCccccCChhheeCCCCEEEEEEEEEECCCCEEEEEEecC
Confidence            45778999999999999999999999999889999999999999999999999999999999999999999999999854

>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=98.99  E-value=7.9e-11  Score=134.45  Aligned_cols=149  Identities=9%  Similarity=0.006  Sum_probs=102.7

Q ss_pred             ccccceeeecccccccccceeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCcceecCCCC
Q 005707           26 NCLTRYNSTRKSTKQTISSQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPS  105 (681)
Q Consensus        26 ~~~~~~~~~r~~~~~~~s~~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s  105 (681)
                      .+.+||||+-.+|.|||||.|++.|+-.+|- |-+...+              ....    ..   ..   .        
T Consensus       480 ~~~~HfgLa~~~YthfTSPIRRY~DLivHR~-l~a~l~~--------------~~~~----~~---~~---~--------  526 (644)
T 2id0_A          480 EPGPHFGLGLEAYATWTSPIRKYGDMINHRL-LKAVIKG--------------ETAT----RP---QD---E--------  526 (644)
T ss_dssp             SCCCBTTTTBSSCBCCSCTTTBHHHHHHHHH-HHHHTTC----------------------CC---CT---T--------
T ss_pred             CCCCchhcCCCceeeeCChhhcchHHHHHHH-HHHHHcC--------------CCCC----cc---HH---H--------
Confidence            4678999999999999999999999877742 2222111              1000    00   00   1        


Q ss_pred             CcccccccccccCCChhhHHhhhchhhhhcCCCCCCcCCCCCCc--EEEEEEEEEecCeeEEEE-CCCeEEEEeccccCC
Q 005707          106 DVETSESSSIKSEASPTLAESRRSRTARKSEMPPVKNEDLIPGA--TFTGKVRSIQPFGAFIDF-GAFTDGLVHVSRLSD  182 (681)
Q Consensus       106 ~v~~ae~ss~~sea~~daek~~~kr~~rk~e~~~lt~~~LkvGd--IVeGkV~sV~d~GaFVdL-gggV~GLVPiSELS~  182 (681)
                         ..++.+.+.+.+.++++...+..  ...     +..-++|+  +++|+|++|.++|+||.| ..+++||||+++|.+
T Consensus       527 ---~~~~~s~~er~a~~aer~~~~~~--~~~-----~l~~~vGe~~~f~g~V~~V~~~G~fV~L~~~gieGlVhis~l~~  596 (644)
T 2id0_A          527 ---ITVQMAERRRLNRMAERDVGDWL--YAR-----FLKDKAGTDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHA  596 (644)
T ss_dssp             ---HHHHHHHHHHHHHHHHHHHHHHH--HHH-----HHGGGTTSCCCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTCS
T ss_pred             ---HHHHHHHHHHHHHHHHHHHHHHH--HHH-----HhhhccCCCceEEEEEEEEeCCceEEEEcCCcEEEEEEchhccC
Confidence               12234444555555554433311  111     33456799  999999999999999999 467999999999974


Q ss_pred             --ccc-c---------CcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707          183 --NFV-K---------DVGSIVSVGQEVKVRLIEANAETGRISLTMR  217 (681)
Q Consensus       183 --~~v-~---------d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK  217 (681)
                        +++ .         +....|++||.|+|+|+.+|..+++|.|++.
T Consensus       597 ~~d~~~~d~~~~~l~~~~~~~~~lGD~V~VkV~~vd~~~~~I~~~l~  643 (644)
T 2id0_A          597 VRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETRSIIARPV  643 (644)
T ss_dssp             CGGGEEEETTTTEEEETTEEEEETTCEEEEEEEEEETTTTEEEEEEC
T ss_pred             cCceeEEcccccEEEecCCCEeCCCCEEEEEEEEEeCCCCEEEEEEc
Confidence              331 1         3456799999999999999999999999874

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=98.97  E-value=6.1e-11  Score=136.83  Aligned_cols=82  Identities=38%  Similarity=0.698  Sum_probs=0.0

Q ss_pred             cCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccch
Q 005707          142 NEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDD  221 (681)
Q Consensus       142 ~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~  221 (681)
                      ...+++|++|.|+|+++.+||+||+|.++++||||+++++|+++.++.+.|++||.|+|+|+++|. +++|.||+|.+..
T Consensus       622 ~~~~~vG~i~~G~V~~i~~fGaFVel~~g~eGLvHiSel~~~~v~~~~~~~~vGd~V~VkVi~vd~-~grI~LS~k~~~~  700 (723)
T 3cdi_A          622 TAEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDR-QGRIRLSIKEATE  700 (723)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hhhhhcCcEEEEEEEEEecceEEEEeCCCceEEEEHHHcCCccccCcccccCCCCEEEEEEEEECC-CCcEEEEEEeccC
Confidence            467899999999999999999999998889999999999999999999999999999999999998 8999999999888


Q ss_pred             hhH
Q 005707          222 ISK  224 (681)
Q Consensus       222 dp~  224 (681)
                      ++|
T Consensus       701 ~~g  703 (723)
T 3cdi_A          701 QSQ  703 (723)
T ss_dssp             ---
T ss_pred             CCC
Confidence            887

>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=98.95  E-value=2.3e-09  Score=103.71  Aligned_cols=77  Identities=29%  Similarity=0.586  Sum_probs=67.3

Q ss_pred             cCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccc-----------cCcccccccCCEEEEEEEEEecc--
Q 005707          142 NEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFV-----------KDVGSIVSVGQEVKVRLIEANAE--  208 (681)
Q Consensus       142 ~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v-----------~d~~e~fkVGd~VkVkVl~VD~e--  208 (681)
                      .....+|++++|+|++++++|+||++++ .+||+|++++.++++           .+....|++||.|+|+|+++|.+  
T Consensus        76 v~~p~~Gev~~G~V~~v~~~G~fv~l~~-~~glvh~s~l~~d~~~~d~~~~~~~g~~~~~~~~~Gd~VrvkV~~v~~~~~  154 (180)
T 4ayb_E           76 TYVPVVQEVVEGEVLQVDNYGVFVNLGP-MDGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISVASTVT  154 (180)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEECSS-SEEEEEGGGSCSSCEEECSSSCCEEETTTCCCCCTTCEEEEEEEEECC---
T ss_pred             eeeccCCCEEEEEEeeeccceEEEEECC-ccceEEeeecCCCccccchhcceEEEeccCeEECCCCEEEEEEEEEeCCCC
Confidence            4578899999999999999999999976 899999999999876           46777899999999999999864  


Q ss_pred             --CCceEEEEecc
Q 005707          209 --TGRISLTMRES  219 (681)
Q Consensus       209 --kgrI~LSlK~l  219 (681)
                        ..+|.||||+.
T Consensus       155 ~~~~rI~ls~k~~  167 (180)
T 4ayb_E          155 GRLPRIALTMRQP  167 (180)
T ss_dssp             ----CEEEECCST
T ss_pred             cccCcEEEEcCCC
Confidence              35899999974

>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=98.95  E-value=3.2e-11  Score=139.67  Aligned_cols=82  Identities=28%  Similarity=0.460  Sum_probs=38.4

Q ss_pred             CCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEecccc----CCccccCcccccccCCEEEEEEEEEeccCCceEEEEec
Q 005707          143 EDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRL----SDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRE  218 (681)
Q Consensus       143 ~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSEL----S~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~  218 (681)
                      ..+++|++|.|+|+++.+||+||+|.++++||||++++    +|+++.++.+.|++||.|+|+|+++|. +++|.||+|.
T Consensus       663 ~~~~vG~i~~G~V~~i~~fGaFV~l~~g~eGLvHiSel~~~~s~~rv~~~~~~~~vGd~V~VkVi~vd~-~grI~LS~k~  741 (757)
T 1e3p_A          663 TSPEVGERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDS-RGKLSLIPVI  741 (757)
T ss_dssp             ----------CBEEECC-CSCEECCC---CCCCC-------------------CCSSCBCCCCCCCCCS-SCC-------
T ss_pred             hhcccccEEEEEEEEccccEEEEEEcCCcEEEEEhHHhccccCCCcccCcccccCCCCEEEEEEEEECC-CCCEEEEEec
Confidence            57899999999999999999999998889999999999    999999999999999999999999998 9999999999


Q ss_pred             cchhhHh
Q 005707          219 SDDISKL  225 (681)
Q Consensus       219 l~~dp~e  225 (681)
                      +..+||.
T Consensus       742 ~~~~pw~  748 (757)
T 1e3p_A          742 EGEEAAS  748 (757)
T ss_dssp             -------
T ss_pred             CCCCchh
Confidence            9999994

>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae}

Probab=98.94  E-value=1.4e-09  Score=131.26  Aligned_cols=79  Identities=11%  Similarity=0.188  Sum_probs=71.5

Q ss_pred             cccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEec
Q 005707          256 KTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKK  333 (681)
Q Consensus       256 ~~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~  333 (681)
                      ...++++|++|.|+|++|++||+||+|+.|++||||+++++|.++ ..++...|++||.|+|+|++||  ++||.||||.
T Consensus       896 t~~~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSelsd~~~-v~~p~~v~kvGd~V~vkVl~VD~~~~rI~LSlk~  974 (1219)
T 3psi_A          896 SEKTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQL-RRPANEIYEIGKTYPAKVIYIDYANITAEVSLLD  974 (1219)
T ss_dssp             CTTTSCTTCEEEEEEEEECSSCEEEECTTSCEEEECTTSSSSTTS-CSCSTTTSCTTCEEEEEEEEEEGGGTEEEEECCH
T ss_pred             cHhhCCCCCEEEEEEEEEecceEEEEeCCCceEEEEHHHcCCCcc-cCCHHHcCCCCCEEEEEEEEEECCCCEEEEEecH
Confidence            458999999999999999999999999999999999999999872 1346899999999999999998  6999999997


Q ss_pred             cC
Q 005707          334 ED  335 (681)
Q Consensus       334 ~~  335 (681)
                      ..
T Consensus       975 ~d  976 (1219)
T 3psi_A          975 HD  976 (1219)
T ss_dssp             HH
T ss_pred             HH
Confidence            63

>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae}

Probab=98.89  E-value=1.7e-10  Score=137.29  Aligned_cols=82  Identities=10%  Similarity=0.135  Sum_probs=0.4

Q ss_pred             CcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCcc-ccCcccccccCCEEEEEEEEEeccCCceEEEEecc
Q 005707          141 KNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNF-VKDVGSIVSVGQEVKVRLIEANAETGRISLTMRES  219 (681)
Q Consensus       141 t~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~-v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l  219 (681)
                      +..++++|++|.|+|++|.+||+||+|+.+++||||+++|++.+ +.++.+.|++||.|+|+|+.+|.++++|.||+|..
T Consensus       899 t~~~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSelsd~~~v~~~~~v~kvGd~V~vkVl~VD~~~~rI~LSlk~~  978 (1030)
T 3psf_A          899 SEKTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAEVSLLDH  978 (1030)
T ss_dssp             C-------------------------------------------------------------------------------
T ss_pred             cHHHhcCCCEEEEEEEEEccCeEEEEeCCCcEEEEEHHHcCCCcccCCHHHcCCCCCEEEEEEEEEECCCCEEEEEechH
Confidence            34789999999999999999999999998899999999999998 89999999999999999999999999999999976


Q ss_pred             chh
Q 005707          220 DDI  222 (681)
Q Consensus       220 ~~d  222 (681)
                      ...
T Consensus       979 dl~  981 (1030)
T 3psf_A          979 DVK  981 (1030)
T ss_dssp             ---
T ss_pred             Hhc
Confidence            553

>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=98.88  E-value=3e-09  Score=106.16  Aligned_cols=77  Identities=19%  Similarity=0.075  Sum_probs=70.3

Q ss_pred             CCCCCCcEEEEEEEEEecCeeEEEEC--------CCeEEEEeccccCCcccc--CcccccccCCEEEEEEEEEeccCCce
Q 005707          143 EDLIPGATFTGKVRSIQPFGAFIDFG--------AFTDGLVHVSRLSDNFVK--DVGSIVSVGQEVKVRLIEANAETGRI  212 (681)
Q Consensus       143 ~~LkvGdIVeGkV~sV~d~GaFVdLg--------ggV~GLVPiSELS~~~v~--d~~e~fkVGd~VkVkVl~VD~ekgrI  212 (681)
                      ..+++|++|.|+|+++.++|+||+|+        .+.+|+||++++++.+..  ++.+.|++||.|+|+|++++..++++
T Consensus        77 y~p~vGDvV~G~V~~v~~~~a~V~I~~v~~~~L~~~~~GlIhisei~~~~~~~~~~~~~l~~GD~V~akVisi~~~~~~i  156 (209)
T 2nn6_I           77 LLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSNY  156 (209)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEETTTTEE
T ss_pred             CCCCCCCEEEEEEEEEECceEEEEECccccccccCCceeEEEHHHcccccccccchhhhcCCCCEEEEEEEEEeCCCCeE
Confidence            36899999999999999999999985        357999999999998887  89999999999999999999877899


Q ss_pred             EEEEecc
Q 005707          213 SLTMRES  219 (681)
Q Consensus       213 ~LSlK~l  219 (681)
                      .||+|..
T Consensus       157 ~LS~k~~  163 (209)
T 2nn6_I          157 LLTTAEN  163 (209)
T ss_dssp             EEECCSS
T ss_pred             EEEEecC
Confidence            9999964

>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=98.88  E-value=4.7e-09  Score=101.99  Aligned_cols=81  Identities=25%  Similarity=0.299  Sum_probs=68.0

Q ss_pred             ccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccc---------cCCCCcccCCCEEEEEEEEEeC---
Q 005707          257 TTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFAN---------MMGGSSLQVGQEVSVRVLRISR---  324 (681)
Q Consensus       257 ~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~---------~~p~~~fkVGqkVkVrVL~IDk---  324 (681)
                      ..+..+|+++.|+|++++++|+||+|+ +++||+|.+++.+.++..         .++...|++||.|+|+|+++|.   
T Consensus        76 ~~~~~~Gev~~G~V~~v~~~G~fV~l~-~~eglvhis~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~  154 (187)
T 1go3_E           76 VYIPEMYELIEGEVVDVVEFGSFVRLG-PLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAE  154 (187)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEECS-SSEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEEECCC-
T ss_pred             EEccCCCCEEEEEEEEEeCcEEEEEEc-CccEEEEhHHhCCCcceECCccceEEecCCCeEEcCCCEEEEEEEEEEcccC
Confidence            456789999999999999999999997 499999999999876531         1346889999999999999973   


Q ss_pred             ----CeEEEEEeccCCCc
Q 005707          325 ----GQVTLTMKKEDDVG  338 (681)
Q Consensus       325 ----gKI~LSLK~~~~DP  338 (681)
                          +++.||||.....+
T Consensus       155 ~p~~~~I~lS~k~~~LG~  172 (187)
T 1go3_E          155 RKRGSKIALTMRQPYLGK  172 (187)
T ss_dssp             ----CEEEEECCSTTCEE
T ss_pred             CCCccEEEEEEcCCCCCc
Confidence                49999999864333

>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=98.83  E-value=1.3e-09  Score=126.67  Aligned_cols=79  Identities=28%  Similarity=0.408  Sum_probs=71.3

Q ss_pred             ccccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEe
Q 005707          255 MKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMK  332 (681)
Q Consensus       255 ~~~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK  332 (681)
                      ..+.++++|+++.|+|++|++||+||+|+.+++||||+++++|.++.  ++...|++||.|+|+|+++|  +++|.||||
T Consensus       647 e~~~~l~vG~iv~G~V~~V~~fGaFV~l~~~~eGLVhiS~Lsd~~v~--d~~~~~~vGd~V~VkVi~VD~~~~rI~LSlk  724 (785)
T 3bzc_A          647 ESLKDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVK--DPYEVVKAGDIVKVKVMEVDIPRNRVGLSMR  724 (785)
T ss_dssp             CSSTTCCTTCBCCCEEEEEETTEEEEECSSSSEEEEETTTSCSSCCS--CHHHHCCTTCCCCCBEEEEETTTTEEEECCS
T ss_pred             cchhhcCCCCEEEEEEEEEecCCeEEEeCCCcEEEEEHHHcCccccC--ChhheeCCCCEEEEEEEEEECCCCEEEEEEe
Confidence            56778999999999999999999999999999999999999997753  45788999999999999998  599999998


Q ss_pred             ccC
Q 005707          333 KED  335 (681)
Q Consensus       333 ~~~  335 (681)
                      ...
T Consensus       725 ~~~  727 (785)
T 3bzc_A          725 MSD  727 (785)
T ss_dssp             SCC
T ss_pred             cCC
Confidence            653

>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A

Probab=98.83  E-value=7.3e-09  Score=100.84  Aligned_cols=70  Identities=24%  Similarity=0.403  Sum_probs=65.6

Q ss_pred             CCCCCcEEEEEEEEEecCeeEEEECC----------CeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceE
Q 005707          144 DLIPGATFTGKVRSIQPFGAFIDFGA----------FTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRIS  213 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~GaFVdLgg----------gV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~  213 (681)
                      ..+ |++|.|+|+++.++|+||+|..          +.+|+||++++++.++.++.+.|++||.|+|+|++     +++.
T Consensus        55 ~p~-GdiV~G~V~~V~~~ga~V~I~~v~~~~~~~~~~~~Gll~isei~~~~~~~~~~~~~~GD~V~akVi~-----~~i~  128 (179)
T 3m7n_A           55 IVK-GDVVLGRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEISEAVGYLDILKARVIG-----DNLR  128 (179)
T ss_dssp             CCT-TCEEEEEEEEECSSEEEEEEEEETTCCSCCTTCEEEEEEGGGTTSSCCSSGGGTCCTTCEEEEEEEE-----TTTE
T ss_pred             cCC-CCEEEEEEEEEeCCcEEEEEccccCcccccccCeeEEEEHHHcCcchhhCHhhcCCCCCEEEEEEEC-----CeEE
Confidence            467 9999999999999999999976          79999999999999999999999999999999997     8999


Q ss_pred             EEEecc
Q 005707          214 LTMRES  219 (681)
Q Consensus       214 LSlK~l  219 (681)
                      ||+|..
T Consensus       129 LS~k~~  134 (179)
T 3m7n_A          129 LSTKEE  134 (179)
T ss_dssp             EECCST
T ss_pred             EEEecC
Confidence            999964

>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=98.82  E-value=5.6e-09  Score=111.24  Aligned_cols=113  Identities=18%  Similarity=0.090  Sum_probs=81.9

Q ss_pred             hhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCChhhHHhhhchhhhhcCCCCCCcCCCC--CCcE
Q 005707           73 LHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASPTLAESRRSRTARKSEMPPVKNEDLI--PGAT  150 (681)
Q Consensus        73 ~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~~daek~~~kr~~rk~e~~~lt~~~Lk--vGdI  150 (681)
                      ....+|+.+.+.|...|..+.    .+.                      ..+.......+..+...+ +..++  .|++
T Consensus        85 ~~~~vGd~ie~~I~~~dfgR~----aa~----------------------~aKqvi~qkireaere~i-~~e~~~~~GeI  137 (344)
T 1hh2_P           85 PLAEVGSIVKKELNVKNFGRI----AAQ----------------------TAKQVLIQRIRELEKEKQ-FEKYSELKGTV  137 (344)
T ss_dssp             TTCCTTCEEEEECCCCCSSSC----SGG----------------------GHHHHHHHHHHHHTTCCS-SCCTTCCTTCE
T ss_pred             ccccCCCEEEEEEccccCccH----HHH----------------------HHHHHHHHHHHHHHHHHH-HHHHhhcCCCE
Confidence            345689999999987765433    111                      112222122333333222 45555  8999


Q ss_pred             EEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCC--ceEEEEecc
Q 005707          151 FTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETG--RISLTMRES  219 (681)
Q Consensus       151 VeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekg--rI~LSlK~l  219 (681)
                      ++|+|.++.++|+||++| +.+|+||.+++.      +.+.|++||.|+|+|+.++++++  +|.||++..
T Consensus       138 V~G~V~ri~~~~v~VDlG-k~EgiLp~sE~i------p~E~~~vGD~Vkv~V~~V~~~~kg~~I~LSRt~p  201 (344)
T 1hh2_P          138 TTAEVIRVMGEWADIRIG-KLETRLPKKEWI------PGEEIKAGDLVKVYIIDVVKTTKGPKILVSRRVP  201 (344)
T ss_dssp             EEEEEEEECSSEEEEEET-TEEEEEEGGGSC------TTCCCCTTCEEEEEEEEEEEETTEEEEEEESSSH
T ss_pred             EEEEEEEEecCcEEEEeC-CeEEEEeHHHcC------CCcCCCCCCEEEEEEEEEEcCCCCcEEEEEeecc
Confidence            999999999999999998 599999999996      45689999999999999997665  677877743

>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=98.82  E-value=9.8e-09  Score=98.85  Aligned_cols=68  Identities=12%  Similarity=0.231  Sum_probs=58.4

Q ss_pred             cCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCc----------ccccccCCEEEEEEEEEeccCC
Q 005707          142 NEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDV----------GSIVSVGQEVKVRLIEANAETG  210 (681)
Q Consensus       142 ~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~----------~e~fkVGd~VkVkVl~VD~ekg  210 (681)
                      +....+|++++|+|++++++|+||+|+. .+||||+++|++.+..++          .+.|++||.|+|+|+++|.+.+
T Consensus        78 ~~~~~~Gev~~G~V~~v~~fG~FV~l~~-~dglvhis~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~  155 (171)
T 1y14_B           78 VFKPFKGEVVDGTVVSCSQHGFEVQVGP-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVS  155 (171)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEEETT-EEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEEEETT
T ss_pred             EccCCCCCEEEEEEEEEecCEEEEEecC-eEEEEEHHHCCCCceECcccCceEEeccceEECCCCEEEEEEEEEEcCCC
Confidence            4467799999999999999999999998 999999999986543222          2669999999999999998774

>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=98.81  E-value=1.1e-08  Score=99.05  Aligned_cols=79  Identities=25%  Similarity=0.358  Sum_probs=66.3

Q ss_pred             cccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccc---------cCCCCcccCCCEEEEEEEEEe---
Q 005707          256 KTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFAN---------MMGGSSLQVGQEVSVRVLRIS---  323 (681)
Q Consensus       256 ~~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~---------~~p~~~fkVGqkVkVrVL~ID---  323 (681)
                      ...+..+|+++.|+|++++++|+||+++ +++||+|.+++.++++..         .+....|++||.|+|||+.+|   
T Consensus        75 iv~~p~~Gev~~G~V~~v~~~G~fv~l~-~~~glvh~s~l~~d~~~~d~~~~~~~g~~~~~~~~~Gd~VrvkV~~v~~~~  153 (180)
T 4ayb_E           75 ITYVPVVQEVVEGEVLQVDNYGVFVNLG-PMDGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISVASTV  153 (180)
T ss_dssp             EEECCCTTCEEEEEEEEEETTEEEEECS-SSEEEEEGGGSCSSCEEECSSSCCEEETTTCCCCCTTCEEEEEEEEECC--
T ss_pred             eeeeccCCCEEEEEEeeeccceEEEEEC-CccceEEeeecCCCccccchhcceEEEeccCeEECCCCEEEEEEEEEeCCC
Confidence            3556789999999999999999999997 699999999999886521         134668999999999999996   


Q ss_pred             ---CCeEEEEEeccC
Q 005707          324 ---RGQVTLTMKKED  335 (681)
Q Consensus       324 ---kgKI~LSLK~~~  335 (681)
                         ..||.||||+.-
T Consensus       154 ~~~~~rI~ls~k~~g  168 (180)
T 4ayb_E          154 TGRLPRIALTMRQPY  168 (180)
T ss_dssp             -----CEEEECCSTT
T ss_pred             CcccCcEEEEcCCCC
Confidence               258999999853

>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=98.80  E-value=2.4e-10  Score=132.68  Aligned_cols=155  Identities=12%  Similarity=0.015  Sum_probs=95.6

Q ss_pred             cccccceeeecccccccccceeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCcceecCCC
Q 005707           25 NNCLTRYNSTRKSTKQTISSQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIP  104 (681)
Q Consensus        25 ~~~~~~~~~~r~~~~~~~s~~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~  104 (681)
                      ..+.+||||+-.+|.|||||.|++.||-.+|-+ -........ ... +..                     .--+.   
T Consensus       585 ~~~~~HfgLa~~~YtHfTSPIRRY~DLivHR~L-~~~l~~~~~-~~~-~~~---------------------~~~l~---  637 (760)
T 2vnu_D          585 YPDFRHYGLAVDIYTHFTSPIRRYCDVVAHRQL-AGAIGYEPL-SLT-HRD---------------------KNKMD---  637 (760)
T ss_dssp             GGGGCBTTTTBSCCCCCSCTTTBHHHHHHHHHH-HHHTTSSCC-CGG-GGC---------------------HHHHH---
T ss_pred             CCCCCceecCCCceeccCchHhhhHHHHHHHHH-HHHHccCCC-ccc-ccC---------------------HHHHH---
Confidence            457899999999999999999999998776432 111111000 000 000                     00011   


