Citrus Sinensis ID: 035754

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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-----
Protein Sequence
LQTIAFEHCTNHDLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLKYQNAVHYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNVYKWTTASHPCLA
Secondary Structure (PSIPRED)
cccccccHHcccccHHcccccHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHccHHHHHHHHHHHcccHHHHHHHHccccHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHccccccHHHHHHHcccccccHHHHHHHHHHHHHHHHccccHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHccccHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHcccHHHHHHHHHcccHHHHHHHHcccHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHcccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHccHHHHHHccccHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHHHHHccccEEEEccccccHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHccHHHHcccccHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHcccHHHHHHHHHHcccHHHHHHHccHHHHHHHHHHHcccHHHHHHHHHHHHHHHHcHHHHHHccccHHHHHHHHHHHccccc
Coil and Loop (DISEMBL)
lqtiafehctnhdlfslaqdqegsQYLQenlssgdsrildKLFWVVSGFTFElmsgqygrfVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMmtkpgssvilqclepsynhkndfIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAaslsrhrsgnyvvqHVLSLEDPFLIDAICFALRGhyvdlsltkcgsFVVQKCLKYQNAVHYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSnvykwttashpcla
Flexible Loop (DISEMBL)
lqtiafehctnhdlfslaQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLKYQNAVHYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNVYKWTtashpcla
Low Complexity Region (SEG)
LQTIAFEHCTNHDLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLKYQNAVHYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNVYKWTTASHPCLA
Disordered region (IsUnstruct)
****AFEHCTNHDLFSL******************SRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLKYQNAVHYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNVYKWTTA******
Disordered Region (DISOPRED)
**TIAFEHCTNHDLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLKYQNAVHYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNVYKWTTASHPCL*
Disordered Region (DISEMBL)
LQTIAFEHCTNHDLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLKYQNAVHYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNVYKWTTASHPCLA
Disordered Region (DISPRO)
LQTIAFEHCTNHDLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLKYQNAVHYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNVYKWTTASHPCL*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
LQTIAFEHCTNHDLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLKYQNAVHYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNVYKWTTASHPCLA
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	335	2.2.26 [Sep-21-2011]
Q9LVC3	596	Pumilio homolog 12 OS=Ara	yes	no	0.910	0.511	0.336	3e-40
Q9LM20	515	Putative pumilio homolog	no	no	0.910	0.592	0.314	2e-32
Q9C9R6	650	Putative pumilio homolog	no	no	0.910	0.469	0.298	2e-29
Q9LDW3	556	Pumilio homolog 11 OS=Ara	no	no	0.904	0.544	0.310	3e-29
Q9LXC5	517	Putative pumilio homolog	no	no	0.746	0.483	0.305	6e-27
Q1PFN9	564	Pumilio homolog 9 OS=Arab	no	no	0.871	0.517	0.296	8e-26
Q9LP21	528	Putative pumilio homolog	no	no	0.871	0.553	0.304	1e-24
Q9LVG3	327	Pumilio homolog 18 OS=Ara	no	no	0.8	0.819	0.315	9e-23
Q92359	681	Pumilio domain-containing	yes	no	0.931	0.458	0.269	6e-22
Q9LSS8	327	Putative pumilio homolog	no	no	0.8	0.819	0.311	8e-22

>sp|Q9LVC3|PUM12_ARATH Pumilio homolog 12 OS=Arabidopsis thaliana GN=APUM12 PE=2 SV=2

 Score =  165 bits (418), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 105/312 (33%), Positives = 172/312 (55%), Gaps = 7/312 (2%)

Query: 14  LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
           ++ LA+DQ G ++LQ   S  D   ++ +F  +  +  ELM   +G ++  K +E CNE 
Sbjct: 282 IYYLAKDQHGCRFLQRIFSEKDGNDIEMIFNEIIDYISELMMDPFGNYLVQKLLEVCNED 341

Query: 74  QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMT 133
           Q   I+  IT +  L +  S D  G+ +V+K+++  A     +  ++SALK     L+  
Sbjct: 342 QRMQIVHSITRKPGLLIKISCDMHGTRAVQKIVET-AKREEEISIIISALKHGIVHLIKN 400

Query: 134 KPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILH 193
             G+ V+ +CL+    +   F+++AA+ HC+ LA    GC  L   +   +G +++ ++ 
Sbjct: 401 VNGNHVVQRCLQYLLPYCGKFLFEAAITHCVELATDRHGCCVLQKCLGYSEGEQKQHLVS 460

Query: 194 LISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLK 253
            I+ NA  LS+   GNYV+Q+V  L+  +    I   L G+Y +LS+ KC S VV+KCLK
Sbjct: 461 EIASNALLLSQDPFGNYVLQYVFELQLQWATFEILEQLEGNYTELSMQKCSSNVVEKCLK 520

Query: 254 YQNAVH--YIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHL 311
             +  H   II EL+N  ++ QV  D YGNYVIQ AL    +Q + +VH  LV  ++ ++
Sbjct: 521 LADDKHRARIIRELINYGRLDQVMLDPYGNYVIQAAL----KQSKGNVHALLVDAIKLNI 576

Query: 312 AALRVMKYGSNV 323
           ++LR   YG  V
Sbjct: 577 SSLRTNPYGKKV 588

Sequence-specific RNA-binding protein that regulates translation and mRNA stability by binding the 3'-UTR of target mRNAs.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9LM20|PUM8_ARATH Putative pumilio homolog 8, chloroplastic OS=Arabidopsis thaliana GN=APUM8 PE=3 SV=2

 Score =  139 bits (351), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 98/312 (31%), Positives = 164/312 (52%), Gaps = 7/312 (2%)

Query: 14  LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
           ++ +A+DQ G ++LQ     G +     +F  V     ELM   +G ++  K ++ CNE 
Sbjct: 203 VYFMAKDQHGCRFLQWIFEDGSALDALVIFSEVIPHVVELMMDPFGNYLMQKLLDVCNEE 262

Query: 74  QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMT 133
           Q   IIL +T +    +  S++ +G+  V++L++ +     +   V SAL+  F  L+  
Sbjct: 263 QRTQIILMVTSEPGQLIRISLNAYGTRVVQRLVESIKTRKQISL-VKSALRPGFLNLIRD 321

Query: 134 KPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILH 193
             G+ VI +CL+      N+FI++ A + C+ +A H  GC  L   I    G +R++++ 
Sbjct: 322 LNGNHVIQRCLQCLSTEDNEFIFEDATKFCIDIATHRHGCCVLQKCIAYSSGLQREKLVT 381

Query: 194 LISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLK 253
            IS N+  L++   GNY VQ VL L D   I A+   L+GHYV+LS+ K  S +V++CL 
Sbjct: 382 EISRNSLFLAQDPYGNYAVQFVLELRDFSAIAAMLAQLKGHYVELSMQKFSSHMVERCLT 441

Query: 254 Y-QNAVHYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLA 312
           +   +   I+ EL++      +  D Y N+VIQ ALA T    + S+H  LV  ++ H +
Sbjct: 442 HCPESRPQIVRELISVPHFDILIQDPYANFVIQAALAVT----KGSLHATLVEVIRPH-S 496

Query: 313 ALRVMKYGSNVY 324
            LR   Y   ++
Sbjct: 497 ILRNNPYCKRIF 508

Sequence-specific RNA-binding protein that regulates translation and mRNA stability by binding the 3'-UTR of target mRNAs.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9C9R6|PUM7_ARATH Putative pumilio homolog 7, chloroplastic OS=Arabidopsis thaliana GN=APUM7 PE=3 SV=2

 Score =  130 bits (326), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 93/312 (29%), Positives = 156/312 (50%), Gaps = 7/312 (2%)

Query: 14  LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
           ++ +A+DQ G ++LQ     G S     +F  V     ELM   +G ++  K ++ C E 
Sbjct: 338 VYLMAKDQHGCRFLQRIFDEGTSVDAMIIFNEVIAHVVELMMDPFGNYLMQKLLDVCTEE 397

Query: 74  QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMT 133
           Q   I+L  T +    +  S++ +G+  V++L++ +     +   V  AL+  F  L+  
Sbjct: 398 QRTQIVLVATEEPGQLIRISLNAYGTRVVQRLVETIRSGKQISL-VKLALRPGFLDLIKD 456

Query: 134 KPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILH 193
             G+ VI +CL+      N FI+ AA + C  +A H  GC  L   I      +R++++ 
Sbjct: 457 LNGNHVIQRCLQCLSTEDNKFIFDAATKFCTEIATHRHGCCVLQKCIAYSMRQQREKLIA 516

Query: 194 LISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLK 253
            IS N+  L++   GNY VQ V+ L  P  +  +   L+GHYV LS+ K  S +V++CL 
Sbjct: 517 EISRNSLLLAQDPFGNYAVQFVIELRIPSAVAMMLAQLKGHYVQLSMQKFSSHMVERCLM 576

Query: 254 Y-QNAVHYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLA 312
           +   +   I+ EL++     Q+  D Y N+VIQ ALA T    +  +H  LV  ++ H +
Sbjct: 577 HCPESRPQIVRELVSVPHFDQLLQDPYANFVIQAALAAT----KGPLHASLVEVIRPH-S 631

Query: 313 ALRVMKYGSNVY 324
            LR   Y   ++
Sbjct: 632 ILRNNPYCKRIF 643

Sequence-specific RNA-binding protein that regulates translation and mRNA stability by binding the 3'-UTR of target mRNAs.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LDW3|PUM11_ARATH Pumilio homolog 11 OS=Arabidopsis thaliana GN=APUM11 PE=3 SV=2

 Score =  129 bits (324), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 97/312 (31%), Positives = 165/312 (52%), Gaps = 9/312 (2%)

Query: 14  LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
           ++ +A+DQ G + LQ+ +  G+   +  +F  V     EL +  +G ++  K IE CNE 
Sbjct: 246 VYLMAKDQLGCRLLQKFVDEGNFVDVMIIFKEVINNVIELGTDPFGNYLIQKLIEVCNEE 305

Query: 74  QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMT 133
           Q   I++++T +  L +  S++ +G+  V+KLI+ V      +  V SAL   F  L   
Sbjct: 306 QRTQILIRLTSKPGLLVKISINNYGTRVVQKLIETVT-TKEQISLVKSALVPGFLSLFRE 364

Query: 134 KPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILH 193
             G+ VIL CL+    + N FI +AA + C+ +A    GC  L   +    G + ++++ 
Sbjct: 365 LNGNHVILNCLKFFSPNDNKFILEAATKFCIEIATTRHGCCVLQRCVSYSVGEQHEKLVD 424

Query: 194 LISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLK 253
            IS N+  L++   GNY+VQ++  +E       + F LRG+YV L+  K GS VV+KCL+
Sbjct: 425 EISRNSLLLAQDPFGNYLVQYI--IEKKVGGVNVLFELRGNYVKLATQKFGSHVVEKCLR 482

Query: 254 -YQNAVHYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLA 312
            Y  +   I+ EL++      +  D Y NYVIQ AL++T    +  V   LV K++++  
Sbjct: 483 YYPESRSQIVNELVSVLNFGYLLQDPYANYVIQCALSKT----KGFVRASLVEKVRRY-E 537

Query: 313 ALRVMKYGSNVY 324
            L++  Y   ++
Sbjct: 538 NLKMTPYCKRIF 549

Sequence-specific RNA-binding protein that regulates translation and mRNA stability by binding the 3'-UTR of target mRNAs.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LXC5|PUM21_ARATH Putative pumilio homolog 21 OS=Arabidopsis thaliana GN=APUM21 PE=3 SV=1

 Score =  121 bits (304), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 78/255 (30%), Positives = 136/255 (53%), Gaps = 5/255 (1%)

Query: 72  ESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLM 131
           ES L  I   +T   ++FL  + +++GS +++ L +    L  LL+    A+   F  LM
Sbjct: 246 ESHLFKIGSALTTTKRIFLHLATNQYGSQALRILFRRSPSLDHLLF---CAVDTNFFLLM 302

Query: 132 MTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQI 191
             K G  +I+  +      K + +Y+   E+ L+LA  E GC+ LNN +  ++G  R  I
Sbjct: 303 SDKYGRGLIIPAIRAVDKTKKESLYKLTYEYTLHLARLETGCLALNNVLQEIRGIYRDLI 362

Query: 192 LHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKC 251
              ++ NA  LS    G +VVQ++L L++P    AI   LRG +  L++ + GS+VV+KC
Sbjct: 363 FECVANNADWLSFDPYGTHVVQNILILQNPVATTAIAERLRGSFFRLAMERQGSYVVEKC 422

Query: 252 LKYQNAVHYIIEELL-NSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQH 310
           LK   A   ++EE   N+ + +++  DK+GN+V+Q+AL     ++   + +  V KL+ H
Sbjct: 423 LKSDFARDQVLEEFRGNAKEWVRMTTDKFGNFVVQSALRVMKEKEMRPLLREFVEKLRPH 482

Query: 311 LAALRVMKYGSNVYK 325
              + + + G N  +
Sbjct: 483 FGKMEIGR-GRNTLR 496

Sequence-specific RNA-binding protein that regulates translation and mRNA stability by binding the 3'-UTR of target mRNAs.

Arabidopsis thaliana (taxid: 3702)

>sp|Q1PFN9|PUM9_ARATH Pumilio homolog 9 OS=Arabidopsis thaliana GN=APUM9 PE=2 SV=1

 Score =  117 bits (294), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 93/314 (29%), Positives = 155/314 (49%), Gaps = 22/314 (7%)

Query: 10  TNHDLFSL----------AQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYG 59
           +N+DL S+          A+DQ G + LQ+ +  G       +   +     EL    +G
Sbjct: 240 SNNDLVSMVEIYGSVNLMAKDQIGCRVLQKLVEEGTFHEAKVILLAIIDHVVELSMDPFG 299

Query: 60  RFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHV 119
            ++  K  +  +E Q  LI+  +T   +  +   ++ +G+  V+K+I+ V     +   V
Sbjct: 300 NYIVQKLFDVSDEEQRTLIVSVLTSNPRELIRICLNTYGTRVVQKMIETVKTKQQIAL-V 358

Query: 120 MSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNF 179
            S LK  F  L+    G+ VI  CL+    + N+F+ +AA ++C  +A H  GC  L   
Sbjct: 359 KSGLKPGFLALVKDLNGNHVIQSCLQTLGPNDNEFVLEAATKYCAEIAIHRHGCCVLQCC 418

Query: 180 IDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAI--CFALRGHYVD 237
           I N  G +R++++  IS N+  LS+   GNYVVQ+++  +    + A+      R HY +
Sbjct: 419 ISNSVGLQRERLVAEISRNSLHLSQDPFGNYVVQYLIDQQ----VSAVKLLVQFRMHYAE 474

Query: 238 LSLTKCGSFVVQKCL-KYQNAVHYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDR 296
           L+  K  S V++KCL KY  +   I+ ELL       +  D Y NYVIQTAL+ T    +
Sbjct: 475 LATQKFSSHVIEKCLRKYPESRAEIVRELLCVPNFEYLLQDPYANYVIQTALSVT----K 530

Query: 297 LSVHQRLVTKLQQH 310
             V  +LV K+ ++
Sbjct: 531 GPVRAKLVAKVYRY 544

Sequence-specific RNA-binding protein that regulates translation and mRNA stability by binding the 3'-UTR of target mRNAs.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LP21|PUM10_ARATH Putative pumilio homolog 10 OS=Arabidopsis thaliana GN=APUM10 PE=3 SV=2

 Score =  114 bits (284), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 95/312 (30%), Positives = 157/312 (50%), Gaps = 20/312 (6%)

Query: 17  LAQDQEGSQYLQENLSSG---DSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
           +A+DQ G + LQ+ +  G   DS+++   F  +     EL     G ++  K +   +E 
Sbjct: 221 MARDQIGCRALQKLVEEGTVLDSKVI---FLEIIDHVVELSMDPLGNYIVQKLLVVSDEE 277

Query: 74  QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMT 133
           Q  +I+  +T + +  +   ++  G+  ++K+IK V     +   V SAL+  F  L+  
Sbjct: 278 QRTMIVSVLTSKPRELIKICLNTNGTRVIQKMIKTVKTKQQIAL-VKSALEPGFLVLVND 336

Query: 134 KPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILH 193
             G  V+  CLE    + N F+ +AA E+C  LA H+ GC  L   + N  G + ++++ 
Sbjct: 337 SNGYHVLQSCLEFLVPNDNKFVVEAATEYCAQLATHQYGCYVLQCSLINTVGLQHERLVA 396

Query: 194 LISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCL- 252
            IS ++  LS+   GNYVVQ ++  +   +   +    R H ++L+  K  S V++KCL 
Sbjct: 397 EISRDSLRLSQDPFGNYVVQCLIDQQVSSV--NLLLPFRTHCIELATQKFSSHVIEKCLR 454

Query: 253 KYQNAVHYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLA 312
           KY  +   I+ ELL+     Q+  D Y NYVIQTAL+ T    + +V  RLV K++    
Sbjct: 455 KYPESRAEIVRELLSYPNFEQLLQDPYANYVIQTALSVT----KGAVRARLVEKVK---- 506

Query: 313 ALRVMKYGSNVY 324
             R  K  SN Y
Sbjct: 507 --RFGKLQSNPY 516

Sequence-specific RNA-binding protein that regulates translation and mRNA stability by binding the 3'-UTR of target mRNAs.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LVG3|PUM18_ARATH Pumilio homolog 18 OS=Arabidopsis thaliana GN=APUM18 PE=2 SV=1

 Score =  107 bits (268), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 87/276 (31%), Positives = 144/276 (52%), Gaps = 8/276 (2%)

Query: 51  FELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVA 110
           F LM+   G   F + I + ++++L  +   +T     F+     KFGS  V+KL+    
Sbjct: 46  FNLMTDGDGVSYFKEMISNSDKTELQRMASLLTSDSDYFMSIVTTKFGSRRVQKLLGKSD 105

Query: 111 HLPPLLYHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHE 170
            +        +A+ R F  +   K  S V ++ +          +Y+  L H L LAC +
Sbjct: 106 DVDAFF---CAAILRRFLHITTDKYASYVTIRAMVVFDKVMKKALYERILYHALDLACDQ 162

Query: 171 QGCINLNNFIDNMKGSR-RKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICF 229
            GCI LN+ I +      R Q+L L++ NA  LS   SGN+VVQHVL+L D   I  I  
Sbjct: 163 HGCIALNDIITDADDPYYRDQLLELVASNALRLSNDASGNFVVQHVLTLYDSRCIHNIAV 222

Query: 230 ALRGHYVDLSLTKCGSFVVQKCLKYQNAVHYIIEELL--NSDQILQVANDKYGNYVIQTA 287
            L G  ++LS  K GS++V+K L+ + ++  ++ ELL  + D+++++A +++GN+V+  A
Sbjct: 223 NLYGQCIELSFKKYGSYIVEKLLEVEESMVVVVVELLGCDGDRLMRLARNEFGNFVVVKA 282

Query: 288 LAETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNV 323
           L  T +  R+ +   LV KL   +  LR   +GSN+
Sbjct: 283 LRFT-KMSRMDLFWGLVQKLMPFIRLLR-RSHGSNI 316

Sequence-specific RNA-binding protein that regulates translation and mRNA stability by binding the 3'-UTR of target mRNAs.

Arabidopsis thaliana (taxid: 3702)

>sp|Q92359|YDHE_SCHPO Pumilio domain-containing protein C6G9.14 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC6G9.14 PE=4 SV=1

 Score =  105 bits (261), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 88/326 (26%), Positives = 155/326 (47%), Gaps = 14/326 (4%)

Query: 11  NHDLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESC 70
           N ++ S  +DQ G +YLQ  L   +   +D +F     +   LM   +G ++  K  E  
Sbjct: 345 NSNILSFCKDQHGCRYLQRLLEKKNQSHIDAVFAETHPYLAVLMVDAFGNYLCQKLFEHA 404

Query: 71  NESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFL 130
           +E+Q +  I  I  +    +  S +  G+ +++K+I +V+  P  +  +++AL+     L
Sbjct: 405 SEAQRSTFIQIIAPK---LVPISFNMHGTRALQKIIDLVSS-PDQISCIVNALRPNVVLL 460

Query: 131 MMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQ 190
                G+ VI +CL         FI+ A  E  L ++ H  GC  +    D+   ++ +Q
Sbjct: 461 TKDLNGNHVIQKCLNKFSQEDCQFIFDAICEDPLDVSTHRHGCCVVQRCFDHASPAQIEQ 520

Query: 191 ILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQK 250
           ++  I  +A +L +   GNYV+Q+VL L +P   +AI          LS  K  S V++K
Sbjct: 521 LVEHIVPHALTLVQDAFGNYVLQYVLELNNPNHTEAIISYFLYKVRALSTQKFSSNVMEK 580

Query: 251 CLKYQNAV--HYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQR--LVTK 306
           C+ +  A     +I EL++   + ++  D + NYVIQTAL      D  SV QR  LV +
Sbjct: 581 CIFFAPAAIKEKLISELMDEKHLPKLLRDSFANYVIQTAL------DNASVKQRAELVER 634

Query: 307 LQQHLAALRVMKYGSNVYKWTTASHP 332
           ++  + +++    G  +       HP
Sbjct: 635 IKPLIPSIKNTPCGRRILSKLERRHP 660

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

>sp|Q9LSS8|PUM19_ARATH Putative pumilio homolog 19 OS=Arabidopsis thaliana GN=APUM19 PE=3 SV=2

 Score =  104 bits (260), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 143/276 (51%), Gaps = 8/276 (2%)

Query: 51  FELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVA 110
           F LM+   G   F + I   ++++L  +   +T     F+     KFGS  V+KL+    
Sbjct: 46  FNLMTDGDGVSYFKEMISKSDKTELQRMASLLTSDSDYFMSIVTTKFGSRRVQKLLGKSD 105

Query: 111 HLPPLLYHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHE 170
            +        +A+ R F  +   K  S V ++ +          +Y+  L H L LAC +
Sbjct: 106 DVDAFF---CAAILRRFLHITTDKYASYVTIRAMVVFDKVMKKALYERILYHALDLACDQ 162

Query: 171 QGCINLNNFIDNMKGSR-RKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICF 229
            GCI LN+ I +      R Q+L L+  NA  LS   SGN+VVQHVL+L D   I  I  
Sbjct: 163 HGCIALNDIITDADDPYYRDQLLELVVSNALRLSNDASGNFVVQHVLTLYDSRCIHNIAV 222

Query: 230 ALRGHYVDLSLTKCGSFVVQKCLKYQNAVHYIIEELL--NSDQILQVANDKYGNYVIQTA 287
            L G  ++LS  K GS++V+K L+ + ++  ++ ELL  + D+++++A +++GN+V+  A
Sbjct: 223 NLYGQCIELSFKKYGSYIVEKLLEVEESMVVVVVELLGCDGDRLMRLARNEFGNFVVVKA 282

Query: 288 LAETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNV 323
           L  T ++ R+ +   LV KL   +  LR   +G+N+
Sbjct: 283 LRFT-KEMRMDLFWGLVQKLMPFIHLLR-RSHGNNI 316

Sequence-specific RNA-binding protein that regulates translation and mRNA stability by binding the 3'-UTR of target mRNAs.

Arabidopsis thaliana (taxid: 3702)

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	335
255553119	471	RNA binding protein, putative [Ricinus c	0.949	0.675	0.412	3e-51
255544718	483	conserved hypothetical protein [Ricinus	0.931	0.645	0.404	7e-50
224117628	502	predicted protein [Populus trichocarpa]	0.919	0.613	0.356	2e-42
147798084	507	hypothetical protein VITISV_039435 [Viti	0.779	0.514	0.378	3e-42
255564824	771	RNA binding protein, putative [Ricinus c	0.910	0.395	0.339	4e-40
297793151	598	APUM12 [Arabidopsis lyrata subsp. lyrata	0.910	0.510	0.342	1e-39
224052863	620	predicted protein [Populus trichocarpa]	0.901	0.487	0.338	1e-38
224056741	497	predicted protein [Populus trichocarpa]	0.919	0.619	0.353	2e-38
22327888	596	pumilio 12 [Arabidopsis thaliana] gi|313	0.910	0.511	0.336	2e-38
302756987	322	hypothetical protein SELMODRAFT_75995 [S	0.904	0.940	0.326	3e-38

>gi|255553119|ref|XP_002517602.1| RNA binding protein, putative [Ricinus communis] gi|223543234|gb|EEF44766.1| RNA binding protein, putative [Ricinus communis]

 Score =  208 bits (530), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 137/332 (41%), Positives = 198/332 (59%), Gaps = 14/332 (4%)

Query: 11  NHDLFSL-AQDQEGSQYLQENLSSGDS-----RILDKLFWVVSGFTF--ELMSGQYGRFV 62
           N D F + A  Q+GS+YLQ+ L++ DS     +ILDK+   V G      LM  Q+G  V
Sbjct: 140 NQDSFIMFASTQQGSEYLQDLLATSDSYLTTSKILDKVTASVVGIPVINYLMVDQHGYHV 199

Query: 63  FGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSA 122
             K I+SCN+ QL LI+ +IT   + F+       GS  +KKLIK V     + Y  +S 
Sbjct: 200 CSKLIDSCNDIQLTLILERITKNTEQFVRICCAINGSKMIKKLIKKVKRSCLISYLTVSL 259

Query: 123 LKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDN 182
            K  ++ L + + GS V++ C++     +N  +Y+AA+ HCL LA    GC++ N FID 
Sbjct: 260 YKGFYQ-LAINQIGSYVVVFCMDCLDIQQNALLYEAAISHCLILATDAIGCVSANKFIDR 318

Query: 183 MKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTK 242
           ++GSRR+ +L LIS NA  LS+  SGN+VVQ VL LE+P +   I   L+GHYV LS  K
Sbjct: 319 IQGSRRQTLLELISDNAVFLSQDPSGNHVVQKVLGLENPIINAKIGAQLKGHYVRLSFQK 378

Query: 243 CGSFVVQKCLKYQNAVHYIIEELL--NSDQILQVANDKYGNYVIQTALAETMRQDRLSVH 300
            GS VV+KCL  Q A+ Y +++LL   S Q+LQ+A D++GNYVIQ AL  T +++ +++H
Sbjct: 379 WGSHVVEKCLVSQ-AMVYAVQDLLTCGSSQLLQIARDQFGNYVIQKALKVTKKKN-IALH 436

Query: 301 QRLVTKLQQHLAALRVMKYGSNVYKWTTASHP 332
           + L+  L+ +L ALR   +G  VY       P
Sbjct: 437 RILLNSLEPNLNALR-NGFGKKVYSLIMDGIP 467

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255544718|ref|XP_002513420.1| conserved hypothetical protein [Ricinus communis] gi|223547328|gb|EEF48823.1| conserved hypothetical protein [Ricinus communis]

 Score =  203 bits (517), Expect = 7e-50,   Method: Compositional matrix adjust.
 Identities = 131/324 (40%), Positives = 192/324 (59%), Gaps = 12/324 (3%)

Query: 17  LAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFE------LMSGQYGRFVFGKFIESC 70
            A  Q+GS++LQ+ L+  +S    KL   V+    E      LM  QYG  V  K I+SC
Sbjct: 156 FASTQQGSKHLQDLLAYSNSDFASKLLETVTASVVEIPVINYLMVDQYGCHVCSKLIDSC 215

Query: 71  NESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFL 130
           N+ QLALI+ +IT  D+ F+    +  GS  +KKLIK V     + Y  +S L + F  L
Sbjct: 216 NDKQLALILERITRNDEQFVQICCNINGSKMIKKLIKKVKRSCLICYMTVS-LYKGFCQL 274

Query: 131 MMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQ 190
            + + GS V++ C++     ++  +Y+AA+ HCL LA    GC+++NNFID ++GS R+ 
Sbjct: 275 AINQIGSYVVVFCMDCLDVKQSALLYEAAISHCLILATDATGCVSINNFIDRIQGSHRQT 334

Query: 191 ILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQK 250
           +L LIS NA  LS+  SGN+VVQ VL LE+P +   I   L+GHY  LS  K GS VV+K
Sbjct: 335 LLELISDNAVFLSQDPSGNHVVQKVLELENPIINAKIGAQLKGHYARLSFQKWGSHVVEK 394

Query: 251 CLKYQNAVHYIIEELL--NSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQ 308
           CL  Q  V Y++++LL   S Q+ Q+A D++GNYVIQ AL  T +++ +++H  L+  L+
Sbjct: 395 CLVSQPIV-YVVQDLLTCGSSQLSQIARDQFGNYVIQKALKVTKKKN-ITLHLILLNSLK 452

Query: 309 QHLAALRVMKYGSNVYKWTTASHP 332
            +L AL+   YG  VY+      P
Sbjct: 453 PNLNALQ-NGYGKKVYRLIMDGIP 475

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224117628|ref|XP_002317626.1| predicted protein [Populus trichocarpa] gi|222860691|gb|EEE98238.1| predicted protein [Populus trichocarpa]

 Score =  179 bits (453), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 114/320 (35%), Positives = 181/320 (56%), Gaps = 12/320 (3%)

Query: 20  DQEGSQYLQENLSSGDSRILDKLFWVVSGFT-------FELMSGQYGRFVFGKFIESCNE 72
           DQ GS+ +Q  L   +  I  +++  V   +        ELM  Q+G  VFG+ I++ N 
Sbjct: 183 DQHGSRTIQGLLRLRNPEITREIYNKVLALSSRGIAVVLELMLDQHGWHVFGELIDALNY 242

Query: 73  SQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMM 132
            QL LI  +IT     F+  ++D  GS+S++K+I+++    PL+  VM+ L+  F  +M 
Sbjct: 243 QQLKLITYEITKNLDNFVSLTLDTHGSNSIRKVIRLLRR-SPLVTLVMNNLRAAFFTIMT 301

Query: 133 TKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQIL 192
            + GS  + +C        N  +Y+AA+E CL LA   +G + L   I+ ++G +R ++L
Sbjct: 302 NRIGSYAVSECFNQLSAEDNRLLYEAAIECCLDLAIDHEGSLALIRVINTIQGLQRYRLL 361

Query: 193 HLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCL 252
            ++S   A LS+   GNYVVQ V+SL +P     IC  LRG+Y  +SL K GS + +KCL
Sbjct: 362 DILSTYVAFLSQDPKGNYVVQKVISLNNPLFTQKICHHLRGYYGTISLQKGGSHIAEKCL 421

Query: 253 KYQNAVHYIIEELL-NSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHL 311
             +    ++IE+ L N++ +LQVA D++GNYVIQ AL  T +     ++Q+L+ +LQ HL
Sbjct: 422 DTE-WKSWVIEDFLSNTNTLLQVAKDEFGNYVIQKALKVTKKSGS-PLYQKLLLRLQPHL 479

Query: 312 AALRVMKYGSNVYKWTTASH 331
           + L+   YG NV+   T   
Sbjct: 480 SILQ-SGYGRNVFNLITGGR 498

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147798084|emb|CAN67257.1| hypothetical protein VITISV_039435 [Vitis vinifera]

 Score =  178 bits (452), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 100/264 (37%), Positives = 164/264 (62%), Gaps = 3/264 (1%)

Query: 62  VFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMS 121
           VF +  E+C+ +QL+ I+ K+       +  S D  GS S+++LI+V+   P L+  V++
Sbjct: 239 VFIRLTEACDANQLSQILSKLILPPSTIIRVSHDPIGSKSIQRLIQVLRRSP-LVVPVVT 297

Query: 122 ALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFID 181
           AL   F  LM  + G+ VI +CL    + +N+ +Y+AA+  C+ LA H +GCI LN+FI+
Sbjct: 298 ALAAGFYELMKDQQGAMVISRCLALLSSEQNEELYRAAILPCVALATHAKGCIALNSFIN 357

Query: 182 NMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLT 241
           N+ G  R  +LH I+ N   LS+   GN+VVQH+L L  P     IC  L+G+YV LS+ 
Sbjct: 358 NVIGPYRDLLLHKITDNTVFLSQDPRGNFVVQHILELHHPVFTSKICHLLQGYYVRLSVQ 417

Query: 242 KCGSFVVQKCLKYQNAVHYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQ 301
           K GS +V+KCLK  + + + ++EL  S ++ Q+A+D++GNYVIQTAL  T +   + +++
Sbjct: 418 KSGSHIVEKCLK-SHWMSFAVKELTTSGRLPQLAHDQFGNYVIQTALRVT-KDANIQLYR 475

Query: 302 RLVTKLQQHLAALRVMKYGSNVYK 325
            L+  L+ +L +L    +G N+++
Sbjct: 476 SLLEALEPYLPSLASHLHGKNLFR 499

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255564824|ref|XP_002523406.1| RNA binding protein, putative [Ricinus communis] gi|223537356|gb|EEF38985.1| RNA binding protein, putative [Ricinus communis]

 Score =  171 bits (434), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 106/312 (33%), Positives = 170/312 (54%), Gaps = 7/312 (2%)

Query: 14  LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
           ++ +A+DQ G ++LQ   S G  + ++K+F  V     ELM+  +G ++  K +E CNE 
Sbjct: 427 VYLMAKDQHGCRFLQRKFSEGTPQDIEKIFLEVIDHIAELMTDPFGNYLVQKLLEVCNED 486

Query: 74  QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMT 133
           Q   I+  IT +    +  S D  G+ +V+K+I+ +   P     V+S+LK     L+  
Sbjct: 487 QRMQILCAITRKAGELVRISCDMHGTRAVQKVIETLK-TPQQFSMVVSSLKPGIVTLIKN 545

Query: 134 KPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILH 193
             G+ V  +CL+      ++F+++AA  +C+ LA    GC  L   + + +G +R+ ++ 
Sbjct: 546 MNGNHVAQRCLQYLTPEHSEFLFEAATTNCVELATDRHGCCVLQKCLSHSEGEQRRCLIS 605

Query: 194 LISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLK 253
            I+ NA  LS+   GNYVVQ V  L  P+    I   L G+Y DLS+ K  S V++KCLK
Sbjct: 606 EITSNALILSQDPFGNYVVQFVFELRLPWATANILDQLEGNYGDLSMQKYSSNVIEKCLK 665

Query: 254 YQNAVH--YIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHL 311
           Y +  H  +II +L+++  + QV  D YGNYVIQ AL     Q + ++H  LV  ++ H+
Sbjct: 666 YASEEHRAHIIRQLISNTHLDQVMQDPYGNYVIQAAL----HQSKGALHAALVEAIRPHV 721

Query: 312 AALRVMKYGSNV 323
             LR   YG  V
Sbjct: 722 PVLRTSPYGKKV 733

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297793151|ref|XP_002864460.1| APUM12 [Arabidopsis lyrata subsp. lyrata] gi|297310295|gb|EFH40719.1| APUM12 [Arabidopsis lyrata subsp. lyrata]

 Score =  170 bits (430), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 107/312 (34%), Positives = 172/312 (55%), Gaps = 7/312 (2%)

Query: 14  LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
           ++ LA+DQ G ++LQ   +  D   ++ +F  +  +  ELM   +G ++  K +E CNE 
Sbjct: 284 IYYLAKDQHGCRFLQRIFAEKDGNDIEMIFDEIIDYISELMIDPFGNYLVQKLLEVCNED 343

Query: 74  QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMT 133
           Q   I+  IT +  L +  S D  G+ +V+K+++  A     +  ++SALK     L+  
Sbjct: 344 QRMQIVHSITRKPGLLIKISCDMHGTRAVQKIVET-AKREEEISIIISALKHGIVNLIKN 402

Query: 134 KPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILH 193
             G+ V+ +CL+    H   F+++AA+ HC+ LA    GC  L   +   +G +++ ++ 
Sbjct: 403 VNGNHVVQRCLQYLLPHCGKFLFEAAITHCVDLATDRHGCCVLQKCLGYSEGEQKQHLVS 462

Query: 194 LISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLK 253
            I+ NA  LS+   GNYV+Q+V  L+  +    I   L G+Y +LS+ KC S VV+KCLK
Sbjct: 463 EIASNALLLSQDPFGNYVLQYVFELQLQWATFEILEQLEGNYTELSMQKCSSNVVEKCLK 522

Query: 254 YQNAVH--YIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHL 311
             +  H   II EL+N  ++ QV  D YGNYVIQ AL    RQ + +VH  LV  ++ H+
Sbjct: 523 LADDKHRARIIRELINYGRLDQVMLDPYGNYVIQAAL----RQSKGNVHALLVDAIKLHI 578

Query: 312 AALRVMKYGSNV 323
           ++LR   YG  V
Sbjct: 579 SSLRTNPYGKKV 590

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224052863|ref|XP_002297618.1| predicted protein [Populus trichocarpa] gi|222844876|gb|EEE82423.1| predicted protein [Populus trichocarpa]

 Score =  166 bits (421), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 109/322 (33%), Positives = 170/322 (52%), Gaps = 20/322 (6%)

Query: 14  LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
           ++ +A+DQ G ++LQ   S G  + ++K+F  +     ELM+  +G ++  K +E CNE 
Sbjct: 299 IYLMAKDQHGCRFLQRTFSEGTPQDVEKIFLEIIDHIVELMTDPFGNYLVQKLLEVCNED 358

Query: 74  QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMT 133
           Q   I+  IT +    +  S D  G+ +V+K+I+ +   P     V+SALK     L+  
Sbjct: 359 QRMQILRTITRKAGELVRISCDMHGTRAVQKVIETL-KTPEQFSMVVSALKPCIVTLIKN 417

Query: 134 KPGSSVILQCLE---PSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQ 190
             G+ V  +CL+   P Y   ++F+++A   +C+ LA    GC  L   +   KG +R+ 
Sbjct: 418 MNGNHVAQRCLQYLMPEY---SEFLFEATTANCVELATDRHGCCVLQKCLSQSKGEQRRC 474

Query: 191 ILHLISVNAASLSRHRSG-------NYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKC 243
           ++  I+ NA  LS+   G       NYVVQ V  L  P+    I   L G+Y DLS+ K 
Sbjct: 475 LVSEITSNALILSQDPFGYCIFLFSNYVVQFVFELRLPWAATDILDQLEGNYGDLSVQKY 534

Query: 244 GSFVVQKCLKYQNAVH--YIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQ 301
            S VV+KCLKY   V    II EL+N+ ++ QV  D +GNYVIQ AL    +Q + ++H 
Sbjct: 535 SSNVVEKCLKYAGEVRRTRIIRELINNSRLDQVMQDPFGNYVIQAAL----QQSKGALHA 590

Query: 302 RLVTKLQQHLAALRVMKYGSNV 323
            LV  ++ H+  L+   YG  V
Sbjct: 591 ALVEAIRPHVPTLQTSPYGKKV 612

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224056741|ref|XP_002299000.1| predicted protein [Populus trichocarpa] gi|222846258|gb|EEE83805.1| predicted protein [Populus trichocarpa]

 Score =  166 bits (419), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 113/320 (35%), Positives = 175/320 (54%), Gaps = 12/320 (3%)

Query: 20  DQEGSQYLQENLSSGDSRILDKLFWVVSGFT-------FELMSGQYGRFVFGKFIESCNE 72
           D++GS+ L   LS  D  I  ++   V   +       FELM  Q+G  VF + I+S N 
Sbjct: 177 DKDGSRTLHGLLSLRDPEITCQICKKVLDLSSRGIPIFFELMLNQHGWQVFSELIDSLNH 236

Query: 73  SQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMM 132
            QL LI   IT    +F+  +    GS+ +KK+I+++     L+  V + L   F  +M 
Sbjct: 237 QQLKLITYVITKDLSIFIALTFHTHGSNLIKKVIRILRR-SHLISFVTNNLCAAFLLIMT 295

Query: 133 TKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQIL 192
            + GS V+ +CL       N  +Y+AA+  CL LA   +G I L   I+ ++G +R ++L
Sbjct: 296 NRIGSYVVSECLNHLRAEDNKALYEAAITWCLDLAIDHEGSIALIRVINTIQGLQRYRLL 355

Query: 193 HLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCL 252
           +++S NA  LS+   GNYV+Q V+SL +P     +C  L GHY  +SL K GS +V+KCL
Sbjct: 356 NILSRNAVFLSQDPEGNYVIQKVISLNNPLFTQNVCHLLIGHYETISLQKGGSHIVEKCL 415

Query: 253 KYQNAVHYIIEELL-NSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHL 311
             +    +IIE  L N++ +L VA D +GNYVIQ AL  T +     ++ +L+++L+ HL
Sbjct: 416 DTE-WKGWIIENFLSNTNTLLHVAKDAFGNYVIQKALKVTKKSGS-PLYHKLLSRLKPHL 473

Query: 312 AALRVMKYGSNVYKWTTASH 331
           + L+   YG NV+   T   
Sbjct: 474 SILQ-SGYGRNVFNLITGGQ 492

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|22327888|ref|NP_200462.2| pumilio 12 [Arabidopsis thaliana] gi|313471423|sp|Q9LVC3.2|PUM12_ARATH RecName: Full=Pumilio homolog 12; Short=APUM-12; Short=AtPUM12 gi|332009392|gb|AED96775.1| pumilio 12 [Arabidopsis thaliana]

 Score =  165 bits (418), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 105/312 (33%), Positives = 172/312 (55%), Gaps = 7/312 (2%)

Query: 14  LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
           ++ LA+DQ G ++LQ   S  D   ++ +F  +  +  ELM   +G ++  K +E CNE 
Sbjct: 282 IYYLAKDQHGCRFLQRIFSEKDGNDIEMIFNEIIDYISELMMDPFGNYLVQKLLEVCNED 341

Query: 74  QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMT 133
           Q   I+  IT +  L +  S D  G+ +V+K+++  A     +  ++SALK     L+  
Sbjct: 342 QRMQIVHSITRKPGLLIKISCDMHGTRAVQKIVET-AKREEEISIIISALKHGIVHLIKN 400

Query: 134 KPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILH 193
             G+ V+ +CL+    +   F+++AA+ HC+ LA    GC  L   +   +G +++ ++ 
Sbjct: 401 VNGNHVVQRCLQYLLPYCGKFLFEAAITHCVELATDRHGCCVLQKCLGYSEGEQKQHLVS 460

Query: 194 LISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLK 253
            I+ NA  LS+   GNYV+Q+V  L+  +    I   L G+Y +LS+ KC S VV+KCLK
Sbjct: 461 EIASNALLLSQDPFGNYVLQYVFELQLQWATFEILEQLEGNYTELSMQKCSSNVVEKCLK 520

Query: 254 YQNAVH--YIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHL 311
             +  H   II EL+N  ++ QV  D YGNYVIQ AL    +Q + +VH  LV  ++ ++
Sbjct: 521 LADDKHRARIIRELINYGRLDQVMLDPYGNYVIQAAL----KQSKGNVHALLVDAIKLNI 576

Query: 312 AALRVMKYGSNV 323
           ++LR   YG  V
Sbjct: 577 SSLRTNPYGKKV 588

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302756987|ref|XP_002961917.1| hypothetical protein SELMODRAFT_75995 [Selaginella moellendorffii] gi|300170576|gb|EFJ37177.1| hypothetical protein SELMODRAFT_75995 [Selaginella moellendorffii]

 Score =  165 bits (418), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 102/312 (32%), Positives = 171/312 (54%), Gaps = 9/312 (2%)

Query: 14  LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
           ++S+A+DQ G ++LQ     G +  L K+F  +     +LM+  +G ++  K +E C E 
Sbjct: 9   IYSIAKDQYGCRFLQRRFDEGVAEDLQKIFEEIIDHIVDLMTDPFGNYLVQKLLEVCTED 68

Query: 74  QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMT 133
           Q  L IL++       +  S++  G+ +V+KLI+ +   P  +  + S+L++    L+  
Sbjct: 69  Q-RLEILRVVCSGDELISISLNMHGTRAVQKLIETLKS-PEQVSMITSSLEQGIVILIKD 126

Query: 134 KPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILH 193
             G+ V+ +CL+   N +N FI+ AA +HC+ +  H  GC  L   +D  KG ++++++ 
Sbjct: 127 LNGNHVVQRCLQRLGNEENQFIFDAAAQHCVEVGTHRHGCCVLQRCVDFSKGVQKERLVG 186

Query: 194 LISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLK 253
            I+ NA  LS+ + GNYVVQ++L  E P++   +   L GH+  L++ K  S VV+KCLK
Sbjct: 187 EIAANALVLSQDQYGNYVVQYILD-EAPWIAPEVMAQLEGHHAHLAMQKFSSNVVEKCLK 245

Query: 254 --YQNAVHYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHL 311
               +    II EL  S  + Q+  D + NYVIQ AL  T    + ++H  LV  ++ HL
Sbjct: 246 QGADDKRARIIHELTKSAFLGQLLQDPFANYVIQCALTVT----KGALHASLVEAIRPHL 301

Query: 312 AALRVMKYGSNV 323
            ALR   YG  +
Sbjct: 302 PALRSSPYGKRI 313

Source: Selaginella moellendorffii

Species: Selaginella moellendorffii

Genus: Selaginella

Family: Selaginellaceae

Order: Selaginellales

Class: Isoetopsida

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	335
TAIR|locus:2167111	596	PUM12 "pumilio 12" [Arabidopsi	0.910	0.511	0.333	6.6e-42
TAIR|locus:2015036	515	PUM8 "pumilio 8" [Arabidopsis	0.904	0.588	0.321	5.1e-35
DICTYBASE|DDB_G0289987	1036	DDB_G0289987 "Pumilio homology	0.901	0.291	0.308	3.8e-34
TAIR|locus:2138258	556	PUM11 "pumilio 11" [Arabidopsi	0.904	0.544	0.310	5.2e-32
TAIR|locus:2194699	650	PUM7 "pumilio 7" [Arabidopsis	0.910	0.469	0.298	1.5e-31
ASPGD|ASPL0000057098	650	AN10071 [Emericella nidulans (	0.907	0.467	0.286	2.5e-31
TAIR|locus:2164165	327	PUM18 "pumilio 18" [Arabidopsi	0.8	0.819	0.315	2.1e-29
TAIR|locus:2011349	564	PUM9 "pumilio 9" [Arabidopsis	0.904	0.537	0.294	2.8e-29
TAIR|locus:2144010	327	PUM19 "pumilio 19" [Arabidopsi	0.8	0.819	0.311	1.9e-28
TAIR|locus:2011360	528	PUM10 "pumilio 10" [Arabidopsi	0.898	0.570	0.296	7.2e-28

TAIR|locus:2167111 PUM12 "pumilio 12" [Arabidopsis thaliana (taxid:3702)]

 Score = 444 (161.4 bits), Expect = 6.6e-42, P = 6.6e-42
 Identities = 104/312 (33%), Positives = 171/312 (54%)

Query:    14 LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
             ++ LA+DQ G ++LQ   S  D   ++ +F  +  +  ELM   +G ++  K +E CNE 
Sbjct:   282 IYYLAKDQHGCRFLQRIFSEKDGNDIEMIFNEIIDYISELMMDPFGNYLVQKLLEVCNED 341

Query:    74 QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMT 133
             Q   I+  IT +  L +  S D  G+ +V+K+++       +   ++SALK     L+  
Sbjct:   342 QRMQIVHSITRKPGLLIKISCDMHGTRAVQKIVETAKREEEISI-IISALKHGIVHLIKN 400

Query:   134 KPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILH 193
               G+ V+ +CL+    +   F+++AA+ HC+ LA    GC  L   +   +G +++ ++ 
Sbjct:   401 VNGNHVVQRCLQYLLPYCGKFLFEAAITHCVELATDRHGCCVLQKCLGYSEGEQKQHLVS 460

Query:   194 LISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLK 253
              I+ NA  LS+   GNYV+Q+V  L+  +    I   L G+Y +LS+ KC S VV+KCLK
Sbjct:   461 EIASNALLLSQDPFGNYVLQYVFELQLQWATFEILEQLEGNYTELSMQKCSSNVVEKCLK 520

Query:   254 YQNAVHY--IIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHL 311
               +  H   II EL+N  ++ QV  D YGNYVIQ AL    +Q + +VH  LV  ++ ++
Sbjct:   521 LADDKHRARIIRELINYGRLDQVMLDPYGNYVIQAAL----KQSKGNVHALLVDAIKLNI 576

Query:   312 AALRVMKYGSNV 323
             ++LR   YG  V
Sbjct:   577 SSLRTNPYGKKV 588

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

GO:0005737 "cytoplasm" evidence=ISM;IDA

GO:0005634 "nucleus" evidence=IDA

TAIR|locus:2015036 PUM8 "pumilio 8" [Arabidopsis thaliana (taxid:3702)]

 Score = 379 (138.5 bits), Expect = 5.1e-35, P = 5.1e-35
 Identities = 101/314 (32%), Positives = 166/314 (52%)

Query:    14 LFSLAQDQEGSQYLQENLSSGDSRILDKL--FWVVSGFTFELMSGQYGRFVFGKFIESCN 71
             ++ +A+DQ G ++LQ     G +  LD L  F  V     ELM   +G ++  K ++ CN
Sbjct:   203 VYFMAKDQHGCRFLQWIFEDGSA--LDALVIFSEVIPHVVELMMDPFGNYLMQKLLDVCN 260

Query:    72 ESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLM 131
             E Q   IIL +T +    +  S++ +G+  V++L++ +     +   V SAL+  F  L+
Sbjct:   261 EEQRTQIILMVTSEPGQLIRISLNAYGTRVVQRLVESIKTRKQISL-VKSALRPGFLNLI 319

Query:   132 MTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQI 191
                 G+ VI +CL+      N+FI++ A + C+ +A H  GC  L   I    G +R+++
Sbjct:   320 RDLNGNHVIQRCLQCLSTEDNEFIFEDATKFCIDIATHRHGCCVLQKCIAYSSGLQREKL 379

Query:   192 LHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKC 251
             +  IS N+  L++   GNY VQ VL L D   I A+   L+GHYV+LS+ K  S +V++C
Sbjct:   380 VTEISRNSLFLAQDPYGNYAVQFVLELRDFSAIAAMLAQLKGHYVELSMQKFSSHMVERC 439

Query:   252 LKY-QNAVHYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQH 310
             L +   +   I+ EL++      +  D Y N+VIQ ALA T    + S+H  LV  ++ H
Sbjct:   440 LTHCPESRPQIVRELISVPHFDILIQDPYANFVIQAALAVT----KGSLHATLVEVIRPH 495

Query:   311 LAALRVMKYGSNVY 324
              + LR   Y   ++
Sbjct:   496 -SILRNNPYCKRIF 508

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

GO:0005737 "cytoplasm" evidence=IDA

DICTYBASE|DDB_G0289987 DDB_G0289987 "Pumilio homology domain family member 4" [Dictyostelium discoideum (taxid:44689)]

 Score = 382 (139.5 bits), Expect = 3.8e-34, P = 3.8e-34
 Identities = 97/314 (30%), Positives = 161/314 (51%)

Query:    14 LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
             ++ L +DQ G ++LQ+ L   D ++ + +F  V  +  ELM+  +G ++  K +E CN+ 
Sbjct:   716 IYPLCRDQHGCRFLQKKLEESDLQLTEIIFKEVCDYMLELMTDPFGNYLCQKLLEHCNDR 775

Query:    74 QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMT 133
             Q   II K+       +  S++  G+ +V+K+I+ +   P  +  +  +LK     L+  
Sbjct:   776 QRLTIIEKVGTD---IVRISMNMHGTRAVQKMIEYLT-TPEQIQLIKRSLKDSVVPLIQD 831

Query:   134 KPGSSVILQCLEPSYNHKNDFIYQAALEH--CLYLACHEQGCINLNNFIDNMKGSRRKQI 191
               G+ VI +CL       N FIY A      C+ +A H  GC  L   ID+   S++ Q+
Sbjct:   832 LNGNHVIQKCLNKLSPQDNQFIYDAVSSDGSCIAVATHRHGCCVLQRCIDHASESQKLQL 891

Query:   192 LHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKC 251
             +  +  N+  L +   GNYVVQ+VL L    L   +     GH   L+  K  S VV+KC
Sbjct:   892 IQEVIANSLVLVQDPYGNYVVQYVLDLPFQGLATEMAKRFVGHVPILATQKFSSNVVEKC 951

Query:   252 LKYQNAVH--YIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQ 309
             L   +A+   Y+I+E+++ D +L +  D Y NYVIQT+L  T+ +     H +LV  ++ 
Sbjct:   952 LHVADAITRGYLIQEVIDYDNLLHLLQDPYANYVIQTSL--TISEPHQ--HTKLVEAIRP 1007

Query:   310 HLAALRVMKYGSNV 323
             HL  L+   YG  +
Sbjct:  1008 HLPLLKNTPYGKRI 1021

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

TAIR|locus:2138258 PUM11 "pumilio 11" [Arabidopsis thaliana (taxid:3702)]

 Score = 354 (129.7 bits), Expect = 5.2e-32, P = 5.2e-32
 Identities = 97/312 (31%), Positives = 166/312 (53%)

Query:    14 LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
             ++ +A+DQ G + LQ+ +  G+   +  +F  V     EL +  +G ++  K IE CNE 
Sbjct:   246 VYLMAKDQLGCRLLQKFVDEGNFVDVMIIFKEVINNVIELGTDPFGNYLIQKLIEVCNEE 305

Query:    74 QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMT 133
             Q   I++++T +  L +  S++ +G+  V+KLI+ V     +   V SAL   F  L   
Sbjct:   306 QRTQILIRLTSKPGLLVKISINNYGTRVVQKLIETVTTKEQISL-VKSALVPGFLSLFRE 364

Query:   134 KPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILH 193
               G+ VIL CL+    + N FI +AA + C+ +A    GC  L   +    G + ++++ 
Sbjct:   365 LNGNHVILNCLKFFSPNDNKFILEAATKFCIEIATTRHGCCVLQRCVSYSVGEQHEKLVD 424

Query:   194 LISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLK 253
              IS N+  L++   GNY+VQ+++  +   +   + F LRG+YV L+  K GS VV+KCL+
Sbjct:   425 EISRNSLLLAQDPFGNYLVQYIIEKKVGGV--NVLFELRGNYVKLATQKFGSHVVEKCLR 482

Query:   254 YQ-NAVHYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLA 312
             Y   +   I+ EL++      +  D Y NYVIQ AL++T    R S    LV K++++  
Sbjct:   483 YYPESRSQIVNELVSVLNFGYLLQDPYANYVIQCALSKTKGFVRAS----LVEKVRRY-E 537

Query:   313 ALRVMKYGSNVY 324
              L++  Y   ++
Sbjct:   538 NLKMTPYCKRIF 549

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

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2194699 PUM7 "pumilio 7" [Arabidopsis thaliana (taxid:3702)]

 Score = 353 (129.3 bits), Expect = 1.5e-31, P = 1.5e-31
 Identities = 93/312 (29%), Positives = 156/312 (50%)

Query:    14 LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
             ++ +A+DQ G ++LQ     G S     +F  V     ELM   +G ++  K ++ C E 
Sbjct:   338 VYLMAKDQHGCRFLQRIFDEGTSVDAMIIFNEVIAHVVELMMDPFGNYLMQKLLDVCTEE 397

Query:    74 QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMT 133
             Q   I+L  T +    +  S++ +G+  V++L++ +     +   V  AL+  F  L+  
Sbjct:   398 QRTQIVLVATEEPGQLIRISLNAYGTRVVQRLVETIRSGKQISL-VKLALRPGFLDLIKD 456

Query:   134 KPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILH 193
               G+ VI +CL+      N FI+ AA + C  +A H  GC  L   I      +R++++ 
Sbjct:   457 LNGNHVIQRCLQCLSTEDNKFIFDAATKFCTEIATHRHGCCVLQKCIAYSMRQQREKLIA 516

Query:   194 LISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLK 253
              IS N+  L++   GNY VQ V+ L  P  +  +   L+GHYV LS+ K  S +V++CL 
Sbjct:   517 EISRNSLLLAQDPFGNYAVQFVIELRIPSAVAMMLAQLKGHYVQLSMQKFSSHMVERCLM 576

Query:   254 Y-QNAVHYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLA 312
             +   +   I+ EL++     Q+  D Y N+VIQ ALA T    +  +H  LV  ++ H +
Sbjct:   577 HCPESRPQIVRELVSVPHFDQLLQDPYANFVIQAALAAT----KGPLHASLVEVIRPH-S 631

Query:   313 ALRVMKYGSNVY 324
              LR   Y   ++
Sbjct:   632 ILRNNPYCKRIF 643

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

GO:0009507 "chloroplast" evidence=ISM

GO:0003729 "mRNA binding" evidence=IPI

GO:0005737 "cytoplasm" evidence=IDA

ASPGD|ASPL0000057098 AN10071 [Emericella nidulans (taxid:162425)]

 Score = 351 (128.6 bits), Expect = 2.5e-31, P = 2.5e-31
 Identities = 90/314 (28%), Positives = 158/314 (50%)

Query:    12 HDLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCN 71
             ++++ L +DQ G +YLQ  L   +   L  +F        ELM+  +G ++  K +E  N
Sbjct:   239 NEIYGLCKDQHGCRYLQRKLEERNDDQLQMIFAETHSHVIELMTDPFGNYLCQKLLEYSN 298

Query:    72 ESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLM 131
             + Q  +++ K     QL  +A +++ G+ +++K+I+ ++        V+ ALK     L+
Sbjct:   299 DEQRTVLVNKAA--PQLVKIA-LNQHGTRALQKMIEFIS-TEEQTQTVIDALKDHVVELV 354

Query:   132 MTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQI 191
                 G+ VI +CL      K+ FIY A    C+ +  H  GC  L   ID+  G++R ++
Sbjct:   355 QDLNGNHVIQKCLNRLTAEKSQFIYDAVGAQCVTVGTHRHGCCVLQRCIDHASGAQRARL 414

Query:   192 LHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKC 251
             +  I+ NA +L +   GNYVVQ++L L +    + +C         LS  K  S V++KC
Sbjct:   415 IEQITENAFALVQDPFGNYVVQYILDLAEARFTEPLCREFLSRIPKLSKHKFSSNVIEKC 474

Query:   252 LKY--QNAVHYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQ 309
             L+   +     +IEE+L  D++ ++  D Y NYV+QTA+       R     R+V  ++ 
Sbjct:   475 LRTADEEMRRQMIEEMLAGDELEKMLRDSYANYVVQTAMDYADPATRA----RIVKYIEP 530

Query:   310 HLAALRVMKYGSNV 323
              L +LR   +G  +
Sbjct:   531 ILPSLRGTPHGRRI 544

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0003723 "RNA binding" evidence=IEA

TAIR|locus:2164165 PUM18 "pumilio 18" [Arabidopsis thaliana (taxid:3702)]

 Score = 326 (119.8 bits), Expect = 2.1e-29, P = 2.1e-29
 Identities = 87/276 (31%), Positives = 144/276 (52%)

Query:    51 FELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVA 110
             F LM+   G   F + I + ++++L  +   +T     F+     KFGS  V+KL+    
Sbjct:    46 FNLMTDGDGVSYFKEMISNSDKTELQRMASLLTSDSDYFMSIVTTKFGSRRVQKLLGKSD 105

Query:   111 HLPPLLYHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHE 170
              +        +A+ R F  +   K  S V ++ +          +Y+  L H L LAC +
Sbjct:   106 DVDAFF---CAAILRRFLHITTDKYASYVTIRAMVVFDKVMKKALYERILYHALDLACDQ 162

Query:   171 QGCINLNNFIDNMKGSR-RKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICF 229
              GCI LN+ I +      R Q+L L++ NA  LS   SGN+VVQHVL+L D   I  I  
Sbjct:   163 HGCIALNDIITDADDPYYRDQLLELVASNALRLSNDASGNFVVQHVLTLYDSRCIHNIAV 222

Query:   230 ALRGHYVDLSLTKCGSFVVQKCLKYQNAVHYIIEELL--NSDQILQVANDKYGNYVIQTA 287
              L G  ++LS  K GS++V+K L+ + ++  ++ ELL  + D+++++A +++GN+V+  A
Sbjct:   223 NLYGQCIELSFKKYGSYIVEKLLEVEESMVVVVVELLGCDGDRLMRLARNEFGNFVVVKA 282

Query:   288 LAETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNV 323
             L  T +  R+ +   LV KL   +  LR   +GSN+
Sbjct:   283 LRFT-KMSRMDLFWGLVQKLMPFIRLLR-RSHGSNI 316

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

GO:0005737 "cytoplasm" evidence=ISM;IDA

GO:0007059 "chromosome segregation" evidence=RCA

GO:0007129 "synapsis" evidence=RCA

GO:0007131 "reciprocal meiotic recombination" evidence=RCA

GO:0042138 "meiotic DNA double-strand break formation" evidence=RCA

TAIR|locus:2011349 PUM9 "pumilio 9" [Arabidopsis thaliana (taxid:3702)]

 Score = 330 (121.2 bits), Expect = 2.8e-29, P = 2.8e-29
 Identities = 92/312 (29%), Positives = 154/312 (49%)

Query:    17 LAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLA 76
             +A+DQ G + LQ+ +  G       +   +     EL    +G ++  K  +  +E Q  
Sbjct:   257 MAKDQIGCRVLQKLVEEGTFHEAKVILLAIIDHVVELSMDPFGNYIVQKLFDVSDEEQRT 316

Query:    77 LIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMTKPG 136
             LI+  +T   +  +   ++ +G+  V+K+I+ V     +   V S LK  F  L+    G
Sbjct:   317 LIVSVLTSNPRELIRICLNTYGTRVVQKMIETVKTKQQIAL-VKSGLKPGFLALVKDLNG 375

Query:   137 SSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLIS 196
             + VI  CL+    + N+F+ +AA ++C  +A H  GC  L   I N  G +R++++  IS
Sbjct:   376 NHVIQSCLQTLGPNDNEFVLEAATKYCAEIAIHRHGCCVLQCCISNSVGLQRERLVAEIS 435

Query:   197 VNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCL-KYQ 255
              N+  LS+   GNYVVQ+++  +   +   + F  R HY +L+  K  S V++KCL KY 
Sbjct:   436 RNSLHLSQDPFGNYVVQYLIDQQVSAVKLLVQF--RMHYAELATQKFSSHVIEKCLRKYP 493

Query:   256 NAVHYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLAALR 315
              +   I+ ELL       +  D Y NYVIQTAL+ T    +  V  +LV K+ ++   L 
Sbjct:   494 ESRAEIVRELLCVPNFEYLLQDPYANYVIQTALSVT----KGPVRAKLVAKVYRY-GKLH 548

Query:   316 VMKYGSNVYKWT 327
                Y   ++  T
Sbjct:   549 SSPYCKKIFSKT 560

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

GO:0005737 "cytoplasm" evidence=ISM;IDA

TAIR|locus:2144010 PUM19 "pumilio 19" [Arabidopsis thaliana (taxid:3702)]

 Score = 317 (116.6 bits), Expect = 1.9e-28, P = 1.9e-28
 Identities = 86/276 (31%), Positives = 143/276 (51%)

Query:    51 FELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVA 110
             F LM+   G   F + I   ++++L  +   +T     F+     KFGS  V+KL+    
Sbjct:    46 FNLMTDGDGVSYFKEMISKSDKTELQRMASLLTSDSDYFMSIVTTKFGSRRVQKLLGKSD 105

Query:   111 HLPPLLYHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHE 170
              +        +A+ R F  +   K  S V ++ +          +Y+  L H L LAC +
Sbjct:   106 DVDAFF---CAAILRRFLHITTDKYASYVTIRAMVVFDKVMKKALYERILYHALDLACDQ 162

Query:   171 QGCINLNNFIDNMKGSR-RKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICF 229
              GCI LN+ I +      R Q+L L+  NA  LS   SGN+VVQHVL+L D   I  I  
Sbjct:   163 HGCIALNDIITDADDPYYRDQLLELVVSNALRLSNDASGNFVVQHVLTLYDSRCIHNIAV 222

Query:   230 ALRGHYVDLSLTKCGSFVVQKCLKYQNAVHYIIEELL--NSDQILQVANDKYGNYVIQTA 287
              L G  ++LS  K GS++V+K L+ + ++  ++ ELL  + D+++++A +++GN+V+  A
Sbjct:   223 NLYGQCIELSFKKYGSYIVEKLLEVEESMVVVVVELLGCDGDRLMRLARNEFGNFVVVKA 282

Query:   288 LAETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNV 323
             L  T ++ R+ +   LV KL   +  LR   +G+N+
Sbjct:   283 LRFT-KEMRMDLFWGLVQKLMPFIHLLR-RSHGNNI 316

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

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2011360 PUM10 "pumilio 10" [Arabidopsis thaliana (taxid:3702)]

 Score = 316 (116.3 bits), Expect = 7.2e-28, P = 7.2e-28
 Identities = 93/314 (29%), Positives = 158/314 (50%)

Query:    17 LAQDQEGSQYLQENLSSGDSRILDK--LFWVVSGFTFELMSGQYGRFVFGKFIESCNESQ 74
             +A+DQ G + LQ+ +  G   +LD   +F  +     EL     G ++  K +   +E Q
Sbjct:   221 MARDQIGCRALQKLVEEGT--VLDSKVIFLEIIDHVVELSMDPLGNYIVQKLLVVSDEEQ 278

Query:    75 LALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMTK 134
               +I+  +T + +  +   ++  G+  ++K+IK V     +   V SAL+  F  L+   
Sbjct:   279 RTMIVSVLTSKPRELIKICLNTNGTRVIQKMIKTVKTKQQIAL-VKSALEPGFLVLVNDS 337

Query:   135 PGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHL 194
              G  V+  CLE    + N F+ +AA E+C  LA H+ GC  L   + N  G + ++++  
Sbjct:   338 NGYHVLQSCLEFLVPNDNKFVVEAATEYCAQLATHQYGCYVLQCSLINTVGLQHERLVAE 397

Query:   195 ISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCL-K 253
             IS ++  LS+   GNYVVQ ++  +   +   +    R H ++L+  K  S V++KCL K
Sbjct:   398 ISRDSLRLSQDPFGNYVVQCLIDQQVSSV--NLLLPFRTHCIELATQKFSSHVIEKCLRK 455

Query:   254 YQNAVHYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLAA 313
             Y  +   I+ ELL+     Q+  D Y NYVIQTAL+ T    + +V  RLV K+++    
Sbjct:   456 YPESRAEIVRELLSYPNFEQLLQDPYANYVIQTALSVT----KGAVRARLVEKVKR-FGK 510

Query:   314 LRVMKYGSNVYKWT 327
             L+   Y   ++  T
Sbjct:   511 LQSNPYCKKIFSKT 524

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

GO:0005737 "cytoplasm" evidence=ISM;IDA

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: eugene3.00111204 hypothetical protein (502 aa) (Populus trichocarpa)

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	335
cd07920	322	cd07920, Pumilio, Pumilio-family RNA binding domai	7e-60
COG5099	777	COG5099, COG5099, RNA-binding protein of the Puf f	4e-29
cd07920	322	cd07920, Pumilio, Pumilio-family RNA binding domai	1e-04

>gnl|CDD|153420 cd07920, Pumilio, Pumilio-family RNA binding domain

 Score =  194 bits (495), Expect = 7e-60
 Identities = 96/317 (30%), Positives = 155/317 (48%), Gaps = 15/317 (4%)

Query: 13  DLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNE 72
            +   A+DQ GS++LQ+ L        + +F  +     ELM   +G +V  K  E   E
Sbjct: 11  HIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTE 70

Query: 73  SQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMM 132
            Q   ++ KI     +  L S+D +G   ++KL++ ++     +  ++  L+     L+ 
Sbjct: 71  EQRLQLLEKIL--GHVVRL-SLDMYGCRVIQKLLESIS--EEQISLLVKELRGHVVELVK 125

Query: 133 TKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQIL 192
            + G+ VI +C+E        FI  A   +C+ L+ H  GC  +   +++    +R+ +L
Sbjct: 126 DQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVALSTHPYGCRVIQRCLEHCSEEQREPLL 185

Query: 193 HLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCL 252
             I  +A  L + + GNYVVQHVL L DP     I   L G+ V LS  K  S VV+KCL
Sbjct: 186 EEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFASNVVEKCL 245

Query: 253 KYQNAVH--YIIEELLNS----DQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTK 306
           K+ +      II+E+L S      +  +  D+YGNYVIQTAL       +    + LV  
Sbjct: 246 KHASKEERELIIDEILASGNETSALDTLMKDQYGNYVIQTALDVA----KEEQRELLVEA 301

Query: 307 LQQHLAALRVMKYGSNV 323
           ++ HL +LR   YG ++
Sbjct: 302 IRPHLPSLRKSPYGKHI 318

Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canonical) repeats. Length = 322

>gnl|CDD|227430 COG5099, COG5099, RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis]

 Score =  117 bits (295), Expect = 4e-29
 Identities = 81/287 (28%), Positives = 138/287 (48%), Gaps = 13/287 (4%)

Query: 12  HDLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCN 71
             +    +DQ GS++LQ+ L S  S  ++ +F  +     EL S  +G ++  K  E  +
Sbjct: 441 PSIIVSCKDQHGSRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFEYGS 500

Query: 72  ESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLM 131
           E Q ++++ K +      +  SV K+G+  ++K I +V      +  ++  L+     L+
Sbjct: 501 EIQKSIMLSKSSKH---LVSLSVHKYGTRVLQKAIDIV-STDIQISLLVEELRPYCLQLI 556

Query: 132 MTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQI 191
             + G+ VI +C+E     KN FI+ +  E+   L+ H  G   +   ++N     ++ +
Sbjct: 557 KDQNGNHVIQKCIEKFNKEKNQFIFDSINENLYDLSTHRYGSRVVQRCLENCNSEDKENL 616

Query: 192 LHLISVNAASLSRHRSGNYVVQHVLSLE-DPFLIDAICFALRGHYVDLSLTKCGSFVVQK 250
           +  I  N+  LS+ + GNYVVQH+L    +P     I   L    V+LS  K  S VV+K
Sbjct: 617 VEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKLLSKRVVELSTHKFASNVVEK 676