Q ss_pred             CCcccccccccccCCChhhHHhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECC-CeEEEEeccccC--
Q 005707          105 SDVETSESSSIKSEASPTLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGA-FTDGLVHVSRLS--  181 (681)
Q Consensus       105 s~v~~ae~ss~~sea~~daek~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgg-gV~GLVPiSELS--  181 (681)
                         ..+++++.+.+.+..+++...+.....       +..-++ +++.|+|++|.++|+||.|.. +++|+||+++|.  
T Consensus       638 ---~~~~~~s~~er~A~~aer~~~~~~~~~-------~l~~~~-~~~~g~V~~V~~~G~fV~l~~~giEGlVhis~L~~~  706 (760)
T 2vnu_D          638 ---MICRNINRKHRNAQFAGRASIEYYVGQ-------VMRNNE-STETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTED  706 (760)
T ss_dssp             ---HHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHTCC-SEEEEEEEEEETTEEEEEETTTTEEEEEEHHHHCSC
T ss_pred             ---HHHHHhhHHHHHHHHHHHHHHHHHHHH-------HhhcCc-eEEEEEEEEEECCeEEEEEeCCCcEEEEEeccccCC
Confidence               113445555566555555443321111       112223 699999999999999999975 799999999996  


Q ss_pred             Cccc-----------cC----cccccccCCEEEEEEEEEecc---CCceEEEEe
Q 005707          182 DNFV-----------KD----VGSIVSVGQEVKVRLIEANAE---TGRISLTMR  217 (681)
Q Consensus       182 ~~~v-----------~d----~~e~fkVGd~VkVkVl~VD~e---kgrI~LSlK  217 (681)
                      ++++           .+    ....|++||.|+|+|+.+|.+   +++|.|++|
T Consensus       707 ~d~~~fd~~~~~l~g~~~~~~~~~~~~lGD~V~VkV~~vd~~~~~~~kI~lslk  760 (760)
T 2vnu_D          707 PNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVMDPITSKRKAELLLK  760 (760)
T ss_dssp             GGGCEEETTTTEEEECCTTCSSCEEEETTCEEEEEEC--------CCEEEC---
T ss_pred             CceeEEcccccEEEEecCCCccCcEEecCCEEEEEEEEEECccccCCcEEEEeC
Confidence            4431           22    257899999999999999988   689999886

>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae}

Probab=98.79  E-value=4.2e-10  Score=133.69  Aligned_cols=155  Identities=12%  Similarity=0.015  Sum_probs=103.5

Q ss_pred             cccccceeeecccccccccceeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCcceecCCC
Q 005707           25 NNCLTRYNSTRKSTKQTISSQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIP  104 (681)
Q Consensus        25 ~~~~~~~~~~r~~~~~~~s~~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~  104 (681)
                      ..+.+||||+-.+|.|||||.|++.|+-.+|-+ -....+... +.. +..                     .-.+.   
T Consensus       802 ~~~~gHfgLa~~~YtHfTSPIRRY~DLivHR~L-~a~L~~~~~-~~~-~~~---------------------~~~l~---  854 (977)
T 2wp8_J          802 YPDFRHYGLAVDIYTHFTSPIRRYCDVVAHRQL-AGAIGYEPL-SLT-HRD---------------------KNKMD---  854 (977)
T ss_dssp             GGGSCBTTTTBSSCCCCSCTTTBHHHHHHHHHH-HHHTTSSCC-CGG-GGC---------------------HHHHH---
T ss_pred             CCCCCceecCCCCeeccCchHhhHHHHHHHHHH-HHHhcCCCC-ccc-ccC---------------------HHHHH---
Confidence            356799999999999999999999998776432 111111000 000 000                     00011   


Q ss_pred             CCcccccccccccCCChhhHHhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECC-CeEEEEeccccC--
Q 005707          105 SDVETSESSSIKSEASPTLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGA-FTDGLVHVSRLS--  181 (681)
Q Consensus       105 s~v~~ae~ss~~sea~~daek~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgg-gV~GLVPiSELS--  181 (681)
                         ..+++.+.+.+.+..+++...+.....       +..-+ |+++.|+|++|.++|+||.|.. +++|+||+++|.  
T Consensus       855 ---~i~~~~s~~er~A~~aeR~~~~~~~~~-------~l~~~-ge~~~g~V~~V~~~G~fV~L~~~giEGlVhis~L~~~  923 (977)
T 2wp8_J          855 ---MICRNINRKHRNAQFAGRASIEYYVGQ-------VMRNN-ESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTED  923 (977)
T ss_dssp             ---HHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHT-TCEEEEEEEEECSSEEEEECTTTCCEEEEEGGGTCSC
T ss_pred             ---HHHHHhCHHHHHHHHHHHHHHHHHHhh-------hhccc-ceEEEEEEEEEcCCeEEEEEcCCCeEEEEEeccccCC
Confidence               113445556666666665544321111       21223 8899999999999999999975 799999999997  


Q ss_pred             Cccc-----------cC----cccccccCCEEEEEEEEEecc---CCceEEEEe
Q 005707          182 DNFV-----------KD----VGSIVSVGQEVKVRLIEANAE---TGRISLTMR  217 (681)
Q Consensus       182 ~~~v-----------~d----~~e~fkVGd~VkVkVl~VD~e---kgrI~LSlK  217 (681)
                      ++++           .+    ....|++||.|+|+|..+|..   +++|.|++|
T Consensus       924 ~d~y~fde~~~~L~g~~~~g~~~~~~~lGD~V~VkV~~vd~~~~~~~kI~Lslk  977 (977)
T 2wp8_J          924 PNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVMDPITSKRKAELLLK  977 (977)
T ss_dssp             GGGCEEETTTTEEEECCTTCCSCEEEETTCEEEEEECCCCCSSSCCCCCCEEEC
T ss_pred             CceeEEcccccEEEeecCCCccCcEEccCCEEEEEEEEEcCcccCCCceEEEeC
Confidence            4431           22    357899999999999999874   489999986

>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=98.79  E-value=1.4e-08  Score=97.62  Aligned_cols=75  Identities=11%  Similarity=0.300  Sum_probs=61.3

Q ss_pred             cCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCc------------ccccccCCEEEEEEEEEeccC
Q 005707          142 NEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDV------------GSIVSVGQEVKVRLIEANAET  209 (681)
Q Consensus       142 ~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~------------~e~fkVGd~VkVkVl~VD~ek  209 (681)
                      +....+|++++|+|++++++|+||+|+. .+||||+++|++.+..++            ...|++||.|+|+|+++|.+.
T Consensus        76 ~~~~~~Gev~~G~V~~v~~fG~fV~l~~-~~glvhis~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~  154 (172)
T 2c35_B           76 VFRPFKGEVVDAVVTQVNKVGLFTEIGP-MSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDK  154 (172)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEEETT-EEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEET
T ss_pred             EeeCCCCCEEEEEEEEEeCCEEEEEECC-EEEEEEHHHCCCCcEECCCCCccEEEeCCCCEEECCCCEEEEEEEEEEcCC
Confidence            3456799999999999999999999975 789999999986544222            447999999999999999876


Q ss_pred             C---ceEEEEec
Q 005707          210 G---RISLTMRE  218 (681)
Q Consensus       210 g---rI~LSlK~  218 (681)
                      +   ++. ||++
T Consensus       155 ~~~~~ig-sm~~  165 (172)
T 2c35_B          155 NDIFAIG-SLMD  165 (172)
T ss_dssp             TEEEEEE-ECCS
T ss_pred             CCcEEEE-EecC
Confidence            6   444 7764

>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=98.77  E-value=1.2e-08  Score=102.35  Aligned_cols=80  Identities=14%  Similarity=0.245  Sum_probs=65.9

Q ss_pred             cCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcc----------cccccCCEEEEEEEEEeccCC-
Q 005707          142 NEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVG----------SIVSVGQEVKVRLIEANAETG-  210 (681)
Q Consensus       142 ~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~----------e~fkVGd~VkVkVl~VD~ekg-  210 (681)
                      +...++|++++|+|++++++|+||+|+. .+||||+++|++.+..++.          +.|++||.|+|+|+++|.+.+ 
T Consensus        78 ~~~p~vGev~~G~V~~vt~fG~FVelg~-~dGlVhiS~l~d~~~~d~~~~~w~~~~~~~~~~~Gd~VrVkV~~vd~~~~~  156 (215)
T 2b8k_G           78 VFKPFKGEVVDGTVVSCSQHGFEVQVGP-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSS  156 (215)
T ss_dssp             EECCCTTEEEEEEEEEEETTEEEEECTT-SEEEEEGGGSCSSCCCBSSCSSCEEECSSCEEETTCEEEEEEEEEEEETTE
T ss_pred             eeccCCCCEEEEEEEEEecceEEEEecC-cEEEEEHHHCCccceeccccccceeeccccEECCCCEEEEEEEEEEcCCCc
Confidence            4466899999999999999999999988 9999999999866443332          569999999999999998875 


Q ss_pred             --ceEEEEeccchhh
Q 005707          211 --RISLTMRESDDIS  223 (681)
Q Consensus       211 --rI~LSlK~l~~dp  223 (681)
                        +|. ||++.-.-+
T Consensus       157 i~~Ig-Smk~~~LG~  170 (215)
T 2b8k_G          157 IHAIG-SIKEDYLGA  170 (215)
T ss_dssp             EEEEE-ECCSTTCEE
T ss_pred             cEEEE-EcCCCCCCC
Confidence              555 887654433

>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae}

Probab=98.77  E-value=8.1e-10  Score=131.46  Aligned_cols=79  Identities=11%  Similarity=0.188  Sum_probs=0.4

Q ss_pred             cccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEec
Q 005707          256 KTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKK  333 (681)
Q Consensus       256 ~~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~  333 (681)
                      ...+|++|++|.|+|++|++||+||+|+.|++||||+++++|.++ ..++...|++||.|+|+|++||  ++||.||||.
T Consensus       899 t~~~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSelsd~~~-v~~~~~v~kvGd~V~vkVl~VD~~~~rI~LSlk~  977 (1030)
T 3psf_A          899 SEKTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQL-RRPANEIYEIGKTYPAKVIYIDYANITAEVSLLD  977 (1030)
T ss_dssp             C-------------------------------------------------------------------------------
T ss_pred             cHHHhcCCCEEEEEEEEEccCeEEEEeCCCcEEEEEHHHcCCCcc-cCCHHHcCCCCCEEEEEEEEEECCCCEEEEEech
Confidence            458899999999999999999999999999999999999999872 1246889999999999999997  6899999997


Q ss_pred             cC
Q 005707          334 ED  335 (681)
Q Consensus       334 ~~  335 (681)
                      ..
T Consensus       978 ~d  979 (1030)
T 3psf_A          978 HD  979 (1030)
T ss_dssp             --
T ss_pred             HH
Confidence            63

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

Probab=98.77  E-value=1.1e-08  Score=91.17  Aligned_cols=86  Identities=29%  Similarity=0.375  Sum_probs=67.6

Q ss_pred             CCCCCcEEEEEEEEE---ecCeeEEEE-CCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEecc
Q 005707          144 DLIPGATFTGKVRSI---QPFGAFIDF-GAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRES  219 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV---~d~GaFVdL-gggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l  219 (681)
                      ..+.++.++|+|+..   +.|| |+.- .++.++|+|++.|.+..+                                  
T Consensus        10 ~~~~~~~~~G~Vk~fn~~kGfG-FI~~~~gg~dvfvH~s~l~~~~~----------------------------------   54 (101)
T 2bh8_A           10 SRLQSGKMTGIVKWFNADKGFG-FITPDDGSKDVFVHFSAGSSGAA----------------------------------   54 (101)
T ss_dssp             ------CEEEEEEEEEGGGTEE-EEEESSSSCEEEEECCCSCSSSC----------------------------------
T ss_pred             cccccccceeEEEEEECCCCCE-EEEeCCCCcEEEEEEEEEecCCc----------------------------------
Confidence            345677899999998   4688 6665 455899999999987631                                  


Q ss_pred             chhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCccc
Q 005707          220 DDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDG  299 (681)
Q Consensus       220 ~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~  299 (681)
                          .                                ...+++|+.|.+.|.++.+||+||+|.++++||||+++++|.+
T Consensus        55 ----~--------------------------------~~~l~~Ge~V~g~V~~i~~fG~fv~l~~~~eGlvhis~i~~~~   98 (101)
T 2bh8_A           55 ----V--------------------------------RGNPQQGDRVEGKIKSITDFGIFIGLDGGIDGLVHLSDISWAQ   98 (101)
T ss_dssp             ----C--------------------------------CCCCCTTCEEEEEEEECCSEEEEECTTSCEEEEEEEEEEEECC
T ss_pred             ----c--------------------------------ccCCCCCCEEEEEEEEeCCcEEEEEcCCCceEEEEHHHCccCc
Confidence                0                                1247899999999999999999999998999999999999876


Q ss_pred             c
Q 005707          300 F  300 (681)
Q Consensus       300 i  300 (681)
                      +
T Consensus        99 ~   99 (101)
T 2bh8_A           99 A   99 (101)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=98.71  E-value=1.5e-08  Score=101.15  Aligned_cols=77  Identities=13%  Similarity=0.069  Sum_probs=67.6

Q ss_pred             cCCccCcEEEEEEEEEecceEEEEeC--------CCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC--CeE
Q 005707          258 TKFVKGQDLEGTVKNLTRSGAFISLP--------EGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR--GQV  327 (681)
Q Consensus       258 sklkvGdIV~G~VknVt~~GaFVeIg--------~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk--gKI  327 (681)
                      ..+++|++|.|+|++|.++|+||+|.        .+.+|+||++++++.+.+..++.+.|++||.|.|+|+++++  +++
T Consensus        77 y~p~vGDvV~G~V~~v~~~~a~V~I~~v~~~~L~~~~~GlIhisei~~~~~~~~~~~~~l~~GD~V~akVisi~~~~~~i  156 (209)
T 2nn6_I           77 LLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSNY  156 (209)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEETTTTEE
T ss_pred             CCCCCCCEEEEEEEEEECceEEEEECccccccccCCceeEEEHHHcccccccccchhhhcCCCCEEEEEEEEEeCCCCeE
Confidence            35789999999999999999999974        57899999999998876534568889999999999999975  579


Q ss_pred             EEEEecc
Q 005707          328 TLTMKKE  334 (681)
Q Consensus       328 ~LSLK~~  334 (681)
                      .||+|..
T Consensus       157 ~LS~k~~  163 (209)
T 2nn6_I          157 LLTTAEN  163 (209)
T ss_dssp             EEECCSS
T ss_pred             EEEEecC
Confidence            9999875

>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A

Probab=98.69  E-value=2.2e-08  Score=97.45  Aligned_cols=69  Identities=22%  Similarity=0.230  Sum_probs=63.1

Q ss_pred             CccCcEEEEEEEEEecceEEEEeCC----------CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCeEEE
Q 005707          260 FVKGQDLEGTVKNLTRSGAFISLPE----------GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQVTL  329 (681)
Q Consensus       260 lkvGdIV~G~VknVt~~GaFVeIg~----------GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgKI~L  329 (681)
                      .+ |++|.|+|++|.++|+||+|..          +.+|+||++++++.+.+  ++.+.|++||.|.++|++   +++.|
T Consensus        56 p~-GdiV~G~V~~V~~~ga~V~I~~v~~~~~~~~~~~~Gll~isei~~~~~~--~~~~~~~~GD~V~akVi~---~~i~L  129 (179)
T 3m7n_A           56 VK-GDVVLGRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVK--EISEAVGYLDILKARVIG---DNLRL  129 (179)
T ss_dssp             CT-TCEEEEEEEEECSSEEEEEEEEETTCCSCCTTCEEEEEEGGGTTSSCCS--SGGGTCCTTCEEEEEEEE---TTTEE
T ss_pred             CC-CCEEEEEEEEEeCCcEEEEEccccCcccccccCeeEEEEHHHcCcchhh--CHhhcCCCCCEEEEEEEC---CeEEE
Confidence            46 9999999999999999999987          89999999999998764  448999999999999998   89999


Q ss_pred             EEecc
Q 005707          330 TMKKE  334 (681)
Q Consensus       330 SLK~~  334 (681)
                      |+|..
T Consensus       130 S~k~~  134 (179)
T 3m7n_A          130 STKEE  134 (179)
T ss_dssp             ECCST
T ss_pred             EEecC
Confidence            99875

>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=98.67  E-value=6.1e-08  Score=97.23  Aligned_cols=81  Identities=15%  Similarity=0.131  Sum_probs=63.0

Q ss_pred             ccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCC--------CCcccCCCEEEEEEEEEe--C--
Q 005707          257 TTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMG--------GSSLQVGQEVSVRVLRIS--R--  324 (681)
Q Consensus       257 ~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p--------~~~fkVGqkVkVrVL~ID--k--  324 (681)
                      ..+..+|+++.|+|+++++||+||+|++ ++||||+++|.+.+.-+...        ...|++||.|+|+|+++|  +  
T Consensus        78 ~~~p~vGev~~G~V~~vt~fG~FVelg~-~dGlVhiS~l~d~~~~d~~~~~w~~~~~~~~~~~Gd~VrVkV~~vd~~~~~  156 (215)
T 2b8k_G           78 VFKPFKGEVVDGTVVSCSQHGFEVQVGP-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSS  156 (215)
T ss_dssp             EECCCTTEEEEEEEEEEETTEEEEECTT-SEEEEEGGGSCSSCCCBSSCSSCEEECSSCEEETTCEEEEEEEEEEEETTE
T ss_pred             eeccCCCCEEEEEEEEEecceEEEEecC-cEEEEEHHHCCccceeccccccceeeccccEECCCCEEEEEEEEEEcCCCc
Confidence            4456899999999999999999999997 99999999997653211111        256999999999999997  3  


Q ss_pred             -CeEEEEEeccCCCcC
Q 005707          325 -GQVTLTMKKEDDVGS  339 (681)
Q Consensus       325 -gKI~LSLK~~~~DP~  339 (681)
                       .++. |||+....++
T Consensus       157 i~~Ig-Smk~~~LG~~  171 (215)
T 2b8k_G          157 IHAIG-SIKEDYLGAI  171 (215)
T ss_dssp             EEEEE-ECCSTTCEEC
T ss_pred             cEEEE-EcCCCCCCCc
Confidence             3566 8877544443

>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=98.67  E-value=5.6e-08  Score=93.58  Aligned_cols=66  Identities=17%  Similarity=0.170  Sum_probs=54.0

Q ss_pred             ccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCC--------CCcccCCCEEEEEEEEEe
Q 005707          257 TTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMG--------GSSLQVGQEVSVRVLRIS  323 (681)
Q Consensus       257 ~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p--------~~~fkVGqkVkVrVL~ID  323 (681)
                      ..+..+|+++.|+|+++++||+||++++ .+||+|.+++++.+.-+...        ...|++||.|+|+|+++|
T Consensus        78 ~~~~~~Gev~~G~V~~v~~fG~FV~l~~-~dglvhis~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd  151 (171)
T 1y14_B           78 VFKPFKGEVVDGTVVSCSQHGFEVQVGP-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCI  151 (171)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEEETT-EEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEE
T ss_pred             EccCCCCCEEEEEEEEEecCEEEEEecC-eEEEEEHHHCCCCceECcccCceEEeccceEECCCCEEEEEEEEEE
Confidence            4456699999999999999999999998 99999999997652111110        266999999999999997

>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=98.64  E-value=3.3e-08  Score=101.15  Aligned_cols=74  Identities=18%  Similarity=0.196  Sum_probs=68.1

Q ss_pred             CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccc---cCcccccccCCEEEEEEEEEeccCCceEEEEec
Q 005707          144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFV---KDVGSIVSVGQEVKVRLIEANAETGRISLTMRE  218 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v---~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~  218 (681)
                      .+++|++|.|+|+++.++|+||+|++..+|+||++++.+.+.   .++.+.|++||.|.|+|++++.. +++.||++.
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 YPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDRS-IDPVLSVKG  147 (251)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEETT-EEEEEECCS
T ss_pred             CCCCCCEEEEEEEEEeCceEEEEcCCCeEEEEEHHHhcCCccccccchhhcCCCCCEEEEEEEEECCC-CcEEEEEcc
Confidence            578999999999999999999999988999999999998777   78888999999999999999864 689999874

>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=98.63  E-value=1.7e-08  Score=107.57  Aligned_cols=110  Identities=21%  Similarity=0.183  Sum_probs=80.5

Q ss_pred             cccccCCEEEEEEEEEeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCc--cCcEEE
Q 005707          190 SIVSVGQEVKVRLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFV--KGQDLE  267 (681)
Q Consensus       190 e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklk--vGdIV~  267 (681)
                      ..+.+||.+.+.|...|.. ++...+.|+......                  |.      ......+..|+  .|+++.
T Consensus        85 ~~~~vGd~ie~~I~~~dfg-R~aa~~aKqvi~qki------------------re------aere~i~~e~~~~~GeIV~  139 (344)
T 1hh2_P           85 PLAEVGSIVKKELNVKNFG-RIAAQTAKQVLIQRI------------------RE------LEKEKQFEKYSELKGTVTT  139 (344)
T ss_dssp             TTCCTTCEEEEECCCCCSS-SCSGGGHHHHHHHHH------------------HH------HTTCCSSCCTTCCTTCEEE
T ss_pred             ccccCCCEEEEEEccccCc-cHHHHHHHHHHHHHH------------------HH------HHHHHHHHHHhhcCCCEEE
Confidence            4488999999999887643 233333344333222                  00      01123456666  899999


Q ss_pred             EEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--C--CeEEEEEec
Q 005707          268 GTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--R--GQVTLTMKK  333 (681)
Q Consensus       268 G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--k--gKI~LSLK~  333 (681)
                      |+|.++.++|+||+++ +.+|+||.+|+.        |.+.|++||.|+|+|++++  +  .++.||.+.
T Consensus       140 G~V~ri~~~~v~VDlG-k~EgiLp~sE~i--------p~E~~~vGD~Vkv~V~~V~~~~kg~~I~LSRt~  200 (344)
T 1hh2_P          140 AEVIRVMGEWADIRIG-KLETRLPKKEWI--------PGEEIKAGDLVKVYIIDVVKTTKGPKILVSRRV  200 (344)
T ss_dssp             EEEEEECSSEEEEEET-TEEEEEEGGGSC--------TTCCCCTTCEEEEEEEEEEEETTEEEEEEESSS
T ss_pred             EEEEEEecCcEEEEeC-CeEEEEeHHHcC--------CCcCCCCCCEEEEEEEEEEcCCCCcEEEEEeec
Confidence            9999999999999998 999999999875        3578999999999999997  3  357777754

>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=98.60  E-value=1.1e-07  Score=96.06  Aligned_cols=74  Identities=16%  Similarity=0.299  Sum_probs=67.6

Q ss_pred             CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCc-cccCcccccccCCEEEEEEEEEeccCCceEEEEec
Q 005707          144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDN-FVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRE  218 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~-~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~  218 (681)
                      .+++|++|.|+|+.+.++|+||+|++..+|+||++++.+. +..++.+.|++||.|.|+|++++.. +++.||++.
T Consensus        54 ~p~~GDiV~G~V~~v~~~~a~V~I~~~~~g~l~isev~~~~~~~~~~~~l~~GD~V~arVi~v~~~-~~i~LS~r~  128 (229)
T 2ba0_A           54 TPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDPK-MKVTLTMKD  128 (229)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECTT-CCEEEECCS
T ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHccccccccchhcccCCCCEEEEEEEEECCC-CcEEEEEcc
Confidence            4789999999999999999999999889999999999964 6788899999999999999999864 789999874

>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=98.60  E-value=3.5e-08  Score=99.84  Aligned_cols=76  Identities=17%  Similarity=0.169  Sum_probs=65.2

Q ss_pred             CCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCccccc--ccCCCCcccCCCEEEEEEEEEeC-CeEEEEEecc
Q 005707          259 KFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFA--NMMGGSSLQVGQEVSVRVLRISR-GQVTLTMKKE  334 (681)
Q Consensus       259 klkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie--~~~p~~~fkVGqkVkVrVL~IDk-gKI~LSLK~~  334 (681)
                      ..++|++|.|+|+++.++|+||+|+.+.+|+||++++.+.+.+  ...+...|++||.|.|+|+++++ +++.||+|..
T Consensus        63 ~p~~GDiV~G~V~~v~~~~~~V~I~~~~~g~l~isei~~~~~~~~~~~~~~~l~~GD~V~a~Vi~v~~~~~i~LS~k~~  141 (235)
T 2z0s_A           63 VPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDKTRSPLLTVQGE  141 (235)
T ss_dssp             CCCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECTTSCEEEECCSS
T ss_pred             CCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHhCCCccccchhhHhhcCCCCCEEEEEEEEECCCCcEEEEEecc
Confidence            4689999999999999999999999999999999999763221  13457799999999999999974 6899999864