Query: 251 CLKYQNAVHY---IIEELLN----SDQILQ-VANDKYGNYVIQTALA 289
           C+KY +       I+ EL N        L  + +D+Y NYVIQ  L 
Sbjct: 677 CIKYASDSFKRSRILNELTNRGIEKPGFLMLILDDQYANYVIQYLLD 723

Length = 777

>gnl|CDD|153420 cd07920, Pumilio, Pumilio-family RNA binding domain

 Score = 42.6 bits (101), Expect = 1e-04
 Identities = 53/269 (19%), Positives = 97/269 (36%), Gaps = 34/269 (12%)

Query: 6   FEHCTNH-----------DLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELM 54
           FEH T              +  L+ D  G + +Q+ L S     +  L   + G   EL+
Sbjct: 65  FEHGTEEQRLQLLEKILGHVVRLSLDMYGCRVIQKLLESISEEQISLLVKELRGHVVELV 124

Query: 55  SGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPP 114
             Q G  V  K IE      L  II           L S   +G   +++ ++  +    
Sbjct: 125 KDQNGNHVIQKCIEKFPPEDLQFIIDAFK--GNCVAL-STHPYGCRVIQRCLEHCS--EE 179

Query: 115 LLYHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHE---- 170
               ++  +      L+  + G+ V+   LE         I +  L + + L+CH+    
Sbjct: 180 QREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFASN 239

Query: 171 --QGCINLNNFIDNMKGSRRKQILHLISVNAASLS------RHRSGNYVVQHVLSLEDPF 222
             + C+   +  +      R+ I+  I  +    S      + + GNYV+Q  L +    
Sbjct: 240 VVEKCLKHASKEE------RELIIDEILASGNETSALDTLMKDQYGNYVIQTALDVAKEE 293

Query: 223 LIDAICFALRGHYVDLSLTKCGSFVVQKC 251
             + +  A+R H   L  +  G  ++ K 
Sbjct: 294 QRELLVEAIRPHLPSLRKSPYGKHILAKL 322

Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canonical) repeats. Length = 322

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	335
KOG1488	503	consensus Translational repressor Pumilio/PUF3 and	100.0
cd07920	322	Pumilio Pumilio-family RNA binding domain. Puf rep	100.0
KOG2049	536	consensus Translational repressor MPT5/PUF4 and re	100.0
COG5099	777	RNA-binding protein of the Puf family, translation	100.0
cd07920	322	Pumilio Pumilio-family RNA binding domain. Puf rep	100.0
KOG1488	503	consensus Translational repressor Pumilio/PUF3 and	100.0
COG5099	777	RNA-binding protein of the Puf family, translation	100.0
KOG2049	536	consensus Translational repressor MPT5/PUF4 and re	100.0
KOG2188	650	consensus Predicted RNA-binding protein, contains	100.0
KOG2050	652	consensus Puf family RNA-binding protein [Translat	99.97
KOG2188	650	consensus Predicted RNA-binding protein, contains	99.95
KOG2050	652	consensus Puf family RNA-binding protein [Translat	99.87
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	99.72
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	99.25
PF00806	35	PUF: Pumilio-family RNA binding repeat; InterPro:	98.52
PF00806	35	PUF: Pumilio-family RNA binding repeat; InterPro:	98.38
smart00025	36	Pumilio Pumilio-like repeats. Pumilio-like repeats	98.11
smart00025	36	Pumilio Pumilio-like repeats. Pumilio-like repeats	97.88
PF08144	148	CPL: CPL (NUC119) domain; InterPro: IPR012959 This	95.13
PRK05686	339	fliG flagellar motor switch protein G; Validated	93.8
PF08144	148	CPL: CPL (NUC119) domain; InterPro: IPR012959 This	92.44

>KOG1488 consensus Translational repressor Pumilio/PUF3 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=7.6e-62  Score=442.80  Aligned_cols=313  Identities=24%  Similarity=0.391  Sum_probs=300.7

Q ss_pred             cCcchhhhccCchhcHHHHHhhcCCCH-HHHHHHHHHHHhhHHhhccCccchHHHHHHhhhcCHHHHHHHHHHHhcccch
Q 035754           10 TNHDLFSLAQDQEGSQYLQENLSSGDS-RILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQL   88 (335)
Q Consensus        10 ~~g~~~~la~~~~~s~~lq~~l~~~~~-e~~~~i~~e~~~~~~~L~~~~~gs~v~q~ll~~~~~~~~~~i~~~l~~~~~~   88 (335)
                      ..|++++++.||+|||++|..++...+ +++..+|+++.+.+..||.|.|||||||+++++++++++..+...+.   ++
T Consensus       177 ~~~~~v~f~~Dq~GsrfiQqkl~~~~~~~ek~~if~ei~~~~~~L~~dvFGNyvIQkffE~gt~~q~~~l~~~~~---g~  253 (503)
T KOG1488|consen  177 IPGHLVEFAKDQHGSRFIQQKLETASDNEEKQAVFDEILPPALELMTDVFGNYVIQKFFEHGTEDQRNLLHSQIK---GH  253 (503)
T ss_pred             cCCCceeecCCcccchHHHHhccccccHHHHHHHHHHHHHHHHHHHHHHhcCchhhhhhccCCHHHHHHHHHHHH---hh
Confidence            349999999999999999999999977 99999999999999999999999999999999999999999999999   99


Q ss_pred             hhhhhccccCcHHHHHHHhhhcCChhHHHHHHHHHHHhhhhhhcCCCccHHHHHHhhcCCcchhHHHHHHHHH--hHHHh
Q 035754           89 FLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALE--HCLYL  166 (335)
Q Consensus        89 ~~~l~~~~~gs~vlq~ll~~~~~~~~~~~~i~~~l~~~~~~l~~d~~g~~vvq~~l~~~~~~~~~~l~~~~~~--~~~~l  166 (335)
                      +..|+.|.|||||+|+.|+. .......+++.+ +.+++..++.|.+||||+|++++..+++....|++.|.+  ++..+
T Consensus       254 v~~Lsld~ygCRVIQkale~-id~~~~~~Li~E-Ld~~vl~~v~DQngnHViQK~ie~~p~~~~~Fiv~~f~~~~~~~~l  331 (503)
T KOG1488|consen  254 VLELSLDMYGCRVIQKALEK-VDVSLQIQLIDE-LDGHLLKCVKDQNGNHVIQKCIETLPPDAWQFIVDFFSGDDNLLEL  331 (503)
T ss_pred             hhhhhcccccchhHHHHHHh-cCHHHHHHHHHH-HHhhHHHHHhhcccceehhhhhhccChHHHHHHHHHhcCCCceeEe
Confidence            99999999999999999999 777777777776 799999999999999999999999999999999999999  99999


Q ss_pred             hcCCCccHHHHHHHhccChHHHHHHHHHHHHhHHhhhcCCChhHHHHHhhccCChhhHHHHHHHHHHhHHHhccCcchhH
Q 035754          167 ACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSF  246 (335)
Q Consensus       167 ~~~~~g~~vlq~~l~~~~~~~~~~l~~~l~~~~~~l~~d~~G~~viq~~l~~~~~~~~~~i~~~l~~~~~~l~~~~~gS~  246 (335)
                      ++|+|||+|+|++++.+.++++..++++|..++..|+.|+|||||||++++++++..+..|++.+.+++.+++.+||+|+
T Consensus       332 s~~~YGCRVIQr~lE~c~~~~~~~i~~ei~~~~~~L~~dQygNYVIQHVie~g~~~~~~~I~~~l~~~ll~~Sq~KfASn  411 (503)
T KOG1488|consen  332 STHKYGCRVIQRILEHCSEDQKQPLMEEIIRNCDQLAQDQYGNYVIQHVIEHGSPYRDTIIIKCLLGNLLSMSQHKFASN  411 (503)
T ss_pred             eccCcccHHHHHHhhcCChHhhhHHHHHHHHHHHHHHhhhhhhHHHHHHHhcCChhhhhhHHHHHHhhHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcCCcH--HHHHHHHhC-----hhhHHhhhcCcchhHHHHHHHhhccCcCcHHHHHHHHHHHHHHHHhhhcCCC
Q 035754          247 VVQKCLKYQNAV--HYIIEELLN-----SDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLAALRVMKY  319 (335)
Q Consensus       247 vve~~l~~~~~~--~~i~~~l~~-----~~~~~~l~~~~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~~~~~L~~~~~  319 (335)
                      |||+|+..++..  ..|++|+++     ++-+..|+.|+|||||||++++.+.+    .+++.|..++++|+..|...+|
T Consensus       412 VVEk~~~~a~~~~r~~i~~Ei~~~~~~~~~~L~~mmkdQYgNYVVQkmi~~~~~----~q~~~i~~rI~~h~~~Lrk~sy  487 (503)
T KOG1488|consen  412 VVEKAFLFAPPLLRALIMNEIFPGYVEHPDALDIMMKDQYGNYVVQKMIDICGP----EQRELIKSRVKPHASRLRKFSY  487 (503)
T ss_pred             HHHHHHhhCCHHHHHHHHHHhcCCccCCccHHHHHHHHhhhhhHHHHHHHhcCH----HHHHHHHHHHHHHHHHHccCcc
Confidence            999999999988  999999998     36899999999999999999999988    8999999999999999999999


Q ss_pred             hHHHHHHHHhhC
Q 035754          320 GSNVYKWTTASH  331 (335)
Q Consensus       320 gs~v~~~l~~~~  331 (335)
                      |+||+.++.+..
T Consensus       488 GKhIia~lek~~  499 (503)
T KOG1488|consen  488 GKHIIAKLEKLR  499 (503)
T ss_pred             HHHHHHHHHHhc
Confidence            999999998864

>cd07920 Pumilio Pumilio-family RNA binding domain

Probab=100.00  E-value=8.2e-60  Score=427.49  Aligned_cols=308  Identities=31%  Similarity=0.457  Sum_probs=298.4

Q ss_pred             CcchhhhccCchhcHHHHHhhcCCCHHHHHHHHHHHHhhHHhhccCccchHHHHHHhhhcCHHHHHHHHHHHhcccchhh
Q 035754           11 NHDLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFL   90 (335)
Q Consensus        11 ~g~~~~la~~~~~s~~lq~~l~~~~~e~~~~i~~e~~~~~~~L~~~~~gs~v~q~ll~~~~~~~~~~i~~~l~~~~~~~~   90 (335)
                      .|++.++|+|++|||++|++++.+++++++.|++++.+++.+|+.|+|||||+|+++++++++++..|++.+.   +++.
T Consensus         9 ~~~~~~l~~~~~gsr~lQ~~l~~~~~~~~~~i~~~l~~~~~~l~~~~~g~~vvq~~l~~~~~~~~~~i~~~~~---~~~~   85 (322)
T cd07920           9 AGHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKIL---GHVV   85 (322)
T ss_pred             CcchhhccCCchhhHHHHHHhccCCHHHHHHHHHHHHHhHHHHhcCccccHHHHHHHHhCCHHHHHHHHHHHH---HHHH
Confidence            3999999999999999999999999999999999999999999999999999999999999999999999999   9999


Q ss_pred             hhhccccCcHHHHHHHhhhcCChhHHHHHHHHHHHhhhhhhcCCCccHHHHHHhhcCCcchhHHHHHHHHHhHHHhhcCC
Q 035754           91 LASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHE  170 (335)
Q Consensus        91 ~l~~~~~gs~vlq~ll~~~~~~~~~~~~i~~~l~~~~~~l~~d~~g~~vvq~~l~~~~~~~~~~l~~~~~~~~~~l~~~~  170 (335)
                      +++.|+|||+++|++++. +. +++...+.+++.+++..|+.|++||||+|++++.++++.++.+++.+.+++..++.|+
T Consensus        86 ~l~~~~~g~~vlqkll~~-~~-~~~~~~i~~~l~~~~~~L~~d~~gn~Vvq~~l~~~~~~~~~~i~~~l~~~~~~l~~~~  163 (322)
T cd07920          86 RLSLDMYGCRVIQKLLES-IS-EEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVALSTHP  163 (322)
T ss_pred             HHcccchhHHHHHHHHHh-cC-HHHHHHHHHHHHHCHHHHhhcccccHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHcCc
Confidence            999999999999999998 54 7788888888999999999999999999999999999999999999999999999999


Q ss_pred             CccHHHHHHHhccChHHHHHHHHHHHHhHHhhhcCCChhHHHHHhhccCChhhHHHHHHHHHHhHHHhccCcchhHHHHH
Q 035754          171 QGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQK  250 (335)
Q Consensus       171 ~g~~vlq~~l~~~~~~~~~~l~~~l~~~~~~l~~d~~G~~viq~~l~~~~~~~~~~i~~~l~~~~~~l~~~~~gS~vve~  250 (335)
                      +||+++|++++.++++++..+++++.+++..|+.|++||||+|++++.++++.+..+++.+.+++.++++++|||+|+|+
T Consensus       164 ~G~~vvq~~l~~~~~~~~~~l~~~l~~~~~~L~~d~~Gn~vvq~~l~~~~~~~~~~i~~~l~~~~~~l~~~k~Gs~Vve~  243 (322)
T cd07920         164 YGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFASNVVEK  243 (322)
T ss_pred             cccHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHhcCCHHHHHHHHHHHHHHHHHHHcCcchHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhcCCcH--HHHHHHHhCh----hhHHhhhcCcchhHHHHHHHhhccCcCcHHHHHHHHHHHHHHHHhhhcCCChHHHH
Q 035754          251 CLKYQNAV--HYIIEELLNS----DQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNVY  324 (335)
Q Consensus       251 ~l~~~~~~--~~i~~~l~~~----~~~~~l~~~~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~~~~~L~~~~~gs~v~  324 (335)
                      |++.+++.  +.++++++..    +++.+|++|+|||||||++|+.+++    ..++.+++.|.+++.+|+.++|||+|+
T Consensus       244 ~l~~~~~~~~~~ii~~l~~~~~~~~~l~~l~~d~~Gn~Viq~~l~~~~~----~~~~~i~~~l~~~~~~L~~~~~G~~v~  319 (322)
T cd07920         244 CLKHASKEERELIIDEILASGNETSALDTLMKDQYGNYVIQTALDVAKE----EQRELLVEAIRPHLPSLRKSPYGKHIL  319 (322)
T ss_pred             HHHHCCHHHHHHHHHHHhcCCCchhHHHHHhCCCcccHHHHHHHHhCCH----HHHHHHHHHHHHHHHHHcCCCcHHHHH
Confidence            99999987  8899999873    4999999999999999999999997    899999999999999999999999999


Q ss_pred             HHH
Q 035754          325 KWT  327 (335)
Q Consensus       325 ~~l  327 (335)
                      ++|
T Consensus       320 ~~~  322 (322)
T cd07920         320 AKL  322 (322)
T ss_pred             HhC
Confidence            985

Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canon

>KOG2049 consensus Translational repressor MPT5/PUF4 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=2.3e-51  Score=377.54  Aligned_cols=317  Identities=36%  Similarity=0.509  Sum_probs=304.3

Q ss_pred             cCcchhhhccCchhcHHHHHhhcCCCHHHHHHHHHHHHhhHHhhccCccchHHHHHHhhhcCHHHHHHHHHHHhcccchh
Q 035754           10 TNHDLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLF   89 (335)
Q Consensus        10 ~~g~~~~la~~~~~s~~lq~~l~~~~~e~~~~i~~e~~~~~~~L~~~~~gs~v~q~ll~~~~~~~~~~i~~~l~~~~~~~   89 (335)
                      .+|.+..+|+|++||+++|+.++.++......|+.++..+..+|+.|+||++++|++++.|+.+++..|+..+..+++.+
T Consensus       215 ~~~~~~~~akd~~gc~~lq~~~~~~~~~~~~~if~~~~~~~~~Lm~d~fGny~vqkl~~~~~~eq~~~i~~~lts~p~~f  294 (536)
T KOG2049|consen  215 IQGSINLIAKDQHGCRLLQKLLSEGTKVSILKIFLETIQDVPELMEDPFGNYLVQKLLEVCDEEQLTKIVSLLTSDPRLF  294 (536)
T ss_pred             cchhhhhhcccccCCcccccCcccCccccHHHHHHHHHHHHHHHHhccchhHHHHHHHHhhCHHHHHHHHHHHhcCccce
Confidence            34899999999999999999999999999999999999999999999999999999999999999999999999889999


Q ss_pred             hhhhccccCcHHHHHHHhhhcCChhHHHHHHHHHHHhhhhhhcCCCccHHHHHHhhcCCcchhHHHHHHHHHhHHHhhcC
Q 035754           90 LLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACH  169 (335)
Q Consensus        90 ~~l~~~~~gs~vlq~ll~~~~~~~~~~~~i~~~l~~~~~~l~~d~~g~~vvq~~l~~~~~~~~~~l~~~~~~~~~~l~~~  169 (335)
                      ..++.+.||++++|++++. ....++...+.+++.+.+..|++|.+|+||+|+|+...+++..+.+++.+..++..+|+|
T Consensus       295 v~i~~N~~GTr~iQkl~~~-~~~~dqI~~~~~ai~~~fl~L~~D~~g~~Viq~cl~~f~~~~~~~l~e~i~~~c~~iA~~  373 (536)
T KOG2049|consen  295 VEICTNMYGTRAVQKLLGK-SDSVDQISLFLDAIKPNFLHLIKDKNGNHVIQRCLRVFSKEKNEFLYEAILRYCLDLATD  373 (536)
T ss_pred             eEeeecCchhHHHHHHHhc-cccHHHHHHHHHHHHhhhHHhhhhcchhHHHHHHHHhcCchhhhHHHHHHHHHHHHHHHh
Confidence            9999999999999999999 888889999999999999999999999999999999999999999999999999999999


Q ss_pred             CCccHHHHHHHhccChHHHHHHHHHHHHhHHhhhcCCChhHHHHHhhccCChhhHHHHHHHHHHhHHHhccCcchhHHHH
Q 035754          170 EQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQ  249 (335)
Q Consensus       170 ~~g~~vlq~~l~~~~~~~~~~l~~~l~~~~~~l~~d~~G~~viq~~l~~~~~~~~~~i~~~l~~~~~~l~~~~~gS~vve  249 (335)
                      ++||.|+|+||....++++..+++++..+...|+.|+|||||+|++++..++.....|++.|.|++.+||.+||||+|||
T Consensus       374 ~hGCcvLq~cl~~~~~~~rd~Lv~~i~~naL~Ls~d~~GNyvVQyvl~L~~~~~t~~i~~~L~g~~veLS~qKfgS~vVE  453 (536)
T KOG2049|consen  374 QHGCCVLQKCLDYSRGEQRDRLVEEISRNALLLSNDPYGNYVVQYVLELNDPSCTVNIAEKLRGHYVELSFQKFGSHVVE  453 (536)
T ss_pred             ccccchhHHHhcchhHHHHHHHHHHHHHHhHhhhcCccccchhhhhhhhcCcchHHHHHHhhhhHHHHHHHHhhccHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhcCCcH-HHHHHHHhChhhHHhhhcCcchhHHHHHHHhhccCcCcHHHHHHHHHHHHHHHHhhhcCCChHHHHHHH
Q 035754          250 KCLKYQNAV-HYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNVYKWT  327 (335)
Q Consensus       250 ~~l~~~~~~-~~i~~~l~~~~~~~~l~~~~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~~~~~L~~~~~gs~v~~~l  327 (335)
                      +||+..+.. ..++.||++-+++.+|+.|+|||||||++|......++...+..++.++++.+..|+.+++|..+..+.
T Consensus       454 k~L~~~~~~~~~iV~ell~~~~~~~Ll~D~ygNyViq~AL~vtk~~~~~~~~~~lv~~~~~~~~~lr~~p~~~~~~~~~  532 (536)
T KOG2049|consen  454 KLLKVRESSRAQIVLELLSCDELDRLLRDPYGNYVIQTALRVTKVKLREDLFGLLVQKLMPRIRLLRNNPGGNIALIKD  532 (536)
T ss_pred             HHHhcCcchhhHHHHHHHccccHHHHhhCccchHHHHHHHHHhhhcccchhhHHHHHHHhhhhHHhhcCcccceeeehh
Confidence            999999999 999999998779999999999999999999998842333789999999999999999999999876654

>COG5099 RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=3.9e-47  Score=366.21  Aligned_cols=308  Identities=27%  Similarity=0.409  Sum_probs=295.2

Q ss_pred             hccCchhcHHHHHhhcCCCHHHHHHHHHHHHhhHHhhccCccchHHHHHHhhhcCHHHHHHHHHHHhcccchhhhhhccc
Q 035754           17 LAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDK   96 (335)
Q Consensus        17 la~~~~~s~~lq~~l~~~~~e~~~~i~~e~~~~~~~L~~~~~gs~v~q~ll~~~~~~~~~~i~~~l~~~~~~~~~l~~~~   96 (335)
                      .++||+|||.||+.|+.-+.+..+.++.++.+...+|+.|.|||||+|++++++++.++..++..+.   +++..++.|+
T Consensus       446 ~~~Dq~g~r~LQk~Lds~s~~~~~~~~~e~~d~~~eLs~d~fGNyliQK~fe~~s~~q~~~ml~~~~---~~~~~ls~~~  522 (777)
T COG5099         446 SCKDQHGSRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSS---KHLVSLSVHK  522 (777)
T ss_pred             ccCCcHHHHHHHHHhcccchHHHHHHHHHHhhhhHHHHHhhhcchhhHHHHHhccHHHHHHHHHHhh---hhHHHhhccc
Confidence            3699999999999999988999999999999999999999999999999999999999999999999   9999999999


Q ss_pred             cCcHHHHHHHhhhcCChhHHHHHHHHHHHhhhhhhcCCCccHHHHHHhhcCCcchhHHHHHHHHHhHHHhhcCCCccHHH
Q 035754           97 FGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINL  176 (335)
Q Consensus        97 ~gs~vlq~ll~~~~~~~~~~~~i~~~l~~~~~~l~~d~~g~~vvq~~l~~~~~~~~~~l~~~~~~~~~~l~~~~~g~~vl  176 (335)
                      ||+||+||+++. +.++++...+.+++.+.+..+++|.+||||+|+|++..+.+....|++.+.++++++++|+|||+|+
T Consensus       523 ~Gtrv~QK~id~-~~t~~qi~~lv~~l~~~~~~li~dqngNHviqKci~~~~~~~~~fif~~~~~~~~~is~~r~Gs~vv  601 (777)
T COG5099         523 YGTRVLQKAIDI-VSTDIQISLLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKEKNQFIFDSINENLYDLSTHRYGSRVV  601 (777)
T ss_pred             cccHHHHHHHhc-cCchhhHHHHHHHhhhhhHHHHHhccCCHHHHHHHHhcCccccchHHHHHHhhhHhhhccccccHHH
Confidence            999999999999 9899999888999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhccChHHHHHHHHHHHHhHHhhhcCCChhHHHHHhhccCChhhHHHHHHHHHH-hHHHhccCcchhHHHHHHHhcC
Q 035754          177 NNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRG-HYVDLSLTKCGSFVVQKCLKYQ  255 (335)
Q Consensus       177 q~~l~~~~~~~~~~l~~~l~~~~~~l~~d~~G~~viq~~l~~~~~~~~~~i~~~l~~-~~~~l~~~~~gS~vve~~l~~~  255 (335)
                      |+|++.+..+....++++|..+...|+.|+|||||||++|+.+.+..++.++..+.. ++.+++++++||.|||+|++.+
T Consensus       602 q~~le~~~~~~~~~~~~~Ii~~~~~L~~dq~GNyvvq~il~~g~~~~k~~i~~~~l~~~v~elS~~kfaSnvVeK~i~~~  681 (777)
T COG5099         602 QRCLENCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKLLSKRVVELSTHKFASNVVEKCIKYA  681 (777)
T ss_pred             HHHHHhccHhHHHHHHHHHHHHHHhhccCCcchhhhhHHhhcCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            999999999999999999999999999999999999999999999999999998888 9999999999999999999999


Q ss_pred             CcH---HHHHHHHhC-----hhhHHhhhcCcchhHHHHHHHhhccCcCcHHHHHHHHHHHHHHHHhhhcCCChHHHHHHH
Q 035754          256 NAV---HYIIEELLN-----SDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNVYKWT  327 (335)
Q Consensus       256 ~~~---~~i~~~l~~-----~~~~~~l~~~~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~~~~~L~~~~~gs~v~~~l  327 (335)
                      ++.   .+|+.++..     +.-+..|+.|.|||||+|+++.....    ..+..+.+.+.+.+..|..++||.++..++
T Consensus       682 ~~~~~~~ril~~~~~~~~~~~~~l~~i~~d~y~Nyv~q~~~~~s~~----~~~~l~~~~i~~~~~~l~~s~~g~~i~~~l  757 (777)
T COG5099         682 SDSFKRSRILNELTNRGIEKPGFLMLILDDQYANYVIQYLLDVSPE----IQRSLLARAIKKVIPSLKKSMYGQHILALL  757 (777)
T ss_pred             CcchHHHHHHHHHhcccccCChHHHHHHHhhhcchHHHHHHhhCch----hhHHHHHHHHHHHHHHHhcCCccHHHHHHH
Confidence            988   488888876     33489999999999999999999999    899999999999999999999999999999


Q ss_pred             HhhCC
Q 035754          328 TASHP  332 (335)
Q Consensus       328 ~~~~~  332 (335)
                      .+.+.
T Consensus       758 e~~~~  762 (777)
T COG5099         758 EKVGS  762 (777)
T ss_pred             HHHhc
Confidence            88764

>cd07920 Pumilio Pumilio-family RNA binding domain

Probab=100.00  E-value=1.2e-43  Score=321.65  Aligned_cols=277  Identities=20%  Similarity=0.261  Sum_probs=264.7

Q ss_pred             HHH-hhHHhhccCccchHHHHHHhhhcCHHHHHHHHHHHhcccchhhhhhccccCcHHHHHHHhhhcCChhHHHHHHHHH
Q 035754           45 VVS-GFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSAL  123 (335)
Q Consensus        45 e~~-~~~~~L~~~~~gs~v~q~ll~~~~~~~~~~i~~~l~~~~~~~~~l~~~~~gs~vlq~ll~~~~~~~~~~~~i~~~l  123 (335)
                      +.. +++.+++.|++||+++|++++.++++++..|+..+.   +++.+++.|+||++|+|++++.  +++++...+.+.+
T Consensus         6 ~~~~~~~~~l~~~~~gsr~lQ~~l~~~~~~~~~~i~~~l~---~~~~~l~~~~~g~~vvq~~l~~--~~~~~~~~i~~~~   80 (322)
T cd07920           6 DIKAGHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEIL---PHVVELMVDPFGNYVIQKLFEH--GTEEQRLQLLEKI   80 (322)
T ss_pred             hccCcchhhccCCchhhHHHHHHhccCCHHHHHHHHHHHH---HhHHHHhcCccccHHHHHHHHh--CCHHHHHHHHHHH
Confidence            344 899999999999999999999999999999999999   9999999999999999999998  5678888888889


Q ss_pred             HHhhhhhhcCCCccHHHHHHhhcCCcchhHHHHHHHHHhHHHhhcCCCccHHHHHHHhccChHHHHHHHHHHHHhHHhhh
Q 035754          124 KRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLS  203 (335)
Q Consensus       124 ~~~~~~l~~d~~g~~vvq~~l~~~~~~~~~~l~~~~~~~~~~l~~~~~g~~vlq~~l~~~~~~~~~~l~~~l~~~~~~l~  203 (335)
                      .+++..++.|++|++++|++++..+++++..+++.+.+++..|+.|++|++|+|++++.++++++..+++.+.+++..++
T Consensus        81 ~~~~~~l~~~~~g~~vlqkll~~~~~~~~~~i~~~l~~~~~~L~~d~~gn~Vvq~~l~~~~~~~~~~i~~~l~~~~~~l~  160 (322)
T cd07920          81 LGHVVRLSLDMYGCRVIQKLLESISEEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVALS  160 (322)
T ss_pred             HHHHHHHcccchhHHHHHHHHHhcCHHHHHHHHHHHHHCHHHHhhcccccHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCChhHHHHHhhccCChhhHHHHHHHHHHhHHHhccCcchhHHHHHHHhcCCcH--HHHHHHHhChhhHHhhhcCcchh
Q 035754          204 RHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLKYQNAV--HYIIEELLNSDQILQVANDKYGN  281 (335)
Q Consensus       204 ~d~~G~~viq~~l~~~~~~~~~~i~~~l~~~~~~l~~~~~gS~vve~~l~~~~~~--~~i~~~l~~~~~~~~l~~~~~g~  281 (335)
                      .|++|++++|++++..+++.++.+++.+.+++..|+.|+||++|+|++++.+++.  +.+++.+.+  ++..|+.|+||+
T Consensus       161 ~~~~G~~vvq~~l~~~~~~~~~~l~~~l~~~~~~L~~d~~Gn~vvq~~l~~~~~~~~~~i~~~l~~--~~~~l~~~k~Gs  238 (322)
T cd07920         161 THPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLG--NIVQLSCHKFAS  238 (322)
T ss_pred             cCccccHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHhcCCHHHHHHHHHHHHH--HHHHHHcCcchH
Confidence            9999999999999999999999999999999999999999999999999999877  889999997  999999999999


Q ss_pred             HHHHHHHhhccCcCcHHHHHHHHHHHH------HHHHhhhcCCChHHHHHHHHhhCC
Q 035754          282 YVIQTALAETMRQDRLSVHQRLVTKLQ------QHLAALRVMKYGSNVYKWTTASHP  332 (335)
Q Consensus       282 ~Viq~~l~~~~~~~~~~~~~~l~~~l~------~~~~~L~~~~~gs~v~~~l~~~~~  332 (335)
                      +|++++++.+++    ..++.+++++.      +++.+|+.++||++|+++++...+
T Consensus       239 ~Vve~~l~~~~~----~~~~~ii~~l~~~~~~~~~l~~l~~d~~Gn~Viq~~l~~~~  291 (322)
T cd07920         239 NVVEKCLKHASK----EERELIIDEILASGNETSALDTLMKDQYGNYVIQTALDVAK  291 (322)
T ss_pred             HHHHHHHHHCCH----HHHHHHHHHHhcCCCchhHHHHHhCCCcccHHHHHHHHhCC
Confidence            999999999998    89999999994      589999999999999999998765

Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canon

>KOG1488 consensus Translational repressor Pumilio/PUF3 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=1.1e-41  Score=310.99  Aligned_cols=241  Identities=21%  Similarity=0.250  Sum_probs=231.3

Q ss_pred             cchhhhhhccccCcHHHHHHHhhhcCChhHHHHHHHHHHHhhhhhhcCCCccHHHHHHhhcCCcchhHHHHHHHHHhHHH
Q 035754           86 DQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLY  165 (335)
Q Consensus        86 ~~~~~~l~~~~~gs~vlq~ll~~~~~~~~~~~~i~~~l~~~~~~l~~d~~g~~vvq~~l~~~~~~~~~~l~~~~~~~~~~  165 (335)
                      .+++.+++.|++||+.+|.-++. ....+....+++.+.+.+.+||.|.+||||||+++++.+.+++..+...+.+++..
T Consensus       178 ~~~~v~f~~Dq~GsrfiQqkl~~-~~~~~ek~~if~ei~~~~~~L~~dvFGNyvIQkffE~gt~~q~~~l~~~~~g~v~~  256 (503)
T KOG1488|consen  178 PGHLVEFAKDQHGSRFIQQKLET-ASDNEEKQAVFDEILPPALELMTDVFGNYVIQKFFEHGTEDQRNLLHSQIKGHVLE  256 (503)
T ss_pred             CCCceeecCCcccchHHHHhccc-cccHHHHHHHHHHHHHHHHHHHHHHhcCchhhhhhccCCHHHHHHHHHHHHhhhhh
Confidence            38899999999999999999998 55547788888889999999999999999999999999999999999999999999


Q ss_pred             hhcCCCccHHHHHHHhccChHHHHHHHHHHHHhHHhhhcCCChhHHHHHhhccCChhhHHHHHHHHHH--hHHHhccCcc
Q 035754          166 LACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRG--HYVDLSLTKC  243 (335)
Q Consensus       166 l~~~~~g~~vlq~~l~~~~~~~~~~l~~~l~~~~~~l~~d~~G~~viq~~l~~~~~~~~~~i~~~l~~--~~~~l~~~~~  243 (335)
                      ||.++|||+|+|+.++..+.+....|+.+|.+++..+++|++||||||++++..+++....|++.|.+  ++..++.|||
T Consensus       257 Lsld~ygCRVIQkale~id~~~~~~Li~ELd~~vl~~v~DQngnHViQK~ie~~p~~~~~Fiv~~f~~~~~~~~ls~~~Y  336 (503)
T KOG1488|consen  257 LSLDMYGCRVIQKALEKVDVSLQIQLIDELDGHLLKCVKDQNGNHVIQKCIETLPPDAWQFIVDFFSGDDNLLELSTHKY  336 (503)
T ss_pred             hhcccccchhHHHHHHhcCHHHHHHHHHHHHhhHHHHHhhcccceehhhhhhccChHHHHHHHHHhcCCCceeEeeccCc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999  9999999999


Q ss_pred             hhHHHHHHHhcCCcH--HHHHHHHhChhhHHhhhcCcchhHHHHHHHhhccCcCcHHHHHHHHHHHHHHHHhhhcCCChH
Q 035754          244 GSFVVQKCLKYQNAV--HYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLAALRVMKYGS  321 (335)
Q Consensus       244 gS~vve~~l~~~~~~--~~i~~~l~~~~~~~~l~~~~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~~~~~L~~~~~gs  321 (335)
                      ||+|+|++++.+.+.  ..++++|..  ++.+|+.|+|||||||++++.+++    ..+..|.+.|.+++..++.++|+|
T Consensus       337 GCRVIQr~lE~c~~~~~~~i~~ei~~--~~~~L~~dQygNYVIQHVie~g~~----~~~~~I~~~l~~~ll~~Sq~KfAS  410 (503)
T KOG1488|consen  337 GCRVIQRILEHCSEDQKQPLMEEIIR--NCDQLAQDQYGNYVIQHVIEHGSP----YRDTIIIKCLLGNLLSMSQHKFAS  410 (503)
T ss_pred             ccHHHHHHhhcCChHhhhHHHHHHHH--HHHHHHhhhhhhHHHHHHHhcCCh----hhhhhHHHHHHhhHHHHHHHHHHH
Confidence            999999999999999  669999999  999999999999999999999999    899999999999999999999999


Q ss_pred             HHHHHHHhhCCC
Q 035754          322 NVYKWTTASHPC  333 (335)
Q Consensus       322 ~v~~~l~~~~~~  333 (335)
                      +|+++|...+|.
T Consensus       411 nVVEk~~~~a~~  422 (503)
T KOG1488|consen  411 NVVEKAFLFAPP  422 (503)
T ss_pred             HHHHHHHhhCCH
Confidence            999999998774

>COG5099 RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=4.8e-34  Score=275.79  Aligned_cols=233  Identities=22%  Similarity=0.302  Sum_probs=219.8