>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=98.59  E-value=2.5e-08  Score=96.40  Aligned_cols=74  Identities=16%  Similarity=0.340  Sum_probs=62.1

Q ss_pred             cCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCc----------ccccccCCEEEEEEEEEeccCCc
Q 005707          142 NEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDV----------GSIVSVGQEVKVRLIEANAETGR  211 (681)
Q Consensus       142 ~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~----------~e~fkVGd~VkVkVl~VD~ekgr  211 (681)
                      +....+|++++|+|++++++|+||+|+. ++||||+++|++.+..+.          ...|++||.|+|+|+++|.+.+.
T Consensus        79 vf~p~~Gev~~G~V~~v~~fG~FV~l~~-~~glVh~s~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~vd~~~~~  157 (172)
T 3h0g_G           79 LWRPFRGEVVDAIVTTVNKMGFFANIGP-LNVFVSSHLVPPDMKFDPTANPPNYSGEDQVIEKGSNVRLKIVGTRTDATE  157 (172)
T ss_dssp             EECCCTTCEEECCCCEEETTEEECCBTT-BCCEEEGGGSCTTCCCBSSSSSCBEESSSCEECSSCCEEEEEEEEEESSSC
T ss_pred             eeccCCCCEEEEEEEEEEcceEEEEeCC-eEEEEEHHHCCCccccCcccccceEecCCcEECCCCEEEEEEEEEECCCCC
Confidence            4567899999999999999999999976 789999999986654443          56899999999999999988753


Q ss_pred             ---eEEEEe
Q 005707          212 ---ISLTMR  217 (681)
Q Consensus       212 ---I~LSlK  217 (681)
                         |. ||+
T Consensus       158 ~~~Ig-tm~  165 (172)
T 3h0g_G          158 IFAIA-TMK  165 (172)
T ss_dssp             EEEEE-ECC
T ss_pred             ceEEE-EcC
Confidence               44 555

>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=98.56  E-value=1.4e-07  Score=90.72  Aligned_cols=75  Identities=11%  Similarity=0.220  Sum_probs=58.1

Q ss_pred             ccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccC----------CCCcccCCCEEEEEEEEEe--C
Q 005707          257 TTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMM----------GGSSLQVGQEVSVRVLRIS--R  324 (681)
Q Consensus       257 ~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~----------p~~~fkVGqkVkVrVL~ID--k  324 (681)
                      ..+-.+|+++.|+|++++++|+||+|+ ..+||+|.++|.+.+.-+..          ....|++||.|+|+|+++|  +
T Consensus        76 ~~~~~~Gev~~G~V~~v~~fG~fV~l~-~~~glvhis~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~  154 (172)
T 2c35_B           76 VFRPFKGEVVDAVVTQVNKVGLFTEIG-PMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDK  154 (172)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEEET-TEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEET
T ss_pred             EeeCCCCCEEEEEEEEEeCCEEEEEEC-CEEEEEEHHHCCCCcEECCCCCccEEEeCCCCEEECCCCEEEEEEEEEEcCC
Confidence            334569999999999999999999997 67799999999764221111          1457999999999999997  3


Q ss_pred             C---eEEEEEec
Q 005707          325 G---QVTLTMKK  333 (681)
Q Consensus       325 g---KI~LSLK~  333 (681)
                      +   ++. |||+
T Consensus       155 ~~~~~ig-sm~~  165 (172)
T 2c35_B          155 NDIFAIG-SLMD  165 (172)
T ss_dssp             TEEEEEE-ECCS
T ss_pred             CCcEEEE-EecC
Confidence            3   444 7765

>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=98.56  E-value=7.4e-08  Score=97.46  Aligned_cols=74  Identities=19%  Similarity=0.284  Sum_probs=66.6

Q ss_pred             CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCc----cccCcccccccCCEEEEEEEEEeccCCceEEEEec
Q 005707          144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDN----FVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRE  218 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~----~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~  218 (681)
                      .+++|++|.|+|+++.++|+||+|++..+|+||++++.+.    +..++.+.|++||.|.|+|++++.. +++.||++.
T Consensus        63 ~p~~GDiV~G~V~~v~~~~~~V~I~~~~~g~l~isei~~~~~~~~~~~~~~~l~~GD~V~a~Vi~v~~~-~~i~LS~k~  140 (235)
T 2z0s_A           63 VPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDKT-RSPLLTVQG  140 (235)
T ss_dssp             CCCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECTT-SCEEEECCS
T ss_pred             CCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHhCCCccccchhhHhhcCCCCCEEEEEEEEECCC-CcEEEEEec
Confidence            6789999999999999999999999889999999999863    4577888999999999999999864 589999873

>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=98.51  E-value=1.2e-07  Score=97.15  Aligned_cols=76  Identities=18%  Similarity=0.159  Sum_probs=66.8

Q ss_pred             CCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccc-cCCCCcccCCCEEEEEEEEEeC-CeEEEEEecc
Q 005707          259 KFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFAN-MMGGSSLQVGQEVSVRVLRISR-GQVTLTMKKE  334 (681)
Q Consensus       259 klkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~-~~p~~~fkVGqkVkVrVL~IDk-gKI~LSLK~~  334 (681)
                      ..++|++|.|+|+.+.++|+||+|+.+.+|+||++++.+.+.+. .++...|++||.|.|+|+++++ +++.||+|..
T Consensus        71 ~p~~GDiV~G~V~~v~~~ga~VdI~~~~~GlL~isei~~~~~~~~~~~~~~l~vGD~V~arVi~v~~~~~i~LS~r~~  148 (251)
T 2je6_I           71 YPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDRSIDPVLSVKGK  148 (251)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEETTEEEEEECCST
T ss_pred             CCCCCCEEEEEEEEEeCceEEEEcCCCeEEEEEHHHhcCCccccccchhhcCCCCCEEEEEEEEECCCCcEEEEEccc
Confidence            45899999999999999999999999999999999998766422 4457899999999999999974 7899999864

>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=98.37  E-value=6.4e-07  Score=90.45  Aligned_cols=74  Identities=27%  Similarity=0.395  Sum_probs=64.3

Q ss_pred             CccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe-CCeEEEEEecc
Q 005707          260 FVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS-RGQVTLTMKKE  334 (681)
Q Consensus       260 lkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID-kgKI~LSLK~~  334 (681)
                      .++|++|.|+|+.+.++|+||+|+...+|+||.+++.+... ..+....|++||.|.|+|++++ .+++.||+|..
T Consensus        55 p~~GDiV~G~V~~v~~~~a~V~I~~~~~g~l~isev~~~~~-~~~~~~~l~~GD~V~arVi~v~~~~~i~LS~r~~  129 (229)
T 2ba0_A           55 PSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKP-NKKPNEVLDIGDAIIAKVLNIDPKMKVTLTMKDR  129 (229)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTTCCT-TSCGGGTCCTTCEEEEEEEEECTTCCEEEECCSS
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHcccccc-ccchhcccCCCCEEEEEEEEECCCCcEEEEEccc
Confidence            58999999999999999999999989999999999985311 1234678999999999999996 48999999865

>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=98.34  E-value=2.7e-07  Score=89.09  Aligned_cols=75  Identities=15%  Similarity=0.207  Sum_probs=59.3

Q ss_pred             ccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCccccccc--------CCCCcccCCCEEEEEEEEEe--C--
Q 005707          257 TTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANM--------MGGSSLQVGQEVSVRVLRIS--R--  324 (681)
Q Consensus       257 ~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~--------~p~~~fkVGqkVkVrVL~ID--k--  324 (681)
                      .-+..+|+++.|+|++++++|+||+++ .++||+|.++|++.+.-+.        +....|++||.|+|+|+++|  +  
T Consensus        79 vf~p~~Gev~~G~V~~v~~fG~FV~l~-~~~glVh~s~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~vd~~~~~  157 (172)
T 3h0g_G           79 LWRPFRGEVVDAIVTTVNKMGFFANIG-PLNVFVSSHLVPPDMKFDPTANPPNYSGEDQVIEKGSNVRLKIVGTRTDATE  157 (172)
T ss_dssp             EECCCTTCEEECCCCEEETTEEECCBT-TBCCEEEGGGSCTTCCCBSSSSSCBEESSSCEECSSCCEEEEEEEEEESSSC
T ss_pred             eeccCCCCEEEEEEEEEEcceEEEEeC-CeEEEEEHHHCCCccccCcccccceEecCCcEECCCCEEEEEEEEEECCCCC
Confidence            455779999999999999999999997 5779999999976532111        22468999999999999997  2  


Q ss_pred             -CeEEEEEec
Q 005707          325 -GQVTLTMKK  333 (681)
Q Consensus       325 -gKI~LSLK~  333 (681)
                       .+|. |||+
T Consensus       158 ~~~Ig-tm~~  166 (172)
T 3h0g_G          158 IFAIA-TMKE  166 (172)
T ss_dssp             EEEEE-ECCS
T ss_pred             ceEEE-EcCC
Confidence             3455 6664

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

Probab=98.19  E-value=4.1e-06  Score=74.45  Aligned_cols=86  Identities=17%  Similarity=0.190  Sum_probs=61.5

Q ss_pred             ccCCccCcEEEEEEEEE---ecceEEEEeCC-CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCeEEEEEe
Q 005707          257 TTKFVKGQDLEGTVKNL---TRSGAFISLPE-GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQVTLTMK  332 (681)
Q Consensus       257 ~sklkvGdIV~G~VknV---t~~GaFVeIg~-GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgKI~LSLK  332 (681)
                      ..+..+++.+.|+|+..   ..|| ||...+ |.++|+|.+.+.+..+                                
T Consensus         8 ~~~~~~~~~~~G~Vk~fn~~kGfG-FI~~~~gg~dvfvH~s~l~~~~~--------------------------------   54 (101)
T 2bh8_A            8 HGSRLQSGKMTGIVKWFNADKGFG-FITPDDGSKDVFVHFSAGSSGAA--------------------------------   54 (101)
T ss_dssp             --------CEEEEEEEEEGGGTEE-EEEESSSSCEEEEECCCSCSSSC--------------------------------
T ss_pred             eccccccccceeEEEEEECCCCCE-EEEeCCCCcEEEEEEEEEecCCc--------------------------------
Confidence            34455788899999987   6789 888655 6999999999987542                                


Q ss_pred             ccCCCcCCcceeeeEEEEeecccEEEEEEcCCeEEEeeCCccccc
Q 005707          333 KEDDVGSNLQLTQGVIHAATNPFVLAFRSNKDISSFLDERDKSAT  377 (681)
Q Consensus       333 ~~~~DP~e~~lv~G~V~~~i~~fGlfV~l~~gI~GfIp~~els~~  377 (681)
                       ....+...+.+.|.|. .+.+||+||.+.++++||+|.+++++.
T Consensus        55 -~~~~l~~Ge~V~g~V~-~i~~fG~fv~l~~~~eGlvhis~i~~~   97 (101)
T 2bh8_A           55 -VRGNPQQGDRVEGKIK-SITDFGIFIGLDGGIDGLVHLSDISWA   97 (101)
T ss_dssp             -CCCCCCTTCEEEEEEE-ECCSEEEEECTTSCEEEEEEEEEEEEC
T ss_pred             -cccCCCCCCEEEEEEE-EeCCcEEEEEcCCCceEEEEHHHCccC
Confidence             0112233455566677 788999999999999999999999976

>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe}

Probab=98.12  E-value=5.3e-06  Score=82.21  Aligned_cols=67  Identities=12%  Similarity=0.165  Sum_probs=57.8

Q ss_pred             cCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccc-------------------cCcccccccCCEEEEEE
Q 005707          142 NEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFV-------------------KDVGSIVSVGQEVKVRL  202 (681)
Q Consensus       142 ~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v-------------------~d~~e~fkVGd~VkVkV  202 (681)
                      +....+|+++.|+|++++++|+||+|+ .++|++|.+++.+++.                   .+....|++|+.|+|+|
T Consensus        76 ~f~p~~GEv~~G~Vs~vt~~GifV~lg-~~eglv~~~~l~~d~~~fd~~~~~~v~~~~~~~~~~~~~~~~~~Gd~VrvrV  154 (203)
T 3ayh_B           76 IFRPFRGEVMLGKIKSCSEEGIRVTIS-FFDDIFIPKDMLFDPCVFRPDERAWVWKIEGEDGSEGTELYFDIDEEIRFQI  154 (203)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEECS-SCCCEEEEGGGBCTTEEEEGGGTEEEEEECCCTTSCCEEEECCTTCEEEEEE
T ss_pred             EEccCCCCEEEEEEEEEeccEEEEEEe-CceEEEEcHHhCCCCceECccCceEEeecccccccccCCcEEcCCCEEEEEE
Confidence            456789999999999999999999995 5999999999987654                   44566799999999999


Q ss_pred             EEEeccC
Q 005707          203 IEANAET  209 (681)
Q Consensus       203 l~VD~ek  209 (681)
                      .++|...
T Consensus       155 ~~v~~~~  161 (203)
T 3ayh_B          155 ESEDFVD  161 (203)
T ss_dssp             EEEEECC
T ss_pred             EEEEccc
Confidence            9998643

>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=98.10  E-value=7.3e-06  Score=87.97  Aligned_cols=81  Identities=12%  Similarity=0.222  Sum_probs=60.8

Q ss_pred             hhhhhcCCCCCCcCCCC--CCcEEEEEEEE----EecCeeEEEECC---CeEEEEeccccCCccccCcccccccCCEEEE
Q 005707          130 RTARKSEMPPVKNEDLI--PGATFTGKVRS----IQPFGAFIDFGA---FTDGLVHVSRLSDNFVKDVGSIVSVGQEVKV  200 (681)
Q Consensus       130 r~~rk~e~~~lt~~~Lk--vGdIVeGkV~s----V~d~GaFVdLgg---gV~GLVPiSELS~~~v~d~~e~fkVGd~VkV  200 (681)
                      .+.+..+...+ |..++  +|++|+|+|.+    +.+.++||+||+   +++|+||.+++.      |.+.|++||.|+|
T Consensus       112 QkiREaEr~~i-~~ef~~r~GeIVtG~V~r~~~~v~~~~v~VdLG~~~~k~EgiLP~~Eqi------P~E~~~~GDrVkv  184 (366)
T 1k0r_A          112 QRFRDAENERT-YGEFSTREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV------PGESYEHGNRLRC  184 (366)
T ss_dssp             HHHHCCC---------CCCTTCEEEEEEECCHHHHHTTCEEEEECCSSSCEEEEECGGGSC------TTCCCCTTCEEEE
T ss_pred             HHHHHHHHHHH-HHHHHhcCCCEEEEEEEEccccccCCeEEEEeCCCccceEEEEcHHHcC------CCccCCCCCEEEE
Confidence            33444443333 66666  99999999999    999999999987   599999999986      3578999999999


Q ss_pred             EEEEEeccCCc--eEEEEe
Q 005707          201 RLIEANAETGR--ISLTMR  217 (681)
Q Consensus       201 kVl~VD~ekgr--I~LSlK  217 (681)
                      .|+.|+...+.  |.||+.
T Consensus       185 yV~~V~~~~kgpqI~LSRT  203 (366)
T 1k0r_A          185 YVVGVTRGAREPLITLSRT  203 (366)
T ss_dssp             EEEEEECCSSSCEEEEESS
T ss_pred             EEEEEecCCCccEEEEEeC
Confidence            99999987654  566655

>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=98.04  E-value=9.1e-06  Score=90.82  Aligned_cols=76  Identities=24%  Similarity=0.449  Sum_probs=65.2

Q ss_pred             CCCCCcEEEEEEEEEecC--eeEEEECCCeEEEEeccccCCccc---------cCcccccccCCEEEEEEEEEeccCCce
Q 005707          144 DLIPGATFTGKVRSIQPF--GAFIDFGAFTDGLVHVSRLSDNFV---------KDVGSIVSVGQEVKVRLIEANAETGRI  212 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~--GaFVdLgggV~GLVPiSELS~~~v---------~d~~e~fkVGd~VkVkVl~VD~ekgrI  212 (681)
                      ...+|.+|.|+|+++.++  |+||++|.+..||||++++++.++         .++.+.+++||.|.|.|+.....++.-
T Consensus        42 ~~~vGnIY~GkV~rv~p~~~aAFVdiG~gk~gfLhisei~~~~~~~~~~~~~~~~i~d~lk~Gq~VlVQV~Ke~~g~KGa  121 (517)
T 2bx2_L           42 EQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGA  121 (517)
T ss_dssp             CCCTTCEEEEEEEEEETTTTEEEEESSSSSCEEEEGGGSCGGGCC-------CCCGGGTCCTTCEEEEEEEECCCTTCCC
T ss_pred             cCCCCCEEEEEEEEeccCCceEEEEeCCCcEEEEEHHHcChhhhccccccccccchhhhccCCCEEEEEEEeeccccCCc
Confidence            456899999999999999  999999998999999999988763         245677999999999999988777777


Q ss_pred             EEEEecc
Q 005707          213 SLTMRES  219 (681)
Q Consensus       213 ~LSlK~l  219 (681)
                      .||..-.
T Consensus       122 ~lTt~is  128 (517)
T 2bx2_L          122 ALTTFIS  128 (517)
T ss_dssp             EEESSCC
T ss_pred             eEEeeEE
Confidence            7776643

>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae}

Probab=98.04  E-value=7.5e-06  Score=82.23  Aligned_cols=69  Identities=10%  Similarity=0.044  Sum_probs=58.6

Q ss_pred             cCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccc--------------cCcccccccCCEEEEEEEEEec
Q 005707          142 NEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFV--------------KDVGSIVSVGQEVKVRLIEANA  207 (681)
Q Consensus       142 ~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v--------------~d~~e~fkVGd~VkVkVl~VD~  207 (681)
                      +....+|+++.|+|++++++|+||+|.|.++|++|.+++.++++              .+....|++||.|+|+|..+|.
T Consensus        76 ~f~p~vGEv~~G~Is~Vt~fGifVeL~g~~eglv~~s~l~~d~~~fd~~~~~~vg~~~e~t~~~~~~Gd~VrvrV~~v~~  155 (218)
T 2ckz_B           76 VFKPFLGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYFDVNEKIRFRIEREVF  155 (218)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEECTTSCCCEEEETTTSCTTCEEETTTTEEEEECC--CEEEECTTCEEEEEEEEEEE
T ss_pred             EecCCCCCEEEEEEEEEccCcEEEEccCccceEEEcHHHCCCCcEEcCcCceEEeeccccCCcEEcCCCEEEEEEEEEEc
Confidence            56778899999999999999999999667999999999976553              3345679999999999999997


Q ss_pred             cCC
Q 005707          208 ETG  210 (681)
Q Consensus       208 ekg  210 (681)
                      ..+
T Consensus       156 ~~~  158 (218)
T 2ckz_B          156 VDV  158 (218)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            654

>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR family, hydrolase; 2.35A {Escherichia coli} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 PDB: 2ix0_A* 2ix1_A

Probab=97.96  E-value=1.3e-05  Score=91.83  Aligned_cols=73  Identities=16%  Similarity=0.306  Sum_probs=59.6

Q ss_pred             CCccCc--EEEEEEEEEecceEEEEeC-CCeEEEEeCCCCCc--ccccc--------cCCCCcccCCCEEEEEEEEEe--
Q 005707          259 KFVKGQ--DLEGTVKNLTRSGAFISLP-EGEEGFLPTSEESD--DGFAN--------MMGGSSLQVGQEVSVRVLRIS--  323 (681)
Q Consensus       259 klkvGd--IV~G~VknVt~~GaFVeIg-~GIeGLLpiSELSd--~~ie~--------~~p~~~fkVGqkVkVrVL~ID--  323 (681)
                      +-++|+  ++.|+|++|+++|+||+|. .|++||||.+++.+  +++..        .+....|++||.|+|+|+++|  
T Consensus       555 ~~~vGe~~~f~g~V~~V~~~G~fV~L~~~gieGlVhis~l~~~~d~~~~d~~~~~l~~~~~~~~~lGD~V~VkV~~vd~~  634 (644)
T 2id0_A          555 KDKAGTDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRME  634 (644)
T ss_dssp             GGGTTSCCCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEEEEEETT
T ss_pred             hhccCCCceEEEEEEEEeCCceEEEEcCCcEEEEEEchhccCcCceeEEcccccEEEecCCCEeCCCCEEEEEEEEEeCC
Confidence            346899  9999999999999999994 69999999999973  22111        023457999999999999998  


Q ss_pred             CCeEEEEE
Q 005707          324 RGQVTLTM  331 (681)
Q Consensus       324 kgKI~LSL  331 (681)
                      +++|.|++
T Consensus       635 ~~~I~~~l  642 (644)
T 2id0_A          635 TRSIIARP  642 (644)
T ss_dssp             TTEEEEEE
T ss_pred             CCEEEEEE
Confidence            58898887

>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe}

Probab=97.86  E-value=2.3e-05  Score=77.58  Aligned_cols=66  Identities=9%  Similarity=0.100  Sum_probs=54.3

Q ss_pred             ccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccc-----------------cCCCCcccCCCEEEEEE
Q 005707          257 TTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFAN-----------------MMGGSSLQVGQEVSVRV  319 (681)
Q Consensus       257 ~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~-----------------~~p~~~fkVGqkVkVrV  319 (681)
                      .-+-.+|+++.|+|++++++|+||+|+ .++|++|.+++.+++...                 ......|++||.|++||
T Consensus        76 ~f~p~~GEv~~G~Vs~vt~~GifV~lg-~~eglv~~~~l~~d~~~fd~~~~~~v~~~~~~~~~~~~~~~~~~Gd~VrvrV  154 (203)
T 3ayh_B           76 IFRPFRGEVMLGKIKSCSEEGIRVTIS-FFDDIFIPKDMLFDPCVFRPDERAWVWKIEGEDGSEGTELYFDIDEEIRFQI  154 (203)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEECS-SCCCEEEEGGGBCTTEEEEGGGTEEEEEECCCTTSCCEEEECCTTCEEEEEE
T ss_pred             EEccCCCCEEEEEEEEEeccEEEEEEe-CceEEEEcHHhCCCCceECccCceEEeecccccccccCCcEEcCCCEEEEEE
Confidence            455678999999999999999999995 899999999997654310                 11245699999999999


Q ss_pred             EEEe
Q 005707          320 LRIS  323 (681)
Q Consensus       320 L~ID  323 (681)
                      ++++
T Consensus       155 ~~v~  158 (203)
T 3ayh_B          155 ESED  158 (203)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            9996

>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=97.80  E-value=3.1e-05  Score=83.17  Aligned_cols=69  Identities=22%  Similarity=0.416  Sum_probs=54.8

Q ss_pred             ccccCCc--cCcEEEEEEEE----EecceEEEEeCC---CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC-
Q 005707          255 MKTTKFV--KGQDLEGTVKN----LTRSGAFISLPE---GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR-  324 (681)
Q Consensus       255 ~~~sklk--vGdIV~G~Vkn----Vt~~GaFVeIg~---GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk-  324 (681)
                      ..+.+|+  +|+++.|+|.+    +.+.++||+|+.   +++|+||.+|+.        |.+.|++||.|+|+|+++++ 
T Consensus       121 ~i~~ef~~r~GeIVtG~V~r~~~~v~~~~v~VdLG~~~~k~EgiLP~~Eqi--------P~E~~~~GDrVkvyV~~V~~~  192 (366)
T 1k0r_A          121 RTYGEFSTREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV--------PGESYEHGNRLRCYVVGVTRG  192 (366)
T ss_dssp             ------CCCTTCEEEEEEECCHHHHHTTCEEEEECCSSSCEEEEECGGGSC--------TTCCCCTTCEEEEEEEEEECC
T ss_pred             HHHHHHHhcCCCEEEEEEEEccccccCCeEEEEeCCCccceEEEEcHHHcC--------CCccCCCCCEEEEEEEEEecC
Confidence            5577777  99999999999    999999999986   599999998865        46799999999999999974 


Q ss_pred             ---CeEEEEE
Q 005707          325 ---GQVTLTM  331 (681)
Q Consensus       325 ---gKI~LSL  331 (681)
                         .+|.||.
T Consensus       193 ~kgpqI~LSR  202 (366)
T 1k0r_A          193 AREPLITLSR  202 (366)
T ss_dssp             SSSCEEEEES
T ss_pred             CCccEEEEEe
Confidence               3455655

>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=97.78  E-value=3.2e-05  Score=86.49  Aligned_cols=74  Identities=27%  Similarity=0.347  Sum_probs=59.2

Q ss_pred             cCCccCcEEEEEEEEEecc--eEEEEeCCCeEEEEeCCCCCcccccc-------cCCCCcccCCCEEEEEEEEEeC--Ce
Q 005707          258 TKFVKGQDLEGTVKNLTRS--GAFISLPEGEEGFLPTSEESDDGFAN-------MMGGSSLQVGQEVSVRVLRISR--GQ  326 (681)
Q Consensus       258 sklkvGdIV~G~VknVt~~--GaFVeIg~GIeGLLpiSELSd~~ie~-------~~p~~~fkVGqkVkVrVL~IDk--gK  326 (681)
                      ....+|.++.|+|++|.++  |+||+++.|..||||.++++|.++..       .+..+.+++||.|.|.|++...  +.
T Consensus        41 ~~~~vGnIY~GkV~rv~p~~~aAFVdiG~gk~gfLhisei~~~~~~~~~~~~~~~~i~d~lk~Gq~VlVQV~Ke~~g~KG  120 (517)
T 2bx2_L           41 HEQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKG  120 (517)
T ss_dssp             SCCCTTCEEEEEEEEEETTTTEEEEESSSSSCEEEEGGGSCGGGCC-------CCCGGGTCCTTCEEEEEEEECCCTTCC
T ss_pred             CcCCCCCEEEEEEEEeccCCceEEEEeCCCcEEEEEHHHcChhhhccccccccccchhhhccCCCEEEEEEEeeccccCC
Confidence            4567999999999999999  99999999999999999998876321       1124569999999999999863  33


Q ss_pred             EEEEE
Q 005707          327 VTLTM  331 (681)
Q Consensus       327 I~LSL  331 (681)
                      -.||.
T Consensus       121 a~lTt  125 (517)
T 2bx2_L          121 AALTT  125 (517)
T ss_dssp             CEEES
T ss_pred             ceEEe
Confidence            44444

>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=97.75  E-value=4.8e-05  Score=77.98  Aligned_cols=70  Identities=11%  Similarity=0.197  Sum_probs=60.8

Q ss_pred             CCCcEEEEEEEE----EecCeeEEEECC---CeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccC--CceEEEE
Q 005707          146 IPGATFTGKVRS----IQPFGAFIDFGA---FTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAET--GRISLTM  216 (681)
Q Consensus       146 kvGdIVeGkV~s----V~d~GaFVdLgg---gV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ek--grI~LSl  216 (681)
                      +.|++|+|+|.+    +.+..+||+||.   +.+|+||.+|+.      |.+.|++||.|+|.|+.++...  .+|.||+
T Consensus         6 r~GeIVtG~V~r~~~~v~~~~ViVdlG~~~~k~EgiLP~~Eqi------p~E~~~~GDrIkayV~~V~~~~~gpqIiLSR   79 (251)
T 2asb_A            6 REGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV------PGESYEHGNRLRCYVVGVTRGAREPLITLSR   79 (251)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSC------TTCCCCTTCEEEEEEEEEECCSSSCEEEEES
T ss_pred             cCCCEEEEEEEEccccccCCeEEEEeCCCCcceEEEEcHHHcC------CCccCCCCCEEEEEEEEEEcCCCCCEEEEEe
Confidence            479999999999    889999999986   599999999985      4678999999999999999865  5899998


Q ss_pred             eccch
Q 005707          217 RESDD  221 (681)
Q Consensus       217 K~l~~  221 (681)
                      .....
T Consensus        80 t~p~l   84 (251)
T 2asb_A           80 THPNL   84 (251)
T ss_dssp             SCHHH
T ss_pred             ccHHH
Confidence            85443

>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae}

Probab=97.71  E-value=4.6e-05  Score=76.49  Aligned_cols=68  Identities=16%  Similarity=0.085  Sum_probs=55.0

Q ss_pred             cccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccc------------cCCCCcccCCCEEEEEEEEEe
Q 005707          256 KTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFAN------------MMGGSSLQVGQEVSVRVLRIS  323 (681)
Q Consensus       256 ~~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~------------~~p~~~fkVGqkVkVrVL~ID  323 (681)
                      .+-+-.+|+++.|+|++++++|+||+|.+.++|++|.+++.++++..            ..-...|++||.|++||.+++
T Consensus        75 ~~f~p~vGEv~~G~Is~Vt~fGifVeL~g~~eglv~~s~l~~d~~~fd~~~~~~vg~~~e~t~~~~~~Gd~VrvrV~~v~  154 (218)
T 2ckz_B           75 VVFKPFLGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYFDVNEKIRFRIEREV  154 (218)
T ss_dssp             EEECCCTTCEEEEEEEEEETTEEEEECTTSCCCEEEETTTSCTTCEEETTTTEEEEECC--CEEEECTTCEEEEEEEEEE
T ss_pred             EEecCCCCCEEEEEEEEEccCcEEEEccCccceEEEcHHHCCCCcEEcCcCceEEeeccccCCcEEcCCCEEEEEEEEEE
Confidence            35556789999999999999999999966789999999996654311            111356999999999999997

>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae}

Probab=97.71  E-value=2.7e-05  Score=92.89  Aligned_cols=70  Identities=20%  Similarity=0.265  Sum_probs=58.5

Q ss_pred             CcEEEEEEEEEecceEEEEeCC-CeEEEEeCCCCC--cccccc---------cC----CCCcccCCCEEEEEEEEEeC--
Q 005707          263 GQDLEGTVKNLTRSGAFISLPE-GEEGFLPTSEES--DDGFAN---------MM----GGSSLQVGQEVSVRVLRISR--  324 (681)
Q Consensus       263 GdIV~G~VknVt~~GaFVeIg~-GIeGLLpiSELS--d~~ie~---------~~----p~~~fkVGqkVkVrVL~IDk--  324 (681)
                      |+++.|+|++|.++|+||.|++ |++||||+++|.  ++++..         ..    ....|++||.|+|+|+.++.  
T Consensus       887 ge~~~g~V~~V~~~G~fV~L~~~giEGlVhis~L~~~~d~y~fde~~~~L~g~~~~g~~~~~~~lGD~V~VkV~~vd~~~  966 (977)
T 2wp8_J          887 ESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVMDPI  966 (977)
T ss_dssp             TCEEEEEEEEECSSEEEEECTTTCCEEEEEGGGTCSCGGGCEEETTTTEEEECCTTCCSCEEEETTCEEEEEECCCCCSS
T ss_pred             ceEEEEEEEEEcCCeEEEEEcCCCeEEEEEeccccCCCceeEEcccccEEEeecCCCccCcEEccCCEEEEEEEEEcCcc
Confidence            9999999999999999999998 999999999997  332100         01    24689999999999999963  


Q ss_pred             ---CeEEEEEe
Q 005707          325 ---GQVTLTMK  332 (681)
Q Consensus       325 ---gKI~LSLK  332 (681)
                         +||.|+||
T Consensus       967 ~~~~kI~Lslk  977 (977)
T 2wp8_J          967 TSKRKAELLLK  977 (977)
T ss_dssp             SCCCCCCEEEC
T ss_pred             cCCCceEEEeC
Confidence               79999997

>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=97.66  E-value=4.1e-05  Score=80.59  Aligned_cols=74  Identities=14%  Similarity=0.129  Sum_probs=61.7

Q ss_pred             CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCc-c---c------cCcccccccCCEEEEEEEEEeccCCceE
Q 005707          144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDN-F---V------KDVGSIVSVGQEVKVRLIEANAETGRIS  213 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~-~---v------~d~~e~fkVGd~VkVkVl~VD~ekgrI~  213 (681)
                      ..++|++|.|+|+.+.++|+||+|+....|++|++++++. .   .      .++...|++||.|.|+|++++. .+.+.
T Consensus        92 ~P~vGDvViG~Vt~V~~~~a~VdI~s~~~~~l~iS~v~f~gg~iR~~~~~D~~~m~~~l~vGDlV~ArVisv~~-~~~i~  170 (308)
T 2nn6_H           92 IGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFS-DGAVS  170 (308)
T ss_dssp             CCCSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEET-TTEEE
T ss_pred             CCCCCCEEEEEEEEEeCceEEEEECCCcCCceechhhccccceeecccchhhhhhhccCCCCCEEEEEEEEcCC-CCCEE
Confidence            6789999999999999999999999778999999998753 2   1      2345689999999999999984 56899


Q ss_pred             EEEec
Q 005707          214 LTMRE  218 (681)
Q Consensus       214 LSlK~  218 (681)
                      ||++.
T Consensus       171 LStr~  175 (308)
T 2nn6_H          171 LHTRS  175 (308)
T ss_dssp             EECCS
T ss_pred             EEecC
Confidence            99883

>2vnu_D Exosome complex exonuclease RRP44; hydrolase-RNA complex, RNA degradation, RNA-binding, RNA Pro; HET: 1PE; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16

Probab=97.58  E-value=4.9e-05  Score=88.51  Aligned_cols=69  Identities=20%  Similarity=0.288  Sum_probs=52.0

Q ss_pred             cEEEEEEEEEecceEEEEeCC-CeEEEEeCCCCC--cccccc---------cC----CCCcccCCCEEEEEEEEEe----
Q 005707          264 QDLEGTVKNLTRSGAFISLPE-GEEGFLPTSEES--DDGFAN---------MM----GGSSLQVGQEVSVRVLRIS----  323 (681)
Q Consensus       264 dIV~G~VknVt~~GaFVeIg~-GIeGLLpiSELS--d~~ie~---------~~----p~~~fkVGqkVkVrVL~ID----  323 (681)
                      +++.|+|++|.++|+||.|.+ |++||||++++.  ++++..         .+    ....|++||.|+|+|+.+|    
T Consensus       671 ~~~~g~V~~V~~~G~fV~l~~~giEGlVhis~L~~~~d~~~fd~~~~~l~g~~~~~~~~~~~~lGD~V~VkV~~vd~~~~  750 (760)
T 2vnu_D          671 STETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVMDPIT  750 (760)
T ss_dssp             SEEEEEEEEEETTEEEEEETTTTEEEEEEHHHHCSCGGGCEEETTTTEEEECCTTCSSCEEEETTCEEEEEEC-------
T ss_pred             eEEEEEEEEEECCeEEEEEeCCCcEEEEEeccccCCCceeEEcccccEEEEecCCCccCcEEecCCEEEEEEEEEECccc
Confidence            799999999999999999998 999999999986  332100         01    1468999999999999996    


Q ss_pred             -CCeEEEEEe
Q 005707          324 -RGQVTLTMK  332 (681)
Q Consensus       324 -kgKI~LSLK  332 (681)
                       ++||.|+||
T Consensus       751 ~~~kI~lslk  760 (760)
T 2vnu_D          751 SKRKAELLLK  760 (760)
T ss_dssp             -CCEEEC---
T ss_pred             cCCcEEEEeC
Confidence             379999986

>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=97.54  E-value=0.00022  Score=69.41  Aligned_cols=72  Identities=13%  Similarity=-0.005  Sum_probs=62.4

Q ss_pred             CCCCCcEEEEEEEEEecCeeEEEECC-CeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707          144 DLIPGATFTGKVRSIQPFGAFIDFGA-FTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR  217 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~GaFVdLgg-gV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK  217 (681)
                      ..++||+|.|+|+.+..++++|+|+. ...|+||.+++. ...++.+..|++||.|.|+|..++.. +.+.||+.
T Consensus         4 ~P~~gDvViG~V~~v~~~~~~VdI~~~~~~a~L~~s~~~-g~~k~~r~~l~~GDlV~ArV~~~~~~-~~~~Ltc~   76 (175)
T 2ja9_A            4 IPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFP-NASKKNRPTLQVGDLVYARVCTAEKE-LEAEIECF   76 (175)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSST-TCCSSSCCCCCTTCEEEEEEEECCTT-SCCEEESS
T ss_pred             cCCCcCEEEEEEEEEECcEEEEEECCCCccEEEEHHHCC-chhhhhhccCCCCCEEEEEEEEecCC-CceEEEec
Confidence            46789999999999999999999998 799999999886 33467788899999999999999753 57888843

>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=97.50  E-value=8.4e-06  Score=90.12  Aligned_cols=138  Identities=13%  Similarity=0.109  Sum_probs=86.7

Q ss_pred             cccceeeecccccccccceeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCcceecCCCCC
Q 005707           27 CLTRYNSTRKSTKQTISSQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSD  106 (681)
Q Consensus        27 ~~~~~~~~r~~~~~~~s~~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~  106 (681)
                      +.+||||+-.+|.||+||.|++.|+-.+|-+. ...              -|.          .+-.   .--+      
T Consensus       324 ~~~HfgL~~~~YthfTSPIRRY~DLivHr~L~-a~l--------------~~~----------~~~~---~~~l------  369 (469)
T 2r7d_A          324 PGPHHGMGLDLYAQATSPMRRYLDLVVHQQLR-AFL--------------AGR----------DPLS---SKVM------  369 (469)
T ss_dssp             CCCBTTTTBSCCCCCSCTTTBHHHHHHHHHHH-HHH--------------TTC----------CCCC---HHHH------
T ss_pred             CCCchhhCccceeeECCcccccHHHHHHHHHH-HHH--------------cCC----------CCCC---HHHH------
Confidence            57899999999999999999999986664221 110              011          0000   0000      


Q ss_pred             cccccccccccCCChhhHHhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCcccc
Q 005707          107 VETSESSSIKSEASPTLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVK  186 (681)
Q Consensus       107 v~~ae~ss~~sea~~daek~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~  186 (681)
                      ...+.+.+.+.+++.++++...+.....       +..-.+|+.++|.|+.+.         + ..|+||++++..+  .
T Consensus       370 ~~~~~~~~~~er~a~~aer~~~~~~~~~-------~l~~~~g~~f~g~vv~l~---------~-~~glV~v~~l~~d--~  430 (469)
T 2r7d_A          370 AAHIAESQMNADATRQAERLSRRHHTLR-------FIAAQPERVWDAVVVDRR---------G-AQATLLIPDLAFD--V  430 (469)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHTCTTCCEEEEEEEEE---------T-TEEEEEEGGGTEE--E
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHhCCCCEEEEEEEEEe---------C-cEEEEEECCCCeE--E
Confidence            0112334445555555554443321111       222357999999875432         3 4789999888765  2


Q ss_pred             CcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707          187 DVGSIVSVGQEVKVRLIEANAETGRISLTMR  217 (681)
Q Consensus       187 d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK  217 (681)
                      .....|++||.|+|+|.++|..+++|.+...
T Consensus       431 ~~~~~~~lGd~V~V~v~~vd~~~~~i~f~~~  461 (469)
T 2r7d_A          431 QVNTPAAPGTALQVQFADIDLPQMRVRARSV  461 (469)
T ss_dssp             EEECCCCTTCEEEEEEEEEETTTTEEEEEEC
T ss_pred             ecCCcCCCCCEEEEEEEEEccCCCEEEEEEE
Confidence            3345799999999999999999999988654

>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=97.46  E-value=0.00021  Score=73.25  Aligned_cols=66  Identities=21%  Similarity=0.412  Sum_probs=57.9

Q ss_pred             ccCcEEEEEEEE----EecceEEEEeCC---CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC----CeEEE
Q 005707          261 VKGQDLEGTVKN----LTRSGAFISLPE---GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR----GQVTL  329 (681)
Q Consensus       261 kvGdIV~G~Vkn----Vt~~GaFVeIg~---GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk----gKI~L  329 (681)
                      +.|++|.|+|.+    +.+..+||+|+.   +.+|+||.+|+.        |.+.|++||.|+|+|+++++    .+|.|
T Consensus         6 r~GeIVtG~V~r~~~~v~~~~ViVdlG~~~~k~EgiLP~~Eqi--------p~E~~~~GDrIkayV~~V~~~~~gpqIiL   77 (251)
T 2asb_A            6 REGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV--------PGESYEHGNRLRCYVVGVTRGAREPLITL   77 (251)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSC--------TTCCCCTTCEEEEEEEEEECCSSSCEEEE
T ss_pred             cCCCEEEEEEEEccccccCCeEEEEeCCCCcceEEEEcHHHcC--------CCccCCCCCEEEEEEEEEEcCCCCCEEEE
Confidence            589999999999    888999999986   599999998764        46889999999999999963    67999


Q ss_pred             EEecc
Q 005707          330 TMKKE  334 (681)
Q Consensus       330 SLK~~  334 (681)
                      |.+..
T Consensus        78 SRt~p   82 (251)
T 2asb_A           78 SRTHP   82 (251)
T ss_dssp             ESSCH
T ss_pred             EeccH
Confidence            98654

>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=97.39  E-value=0.00016  Score=76.09  Aligned_cols=75  Identities=17%  Similarity=0.131  Sum_probs=60.2

Q ss_pred             CCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcc-c---ccc----cCCCCcccCCCEEEEEEEEEe-CCeEEE
Q 005707          259 KFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDD-G---FAN----MMGGSSLQVGQEVSVRVLRIS-RGQVTL  329 (681)
Q Consensus       259 klkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~-~---ie~----~~p~~~fkVGqkVkVrVL~ID-kgKI~L  329 (681)
                      ..++|++|.|+|+.+..+|+||+|+....|++|.+++.+. .   ..+    .+....|++||.|.++|+.++ .+++.|
T Consensus        92 ~P~vGDvViG~Vt~V~~~~a~VdI~s~~~~~l~iS~v~f~gg~iR~~~~~D~~~m~~~l~vGDlV~ArVisv~~~~~i~L  171 (308)
T 2nn6_H           92 IGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSL  171 (308)
T ss_dssp             CCCSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEETTTEEEE
T ss_pred             CCCCCCEEEEEEEEEeCceEEEEECCCcCCceechhhccccceeecccchhhhhhhccCCCCCEEEEEEEEcCCCCCEEE
Confidence            4679999999999999999999999888999999998753 1   110    011357999999999999997 588999


Q ss_pred             EEec
Q 005707          330 TMKK  333 (681)
Q Consensus       330 SLK~  333 (681)
                      |+|.
T Consensus       172 Str~  175 (308)
T 2nn6_H          172 HTRS  175 (308)
T ss_dssp             ECCS
T ss_pred             EecC
Confidence            9985

>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=97.30  E-value=0.00081  Score=65.48  Aligned_cols=68  Identities=16%  Similarity=0.086  Sum_probs=58.8

Q ss_pred             CccCcEEEEEEEEEecceEEEEeCC-CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC-CeEEEE
Q 005707          260 FVKGQDLEGTVKNLTRSGAFISLPE-GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR-GQVTLT  330 (681)
Q Consensus       260 lkvGdIV~G~VknVt~~GaFVeIg~-GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk-gKI~LS  330 (681)
                      .++||+|.|+|+.+..++++|+|+. ...|+||.+.+....   .+....|++||.|.++|+.++. +.+.|+
T Consensus         5 P~~gDvViG~V~~v~~~~~~VdI~~~~~~a~L~~s~~~g~~---k~~r~~l~~GDlV~ArV~~~~~~~~~~Lt   74 (175)
T 2ja9_A            5 PSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNAS---KKNRPTLQVGDLVYARVCTAEKELEAEIE   74 (175)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSSTTCC---SSSCCCCCTTCEEEEEEEECCTTSCCEEE
T ss_pred             CCCcCEEEEEEEEEECcEEEEEECCCCccEEEEHHHCCchh---hhhhccCCCCCEEEEEEEEecCCCceEEE
Confidence            4689999999999999999999998 799999999876321   2346789999999999999974 789999

>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=96.34  E-value=0.0065  Score=63.48  Aligned_cols=72  Identities=15%  Similarity=0.062  Sum_probs=62.0

Q ss_pred             CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707          144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR  217 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK  217 (681)
                      -.++|++|-|+|+.+....+.|+|+....|+||.+++. +..++.+..|++||.|.++|+.++. .+.+.||+.
T Consensus       124 iP~vGDiVIG~Vt~v~~~~~~VdI~s~~~a~L~~~~f~-Gatk~~r~~f~~GDlV~ArV~s~~~-~~~~eLsc~  195 (289)
T 2nn6_G          124 VPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFE-GATKRNRPNVQVGDLIYGQFVVANK-DMEPEMVCI  195 (289)
T ss_dssp             CCCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSS-CCSSCSSSSSCTTCEEEEEEEECCT-TSCCEEECS
T ss_pred             CCCCCCEEEEEEEEEeCcEEEEEECCCceeEEehhhcC-cchhhhhhhcCCCCEEEEEEEEcCC-CCceEEEec
Confidence            46899999999999999999999998889999999876 2346677889999999999999864 346788874

>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=94.97  E-value=0.044  Score=57.26  Aligned_cols=69  Identities=14%  Similarity=0.090  Sum_probs=59.0

Q ss_pred             CccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC-CeEEEEE
Q 005707          260 FVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR-GQVTLTM  331 (681)
Q Consensus       260 lkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk-gKI~LSL  331 (681)
                      .++||+|-|+|+.+....+.|+|..-..|+||.+++....   .+....|++||.|.++|+.+++ +...|++
T Consensus       125 P~vGDiVIG~Vt~v~~~~~~VdI~s~~~a~L~~~~f~Gat---k~~r~~f~~GDlV~ArV~s~~~~~~~eLsc  194 (289)
T 2nn6_G          125 PVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGAT---KRNRPNVQVGDLIYGQFVVANKDMEPEMVC  194 (289)
T ss_dssp             CCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSSCCS---SCSSSSSCTTCEEEEEEEECCTTSCCEEEC
T ss_pred             CCCCCEEEEEEEEEeCcEEEEEECCCceeEEehhhcCcch---hhhhhhcCCCCEEEEEEEEcCCCCceEEEe
Confidence            4799999999999999999999998899999998766221   1336789999999999999975 6788988

>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=91.89  E-value=0.55  Score=46.72  Aligned_cols=72  Identities=4%  Similarity=-0.028  Sum_probs=53.4

Q ss_pred             CCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcc------------cccccCCEEEEEEEEEeccCC
Q 005707          143 EDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVG------------SIVSVGQEVKVRLIEANAETG  210 (681)
Q Consensus       143 ~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~------------e~fkVGd~VkVkVl~VD~ekg  210 (681)
                      -....|+++.|+|..+.+.|+.+-+-|....+||...|..++.-++.            +--++|+.|+++|.+++..++
T Consensus       125 FrPf~GevL~G~V~~~s~~~Ig~~~~G~Fn~~Ip~~~ip~~~~f~~~~~~~~~~~wv~~~~~~ig~~IRFrV~~~~~~~~  204 (214)
T 2rf4_A          125 WQPQVGDVLEGYIFIQSASHIGLLIHDAFNASIKKNNIPVDWTFVHNDGNRSLGHWVDSNGEPIDGKLRFTVRNVHTTGR  204 (214)
T ss_dssp             ECCCTTCEEEEEECCCCSSCEEEEETTTEEEEECSTTSCSSCBCCCCSCC-CCCCCBCSSCCBCCSEEEEEEEEEECCSS
T ss_pred             EecCCCCEEEEEEEEECCCcEEEEEeCCEEEEEcHHHCCCcccccccccccCCCceEcCCCCCCCCEEEEEEEEEEecCC
Confidence            36789999999999999988877666668899999998644322111            112369999999999987655


Q ss_pred             ceEE
Q 005707          211 RISL  214 (681)
Q Consensus       211 rI~L  214 (681)
                      .+.+
T Consensus       205 ~lsI  208 (214)
T 2rf4_A          205 VVSV  208 (214)
T ss_dssp             SCEE
T ss_pred             EEEE
Confidence            5443

>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=87.51  E-value=4.3  Score=35.19  Aligned_cols=59  Identities=24%  Similarity=0.318  Sum_probs=44.9

Q ss_pred             CccCcEEEEEEEEEecceE-EEEeCCC-eEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC-Ce
Q 005707          260 FVKGQDLEGTVKNLTRSGA-FISLPEG-EEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR-GQ  326 (681)
Q Consensus       260 lkvGdIV~G~VknVt~~Ga-FVeIg~G-IeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk-gK  326 (681)
                      ....+...|+|+... .|. ||.-.+| -+-|+|.+.+...       ...+..||.|.+.|..-++ +|
T Consensus        13 ~s~~~~~~G~Vkwf~-KGfGFI~~ddgg~DVFvH~s~i~~~-------~~~L~~G~~V~F~v~~~~k~Gk   74 (89)
T 1wfq_A           13 TSAALRETGVIEKLL-TSYGFIQCSERQARLFFHCSQYNGN-------LQDLKVGDDVEFEVSSDRRTGK   74 (89)
T ss_dssp             SSCCCEEEEEEEEEC-SSEEEEEETTTTEEEEEETTTCSSC-------TTTCCTTCCEEEEEEECSSSCC
T ss_pred             CCcccccceEEEEEe-CCeeEEecCCCCccEEEEhHHhhCc-------cCCCCCCCEEEEEEEECCCCCC
Confidence            445567899999985 433 7877665 8999999998753       2578999999999877666 64

>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=87.41  E-value=1.5  Score=38.58  Aligned_cols=55  Identities=11%  Similarity=-0.050  Sum_probs=47.3