Q ss_pred             hccccCcHHHHHHHhhhcCChhHHHHHHHHHHHhhhhhhcCCCccHHHHHHhhcCCcchhHHHHHHHHHhHHHhhcCCCc
Q 035754           93 SVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQG  172 (335)
Q Consensus        93 ~~~~~gs~vlq~ll~~~~~~~~~~~~i~~~l~~~~~~l~~d~~g~~vvq~~l~~~~~~~~~~l~~~~~~~~~~l~~~~~g  172 (335)
                      +.|++|||.||+.++.  ...+..+.+..++.+...+||.|.+||||+|++++.++..++..++..+.+++..++.|++|
T Consensus       447 ~~Dq~g~r~LQk~Lds--~s~~~~~~~~~e~~d~~~eLs~d~fGNyliQK~fe~~s~~q~~~ml~~~~~~~~~ls~~~~G  524 (777)
T COG5099         447 CKDQHGSRFLQKLLDS--NSSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKHLVSLSVHKYG  524 (777)
T ss_pred             cCCcHHHHHHHHHhcc--cchHHHHHHHHHHhhhhHHHHHhhhcchhhHHHHHhccHHHHHHHHHHhhhhHHHhhccccc
Confidence            6999999999999998  55566777777799999999999999999999999999999999999999999999999999


Q ss_pred             cHHHHHHHhccChHH-HHHHHHHHHHhHHhhhcCCChhHHHHHhhccCChhhHHHHHHHHHHhHHHhccCcchhHHHHHH
Q 035754          173 CINLNNFIDNMKGSR-RKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKC  251 (335)
Q Consensus       173 ~~vlq~~l~~~~~~~-~~~l~~~l~~~~~~l~~d~~G~~viq~~l~~~~~~~~~~i~~~l~~~~~~l~~~~~gS~vve~~  251 (335)
                      |+++|++++....+. ...++.++.+++..+++|++||+|+|++++...++....|++.+.+++.+++.++|||+|+|+|
T Consensus       525 trv~QK~id~~~t~~qi~~lv~~l~~~~~~li~dqngNHviqKci~~~~~~~~~fif~~~~~~~~~is~~r~Gs~vvq~~  604 (777)
T COG5099         525 TRVLQKAIDIVSTDIQISLLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKEKNQFIFDSINENLYDLSTHRYGSRVVQRC  604 (777)
T ss_pred             cHHHHHHHhccCchhhHHHHHHHhhhhhHHHHHhccCCHHHHHHHHhcCccccchHHHHHHhhhHhhhccccccHHHHHH
Confidence            999999999987655 5589999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhcCCcH--HHHHHHHhChhhHHhhhcCcchhHHHHHHHhhccCcCcHHHHHHHHHHHHH-HHHhhhcCCChHHHHHHHH
Q 035754          252 LKYQNAV--HYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQ-HLAALRVMKYGSNVYKWTT  328 (335)
Q Consensus       252 l~~~~~~--~~i~~~l~~~~~~~~l~~~~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~-~~~~L~~~~~gs~v~~~l~  328 (335)
                      ++.+...  +.++++++.  +...|++|+|||||||++++.+..    ..+++++..+.. ++.+|+.++||+.|++||.
T Consensus       605 le~~~~~~~~~~~~~Ii~--~~~~L~~dq~GNyvvq~il~~g~~----~~k~~i~~~~l~~~v~elS~~kfaSnvVeK~i  678 (777)
T COG5099         605 LENCNSEDKENLVEEIIS--NSKYLSQDQYGNYVVQHILDNGAE----PNKERIIIKLLSKRVVELSTHKFASNVVEKCI  678 (777)
T ss_pred             HHhccHhHHHHHHHHHHH--HHHhhccCCcchhhhhHHhhcCCC----cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999998  789999999  999999999999999999999999    788999998888 9999999999999999999


Q ss_pred             hhCCC
Q 035754          329 ASHPC  333 (335)
Q Consensus       329 ~~~~~  333 (335)
                      ++.+.
T Consensus       679 ~~~~~  683 (777)
T COG5099         679 KYASD  683 (777)
T ss_pred             hcCCc
Confidence            98764

>KOG2049 consensus Translational repressor MPT5/PUF4 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=6e-34  Score=262.60  Aligned_cols=239  Identities=22%  Similarity=0.263  Sum_probs=225.2

Q ss_pred             chhhhhhccccCcHHHHHHHhhhcCChhHHHHHHHHHHHhhhhhhcCCCccHHHHHHhhcCCcchhHHHHHHHHH---hH
Q 035754           87 QLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALE---HC  163 (335)
Q Consensus        87 ~~~~~l~~~~~gs~vlq~ll~~~~~~~~~~~~i~~~l~~~~~~l~~d~~g~~vvq~~l~~~~~~~~~~l~~~~~~---~~  163 (335)
                      +.+..+++|++||+++|+.++.  ++......+...+..++.+||.|++|++++|++++.++.+++..|.+.+..   .+
T Consensus       217 ~~~~~~akd~~gc~~lq~~~~~--~~~~~~~~if~~~~~~~~~Lm~d~fGny~vqkl~~~~~~eq~~~i~~~lts~p~~f  294 (536)
T KOG2049|consen  217 GSINLIAKDQHGCRLLQKLLSE--GTKVSILKIFLETIQDVPELMEDPFGNYLVQKLLEVCDEEQLTKIVSLLTSDPRLF  294 (536)
T ss_pred             hhhhhhcccccCCcccccCccc--CccccHHHHHHHHHHHHHHHHhccchhHHHHHHHHhhCHHHHHHHHHHHhcCccce
Confidence            7889999999999999999997  666667777777999999999999999999999999999999999999987   48


Q ss_pred             HHhhcCCCccHHHHHHHhccC-hHHHHHHHHHHHHhHHhhhcCCChhHHHHHhhccCChhhHHHHHHHHHHhHHHhccCc
Q 035754          164 LYLACHEQGCINLNNFIDNMK-GSRRKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTK  242 (335)
Q Consensus       164 ~~l~~~~~g~~vlq~~l~~~~-~~~~~~l~~~l~~~~~~l~~d~~G~~viq~~l~~~~~~~~~~i~~~l~~~~~~l~~~~  242 (335)
                      ..++.+.+|++++|++++... .+++..++..+.+.+..|++|.||+||+|.+++..++...+.+++.......++|.++
T Consensus       295 v~i~~N~~GTr~iQkl~~~~~~~dqI~~~~~ai~~~fl~L~~D~~g~~Viq~cl~~f~~~~~~~l~e~i~~~c~~iA~~~  374 (536)
T KOG2049|consen  295 VEICTNMYGTRAVQKLLGKSDSVDQISLFLDAIKPNFLHLIKDKNGNHVIQRCLRVFSKEKNEFLYEAILRYCLDLATDQ  374 (536)
T ss_pred             eEeeecCchhHHHHHHHhccccHHHHHHHHHHHHhhhHHhhhhcchhHHHHHHHHhcCchhhhHHHHHHHHHHHHHHHhc
Confidence            999999999999999999874 5678889999999999999999999999999999999999999999999999999999


Q ss_pred             chhHHHHHHHhcCCcH--HHHHHHHhChhhHHhhhcCcchhHHHHHHHhhccCcCcHHHHHHHHHHHHHHHHhhhcCCCh
Q 035754          243 CGSFVVQKCLKYQNAV--HYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLAALRVMKYG  320 (335)
Q Consensus       243 ~gS~vve~~l~~~~~~--~~i~~~l~~~~~~~~l~~~~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~~~~~L~~~~~g  320 (335)
                      +|+.|+++|+......  +.+++++..  +...|+.|+|||||+|++++.-+.    .....|+..|.|+..+|+..+||
T Consensus       375 hGCcvLq~cl~~~~~~~rd~Lv~~i~~--naL~Ls~d~~GNyvVQyvl~L~~~----~~t~~i~~~L~g~~veLS~qKfg  448 (536)
T KOG2049|consen  375 HGCCVLQKCLDYSRGEQRDRLVEEISR--NALLLSNDPYGNYVVQYVLELNDP----SCTVNIAEKLRGHYVELSFQKFG  448 (536)
T ss_pred             cccchhHHHhcchhHHHHHHHHHHHHH--HhHhhhcCccccchhhhhhhhcCc----chHHHHHHhhhhHHHHHHHHhhc
Confidence            9999999999999988  999999999  999999999999999999999998    67899999999999999999999


Q ss_pred             HHHHHHHHhhCCC
Q 035754          321 SNVYKWTTASHPC  333 (335)
Q Consensus       321 s~v~~~l~~~~~~  333 (335)
                      |+||++|++..|.
T Consensus       449 S~vVEk~L~~~~~  461 (536)
T KOG2049|consen  449 SHVVEKLLKVRES  461 (536)
T ss_pred             cHHHHHHHhcCcc
Confidence            9999999998764

>KOG2188 consensus Predicted RNA-binding protein, contains Pumilio domains [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=5.9e-31  Score=241.05  Aligned_cols=312  Identities=19%  Similarity=0.246  Sum_probs=243.6

Q ss_pred             ccccccCcchhhhccCchhcHHHHHhhcCCCHHHHHHHHHHHHhhHHhhccCccchHHHHHHhhhc--------------
Q 035754            5 AFEHCTNHDLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESC--------------   70 (335)
Q Consensus         5 ~~~~~~~g~~~~la~~~~~s~~lq~~l~~~~~e~~~~i~~e~~~~~~~L~~~~~gs~v~q~ll~~~--------------   70 (335)
                      .|+|.. |++.++|+++.||..||+++..++..+...++.++.+++..+++|+|||||+|.++...              
T Consensus        93 i~ee~~-grel~l~tnqi~Sk~le~l~~f~d~~ql~~ff~~~~g~lr~i~~~r~gshVle~~L~~~a~~vg~e~~~~s~d  171 (650)
T KOG2188|consen   93 IFEEVY-GRELDLATNQIGSKVLEDLLGFSDSRQLCDFFSALNGVLRSIAQHRFGSHVLESALEKLAALVGQEAALLSED  171 (650)
T ss_pred             HHHHhc-cceeehhccchhHHHHHHHhccCCchhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHhCccccccchh
Confidence            577777 99999999999999999999999999999999999999999999999999999999874              


Q ss_pred             ------------CHHHHHHHHHHHhcccchhh-hhhccccCcHHHHHHHhhhcCCh------------------------
Q 035754           71 ------------NESQLALIILKITFQDQLFL-LASVDKFGSSSVKKLIKVVAHLP------------------------  113 (335)
Q Consensus        71 ------------~~~~~~~i~~~l~~~~~~~~-~l~~~~~gs~vlq~ll~~~~~~~------------------------  113 (335)
                                  -++...-+..++.   +++. .++.|.+|+||+++++-. +.+.                        
T Consensus       172 ea~~~ke~p~~t~e~~~~~m~nei~---~~~~~~l~~~~~gshv~rt~~l~-l~s~~~~~~~~~~~~~~~~~~~~~~~~~  247 (650)
T KOG2188|consen  172 EAAVEKEGPFVTCENLLLLMLNEIS---PHVLKTLMELIFGSHVLRTILLL-LFSMCPIAESEHKLALRKAAHRGMDDWD  247 (650)
T ss_pred             hhcccccCcccccchHHHHHHHHhh---HHHHHHHHHHHHhHHHHHHHHHH-HccCcchhhhHHHHHHHHHhhccccchh
Confidence                        1133445566777   8887 999999999999998865 3220                        


Q ss_pred             ---------------------------------hHH------------HHHHHHHH------------------------
Q 035754          114 ---------------------------------PLL------------YHVMSALK------------------------  124 (335)
Q Consensus       114 ---------------------------------~~~------------~~i~~~l~------------------------  124 (335)
                                                       +..            +..+....                        
T Consensus       248 ~~~~~pqsFp~~l~~~i~~~l~~~~~~s~~~~~~~k~~~vDk~~s~v~q~~i~l~~~~~~~~~~~~~~~lv~~~~~~~e~  327 (650)
T KOG2188|consen  248 AVTTPPQSFPQRLIVWICTGLSALQDVSESKKRDLKGYEVDKSSSNVLQKAIRLAFDENKNDQFMESPRLVTKFQLFNEK  327 (650)
T ss_pred             hhhcChhhccHHHHHHHhhhccccccchhhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhcchhhhhhhhHHHhhhhcccc
Confidence                                             000            00000000                        


Q ss_pred             --------HhhhhhhcCCCccHHHHHHhhcCCcchhHHHHHHHHHhHHHhhcCCCccHHHHHHHhccC-hHHHHHHHHHH
Q 035754          125 --------RLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMK-GSRRKQILHLI  195 (335)
Q Consensus       125 --------~~~~~l~~d~~g~~vvq~~l~~~~~~~~~~l~~~~~~~~~~l~~~~~g~~vlq~~l~~~~-~~~~~~l~~~l  195 (335)
                              +....+..|+.|||+++.+++.++++....++..+.+++.+||.|+.++++||+++++.. .++...+++++
T Consensus       328 d~~~~kE~~~~k~~l~d~tgSrllE~Imeva~~~~~~lf~~~f~~rl~~La~~p~aNF~lQrli~h~~~~e~v~~v~eeL  407 (650)
T KOG2188|consen  328 DGLWGKERSFLKELLSDQTGSRLLEVIMEVASESLLSLFYIVFCGRLDELAVHPIANFPLQRLINHLTSLEDVGSVIEEL  407 (650)
T ss_pred             CcccccccHHHHHHHhcCcccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhCccccchHHHHHHhccCHHHHHHHHHHH
Confidence                    013366779999999999999999999988888899999999999999999999999986 78899999999


Q ss_pred             HHhHHhhhcCC-----------------------------------------------------------------ChhH
Q 035754          196 SVNAASLSRHR-----------------------------------------------------------------SGNY  210 (335)
Q Consensus       196 ~~~~~~l~~d~-----------------------------------------------------------------~G~~  210 (335)
                      .+++..|....                                                                 .|+.
T Consensus       408 ~P~~~~LL~~g~~gVv~sLia~~~rl~s~q~~~l~~Li~a~~~~~~~~k~il~~lL~~~~~~g~~~~~~~t~~~h~~ga~  487 (650)
T KOG2188|consen  408 APKLSSLLEQGNSGVVASLIAASARLGSYQDKMLQQLIQAFHAASESKKNILPCLLFSLTLFGCVGEWFLTEKFHQKGAV  487 (650)
T ss_pred             hHHHHHHHHcCCchHhHHHHHHHHhhchhHHHHHHHHHHHHhcCChhhcchHHHHHHHhhhcccccccccHHHHhhchhH
Confidence            88877666522                                                                 3455


Q ss_pred             HHHHhhccCChh---hHHHHHHHHHHhHHHhccCcchhHHHHHHHhcCC--cH--HHHHHHHhChhhHHhhhcCcchhHH
Q 035754          211 VVQHVLSLEDPF---LIDAICFALRGHYVDLSLTKCGSFVVQKCLKYQN--AV--HYIIEELLNSDQILQVANDKYGNYV  283 (335)
Q Consensus       211 viq~~l~~~~~~---~~~~i~~~l~~~~~~l~~~~~gS~vve~~l~~~~--~~--~~i~~~l~~~~~~~~l~~~~~g~~V  283 (335)
                      ++|.+++...+.   ....+.+...+++.+++++++||||||.+++...  ..  ++++..|-+  .+.+|+.+.+||+|
T Consensus       488 lle~lv~f~k~~i~~litsll~L~~eqi~e~~~~~~~ShlIeavL~S~~l~~~~~~kLi~~l~g--~~~~La~~~~GSrv  565 (650)
T KOG2188|consen  488 LLEELVNFSKTHIQTLITSLLSLSEEQILEMSCNGVGSHLIEAVLASKDLGEKIKEKLINILDG--SFVTLALSTFGSRV  565 (650)
T ss_pred             HHHHHHhhchhhhHHHHHHHHhhhHHHHHHHhcCCchHHHHHHHHHhccccHHHHHHHHHHhhc--cchheeecCcccHH
Confidence            555555543331   2233444445678888888888888888888833  33  777777776  88888888888888


Q ss_pred             HHHHHhhccCcCcHHHHHHHHHHHHHHHHhhhcCCChHHHHHHH
Q 035754          284 IQTALAETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNVYKWT  327 (335)
Q Consensus       284 iq~~l~~~~~~~~~~~~~~l~~~l~~~~~~L~~~~~gs~v~~~l  327 (335)
                      +.++|+.++.    .+|++|+.+|.+.-.++..++||++|+.++
T Consensus       566 ~eK~wea~~~----~~k~rIakeL~~~~~~vk~s~~gk~v~~~~  605 (650)
T KOG2188|consen  566 FEKCWEATDV----LYKERIAKELVGIHNDVKSSKYGKFVMLNW  605 (650)
T ss_pred             HHHHHHHhhH----HHHHHHHHHHHhhccccccCcchHHHHHhc
Confidence            8888888887    888888888888888888888888888765

>KOG2050 consensus Puf family RNA-binding protein [Translation, ribosomal structure and biogenesis]

Probab=99.97  E-value=1.6e-30  Score=236.00  Aligned_cols=282  Identities=18%  Similarity=0.167  Sum_probs=211.1

Q ss_pred             cccCcchhhhccCchhcHHHHHhhcCCCHHHHHHHHHHHHhhHHhhccCccchHHHHHHhhhcCHHHHHHHHHHHhcccc
Q 035754            8 HCTNHDLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQ   87 (335)
Q Consensus         8 ~~~~g~~~~la~~~~~s~~lq~~l~~~~~e~~~~i~~e~~~~~~~L~~~~~gs~v~q~ll~~~~~~~~~~i~~~l~~~~~   87 (335)
                      .+.+|++.+++..++.||++|++++++++.+|+.||+|+.|.+.+||.++||-|++|+++.++++.++..|+..+.   |
T Consensus       160 ~likg~i~~lv~aHDtSRViQt~Vky~s~~~r~~if~eL~p~~v~l~kskY~k~~v~KmLkyGsk~q~a~iI~sl~---G  236 (652)
T KOG2050|consen  160 KLIKGKISKLVFAHDTSRVIQTCVKYGSEAQREQIFEELLPFFVELAKSKYAKFFVQKMLKYGSKAQKAKIINSLR---G  236 (652)
T ss_pred             HHHhhhHHHHHHHhhhHHHHHHHHHhcCHHHHHHHHHHHhHHHHHHHHhHHHHHHHHHHHhcCCHHHHHHHHHHHh---h
Confidence            3456999999999999999999999999999999999999999999999999999999999999999999999999   9


Q ss_pred             hhhhhhccccCcHHHHHHHhhhcCChhHHHHHHHHHHHhhhhhhcCCCccHHHHHHhhcCCcchhHHHHHHHHHhHHHhh
Q 035754           88 LFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLA  167 (335)
Q Consensus        88 ~~~~l~~~~~gs~vlq~ll~~~~~~~~~~~~i~~~l~~~~~~l~~d~~g~~vvq~~l~~~~~~~~~~l~~~~~~~~~~l~  167 (335)
                      |++.|+-|+.|+.|++.++.. .++.++...++.++.+....++++.+--++...+.+.  ++.+..|...+.+.+..++
T Consensus       237 hv~kLlRH~eaa~Vve~ay~~-~A~l~Qr~~li~EfYG~efqlfK~sn~~Tl~kil~~~--pekk~~I~~~l~~~I~~v~  313 (652)
T KOG2050|consen  237 HVVKLLRHREAAYVVEYAYND-FATLEQRQYLIQEFYGDEFQLFKDSNDKTLDKILAEA--PEKKASILRHLKAIITPVA  313 (652)
T ss_pred             hHHHHHhhhHHHHHHHHHHHh-hccHHHHHHHHHHHhhHHHHHHhccCcccHHHHHHhC--hHhHHHHHHHHHHHhHHHh
Confidence            999999999999999999998 8889999999998999999999985544444433333  5556666555544332221


Q ss_pred             cCCCccHHHHHHHhccChHHHHHHHHHHHHhHHhhhcCCChhHHHHHhhccCChhhHHHHHHHHHHhHHHhccCcchhHH
Q 035754          168 CHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFV  247 (335)
Q Consensus       168 ~~~~g~~vlq~~l~~~~~~~~~~l~~~l~~~~~~l~~d~~G~~viq~~l~~~~~~~~~~i~~~l~~~~~~l~~~~~gS~v  247 (335)
                      .-               +.....|+..                ++.-.+..++++.+.++++.+.+.+++|.+++.||+|
T Consensus       314 eK---------------g~v~~tivHk----------------~mlEy~~~ade~e~~e~l~ll~elv~e~vHT~dGS~v  362 (652)
T KOG2050|consen  314 EK---------------GSVDHTIVHK----------------LMLEYLTIADEEEKSELLELLKELVPEMVHTRDGSRV  362 (652)
T ss_pred             hc---------------chhHHHHHHH----------------HHHHHHHhCCHHHHHHHHHHHHHHHHHHhcCCchHHH
Confidence            10               0011112111                1112234456666677777777777777777777777


Q ss_pred             HHHHHhcCCcH--HHHHHHHhChhhHHhhhcCcchhHHHHHHHhhccCcCcHHHHHHHHHHHHHHHHhhhcCCChHHHHH
Q 035754          248 VQKCLKYQNAV--HYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNVYK  325 (335)
Q Consensus       248 ve~~l~~~~~~--~~i~~~l~~~~~~~~l~~~~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~~~~~L~~~~~gs~v~~  325 (335)
                      ...|+..++++  +.|++.+..  ++..+|+|+||+.|+-++|+..++|+  ..++.|+.++.+.+..+..++||++|+.
T Consensus       363 Am~li~~a~aKeRK~IiK~~K~--h~~K~A~~~yGh~vlia~ldc~DDT~--l~kk~i~~e~~~el~~li~Dk~Grrv~l  438 (652)
T KOG2050|consen  363 AMKLIWHATAKERKLIIKNMKE--HVEKIANDEYGHLVLIALLDCTDDTK--LLKKLIYDELKSELKSLISDKYGRRVIL  438 (652)
T ss_pred             HHHHHhhCCHHHHHHHHHHHHH--HHHHHHhhccCceehhhhhcccchHH--HHHHHHHHHHHHHHHHHhccchhhhhhh
Confidence            77777777776  666677766  77777777777777777777777642  5666667777777777777777777777


Q ss_pred             HHHhh
Q 035754          326 WTTAS  330 (335)
Q Consensus       326 ~l~~~  330 (335)
                      .++..
T Consensus       439 yll~p  443 (652)
T KOG2050|consen  439 YLLAP  443 (652)
T ss_pred             hhccC
Confidence            76654

>KOG2188 consensus Predicted RNA-binding protein, contains Pumilio domains [Translation, ribosomal structure and biogenesis]

Probab=99.95  E-value=1.8e-26  Score=211.77  Aligned_cols=309  Identities=17%  Similarity=0.238  Sum_probs=238.1

Q ss_pred             ccCchhcHHHHHhhcC---CCH--H----HH-HHHHHHHHhhHHhhccCccchHHHHHHhhhcCHHHHHHHHHHHhcccc
Q 035754           18 AQDQEGSQYLQENLSS---GDS--R----IL-DKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQ   87 (335)
Q Consensus        18 a~~~~~s~~lq~~l~~---~~~--e----~~-~~i~~e~~~~~~~L~~~~~gs~v~q~ll~~~~~~~~~~i~~~l~~~~~   87 (335)
                      ..||.+..+.+.....   +..  +    .. +.|++|..+...++++++.||+++|.++..|+..+...+++.+.   +
T Consensus        59 ~~dpE~~~YF~~a~~a~~~~~~~~eEr~~~f~n~i~ee~~grel~l~tnqi~Sk~le~l~~f~d~~ql~~ff~~~~---g  135 (650)
T KOG2188|consen   59 GLDPEELGYFRRAESAFKGGFERGEERNRMFVNSIFEEVYGRELDLATNQIGSKVLEDLLGFSDSRQLCDFFSALN---G  135 (650)
T ss_pred             CcChhhhhHHHHHHHHhhcCccccccceeeeehhHHHHhccceeehhccchhHHHHHHHhccCCchhHHHHHHHHh---h
Confidence            4567776666555543   211  1    23 34999999999999999999999999999999999999999999   9


Q ss_pred             hhhhhhccccCcHHHHHHHhhhcC------------------------ChhHHHHHHHHHHHhhh-hhhcCCCccHHHHH
Q 035754           88 LFLLASVDKFGSSSVKKLIKVVAH------------------------LPPLLYHVMSALKRLFK-FLMMTKPGSSVILQ  142 (335)
Q Consensus        88 ~~~~l~~~~~gs~vlq~ll~~~~~------------------------~~~~~~~i~~~l~~~~~-~l~~d~~g~~vvq~  142 (335)
                      +++.+++|++||||+|++++.+++                        .++....+.+++.+++. .+|.|.+|+||++.
T Consensus       136 ~lr~i~~~r~gshVle~~L~~~a~~vg~e~~~~s~dea~~~ke~p~~t~e~~~~~m~nei~~~~~~~l~~~~~gshv~rt  215 (650)
T KOG2188|consen  136 VLRSIAQHRFGSHVLESALEKLAALVGQEAALLSEDEAAVEKEGPFVTCENLLLLMLNEISPHVLKTLMELIFGSHVLRT  215 (650)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhCccccccchhhhcccccCcccccchHHHHHHHHhhHHHHHHHHHHHHhHHHHHH
Confidence            999999999999999999987421                        13344566677999998 99999999999998


Q ss_pred             HhhcCCcc----------------------------------------------------------------------hh
Q 035754          143 CLEPSYNH----------------------------------------------------------------------KN  152 (335)
Q Consensus       143 ~l~~~~~~----------------------------------------------------------------------~~  152 (335)
                      ++-.....                                                                      ..
T Consensus       216 ~~l~l~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pqsFp~~l~~~i~~~l~~~~~~s~~~~~~~k~~~vDk~~s~v~  295 (650)
T KOG2188|consen  216 ILLLLFSMCPIAESEHKLALRKAAHRGMDDWDAVTTPPQSFPQRLIVWICTGLSALQDVSESKKRDLKGYEVDKSSSNVL  295 (650)
T ss_pred             HHHHHccCcchhhhHHHHHHHHHhhccccchhhhhcChhhccHHHHHHHhhhccccccchhhhhhHHHHHHHHHHHHHHH
Confidence            88763220                                                                      00


Q ss_pred             HHHHHH---------HHH-----------------------hHHHhhcCCCccHHHHHHHhccChHHHHHHHHHHHHhHH
Q 035754          153 DFIYQA---------ALE-----------------------HCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAA  200 (335)
Q Consensus       153 ~~l~~~---------~~~-----------------------~~~~l~~~~~g~~vlq~~l~~~~~~~~~~l~~~l~~~~~  200 (335)
                      +.++..         +..                       -...+..|+.||++++.+++.++++....+...+.+.+.
T Consensus       296 q~~i~l~~~~~~~~~~~~~~~lv~~~~~~~e~d~~~~kE~~~~k~~l~d~tgSrllE~Imeva~~~~~~lf~~~f~~rl~  375 (650)
T KOG2188|consen  296 QKAIRLAFDENKNDQFMESPRLVTKFQLFNEKDGLWGKERSFLKELLSDQTGSRLLEVIMEVASESLLSLFYIVFCGRLD  375 (650)
T ss_pred             HHHHHHHhhhhcchhhhhhhhHHHhhhhccccCcccccccHHHHHHHhcCcccHHHHHHHHhcCHHHHHHHHHHHHHHHH
Confidence            000000         000                       012444678899999999999998888555555678999


Q ss_pred             hhhcCCChhHHHHHhhccCC-hhhHHHHHHHHHHhHHHh-----------------------------------------
Q 035754          201 SLSRHRSGNYVVQHVLSLED-PFLIDAICFALRGHYVDL-----------------------------------------  238 (335)
Q Consensus       201 ~l~~d~~G~~viq~~l~~~~-~~~~~~i~~~l~~~~~~l-----------------------------------------  238 (335)
                      .|+.++.+|+++|++|++.. ++....+++.+.+++..|                                         
T Consensus       376 ~La~~p~aNF~lQrli~h~~~~e~v~~v~eeL~P~~~~LL~~g~~gVv~sLia~~~rl~s~q~~~l~~Li~a~~~~~~~~  455 (650)
T KOG2188|consen  376 ELAVHPIANFPLQRLINHLTSLEDVGSVIEELAPKLSSLLEQGNSGVVASLIAASARLGSYQDKMLQQLIQAFHAASESK  455 (650)
T ss_pred             HHHhCccccchHHHHHHhccCHHHHHHHHHHHhHHHHHHHHcCCchHhHHHHHHHHhhchhHHHHHHHHHHHHhcCChhh
Confidence            99999999999999999875 777777777766633220                                         


Q ss_pred             ------------------------ccCcchhHHHHHHHhcCCcH-HHHHHHHhC--hhhHHhhhcCcchhHHHHHHHhhc
Q 035754          239 ------------------------SLTKCGSFVVQKCLKYQNAV-HYIIEELLN--SDQILQVANDKYGNYVIQTALAET  291 (335)
Q Consensus       239 ------------------------~~~~~gS~vve~~l~~~~~~-~~i~~~l~~--~~~~~~l~~~~~g~~Viq~~l~~~  291 (335)
                                              -.+..|+.++|.+++...+. +.++..+++  ..++.+++.+++|++||+++|++.
T Consensus       456 k~il~~lL~~~~~~g~~~~~~~t~~~h~~ga~lle~lv~f~k~~i~~litsll~L~~eqi~e~~~~~~~ShlIeavL~S~  535 (650)
T KOG2188|consen  456 KNILPCLLFSLTLFGCVGEWFLTEKFHQKGAVLLEELVNFSKTHIQTLITSLLSLSEEQILEMSCNGVGSHLIEAVLASK  535 (650)
T ss_pred             cchHHHHHHHhhhcccccccccHHHHhhchhHHHHHHHhhchhhhHHHHHHHHhhhHHHHHHHhcCCchHHHHHHHHHhc
Confidence                                    01235677778888777776 666666655  469999999999999999999996


Q ss_pred             cCcCcHHHHHHHHHHHHHHHHhhhcCCChHHHHHHHHhhC
Q 035754          292 MRQDRLSVHQRLVTKLQQHLAALRVMKYGSNVYKWTTASH  331 (335)
Q Consensus       292 ~~~~~~~~~~~l~~~l~~~~~~L~~~~~gs~v~~~l~~~~  331 (335)
                      +.  .+..++++++.+.+...+|+.+.+||||++|||+..
T Consensus       536 ~l--~~~~~~kLi~~l~g~~~~La~~~~GSrv~eK~wea~  573 (650)
T KOG2188|consen  536 DL--GEKIKEKLINILDGSFVTLALSTFGSRVFEKCWEAT  573 (650)
T ss_pred             cc--cHHHHHHHHHHhhccchheeecCcccHHHHHHHHHh
Confidence            54  238999999999999999999999999999999853

>KOG2050 consensus Puf family RNA-binding protein [Translation, ribosomal structure and biogenesis]

Probab=99.87  E-value=2.3e-20  Score=170.20  Aligned_cols=248  Identities=15%  Similarity=0.154  Sum_probs=206.9

Q ss_pred             ccccccccCcchhhhccCchhcHHHHHhhcCCCHHHHHHHHHHHHhhHHhhccCccchHHHHHHhhh-cCHHHHHHHHHH
Q 035754            3 TIAFEHCTNHDLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIES-CNESQLALIILK   81 (335)
Q Consensus         3 ~~~~~~~~~g~~~~la~~~~~s~~lq~~l~~~~~e~~~~i~~e~~~~~~~L~~~~~gs~v~q~ll~~-~~~~~~~~i~~~   81 (335)
                      +.+|+++. |..++||.+++|-.++|++|.+|++.+++.|++++.|++..|+.|+.|++|++-++.. .+.+||..++.+
T Consensus       192 ~~if~eL~-p~~v~l~kskY~k~~v~KmLkyGsk~q~a~iI~sl~Ghv~kLlRH~eaa~Vve~ay~~~A~l~Qr~~li~E  270 (652)
T KOG2050|consen  192 EQIFEELL-PFFVELAKSKYAKFFVQKMLKYGSKAQKAKIINSLRGHVVKLLRHREAAYVVEYAYNDFATLEQRQYLIQE  270 (652)
T ss_pred             HHHHHHHh-HHHHHHHHhHHHHHHHHHHHhcCCHHHHHHHHHHHhhhHHHHHhhhHHHHHHHHHHHhhccHHHHHHHHHH
Confidence            45789999 9999999999999999999999999999999999999999999999999999988866 899999999999


Q ss_pred             HhcccchhhhhhccccCcHHHHHHHhhhcCChhHHHHHHHHHHHhhhhhhc-CCCcc----HHHHHHhhcCCcchhHHHH
Q 035754           82 ITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMM-TKPGS----SVILQCLEPSYNHKNDFIY  156 (335)
Q Consensus        82 l~~~~~~~~~l~~~~~gs~vlq~ll~~~~~~~~~~~~i~~~l~~~~~~l~~-d~~g~----~vvq~~l~~~~~~~~~~l~  156 (335)
                      |.   +.-..+..+. --.-+.+++..   .++....|...+...+..... ...|.    -++...+..++++.+..++
T Consensus       271 fY---G~efqlfK~s-n~~Tl~kil~~---~pekk~~I~~~l~~~I~~v~eKg~v~~tivHk~mlEy~~~ade~e~~e~l  343 (652)
T KOG2050|consen  271 FY---GDEFQLFKDS-NDKTLDKILAE---APEKKASILRHLKAIITPVAEKGSVDHTIVHKLMLEYLTIADEEEKSELL  343 (652)
T ss_pred             Hh---hHHHHHHhcc-CcccHHHHHHh---ChHhHHHHHHHHHHHhHHHhhcchhHHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            99   9888888873 33355566654   366677777666665554442 22332    3455566678888888899


Q ss_pred             HHHHHhHHHhhcCCCccHHHHHHHhccChHHHHHHHHHHHHhHHhhhcCCChhHHHHHhhccCChh--hHHHHHHHHHHh
Q 035754          157 QAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPF--LIDAICFALRGH  234 (335)
Q Consensus       157 ~~~~~~~~~l~~~~~g~~vlq~~l~~~~~~~~~~l~~~l~~~~~~l~~d~~G~~viq~~l~~~~~~--~~~~i~~~l~~~  234 (335)
                      +.+...+..+.-.+.|+++-.++|..+++++|+.|+.++.+++..++.|.||+.|+-++|+..+..  ..+-|.+.+.+.
T Consensus       344 ~ll~elv~e~vHT~dGS~vAm~li~~a~aKeRK~IiK~~K~h~~K~A~~~yGh~vlia~ldc~DDT~l~kk~i~~e~~~e  423 (652)
T KOG2050|consen  344 ELLKELVPEMVHTRDGSRVAMKLIWHATAKERKLIIKNMKEHVEKIANDEYGHLVLIALLDCTDDTKLLKKLIYDELKSE  423 (652)
T ss_pred             HHHHHHHHHHhcCCchHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHhhccCceehhhhhcccchHHHHHHHHHHHHHHH
Confidence            988888899999999999999999999999999999999999999999999999999999976543  567788889999