Q ss_pred             CCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccc-----cC-cccccccCCEEEEE
Q 005707          147 PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFV-----KD-VGSIVSVGQEVKVR  201 (681)
Q Consensus       147 vGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v-----~d-~~e~fkVGd~VkVk  201 (681)
                      .|..+.|.|+++.+.++-|.+.++-.+.|+...+.|.+-     .. +.+.+++|+.|.|+
T Consensus        33 ~~~~~~AvV~~v~~~~~~v~~~~g~~~~l~~~~~~WA~~~~~~~~~~~~~~l~~GdvI~V~   93 (106)
T 3d0f_A           33 SDDILAAVVLSATPGAVEAFRKNGETIRITGDGLKAAHRFLSNDPKIGEKRIRPGALIRVK   93 (106)
T ss_dssp             TTTCEEEEEEEEETTEEEEEETTSCEEEECGGGGSTTGGGTTTCTTTGGGSCCTTEEEEEE
T ss_pred             cCCeEEEEEEEeCCCeEEEEEcCCCeEEEcHHHChhhhhcccccccchhccCCCCCEEEEE
Confidence            388999999999999999999776888899999998742     33 56779999999998

>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=85.87  E-value=2  Score=37.19  Aligned_cols=64  Identities=27%  Similarity=0.271  Sum_probs=47.6

Q ss_pred             ccccCCccCcEEEEEEEEEec-ceEEEEeCC-CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCe
Q 005707          255 MKTTKFVKGQDLEGTVKNLTR-SGAFISLPE-GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQ  326 (681)
Q Consensus       255 ~~~sklkvGdIV~G~VknVt~-~GaFVeIg~-GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgK  326 (681)
                      ..+.....++...|+|+...+ || ||.-.+ |-+-|+|.+.+...       ...+..||.|.+.+..-.++|
T Consensus         8 ~l~~~~~~~~~~~G~Vk~f~kGfG-FI~~ddgg~DvFvH~S~i~~~-------~~~L~~G~~V~F~~~~g~~Gk   73 (88)
T 2yty_A            8 RLLGRNSNSKRLLGYVATLKDNFG-FIETANHDKEIFFHYSEFSGD-------VDSLELGDMVEYSLSKGKGNK   73 (88)
T ss_dssp             SCCCCCSSCCCEEEEEEEECSSEE-EEECSSSSCEEEEETTTCCSC-------TTTCCTTCEEEECCCCCSCSC
T ss_pred             EEEeccCCCCceeEEEEEEECCcc-EEecCCCCceEEEEEhhhccc-------cCcCCCCCEEEEEEEECCCCC
Confidence            345555578889999999973 34 888765 69999999988754       257899999998875544453

>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=84.15  E-value=1.7  Score=38.11  Aligned_cols=58  Identities=14%  Similarity=0.040  Sum_probs=48.0

Q ss_pred             ccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccc-cc--cC-CCCcccCCCEEEEE
Q 005707          261 VKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGF-AN--MM-GGSSLQVGQEVSVR  318 (681)
Q Consensus       261 kvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~i-e~--~~-p~~~fkVGqkVkVr  318 (681)
                      ..|+.+.+.|.++.+.++-|.+.+|-.+.|+...|.|.+- ..  .. +...|++||.|.|+
T Consensus        32 ~~~~~~~AvV~~v~~~~~~v~~~~g~~~~l~~~~~~WA~~~~~~~~~~~~~~l~~GdvI~V~   93 (106)
T 3d0f_A           32 NSDDILAAVVLSATPGAVEAFRKNGETIRITGDGLKAAHRFLSNDPKIGEKRIRPGALIRVK   93 (106)
T ss_dssp             TTTTCEEEEEEEEETTEEEEEETTSCEEEECGGGGSTTGGGTTTCTTTGGGSCCTTEEEEEE
T ss_pred             ccCCeEEEEEEEeCCCeEEEEEcCCCeEEEcHHHChhhhhcccccccchhccCCCCCEEEEE
Confidence            3489999999999999999999888999999999999852 00  11 34669999999998

>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=83.17  E-value=3.5  Score=40.92  Aligned_cols=68  Identities=10%  Similarity=-0.023  Sum_probs=48.3

Q ss_pred             cccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCC----------CCcccCCCEEEEEEEEEe
Q 005707          256 KTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMG----------GSSLQVGQEVSVRVLRIS  323 (681)
Q Consensus       256 ~~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p----------~~~fkVGqkVkVrVL~ID  323 (681)
                      ..-+-.+|+++.|+|+.+.+.|+.+-+-+-.+.+||...+...+.-+...          ...-++|+.|++||..++
T Consensus       123 iVFrPf~GevL~G~V~~~s~~~Ig~~~~G~Fn~~Ip~~~ip~~~~f~~~~~~~~~~~wv~~~~~~ig~~IRFrV~~~~  200 (214)
T 2rf4_A          123 YVWQPQVGDVLEGYIFIQSASHIGLLIHDAFNASIKKNNIPVDWTFVHNDGNRSLGHWVDSNGEPIDGKLRFTVRNVH  200 (214)
T ss_dssp             EEECCCTTCEEEEEECCCCSSCEEEEETTTEEEEECSTTSCSSCBCCCCSCC-CCCCCBCSSCCBCCSEEEEEEEEEE
T ss_pred             EEEecCCCCEEEEEEEEECCCcEEEEEeCCEEEEEcHHHCCCcccccccccccCCCceEcCCCCCCCCEEEEEEEEEE
Confidence            45567799999999999999877765555778899998875332101000          111236999999999997

>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=82.52  E-value=6.5  Score=31.89  Aligned_cols=54  Identities=31%  Similarity=0.500  Sum_probs=41.2

Q ss_pred             EEEEEEEEec---ceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCe
Q 005707          266 LEGTVKNLTR---SGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQ  326 (681)
Q Consensus       266 V~G~VknVt~---~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgK  326 (681)
                      ..|+|+...+   || ||.-.+|-+-|+|.+.+....      ...+..||.|.+.+..-++|.
T Consensus         2 ~~G~Vk~fn~~kGfG-FI~~~~g~dvFvH~s~i~~~g------~~~l~~G~~V~f~~~~~~kG~   58 (66)
T 1c9o_A            2 QRGKVKWFNNEKGYG-FIEVEGGSDVFVHFTAIQGEG------FKTLEEGQEVSFEIVQGNRGP   58 (66)
T ss_dssp             EEEEEEEEETTTTEE-EEEETTEEEEEEEGGGBCSSS------CCCCCTTCEEEEEEEEETTEE
T ss_pred             CceEEEEEECCCCeE-EEecCCCccEEEEHHHccccC------CCCCCCCCEEEEEEEECCCCc
Confidence            3689999853   45 888777899999999887543      246899999999987655553

>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=81.26  E-value=2.9  Score=36.76  Aligned_cols=51  Identities=27%  Similarity=0.325  Sum_probs=39.9

Q ss_pred             cCcEEEEEEEEEecceE-EEEeCCC-eEEEEeCCCCCcccccccCCCCcccCCCEEEEEEE
Q 005707          262 KGQDLEGTVKNLTRSGA-FISLPEG-EEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVL  320 (681)
Q Consensus       262 vGdIV~G~VknVt~~Ga-FVeIg~G-IeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL  320 (681)
                      ......|+|+.. ..|. ||.-.+| -+-|+|.+.+...       ...+..||.|.+.+.
T Consensus        15 ~~~~~~G~Vkwf-~KGfGFI~~ddg~~DvFvH~s~i~~~-------~~~L~~G~~V~F~v~   67 (97)
T 2ytx_A           15 KQARCQGVVCAM-KEAFGFIERGDVVKEIFFHYSEFKGD-------LETLQPGDDVEFTIK   67 (97)
T ss_dssp             CCCCEEEEECCC-CSSEEEEECSSSCCCEEEETTTCCSC-------TTSCCSCCEEEEEEC
T ss_pred             CCcceeEEEEEE-eCCceEEecCCCCceEEEEehHhccc-------cCCCCCCCEEEEEEE
Confidence            367789999998 4444 8887664 8999999988754       246899999999884

>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=80.61  E-value=2.1  Score=47.28  Aligned_cols=57  Identities=14%  Similarity=0.102  Sum_probs=41.9

Q ss_pred             ccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEE
Q 005707          261 VKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTM  331 (681)
Q Consensus       261 kvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSL  331 (681)
                      .+|+.+.|.|..+.          +..|+++++++..+.    .....|+.||.|+|+|.++|  +++|.+..
T Consensus       402 ~~g~~f~g~vv~l~----------~~~glV~v~~l~~d~----~~~~~~~lGd~V~V~v~~vd~~~~~i~f~~  460 (469)
T 2r7d_A          402 QPERVWDAVVVDRR----------GAQATLLIPDLAFDV----QVNTPAAPGTALQVQFADIDLPQMRVRARS  460 (469)
T ss_dssp             CTTCCEEEEEEEEE----------TTEEEEEEGGGTEEE----EEECCCCTTCEEEEEEEEEETTTTEEEEEE
T ss_pred             CCCCEEEEEEEEEe----------CcEEEEEECCCCeEE----ecCCcCCCCCEEEEEEEEEccCCCEEEEEE
Confidence            57999999875532          346888888876542    11358999999999999998  57776654

---

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	681
d1sroa_	76	b.40.4.5 (A:) S1 RNA-binding domain of polyribonuc	4e-18
d1sroa_	76	b.40.4.5 (A:) S1 RNA-binding domain of polyribonuc	6e-10
d3bzka4	94	b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas ae	5e-18
d3bzka4	94	b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas ae	3e-10
d2z0sa1	88	b.40.4.5 (A:60-147) S1-domain of exosome complex R	6e-14
d2z0sa1	88	b.40.4.5 (A:60-147) S1-domain of exosome complex R	2e-09
d1y14b1	91	b.40.4.5 (B:81-171) C-terminal domain of RNA polym	3e-13
d1y14b1	91	b.40.4.5 (B:81-171) C-terminal domain of RNA polym	2e-06
d1e3pa2	62	b.40.4.5 (A:656-717) S1 RNA-binding domain of poly	5e-13
d1e3pa2	62	b.40.4.5 (A:656-717) S1 RNA-binding domain of poly	1e-08
d2je6i1	87	b.40.4.5 (I:66-152) S1-domain of exosome complex R	5e-13
d2je6i1	87	b.40.4.5 (I:66-152) S1-domain of exosome complex R	1e-09
d2ahob2	84	b.40.4.5 (B:1-84) Eukaryotic initiation factor 2al	1e-12
d2ahob2	84	b.40.4.5 (B:1-84) Eukaryotic initiation factor 2al	2e-07
d1kl9a2	86	b.40.4.5 (A:3-88) Eukaryotic initiation factor 2al	1e-12
d1kl9a2	86	b.40.4.5 (A:3-88) Eukaryotic initiation factor 2al	6e-08
d2nn6h1	95	b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-pro	4e-12
d2nn6h1	95	b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-pro	6e-08
d2ba0a1	83	b.40.4.5 (A:53-135) S1-domain of exosome complex R	6e-12
d2ba0a1	83	b.40.4.5 (A:53-135) S1-domain of exosome complex R	1e-07
d2c35b1	94	b.40.4.5 (B:78-171) C-terminal domain of RNA polym	6e-10
d2c35b1	94	b.40.4.5 (B:78-171) C-terminal domain of RNA polym	6e-04
d1go3e1	106	b.40.4.5 (E:79-184) C-terminal domain of RNA polym	1e-09
d1go3e1	106	b.40.4.5 (E:79-184) C-terminal domain of RNA polym	6e-06
d2ja9a1	90	b.40.4.5 (A:62-151) S1-domain of exosome component	2e-08
d2nn6g1	88	b.40.4.5 (G:107-194) S1-domain of exosome componen	3e-08
d2ix0a3	87	b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Esche	4e-08
d2ix0a3	87	b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Esche	7e-05
d1wi5a_	119	b.40.4.5 (A:) S1-domain of RRP5 protein homolog (P	5e-08

>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 = 76.7 bits (189), Expect = 4e-18
 Identities = 30/76 (39%), Positives = 51/76 (67%), Gaps = 1/76 (1%)

Query: 144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLI 203
           ++  G  +TGKV  I  FGAF+  G   +GLVH+S+++D  V+ V   + +GQEV V+++
Sbjct: 2   EIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVL 61

Query: 204 EANAETGRISLTMRES 219
           E + + GRI L+++E+
Sbjct: 62  EVDRQ-GRIRLSIKEA 76

>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 = 53.6 bits (129), Expect = 6e-10
 Identities = 23/72 (31%), Positives = 42/72 (58%), Gaps = 3/72 (4%)

Query: 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI 322
           G+   G V  +   GAF+++  G+EG +  S+ +D     +     LQ+GQEV V+VL +
Sbjct: 6   GRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKV--TDYLQMGQEVPVKVLEV 63

Query: 323 -SRGQVTLTMKK 333
             +G++ L++K+
Sbjct: 64  DRQGRIRLSIKE 75

>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 = 77.2 bits (190), Expect = 5e-18
 Identities = 36/79 (45%), Positives = 49/79 (62%)

Query: 143 EDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRL 202
           +DL PG    G V ++  FGAF+D G   DGLVH+S LS+ FVKD   +V  G  VKV++
Sbjct: 14  KDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKV 73

Query: 203 IEANAETGRISLTMRESDD 221
           +E +    R+ L+MR SD 
Sbjct: 74  MEVDIPRNRVGLSMRMSDT 92

>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 = 55.3 bits (133), Expect = 3e-10
 Identities = 26/95 (27%), Positives = 49/95 (51%), Gaps = 5/95 (5%)

Query: 247 KPGQKRDEMKTTKFVK-GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMG 305
           K  + ++ +++ K +K G  LEG V N+T  GAF+ +   ++G +  S  S+    +   
Sbjct: 2   KTAEFQEGVESLKDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPY- 60

Query: 306 GSSLQVGQEVSVRVLRI--SRGQVTLTMKKEDDVG 338
              ++ G  V V+V+ +   R +V L+M+  D  G
Sbjct: 61  -EVVKAGDIVKVKVMEVDIPRNRVGLSMRMSDTPG 94

>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 = 65.7 bits (160), Expect = 6e-14
 Identities = 14/78 (17%), Positives = 32/78 (41%), Gaps = 5/78 (6%)

Query: 147 PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVK----DVGSIVSVGQEVKVRL 202
            G    G ++S+     F+D  +    ++ V             D+ S++ VG  +K ++
Sbjct: 7   AGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKV 66

Query: 203 IEANAETGRISLTMRESD 220
           +  + +T    LT++   
Sbjct: 67  VAFD-KTRSPLLTVQGEG 83

>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 = 52.6 bits (126), Expect = 2e-09
 Identities = 13/77 (16%), Positives = 28/77 (36%), Gaps = 3/77 (3%)

Query: 262 KGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMG--GSSLQVGQEVSVRV 319
            G  + G ++++     F+ +       L   +     F   +    S L+VG  +  +V
Sbjct: 7   AGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKV 66

Query: 320 LRIS-RGQVTLTMKKED 335
           +         LT++ E 
Sbjct: 67  VAFDKTRSPLLTVQGEG 83

>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]} Length = 91

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]

 Score = 63.7 bits (155), Expect = 3e-13
 Identities = 10/84 (11%), Positives = 25/84 (29%), Gaps = 11/84 (13%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFV----------KDVGSIVSVGQE 197
           G    G V S    G  +  G      V    +  +            +    ++++   
Sbjct: 4   GEVVDGTVVSCSQHGFEVQVG-PMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSR 62

Query: 198 VKVRLIEANAETGRISLTMRESDD 221
           ++V++    ++   I       +D
Sbjct: 63  IRVKIEGCISQVSSIHAIGSIKED 86

>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]} Length = 91

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]

 Score = 44.5 bits (105), Expect = 2e-06
 Identities = 11/86 (12%), Positives = 29/86 (33%), Gaps = 11/86 (12%)

Query: 261 VKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMG--------GSSLQVG 312
            KG+ ++GTV + ++ G  + +    + F+       D   N              + + 
Sbjct: 2   FKGEVVDGTVVSCSQHGFEVQV-GPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIK 60

Query: 313 QEVSVRVLRIS--RGQVTLTMKKEDD 336
             + V++         +      ++D
Sbjct: 61  SRIRVKIEGCISQVSSIHAIGSIKED 86

>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 = 62.0 bits (151), Expect = 5e-13
 Identities = 19/60 (31%), Positives = 33/60 (55%), Gaps = 4/60 (6%)

Query: 153 GKVRSIQPFGAFIDFGAFTDGLVHVSRLSDN----FVKDVGSIVSVGQEVKVRLIEANAE 208
           G V     FGAF+      DGL+H+S++        V++V  ++ VGQ+V+V + E ++ 
Sbjct: 1   GSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSR 60

>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 = 49.3 bits (118), Expect = 1e-08
 Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 2/59 (3%)

Query: 268 GTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMG--GSSLQVGQEVSVRVLRISR 324
           G+V   T  GAF+SL  G++G L  S+         +      L VGQ+V V +  I  
Sbjct: 1   GSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDS 59

>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 = 62.7 bits (152), Expect = 5e-13
 Identities = 13/77 (16%), Positives = 26/77 (33%), Gaps = 4/77 (5%)

Query: 147 PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDV---GSIVSVGQEVKVRLI 203
                 G V  ++ +G  +D  A     +  S L    +         + VG  V  R+ 
Sbjct: 7   INDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIE 66

Query: 204 EANAETGRISLTMRESD 220
             +  +    L+++  D
Sbjct: 67  NFD-RSIDPVLSVKGKD 82

>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 = 53.5 bits (128), Expect = 1e-09
 Identities = 14/76 (18%), Positives = 26/76 (34%), Gaps = 2/76 (2%)

Query: 262 KGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSS-LQVGQEVSVRVL 320
               + G V+++   G  + +    + +LP S                L VG  V  R+ 
Sbjct: 7   INDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIE 66

Query: 321 RI-SRGQVTLTMKKED 335
                    L++K +D
Sbjct: 67  NFDRSIDPVLSVKGKD 82

>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 = 62.0 bits (150), Expect = 1e-12
 Identities = 11/80 (13%), Positives = 39/80 (48%), Gaps = 2/80 (2%)

Query: 141 KNEDLIPGATFTGKVRSIQPFGAFIDFGAFT--DGLVHVSRLSDNFVKDVGSIVSVGQEV 198
           +++    G      V+ +  +G+++    +      +  S +S  +VK++  ++   ++V
Sbjct: 5   RSKLPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKV 64

Query: 199 KVRLIEANAETGRISLTMRE 218
            V++I  +   G + +++++
Sbjct: 65  IVKVIRVDRRKGTVDVSLKK 84

>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 = 46.9 bits (111), Expect = 2e-07
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 6/75 (8%)

Query: 263 GQDLEGTVKNLTRSGAFISLPE--GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVL 320
           G+ L  TVK +   G+++SL E  G + FLP SE S            L+  ++V V+V+
Sbjct: 12  GEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSS--KWVKNIRDVLKENRKVIVKVI 69

Query: 321 RI--SRGQVTLTMKK 333
           R+   +G V +++KK
Sbjct: 70  RVDRRKGTVDVSLKK 84

>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 = 61.5 bits (149), Expect = 1e-12
 Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 2/73 (2%)

Query: 147 PGATFTGKVRSIQPFGAFIDFGAF--TDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIE 204
                   VRSI   GA++    +   +G++ +S LS   ++ +  ++ +G+   V +I 
Sbjct: 13  VEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIR 72

Query: 205 ANAETGRISLTMR 217
            + E G I L+ R
Sbjct: 73  VDKEKGYIDLSKR 85

>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 = 48.5 bits (115), Expect = 6e-08
 Identities = 19/85 (22%), Positives = 39/85 (45%), Gaps = 7/85 (8%)

Query: 254 EMKTTKFVK-GQDLEGTVKNLTRSGAFISLPE--GEEGFLPTSEESDDGFANMMGGSSLQ 310
                KF +    +   V+++   GA++SL E    EG +  SE S     ++      +
Sbjct: 4   RFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLI--R 61

Query: 311 VGQEVSVRVLRI--SRGQVTLTMKK 333
           +G+   V V+R+   +G + L+ ++
Sbjct: 62  IGRNECVVVIRVDKEKGYIDLSKRR 86

>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 = 60.7 bits (147), Expect = 4e-12
 Identities = 10/82 (12%), Positives = 28/82 (34%), Gaps = 11/82 (13%)

Query: 147 PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLS----------DNFVKDVGSIVSVGQ 196
            G    G++  +Q     ++  +  D ++ +S ++                +   +  G 
Sbjct: 8   VGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGD 67

Query: 197 EVKVRLIEANAETGRISLTMRE 218
            +   +    ++ G +SL  R 
Sbjct: 68  LISAEVQAVFSD-GAVSLHTRS 88

>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 = 48.8 bits (116), Expect = 6e-08
 Identities = 14/86 (16%), Positives = 29/86 (33%), Gaps = 11/86 (12%)

Query: 258 TKFV--KGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSS------- 308
           T+++   G  + G +  + +    +      +  L  S  +  G       +        
Sbjct: 2   TRYIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRG 61

Query: 309 -LQVGQEVSVRVLRISR-GQVTLTMK 332
            LQ G  +S  V  +   G V+L  +
Sbjct: 62  FLQEGDLISAEVQAVFSDGAVSLHTR 87

>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 = 59.6 bits (144), Expect = 6e-12
 Identities = 12/75 (16%), Positives = 30/75 (40%), Gaps = 2/75 (2%)

Query: 147 PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLS-DNFVKDVGSIVSVGQEVKVRLIEA 205
            G    G +R +   G  +D  +     + VS        K    ++ +G  +  +++  
Sbjct: 5   VGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNI 64

Query: 206 NAETGRISLTMRESD 220
           +    +++LTM++  
Sbjct: 65  D-PKMKVTLTMKDRI 78

>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 = 47.7 bits (113), Expect = 1e-07
 Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 2/75 (2%)

Query: 262 KGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLR 321
            G  + G ++ +  +G  + +    + FLP SE  +    N      L +G  +  +VL 
Sbjct: 5   VGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKP-NKKPNEVLDIGDAIIAKVLN 63

Query: 322 I-SRGQVTLTMKKED 335
           I  + +VTLTMK   
Sbjct: 64  IDPKMKVTLTMKDRI 78

>d2c35b1 b.40.4.5 (B:78-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Human (Homo sapiens) [TaxId: 9606]} Length = 94

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]

 Score = 54.5 bits (131), Expect = 6e-10
 Identities = 8/85 (9%), Positives = 24/85 (28%), Gaps = 15/85 (17%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFV------------KDVGSIVSVG 195
           G      V  +   G F + G      +    +                  D   ++   
Sbjct: 5   GEVVDAVVTQVNKVGLFTEIG-PMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQD 63

Query: 196 QEVKVRLIEANAETGRIS--LTMRE 218
            E++++++    +   I    ++ +
Sbjct: 64  DEIRLKIVGTRVDKNDIFAIGSLMD 88

>d2c35b1 b.40.4.5 (B:78-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Human (Homo sapiens) [TaxId: 9606]} Length = 94

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]

 Score = 37.2 bits (86), Expect = 6e-04
 Identities = 9/85 (10%), Positives = 26/85 (30%), Gaps = 15/85 (17%)

Query: 262 KGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDG----------FANMMGGSSLQV 311
           KG+ ++  V  + + G F  +      F+       +           +  M     +Q 
Sbjct: 4   KGEVVDAVVTQVNKVGLFTEI-GPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQ 62

Query: 312 GQEVSVRVLRIS----RGQVTLTMK 332
             E+ ++++             ++ 
Sbjct: 63  DDEIRLKIVGTRVDKNDIFAIGSLM 87

>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 = 53.5 bits (128), Expect = 1e-09
 Identities = 25/87 (28%), Positives = 45/87 (51%), Gaps = 17/87 (19%)

Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFV-----------KDVGSIVSVGQ 196
                G+V  +  FG+F+  G   DGL+HVS++ D++V           K+ G ++ +G 
Sbjct: 4   YELIEGEVVDVVEFGSFVRLGPL-DGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGD 62

Query: 197 EVKVRLIEANAETGR-----ISLTMRE 218
            V+ R++  + +  R     I+LTMR+
Sbjct: 63  YVRARIVAISLKAERKRGSKIALTMRQ 89

>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 = 43.5 bits (102), Expect = 6e-06
 Identities = 17/87 (19%), Positives = 37/87 (42%), Gaps = 17/87 (19%)

Query: 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSL---------QVGQ 313
            + +EG V ++   G+F+ L    +G +  S+  DD  +      ++         ++G 
Sbjct: 4   YELIEGEVVDVVEFGSFVRL-GPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGD 62

Query: 314 EVSVRVL-------RISRGQVTLTMKK 333
            V  R++       R    ++ LTM++
Sbjct: 63  YVRARIVAISLKAERKRGSKIALTMRQ 89

>d2ja9a1 b.40.4.5 (A:62-151) S1-domain of exosome component 3 (RRP40) {Saccharomyces cerevisiae [TaxId: 4932]} Length = 90

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]

 Score = 49.4 bits (118), Expect = 2e-08
 Identities = 11/73 (15%), Positives = 19/73 (26%), Gaps = 1/73 (1%)

Query: 147 PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEAN 206
                 G +         +    F+  +        N  K     + VG  V  R+  A 
Sbjct: 7   VNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAE 66

Query: 207 AETGRISLTMRES 219
            E     +   +S
Sbjct: 67  KE-LEAEIECFDS 78

>d2nn6g1 b.40.4.5 (G:107-194) S1-domain of exosome component 3 (RRP40) {Human (Homo sapiens) [TaxId: 9606]} 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 component 3 (RRP40)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.1 bits (117), Expect = 3e-08
 Identities = 12/73 (16%), Positives = 22/73 (30%), Gaps = 2/73 (2%)

Query: 147 PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEAN 206
            G    G V +       +D G      +      +   K     V VG  +  + + AN
Sbjct: 6   KGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSF-EGATKRNRPNVQVGDLIYGQFVVAN 64

Query: 207 AETGRISLTMRES 219
            +     +   +S
Sbjct: 65  KD-MEPEMVCIDS 76

>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 = 49.0 bits (117), Expect = 4e-08
 Identities = 13/82 (15%), Positives = 21/82 (25%), Gaps = 17/82 (20%)

Query: 148 GATFTGKVRSIQPFGAFI---DFGAFTDGLVHVSRLSDNF------------VKDVGSIV 192
              F  ++  I   G  +   D GA     +    L                     ++ 
Sbjct: 4   DTRFAAEIVDISRGGMRVRLVDNGA--IAFIPAPFLHAVRDELVCSQENGTVQIKGETVY 61

Query: 193 SVGQEVKVRLIEANAETGRISL 214
            V   + V + E   ET  I  
Sbjct: 62  KVTDVIDVTIAEVRMETRSIIA 83

>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 = 39.8 bits (93), Expect = 7e-05
 Identities = 9/71 (12%), Positives = 20/71 (28%), Gaps = 11/71 (15%)

Query: 263 GQDLEGTVKNLTRSGAFISLPE-GEEGFLPTSEESDD------GFANMMGGSS----LQV 311
                  + +++R G  + L + G   F+P                N           +V
Sbjct: 4   DTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKV 63

Query: 312 GQEVSVRVLRI 322
              + V +  +
Sbjct: 64  TDVIDVTIAEV 74

>d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {Human (Homo sapiens) [TaxId: 9606]} Length = 119

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]

 Score = 49.7 bits (118), Expect = 5e-08
 Identities = 20/92 (21%), Positives = 42/92 (45%), Gaps = 2/92 (2%)

Query: 143 EDLIPGATFTGKVRSIQPFGAFIDFGAFT-DGLVHVSRLSDNF-VKDVGSIVSVGQEVKV 200
           E L PG   TG V S++  G  +D G       + + +  +    K+ G+ + VGQ +  
Sbjct: 17  EALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNC 76

Query: 201 RLIEANAETGRISLTMRESDDISKLQQQKDAT 232
            + +     G +SL++  S+  + +  ++ + 
Sbjct: 77  IVEKVKGNGGVVSLSVGHSEVSTAIATEQQSW 108

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	681
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	99.62
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	99.6
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	99.58
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.55
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	99.55
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.55
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.49
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.45
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	99.43
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	99.42
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	99.42
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	99.4
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	99.38
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	99.34
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	99.33
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	99.32
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	99.3
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	99.27
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	99.05
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	99.0
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	98.97
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	98.93
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	98.93
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	98.86
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	98.78
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	98.73
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	98.63
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	98.51
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	98.45
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	98.32
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	98.31
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	98.23
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	98.08
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	98.07
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	97.84
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	97.83
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	97.66
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	97.45
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	97.1
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	97.06
d1c9oa_	66	Major cold shock protein {Bacillus caldolyticus [T	88.99
d1k3ra1	71	Hypothetical protein MTH1 (MT0001), insert domain	88.3
d1jjga_	102	Viral structural mimic of eIF2alpha {Myxoma virus,	88.07
d1luza_	85	Viral structural mimic of eIF2alpha {Vaccinia viru	87.85
d1k3ra1	71	Hypothetical protein MTH1 (MT0001), insert domain	87.1
d1wfqa_	89	Cold shock domain protein E1 (UNR) {Human (Homo sa	85.11
d1jjga_	102	Viral structural mimic of eIF2alpha {Myxoma virus,	83.05
d1g6pa_	66	Major cold shock protein {Thermotoga maritima [Tax	83.05
d1wfqa_	89	Cold shock domain protein E1 (UNR) {Human (Homo sa	80.56
d3d31a1	119	Sulfate/molybdate ABC transporter, ATP-binding pro	80.34
d1h95a_	79	Y-box protein 1 cold shock domain (YB1-CSD) {Human	80.1

>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=99.62  E-value=2e-16  Score=132.04  Aligned_cols=76  Identities=39%  Similarity=0.731  Sum_probs=71.8

Q ss_pred             CCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEecc
Q 005707          143 EDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRES  219 (681)
Q Consensus       143 ~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l  219 (681)
                      +++++|+++.|+|+++.+||+||+|+++++||||.++++|+++.++.+.|++||.|+|+|+++|+ ++||.||+|++
T Consensus         1 ad~kvG~iv~G~V~~v~~~G~fV~l~~~~~Glv~~sels~~~~~~~~~~~~~G~~v~v~Vi~id~-~~ri~LS~k~a   76 (76)
T d1sroa_           1 AEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDR-QGRIRLSIKEA   76 (76)
T ss_dssp             CCCCTTSEEEEEEEEEETTEEEEECSSSCCCBCCTTSSCSSCCSCHHHHCCTTCEEEEEEEECCT-TCCCEEEECCC
T ss_pred             CCCCCCCEEEEEEEEEeCcEEEEEeCCCCEEEEEhHHhCccccCCHHHccCCCCEEEEEEEEECC-CCCEEEEEEcC
Confidence            37899999999999999999999999889999999999999999999999999999999999996 57899999963

>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=99.60  E-value=2.6e-16  Score=131.33  Aligned_cols=74  Identities=31%  Similarity=0.548  Sum_probs=68.8

Q ss_pred             CCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe-CCeEEEEEecc
Q 005707          259 KFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS-RGQVTLTMKKE  334 (681)
Q Consensus       259 klkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID-kgKI~LSLK~~  334 (681)
                      ++++|+++.|+|++|.+||+||+|+++++||||.++++|.++.  +|...|++||.|+|+|+++| ++|+.||||++
T Consensus         2 d~kvG~iv~G~V~~v~~~G~fV~l~~~~~Glv~~sels~~~~~--~~~~~~~~G~~v~v~Vi~id~~~ri~LS~k~a   76 (76)
T d1sroa_           2 EIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVE--KVTDYLQMGQEVPVKVLEVDRQGRIRLSIKEA   76 (76)
T ss_dssp             CCCTTSEEEEEEEEEETTEEEEECSSSCCCBCCTTSSCSSCCS--CHHHHCCTTCEEEEEEEECCTTCCCEEEECCC
T ss_pred             CCCCCCEEEEEEEEEeCcEEEEEeCCCCEEEEEhHHhCccccC--CHHHccCCCCEEEEEEEEECCCCCEEEEEEcC
Confidence            6899999999999999999999999999999999999999865  45888999999999999997 58999999974

>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=99.58  E-value=1.1e-15  Score=132.10  Aligned_cols=79  Identities=44%  Similarity=0.751  Sum_probs=76.2

Q ss_pred             CcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEecc
Q 005707          141 KNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRES  219 (681)
Q Consensus       141 t~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l  219 (681)
                      ++.++++|+++.|+|+++.++|+||+|+++++||||.++++|.++.++.+.|++||.|+|+|+.+|+++++|.||+|+.
T Consensus        12 ~~~~~k~G~iv~g~V~~v~~~G~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~vGq~v~~~V~~id~~~~~i~LS~K~~   90 (94)
T d3bzka4          12 SLKDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGLSMRMS   90 (94)
T ss_dssp             CGGGCCTTCEEEEEEEEEETTEEEEECSSSSCEEEEGGGGCSSCCSCHHHHCCTTCEEEEEEEEEETTTTEEEEESCTT
T ss_pred             HHhcCCCCCEEEEEEEEEECcEEEEEeCCCceEEeehhhhhcccccChhhhhccCcEEEEEEEEEECCCCEEEEEEecc
Confidence            4789999999999999999999999999899999999999999999999999999999999999999999999999964

>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=99.55  E-value=6.6e-15  Score=125.05  Aligned_cols=74  Identities=24%  Similarity=0.411  Sum_probs=58.7

Q ss_pred             CCCCcEEEEEEEEEecCeeEEEEC--CCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEec
Q 005707          145 LIPGATFTGKVRSIQPFGAFIDFG--AFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRE  218 (681)
Q Consensus       145 LkvGdIVeGkV~sV~d~GaFVdLg--ggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~  218 (681)
                      .++|+++.|+|+++.++|+||+|.  ++++||||.++++|++..++.+.|++||.|+|+|+++|+++++|.||+|+
T Consensus        11 p~~G~iv~G~V~~i~~~G~fV~l~~~~~i~G~i~~sels~~~~~~~~~~~~~Gd~v~~kV~~vd~~~~ki~LS~Kq   86 (86)
T d1kl9a2          11 PEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRR   86 (86)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC------------CTTCEEEEEEEEEETTTTEEEEESTT
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEEecCCCEEEEEEeeeccccccccceEEeecccEEEEEEEEEECCCCEEEEEeeC
Confidence            368999999999999999999996  46999999999999999999999999999999999999999999999984

>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=99.55  E-value=3.7e-15  Score=128.78  Aligned_cols=81  Identities=27%  Similarity=0.413  Sum_probs=74.0

Q ss_pred             ccccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEe
Q 005707          255 MKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMK  332 (681)
Q Consensus       255 ~~~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK  332 (681)
                      ..++++++|+++.|+|++|.++|+||+|++|++||||.++++|.+.++  +...|++||.|.|+|+++|  ++||.||||
T Consensus        11 e~~~~~k~G~iv~g~V~~v~~~G~~V~l~~~i~G~i~~~~ls~~~~~~--~~~~~~vGq~v~~~V~~id~~~~~i~LS~K   88 (94)
T d3bzka4          11 ESLKDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKD--PYEVVKAGDIVKVKVMEVDIPRNRVGLSMR   88 (94)
T ss_dssp             CCGGGCCTTCEEEEEEEEEETTEEEEECSSSSCEEEEGGGGCSSCCSC--HHHHCCTTCEEEEEEEEEETTTTEEEEESC
T ss_pred             hHHhcCCCCCEEEEEEEEEECcEEEEEeCCCceEEeehhhhhcccccC--hhhhhccCcEEEEEEEEEECCCCEEEEEEe
Confidence            457899999999999999999999999999999999999999988654  4789999999999999997  699999999


Q ss_pred             ccCCCc
Q 005707          333 KEDDVG  338 (681)
Q Consensus       333 ~~~~DP  338 (681)
                      +. ++|
T Consensus        89 ~~-e~P   93 (94)
T d3bzka4          89 MS-DTP   93 (94)
T ss_dssp             TT-CCC
T ss_pred             cc-CCC
Confidence            85 665

>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=99.55  E-value=5e-15  Score=125.03  Aligned_cols=76  Identities=14%  Similarity=0.399  Sum_probs=66.6

Q ss_pred             CCCCCCcEEEEEEEEEecCeeEEEEC--CCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEec
Q 005707          143 EDLIPGATFTGKVRSIQPFGAFIDFG--AFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRE  218 (681)
Q Consensus       143 ~~LkvGdIVeGkV~sV~d~GaFVdLg--ggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~  218 (681)
                      ...++|+++.|+|+++.++|+||+|+  ++++||||.++++|.+..++.+.|++||.|+|+|+++|+++++|.||+|+
T Consensus         7 ~~p~~G~iv~G~V~~v~~~G~fV~l~~~~gi~Gli~~sels~~~~~~~~~~~~~G~~v~~kV~~vd~~~~~i~LS~Kq   84 (84)
T d2ahob2           7 KLPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDVSLKK   84 (84)
T ss_dssp             SSCCTTCCCEEEEEEEETTEEEEEETTTTTEEEEECGGGCC-----CHHHHTCSSCEEECEEEEEETTTTEEEEESSS
T ss_pred             cCCCCCCEEEEEEEEEECCEEEEEECCcCCEEEEEEccccccccccccceEeecccEEEEEEEEEECCCCEEEEEEcC
Confidence            34578999999999999999999996  46999999999999999999999999999999999999999999999984

>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=99.49  E-value=2.9e-14  Score=121.00  Aligned_cols=75  Identities=24%  Similarity=0.391  Sum_probs=57.7

Q ss_pred             ccCC-ccCcEEEEEEEEEecceEEEEeC--CCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEE
Q 005707          257 TTKF-VKGQDLEGTVKNLTRSGAFISLP--EGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTM  331 (681)
Q Consensus       257 ~skl-kvGdIV~G~VknVt~~GaFVeIg--~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSL  331 (681)
                      .+++ ++|+++.|+|++++++|+||+|.  +|++||||.++++|.+..  ++...|++||.|.|+|+++|  ++||.||+
T Consensus         7 ~~~~p~~G~iv~G~V~~i~~~G~fV~l~~~~~i~G~i~~sels~~~~~--~~~~~~~~Gd~v~~kV~~vd~~~~ki~LS~   84 (86)
T d1kl9a2           7 QHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIR--SINKLIRIGRNECVVVIRVDKEKGYIDLSK   84 (86)
T ss_dssp             SSSSCCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC--------------CTTCEEEEEEEEEETTTTEEEEES
T ss_pred             hhcCCCCCCEEEEEEEEEeCCeEEEEEecCCCEEEEEEeeeccccccc--cceEEeecccEEEEEEEEEECCCCEEEEEe
Confidence            3445 58999999999999999999997  589999999999998854  45889999999999999997  69999999


Q ss_pred             ec
Q 005707          332 KK  333 (681)
Q Consensus       332 K~  333 (681)
                      |+
T Consensus        85 Kq   86 (86)
T d1kl9a2          85 RR   86 (86)
T ss_dssp             TT
T ss_pred             eC
Confidence            85

>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=99.45  E-value=3.6e-14  Score=119.68  Aligned_cols=71  Identities=34%  Similarity=0.490  Sum_probs=61.2

Q ss_pred             ccCcEEEEEEEEEecceEEEEeC--CCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEec
Q 005707          261 VKGQDLEGTVKNLTRSGAFISLP--EGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKK  333 (681)
Q Consensus       261 kvGdIV~G~VknVt~~GaFVeIg--~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~  333 (681)
                      ++|+++.|+|++|+++|+||+|+  +|++||||.++++|.+..  ++.+.|++||.|+|+|+++|  ++|+.||+|+
T Consensus        10 ~~G~iv~G~V~~v~~~G~fV~l~~~~gi~Gli~~sels~~~~~--~~~~~~~~G~~v~~kV~~vd~~~~~i~LS~Kq   84 (84)
T d2ahob2          10 SEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVK--NIRDVLKENRKVIVKVIRVDRRKGTVDVSLKK   84 (84)
T ss_dssp             CTTCCCEEEEEEEETTEEEEEETTTTTEEEEECGGGCC-------CHHHHTCSSCEEECEEEEEETTTTEEEEESSS
T ss_pred             CCCCEEEEEEEEEECCEEEEEECCcCCEEEEEEcccccccccc--ccceEeecccEEEEEEEEEECCCCEEEEEEcC
Confidence            58999999999999999999997  489999999999998854  45788999999999999997  5999999985

>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=99.43  E-value=1.1e-13  Score=116.32  Aligned_cols=78  Identities=26%  Similarity=0.339  Sum_probs=68.8

Q ss_pred             ccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe-CCeEEEEEeccCCCcC
Q 005707          261 VKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS-RGQVTLTMKKEDDVGS  339 (681)
Q Consensus       261 kvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID-kgKI~LSLK~~~~DP~  339 (681)
                      ++|++|.|+|++++++|+||+|++++.||||.++++|... ..++...|++||.|.|+|+++| .+|+.||||.....|+
T Consensus         4 k~Gd~V~G~V~~v~~~g~~V~i~~~~~g~l~~se~s~~~~-~~~~~~~~~vGd~V~~kV~~vd~~~~i~LS~k~~~~~k~   82 (83)
T d2ba0a1           4 SVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKP-NKKPNEVLDIGDAIIAKVLNIDPKMKVTLTMKDRICRPI   82 (83)
T ss_dssp             CTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTTCCT-TSCGGGTCCTTCEEEEEEEEECTTCCEEEECCSSSCEEE
T ss_pred             CCCCEEEEEEEEEECCEEEEecCCCeeEEEeccccccccc-ccChhhhcccccEEEEEEEEECCCCCEEEEecCCCCCCC
Confidence            6899999999999999999999999999999999998753 2245788999999999999997 5899999998765543

>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=99.42  E-value=2.1e-13  Score=114.69  Aligned_cols=76  Identities=16%  Similarity=0.257  Sum_probs=69.3

Q ss_pred             CCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCcc-ccCcccccccCCEEEEEEEEEeccCCceEEEEeccch
Q 005707          145 LIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNF-VKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDD  221 (681)
Q Consensus       145 LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~-v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~  221 (681)
                      .++|++|.|+|+++.++|+||+|++++.||||+++++|.. ..++...|++||.|.|+|+++|+ .++|.||+|....
T Consensus         3 Pk~Gd~V~G~V~~v~~~g~~V~i~~~~~g~l~~se~s~~~~~~~~~~~~~vGd~V~~kV~~vd~-~~~i~LS~k~~~~   79 (83)
T d2ba0a1           3 PSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDP-KMKVTLTMKDRIC   79 (83)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECT-TCCEEEECCSSSC
T ss_pred             CCCCCEEEEEEEEEECCEEEEecCCCeeEEEecccccccccccChhhhcccccEEEEEEEEECC-CCCEEEEecCCCC
Confidence            4789999999999999999999999999999999999865 67899999999999999999985 5789999997543

>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=99.42  E-value=8.1e-14  Score=125.30  Aligned_cols=85  Identities=25%  Similarity=0.403  Sum_probs=76.9

Q ss_pred             CCCcCCCCCCcEEEEEEEEEecCeeEEEEC-CCeEEEEeccccCCcc-ccCcccccccCCEEEEEEEEEeccCCceEEEE
Q 005707          139 PVKNEDLIPGATFTGKVRSIQPFGAFIDFG-AFTDGLVHVSRLSDNF-VKDVGSIVSVGQEVKVRLIEANAETGRISLTM  216 (681)
Q Consensus       139 ~lt~~~LkvGdIVeGkV~sV~d~GaFVdLg-ggV~GLVPiSELS~~~-v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSl  216 (681)
                      .+++++|++|+++.|+|++|.++|+||+|+ .+++||||++++++.+ ..++...|++||.|+|+|+++|+.+++|.||+
T Consensus        13 ~ls~~~l~~G~iv~G~V~~i~~~G~~V~lg~~~~~G~l~~~els~~~~~~~~~~~~~vGq~v~~~V~~vd~~~~~i~LS~   92 (119)
T d1wi5a_          13 VLSAEALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSV   92 (119)
T ss_dssp             CCCTTTCCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCTTSCEEEEEC
T ss_pred             hcCHhhcCCCCEEEEEEEEEeccEEEEEEeccccceEEeHHHhccccccCCHHHhcccceEEEEEEEEEeCCCCEEEEEe
Confidence            345789999999999999999999999996 6799999999999874 67888899999999999999999999999999


Q ss_pred             eccchhh
Q 005707          217 RESDDIS  223 (681)
Q Consensus       217 K~l~~dp  223 (681)
                      |+.....
T Consensus        93 k~~~~~~   99 (119)
T d1wi5a_          93 GHSEVST   99 (119)
T ss_dssp             CCCCSCC
T ss_pred             cHHHhhh
Confidence            9765533

>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=99.40  E-value=3.7e-13  Score=118.75  Aligned_cols=79  Identities=32%  Similarity=0.572  Sum_probs=70.0

Q ss_pred             CCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccc-----------cCcccccccCCEEEEEEEEEeccCCc---
Q 005707          146 IPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFV-----------KDVGSIVSVGQEVKVRLIEANAETGR---  211 (681)
Q Consensus       146 kvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v-----------~d~~e~fkVGd~VkVkVl~VD~ekgr---  211 (681)
                      ++|++|+|+|++|.+||+||+|++ ++||||+++|+++++           .++...|++||.|+|+|+++|.++++   
T Consensus         2 ~~gei~~g~V~~v~~~G~FVel~~-ieGlv~~s~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkV~~vd~~~~~~~~   80 (106)
T d1go3e1           2 EMYELIEGEVVDVVEFGSFVRLGP-LDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAERKRG   80 (106)
T ss_dssp             CTTCEEEEEEEEEETTEEEEECSS-SEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEEECCC-----
T ss_pred             CCCCEEEEEEEEEeeeEEEEEeeC-eEEEEEeecccCceeeeccceeEEeecccccceeecceEEEEEEEEchhhccccC
Confidence            689999999999999999999975 999999999999877           47788999999999999999998876   


Q ss_pred             --eEEEEeccchhhHh
Q 005707          212 --ISLTMRESDDISKL  225 (681)
Q Consensus       212 --I~LSlK~l~~dp~e  225 (681)
                        |.||+|+....+|+
T Consensus        81 ~~i~ls~K~~~~~~~e   96 (106)
T d1go3e1          81 SKIALTMRQPYLGKLE   96 (106)
T ss_dssp             CEEEEECCSTTCEEHH
T ss_pred             ceeecccccCCCCcch
Confidence              78899988777773

>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=99.38  E-value=2.6e-13  Score=121.91  Aligned_cols=83  Identities=24%  Similarity=0.382  Sum_probs=72.6

Q ss_pred             ccccCCccCcEEEEEEEEEecceEEEEeC-CCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEE
Q 005707          255 MKTTKFVKGQDLEGTVKNLTRSGAFISLP-EGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTM  331 (681)
Q Consensus       255 ~~~sklkvGdIV~G~VknVt~~GaFVeIg-~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSL  331 (681)
                      ..+.+|++|+++.|+|++|.++|+||+|+ +++.||||+++++|.+. ..+|...|++||.|.|+|+++|  ++++.||+
T Consensus        14 ls~~~l~~G~iv~G~V~~i~~~G~~V~lg~~~~~G~l~~~els~~~~-~~~~~~~~~vGq~v~~~V~~vd~~~~~i~LS~   92 (119)
T d1wi5a_          14 LSAEALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIR-QKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSV   92 (119)
T ss_dssp             CCTTTCCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHHHHH-HHSSSCCCCTTCEEEEEEEECCTTSCEEEEEC
T ss_pred             cCHhhcCCCCEEEEEEEEEeccEEEEEEeccccceEEeHHHhccccc-cCCHHHhcccceEEEEEEEEEeCCCCEEEEEe
Confidence            56789999999999999999999999996 79999999999998642 2246789999999999999997  58899999


Q ss_pred             eccCCCc
Q 005707          332 KKEDDVG  338 (681)
Q Consensus       332 K~~~~DP  338 (681)
                      |+.....
T Consensus        93 k~~~~~~   99 (119)
T d1wi5a_          93 GHSEVST   99 (119)
T ss_dssp             CCCCSCC
T ss_pred             cHHHhhh
Confidence            9885543

>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=99.34  E-value=9.7e-13  Score=116.01  Aligned_cols=79  Identities=25%  Similarity=0.336  Sum_probs=68.6

Q ss_pred             ccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccc---------cCCCCcccCCCEEEEEEEEEe--CC----
Q 005707          261 VKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFAN---------MMGGSSLQVGQEVSVRVLRIS--RG----  325 (681)
Q Consensus       261 kvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~---------~~p~~~fkVGqkVkVrVL~ID--kg----  325 (681)
                      ++|+++.|+|++|++||+||+|+ +++||||.++|+|+++..         .++...|++||.|+|+|++||  ++    
T Consensus         2 ~~gei~~g~V~~v~~~G~FVel~-~ieGlv~~s~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkV~~vd~~~~~~~~   80 (106)
T d1go3e1           2 EMYELIEGEVVDVVEFGSFVRLG-PLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAERKRG   80 (106)
T ss_dssp             CTTCEEEEEEEEEETTEEEEECS-SSEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEEECCC-----
T ss_pred             CCCCEEEEEEEEEeeeEEEEEee-CeEEEEEeecccCceeeeccceeEEeecccccceeecceEEEEEEEEchhhccccC
Confidence            58999999999999999999996 799999999999987632         245689999999999999997  33    


Q ss_pred             -eEEEEEeccCCCcCC
Q 005707          326 -QVTLTMKKEDDVGSN  340 (681)
Q Consensus       326 -KI~LSLK~~~~DP~e  340 (681)
                       ++.||+|+...+||+
T Consensus        81 ~~i~ls~K~~~~~~~e   96 (106)
T d1go3e1          81 SKIALTMRQPYLGKLE   96 (106)
T ss_dssp             CEEEEECCSTTCEEHH
T ss_pred             ceeecccccCCCCcch
Confidence             488999999888876