Q ss_pred             HHHhccCcchhHHHHHHHhcCCcH
Q 035754          235 YVDLSLTKCGSFVVQKCLKYQNAV  258 (335)
Q Consensus       235 ~~~l~~~~~gS~vve~~l~~~~~~  258 (335)
                      +..+..|+||-+|++.++...+..
T Consensus       424 l~~li~Dk~Grrv~lyll~p~D~~  447 (652)
T KOG2050|consen  424 LKSLISDKYGRRVILYLLAPRDGR  447 (652)
T ss_pred             HHHHhccchhhhhhhhhccCCccc
Confidence            999999999999999888875443

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=99.72  E-value=4.6e-17  Score=153.60  Aligned_cols=285  Identities=19%  Similarity=0.203  Sum_probs=238.0

Q ss_pred             HHHHHHHHHHHhhHHhhccCccchHHHHHHhhhcCHHHHHHHHHHHhcccchhhhhhccccCcHHHHHHHhhhcCChhHH
Q 035754           37 RILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLL  116 (335)
Q Consensus        37 e~~~~i~~e~~~~~~~L~~~~~gs~v~q~ll~~~~~~~~~~i~~~l~~~~~~~~~l~~~~~gs~vlq~ll~~~~~~~~~~  116 (335)
                      .+.+.+.-++.+...++..|=-|+-|+|+++++++...+....+...   ..+..+..|++|.+..|++++. +-.+.+.
T Consensus       535 pEied~ai~mLDe~~elsSdylGNtVvqkfFe~sS~~ik~aml~r~s---~ylts~gvHknGtw~~qk~ik~-a~te~qi  610 (1007)
T KOG4574|consen  535 PEIEDLAILMLDELPELSSDYLGNTVVQKFFELSSDIIKDAMLRRGS---KYLTSMGVHKNGTWACQKIIKM-AFTERQI  610 (1007)
T ss_pred             hhHHHHHHHHhccCCcchhhhhcchhhHHHHhhccHHHHHHHHhhhh---hhhhhccccccchHHHHHHHHH-hhchhhh
Confidence            45666677777888999999999999999999999999999999999   9999999999999999999999 8888889


Q ss_pred             HHHHHHHHHhhhhhhcCCCccHHHHHHhhcCCcchhHHHHHHHHHhHHHhhcCCCccHHHHHHHhccC--hHHHHHHHHH
Q 035754          117 YHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMK--GSRRKQILHL  194 (335)
Q Consensus       117 ~~i~~~l~~~~~~l~~d~~g~~vvq~~l~~~~~~~~~~l~~~~~~~~~~l~~~~~g~~vlq~~l~~~~--~~~~~~l~~~  194 (335)
                      +.+.....+....++.|.+||||+|.+|... -.-..++++.+..+++++...++|++.+.+|++.-.  .+........
T Consensus       611 k~iv~g~dpyc~~l~~dqfgnyvaqd~LkF~-fp~nsFVfE~v~s~~~~ivQsrfGsravrAcle~lNa~~e~qsl~~~s  689 (1007)
T KOG4574|consen  611 KLIVRGVDPYCTPLLNDQFGNYVAQDSLKFG-FPWNSFVFESVFSHFWDIVQSRFGSRAVRACLEALNANTEDQSLVRES  689 (1007)
T ss_pred             heeeeccCcchhhHHHHhhcceeeeeehhcc-CccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHhccCchhhhhhhhh
Confidence            9999989999999999999999999999985 334556789999999999999999999999998642  2332222222


Q ss_pred             -HHHhHHhhhcCCChhHHHHHhhccCChhhH-HHHHHHHHHhHHHhccCcchhHHHHHHHhcCCcH---HHHHHHHhC--
Q 035754          195 -ISVNAASLSRHRSGNYVVQHVLSLEDPFLI-DAICFALRGHYVDLSLTKCGSFVVQKCLKYQNAV---HYIIEELLN--  267 (335)
Q Consensus       195 -l~~~~~~l~~d~~G~~viq~~l~~~~~~~~-~~i~~~l~~~~~~l~~~~~gS~vve~~l~~~~~~---~~i~~~l~~--  267 (335)
                       +......++.+..|-..|..+++.+....+ ..++..+.++++.+|+|+-||-++.|+++.+.+.   ++|++.|+.  
T Consensus       690 ~iIs~ss~latnsng~llvtw~lDns~~~nrh~~l~~~lt~el~~lC~h~Lgsttv~Kl~n~~qepvs~ekii~hlf~~~  769 (1007)
T KOG4574|consen  690 CIISKSSYLATNSNGLLLVTWLLDNSSLPNRHTILAHGLTKELVMLCFHKLGSTTVLKLLNLRQEPVSREKIIEHLFHLR  769 (1007)
T ss_pred             hhhhchhhhhhcCccceeeeeecccccccchhhHHhhhhhhccchhhhhhccchhhhhhhhcCCChHHHHHHHHHHhhcc
Confidence             344577899999999999999998754433 3445677799999999999999999999999887   888888884  


Q ss_pred             --------------------------hhhHHhhhcCcchhHHHHHHHhhccCcCcHHHHHHHHHHHHHHHHhhhcCCChH
Q 035754          268 --------------------------SDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLAALRVMKYGS  321 (335)
Q Consensus       268 --------------------------~~~~~~l~~~~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~~~~~L~~~~~gs  321 (335)
                                                .+.+.....|+++++|.|.++......      ...++.|...+.-.+.+++|+
T Consensus       770 n~kd~~lt~Vl~~~~~gpmfiikvi~~p~iel~f~dQf~kvvrq~il~~~a~~------narv~~LleevgliSasksgs  843 (1007)
T KOG4574|consen  770 NFKDSALTEVLTEANYGPMFIIKVITKPTIELAFRDQFIKVVRQVILNSPAVS------NARVQRLLEEVGLISASKSGS  843 (1007)
T ss_pred             ccccchhhhhhhhhccccceeeeeeccccchHHHHHHHHHHHHHHHHhcCCcc------HHHHHHHHHHHhhhccccchh
Confidence                                      035667778999999999999988763      222266666777788999999


Q ss_pred             HHHHHHHhhCC
Q 035754          322 NVYKWTTASHP  332 (335)
Q Consensus       322 ~v~~~l~~~~~  332 (335)
                      +-++.+...++
T Consensus       844 ~s~q~~~sss~  854 (1007)
T KOG4574|consen  844 QSIQMHISSSK  854 (1007)
T ss_pred             HHHHhhhccCC
Confidence            99999988765

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=99.25  E-value=5.8e-12  Score=119.67  Aligned_cols=199  Identities=20%  Similarity=0.242  Sum_probs=155.2

Q ss_pred             hhHHHHHHHHHHHhhhhhhcCCCccHHHHHHhhcCCcchhHHHHHHHHHhHHHhhcCCCccHHHHHHHhccC-hHHHHHH
Q 035754          113 PPLLYHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMK-GSRRKQI  191 (335)
Q Consensus       113 ~~~~~~i~~~l~~~~~~l~~d~~g~~vvq~~l~~~~~~~~~~l~~~~~~~~~~l~~~~~g~~vlq~~l~~~~-~~~~~~l  191 (335)
                      +|..++.+. +.++..++-.|..||.|+|++++..+...++.+...-..++.....|++|++..|++++.+. +.+.+.+
T Consensus       535 pEied~ai~-mLDe~~elsSdylGNtVvqkfFe~sS~~ik~aml~r~s~ylts~gvHknGtw~~qk~ik~a~te~qik~i  613 (1007)
T KOG4574|consen  535 PEIEDLAIL-MLDELPELSSDYLGNTVVQKFFELSSDIIKDAMLRRGSKYLTSMGVHKNGTWACQKIIKMAFTERQIKLI  613 (1007)
T ss_pred             hhHHHHHHH-HhccCCcchhhhhcchhhHHHHhhccHHHHHHHHhhhhhhhhhccccccchHHHHHHHHHhhchhhhhee
Confidence            454455544 77889999999999999999999999999999999888999999999999999999999985 4567777


Q ss_pred             HHHHHHhHHhhhcCCChhHHHHHhhccCChhhHHHHHHHHHHhHHHhccCcchhHHHHHHHhcCCcH---HHHHHHHh--
Q 035754          192 LHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLKYQNAV---HYIIEELL--  266 (335)
Q Consensus       192 ~~~l~~~~~~l~~d~~G~~viq~~l~~~~~~~~~~i~~~l~~~~~~l~~~~~gS~vve~~l~~~~~~---~~i~~~l~--  266 (335)
                      +.-..+....++.|++|||++|..|..+-| -...+++....++..+....||++-+.+|++.....   +.+..+..  
T Consensus       614 v~g~dpyc~~l~~dqfgnyvaqd~LkF~fp-~nsFVfE~v~s~~~~ivQsrfGsravrAcle~lNa~~e~qsl~~~s~iI  692 (1007)
T KOG4574|consen  614 VRGVDPYCTPLLNDQFGNYVAQDSLKFGFP-WNSFVFESVFSHFWDIVQSRFGSRAVRACLEALNANTEDQSLVRESCII  692 (1007)
T ss_pred             eeccCcchhhHHHHhhcceeeeeehhccCc-cchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHhccCchhhhhhhhhhhh
Confidence            777888999999999999999999998866 345668888899999999999999999999986554   22222111  


Q ss_pred             --------------------C---------------hhhHHhhhcCcchhHHHHHHHhhccCcCcHHHHHHHHHHHHHHH
Q 035754          267 --------------------N---------------SDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHL  311 (335)
Q Consensus       267 --------------------~---------------~~~~~~l~~~~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~~~  311 (335)
                                          +               .+++..+|.|.-|+-+++++++...++    .   ..+++.+++
T Consensus       693 s~ss~latnsng~llvtw~lDns~~~nrh~~l~~~lt~el~~lC~h~Lgsttv~Kl~n~~qep----v---s~ekii~hl  765 (1007)
T KOG4574|consen  693 SKSSYLATNSNGLLLVTWLLDNSSLPNRHTILAHGLTKELVMLCFHKLGSTTVLKLLNLRQEP----V---SREKIIEHL  765 (1007)
T ss_pred             hchhhhhhcCccceeeeeecccccccchhhHHhhhhhhccchhhhhhccchhhhhhhhcCCCh----H---HHHHHHHHH
Confidence                                1               146777788888888888888877762    2   334444555


Q ss_pred             HhhhcCCCh
Q 035754          312 AALRVMKYG  320 (335)
Q Consensus       312 ~~L~~~~~g  320 (335)
                      ..+..++-|
T Consensus       766 f~~~n~kd~  774 (1007)
T KOG4574|consen  766 FHLRNFKDS  774 (1007)
T ss_pred             hhccccccc
Confidence            555555544

>PF00806 PUF: Pumilio-family RNA binding repeat; InterPro: IPR001313 The drosophila pumilio gene codes for an unusual protein that binds through the Puf domain that usually occurs as a tandem repeat of eight domains

Probab=98.52  E-value=8.3e-08  Score=56.39  Aligned_cols=35  Identities=34%  Similarity=0.532  Sum_probs=29.3

Q ss_pred             HHHhhHHhhccCccchHHHHHHhhhcCHHHHHHHH
Q 035754           45 VVSGFTFELMSGQYGRFVFGKFIESCNESQLALII   79 (335)
Q Consensus        45 e~~~~~~~L~~~~~gs~v~q~ll~~~~~~~~~~i~   79 (335)
                      ++.+++.+|+.|+|||||+|++++.++++++..|+
T Consensus         1 ~i~~~~~~l~~d~~Gn~VvQk~le~~~~~~~~~il   35 (35)
T PF00806_consen    1 EIKGNLVELSKDQYGNYVVQKCLEHASPEQRQLIL   35 (35)
T ss_dssp             CHTTTHHHHHTSTTHHHHHHHHHHHSSHHHHHHHH
T ss_pred             ChHHHHHHHHhccccCHHHHHHHHHCCHHHHHhhC
Confidence            36688889999999999999999998888877664

The FBF-2 protein of Caenorhabditis elegans also has a Puf domain. Both proteins function as translational repressors in early embryonic development by binding sequences in the 3' UTR of target mRNAs [, ]. The same type of repetitive domain has been found in in a number of other proteins from all eukaryotic kingdoms. The Puf proteins characterised to date have been reported to bind to 3'-untranslated region (UTR) sequences encompassing a so-called UGUR tetranucleotide motif and thereby to repress gene expression by affecting mRNA translation or stability. In Saccharomyces cerevisiae (Baker's yeast), five proteins, termed Puf1p to Puf5p, bear six to eight Puf repeats []. Puf3p binds nearly exclusively to cytoplasmic mRNAs that encode mitochondrial proteins; Puf1p and Puf2p interact preferentially with mRNAs encoding membrane-associated proteins; Puf4p preferentially binds mRNAs encoding nucleolar ribosomal RNA-processing factors; and Puf5p is associated with mRNAs encoding chromatin modifiers and components of the spindle pole body. This suggests the existence of an extensive network of RNA-protein interactions that coordinate the post-transcriptional fate of large sets of cytotopically and functionally related RNAs through each stage of its lifecycle.; GO: 0003723 RNA binding; PDB: 3BX2_A 4DZS_B 3BX3_B 3BWT_A 3GVT_B 3GVO_A 1IB2_A 3Q0N_A 2YJY_A 1M8Z_A ....

>PF00806 PUF: Pumilio-family RNA binding repeat; InterPro: IPR001313 The drosophila pumilio gene codes for an unusual protein that binds through the Puf domain that usually occurs as a tandem repeat of eight domains

Probab=98.38  E-value=3.3e-07  Score=53.82  Aligned_cols=30  Identities=30%  Similarity=0.645  Sum_probs=25.8

Q ss_pred             hHHhhhcCcchhHHHHHHHhhccCcCcHHHHHHH
Q 035754          270 QILQVANDKYGNYVIQTALAETMRQDRLSVHQRL  303 (335)
Q Consensus       270 ~~~~l~~~~~g~~Viq~~l~~~~~~~~~~~~~~l  303 (335)
                      ++.+|+.|+|||||||++|+..++    .+++.+
T Consensus         5 ~~~~l~~d~~Gn~VvQk~le~~~~----~~~~~i   34 (35)
T PF00806_consen    5 NLVELSKDQYGNYVVQKCLEHASP----EQRQLI   34 (35)
T ss_dssp             THHHHHTSTTHHHHHHHHHHHSSH----HHHHHH
T ss_pred             HHHHHHhccccCHHHHHHHHHCCH----HHHHhh
Confidence            899999999999999999999776    666655

The FBF-2 protein of Caenorhabditis elegans also has a Puf domain. Both proteins function as translational repressors in early embryonic development by binding sequences in the 3' UTR of target mRNAs [, ]. The same type of repetitive domain has been found in in a number of other proteins from all eukaryotic kingdoms. The Puf proteins characterised to date have been reported to bind to 3'-untranslated region (UTR) sequences encompassing a so-called UGUR tetranucleotide motif and thereby to repress gene expression by affecting mRNA translation or stability. In Saccharomyces cerevisiae (Baker's yeast), five proteins, termed Puf1p to Puf5p, bear six to eight Puf repeats []. Puf3p binds nearly exclusively to cytoplasmic mRNAs that encode mitochondrial proteins; Puf1p and Puf2p interact preferentially with mRNAs encoding membrane-associated proteins; Puf4p preferentially binds mRNAs encoding nucleolar ribosomal RNA-processing factors; and Puf5p is associated with mRNAs encoding chromatin modifiers and components of the spindle pole body. This suggests the existence of an extensive network of RNA-protein interactions that coordinate the post-transcriptional fate of large sets of cytotopically and functionally related RNAs through each stage of its lifecycle.; GO: 0003723 RNA binding; PDB: 3BX2_A 4DZS_B 3BX3_B 3BWT_A 3GVT_B 3GVO_A 1IB2_A 3Q0N_A 2YJY_A 1M8Z_A ....

>smart00025 Pumilio Pumilio-like repeats

Probab=98.11  E-value=2e-06  Score=50.68  Aligned_cols=34  Identities=41%  Similarity=0.579  Sum_probs=26.8

Q ss_pred             HHhhHHhhccCccchHHHHHHhhhcCHHHHHHHH
Q 035754           46 VSGFTFELMSGQYGRFVFGKFIESCNESQLALII   79 (335)
Q Consensus        46 ~~~~~~~L~~~~~gs~v~q~ll~~~~~~~~~~i~   79 (335)
                      +.+++.+|+.|+|||+|+|++++.+++.++..++
T Consensus         2 ~~~~~~~l~~~~~g~~viqk~l~~~~~~~~~~i~   35 (36)
T smart00025        2 IKGHLLELSKDQYGNRVVQKLLEHASESQREQII   35 (36)
T ss_pred             chHHHHHHHhcchhhHHHHHHHHHCCHHHHHHhh
Confidence            4577888888888888888888888887776654

Pumilio-like repeats that bind RNA.

>smart00025 Pumilio Pumilio-like repeats

Probab=97.88  E-value=1.1e-05  Score=47.35  Aligned_cols=31  Identities=29%  Similarity=0.629  Sum_probs=26.0

Q ss_pred             hHHhhhcCcchhHHHHHHHhhccCcCcHHHHHHHH
Q 035754          270 QILQVANDKYGNYVIQTALAETMRQDRLSVHQRLV  304 (335)
Q Consensus       270 ~~~~l~~~~~g~~Viq~~l~~~~~~~~~~~~~~l~  304 (335)
                      ++.+|+.|+|||||+|++++..+.    .++..++
T Consensus         5 ~~~~l~~~~~g~~viqk~l~~~~~----~~~~~i~   35 (36)
T smart00025        5 HLLELSKDQYGNRVVQKLLEHASE----SQREQII   35 (36)
T ss_pred             HHHHHHhcchhhHHHHHHHHHCCH----HHHHHhh
Confidence            788999999999999999999887    6666554

Pumilio-like repeats that bind RNA.

>PF08144 CPL: CPL (NUC119) domain; InterPro: IPR012959 This C-terminal domain is found in Penguin-like proteins (CPL) and is associated with Pumilio like repeats []

Probab=95.13  E-value=0.1  Score=41.40  Aligned_cols=125  Identities=14%  Similarity=0.130  Sum_probs=64.9

Q ss_pred             hcCCChhHHHHHhhccCChhhHH-HHHHHHHHhHHHhccCcchhHH-HHHHHhcCCcHHHHHHHHhChhhHHhhhcCcch
Q 035754          203 SRHRSGNYVVQHVLSLEDPFLID-AICFALRGHYVDLSLTKCGSFV-VQKCLKYQNAVHYIIEELLNSDQILQVANDKYG  280 (335)
Q Consensus       203 ~~d~~G~~viq~~l~~~~~~~~~-~i~~~l~~~~~~l~~~~~gS~v-ve~~l~~~~~~~~i~~~l~~~~~~~~l~~~~~g  280 (335)
                      +.|+||..++..++...++.+.. .+++.|.+.- .-.+.|--..+ -+.+++...  ..+++.+..  +...|+.+++|
T Consensus         1 i~dk~gRr~llYLl~~~d~~~f~p~~i~~L~~~d-~~~tSKKd~~~Rr~ELl~~~s--p~Ll~~i~~--~~~~ll~~~~g   75 (148)
T PF08144_consen    1 INDKYGRRVLLYLLSPRDPRYFSPEIIKLLKEGD-RNATSKKDPEVRRKELLEAIS--PPLLEAIAE--NAEELLSSSFG   75 (148)
T ss_pred             CCCccCceeeeeeccCCCcccCCHHHHHHHhhhc-ccccccCCHHHHHHHHHHHhh--HHHHHHHHH--hHHHHHhcCcc
Confidence            36788888888888866654332 2222222111 00000100011 011111111  233434444  77788888888


Q ss_pred             hHHHHHHHhhccCcCcHHHHHHHHHHHHHH--------HHhhhcCCChHHHHHHHHhhCCC
Q 035754          281 NYVIQTALAETMRQDRLSVHQRLVTKLQQH--------LAALRVMKYGSNVYKWTTASHPC  333 (335)
Q Consensus       281 ~~Viq~~l~~~~~~~~~~~~~~l~~~l~~~--------~~~L~~~~~gs~v~~~l~~~~~~  333 (335)
                      ..+|.-+|..+...+. ...+.|+..+...        -..+..+++|++++.+|.....+
T Consensus        76 ~~~i~eiL~~~~gdk~-~a~~Aia~~~~~~~~~~~~~~e~H~i~~p~~~r~lK~Liq~~~~  135 (148)
T PF08144_consen   76 CQFITEILLSATGDKS-AALEAIASLAAEPLFPGDIDEEYHLIEHPFGHRMLKKLIQGDKK  135 (148)
T ss_pred             cHHHHHHHhccCccHH-HHHHHHHHHHhhccCCCCCcCccchhcCchHHHHHHHHHHCCCc
Confidence            8888888877654111 2222444444332        23467889999999988876653

; GO: 0003723 RNA binding

>PRK05686 fliG flagellar motor switch protein G; Validated

Probab=93.80  E-value=5.2  Score=36.53  Aligned_cols=220  Identities=13%  Similarity=0.077  Sum_probs=115.3

Q ss_pred             CCHHHHHHHHHHHHhhHHhhcc-CccchHHHHHHhhh-cCHHHHHHHHHHHhcccc--hhhhhhccccCcHHHHHHHhhh
Q 035754           34 GDSRILDKLFWVVSGFTFELMS-GQYGRFVFGKFIES-CNESQLALIILKITFQDQ--LFLLASVDKFGSSSVKKLIKVV  109 (335)
Q Consensus        34 ~~~e~~~~i~~e~~~~~~~L~~-~~~gs~v~q~ll~~-~~~~~~~~i~~~l~~~~~--~~~~l~~~~~gs~vlq~ll~~~  109 (335)
                      -+++..+.+++++...+..-.. ..-|.-.+..++.. .+++.-..|+..+...++  .|..|.  .-....++.++.. 
T Consensus        55 vs~~~~~~vL~ef~~~~~~~~~~~~gg~~~~~~iL~~~l~~~~a~~il~~i~~~~~~~~fe~L~--~ld~~~l~~lL~~-  131 (339)
T PRK05686         55 VSPEQVEAVLEEFEDEFEAGAYILMGGIDYARSLLEKALGEEKADSILERILESLGTSGFDFLR--KMDPQQLANFIRN-  131 (339)
T ss_pred             CCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHcCHHHHHHHHHHHhccccCchHHHHh--cCCHHHHHHHHHh-
Confidence            3566777777777776654332 33444457778775 677777888888774322  222222  2345566666665 


Q ss_pred             cCChhHHHHHHHHHHH----hhhhhhcCCCccHHHHHHhhc--CCcchhHHHHHHHHHhHHHhh----cCCCccHHHHHH
Q 035754          110 AHLPPLLYHVMSALKR----LFKFLMMTKPGSSVILQCLEP--SYNHKNDFIYQAALEHCLYLA----CHEQGCINLNNF  179 (335)
Q Consensus       110 ~~~~~~~~~i~~~l~~----~~~~l~~d~~g~~vvq~~l~~--~~~~~~~~l~~~~~~~~~~l~----~~~~g~~vlq~~  179 (335)
                       -+++....+...+.+    .+...+......-|+.++...  .+++..+.+-+.+...+....    ....|...+-.+
T Consensus       132 -EhpqtiA~iLs~l~~~~aa~vL~~l~~~~~~~v~~ria~l~~v~~~~~~~i~~~L~~~l~~~~~~~~~~~~g~~~~a~I  210 (339)
T PRK05686        132 -EHPQTIALILSYLKPDQAAEILSLLPEELRADVMMRIATLEGVSPEALKEVEEVLEKKLSSMANADRTKMGGVKTVAEI  210 (339)
T ss_pred             -cCHHHHHHHHhCCCHHHHHHHHHhCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHhhcccccccccCcHHHHHHH
Confidence             344444444433332    233333333344444444443  223333333344444443322    233466778888


Q ss_pred             HhccChHHHHHHHHHHHHhHHhhhcCCC-hhHHHHHhhccCChhhHHHHHHHHHHhHHHhccCcchhHHHHHHHhcCCcH
Q 035754          180 IDNMKGSRRKQILHLISVNAASLSRHRS-GNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLKYQNAV  258 (335)
Q Consensus       180 l~~~~~~~~~~l~~~l~~~~~~l~~d~~-G~~viq~~l~~~~~~~~~~i~~~l~~~~~~l~~~~~gS~vve~~l~~~~~~  258 (335)
                      +...+.+....++..+...=..++..-- --|+..-++. -++.....+++.+......++..--..-+.++++..-+..
T Consensus       211 ln~~~~~~~~~il~~L~~~d~~~a~~Ir~~mF~Fedl~~-l~~~~l~~ll~~v~~~~L~~ALkga~~~~~~~il~nmS~R  289 (339)
T PRK05686        211 LNNLDRQTEKTILESLEEEDPELAEKIKDLMFVFEDLVD-LDDRSIQRLLREVDNDVLALALKGASEELREKFLSNMSKR  289 (339)
T ss_pred             HhcCCchHHHHHHHHHHhhCHHHHHHHHHHhcCHHHHhc-CCHHHHHHHHHhCCHHHHHHHHCCCCHHHHHHHHHhcCHH
Confidence            8888877777777766543333322110 1122222322 3445566777666666666665555556666666666655

>PF08144 CPL: CPL (NUC119) domain; InterPro: IPR012959 This C-terminal domain is found in Penguin-like proteins (CPL) and is associated with Pumilio like repeats []

Probab=92.44  E-value=0.35  Score=38.38  Aligned_cols=26  Identities=15%  Similarity=0.201  Sum_probs=15.4

Q ss_pred             HHHhHHHhhcCCCccHHHHHHHhccC
Q 035754          159 ALEHCLYLACHEQGCINLNNFIDNMK  184 (335)
Q Consensus       159 ~~~~~~~l~~~~~g~~vlq~~l~~~~  184 (335)
                      +..+..++..++.||.++..++..+.
T Consensus        62 i~~~~~~ll~~~~g~~~i~eiL~~~~   87 (148)
T PF08144_consen   62 IAENAEELLSSSFGCQFITEILLSAT   87 (148)
T ss_pred             HHHhHHHHHhcCcccHHHHHHHhccC
Confidence            33445566666666666666666654

; GO: 0003723 RNA binding

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	335
3bwt_A	333	Crystal Structure Of The Rna Binding Domain Of Puf4		1e-21
3bwt_A	333	Crystal Structure Of The Rna Binding Domain Of Puf4		2e-07
3bx2_A	335	Puf4 Rna Binding Domain Bound To Ho Endonuclease Rn		1e-21
3bx2_A	335	Puf4 Rna Binding Domain Bound To Ho Endonuclease Rn		2e-07
4dzs_A	357	Crystal Structure Of Yeast Puf4p Rna Binding Domain		1e-21
4dzs_A	357	Crystal Structure Of Yeast Puf4p Rna Binding Domain		2e-07
3bx3_A	335	Puf4 T650cC724R MUTANT BOUND TO COX17 RNA 3' UTR Re		4e-21
3bx3_A	335	Puf4 T650cC724R MUTANT BOUND TO COX17 RNA 3' UTR Re		1e-08
3q0q_A	351	Crystal Structure Of The Pumilio-Homology Domain Fr		2e-16
3gvo_A	351	Structure And Rna Binding Of The Mouse Pumilio-2 Pu		1e-15
3bsb_A	343	Crystal Structure Of Human Pumilio1 In Complex With		2e-14
1ib2_A	349	Crystal Structure Of A Pumilio-Homology Domain Leng		3e-14
3h3d_X	323	Drosophila Pumilio Rna Binding Domain (Puf Domain)		5e-14
3h3d_X	323	Drosophila Pumilio Rna Binding Domain (Puf Domain)		6e-10
2yjy_A	350	A Specific And Modular Binding Code For Cytosine Re		4e-13
3k49_A	369	Puf3 Rna Binding Domain Bound To Cox17 Rna 3' Utr R		9e-08
3k49_A	369	Puf3 Rna Binding Domain Bound To Cox17 Rna 3' Utr R		4e-07

>pdb|3BWT|A Chain A, Crystal Structure Of The Rna Binding Domain Of Puf4 From Saccharomyces Cerevisiae Length = 333

Iteration: 1
 Score =  100 bits (249), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 81/289 (28%), Positives = 141/289 (48%), Gaps = 11/289 (3%)
Query: 14  LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
           + SL +DQ G ++LQ+ L    S+  D +F     +T ELM+  +G ++  K +E     
Sbjct: 15  IHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTE 74
Query: 74  QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMT 133
           Q  +++ KI+     F+  S++  G+ +++KLI+ +         V+ +L+     L   
Sbjct: 75  Q-RIVLTKISSPH--FVEISLNPHGTRALQKLIECIKTDEEAQI-VVDSLRPYTVQLSKD 130
Query: 134 KPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILH 193
             G+ VI +CL+        FI+ A  + C+ +A H  GC  L   +D+    +   +  
Sbjct: 131 LNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCD 190
Query: 194 LISVNAASLSRHRSGNYVVQHVLSLEDPF----LIDAICFALRGHYVDLSLTKCGSFVVQ 249
            +      L+    GNYVVQ++++ E           I   L+   ++LS+ K GS V++
Sbjct: 191 KLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIE 250
Query: 250 KCLKYQNAVHYIIEELLNSD---QILQVANDKYGNYVIQTALAETMRQD 295
           K LK       +I E+LN+     I  + ND YGNYV+QTAL  + +Q+
Sbjct: 251 KILKTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDISHKQN 299

>pdb|3BWT|A Chain A, Crystal Structure Of The Rna Binding Domain Of Puf4 From Saccharomyces Cerevisiae Length = 333

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 50/204 (24%), Positives = 94/204 (46%), Gaps = 19/204 (9%)
Query: 130 LMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRK 189
           LM    G+ +I + LE     +   + + +  H + ++ +  G   L   I+ +K     
Sbjct: 54  LMTDSFGNYLIQKLLEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEA 113
Query: 190 QIL-HLISVNAASLSRHRSGNYVVQHVLSLEDP----FLIDAICFALRGHYVDLSLTKCG 244
           QI+   +      LS+  +GN+V+Q  L    P    F+ DAI  +     +D++  + G
Sbjct: 114 QIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSC----IDIATHRHG 169
Query: 245 SFVVQKCLKYQNAVHYIIEELLN-SDQILQVAN----DKYGNYVIQTALAETMRQDRLSV 299
             V+Q+CL      H   E+  N  D++L + +    D +GNYV+Q  + +   +++   
Sbjct: 170 CCVLQRCLD-----HGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDY 224
Query: 300 HQRLVTKLQQHLAALRVMKYGSNV 323
             ++V  L+     L + K+GSNV
Sbjct: 225 THKIVHLLKPRAIELSIHKFGSNV 248

>pdb|3BX2|A Chain A, Puf4 Rna Binding Domain Bound To Ho Endonuclease Rna 3' Utr Recognition Sequence Length = 335

Iteration: 1
 Score =  100 bits (249), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 81/289 (28%), Positives = 141/289 (48%), Gaps = 11/289 (3%)
Query: 14  LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
           + SL +DQ G ++LQ+ L    S+  D +F     +T ELM+  +G ++  K +E     
Sbjct: 15  IHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTE 74
Query: 74  QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMT 133
           Q  +++ KI+     F+  S++  G+ +++KLI+ +         V+ +L+     L   
Sbjct: 75  Q-RIVLTKISSPH--FVEISLNPHGTRALQKLIECIKTDEEAQI-VVDSLRPYTVQLSKD 130
Query: 134 KPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILH 193
             G+ VI +CL+        FI+ A  + C+ +A H  GC  L   +D+    +   +  
Sbjct: 131 LNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCD 190
Query: 194 LISVNAASLSRHRSGNYVVQHVLSLEDPF----LIDAICFALRGHYVDLSLTKCGSFVVQ 249
            +      L+    GNYVVQ++++ E           I   L+   ++LS+ K GS V++
Sbjct: 191 KLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIE 250
Query: 250 KCLKYQNAVHYIIEELLNSD---QILQVANDKYGNYVIQTALAETMRQD 295
           K LK       +I E+LN+     I  + ND YGNYV+QTAL  + +Q+
Sbjct: 251 KILKTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDISHKQN 299

>pdb|3BX2|A Chain A, Puf4 Rna Binding Domain Bound To Ho Endonuclease Rna 3' Utr Recognition Sequence Length = 335

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 50/204 (24%), Positives = 94/204 (46%), Gaps = 19/204 (9%)
Query: 130 LMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRK 189
           LM    G+ +I + LE     +   + + +  H + ++ +  G   L   I+ +K     
Sbjct: 54  LMTDSFGNYLIQKLLEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEA 113
Query: 190 QIL-HLISVNAASLSRHRSGNYVVQHVLSLEDP----FLIDAICFALRGHYVDLSLTKCG 244
           QI+   +      LS+  +GN+V+Q  L    P    F+ DAI  +     +D++  + G
Sbjct: 114 QIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSC----IDIATHRHG 169
Query: 245 SFVVQKCLKYQNAVHYIIEELLN-SDQILQVAN----DKYGNYVIQTALAETMRQDRLSV 299
             V+Q+CL      H   E+  N  D++L + +    D +GNYV+Q  + +   +++   
Sbjct: 170 CCVLQRCLD-----HGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDY 224
Query: 300 HQRLVTKLQQHLAALRVMKYGSNV 323
             ++V  L+     L + K+GSNV
Sbjct: 225 THKIVHLLKPRAIELSIHKFGSNV 248

>pdb|4DZS|A Chain A, Crystal Structure Of Yeast Puf4p Rna Binding Domain In Complex With Ho-4be Mutant Rna Length = 357

Iteration: 1
 Score =  100 bits (248), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 81/289 (28%), Positives = 141/289 (48%), Gaps = 11/289 (3%)
Query: 14  LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
           + SL +DQ G ++LQ+ L    S+  D +F     +T ELM+  +G ++  K +E     
Sbjct: 37  IHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTE 96
Query: 74  QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMT 133
           Q  +++ KI+     F+  S++  G+ +++KLI+ +         V+ +L+     L   
Sbjct: 97  Q-RIVLTKISSPH--FVEISLNPHGTRALQKLIECIKTDEEAQI-VVDSLRPYTVQLSKD 152
Query: 134 KPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILH 193
             G+ VI +CL+        FI+ A  + C+ +A H  GC  L   +D+    +   +  
Sbjct: 153 LNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCD 212
Query: 194 LISVNAASLSRHRSGNYVVQHVLSLEDPF----LIDAICFALRGHYVDLSLTKCGSFVVQ 249
            +      L+    GNYVVQ++++ E           I   L+   ++LS+ K GS V++
Sbjct: 213 KLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIE 272
Query: 250 KCLKYQNAVHYIIEELLNSD---QILQVANDKYGNYVIQTALAETMRQD 295
           K LK       +I E+LN+     I  + ND YGNYV+QTAL  + +Q+
Sbjct: 273 KILKTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDISHKQN 321

>pdb|4DZS|A Chain A, Crystal Structure Of Yeast Puf4p Rna Binding Domain In Complex With Ho-4be Mutant Rna Length = 357