>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=99.33  E-value=6.4e-13  Score=112.81  Aligned_cols=75  Identities=19%  Similarity=0.163  Sum_probs=67.1

Q ss_pred             CccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCccccccc-CCCCcccCCCEEEEEEEEEeC-CeEEEEEecc
Q 005707          260 FVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANM-MGGSSLQVGQEVSVRVLRISR-GQVTLTMKKE  334 (681)
Q Consensus       260 lkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~-~p~~~fkVGqkVkVrVL~IDk-gKI~LSLK~~  334 (681)
                      -++|+++.|+|++++++|+||+|+++++||||.++++|.+.... ++...|++||.|.|+|+++|+ +++.||||..
T Consensus         5 Pk~Gdiv~G~V~~i~~~g~fV~i~~~~~gll~~s~~~~~~~~~~~~~~~~~~~Gd~v~~kV~~vd~~~~i~LS~k~~   81 (87)
T d2je6i1           5 PKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDRSIDPVLSVKGK   81 (87)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEETTEEEEEECCST
T ss_pred             CCCCCEEEEEEEEEECCEEEEEeCCCEEEEEehHHhCCceeccccccchhhcccceEEEEEEEECCCCCEEEEEecC
Confidence            45799999999999999999999999999999999999865432 367889999999999999984 7899999876

>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=99.32  E-value=1.2e-12  Score=111.05  Aligned_cols=75  Identities=17%  Similarity=0.198  Sum_probs=68.0

Q ss_pred             CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCcccc---CcccccccCCEEEEEEEEEeccCCceEEEEecc
Q 005707          144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVK---DVGSIVSVGQEVKVRLIEANAETGRISLTMRES  219 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~---d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l  219 (681)
                      ..++|++|.|+|+++.++|+||+|+++++||||.++++|.++.   ++...|++||.|.|+|+++|+ .+++.||+|..
T Consensus         4 ~Pk~Gdiv~G~V~~i~~~g~fV~i~~~~~gll~~s~~~~~~~~~~~~~~~~~~~Gd~v~~kV~~vd~-~~~i~LS~k~~   81 (87)
T d2je6i1           4 YPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDR-SIDPVLSVKGK   81 (87)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEET-TEEEEEECCST
T ss_pred             cCCCCCEEEEEEEEEECCEEEEEeCCCEEEEEehHHhCCceeccccccchhhcccceEEEEEEEECC-CCCEEEEEecC
Confidence            4678999999999999999999999889999999999998664   677889999999999999996 47899999854

>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=99.30  E-value=1.6e-12  Score=110.50  Aligned_cols=75  Identities=17%  Similarity=0.261  Sum_probs=68.0

Q ss_pred             CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCcccc----CcccccccCCEEEEEEEEEeccCCceEEEEecc
Q 005707          144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVK----DVGSIVSVGQEVKVRLIEANAETGRISLTMRES  219 (681)
Q Consensus       144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~----d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l  219 (681)
                      ..++|++|.|+|+++.++|+||+|+++..||||.+++++.++.    +++..|++||.|+|+|+++|++ +++.||+|..
T Consensus         4 ~Pk~GdvV~G~V~~v~~~g~fV~i~~~~~g~l~~se~~~~~~~~~~~~~~~~~~vGd~V~~kV~~vd~~-~~i~Ls~k~~   82 (88)
T d2z0sa1           4 VPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDKT-RSPLLTVQGE   82 (88)
T ss_dssp             CCCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECTT-SCEEEECCSS
T ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEehHHhCcccccccccchhhhcccCcEEEEEEEEECCC-CCEEEEEecC
Confidence            4678999999999999999999999989999999999988764    6778899999999999999964 6899999953

>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=99.27  E-value=1.8e-12  Score=110.05  Aligned_cols=75  Identities=17%  Similarity=0.182  Sum_probs=66.8

Q ss_pred             CccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCccccccc--CCCCcccCCCEEEEEEEEEe-CCeEEEEEecc
Q 005707          260 FVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANM--MGGSSLQVGQEVSVRVLRIS-RGQVTLTMKKE  334 (681)
Q Consensus       260 lkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~--~p~~~fkVGqkVkVrVL~ID-kgKI~LSLK~~  334 (681)
                      -++|++|.|+|++++++|+||+|+++++||||.++++|.++...  +++..|++||.|.|+|+++| .+++.||||..
T Consensus         5 Pk~GdvV~G~V~~v~~~g~fV~i~~~~~g~l~~se~~~~~~~~~~~~~~~~~~vGd~V~~kV~~vd~~~~i~Ls~k~~   82 (88)
T d2z0sa1           5 PQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDKTRSPLLTVQGE   82 (88)
T ss_dssp             CCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECTTSCEEEECCSS
T ss_pred             CCCCCEEEEEEEEEECCeEEEEeCCCeEEEEehHHhCcccccccccchhhhcccCcEEEEEEEEECCCCCEEEEEecC
Confidence            36899999999999999999999999999999999998775422  35678999999999999997 58999999875

>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=99.05  E-value=2.7e-12  Score=103.26  Aligned_cols=58  Identities=33%  Similarity=0.564  Sum_probs=36.4

Q ss_pred             EEEEEEecCeeEEEECCCeEEEEeccccCCc----cccCcccccccCCEEEEEEEEEeccCC
Q 005707          153 GKVRSIQPFGAFIDFGAFTDGLVHVSRLSDN----FVKDVGSIVSVGQEVKVRLIEANAETG  210 (681)
Q Consensus       153 GkV~sV~d~GaFVdLgggV~GLVPiSELS~~----~v~d~~e~fkVGd~VkVkVl~VD~ekg  210 (681)
                      |+|++|.+||+||+|+++++||||+++|++.    ++.++.+.|++||.|+|+|+++|++++
T Consensus         1 G~V~~i~~fG~FV~l~~g~~Glihiseis~~~~~~~v~~~~~~~~~G~~V~vkV~~iD~~~r   62 (62)
T d1e3pa2           1 GSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSRGK   62 (62)
T ss_dssp             CBEEECC-CSCEECCC---CCCCC-------------------CCSSCBCCCCCCCCCSSCC
T ss_pred             CEEEEEEeceEEEEecCCceEEEEHHHcccccccccccCHHHhcCCCCEEEEEEEEEcCCCC
Confidence            7899999999999999889999999999863    678999999999999999999997653

>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=99.00  E-value=1.1e-10  Score=100.67  Aligned_cols=74  Identities=14%  Similarity=0.152  Sum_probs=64.0

Q ss_pred             CCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCc----------cccCcccccccCCEEEEEEEEEeccCCceEE
Q 005707          145 LIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDN----------FVKDVGSIVSVGQEVKVRLIEANAETGRISL  214 (681)
Q Consensus       145 LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~----------~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~L  214 (681)
                      .++|++|.|+|+++.++|+||+|+....|+||++++.|.          +..++.+.|++||.|.|+|+++|.+ ++|.|
T Consensus         6 P~vGdiV~G~V~~v~~~g~~V~I~~~~~g~l~is~i~~~~~~~rr~~~~~~~~~~~~~~~Gd~V~~kV~~v~~d-g~i~L   84 (95)
T d2nn6h1           6 GEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFSD-GAVSL   84 (95)
T ss_dssp             CCSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEETT-TEEEE
T ss_pred             CCCCCEEEEEEEEEecCcEEEEeCCCceEEEEHHHccccccccccccchhhhhhhhhcccccEEEEEEEEECCC-CCEEE
Confidence            578999999999999999999999889999999999763          2345677899999999999999974 89999


Q ss_pred             EEecc
Q 005707          215 TMRES  219 (681)
Q Consensus       215 SlK~l  219 (681)
                      |++..
T Consensus        85 s~r~~   89 (95)
T d2nn6h1          85 HTRSL   89 (95)
T ss_dssp             ECCSS
T ss_pred             Eeccc
Confidence            99853

>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=98.97  E-value=3.2e-10  Score=97.83  Aligned_cols=74  Identities=18%  Similarity=0.105  Sum_probs=60.5

Q ss_pred             ccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccC--------CCCcccCCCEEEEEEEEEe-CCeEEEEE
Q 005707          261 VKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMM--------GGSSLQVGQEVSVRVLRIS-RGQVTLTM  331 (681)
Q Consensus       261 kvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~--------p~~~fkVGqkVkVrVL~ID-kgKI~LSL  331 (681)
                      ++|++|.|+|+++.++|+||+|+.+.+|+||++++.|.+.....        +...|++||.|.|+|++++ ++++.||+
T Consensus         7 ~vGdiV~G~V~~v~~~g~~V~I~~~~~g~l~is~i~~~~~~~rr~~~~~~~~~~~~~~~Gd~V~~kV~~v~~dg~i~Ls~   86 (95)
T d2nn6h1           7 EVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSLHT   86 (95)
T ss_dssp             CSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEETTTEEEEEC
T ss_pred             CCCCEEEEEEEEEecCcEEEEeCCCceEEEEHHHccccccccccccchhhhhhhhhcccccEEEEEEEEECCCCCEEEEe
Confidence            57999999999999999999999999999999999875432211        2346999999999999997 59999999


Q ss_pred             ecc
Q 005707          332 KKE  334 (681)
Q Consensus       332 K~~  334 (681)
                      |..
T Consensus        87 r~~   89 (95)
T d2nn6h1          87 RSL   89 (95)
T ss_dssp             CSS
T ss_pred             ccc
Confidence            865

>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=98.93  E-value=1.5e-09  Score=92.57  Aligned_cols=69  Identities=14%  Similarity=0.127  Sum_probs=60.0

Q ss_pred             CCcEEEEEEEEEecCeeEEEE-CCCeEEEEeccccCCcccc------------CcccccccCCEEEEEEEEEeccCCceE
Q 005707          147 PGATFTGKVRSIQPFGAFIDF-GAFTDGLVHVSRLSDNFVK------------DVGSIVSVGQEVKVRLIEANAETGRIS  213 (681)
Q Consensus       147 vGdIVeGkV~sV~d~GaFVdL-gggV~GLVPiSELS~~~v~------------d~~e~fkVGd~VkVkVl~VD~ekgrI~  213 (681)
                      .|+.++|.|++|.++|+||+| ..+++||||+++|.+++..            +....|++||.|+|+|+++|+++++|.
T Consensus         3 ~~~~F~g~Is~v~~~GifV~L~e~~~eGlI~~s~L~~d~y~~d~~~~~l~~~~~~~~~~~~Gd~V~V~v~~vd~~~r~I~   82 (87)
T d2ix0a3           3 TDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETRSII   82 (87)
T ss_dssp             SCCCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEEEEEETTTTEEE
T ss_pred             CCCEEEEEEEEEEcCeEEEEEecCCcEEEEEehhCCCceEEEeccceEEEEEEcccEEEECCCEEEEEEEEEecccCeEE
Confidence            478899999999999999999 5679999999999987542            234579999999999999999999997


Q ss_pred             EE
Q 005707          214 LT  215 (681)
Q Consensus       214 LS  215 (681)
                      +.
T Consensus        83 ~~   84 (87)
T d2ix0a3          83 AR   84 (87)
T ss_dssp             EE
T ss_pred             EE
Confidence            63

>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=98.93  E-value=1.1e-11  Score=99.58  Aligned_cols=57  Identities=33%  Similarity=0.387  Sum_probs=34.7

Q ss_pred             EEEEEEecceEEEEeCCCeEEEEeCCCCCccccc--ccCCCCcccCCCEEEEEEEEEeC
Q 005707          268 GTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFA--NMMGGSSLQVGQEVSVRVLRISR  324 (681)
Q Consensus       268 G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie--~~~p~~~fkVGqkVkVrVL~IDk  324 (681)
                      |+|++|.+||+||+|++|++||||+++|+|.+..  ..+++..|++||.|+|+|++||+
T Consensus         1 G~V~~i~~fG~FV~l~~g~~Glihiseis~~~~~~~v~~~~~~~~~G~~V~vkV~~iD~   59 (62)
T d1e3pa2           1 GSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDS   59 (62)
T ss_dssp             CBEEECC-CSCEECCC---CCCCC-------------------CCSSCBCCCCCCCCCS
T ss_pred             CEEEEEEeceEEEEecCCceEEEEHHHcccccccccccCHHHhcCCCCEEEEEEEEEcC
Confidence            7899999999999999999999999999875211  23568999999999999999985

>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=98.86  E-value=4.5e-09  Score=89.23  Aligned_cols=67  Identities=13%  Similarity=0.290  Sum_probs=59.9

Q ss_pred             CCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccc----------cCcccccccCCEEEEEEEEEeccCCceEE
Q 005707          147 PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFV----------KDVGSIVSVGQEVKVRLIEANAETGRISL  214 (681)
Q Consensus       147 vGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v----------~d~~e~fkVGd~VkVkVl~VD~ekgrI~L  214 (681)
                      .|++++|+|++++++|+||+++. ++||||+++|.+++.          ++....|++|+.|+|+|+++|.+.++|.+
T Consensus         3 ~Gev~~g~I~~v~~~G~fv~lg~-~eg~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~~i~~   79 (91)
T d1y14b1           3 KGEVVDGTVVSCSQHGFEVQVGP-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHA   79 (91)
T ss_dssp             TTCEEEEEEEEEETTEEEEEETT-EEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEEEETTEEEE
T ss_pred             CCCEEEEEEEEEEeeEEEEEEcC-eEEEEEhhhcCcceEEccccceeEecccCeEEeCCCEEEEEEEEEecccCccEE
Confidence            69999999999999999999976 899999999998765          34456799999999999999999998855

>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=98.78  E-value=5.5e-09  Score=88.97  Aligned_cols=67  Identities=13%  Similarity=0.257  Sum_probs=55.0

Q ss_pred             cCcEEEEEEEEEecceEEEEeCC-CeEEEEeCCCCCccccccc----------CCCCcccCCCEEEEEEEEEeC--CeEE
Q 005707          262 KGQDLEGTVKNLTRSGAFISLPE-GEEGFLPTSEESDDGFANM----------MGGSSLQVGQEVSVRVLRISR--GQVT  328 (681)
Q Consensus       262 vGdIV~G~VknVt~~GaFVeIg~-GIeGLLpiSELSd~~ie~~----------~p~~~fkVGqkVkVrVL~IDk--gKI~  328 (681)
                      .|+.++|.|++|+++|+||+|.+ +++||||.++|.|+++...          ++...|++||+|+|+|+++|.  +||.
T Consensus         3 ~~~~F~g~Is~v~~~GifV~L~e~~~eGlI~~s~L~~d~y~~d~~~~~l~~~~~~~~~~~~Gd~V~V~v~~vd~~~r~I~   82 (87)
T d2ix0a3           3 TDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETRSII   82 (87)
T ss_dssp             SCCCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEEEEEETTTTEEE
T ss_pred             CCCEEEEEEEEEEcCeEEEEEecCCcEEEEEehhCCCceEEEeccceEEEEEEcccEEEECCCEEEEEEEEEecccCeEE
Confidence            47889999999999999999964 8999999999998764311          123569999999999999985  5553

>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=98.73  E-value=2.2e-08  Score=85.62  Aligned_cols=68  Identities=12%  Similarity=0.336  Sum_probs=59.6

Q ss_pred             CCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccc------------cCcccccccCCEEEEEEEEEeccCCceE
Q 005707          146 IPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFV------------KDVGSIVSVGQEVKVRLIEANAETGRIS  213 (681)
Q Consensus       146 kvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v------------~d~~e~fkVGd~VkVkVl~VD~ekgrI~  213 (681)
                      -.|++++|+|++++++|+||+++. ++||||.++|.+++.            .+....|+.||.|++||++++.+.++|.
T Consensus         3 f~Gev~~g~V~~v~~~G~fv~lg~-~~~~v~~~~l~~d~~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~~I~   81 (94)
T d2c35b1           3 FKGEVVDAVVTQVNKVGLFTEIGP-MSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIF   81 (94)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEETT-EEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEETTEEE
T ss_pred             CCCCEEEEEEEEEEeeEEEEEecC-ceEEEEhhhcCcceeecccccceEEEcccceEEEeCCCEEEEEEEEEecCcCcce
Confidence            369999999999999999999975 899999999998863            3445579999999999999999998876


Q ss_pred             E
Q 005707          214 L  214 (681)
Q Consensus       214 L  214 (681)
                      +
T Consensus        82 ~   82 (94)
T d2c35b1          82 A   82 (94)
T ss_dssp             E
T ss_pred             E
Confidence            3

>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=98.63  E-value=8.3e-08  Score=81.26  Aligned_cols=67  Identities=15%  Similarity=0.186  Sum_probs=55.9

Q ss_pred             cCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccc--------cCCCCcccCCCEEEEEEEEEe--CCeEEE
Q 005707          262 KGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFAN--------MMGGSSLQVGQEVSVRVLRIS--RGQVTL  329 (681)
Q Consensus       262 vGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~--------~~p~~~fkVGqkVkVrVL~ID--kgKI~L  329 (681)
                      +|+++.|+|++++++|+||+++ .++||+|.+.|.+++.-+        ......|+.||.|+++|+.++  ++++..
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            6999999999999999999997 799999999998764211        123568999999999999995  677754

>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=98.51  E-value=2e-07  Score=79.42  Aligned_cols=67  Identities=15%  Similarity=0.317  Sum_probs=55.6

Q ss_pred             cCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCccc-ccc---------cCCCCcccCCCEEEEEEEEEe--CCeEEE
Q 005707          262 KGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDG-FAN---------MMGGSSLQVGQEVSVRVLRIS--RGQVTL  329 (681)
Q Consensus       262 vGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~-ie~---------~~p~~~fkVGqkVkVrVL~ID--kgKI~L  329 (681)
                      .|++++|+|++++++|+||+++ .++||+|.+.|.++. +..         ......|+.||.|++||+.++  .+++..
T Consensus         4 ~Gev~~g~V~~v~~~G~fv~lg-~~~~~v~~~~l~~d~~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~~I~~   82 (94)
T d2c35b1           4 KGEVVDAVVTQVNKVGLFTEIG-PMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFA   82 (94)
T ss_dssp             TTCEEEEEEEEEETTEEEEEET-TEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEETTEEEE
T ss_pred             CCCEEEEEEEEEEeeEEEEEec-CceEEEEhhhcCcceeecccccceEEEcccceEEEeCCCEEEEEEEEEecCcCcceE
Confidence            6999999999999999999997 799999999999875 211         122457999999999999985  677653

>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=98.45  E-value=1.7e-07  Score=79.70  Aligned_cols=73  Identities=16%  Similarity=0.097  Sum_probs=65.8

Q ss_pred             CCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEecc
Q 005707          145 LIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRES  219 (681)
Q Consensus       145 LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l  219 (681)
                      .++|++|.|+|+++..++.||+|+....|+||++++. ...++.+..|++||.|.|+|.++|+ .+++.||+...
T Consensus         4 P~~GD~ViG~V~~~~~~~~~VdI~s~~~a~L~~~~f~-g~~k~~r~~l~~GD~V~arV~~v~~-~~~~~Lscvd~   76 (88)
T d2nn6g1           4 PVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFE-GATKRNRPNVQVGDLIYGQFVVANK-DMEPEMVCIDS   76 (88)
T ss_dssp             CCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSS-CCSSCSSSSSCTTCEEEEEEEECCT-TSCCEEECSBT
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEcCCCeeEEEeHHHcC-ccccccCcccCCCCEEEEEEEEeCC-CCCEEEEEEcc
Confidence            5789999999999999999999999899999999996 4577888899999999999999985 57899998754

>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=98.32  E-value=5.5e-07  Score=76.54  Aligned_cols=72  Identities=14%  Similarity=0.079  Sum_probs=62.5

Q ss_pred             CccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC-CeEEEEEecc
Q 005707          260 FVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR-GQVTLTMKKE  334 (681)
Q Consensus       260 lkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk-gKI~LSLK~~  334 (681)
                      -++||+|-|+|++++.+|.||+|+....|+||.+++.+. ..  ..+..|++||.|.|+|+++++ +++.||+...
T Consensus         4 P~~GD~ViG~V~~~~~~~~~VdI~s~~~a~L~~~~f~g~-~k--~~r~~l~~GD~V~arV~~v~~~~~~~Lscvd~   76 (88)
T d2nn6g1           4 PVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGA-TK--RNRPNVQVGDLIYGQFVVANKDMEPEMVCIDS   76 (88)
T ss_dssp             CCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSSCC-SS--CSSSSSCTTCEEEEEEEECCTTSCCEEECSBT
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEcCCCeeEEEeHHHcCcc-cc--ccCcccCCCCEEEEEEEEeCCCCCEEEEEEcc
Confidence            358999999999999999999999999999999998653 22  336789999999999999984 7899998654

>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=98.31  E-value=1.3e-06  Score=71.69  Aligned_cols=63  Identities=22%  Similarity=0.231  Sum_probs=54.8

Q ss_pred             CCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCC--ceEEE
Q 005707          146 IPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETG--RISLT  215 (681)
Q Consensus       146 kvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekg--rI~LS  215 (681)
                      ++|+++.|+|.++.+.+++|+|++ ++|+||.++..      |.+.|++||.|+|.|.+|+...+  +|.||
T Consensus         7 ~~geiv~G~V~r~~~~~~~Vdlg~-~eaiLp~~eqi------p~E~~~~Gdrik~~i~~V~~~~kgpqI~lS   71 (72)
T d1hh2p1           7 LKGTVTTAEVIRVMGEWADIRIGK-LETRLPKKEWI------PGEEIKAGDLVKVYIIDVVKTTKGPKILVS   71 (72)
T ss_dssp             CTTCEEEEEEEEECSSEEEEEETT-EEEEEEGGGSC------TTCCCCTTCEEEEEEEEEEEETTEEEEEEE
T ss_pred             ccCcEEEEEEEEEcCCCEEEEECC-cEEECCHHHcC------CCCCCCCCCEEEEEEEEEEEcCCCCeEEEe
Confidence            579999999999999999999986 99999998864      46779999999999999987665  46665

>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=98.23  E-value=1.3e-06  Score=74.50  Aligned_cols=73  Identities=12%  Similarity=0.028  Sum_probs=66.2

Q ss_pred             CCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEec
Q 005707          145 LIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRE  218 (681)
Q Consensus       145 LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~  218 (681)
                      .++|++|-|+|..+...+.||+|++...|++|.+.......++.+..|++||.|.|+|.++|+ .+.+.||++.
T Consensus         5 P~~gD~ViG~V~~~~~~~~~vdI~~~~~~~L~~~~~f~g~~k~~r~~l~~GDlV~arV~~v~~-~~~~~Lsc~~   77 (90)
T d2ja9a1           5 PSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAEK-ELEAEIECFD   77 (90)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSSTTCCSSSCCCCCTTCEEEEEEEECCT-TSCCEEESSC
T ss_pred             CCCCCEEEEEEEEEeCCcEEEEcCCcchhhhhhhhccCccccccCCccCCCCEEEEEEEEECC-CCCEEEEEec
Confidence            578999999999999999999999889999998888888888889999999999999999985 5679999874

>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=98.08  E-value=3.5e-06  Score=71.74  Aligned_cols=72  Identities=14%  Similarity=0.055  Sum_probs=62.6

Q ss_pred             ccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC-CeEEEEEecc
Q 005707          261 VKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR-GQVTLTMKKE  334 (681)
Q Consensus       261 kvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk-gKI~LSLK~~  334 (681)
                      ++||+|-|+|.++..+|.||+|+....|++|.++..+....+  ....|.+||.|.|+|.++++ +++.||++..
T Consensus         6 ~~gD~ViG~V~~~~~~~~~vdI~~~~~~~L~~~~~f~g~~k~--~r~~l~~GDlV~arV~~v~~~~~~~Lsc~~~   78 (90)
T d2ja9a1           6 SVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKK--NRPTLQVGDLVYARVCTAEKELEAEIECFDS   78 (90)
T ss_dssp             CTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSSTTCCSS--SCCCCCTTCEEEEEEEECCTTSCCEEESSCT
T ss_pred             CCCCEEEEEEEEEeCCcEEEEcCCcchhhhhhhhccCccccc--cCCccCCCCEEEEEEEEECCCCCEEEEEecc
Confidence            689999999999999999999998899999988777766433  36789999999999999984 7899998543

>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=98.07  E-value=6.7e-06  Score=67.38  Aligned_cols=61  Identities=21%  Similarity=0.289  Sum_probs=53.0

Q ss_pred             ccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC----CeEEEE
Q 005707          261 VKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR----GQVTLT  330 (681)
Q Consensus       261 kvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk----gKI~LS  330 (681)
                      ++|+++.|+|..+.+.+++|+|+ +.+|+||.+|.        .|.+.|++||.|+|.|.+|++    -+|.||
T Consensus         7 ~~geiv~G~V~r~~~~~~~Vdlg-~~eaiLp~~eq--------ip~E~~~~Gdrik~~i~~V~~~~kgpqI~lS   71 (72)
T d1hh2p1           7 LKGTVTTAEVIRVMGEWADIRIG-KLETRLPKKEW--------IPGEEIKAGDLVKVYIIDVVKTTKGPKILVS   71 (72)
T ss_dssp             CTTCEEEEEEEEECSSEEEEEET-TEEEEEEGGGS--------CTTCCCCTTCEEEEEEEEEEEETTEEEEEEE
T ss_pred             ccCcEEEEEEEEEcCCCEEEEEC-CcEEECCHHHc--------CCCCCCCCCCEEEEEEEEEEEcCCCCeEEEe
Confidence            58999999999999999999998 89999998864        357899999999999999952    346665

>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=97.84  E-value=2e-05  Score=70.64  Aligned_cols=74  Identities=20%  Similarity=0.107  Sum_probs=63.1

Q ss_pred             CCCCcEEEEEEEEEecCeeEEEEC--------CCeEEEEeccccC--CccccCcccccccCCEEEEEEEEEeccCCceEE
Q 005707          145 LIPGATFTGKVRSIQPFGAFIDFG--------AFTDGLVHVSRLS--DNFVKDVGSIVSVGQEVKVRLIEANAETGRISL  214 (681)
Q Consensus       145 LkvGdIVeGkV~sV~d~GaFVdLg--------ggV~GLVPiSELS--~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~L  214 (681)
                      .++|++|.|+|+++....++|+|.        ....|++|.+++.  ..+..++.+.|++||.|+|+|+++...+..+.|
T Consensus         5 P~vGDiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~g~i~~~dvr~te~d~~~m~~~fr~GDiV~A~Vis~~~~~~~~~L   84 (125)
T d2nn6i1           5 PDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSNYLL   84 (125)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEETTTTEEEE
T ss_pred             CCCCCEEEEEEEEecCCEEEEEEeEecCcccccCccccccHHHcccchhhhhhHHHhcCCCCEEEEEEEEccCCCccEEE
Confidence            468999999999999999999993        3577999999985  334557889999999999999999876677999


Q ss_pred             EEec
Q 005707          215 TMRE  218 (681)
Q Consensus       215 SlK~  218 (681)
                      |++.
T Consensus        85 st~~   88 (125)
T d2nn6i1          85 TTAE   88 (125)
T ss_dssp             ECCS
T ss_pred             EecC
Confidence            9874

>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=97.83  E-value=1.6e-05  Score=65.75  Aligned_cols=64  Identities=13%  Similarity=0.240  Sum_probs=52.3

Q ss_pred             CCCcEEEEEEEEEecC----eeEEEEC---CCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCC--ceEEE
Q 005707          146 IPGATFTGKVRSIQPF----GAFIDFG---AFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETG--RISLT  215 (681)
Q Consensus       146 kvGdIVeGkV~sV~d~----GaFVdLg---ggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekg--rI~LS  215 (681)
                      ++|+++.|+|..+...    .++|+||   ++++|+||.++.-      |.+.|++||.|+|.|.+|+...+  .|.||
T Consensus         3 r~geiv~G~V~r~~~~~~~~~v~vdlG~~~~~~EaiLp~~eqi------p~E~y~~Gdrik~~i~~V~~~~kGp~IilS   75 (76)
T d2asba1           3 REGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV------PGESYEHGNRLRCYVVGVTRGAREPLITLS   75 (76)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSC------TTCCCCTTCEEEEEEEEEECCSSSCEEEEE
T ss_pred             ccceEEEEEEEEEecCCCceEEEEECCCCCCCEEEECCHHHcC------CCcccCCCCEEEEEEEEEEecCCCCEEEEe
Confidence            5799999999999753    2799997   5699999988763      45679999999999999987654  45665

>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=97.66  E-value=6.2e-05  Score=62.16  Aligned_cols=62  Identities=23%  Similarity=0.497  Sum_probs=51.3

Q ss_pred             ccCcEEEEEEEEEecce----EEEEeC---CCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC----CeEEE
Q 005707          261 VKGQDLEGTVKNLTRSG----AFISLP---EGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR----GQVTL  329 (681)
Q Consensus       261 kvGdIV~G~VknVt~~G----aFVeIg---~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk----gKI~L  329 (681)
                      ++|+++.|+|..+.+..    ++|+|+   ++++|+||.+|.        .|.+.|+.||.|+|.|.++++    -+|.|
T Consensus         3 r~geiv~G~V~r~~~~~~~~~v~vdlG~~~~~~EaiLp~~eq--------ip~E~y~~Gdrik~~i~~V~~~~kGp~Iil   74 (76)
T d2asba1           3 REGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQ--------VPGESYEHGNRLRCYVVGVTRGAREPLITL   74 (76)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGS--------CTTCCCCTTCEEEEEEEEEECCSSSCEEEE
T ss_pred             ccceEEEEEEEEEecCCCceEEEEECCCCCCCEEEECCHHHc--------CCCcccCCCCEEEEEEEEEEecCCCCEEEE
Confidence            57999999999997543    899998   589999998763        468899999999999999963    34666


Q ss_pred             E
Q 005707          330 T  330 (681)
Q Consensus       330 S  330 (681)
                      |
T Consensus        75 S   75 (76)
T d2asba1          75 S   75 (76)
T ss_dssp             E
T ss_pred             e
Confidence            5

>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=97.45  E-value=8.2e-05  Score=66.58  Aligned_cols=73  Identities=14%  Similarity=0.110  Sum_probs=58.9

Q ss_pred             ccCcEEEEEEEEEecceEEEEe--------CCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC--CeEEEE
Q 005707          261 VKGQDLEGTVKNLTRSGAFISL--------PEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR--GQVTLT  330 (681)
Q Consensus       261 kvGdIV~G~VknVt~~GaFVeI--------g~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk--gKI~LS  330 (681)
                      ++|++|.|+|+++....++|+|        .....|++|.+++...........+.|++||.|.++|+++..  ..+.||
T Consensus         6 ~vGDiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~g~i~~~dvr~te~d~~~m~~~fr~GDiV~A~Vis~~~~~~~~~Ls   85 (125)
T d2nn6i1           6 DVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSNYLLT   85 (125)
T ss_dssp             CTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEETTTTEEEEE
T ss_pred             CCCCEEEEEEEEecCCEEEEEEeEecCcccccCccccccHHHcccchhhhhhHHHhcCCCCEEEEEEEEccCCCccEEEE
Confidence            5799999999999999999998        346779999888744332233457899999999999999964  348898


Q ss_pred             Eec
Q 005707          331 MKK  333 (681)
Q Consensus       331 LK~  333 (681)
                      .+.
T Consensus        86 t~~   88 (125)
T d2nn6i1          86 TAE   88 (125)
T ss_dssp             CCS
T ss_pred             ecC
Confidence            854

>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=97.10  E-value=0.00041  Score=58.40  Aligned_cols=60  Identities=27%  Similarity=0.376  Sum_probs=48.8

Q ss_pred             cEEEEEEEEEecc--eEEEEeCCCeEEEEeCCCCCccccccc-------CCCCcccCCCEEEEEEEEEe
Q 005707          264 QDLEGTVKNLTRS--GAFISLPEGEEGFLPTSEESDDGFANM-------MGGSSLQVGQEVSVRVLRIS  323 (681)
Q Consensus       264 dIV~G~VknVt~~--GaFVeIg~GIeGLLpiSELSd~~ie~~-------~p~~~fkVGqkVkVrVL~ID  323 (681)
                      .++.|+|.+|.+.  ++||+++.+-.||||.+++.+..+...       +....++.||.|-|.|.+-.
T Consensus         2 NIY~G~V~~V~pgl~AAFVDiG~~k~gFL~~~di~~~~~~~~~~~~~~~~i~~~l~~G~~ilVQV~Ke~   70 (87)
T d1smxa_           2 NIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEE   70 (87)
T ss_dssp             CCEEEEEEEEEGGGTEEEEESSSSSCEEEEGGGSCGGGCSSCCCSSSCCCGGGTCCTTCEEEEEEEECC
T ss_pred             CcEEEEEEEecCCceEEEEEeCCCccceeEecccceeeeccccccccccchhhhccCCCeEEEEEeecc
Confidence            5789999999987  999999999999999999876543211       12457899999999998863

>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=97.06  E-value=0.00071  Score=56.92  Aligned_cols=69  Identities=25%  Similarity=0.497  Sum_probs=54.8

Q ss_pred             cEEEEEEEEEec--CeeEEEECCCeEEEEeccccCCccc---------cCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707          149 ATFTGKVRSIQP--FGAFIDFGAFTDGLVHVSRLSDNFV---------KDVGSIVSVGQEVKVRLIEANAETGRISLTMR  217 (681)
Q Consensus       149 dIVeGkV~sV~d--~GaFVdLgggV~GLVPiSELS~~~v---------~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK  217 (681)
                      .||.|+|.+|.+  .++|||+|.+..||||..++...+.         ....+.++.||.|-|.|+.=-..++--.||..
T Consensus         2 NIY~G~V~~V~pgl~AAFVDiG~~k~gFL~~~di~~~~~~~~~~~~~~~~i~~~l~~G~~ilVQV~Ke~~~~KGprlT~~   81 (87)
T d1smxa_           2 NIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTTF   81 (87)
T ss_dssp             CCEEEEEEEEEGGGTEEEEESSSSSCEEEEGGGSCGGGCSSCCCSSSCCCGGGTCCTTCEEEEEEEECCBTTBCCEEESC
T ss_pred             CcEEEEEEEecCCceEEEEEeCCCccceeEecccceeeeccccccccccchhhhccCCCeEEEEEeecccCCCCceEEEE
Confidence            479999999998  4999999999999999999876544         24456789999999999984444455556554

>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=88.99  E-value=0.72  Score=35.85  Aligned_cols=56  Identities=30%  Similarity=0.472  Sum_probs=41.8

Q ss_pred             EEEEEEEe---cceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCeEEE
Q 005707          267 EGTVKNLT---RSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQVTL  329 (681)
Q Consensus       267 ~G~VknVt---~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgKI~L  329 (681)
                      .|+|+-..   .|| ||...+|-+-|+|.+.+....      ...+..||.|++.+..-++|.-..
T Consensus         3 ~G~Vk~fn~~kGfG-FI~~d~g~DiF~H~s~l~~~~------~~~L~~G~~V~f~~~~~~~G~~A~   61 (66)
T d1c9oa_           3 RGKVKWFNNEKGYG-FIEVEGGSDVFVHFTAIQGEG------FKTLEEGQEVSFEIVQGNRGPQAA   61 (66)
T ss_dssp             EEEEEEEETTTTEE-EEEETTEEEEEEEGGGBCSSS------CCCCCTTCEEEEEEEEETTEEEEE
T ss_pred             CeEEEEEECCCCEE-EEEecCCceEEEEehhccccc------CCcCCCCCEEEEEEEECCCCCEEE
Confidence            58898874   345 788888899999999986543      246899999999987666654333

>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=88.30  E-value=0.63  Score=37.15  Aligned_cols=50  Identities=18%  Similarity=0.226  Sum_probs=41.3

Q ss_pred             CCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEE
Q 005707          143 EDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEA  205 (681)
Q Consensus       143 ~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~V  205 (681)
                      ...++|++=+|.+.+....|+|||+|-.--+++             ...|++|+.+.++|+++
T Consensus         6 g~p~vGEiReG~~~rr~~~g~~vDiGlD~la~~-------------k~~~~~~~r~tfrIvs~   55 (71)
T d1k3ra1           6 GKPVTGEYRQGLTVKRVKKGTLVDIGADKLALC-------------REKLTVNRIMSFRVVRL   55 (71)
T ss_dssp             SSCCTTCEEEEEEEEECSSSEEEESSSSCEEEC-------------SSCCCSSCEEEEEEEEC
T ss_pred             CCCcccceeeEEEEEecCCcEEEEecCCceeee-------------ecccccCcEEEEEEEEc
Confidence            568999999999999999999999986333332             23488999999999997

>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=88.07  E-value=0.61  Score=39.12  Aligned_cols=64  Identities=17%  Similarity=0.233  Sum_probs=48.3

Q ss_pred             cCCCCCCcEEEEEEEEEecCeeEEEECC--CeEEEE-eccccCCccccCcccccccCCEEEEEEEEEec
Q 005707          142 NEDLIPGATFTGKVRSIQPFGAFIDFGA--FTDGLV-HVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA  207 (681)
Q Consensus       142 ~~~LkvGdIVeGkV~sV~d~GaFVdLgg--gV~GLV-PiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~  207 (681)
                      ..+|-+|++.+|.|. +.++-++|.|.+  +.+++| ..-++-.++..++++.+ +|..|+|+|+.+|.
T Consensus        27 ~~~~~~G~V~kGiVy-~rd~~fyV~L~dY~g~eail~dY~n~~~dr~~klkkkL-VGKTIkVqVIRvDk   93 (102)
T d1jjga_          27 AMDLSPGSVHEGIVY-FKDGIFKVRLLGYEGHECILLDYLNYRQDTLDRLKERL-VGRVIKTRVVRADG   93 (102)
T ss_dssp             CCCCCSSCEEEEEEE-EETTEEEEECTTTSSCEEEECTTCCSSCCCCCHHHHHH-TTCEEEEEEEEECS
T ss_pred             ecccCCCcEeeeEEE-EeCCEEEEEecCCCCceeeeeehhhhhHHHHHHHHHHh-cCceEEEEEEEecc
Confidence            568999999999875 678888999943  577774 44444445556666655 89999999999983

>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=87.85  E-value=0.76  Score=37.65  Aligned_cols=75  Identities=16%  Similarity=0.266  Sum_probs=55.9

Q ss_pred             CCCCCCcEEEEEEEEEecCeeEEEECC--CeEEEEec-cccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEecc
Q 005707          143 EDLIPGATFTGKVRSIQPFGAFIDFGA--FTDGLVHV-SRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRES  219 (681)
Q Consensus       143 ~~LkvGdIVeGkV~sV~d~GaFVdLgg--gV~GLVPi-SELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l  219 (681)
                      .-..+|++.+|.|. ++++-++|.|.+  +.+++|-- -++..++..++++.+ +|.+|+++|+.+|.-+|-|.+.-|.+
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            34568999999875 678888999943  47777642 223334445555555 89999999999999999999988754

>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=87.10  E-value=0.7  Score=36.88  Aligned_cols=51  Identities=22%  Similarity=0.348  Sum_probs=42.0

Q ss_pred             cCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe
Q 005707          258 TKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS  323 (681)
Q Consensus       258 sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID  323 (681)
                      ...++|++=.|.+.+..+.|+||+++-+--++|.               ..|.+|+.++++|.++.
T Consensus         6 g~p~vGEiReG~~~rr~~~g~~vDiGlD~la~~k---------------~~~~~~~r~tfrIvs~~   56 (71)
T d1k3ra1           6 GKPVTGEYRQGLTVKRVKKGTLVDIGADKLALCR---------------EKLTVNRIMSFRVVRLG   56 (71)
T ss_dssp             SSCCTTCEEEEEEEEECSSSEEEESSSSCEEECS---------------SCCCSSCEEEEEEEECS
T ss_pred             CCCcccceeeEEEEEecCCcEEEEecCCceeeee---------------cccccCcEEEEEEEEcC
Confidence            5688999999999999999999999744444432               46799999999999983

>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=85.11  E-value=2  Score=35.20  Aligned_cols=54  Identities=17%  Similarity=0.225  Sum_probs=40.6

Q ss_pred             CCCcEEEEEEEEEec-CeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEE
Q 005707          146 IPGATFTGKVRSIQP-FGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIE  204 (681)
Q Consensus       146 kvGdIVeGkV~sV~d-~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~  204 (681)
                      ..+....|+|...++ ||++-...+.-+.|+|++++....     ..+++||.|.+.|..
T Consensus        14 ~~~~r~~G~I~~~~~gfGFI~~~~~~~dvF~H~s~~~~~~-----~~l~~G~~VeF~v~~   68 (89)
T d1wfqa_          14 SAALRETGVIEKLLTSYGFIQCSERQARLFFHCSQYNGNL-----QDLKVGDDVEFEVSS   68 (89)
T ss_dssp             SCCCEEEEEEEEECSSEEEEEETTTTEEEEEETTTCSSCT-----TTCCTTCCEEEEEEE
T ss_pred             CccceEEEEEEEecCccceEEeCCCCceEEEEeehhhccC-----CcccCCCEEEEEEEE
Confidence            456778999999975 444444456679999999996432     347899999999876

>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=83.05  E-value=1.9  Score=36.03  Aligned_cols=70  Identities=21%  Similarity=0.223  Sum_probs=48.0

Q ss_pred             ccccCCccCcEEEEEEEEEecceEEEEeCC--CeEEEEeC-CCCCcccccccCCCCcccCCCEEEEEEEEEeCCeEE
Q 005707          255 MKTTKFVKGQDLEGTVKNLTRSGAFISLPE--GEEGFLPT-SEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQVT  328 (681)
Q Consensus       255 ~~~sklkvGdIV~G~VknVt~~GaFVeIg~--GIeGLLpi-SELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgKI~  328 (681)
                      ....++-+|++.+|.|. +.++-++|.|.+  |.++++-- -.+..++.+.+  ++. =+|..|+++|+++|+.-|.
T Consensus        25 ~~~~~~~~G~V~kGiVy-~rd~~fyV~L~dY~g~eail~dY~n~~~dr~~kl--kkk-LVGKTIkVqVIRvDklYID   97 (102)
T d1jjga_          25 TSAMDLSPGSVHEGIVY-FKDGIFKVRLLGYEGHECILLDYLNYRQDTLDRL--KER-LVGRVIKTRVVRADGLYVD   97 (102)
T ss_dssp             SCCCCCCSSCEEEEEEE-EETTEEEEECTTTSSCEEEECTTCCSSCCCCCHH--HHH-HTTCEEEEEEEEECSSEEE
T ss_pred             eeecccCCCcEeeeEEE-EeCCEEEEEecCCCCceeeeeehhhhhHHHHHHH--HHH-hcCceEEEEEEEeccEEEE
Confidence            45678999999999886 567778899875  88888542 22222222211  122 3799999999999976443

>d1g6pa_ b.40.4.5 (A:) Major cold shock protein {Thermotoga maritima [TaxId: 2336]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Major cold shock protein
species: Thermotoga maritima [TaxId: 2336]

Probab=83.05  E-value=0.64  Score=36.18  Aligned_cols=54  Identities=30%  Similarity=0.379  Sum_probs=39.4

Q ss_pred             EEEEEEEe---cceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCeE
Q 005707          267 EGTVKNLT---RSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQV  327 (681)
Q Consensus       267 ~G~VknVt---~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgKI  327 (681)
                      .|+|+...   -|| ||.-.+|-+-|+|.+.+....      ...+..||.|.+.+..-++|..
T Consensus         2 ~G~Vk~f~~~kGfG-FI~~~~g~diFvH~s~l~~~g------~~~l~~G~~V~f~~~~~~~G~~   58 (66)
T d1g6pa_           2 RGKVKWFDSKKGYG-FITKDEGGDVFVHWSAIEMEG------FKTLKEGQVVEFEIQEGKKGPQ   58 (66)
T ss_dssp             CEEEEEEETTTTEE-EEEETTSCBCBBCSSSSCCSS------CCCCCSSSEEEEEEECSSSCCE
T ss_pred             eEEEEEEeCCCCee-EEEecCCceEEEEhHHhcccC------CCcCCCCCEEEEEEEECCCCCE
Confidence            58888763   345 677677889999999987543      2458999999998755455543

>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=80.56  E-value=5.6  Score=32.34  Aligned_cols=60  Identities=23%  Similarity=0.292  Sum_probs=45.0

Q ss_pred             ccCCccCcEEEEEEEEEec-ceEEEEeCC-CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC
Q 005707          257 TTKFVKGQDLEGTVKNLTR-SGAFISLPE-GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR  324 (681)
Q Consensus       257 ~sklkvGdIV~G~VknVt~-~GaFVeIg~-GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk  324 (681)
                      ...-..+....|+|+...+ || ||.-.+ +.+-|+|.+.+...       ...+++||.|++.|..-++
T Consensus        10 ~~~~~~~~r~~G~I~~~~~gfG-FI~~~~~~~dvF~H~s~~~~~-------~~~l~~G~~VeF~v~~~~k   71 (89)
T d1wfqa_          10 PNGTSAALRETGVIEKLLTSYG-FIQCSERQARLFFHCSQYNGN-------LQDLKVGDDVEFEVSSDRR   71 (89)
T ss_dssp             SCSSSCCCEEEEEEEEECSSEE-EEEETTTTEEEEEETTTCSSC-------TTTCCTTCCEEEEEEECSS
T ss_pred             CCCCCccceEEEEEEEecCccc-eEEeCCCCceEEEEeehhhcc-------CCcccCCCEEEEEEEECCC
Confidence            3445567788999999964 45 787665 56899999998643       2568999999999766544

>d3d31a1 b.40.6.3 (A:230-348) Sulfate/molybdate ABC transporter, ATP-binding protein {Methanosarcina acetivorans [TaxId: 2214]}

class: All beta proteins
fold: OB-fold
superfamily: MOP-like
family: ABC-transporter additional domain
domain: Sulfate/molybdate ABC transporter, ATP-binding protein
species: Methanosarcina acetivorans [TaxId: 2214]

Probab=80.34  E-value=11  Score=30.15  Aligned_cols=103  Identities=19%  Similarity=0.145  Sum_probs=59.9

Q ss_pred             EEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccchhhHhhhhc
Q 005707          150 TFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDISKLQQQK  229 (681)
Q Consensus       150 IVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~dp~ek~~~  229 (681)
                      ++.|+|.+..+..+.|++++ ..-.++.             .+.+|+.+.+.|-   +  ..|.++...           
T Consensus         4 ~l~g~v~~~~~~~~~v~~~~-~~l~~~~-------------~~~~g~~v~~~iR---P--E~i~l~~~~-----------   53 (119)
T d3d31a1           4 VLKGRVISAEQGLLRIRVGE-VVIDAAG-------------DMEVGDQVYAFLR---P--ENIALSKSS-----------   53 (119)
T ss_dssp             EEEEEEEEEETTEEEEEETT-EEEEEES-------------SCCTTCEEEEEEC---G--GGEEEESSC-----------
T ss_pred             EEEEEEEEecCCEEEEEECC-EEEECCC-------------CCCCCCEEEEEEc---h--HHccccccc-----------
Confidence            58999999999889999976 4443331             1457887654442   2  233333210           


Q ss_pred             cccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEEE----eCCCeEEEEeCCCCCcccccccCC
Q 005707          230 DATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFIS----LPEGEEGFLPTSEESDDGFANMMG  305 (681)
Q Consensus       230 ~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFVe----Ig~GIeGLLpiSELSd~~ie~~~p  305 (681)
                                                  ..-.....+.|+|..+...|..+.    ++..+...+....  ..       
T Consensus        54 ----------------------------~~~~~~N~l~g~V~~~~~~G~~~~v~l~~g~~~~~~v~~~~--~~-------   96 (119)
T d3d31a1          54 ----------------------------TQSSIRNSLQGRVTEAWVLGALVRVKVDCGVPLNVLITRRS--AE-------   96 (119)
T ss_dssp             ----------------------------CCBSCSEEEEEEEEEEEECSSEEEEEEESSSEEEEEEETTH--HH-------
T ss_pred             ----------------------------cccccceEEEEEEEEEEECCCeEEEEEEeCCEEEEEEecCc--hh-------
Confidence                                        001122478999999988775544    3333333343221  11       


Q ss_pred             CCcccCCCEEEEEE
Q 005707          306 GSSLQVGQEVSVRV  319 (681)
Q Consensus       306 ~~~fkVGqkVkVrV  319 (681)
                      ...+++|+.|.+.+
T Consensus        97 ~~~l~~G~~V~v~~  110 (119)
T d3d31a1          97 EMELSPGVQIYARF  110 (119)
T ss_dssp             HSCCCTTCEEEEEE
T ss_pred             hcCcCCCCEEEEEE
Confidence            23578999998653

>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=80.10  E-value=2.6  Score=33.76  Aligned_cols=56  Identities=20%  Similarity=0.255  Sum_probs=40.5

Q ss_pred             cEEEEEEEEEec---CeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEE
Q 005707          149 ATFTGKVRSIQP---FGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIE  204 (681)
Q Consensus       149 dIVeGkV~sV~d---~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~  204 (681)
                      ..+.|+|+-..+   ||++..-.++-+.|+|.+.|...-....-..+..|+.|.+.+..
T Consensus         7 ~r~~G~VKwfn~~KGfGFI~~ddg~~DvFvH~s~i~~~g~~~~~~~L~~G~~V~f~~~~   65 (79)
T d1h95a_           7 TKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVE   65 (79)
T ss_dssp             EEEEEEEEEEETTTTEEEEEEGGGTEEEEEEGGGBCSCCCSCCSCSCCSSCEEEEEEEE
T ss_pred             CcccEEEEEEcCCCCeEEEEECCCCccEEEEhhHcccCCCcceeeecCCCCEEEEEEEe
Confidence            458899998863   56555456668999999999765322223346789999998876