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 50/204 (24%), Positives = 94/204 (46%), Gaps = 19/204 (9%)
Query: 130 LMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRK 189
           LM    G+ +I + LE     +   + + +  H + ++ +  G   L   I+ +K     
Sbjct: 76  LMTDSFGNYLIQKLLEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEA 135
Query: 190 QIL-HLISVNAASLSRHRSGNYVVQHVLSLEDP----FLIDAICFALRGHYVDLSLTKCG 244
           QI+   +      LS+  +GN+V+Q  L    P    F+ DAI  +     +D++  + G
Sbjct: 136 QIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSC----IDIATHRHG 191
Query: 245 SFVVQKCLKYQNAVHYIIEELLN-SDQILQVAN----DKYGNYVIQTALAETMRQDRLSV 299
             V+Q+CL      H   E+  N  D++L + +    D +GNYV+Q  + +   +++   
Sbjct: 192 CCVLQRCLD-----HGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDY 246
Query: 300 HQRLVTKLQQHLAALRVMKYGSNV 323
             ++V  L+     L + K+GSNV
Sbjct: 247 THKIVHLLKPRAIELSIHKFGSNV 270

>pdb|3BX3|A Chain A, Puf4 T650cC724R MUTANT BOUND TO COX17 RNA 3' UTR Recognition Sequence Length = 335

Iteration: 1
 Score = 98.6 bits (244), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 81/289 (28%), Positives = 140/289 (48%), Gaps = 11/289 (3%)
Query: 14  LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
           + SL +DQ G ++LQ+ L    S+  D +F     +T ELM+  +G ++  K +E     
Sbjct: 15  IHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTE 74
Query: 74  QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMT 133
           Q  +++ KI+     F+  S++  G  +++KLI+ +         V+ +L+     L   
Sbjct: 75  Q-RIVLTKISSPH--FVEISLNPHGCRALQKLIECIKTDEEAQI-VVDSLRPYTVQLSKD 130
Query: 134 KPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILH 193
             G+ VI +CL+        FI+ A  + C+ +A H  GC  L   +D+    +   +  
Sbjct: 131 LNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCRVLQRCLDHGTTEQCDNLCD 190
Query: 194 LISVNAASLSRHRSGNYVVQHVLSLEDPF----LIDAICFALRGHYVDLSLTKCGSFVVQ 249
            +      L+    GNYVVQ++++ E           I   L+   ++LS+ K GS V++
Sbjct: 191 KLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIE 250
Query: 250 KCLKYQNAVHYIIEELLNSD---QILQVANDKYGNYVIQTALAETMRQD 295
           K LK       +I E+LN+     I  + ND YGNYV+QTAL  + +Q+
Sbjct: 251 KILKTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDISHKQN 299

>pdb|3BX3|A Chain A, Puf4 T650cC724R MUTANT BOUND TO COX17 RNA 3' UTR Recognition Sequence Length = 335

Iteration: 1
 Score = 57.4 bits (137), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 51/204 (25%), Positives = 95/204 (46%), Gaps = 19/204 (9%)
Query: 130 LMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRK 189
           LM    G+ +I + LE     +   + + +  H + ++ +  GC  L   I+ +K     
Sbjct: 54  LMTDSFGNYLIQKLLEEVTTEQRIVLTKISSPHFVEISLNPHGCRALQKLIECIKTDEEA 113
Query: 190 QIL-HLISVNAASLSRHRSGNYVVQHVLSLEDP----FLIDAICFALRGHYVDLSLTKCG 244
           QI+   +      LS+  +GN+V+Q  L    P    F+ DAI  +     +D++  + G
Sbjct: 114 QIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSC----IDIATHRHG 169
Query: 245 SFVVQKCLKYQNAVHYIIEELLN-SDQILQVAN----DKYGNYVIQTALAETMRQDRLSV 299
             V+Q+CL      H   E+  N  D++L + +    D +GNYV+Q  + +   +++   
Sbjct: 170 CRVLQRCLD-----HGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDY 224
Query: 300 HQRLVTKLQQHLAALRVMKYGSNV 323
             ++V  L+     L + K+GSNV
Sbjct: 225 THKIVHLLKPRAIELSIHKFGSNV 248

>pdb|3Q0Q|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From Human Pumilio2 In Complex With P38alpha Nrea Length = 351

Iteration: 1
 Score = 82.8 bits (203), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 72/319 (22%), Positives = 140/319 (43%), Gaps = 18/319 (5%)
Query: 14  LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
           +   +QDQ GS+++Q+ L          +F  +    ++LM+  +G +V  KF E  +  
Sbjct: 26  IVEFSQDQHGSRFIQQKLERATPAERQMVFNEILQAAYQLMTDVFGNYVIQKFFEFGSLD 85
Query: 74  QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMT 133
           Q   +  +I       L  ++  +G   ++K ++ ++    ++  ++  L       +  
Sbjct: 86  QKLALATRIRGH---VLPLALQMYGCRVIQKALESISSDQQVISEMVKELDGHVLKCVKD 142
Query: 134 KPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILH 193
           + G+ V+ +C+E        FI  A       L+ H  GC  +   +++    +   IL 
Sbjct: 143 QNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILE 202
Query: 194 LISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLK 253
            +  +   L + + GNYV+QHVL    P     I   +RG  + LS  K  S VV+KC+ 
Sbjct: 203 ELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKCVT 262
Query: 254 YQNAVHY--IIEELLNSDQ-----ILQVANDKYGNYVIQTALAETMRQDRLSVHQR--LV 304
           + +      +I+E+   +      +  +  D+Y NYV+Q  +      D     QR  ++
Sbjct: 263 HASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMI------DMAEPAQRKIIM 316
Query: 305 TKLQQHLAALRVMKYGSNV 323
            K++ H+  LR   YG ++
Sbjct: 317 HKIRPHITTLRKYTYGKHI 335

>pdb|3GVO|A Chain A, Structure And Rna Binding Of The Mouse Pumilio-2 Puf Domain Length = 351

Iteration: 1
 Score = 80.5 bits (197), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 75/325 (23%), Positives = 141/325 (43%), Gaps = 32/325 (9%)
Query: 14  LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
           +   +QDQ GS+++Q+ L          +F  +    ++LM+  +G +V  KF E  +  
Sbjct: 28  IVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQAAYQLMTDVFGNYVIQKFFEFGSLD 87
Query: 74  QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAH------LPPLLYHVMSALKRLF 127
           Q   +  +I       L  ++  +G   ++K ++ ++       +  L  HV+  +K   
Sbjct: 88  QKLALATRIRGH---VLPLALQMYGCRVIQKALESISSDQQSEMVKELDGHVLKCVK--- 141
Query: 128 KFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSR 187
                 + G+ V+ +C+E        FI  A       L+ H  GC  +   +++    +
Sbjct: 142 -----DQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQ 196
Query: 188 RKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFV 247
              IL  +  +   L + + GNYV+QHVL    P     I   +RG  + LS  K  S V
Sbjct: 197 TLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNV 256
Query: 248 VQKCLKYQNAVHY--IIEELLNSDQ-----ILQVANDKYGNYVIQTALAETMRQDRLSVH 300
           V+KC+ + +      +I+E+   +      +  +  D+Y NYV+Q  +      D     
Sbjct: 257 VEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMI------DMAEPA 310
Query: 301 QR--LVTKLQQHLAALRVMKYGSNV 323
           QR  ++ K++ H+  LR   YG ++
Sbjct: 311 QRKIIMHKIRPHITTLRKYTYGKHI 335

>pdb|3BSB|A Chain A, Crystal Structure Of Human Pumilio1 In Complex With Cyclinb Reverse Rna Length = 343

Iteration: 1
 Score = 76.3 bits (186), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 77/325 (23%), Positives = 142/325 (43%), Gaps = 32/325 (9%)
Query: 14  LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
           +   +QDQ GS+++Q  L          +F  +    ++LM   +G +V  KF E  +  
Sbjct: 26  IMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLE 85
Query: 74  QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAH------LPPLLYHVMSALKRLF 127
           Q   +  +I       L  ++  +G   ++K ++ +        +  L  HV+  +K   
Sbjct: 86  QKLALAERIRGH---VLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVK--- 139
Query: 128 KFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSR 187
                 + G+ V+ +C+E        FI  A       L+ H  GC  +   +++    +
Sbjct: 140 -----DQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQ 194
Query: 188 RKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFV 247
              IL  +  +   L + + GNYV+QHVL    P     I   +RG+ + LS  K  S V
Sbjct: 195 TLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNV 254
Query: 248 VQKCLKYQNAVH--YIIEELLNSDQ-----ILQVANDKYGNYVIQTAL--AETMRQDRLS 298
           V+KC+ + +      +I+E+   +      +  +  D+Y NYV+Q  +  AE   Q ++ 
Sbjct: 255 VEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPG-QRKIV 313
Query: 299 VHQRLVTKLQQHLAALRVMKYGSNV 323
           +H     K++ H+A LR   YG ++
Sbjct: 314 MH-----KIRPHIATLRKYTYGKHI 333

>pdb|1IB2|A Chain A, Crystal Structure Of A Pumilio-Homology Domain Length = 349

Iteration: 1
 Score = 76.3 bits (186), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 76/325 (23%), Positives = 139/325 (42%), Gaps = 32/325 (9%)
Query: 14  LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
           +   +QDQ GS+++Q  L          +F  +    ++LM   +G +V  KF E  +  
Sbjct: 26  IMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLE 85
Query: 74  QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAH------LPPLLYHVMSALKRLF 127
           Q   +  +I       L  ++  +G   ++K ++ +        +  L  HV+  +K   
Sbjct: 86  QKLALAERIRGH---VLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVK--- 139
Query: 128 KFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSR 187
                 + G+ V+ +C+E        FI  A       L+ H  GC  +   +++    +
Sbjct: 140 -----DQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQ 194
Query: 188 RKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFV 247
              IL  +  +   L + + GNYV+QHVL    P     I   +RG+ + LS  K  S V
Sbjct: 195 TLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNV 254
Query: 248 VQKCLKYQNAVH--YIIEELLNSDQ-----ILQVANDKYGNYVIQTALAETMRQDRLSVH 300
           V+KC+ + +      +I+E+   +      +  +  D+Y NYV+Q  +      D     
Sbjct: 255 VEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMI------DVAEPG 308
Query: 301 QRLVT--KLQQHLAALRVMKYGSNV 323
           QR +   K++ H+A LR   YG ++
Sbjct: 309 QRKIVMHKIRPHIATLRKYTYGKHI 333

>pdb|3H3D|X Chain X, Drosophila Pumilio Rna Binding Domain (Puf Domain) Length = 323

Iteration: 1
 Score = 75.1 bits (183), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 75/313 (23%), Positives = 147/313 (46%), Gaps = 22/313 (7%)
Query: 10  TNHDLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIES 69
            NH +   +QDQ GS+++Q+ L    +     +F  +    + LM+  +G +V  KF E 
Sbjct: 25  ANH-IVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKFFEF 83
Query: 70  CNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKF 129
               Q   + +++       L  ++  +G   ++K ++ ++  P     ++  L      
Sbjct: 84  GTPEQKNTLGMQVKGH---VLQLALQMYGCRVIQKALESIS--PEQQQEIVHELDGHVLK 138
Query: 130 LMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRK 189
            +  + G+ V+ +C+E        FI  A       L+ H  GC  +   +++    +  
Sbjct: 139 CVKDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLSTHPYGCRVIQRILEHCTAEQTT 198
Query: 190 QILHLISVNAASLSRHRSGNYVVQHVLS---LEDP-FLIDAICFALRGHYVDLSLTKCGS 245
            IL  +  +   L + + GNYV+QHVL     ED   LI+++    RG  + LS  K  S
Sbjct: 199 PILDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSV----RGKVLVLSQHKFAS 254
Query: 246 FVVQKCLKY--QNAVHYIIEEL--LNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQ 301
            VV+KC+ +  +     +I+E+   N + +  +  D+Y NYV+Q  + +     +L   +
Sbjct: 255 NVVEKCVTHATRGERTGLIDEVCTFNDNALHVMMKDQYANYVVQ-KMIDVSEPTQL---K 310
Query: 302 RLVTKLQQHLAAL 314
           +L+TK+++++AAL
Sbjct: 311 KLMTKIRKNMAAL 323

>pdb|3H3D|X Chain X, Drosophila Pumilio Rna Binding Domain (Puf Domain) Length = 323

Iteration: 1
 Score = 61.6 bits (148), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 53/197 (26%), Positives = 98/197 (49%), Gaps = 10/197 (5%)
Query: 130 LMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRK 189
           LM    G+ VI +  E     + + +      H L LA    GC  +   ++++   +++
Sbjct: 67  LMTDVFGNYVIQKFFEFGTPEQKNTLGMQVKGHVLQLALQMYGCRVIQKALESISPEQQQ 126
Query: 190 QILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQ 249
           +I+H +  +     + ++GN+VVQ  +   DP  +  I  A +G    LS    G  V+Q
Sbjct: 127 EIVHELDGHVLKCVKDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLSTHPYGCRVIQ 186
Query: 250 KCLKYQNAVHY--IIEEL-LNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTK 306
           + L++  A     I++EL  +++Q++Q   D+YGNYVIQ  L    ++D+ S+   L+  
Sbjct: 187 RILEHCTAEQTTPILDELHEHTEQLIQ---DQYGNYVIQHVLEHGKQEDK-SI---LINS 239
Query: 307 LQQHLAALRVMKYGSNV 323
           ++  +  L   K+ SNV
Sbjct: 240 VRGKVLVLSQHKFASNV 256

>pdb|2YJY|A Chain A, A Specific And Modular Binding Code For Cytosine Recognition In Puf Domains Length = 350

Iteration: 1
 Score = 72.4 bits (176), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 74/325 (22%), Positives = 139/325 (42%), Gaps = 32/325 (9%)
Query: 14  LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
           +   +QDQ GS+++Q  L          +F  +    ++LM   +G +V  KF E  +  
Sbjct: 27  IMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLE 86
Query: 74  QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAH------LPPLLYHVMSALKRLF 127
           Q   +  +I       L  ++  +G   ++K ++ +        +  L  HV+  +K   
Sbjct: 87  QKLALAERIRGH---VLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVK--- 140
Query: 128 KFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSR 187
                 + G+ V+ +C+E        FI  A       L+ H  GC  +   +++    +
Sbjct: 141 -----DQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQ 195
Query: 188 RKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFV 247
              IL  +  +   L + + G+YV++HVL    P     I   +RG+ + LS  K  S V
Sbjct: 196 TLPILEELHQHTEQLVQDQYGSYVIRHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNV 255
Query: 248 VQKCLKYQNAVH--YIIEELLNSDQ-----ILQVANDKYGNYVIQTALAETMRQDRLSVH 300
           V+KC+ + +      +I+E+   +      +  +  D+Y NYV+Q  +      D     
Sbjct: 256 VEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMI------DVAEPG 309
Query: 301 QRLVT--KLQQHLAALRVMKYGSNV 323
           QR +   K++ H+A LR   YG ++
Sbjct: 310 QRKIVMHKIRPHIATLRKYTYGKHI 334

>pdb|3K49|A Chain A, Puf3 Rna Binding Domain Bound To Cox17 Rna 3' Utr Recognition Sequence Site B Length = 369

Iteration: 1
 Score = 54.3 bits (129), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 68/292 (23%), Positives = 131/292 (44%), Gaps = 36/292 (12%)
Query: 19  QDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALI 78
           +DQ GS+++Q  L++  +   + +F  +     EL +  +G +V  KF E  ++ Q    
Sbjct: 38  KDQHGSRFIQRELATSPASEKEVIFNEIRDDAIELSNDVFGNYVIQKFFEFGSKIQ---- 93
Query: 79  ILKITFQDQL---FLLASVDKFGSSSVKKLIKVVA--HLPPLLYHVMSALKRLFKFLMMT 133
             K T  DQ        S+  +    ++K ++ +       L+  +  ++ ++ K     
Sbjct: 94  --KNTLVDQFKGNMKQLSLQMYACRVIQKALEYIDSNQRIELVLELSDSVLQMIK----D 147
Query: 134 KPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILH 193
           + G+ VI + +E     K  FI  +   H  +L+ H  GC  +   ++      ++ IL+
Sbjct: 148 QNGNHVIQKAIETIPIEKLPFILSSLTGHIYHLSTHSYGCRVIQRLLEFGSSEDQESILN 207
Query: 194 LISVNAASLSRHRSGNYVVQHVLSLEDPF----LID---AICFALRGHYVDLSLTKCGSF 246
            +      L + + GNYV+Q+VL  +D F    ++D    I   +  + V+ S  K  S 
Sbjct: 208 ELKDFIPYLIQDQYGNYVIQYVLQ-QDQFTNKEMVDIKQEIIETVANNVVEYSKHKFASN 266
Query: 247 VVQKCLKY--QNAVHYIIEELLNSDQ-----------ILQVANDKYGNYVIQ 285
           VV+K + Y  +N    II ++L  D+           ++ +  D++ NYVIQ
Sbjct: 267 VVEKSILYGSKNQKDLIISKILPRDKNHALNLEDDSPMILMIKDQFANYVIQ 318

>pdb|3K49|A Chain A, Puf3 Rna Binding Domain Bound To Cox17 Rna 3' Utr Recognition Sequence Site B Length = 369

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 36/160 (22%), Positives = 78/160 (48%), Gaps = 6/160 (3%)
Query: 172 GCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFAL 231
            C  +   ++ +  ++R +++  +S +   + + ++GN+V+Q  +       +  I  +L
Sbjct: 114 ACRVIQKALEYIDSNQRIELVLELSDSVLQMIKDQNGNHVIQKAIETIPIEKLPFILSSL 173
Query: 232 RGHYVDLSLTKCGSFVVQKCLKYQNAVHYIIEELLNS--DQILQVANDKYGNYVIQTALA 289
            GH   LS    G  V+Q+ L++ ++     E +LN   D I  +  D+YGNYVIQ  L 
Sbjct: 174 TGHIYHLSTHSYGCRVIQRLLEFGSSEDQ--ESILNELKDFIPYLIQDQYGNYVIQYVLQ 231
Query: 290 ET--MRQDRLSVHQRLVTKLQQHLAALRVMKYGSNVYKWT 327
           +     ++ + + Q ++  +  ++      K+ SNV + +
Sbjct: 232 QDQFTNKEMVDIKQEIIETVANNVVEYSKHKFASNVVEKS 271

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	335
3gvo_A	351	Pumilio 2, pumilio homolog 2; RNA-binding, PUF dom	6e-64
3gvo_A	351	Pumilio 2, pumilio homolog 2; RNA-binding, PUF dom	6e-20
3gvo_A	351	Pumilio 2, pumilio homolog 2; RNA-binding, PUF dom	6e-18
3bwt_A	333	Protein PUF4; pumilio, RNA binding, HO endonucleas	1e-62
3bwt_A	333	Protein PUF4; pumilio, RNA binding, HO endonucleas	4e-20
3bwt_A	333	Protein PUF4; pumilio, RNA binding, HO endonucleas	2e-18
3bwt_A	333	Protein PUF4; pumilio, RNA binding, HO endonucleas	4e-08
3k49_A	369	MRNA-binding protein PUF3; PUF3, pumilio, RNA bind	4e-58
3k49_A	369	MRNA-binding protein PUF3; PUF3, pumilio, RNA bind	4e-18
3v71_A	382	PUF (pumilio/FBF) domain-containing protein 7, CO	6e-45
3v71_A	382	PUF (pumilio/FBF) domain-containing protein 7, CO	1e-12
3v71_A	382	PUF (pumilio/FBF) domain-containing protein 7, CO	6e-07
3v71_A	382	PUF (pumilio/FBF) domain-containing protein 7, CO	8e-06
3k62_A	412	FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding fa	4e-36
3k62_A	412	FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding fa	7e-16
3k62_A	412	FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding fa	4e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04

>3gvo_A Pumilio 2, pumilio homolog 2; RNA-binding, PUF domain, RNA binding protein; HET: DTD; 1.60A {Mus musculus} PDB: 3gvt_A 3q0q_A 3q0r_A 3q0s_A 1ib2_A 1m8w_A 1m8x_A 1m8y_A 1m8z_A 3q0l_A 3q0m_A 3q0n_A 3q0o_A 3q0p_A 2yjy_A 3bsx_A 3bsb_A 3h3d_X Length = 351

 Score =  205 bits (524), Expect = 6e-64
 Identities = 71/325 (21%), Positives = 138/325 (42%), Gaps = 17/325 (5%)

Query: 6   FEHCTNHDLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGK 65
                 H +   +QDQ GS+++Q+ L          +F  +    ++LM+  +G +V  K
Sbjct: 21  LRDLIGH-IVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQAAYQLMTDVFGNYVIQK 79

Query: 66  FIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKR 125
           F E  +  Q   +  +I     +  L ++  +G   ++K ++ ++        ++  L  
Sbjct: 80  FFEFGSLDQKLALATRIR--GHVLPL-ALQMYGCRVIQKALESIS--SDQQSEMVKELDG 134

Query: 126 LFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKG 185
                +  + G+ V+ +C+E        FI  A       L+ H  GC  +   +++   
Sbjct: 135 HVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTA 194

Query: 186 SRRKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGS 245
            +   IL  +  +   L + + GNYV+QHVL    P     I   +RG  + LS  K  S
Sbjct: 195 EQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFAS 254

Query: 246 FVVQKCLKY--QNAVHYIIEELL-----NSDQILQVANDKYGNYVIQTALAETMRQDRLS 298
            VV+KC+ +  +     +I+E+          +  +  D+Y NYV+Q  +       R  
Sbjct: 255 NVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMAEPAQR-- 312

Query: 299 VHQRLVTKLQQHLAALRVMKYGSNV 323
             + ++ K++ H+  LR   YG ++
Sbjct: 313 --KIIMHKIRPHITTLRKYTYGKHI 335

>3gvo_A Pumilio 2, pumilio homolog 2; RNA-binding, PUF domain, RNA binding protein; HET: DTD; 1.60A {Mus musculus} PDB: 3gvt_A 3q0q_A 3q0r_A 3q0s_A 1ib2_A 1m8w_A 1m8x_A 1m8y_A 1m8z_A 3q0l_A 3q0m_A 3q0n_A 3q0o_A 3q0p_A 2yjy_A 3bsx_A 3bsb_A 3h3d_X Length = 351

 Score = 88.1 bits (219), Expect = 6e-20
 Identities = 50/267 (18%), Positives = 98/267 (36%), Gaps = 23/267 (8%)

Query: 6   FEHCTNH-----------DLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELM 54
           FE  +              +  LA    G + +Q+ L S  S    ++   + G   + +
Sbjct: 81  FEFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQQSEMVKELDGHVLKCV 140

Query: 55  SGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPP 114
             Q G  V  K IE      L  II    F+ Q+F+L++   +G   ++++++       
Sbjct: 141 KDQNGNHVVQKCIECVQPQSLQFII--DAFKGQVFVLST-HPYGCRVIQRILEHCT--AE 195

Query: 115 LLYHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCI 174
               ++  L +  + L+  + G+ VI   LE         I        L L+ H+    
Sbjct: 196 QTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASN 255

Query: 175 NLNNFIDNMKGSRRKQILHLISVNAAS-------LSRHRSGNYVVQHVLSLEDPFLIDAI 227
            +   + +   + R  ++  +             + + +  NYVVQ ++ + +P     I
Sbjct: 256 VVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMAEPAQRKII 315

Query: 228 CFALRGHYVDLSLTKCGSFVVQKCLKY 254
              +R H   L     G  ++ K  KY
Sbjct: 316 MHKIRPHITTLRKYTYGKHILAKLEKY 342

>3gvo_A Pumilio 2, pumilio homolog 2; RNA-binding, PUF domain, RNA binding protein; HET: DTD; 1.60A {Mus musculus} PDB: 3gvt_A 3q0q_A 3q0r_A 3q0s_A 1ib2_A 1m8w_A 1m8x_A 1m8y_A 1m8z_A 3q0l_A 3q0m_A 3q0n_A 3q0o_A 3q0p_A 2yjy_A 3bsx_A 3bsb_A 3h3d_X Length = 351

 Score = 82.4 bits (204), Expect = 6e-18
 Identities = 41/191 (21%), Positives = 80/191 (41%), Gaps = 10/191 (5%)

Query: 135 PGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHL 194
            G S +L+      N   +   +  + H +  +  + G   +   ++    + R+ + + 
Sbjct: 2   TGRSRLLEDFRN--NRFPNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQIVFNE 59

Query: 195 ISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLKY 254
           I   A  L     GNYV+Q            A+   +RGH + L+L   G  V+QK L+ 
Sbjct: 60  ILQAAYQLMTDVFGNYVIQKFFEFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKALES 119

Query: 255 QNA--VHYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLA 312
            ++     +++EL     +L+   D+ GN+V+Q  + E ++   L   Q ++   +  + 
Sbjct: 120 ISSDQQSEMVKEL--DGHVLKCVKDQNGNHVVQKCI-ECVQPQSL---QFIIDAFKGQVF 173

Query: 313 ALRVMKYGSNV 323
            L    YG  V
Sbjct: 174 VLSTHPYGCRV 184

>3bwt_A Protein PUF4; pumilio, RNA binding, HO endonuclease, transcription, RNA binding protein; 2.69A {Saccharomyces cerevisiae} PDB: 4dzs_A 3bx2_A 3bx3_A Length = 333

 Score =  201 bits (513), Expect = 1e-62
 Identities = 82/319 (25%), Positives = 147/319 (46%), Gaps = 13/319 (4%)

Query: 13  DLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNE 72
            + SL +DQ G ++LQ+ L    S+  D +F     +T ELM+  +G ++  K +E    
Sbjct: 14  SIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTT 73

Query: 73  SQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMM 132
            Q  ++    +       + S++  G+ +++KLI+ +         V+ +L+     L  
Sbjct: 74  EQRIVLTKISS--PHFVEI-SLNPHGTRALQKLIECIKT-DEEAQIVVDSLRPYTVQLSK 129

Query: 133 TKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQIL 192
              G+ VI +CL+        FI+ A  + C+ +A H  GC  L   +D+    +   + 
Sbjct: 130 DLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLC 189

Query: 193 HLISVNAASLSRHRSGNYVVQHVLSLEDP----FLIDAICFALRGHYVDLSLTKCGSFVV 248
             +      L+    GNYVVQ++++ E           I   L+   ++LS+ K GS V+
Sbjct: 190 DKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVI 249

Query: 249 QKCLKYQNAVHYIIEELLNS---DQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVT 305
           +K LK       +I E+LN+     I  + ND YGNYV+QTAL +   +    +++RL  
Sbjct: 250 EKILKTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTAL-DISHKQNDYLYKRLSE 308

Query: 306 KLQQHLA-ALRVMKYGSNV 323
            +   L   +R   +G  +
Sbjct: 309 IVAPLLVGPIRNTPHGKRI 327

>3bwt_A Protein PUF4; pumilio, RNA binding, HO endonuclease, transcription, RNA binding protein; 2.69A {Saccharomyces cerevisiae} PDB: 4dzs_A 3bx2_A 3bx3_A Length = 333

 Score = 88.7 bits (220), Expect = 4e-20
 Identities = 32/175 (18%), Positives = 62/175 (35%), Gaps = 9/175 (5%)

Query: 152 NDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYV 211
            D +    +     L   + GC  L   +D +       I          L     GNY+
Sbjct: 4   ADAVLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYL 63

Query: 212 VQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLKYQNA---VHYIIEELLNS 268
           +Q +L          +      H+V++SL   G+  +QK ++          +++ L   
Sbjct: 64  IQKLLEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSL--R 121

Query: 269 DQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNV 323
              +Q++ D  GN+VIQ  L     ++     Q +   +      +   ++G  V
Sbjct: 122 PYTVQLSKDLNGNHVIQKCLQRLKPENF----QFIFDAISDSCIDIATHRHGCCV 172

>3bwt_A Protein PUF4; pumilio, RNA binding, HO endonuclease, transcription, RNA binding protein; 2.69A {Saccharomyces cerevisiae} PDB: 4dzs_A 3bx2_A 3bx3_A Length = 333

 Score = 83.3 bits (206), Expect = 2e-18
 Identities = 37/208 (17%), Positives = 83/208 (39%), Gaps = 9/208 (4%)

Query: 119 VMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNN 178
           V+         L   + G   + + L+   +   D I++   ++ + L     G   +  
Sbjct: 7   VLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQK 66

Query: 179 FIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVL-SLEDPFLIDAICFALRGHYVD 237
            ++ +   +R  +  + S +   +S +  G   +Q ++  ++       +  +LR + V 
Sbjct: 67  LLEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQ 126

Query: 238 LSLTKCGSFVVQKCLKYQNAVH--YIIEELLNSDQILQVANDKYGNYVIQTALAETMRQD 295
           LS    G+ V+QKCL+     +  +I + +   D  + +A  ++G  V+Q  L     + 
Sbjct: 127 LSKDLNGNHVIQKCLQRLKPENFQFIFDAIS--DSCIDIATHRHGCCVLQRCLDHGTTEQ 184

Query: 296 RLSVHQRLVTKLQQHLAALRVMKYGSNV 323
                  L  KL   +  L +  +G+ V
Sbjct: 185 C----DNLCDKLLALVDKLTLDPFGNYV 208

>3bwt_A Protein PUF4; pumilio, RNA binding, HO endonuclease, transcription, RNA binding protein; 2.69A {Saccharomyces cerevisiae} PDB: 4dzs_A 3bx2_A 3bx3_A Length = 333

 Score = 53.3 bits (128), Expect = 4e-08
 Identities = 24/105 (22%), Positives = 40/105 (38%), Gaps = 12/105 (11%)

Query: 223 LIDAICFALRGHYVDLSLTKCGSFVVQKCLKYQNA--VHYIIEELLNSDQILQVANDKYG 280
             DA+     G    L   + G   +QK L    +     I EE    D  +++  D +G
Sbjct: 3   FADAVLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETK--DYTVELMTDSFG 60

Query: 281 NYVIQTALAETMRQDRLSVHQR--LVTKLQQHLAALRVMKYGSNV 323
           NY+IQ  L      + ++  QR  L      H   + +  +G+  
Sbjct: 61  NYLIQKLL------EEVTTEQRIVLTKISSPHFVEISLNPHGTRA 99

>3k49_A MRNA-binding protein PUF3; PUF3, pumilio, RNA binding, mitochondrial mRNA,, membrane, mitochondrion; HET: CIT; 2.50A {Saccharomyces cerevisiae} PDB: 3k4e_A Length = 369

 Score =  191 bits (486), Expect = 4e-58
 Identities = 64/331 (19%), Positives = 139/331 (41%), Gaps = 29/331 (8%)

Query: 13  DLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNE 72
                 +DQ GS+++Q  L++  +   + +F  +     EL +  +G +V  KF E  ++
Sbjct: 32  HSLEFCKDQHGSRFIQRELATSPASEKEVIFNEIRDDAIELSNDVFGNYVIQKFFEFGSK 91

Query: 73  SQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMM 132
            Q   ++ +      +  L S+  +    ++K ++ +         ++  L      ++ 
Sbjct: 92  IQKNTLVDQFK--GNMKQL-SLQMYACRVIQKALEYI--DSNQRIELVLELSDSVLQMIK 146

Query: 133 TKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQIL 192
            + G+ VI + +E     K  FI  +   H  +L+ H  GC  +   ++      ++ IL
Sbjct: 147 DQNGNHVIQKAIETIPIEKLPFILSSLTGHIYHLSTHSYGCRVIQRLLEFGSSEDQESIL 206

Query: 193 HLISVNAASLSRHRSGNYVVQHVLSLEDP------FLIDAICFALRGHYVDLSLTKCGSF 246
           + +      L + + GNYV+Q+VL  +         +   I   +  + V+ S  K  S 
Sbjct: 207 NELKDFIPYLIQDQYGNYVIQYVLQQDQFTNKEMVDIKQEIIETVANNVVEYSKHKFASN 266

Query: 247 VVQKCLKY--QNAVHYIIEELL-----------NSDQILQVANDKYGNYVIQTALAETMR 293
           VV+K + Y  +N    II ++L           +   ++ +  D++ NYVIQ  +  +  
Sbjct: 267 VVEKSILYGSKNQKDLIISKILPRDKNHALNLEDDSPMILMIKDQFANYVIQKLVNVSEG 326

Query: 294 QDRLSVHQRLVTKLQQHLAAL-RVMKYGSNV 323
           + +    + +V  ++ +L  L +    G+  
Sbjct: 327 EGK----KLIVIAIRAYLDKLNKSNSLGNRH 353

>3k49_A MRNA-binding protein PUF3; PUF3, pumilio, RNA binding, mitochondrial mRNA,, membrane, mitochondrion; HET: CIT; 2.50A {Saccharomyces cerevisiae} PDB: 3k4e_A Length = 369

 Score = 83.2 bits (206), Expect = 4e-18
 Identities = 47/185 (25%), Positives = 81/185 (43%), Gaps = 8/185 (4%)

Query: 141 LQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAA 200
           L+      N  ++   +    H L     + G   +   +     S ++ I + I  +A 
Sbjct: 11  LRNSSSDKNSNSNMSLKDIFGHSLEFCKDQHGSRFIQRELATSPASEKEVIFNEIRDDAI 70

Query: 201 SLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLKYQNAVH- 259
            LS    GNYV+Q           + +    +G+   LSL      V+QK L+Y ++   
Sbjct: 71  ELSNDVFGNYVIQKFFEFGSKIQKNTLVDQFKGNMKQLSLQMYACRVIQKALEYIDSNQR 130

Query: 260 -YIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLAALRVMK 318
             ++ EL  SD +LQ+  D+ GN+VIQ A+ ET+  ++L     +++ L  H+  L    
Sbjct: 131 IELVLEL--SDSVLQMIKDQNGNHVIQKAI-ETIPIEKL---PFILSSLTGHIYHLSTHS 184

Query: 319 YGSNV 323
           YG  V
Sbjct: 185 YGCRV 189

>3v71_A PUF (pumilio/FBF) domain-containing protein 7, CO transcript evidence; PUF repeats, RNA binding protein-RNA complex; HET: EPE; 2.90A {Caenorhabditis elegans} Length = 382

 Score =  156 bits (396), Expect = 6e-45
 Identities = 54/357 (15%), Positives = 123/357 (34%), Gaps = 49/357 (13%)

Query: 13  DLFSLAQDQEGSQYLQENLSSGDS----RILDKLFWVVSGFTFELMSGQYGRFVFGKFIE 68
            L   A D  G ++L+ N          + + + F   +     L   + G F+  K +E
Sbjct: 21  QLIDFAIDPSGVKFLEANYPLDSEDQIRKAVFEKFTESTTLFVGLCHSRNGNFIVQKLVE 80

Query: 69  SCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFK 128
               ++   ++ ++     L  +   DKF    V+  ++       +   +         
Sbjct: 81  LATPAEQRELLRQM-IDGGLLAM-CKDKFACRVVQLALQKF-DHSNVFQLIQELSTFDLA 137

Query: 129 FLMMTKPGSSVILQCLEPSYNHKNDFIYQA--ALEHCLYLACHEQGCINLNNFIDNMKGS 186
            +   +    VI + ++        F      + +  + +   + GC  +   ID +  +
Sbjct: 138 AMCTDQISIHVIQRVVKQLPVDMWTFFVHFLSSGDSLMAVCQDKYGCRLVQQVIDRLAEN 197

Query: 187 RRK-----------QILHLISVNAASLSRHRSGNYVVQHVL---SLEDPFLIDAICFALR 232
            +             ++  I  N   LS +   NYV+Q+V+    + + +    I   L 
Sbjct: 198 PKLPCFKFRIQLLHSLMTCIVRNCYRLSSNEFANYVIQYVIKSSGIMEMYRDTIIDKCLL 257

Query: 233 GHYVDLSLTKCGSFVVQKCLKYQN--AVHYIIEELL---------NSDQILQVANDKYGN 281
            + + +S  K  S V++    +     +H ++EE+          N D +  +   +YGN
Sbjct: 258 RNLLSMSQDKYASHVIEGAFLFAPPALLHEMMEEIFSGYVKDVESNRDALDILLFHQYGN 317

Query: 282 YVIQTALAETMRQDR---------------LSVHQRLVTKLQQHLAALRVMKYGSNV 323
           YV+Q  ++                         ++++  ++ QH + L     G  +
Sbjct: 318 YVVQQMISICTAALIGKEERELPPAILLLYSGWYEKMKQRVLQHASRLERFSSGKKI 374

>3v71_A PUF (pumilio/FBF) domain-containing protein 7, CO transcript evidence; PUF repeats, RNA binding protein-RNA complex; HET: EPE; 2.90A {Caenorhabditis elegans} Length = 382

 Score = 67.4 bits (164), Expect = 1e-12
 Identities = 44/309 (14%), Positives = 98/309 (31%), Gaps = 42/309 (13%)

Query: 2   QTIAFEHCTNHDLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTF-ELMSGQYGR 60
           Q        +  L ++ +D+   + +Q  L   D   + +L   +S F    + + Q   
Sbjct: 87  QRELLRQMIDGGLLAMCKDKFACRVVQLALQKFDHSNVFQLIQELSTFDLAAMCTDQISI 146

Query: 61  FVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIK---------VVAH 111
            V  + ++          +  ++  D L  +   DK+G   V+++I              
Sbjct: 147 HVIQRVVKQLPVDMWTFFVHFLSSGDSLMAVCQ-DKYGCRLVQQVIDRLAENPKLPCFKF 205

Query: 112 LPPLLYHVMSALKRLFKFLMMTKPGSSVILQCLE---PSYNHKNDFIYQAALEHCLYLAC 168
              LL+ +M+ + R    L   +  + VI   ++       +++  I +  L + L ++ 
Sbjct: 206 RIQLLHSLMTCIVRNCYRLSSNEFANYVIQYVIKSSGIMEMYRDTIIDKCLLRNLLSMSQ 265

Query: 169 HEQGCINLNNFIDNMKGSRRKQILHLISVNAAS-----------LSRHRSGNYVVQHVLS 217
            +     +         +   +++  I                 L  H+ GNYVVQ ++S
Sbjct: 266 DKYASHVIEGAFLFAPPALLHEMMEEIFSGYVKDVESNRDALDILLFHQYGNYVVQQMIS 325

Query: 218 LEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLKYQNAVHYIIEELLNSDQILQVAND 277
           +    LI      L    + L          +                       ++   
Sbjct: 326 ICTAALIGKEERELPPAILLLYSGWYEKMKQRVLQ-----------------HASRLERF 368

Query: 278 KYGNYVIQT 286
             G  +I +
Sbjct: 369 SSGKKIIDS 377

>3v71_A PUF (pumilio/FBF) domain-containing protein 7, CO transcript evidence; PUF repeats, RNA binding protein-RNA complex; HET: EPE; 2.90A {Caenorhabditis elegans} Length = 382

 Score = 49.7 bits (118), Expect = 6e-07
 Identities = 34/227 (14%), Positives = 79/227 (34%), Gaps = 19/227 (8%)

Query: 1   LQTIAFEHCTNHDLFSLAQDQEGSQYLQENLSSGDS-----------RILDKLFWVVSGF 49
                    +   L ++ QD+ G + +Q+ +                ++L  L   +   
Sbjct: 161 WTFFVHFLSSGDSLMAVCQDKYGCRLVQQVIDRLAENPKLPCFKFRIQLLHSLMTCIVRN 220

Query: 50  TFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVV 109
            + L S ++  +V    I+S    ++    +      +  L  S DK+ S  ++      
Sbjct: 221 CYRLSSNEFANYVIQYVIKSSGIMEMYRDTIIDKCLLRNLLSMSQDKYASHVIEGAFLFA 280

Query: 110 AHLPPLLYHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACH 169
              P LL+ +M  +     ++   +     +   L   Y +   ++ Q  +  C   A  
Sbjct: 281 P--PALLHEMMEEI--FSGYVKDVESNRDALDILLFHQYGN---YVVQQMISICTA-ALI 332

Query: 170 EQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVL 216
            +    L   I  +     +++   +  +A+ L R  SG  ++  V+
Sbjct: 333 GKEERELPPAILLLYSGWYEKMKQRVLQHASRLERFSSGKKIIDSVM 379

>3v71_A PUF (pumilio/FBF) domain-containing protein 7, CO transcript evidence; PUF repeats, RNA binding protein-RNA complex; HET: EPE; 2.90A {Caenorhabditis elegans} Length = 382

 Score = 46.2 bits (109), Expect = 8e-06
 Identities = 15/99 (15%), Positives = 35/99 (35%), Gaps = 11/99 (11%)

Query: 231 LRGHYVDLSLTKCGSFVVQKCLKY------QNAVHYIIEELLNSDQILQVANDKYGNYVI 284
           L G  +D ++   G   ++           + AV     E       + + + + GN+++
Sbjct: 18  LNGQLIDFAIDPSGVKFLEANYPLDSEDQIRKAVFEKFTEST--TLFVGLCHSRNGNFIV 75

Query: 285 QTALAETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNV 323
           Q  +      ++    + L   +   L A+   K+   V
Sbjct: 76  QKLVELATPAEQR---ELLRQMIDGGLLAMCKDKFACRV 111

>3k62_A FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding factor, PUF, RNA-binding specificity, base flipping, base stacking; 1.90A {Caenorhabditis elegans} PDB: 3k5y_A 3k5z_A 3k61_A 3k5q_A 3k64_A 3qg9_A 3v6y_A 3v74_A 3qgc_A 3qgb_A Length = 412

 Score =  134 bits (337), Expect = 4e-36
 Identities = 64/354 (18%), Positives = 134/354 (37%), Gaps = 49/354 (13%)

Query: 13  DLFSLAQDQEGSQYLQENL-SSGDSRILDKLFWVV---SGFTFELMSGQYGRFVFGKFIE 68
           DL   A D+ G Q+L++ +  S  S    +LF  V        +L +  +G ++    I 
Sbjct: 30  DLMKFAVDKTGCQFLEKAVKGSLTSYQKFQLFEQVIGRKDDFLKLSTNIFGNYLVQSVIG 89

Query: 69  SCNESQ-----LALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSAL 123
               +           LK     Q+  +  +DKF    ++  ++ +     L   ++ AL
Sbjct: 90  ISLATNDDGYTKRQEKLKNFISSQMTDM-CLDKFACRVIQSSLQNMD--LSLACKLVQAL 146

Query: 124 KRLFKF--LMMTKPGSSVILQCLEPSYNHKNDFIYQ--AALEHCLYLACHEQGCINLNNF 179
            R  +   + + +  + VI + +        +FI    A  EH   +   + GC  +   
Sbjct: 147 PRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIVDFVATPEHLRQICSDKYGCRVVQTI 206

Query: 180 IDNMKGSRR----------------KQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFL 223
           I+ +                     ++++  ++     L+ +   NY++QH++S +D  +
Sbjct: 207 IEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQHIVSNDDLAV 266

Query: 224 ID--AICFALRGHYVDLSLTKCGSFVVQKCLKY--QNAVHYIIEELLN---------SDQ 270
                I   L  + + LS  K  S VV+K   +     +  +++E+ +          D 
Sbjct: 267 YRECIIEKCLMRNLLSLSQEKFASHVVEKAFLHAPLELLAEMMDEIFDGYIPHPDTGKDA 326

Query: 271 ILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNVY 324
           +  +   ++GNYV+Q  L         +V  R  TK   +  A+    +   ++
Sbjct: 327 LDIMMFHQFGNYVVQCMLTIC----CDAVSGRRQTKEGGYDHAISFQDWLKKLH 376

>3k62_A FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding factor, PUF, RNA-binding specificity, base flipping, base stacking; 1.90A {Caenorhabditis elegans} PDB: 3k5y_A 3k5z_A 3k61_A 3k5q_A 3k64_A 3qg9_A 3v6y_A 3v74_A 3qgc_A 3qgb_A Length = 412

 Score = 77.1 bits (189), Expect = 7e-16
 Identities = 46/348 (13%), Positives = 114/348 (32%), Gaps = 41/348 (11%)

Query: 10  TNHDLFSLAQDQEGSQYLQENLSS-------GDSRILDKLFWVVSGFTFELMSGQYGRFV 62
              D   L+ +  G+  +Q  +         G ++  +KL   +S    ++   ++   V
Sbjct: 67  RKDDFLKLSTNIFGNYLVQSVIGISLATNDDGYTKRQEKLKNFISSQMTDMCLDKFACRV 126

Query: 63  FGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVV--AHLPPLLYHVM 120
               +++ + S    ++  +    +L  +  VD+  +  ++K++ V+   +   ++  V 
Sbjct: 127 IQSSLQNMDLSLACKLVQALPRDARLIAIC-VDQNANHVIQKVVAVIPLKNWEFIVDFV- 184

Query: 121 SALKRLFKFLMMTKPGSSVILQCLEPSYNHKN----------------DFIYQAALEHCL 164
            A     + +   K G  V+   +E                         +  +    C 
Sbjct: 185 -ATPEHLRQICSDKYGCRVVQTIIEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQ 243

Query: 165 YLACHEQGCINLNNFIDNMKGS--RRKQILHLISVNAASLSRHRSGNYVVQHVLSLEDP- 221
            LA +E     + + + N   +  R   I   +  N  SLS+ +  ++VV+         
Sbjct: 244 ELATNEYANYIIQHIVSNDDLAVYRECIIEKCLMRNLLSLSQEKFASHVVEKAFLHAPLE 303

Query: 222 ---FLIDAICFAL-------RGHYVDLSLTKCGSFVVQKCLKYQNAVHYIIEELLNSDQI 271
               ++D I           +     +   + G++VVQ  L           +       
Sbjct: 304 LLAEMMDEIFDGYIPHPDTGKDALDIMMFHQFGNYVVQCMLTICCDAVSGRRQTKEGGYD 363

Query: 272 LQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLAALRVMKY 319
             ++   +   +      E  R  R S  ++++  L    +   + + 
Sbjct: 364 HAISFQDWLKKLHSRVTKERHRLSRFSSGKKMIETLANLRSTHPIYEL 411

>3k62_A FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding factor, PUF, RNA-binding specificity, base flipping, base stacking; 1.90A {Caenorhabditis elegans} PDB: 3k5y_A 3k5z_A 3k61_A 3k5q_A 3k64_A 3qg9_A 3v6y_A 3v74_A 3qgc_A 3qgb_A Length = 412

 Score = 50.2 bits (119), Expect = 4e-07
 Identities = 16/100 (16%), Positives = 45/100 (45%), Gaps = 7/100 (7%)

Query: 231 LRGHYVDLSLTKCGSFVVQKCLKYQNAVHY---IIEELL-NSDQILQVANDKYGNYVIQT 286
             G  +  ++ K G   ++K +K     +    + E+++   D  L+++ + +GNY++Q+
Sbjct: 27  DSGDLMKFAVDKTGCQFLEKAVKGSLTSYQKFQLFEQVIGRKDDFLKLSTNIFGNYLVQS 86

Query: 287 ALAETMR-QDRLSVHQR--LVTKLQQHLAALRVMKYGSNV 323
            +  ++   D     ++  L   +   +  + + K+   V
Sbjct: 87  VIGISLATNDDGYTKRQEKLKNFISSQMTDMCLDKFACRV 126

>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 = 56.8 bits (136), Expect = 5e-09
 Identities = 48/300 (16%), Positives = 94/300 (31%), Gaps = 73/300 (24%)

Query: 51  FELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVA 110
           FE    QY    +   +    ++     +     +D   +  S+       +  +I    
Sbjct: 9   FETGEHQYQ---YKDILSVFEDA----FVDNFDCKDVQDMPKSI--LSKEEIDHIIMS-- 57

Query: 111 HLPPLLYHVMSALKRLFKFLMMTKPGSSV---ILQCLEPSYNHKNDFIY--------QAA 159
                    +S   RLF + +++K    V   + + L  +Y     F+         Q +
Sbjct: 58  ---K---DAVSGTLRLF-WTLLSKQEEMVQKFVEEVLRINY----KFLMSPIKTEQRQPS 106

Query: 160 LEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQH----- 214
           +   +Y+   ++   N N        SR +  L L      +L   R    V+       
Sbjct: 107 MMTRMYIEQRDRLY-NDNQVFAKYNVSRLQPYLKLRQ----ALLELRPAKNVLIDGVLGS 161

Query: 215 ---VLSLE---DPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLKYQNAVHYIIEELLNS 268
               ++L+      +   + F +   +  L+L  C S   +  L+    + Y I      
Sbjct: 162 GKTWVALDVCLSYKVQCKMDFKI--FW--LNLKNCNS--PETVLEMLQKLLYQI------ 209

Query: 269 DQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNVY-KWT 327
           D      +D   N  ++        Q  L    RL+ K + +   L V+    NV     
Sbjct: 210 DPNWTSRSDHSSNIKLRIHSI----QAELR---RLL-KSKPYENCLLVL---LNVQNAKA 258

>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 = 41.8 bits (97), Expect = 3e-04
 Identities = 49/317 (15%), Positives = 89/317 (28%), Gaps = 101/317 (31%)

Query: 60  RFVFGKF---IESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLL 116
           +  F  F   +++CN  +  L +L    Q    LL  +D   +S              L 
Sbjct: 179 KMDFKIFWLNLKNCNSPETVLEML----QK---LLYQIDPNWTSRSDHSSN-----IKLR 226

Query: 117 YH-VMSALKRLFKFLMMTKPGSSVIL--------------QC--LEPSYNHKN-DFI--- 155
            H + + L+RL K          ++L               C  L  +   +  DF+   
Sbjct: 227 IHSIQAELRRLLK--SKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAA 284

Query: 156 --YQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILH----LISVNAASLSRH--RS 207
                +L+H       ++    L  ++D       +++L      +S+ A S+       
Sbjct: 285 TTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATW 344

Query: 208 GNYVVQHV----------LSLE--DPFLIDAICFALRGHYVDLSL--------------- 240
            N+  +HV           SL   +P          R  +  LS+               
Sbjct: 345 DNW--KHVNCDKLTTIIESSLNVLEPAE-------YRKMFDRLSVFPPSAHIPTILLSLI 395

Query: 241 -----TKCGSFVVQKCLKYQNAVHYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQD 295
                      VV K  KY          L+                 I   L   +  +
Sbjct: 396 WFDVIKSDVMVVVNKLHKYS---------LVEKQP----KESTISIPSIYLELKVKLENE 442

Query: 296 RLSVHQRLVTKLQQHLA 312
             ++H+ +V        
Sbjct: 443 Y-ALHRSIVDHYNIPKT 458

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	335
3gvo_A	351	Pumilio 2, pumilio homolog 2; RNA-binding, PUF dom	100.0
3bwt_A	333	Protein PUF4; pumilio, RNA binding, HO endonucleas	100.0
3k49_A	369	MRNA-binding protein PUF3; PUF3, pumilio, RNA bind	100.0
3k62_A	412	FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding fa	100.0
3v71_A	382	PUF (pumilio/FBF) domain-containing protein 7, CO	100.0
3gvo_A	351	Pumilio 2, pumilio homolog 2; RNA-binding, PUF dom	100.0
3k49_A	369	MRNA-binding protein PUF3; PUF3, pumilio, RNA bind	100.0
3bwt_A	333	Protein PUF4; pumilio, RNA binding, HO endonucleas	100.0
3v71_A	382	PUF (pumilio/FBF) domain-containing protein 7, CO	100.0
3k62_A	412	FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding fa	100.0
3hjl_A	329	Flagellar motor switch protein FLIG; armadillo rep	86.72

>3gvo_A Pumilio 2, pumilio homolog 2; RNA-binding, PUF domain, RNA binding protein; HET: DTD; 1.60A {Mus musculus} SCOP: a.118.1.8 PDB: 3gvt_A 3q0q_A 3q0r_A 3q0s_A 1ib2_A 1m8w_A 1m8x_A 1m8y_A 1m8z_A 3q0l_A 3q0m_A 3q0n_A 3q0o_A 3q0p_A 2yjy_A 3bsx_A 3bsb_A 3h3d_X

Probab=100.00  E-value=5.8e-65  Score=464.07  Aligned_cols=319  Identities=22%  Similarity=0.367  Sum_probs=303.7

Q ss_pred             ccccccccCcchhhhccCchhcHHHHHhhcCCCHHHHHHHHHHHHhhHHhhccCccchHHHHHHhhhcCHHHHHHHHHHH
Q 035754            3 TIAFEHCTNHDLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKI   82 (335)
Q Consensus         3 ~~~~~~~~~g~~~~la~~~~~s~~lq~~l~~~~~e~~~~i~~e~~~~~~~L~~~~~gs~v~q~ll~~~~~~~~~~i~~~l   82 (335)
                      +..++++. |+++++|+||+|||+||++|+.+++++++.|++++.+++.+||.|+|||||+|+++++++++++..|++.+
T Consensus        18 ~~~l~~~~-g~i~~la~dq~gsR~lQ~~l~~~~~~~~~~i~~ei~~~~~~L~~d~~gn~vvQklle~~~~~~~~~i~~~i   96 (351)
T 3gvo_A           18 NLQLRDLI-GHIVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQAAYQLMTDVFGNYVIQKFFEFGSLDQKLALATRI   96 (351)
T ss_dssp             TCCGGGGT-TCHHHHHTSHHHHHHHHHHHHHCCHHHHHHHHHHHGGGHHHHHTSTTHHHHHHHHHHHCCHHHHHHHHHHH
T ss_pred             CcCHHHHH-hHHHHHhcCCcchHHHHHHHhhCCHHHHHHHHHHHHHhHHHHHhChhhhHHHHHHHhhCCHHHHHHHHHHH
Confidence            34677877 99999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hcccchhhhhhccccCcHHHHHHHhhhcCChhHHHHHHHHHHHhhhhhhcCCCccHHHHHHhhcCCcchhHHHHHHHHHh
Q 035754           83 TFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEH  162 (335)
Q Consensus        83 ~~~~~~~~~l~~~~~gs~vlq~ll~~~~~~~~~~~~i~~~l~~~~~~l~~d~~g~~vvq~~l~~~~~~~~~~l~~~~~~~  162 (335)
                      .   +++.+++.|+|||+|+|++++. +.++ +...+.+++.+++..|+.|++||||+|++++..+++.+..|++.+.++
T Consensus        97 ~---g~~~~l~~~~~G~rvvQk~le~-~~~~-~~~~i~~el~~~~~~L~~d~~Gn~ViQk~l~~~~~~~~~~i~~~~~~~  171 (351)
T 3gvo_A           97 R---GHVLPLALQMYGCRVIQKALES-ISSD-QQSEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQ  171 (351)
T ss_dssp             T---TCHHHHHTSTTHHHHHHHHHHH-SCHH-HHHHHHGGGTTCHHHHHHSTTHHHHHHHHHHHSCGGGTHHHHHHTTTT
T ss_pred             H---hhHHHHhhCHHhHHHHHHHHHh-CCHH-HHHHHHHHhhhhHHHHHHhhhhhHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            9   9999999999999999999999 6554 455666779999999999999999999999999999999999999999


Q ss_pred             HHHhhcCCCccHHHHHHHhccChHHHHHHHHHHHHhHHhhhcCCChhHHHHHhhccCChhhHHHHHHHHHHhHHHhccCc
Q 035754          163 CLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTK  242 (335)
Q Consensus       163 ~~~l~~~~~g~~vlq~~l~~~~~~~~~~l~~~l~~~~~~l~~d~~G~~viq~~l~~~~~~~~~~i~~~l~~~~~~l~~~~  242 (335)
                      +..++.|++||+|+|++++.++++++..+++++.+++..|++|+|||||+|++|+.++|+.+..|++.+.+++..|++++
T Consensus       172 ~~~ls~~~~G~~Vvq~~le~~~~~~~~~ii~~l~~~~~~L~~d~~Gn~ViQ~~l~~~~~~~~~~i~~~l~~~~~~Ls~~k  251 (351)
T 3gvo_A          172 VFVLSTHPYGCRVIQRILEHCTAEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHK  251 (351)
T ss_dssp             HHHHHTSTTHHHHHHHHHHHSCHHHHHHHHHHHHTTHHHHHTSTTHHHHHHHHHHHSCHHHHHHHHHTTTTCHHHHHTST
T ss_pred             HHHHHhCcHhHHHHHHHHHHCCHHHHHHHHHHHhhhHHhcCCCchHHHHHHHHHHhCchhhHHHHHHHHHHHHHHHhcCc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             chhHHHHHHHhcCCcH--HHHHHHHhCh-----hhHHhhhcCcchhHHHHHHHhhccCcCcHHHHHHHHHHHHHHHHhhh
Q 035754          243 CGSFVVQKCLKYQNAV--HYIIEELLNS-----DQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLAALR  315 (335)
Q Consensus       243 ~gS~vve~~l~~~~~~--~~i~~~l~~~-----~~~~~l~~~~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~~~~~L~  315 (335)
                      |||+|+|+|++.+++.  +.|+++++..     +.+..|++|+|||||||++|+.+++    .+++.+++.++|++..|+
T Consensus       252 ~gs~Vvek~l~~~~~~~r~~ii~el~~~~~~~~~~l~~l~~d~ygnyViq~~L~~~~~----~~r~~i~~~i~~~~~~L~  327 (351)
T 3gvo_A          252 FASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMAEP----AQRKIIMHKIRPHITTLR  327 (351)
T ss_dssp             THHHHHHHHHHHSCHHHHHHHHHHHHSCEETTEEHHHHHHHSTTHHHHHHHHHHHCCH----HHHHHHHHHHGGGHHHHT
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHhcccCCCChHHHHccCCcchHHHHHHHHHhCCH----HHHHHHHHHHHHHHHHHh
Confidence            9999999999999988  8899999861     2799999999999999999999988    899999999999999999


Q ss_pred             cCCChHHHHHHHHhhC
Q 035754          316 VMKYGSNVYKWTTASH  331 (335)
Q Consensus       316 ~~~~gs~v~~~l~~~~  331 (335)
                      .++||++|++++.+.-
T Consensus       328 ~~~~g~~i~~kl~~~~  343 (351)
T 3gvo_A          328 KYTYGKHILAKLEKYY  343 (351)
T ss_dssp             TSTTTHHHHHHHHHHT
T ss_pred             cCCchHHHHHHHHHHH
Confidence            9999999999998764

>3bwt_A Protein PUF4; pumilio, RNA binding, HO endonuclease, transcription, RNA binding protein; 2.69A {Saccharomyces cerevisiae} PDB: 4dzs_A 3bx2_A 3bx3_A

Probab=100.00  E-value=2.2e-63  Score=451.27  Aligned_cols=320  Identities=26%  Similarity=0.393  Sum_probs=301.3

Q ss_pred             cccccccccCcchhhhccCchhcHHHHHhhcCCCHHHHHHHHHHHHhhHHhhccCccchHHHHHHhhhcCHHHHHHHHHH
Q 035754            2 QTIAFEHCTNHDLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILK   81 (335)
Q Consensus         2 ~~~~~~~~~~g~~~~la~~~~~s~~lq~~l~~~~~e~~~~i~~e~~~~~~~L~~~~~gs~v~q~ll~~~~~~~~~~i~~~   81 (335)
                      .+.+++++. |+++++|.||+|||++|++|+.+++++++.|++|+.+++.+|+.|+|||||+|+++++++++++..|++.
T Consensus         4 ~~~~l~~~~-g~i~~l~~~q~gsr~iQ~~l~~~~~~~~~~i~~el~~~~~~L~~d~~gn~vvQkll~~~~~~~~~~i~~~   82 (333)
T 3bwt_A            4 ADAVLDQYI-GSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQRIVLTKI   82 (333)
T ss_dssp             TTCCGGGTT-TCHHHHTSSHHHHHHHHHHHHHSCHHHHHHHHHHHGGGHHHHHTSTTHHHHHHHHHHHSCHHHHHHHHHH
T ss_pred             ccCcHHHHH-HHHHHHhcCcHhhHHHHHHHccCCHHHHHHHHHHHHHHHHHHhcCcccHHHHHHHHhhCCHHHHHHHHHH
Confidence            577899998 9999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhcccchhhhhhccccCcHHHHHHHhhhcCChhHHHHHHHHHHHhhhhhhcCCCccHHHHHHhhcCCcchhHHHHHHHHH
Q 035754           82 ITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALE  161 (335)
Q Consensus        82 l~~~~~~~~~l~~~~~gs~vlq~ll~~~~~~~~~~~~i~~~l~~~~~~l~~d~~g~~vvq~~l~~~~~~~~~~l~~~~~~  161 (335)
                      +.   +++.+++.|+|||||+|++++. ++++++...+.+++.+++..|+.|++||||+|++++..+++.++.+++.+.+
T Consensus        83 ~~---~~~~~l~~~~~G~rviQ~~l~~-~~~~~~~~~i~~el~~~~~~L~~d~~gn~Viqk~l~~~~~~~~~~i~~~l~~  158 (333)
T 3bwt_A           83 SS---PHFVEISLNPHGTRALQKLIEC-IKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISD  158 (333)
T ss_dssp             HG---GGHHHHHHSTTHHHHHHHHHHH-CCSHHHHHHHHHHHGGGHHHHHTSTTHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             HH---hHHHHHHhcccccHHHHHHHHh-cCcHHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHCCHHHHHHHHHHHHH
Confidence            99   9999999999999999999999 8888888989999999999999999999999999999999999999999999


Q ss_pred             hHHHhhcCCCccHHHHHHHhccChHHHHHHHHHHHHhHHhhhcCCChhHHHHHhhccCChh----hHHHHHHHHHHhHHH
Q 035754          162 HCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPF----LIDAICFALRGHYVD  237 (335)
Q Consensus       162 ~~~~l~~~~~g~~vlq~~l~~~~~~~~~~l~~~l~~~~~~l~~d~~G~~viq~~l~~~~~~----~~~~i~~~l~~~~~~  237 (335)
                      ++..++.|++||+|+|++++.++++++..+++++.+++..|++|+|||||+|++++.++++    .++.+++.+.+++.+
T Consensus       159 ~~~~l~~~~~Gs~Vvq~~l~~~~~~~~~~l~~el~~~~~~L~~d~~GnyVvQ~~L~~~~~~~~~~~~~~ii~~l~~~~~~  238 (333)
T 3bwt_A          159 SCIDIATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIE  238 (333)
T ss_dssp             SHHHHHTSTTHHHHHHHHHHHCCHHHHHHHHHHHHTTHHHHHTSTTHHHHHHHHHHHHHHHTCCSHHHHHHHHHGGGHHH
T ss_pred             HHHHHhcCchhHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHhCCccccchhHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999987664    368999999999999


Q ss_pred             hccCcchhHHHHHHHhcCCcHHHHHHHHhC---hhhHHhhhcCcchhHHHHHHHhhccCcCcHHHHHHHHHHHHHHH-Hh
Q 035754          238 LSLTKCGSFVVQKCLKYQNAVHYIIEELLN---SDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHL-AA  313 (335)
Q Consensus       238 l~~~~~gS~vve~~l~~~~~~~~i~~~l~~---~~~~~~l~~~~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~~~-~~  313 (335)
                      |+.++|||+|+++|++.++..+.++.+++.   ++++..|++|+|||||||++|+.++++ +...++.+++++.|++ .+
T Consensus       239 Ls~~k~gs~Vvek~l~~~~~~~~ii~ell~~~~~~~l~~L~~d~~gnyViq~~l~~~~~~-~~~~~~~l~~~l~p~l~~~  317 (333)
T 3bwt_A          239 LSIHKFGSNVIEKILKTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDISHKQ-NDYLYKRLSEIVAPLLVGP  317 (333)
T ss_dssp             HHTSTTHHHHHHHHHTSHHHHHHHHHHHHHTTHHHHHHHHHTSTTHHHHHHHHHHHHHHH-CHHHHHHHHHHHGGGCCGG
T ss_pred             HHcccHHHHHHHHHHcccchhHHHHHHHHhccCchHHHHHHcCChHHHHHHHHHHhccCc-cHHHHHHHHHHHHHhchhh
Confidence            999999999999999976544778888875   358999999999999999999998762 1257899999999998 89


Q ss_pred             hhcCCChHHHHHHH
Q 035754          314 LRVMKYGSNVYKWT  327 (335)
Q Consensus       314 L~~~~~gs~v~~~l  327 (335)
                      |+.++||++|+.++
T Consensus       318 lr~~~~G~~i~~~l  331 (333)
T 3bwt_A          318 IRNTPHGKRIIGML  331 (333)
T ss_dssp             GGGSHHHHHHHTTS
T ss_pred             hcCCCCHHHHHHHh
Confidence            99999999999875

>3k49_A MRNA-binding protein PUF3; PUF3, pumilio, RNA binding, mitochondrial mRNA,, membrane, mitochondrion; HET: CIT; 2.50A {Saccharomyces cerevisiae} SCOP: a.118.1.0 PDB: 3k4e_A

Probab=100.00  E-value=8.8e-63  Score=452.63  Aligned_cols=317  Identities=20%  Similarity=0.282  Sum_probs=296.2

Q ss_pred             ccccccccCcchhhhccCchhcHHHHHhhcCCCHHHHHHHHHHHHhhHHhhccCccchHHHHHHhhhcCHHHHHHHHHHH
Q 035754            3 TIAFEHCTNHDLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKI   82 (335)
Q Consensus         3 ~~~~~~~~~g~~~~la~~~~~s~~lq~~l~~~~~e~~~~i~~e~~~~~~~L~~~~~gs~v~q~ll~~~~~~~~~~i~~~l   82 (335)
                      +..++++. |+++++|+||+|||++|++|+.+++++++.|++|+.|++.+|+.|+|||||+|+++++++++++..|++.+
T Consensus        23 ~~~l~~i~-g~i~~l~~d~~gsR~lQ~~l~~~~~~~~~~I~~el~~~~~~L~~d~~gn~vvQkll~~~~~~~~~~i~~~~  101 (369)
T 3k49_A           23 NMSLKDIF-GHSLEFCKDQHGSRFIQRELATSPASEKEVIFNEIRDDAIELSNDVFGNYVIQKFFEFGSKIQKNTLVDQF  101 (369)
T ss_dssp             CCCGGGGT-TCHHHHHTSHHHHHHHHHHHTTCCHHHHHHHHHHHGGGHHHHHHSTTTHHHHHHHHHHCCHHHHHHHHHHH
T ss_pred             ceeHHHHH-HHHHHHHcCCcchHHHHHHhccCCHHHHHHHHHHHHHHHHHHhhCcccccHHHHHHHhCCHHHHHHHHHHH
Confidence            45788998 99999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hcccchhhhhhccccCcHHHHHHHhhhcCChhHHHHHHHHHHHhhhhhhcCCCccHHHHHHhhcCCcchhHHHHHHHHHh
Q 035754           83 TFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEH  162 (335)
Q Consensus        83 ~~~~~~~~~l~~~~~gs~vlq~ll~~~~~~~~~~~~i~~~l~~~~~~l~~d~~g~~vvq~~l~~~~~~~~~~l~~~~~~~  162 (335)
                      .   +++..++.|+|||+|+|++++. +. +++...+.+++.+++..|+.|++||||+|++++.++++.++.|++.+.++
T Consensus       102 ~---g~~~~L~~~~~G~rVlQk~le~-~~-~~q~~~ii~el~~~~~~L~~d~~Gn~ViQ~~l~~~~~~~~~~i~~~~~~~  176 (369)
T 3k49_A          102 K---GNMKQLSLQMYACRVIQKALEY-ID-SNQRIELVLELSDSVLQMIKDQNGNHVIQKAIETIPIEKLPFILSSLTGH  176 (369)
T ss_dssp             T---TCHHHHHHSTTHHHHHHHHHHH-SC-HHHHHHHHGGGTTCHHHHHHSTTHHHHHHHHHHHSCGGGCHHHHHHHTTT
T ss_pred             h---hhHHHHhcChhhHHHHHHHHHh-CC-HHHHHHHHHHHHHHHHHHhcCcccchHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            9   9999999999999999999998 54 55566666779999999999999999999999999999999999999999


Q ss_pred             HHHhhcCCCccHHHHHHHhccChHHHHHHHHHHHHhHHhhhcCCChhHHHHHhhccCChhh------HHHHHHHHHHhHH
Q 035754          163 CLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFL------IDAICFALRGHYV  236 (335)
Q Consensus       163 ~~~l~~~~~g~~vlq~~l~~~~~~~~~~l~~~l~~~~~~l~~d~~G~~viq~~l~~~~~~~------~~~i~~~l~~~~~  236 (335)
                      +..++.|++||+|+|++++.++++++..+++++.+++..|++|+|||||+|++++.+++..      +..+++.+.+++.
T Consensus       177 ~~~ls~~~~Gs~Vvq~~l~~~~~~~~~~i~~~l~~~~~~L~~d~~GnyViQ~~l~~~~~~~~~~~~~~~~i~~~l~~~~~  256 (369)
T 3k49_A          177 IYHLSTHSYGCRVIQRLLEFGSSEDQESILNELKDFIPYLIQDQYGNYVIQYVLQQDQFTNKEMVDIKQEIIETVANNVV  256 (369)
T ss_dssp             HHHHHTSTTHHHHHHHHHHHSCHHHHHHHHHTTTTCHHHHHHSTTHHHHHHHHHTCCTTSCHHHHHHHHHHHHHHHTTHH
T ss_pred             HHHHhCCCccCcHHHHHHHhCCHHHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHhcCCchhhhhHhHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999998764      6789999999999


Q ss_pred             HhccCcchhHHHHHHHhcCCcH--HHHHHHHhCh-----------hhHHhhhcCcchhHHHHHHHhhccCcCcHHHHHHH
Q 035754          237 DLSLTKCGSFVVQKCLKYQNAV--HYIIEELLNS-----------DQILQVANDKYGNYVIQTALAETMRQDRLSVHQRL  303 (335)
Q Consensus       237 ~l~~~~~gS~vve~~l~~~~~~--~~i~~~l~~~-----------~~~~~l~~~~~g~~Viq~~l~~~~~~~~~~~~~~l  303 (335)
                      +|++++|||+|+|+|++.+++.  +.|+++++..           +.+..|++|+|||||||++|+.+++    .+++.+
T Consensus       257 ~Ls~~k~gS~Vvek~l~~~~~~~r~~ii~~l~~~~~~~~~~~~~~~~l~~L~~D~~gNyViq~~l~~~~~----~~~~~l  332 (369)
T 3k49_A          257 EYSKHKFASNVVEKSILYGSKNQKDLIISKILPRDKNHALNLEDDSPMILMIKDQFANYVIQKLVNVSEG----EGKKLI  332 (369)
T ss_dssp             HHHTSTTHHHHHHHHHHHSCHHHHHHHHTTTSCSSHHHHHTCCTTSHHHHHHTSTTHHHHHHHHHHHCCH----HHHHHH
T ss_pred             HHHhhhHhhHHHHHHHHhCCHHHHHHHHHHHhccccccccccccccHHHHHHhCcchHHHHHHHHHhCCH----HHHHHH
Confidence            9999999999999999999887  8899999862           2578999999999999999999998    899999


Q ss_pred             HHHHHHHHHhhhc-CCChHHHHHHHHh
Q 035754          304 VTKLQQHLAALRV-MKYGSNVYKWTTA  329 (335)
Q Consensus       304 ~~~l~~~~~~L~~-~~~gs~v~~~l~~  329 (335)
                      ++.++|++..|+. ++||++++..+.+
T Consensus       333 ~~~i~p~l~~L~~~~~~G~~~~~~~e~  359 (369)
T 3k49_A          333 VIAIRAYLDKLNKSNSLGNRHLASVEK  359 (369)
T ss_dssp             HHHHHHHHHHHHHCC--CCCCCHHHHH
T ss_pred             HHHHHHHHHHHhccccCcchHHHHHHH
Confidence            9999999999986 5999998877654

>3k62_A FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding factor, PUF, RNA-binding specificity, base flipping, base stacking; 1.90A {Caenorhabditis elegans} PDB: 3k5y_A 3k5z_A 3k61_A 3k5q_A 3k64_A 3qg9_A 3v6y_A 3v74_A 3qgc_A 3qgb_A

Probab=100.00  E-value=8.8e-61  Score=441.62  Aligned_cols=320  Identities=18%  Similarity=0.272  Sum_probs=286.9

Q ss_pred             ccccc-CcchhhhccCchhcHHHHHhhcCC-CHHHHHHHHHHHHhh---HHhhccCccchHHHHHHhhhcCH-------H
Q 035754            6 FEHCT-NHDLFSLAQDQEGSQYLQENLSSG-DSRILDKLFWVVSGF---TFELMSGQYGRFVFGKFIESCNE-------S   73 (335)
Q Consensus         6 ~~~~~-~g~~~~la~~~~~s~~lq~~l~~~-~~e~~~~i~~e~~~~---~~~L~~~~~gs~v~q~ll~~~~~-------~   73 (335)
                      +..+. +|+++++|+||+|||+||+.|+.+ ++++++.||+|+.++   +.+||.|+|||||+|+++++|++       +
T Consensus        22 L~~~~~~G~i~~la~Dq~GsR~lQ~~l~~~~~~e~~~~If~el~~~~~~~~~L~~d~fGNyvvQKlle~~~~~~~~~~~~  101 (412)
T 3k62_A           22 LSEVLDSGDLMKFAVDKTGCQFLEKAVKGSLTSYQKFQLFEQVIGRKDDFLKLSTNIFGNYLVQSVIGISLATNDDGYTK  101 (412)
T ss_dssp             HHHHHHHTCHHHHHTSHHHHHHHHHHTTSCCCHHHHHHHHHHHSSSHHHHHHHHTSTTHHHHHHHHHHHHHHCCSTTHHH
T ss_pred             HHHHHhCCCcHHHhcCChhHHHHHHHhccCCCHHHHHHHHHHHHhhhhHHHHHHhCcHHHHHHHHHHHhCCcccccccHH
Confidence            44443 799999999999999999999997 899999999999875   89999999999999999999999       8


Q ss_pred             HHHHHHHHHhcccchhhhhhccccCcHHHHHHHhhhcCChhHHHHHHHHH--HHhhhhhhcCCCccHHHHHHhhcCCcch
Q 035754           74 QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSAL--KRLFKFLMMTKPGSSVILQCLEPSYNHK  151 (335)
Q Consensus        74 ~~~~i~~~l~~~~~~~~~l~~~~~gs~vlq~ll~~~~~~~~~~~~i~~~l--~~~~~~l~~d~~g~~vvq~~l~~~~~~~  151 (335)
                      ++..|++.+.   +++.+++.|++||||+|++++. +. +++...+.+++  .+++..|++|++||||+|++++.++++.
T Consensus       102 q~~~i~~~l~---g~v~~L~~~~~GsrvvQk~le~-~~-~~~~~~iv~eL~~~~~i~~L~~D~~GNhVIQK~Le~~~~~~  176 (412)
T 3k62_A          102 RQEKLKNFIS---SQMTDMCLDKFACRVIQSSLQN-MD-LSLACKLVQALPRDARLIAICVDQNANHVIQKVVAVIPLKN  176 (412)
T ss_dssp             HHHHHHHHHH---HTHHHHHHSTTHHHHHHHHHHH-SC-HHHHHHHHHTSCCSHHHHHHHHCTTTHHHHHHHHHHSCHHH
T ss_pred             HHHHHHHHHH---HHHHHHHcChhhhHHHHHHHHh-CC-HHHHHHHHHHHhccccHHHHHhCccccHHHHHHHHhCCHHH
Confidence            9999999999   9999999999999999999998 54 55666777778  6899999999999999999999999999


Q ss_pred             hHHHHHHHH--HhHHHhhcCCCccHHHHHHHhccCh------------HHHH----HHHHHHHHhHHhhhcCCChhHHHH
Q 035754          152 NDFIYQAAL--EHCLYLACHEQGCINLNNFIDNMKG------------SRRK----QILHLISVNAASLSRHRSGNYVVQ  213 (335)
Q Consensus       152 ~~~l~~~~~--~~~~~l~~~~~g~~vlq~~l~~~~~------------~~~~----~l~~~l~~~~~~l~~d~~G~~viq  213 (335)
                      ++.|++.+.  +++..+++|++||+|+|++++.+++            +++.    .+++++..++..|+.|+|||||+|
T Consensus       177 ~~~I~~~~~~~~~~~~la~h~~GcrVvQk~le~~~~~~~~~~~~~~~~~qr~~il~~L~~~I~~~~~~L~~dq~GNyViQ  256 (412)
T 3k62_A          177 WEFIVDFVATPEHLRQICSDKYGCRVVQTIIEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQ  256 (412)
T ss_dssp             HHHHHHHHHSHHHHHHHHTSHHHHHHHHHHHHHTSCSGGGTTSCHHHHHHHHHHHHHHHHHHHHTHHHHHHSTTTHHHHH
T ss_pred             HHHHHHHHhcchhHHHHhcCcchHHHHHHHHHhcCcccccchhhhhhHHHHHHHHHHHHHHHHHHHHHHhhCccccHHHH
Confidence            999999998  6999999999999999999999863            3443    466778889999999999999999


Q ss_pred             HhhccCChh-hHHHHHH-HHHHhHHHhccCcchhHHHHHHHhcCCcH--HHHHHHHhC---------hhhHHhhhcCcch
Q 035754          214 HVLSLEDPF-LIDAICF-ALRGHYVDLSLTKCGSFVVQKCLKYQNAV--HYIIEELLN---------SDQILQVANDKYG  280 (335)
Q Consensus       214 ~~l~~~~~~-~~~~i~~-~l~~~~~~l~~~~~gS~vve~~l~~~~~~--~~i~~~l~~---------~~~~~~l~~~~~g  280 (335)
                      ++|+++.++ .+..+++ .+.+++.+||++||||+|||+|++.+++.  +.|++++++         ++.+..|++|+||
T Consensus       257 ~iL~~g~~~~~r~~ii~~~l~~~~~~LS~~KfgSnVVek~L~~~~~~~r~~ii~ei~~~~~~~~~~~~~~l~~L~~DqyG  336 (412)
T 3k62_A          257 HIVSNDDLAVYRECIIEKCLMRNLLSLSQEKFASHVVEKAFLHAPLELLAEMMDEIFDGYIPHPDTGKDALDIMMFHQFG  336 (412)
T ss_dssp             HHHHCGGGHHHHHHHHHHHTTTCHHHHHTSTTHHHHHHHHHHHCCHHHHHHHHHHHHHSSCCCTTTCCCHHHHHHHSTTH
T ss_pred             HHHhcCCchhHHHHHHHHHHHHHHHHHhcccHhHHHHHHHHHhCCHHHHHHHHHHHHhhccCCccccchHHHHHhcCCch
Confidence            999999876 5788887 69999999999999999999999999887  789999884         2368999999999


Q ss_pred             hHHHHHHHhhccCc---C-------------cHHHHHHHHHHHHHHHHhhhcCCChHHHHHHHHhh
Q 035754          281 NYVIQTALAETMRQ---D-------------RLSVHQRLVTKLQQHLAALRVMKYGSNVYKWTTAS  330 (335)
Q Consensus       281 ~~Viq~~l~~~~~~---~-------------~~~~~~~l~~~l~~~~~~L~~~~~gs~v~~~l~~~  330 (335)
                      |||||++|+.++++   +             ...+++.|+.+++++...|...+||++|++++.+-
T Consensus       337 NYViQ~~L~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~l~~~i~~~~~~L~~~~~Gk~i~~~l~~~  402 (412)
T 3k62_A          337 NYVVQCMLTICCDAVSGRRQTKEGGYDHAISFQDWLKKLHSRVTKERHRLSRFSSGKKMIETLANL  402 (412)
T ss_dssp             HHHHHHHHHHHHHHHTTSSCCEETTEETHHHHHHHHHHHHHHHHHTHHHHTTSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHccccccchhhccccchhhhhhhHHHHHHHHHHHHHHHHHhccCCCccHHHHHHHHh
Confidence            99999999998552   0             01357899999999999999999999999988653

>3v71_A PUF (pumilio/FBF) domain-containing protein 7, CO transcript evidence; PUF repeats, RNA binding protein-RNA complex; HET: EPE; 2.90A {Caenorhabditis elegans}

Probab=100.00  E-value=6.5e-60  Score=433.27  Aligned_cols=322  Identities=19%  Similarity=0.272  Sum_probs=284.9

Q ss_pred             ccccccc-CcchhhhccCchhcHHHHHhhcCCCHH-HHHHHHHHHH---hhHHhhccCccchHHHHHHhhhcCHHHHHHH
Q 035754            4 IAFEHCT-NHDLFSLAQDQEGSQYLQENLSSGDSR-ILDKLFWVVS---GFTFELMSGQYGRFVFGKFIESCNESQLALI   78 (335)
Q Consensus         4 ~~~~~~~-~g~~~~la~~~~~s~~lq~~l~~~~~e-~~~~i~~e~~---~~~~~L~~~~~gs~v~q~ll~~~~~~~~~~i   78 (335)
                      +.+.++. +|+++++|.||+|||++|+.|+.++++ .++.||+++.   +++.+||.|+|||||+|+++++|+++++..+
T Consensus        11 ~~L~~~~~~G~i~~~a~Dq~Gsr~lQ~~l~~~~~~~~~~~if~~l~e~~~~~~~L~~d~~Gn~vvQklle~~~~~~~~~l   90 (382)
T 3v71_A           11 ISLEDVLLNGQLIDFAIDPSGVKFLEANYPLDSEDQIRKAVFEKFTESTTLFVGLCHSRNGNFIVQKLVELATPAEQREL   90 (382)
T ss_dssp             CCHHHHHHTTCHHHHHHSHHHHHHHHHTSCSCTTCHHHHHHHHHHHSCHHHHHHHHSSTTHHHHHHHHHHTCCHHHHHHH
T ss_pred             CcHHHHhhCCCEehhccCCcccHHHHHHcccCChHHHHHHHHHHHHhhHHHHHHHhcCcHHHHHHHHHHHhCCHHHHHHH
Confidence            3455563 799999999999999999999998765 5789999996   6789999999999999999999999999998


Q ss_pred             HHH-HhcccchhhhhhccccCcHHHHHHHhhhcCChhHHHHHHHHHHH-hhhhhhcCCCccHHHHHHhhcCCcchhHHHH
Q 035754           79 ILK-ITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKR-LFKFLMMTKPGSSVILQCLEPSYNHKNDFIY  156 (335)
Q Consensus        79 ~~~-l~~~~~~~~~l~~~~~gs~vlq~ll~~~~~~~~~~~~i~~~l~~-~~~~l~~d~~g~~vvq~~l~~~~~~~~~~l~  156 (335)
                      +.. +.   +++..++.|+|||||+|++++. +..+++. .+.+++.+ ++..++.|++||||+|++++..+++.++.|+
T Consensus        91 i~~~l~---g~v~~Ls~~~~G~rvvQk~ie~-~~~~~~~-~li~eL~~~~~~~L~~D~~GnhVIQk~le~~~~~~~~~Ii  165 (382)
T 3v71_A           91 LRQMID---GGLLAMCKDKFACRVVQLALQK-FDHSNVF-QLIQELSTFDLAAMCTDQISIHVIQRVVKQLPVDMWTFFV  165 (382)
T ss_dssp             HHHHHH---TCHHHHHTSTTHHHHHHHHHHH-SCHHHHH-HHHHHHHTSCHHHHHHSTTTHHHHHHHHTTSCTTTSHHHH
T ss_pred             HHHHhc---chHHHHHhCccchHHHHHHHHH-CCHHHHH-HHHHHhcccchHHHhcCcccccHHHHHHHHCCHHHHHHHH
Confidence            876 68   9999999999999999999999 6655544 45566887 8999999999999999999999999999999


Q ss_pred             HHHH--HhHHHhhcCCCccHHHHHHHhccChHH-----------HHHHHHHHHHhHHhhhcCCChhHHHHHhhccCCh--
Q 035754          157 QAAL--EHCLYLACHEQGCINLNNFIDNMKGSR-----------RKQILHLISVNAASLSRHRSGNYVVQHVLSLEDP--  221 (335)
Q Consensus       157 ~~~~--~~~~~l~~~~~g~~vlq~~l~~~~~~~-----------~~~l~~~l~~~~~~l~~d~~G~~viq~~l~~~~~--  221 (335)
                      +.+.  +++..+++|++||+|+|++++.+++++           ...++.++.++...|+.|+|||||||++|+.+++  
T Consensus       166 ~~~~~~~~~~~la~h~~Gc~VlQ~~le~~~~~~k~~~~~~r~~~l~~l~~~I~~~~~~L~~d~~GNyVIQ~iL~~~~~~e  245 (382)
T 3v71_A          166 HFLSSGDSLMAVCQDKYGCRLVQQVIDRLAENPKLPCFKFRIQLLHSLMTCIVRNCYRLSSNEFANYVIQYVIKSSGIME  245 (382)
T ss_dssp             HHHHSTTHHHHHHHSTTHHHHHHHHHHHHTCCSSSTTHHHHHHHHHHHHHHHHTTHHHHHTSTTTHHHHHHHHTCCSTHH
T ss_pred             HHHhcccchHhHhcCchhhHHHHHHHHhCCHhhhhhhhhHHHHHHHHHHHHHHHHHHHHhhCccccHHHHHHHhcCCCcH
Confidence            9997  689999999999999999999986542           2346677888899999999999999999999864  


Q ss_pred             hhHHHHHH-HHHHhHHHhccCcchhHHHHHHHhcCCcH--HHHHHHHhC---------hhhHHhhhcCcchhHHHHHHHh
Q 035754          222 FLIDAICF-ALRGHYVDLSLTKCGSFVVQKCLKYQNAV--HYIIEELLN---------SDQILQVANDKYGNYVIQTALA  289 (335)
Q Consensus       222 ~~~~~i~~-~l~~~~~~l~~~~~gS~vve~~l~~~~~~--~~i~~~l~~---------~~~~~~l~~~~~g~~Viq~~l~  289 (335)
                      +.+..+++ .+.+++.+||++||||+|+|+|++.+++.  +.|++++++         ++.+..|++|+|||||||++|+
T Consensus       246 ~~r~~ii~~~l~~~~~~Ls~~k~gS~Vvek~l~~~~~~~r~~ii~el~~~~~~~~~~~~~~l~~l~~D~ygNyVvQ~~L~  325 (382)
T 3v71_A          246 MYRDTIIDKCLLRNLLSMSQDKYASHVIEGAFLFAPPALLHEMMEEIFSGYVKDVESNRDALDILLFHQYGNYVVQQMIS  325 (382)
T ss_dssp             HHHHHHHHHTTTTCHHHHTTSTTHHHHHHHHHHHCCHHHHHHHHHHHCC--CCCSSSCCCHHHHHHTCTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhcCchHhHHHHHHHHhCCHHHHHHHHHHHHhhccccccccchHHHHHHCCCCccHHHHHHHH
Confidence            46889997 59999999999999999999999999988  889999985         2489999999999999999999


Q ss_pred             hccCcC---------------cHHHHHHHHHHHHHHHHhhhcCCChHHHHHHHHhh
Q 035754          290 ETMRQD---------------RLSVHQRLVTKLQQHLAALRVMKYGSNVYKWTTAS  330 (335)
Q Consensus       290 ~~~~~~---------------~~~~~~~l~~~l~~~~~~L~~~~~gs~v~~~l~~~  330 (335)
                      .+++..               ...++++|+.++++++..|+.++||++|++++.++
T Consensus       326 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~~~l~~~~~Gk~i~~~l~~~  381 (382)
T 3v71_A          326 ICTAALIGKEERELPPAILLLYSGWYEKMKQRVLQHASRLERFSSGKKIIDSVMRH  381 (382)
T ss_dssp             HHHHHCC-----CCCTTTHHHHHHHHHHHHHHHHHHHHHHTTSHHHHHHHHHHHHC
T ss_pred             HcccccccchhcccchhHHhhhhHHHHHHHHHHHHHHHHhhhCCchHHHHHHHHhc
Confidence            987510               01356899999999999999999999999999875

>3gvo_A Pumilio 2, pumilio homolog 2; RNA-binding, PUF domain, RNA binding protein; HET: DTD; 1.60A {Mus musculus} SCOP: a.118.1.8 PDB: 3gvt_A 3q0q_A 3q0r_A 3q0s_A 1ib2_A 1m8w_A 1m8x_A 1m8y_A 1m8z_A 3q0l_A 3q0m_A 3q0n_A 3q0o_A 3q0p_A 2yjy_A 3bsx_A 3bsb_A 3h3d_X

Probab=100.00  E-value=1.4e-45  Score=336.22  Aligned_cols=294  Identities=17%  Similarity=0.186  Sum_probs=273.4

Q ss_pred             cHHHHHhhcCCCHHHHHHHHHHHHhhHHhhccCccchHHHHHHhhhcCHHHHHHHHHHHhcccchhhhhhccccCcHHHH
Q 035754           24 SQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVK  103 (335)
Q Consensus        24 s~~lq~~l~~~~~e~~~~i~~e~~~~~~~L~~~~~gs~v~q~ll~~~~~~~~~~i~~~l~~~~~~~~~l~~~~~gs~vlq  103 (335)
                      |.+++..=....   ....++++.|++.+++.|++||+++|++++.++++++..|+.++.   +++.+|+.|+||++|+|
T Consensus         5 ~~l~e~~r~~~~---~~~~l~~~~g~i~~la~dq~gsR~lQ~~l~~~~~~~~~~i~~ei~---~~~~~L~~d~~gn~vvQ   78 (351)
T 3gvo_A            5 SRLLEDFRNNRF---PNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQIVFNEIL---QAAYQLMTDVFGNYVIQ   78 (351)
T ss_dssp             CHHHHHHHTTCC---TTCCGGGGTTCHHHHHTSHHHHHHHHHHHHHCCHHHHHHHHHHHG---GGHHHHHTSTTHHHHHH
T ss_pred             cHHHHHHhCCCC---CCcCHHHHHhHHHHHhcCCcchHHHHHHHhhCCHHHHHHHHHHHH---HhHHHHHhChhhhHHHH
Confidence            445554444322   223467889999999999999999999999999999999999999   99999999999999999


Q ss_pred             HHHhhhcCChhHHHHHHHHHHHhhhhhhcCCCccHHHHHHhhcCCcchhHHHHHHHHHhHHHhhcCCCccHHHHHHHhcc
Q 035754          104 KLIKVVAHLPPLLYHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNM  183 (335)
Q Consensus       104 ~ll~~~~~~~~~~~~i~~~l~~~~~~l~~d~~g~~vvq~~l~~~~~~~~~~l~~~~~~~~~~l~~~~~g~~vlq~~l~~~  183 (335)
                      ++++.  +++++...+.+.+.+++.+++.|++|++|+|++++..+++++..+++.+.+++..++.|++|++|+|++++.+
T Consensus        79 klle~--~~~~~~~~i~~~i~g~~~~l~~~~~G~rvvQk~le~~~~~~~~~i~~el~~~~~~L~~d~~Gn~ViQk~l~~~  156 (351)
T 3gvo_A           79 KFFEF--GSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQQSEMVKELDGHVLKCVKDQNGNHVVQKCIECV  156 (351)
T ss_dssp             HHHHH--CCHHHHHHHHHHHTTCHHHHHTSTTHHHHHHHHHHHSCHHHHHHHHGGGTTCHHHHHHSTTHHHHHHHHHHHS
T ss_pred             HHHhh--CCHHHHHHHHHHHHhhHHHHhhCHHhHHHHHHHHHhCCHHHHHHHHHHhhhhHHHHHHhhhhhHHHHHHHHhC
Confidence            99998  6788888888889999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ChHHHHHHHHHHHHhHHhhhcCCChhHHHHHhhccCChhhHHHHHHHHHHhHHHhccCcchhHHHHHHHhcCCcH--HHH
Q 035754          184 KGSRRKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLKYQNAV--HYI  261 (335)
Q Consensus       184 ~~~~~~~l~~~l~~~~~~l~~d~~G~~viq~~l~~~~~~~~~~i~~~l~~~~~~l~~~~~gS~vve~~l~~~~~~--~~i  261 (335)
                      +++.+..+++.+.+++..++.+++|++|+|++++.++++.+..+++.+.+++..|+.|+||++|+|++++.+++.  +.|
T Consensus       157 ~~~~~~~i~~~~~~~~~~ls~~~~G~~Vvq~~le~~~~~~~~~ii~~l~~~~~~L~~d~~Gn~ViQ~~l~~~~~~~~~~i  236 (351)
T 3gvo_A          157 QPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKI  236 (351)
T ss_dssp             CGGGTHHHHHHTTTTHHHHHTSTTHHHHHHHHHHHSCHHHHHHHHHHHHTTHHHHHTSTTHHHHHHHHHHHSCHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHHHhCcHhHHHHHHHHHHCCHHHHHHHHHHHhhhHHhcCCCchHHHHHHHHHHhCchhhHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999887  889


Q ss_pred             HHHHhChhhHHhhhcCcchhHHHHHHHhhccCcCcHHHHHHHHHHHHH-------HHHhhhcCCChHHHHHHHHhhC
Q 035754          262 IEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQ-------HLAALRVMKYGSNVYKWTTASH  331 (335)
Q Consensus       262 ~~~l~~~~~~~~l~~~~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~-------~~~~L~~~~~gs~v~~~l~~~~  331 (335)
                      ++.+.+  ++..|++|+||++|++++|+.+++    .+++.+++++.+       .+..|..++||.+|+++++...
T Consensus       237 ~~~l~~--~~~~Ls~~k~gs~Vvek~l~~~~~----~~r~~ii~el~~~~~~~~~~l~~l~~d~ygnyViq~~L~~~  307 (351)
T 3gvo_A          237 VSEIRG--KVLALSQHKFASNVVEKCVTHASR----AERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMA  307 (351)
T ss_dssp             HHTTTT--CHHHHHTSTTHHHHHHHHHHHSCH----HHHHHHHHHHHSCEETTEEHHHHHHHSTTHHHHHHHHHHHC
T ss_pred             HHHHHH--HHHHHhcCcHHHHHHHHHHHhCCH----HHHHHHHHHHhcccCCCChHHHHccCCcchHHHHHHHHHhC
Confidence            999998  999999999999999999999998    899999999986       7899999999999999998654

>3k49_A MRNA-binding protein PUF3; PUF3, pumilio, RNA binding, mitochondrial mRNA,, membrane, mitochondrion; HET: CIT; 2.50A {Saccharomyces cerevisiae} SCOP: a.118.1.0 PDB: 3k4e_A

Probab=100.00  E-value=4.2e-46  Score=341.85  Aligned_cols=299  Identities=16%  Similarity=0.183  Sum_probs=277.6

Q ss_pred             hhcHHHHHhhcCCC--HHHHHHHHHHHHhhHHhhccCccchHHHHHHhhhcCHHHHHHHHHHHhcccchhhhhhccccCc
Q 035754           22 EGSQYLQENLSSGD--SRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGS   99 (335)
Q Consensus        22 ~~s~~lq~~l~~~~--~e~~~~i~~e~~~~~~~L~~~~~gs~v~q~ll~~~~~~~~~~i~~~l~~~~~~~~~l~~~~~gs   99 (335)
                      ..|++|+++.....  +.++...++++.|++.+++.|++||+++|+++++++++++..|++++.   +++.+|+.|+||+
T Consensus         3 ~~s~lle~~~~~~~~~~~~~~~~l~~i~g~i~~l~~d~~gsR~lQ~~l~~~~~~~~~~I~~el~---~~~~~L~~d~~gn   79 (369)
T 3k49_A            3 HRSPLLEQLRNSSSDKNSNSNMSLKDIFGHSLEFCKDQHGSRFIQRELATSPASEKEVIFNEIR---DDAIELSNDVFGN   79 (369)
T ss_dssp             --CHHHHHHHTTCC------CCCGGGGTTCHHHHHTSHHHHHHHHHHHTTCCHHHHHHHHHHHG---GGHHHHHHSTTTH
T ss_pred             CcchhHHHHhCCCCccccccceeHHHHHHHHHHHHcCCcchHHHHHHhccCCHHHHHHHHHHHH---HHHHHHhhCcccc
Confidence            46889999998774  478889999999999999999999999999999999999999999999   9999999999999


Q ss_pred             HHHHHHHhhhcCChhHHHHHHHHHHHhhhhhhcCCCccHHHHHHhhcCCcchhHHHHHHHHHhHHHhhcCCCccHHHHHH
Q 035754          100 SSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNF  179 (335)
Q Consensus       100 ~vlq~ll~~~~~~~~~~~~i~~~l~~~~~~l~~d~~g~~vvq~~l~~~~~~~~~~l~~~~~~~~~~l~~~~~g~~vlq~~  179 (335)
                      +|+|++++.  +++++...+.+.+.+++..++.|++|++|+|++++.++++++..+++.+.+++..++.|++|++|+|++
T Consensus        80 ~vvQkll~~--~~~~~~~~i~~~~~g~~~~L~~~~~G~rVlQk~le~~~~~q~~~ii~el~~~~~~L~~d~~Gn~ViQ~~  157 (369)
T 3k49_A           80 YVIQKFFEF--GSKIQKNTLVDQFKGNMKQLSLQMYACRVIQKALEYIDSNQRIELVLELSDSVLQMIKDQNGNHVIQKA  157 (369)
T ss_dssp             HHHHHHHHH--CCHHHHHHHHHHHTTCHHHHHHSTTHHHHHHHHHHHSCHHHHHHHHGGGTTCHHHHHHSTTHHHHHHHH
T ss_pred             cHHHHHHHh--CCHHHHHHHHHHHhhhHHHHhcChhhHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhcCcccchHHHHH
Confidence            999999998  678888888999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhccChHHHHHHHHHHHHhHHhhhcCCChhHHHHHhhccCChhhHHHHHHHHHHhHHHhccCcchhHHHHHHHhcCCcH-
Q 035754          180 IDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLKYQNAV-  258 (335)
Q Consensus       180 l~~~~~~~~~~l~~~l~~~~~~l~~d~~G~~viq~~l~~~~~~~~~~i~~~l~~~~~~l~~~~~gS~vve~~l~~~~~~-  258 (335)
                      ++.++++.+..+++.+.+++..++.+++|++|+|++++.++++.+..+++.+.+++..|+.|+||++|+|++++.+++. 
T Consensus       158 l~~~~~~~~~~i~~~~~~~~~~ls~~~~Gs~Vvq~~l~~~~~~~~~~i~~~l~~~~~~L~~d~~GnyViQ~~l~~~~~~~  237 (369)
T 3k49_A          158 IETIPIEKLPFILSSLTGHIYHLSTHSYGCRVIQRLLEFGSSEDQESILNELKDFIPYLIQDQYGNYVIQYVLQQDQFTN  237 (369)
T ss_dssp             HHHSCGGGCHHHHHHHTTTHHHHHTSTTHHHHHHHHHHHSCHHHHHHHHHTTTTCHHHHHHSTTHHHHHHHHHTCCTTSC
T ss_pred             HHhCCHHHHHHHHHHHHHHHHHHhCCCccCcHHHHHHHhCCHHHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHhcCCchh
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999998874 


Q ss_pred             -------HHHHHHHhChhhHHhhhcCcchhHHHHHHHhhccCcCcHHHHHHHHHHHHH-------------HHHhhhcCC
Q 035754          259 -------HYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQ-------------HLAALRVMK  318 (335)
Q Consensus       259 -------~~i~~~l~~~~~~~~l~~~~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~-------------~~~~L~~~~  318 (335)
                             +.|++.+.+  ++..|++|+||++|++++|+.+++    .+++.+++++.+             .+..|..++
T Consensus       238 ~~~~~~~~~i~~~l~~--~~~~Ls~~k~gS~Vvek~l~~~~~----~~r~~ii~~l~~~~~~~~~~~~~~~~l~~L~~D~  311 (369)
T 3k49_A          238 KEMVDIKQEIIETVAN--NVVEYSKHKFASNVVEKSILYGSK----NQKDLIISKILPRDKNHALNLEDDSPMILMIKDQ  311 (369)
T ss_dssp             HHHHHHHHHHHHHHHT--THHHHHTSTTHHHHHHHHHHHSCH----HHHHHHHTTTSCSSHHHHHTCCTTSHHHHHHTST
T ss_pred             hhhHhHHHHHHHHHHH--HHHHHHhhhHhhHHHHHHHHhCCH----HHHHHHHHHHhccccccccccccccHHHHHHhCc
Confidence                   467888888  999999999999999999999987    899999999854             367899999


Q ss_pred             ChHHHHHHHHhhC
Q 035754          319 YGSNVYKWTTASH  331 (335)
Q Consensus       319 ~gs~v~~~l~~~~  331 (335)
                      ||.+|+++++...
T Consensus       312 ~gNyViq~~l~~~  324 (369)
T 3k49_A          312 FANYVIQKLVNVS  324 (369)
T ss_dssp             THHHHHHHHHHHC
T ss_pred             chHHHHHHHHHhC
Confidence            9999999998764

>3bwt_A Protein PUF4; pumilio, RNA binding, HO endonuclease, transcription, RNA binding protein; 2.69A {Saccharomyces cerevisiae} PDB: 4dzs_A 3bx2_A 3bx3_A

Probab=100.00  E-value=8.1e-44  Score=322.71  Aligned_cols=277  Identities=17%  Similarity=0.208  Sum_probs=255.7

Q ss_pred             HHHHHHHhhHHhhccCccchHHHHHHhhhcCHHHHHHHHHHHhcccchhhhhhccccCcHHHHHHHhhhcCChhHHHHHH
Q 035754           41 KLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVM  120 (335)
Q Consensus        41 ~i~~e~~~~~~~L~~~~~gs~v~q~ll~~~~~~~~~~i~~~l~~~~~~~~~l~~~~~gs~vlq~ll~~~~~~~~~~~~i~  120 (335)
                      .+++++.|++.+++.|++||+++|++++.++++++..|++++.   +++.+|+.|+||++|+|++++.  .++++...+.
T Consensus         6 ~~l~~~~g~i~~l~~~q~gsr~iQ~~l~~~~~~~~~~i~~el~---~~~~~L~~d~~gn~vvQkll~~--~~~~~~~~i~   80 (333)
T 3bwt_A            6 AVLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETK---DYTVELMTDSFGNYLIQKLLEE--VTTEQRIVLT   80 (333)
T ss_dssp             CCGGGTTTCHHHHTSSHHHHHHHHHHHHHSCHHHHHHHHHHHG---GGHHHHHTSTTHHHHHHHHHHH--SCHHHHHHHH
T ss_pred             CcHHHHHHHHHHHhcCcHhhHHHHHHHccCCHHHHHHHHHHHH---HHHHHHhcCcccHHHHHHHHhh--CCHHHHHHHH
Confidence            4577899999999999999999999999999999999999999   9999999999999999999998  5677777888


Q ss_pred             HHHHHhhhhhhcCCCccHHHHHHhhcCCc-chhHHHHHHHHHhHHHhhcCCCccHHHHHHHhccChHHHHHHHHHHHHhH
Q 035754          121 SALKRLFKFLMMTKPGSSVILQCLEPSYN-HKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNA  199 (335)
Q Consensus       121 ~~l~~~~~~l~~d~~g~~vvq~~l~~~~~-~~~~~l~~~~~~~~~~l~~~~~g~~vlq~~l~~~~~~~~~~l~~~l~~~~  199 (335)
                      +.+.+++.+++.|++|++|+|++++.++. +++..+++.+.+++..++.|++|++|+|++++..+++.+..+++.+.+++
T Consensus        81 ~~~~~~~~~l~~~~~G~rviQ~~l~~~~~~~~~~~i~~el~~~~~~L~~d~~gn~Viqk~l~~~~~~~~~~i~~~l~~~~  160 (333)
T 3bwt_A           81 KISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSC  160 (333)
T ss_dssp             HHHGGGHHHHHHSTTHHHHHHHHHHHCCSHHHHHHHHHHHGGGHHHHHTSTTHHHHHHHHHHHSCHHHHHHHHHHHHHSH
T ss_pred             HHHHhHHHHHHhcccccHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHCCHHHHHHHHHHHHHHH
Confidence            88999999999999999999999999754 56778899999999999999999999999999999999999999999999


Q ss_pred             HhhhcCCChhHHHHHhhccCChhhHHHHHHHHHHhHHHhccCcchhHHHHHHHhcCCcH------HHHHHHHhChhhHHh
Q 035754          200 ASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLKYQNAV------HYIIEELLNSDQILQ  273 (335)
Q Consensus       200 ~~l~~d~~G~~viq~~l~~~~~~~~~~i~~~l~~~~~~l~~~~~gS~vve~~l~~~~~~------~~i~~~l~~~~~~~~  273 (335)
                      ..++.+++|++|+|++++.++++.+..+++.+.+++..|+.|+||++|+|++++.+++.      +.|++.+.+  ++..
T Consensus       161 ~~l~~~~~Gs~Vvq~~l~~~~~~~~~~l~~el~~~~~~L~~d~~GnyVvQ~~L~~~~~~~~~~~~~~ii~~l~~--~~~~  238 (333)
T 3bwt_A          161 IDIATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKP--RAIE  238 (333)
T ss_dssp             HHHHTSTTHHHHHHHHHHHCCHHHHHHHHHHHHTTHHHHHTSTTHHHHHHHHHHHHHHHTCCSHHHHHHHHHGG--GHHH
T ss_pred             HHHhcCchhHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHhCCccccchhHHHHHHHHHH--HHHH
Confidence            99999999999999999999999999999999999999999999999999999987653      578888887  9999


Q ss_pred             hhcCcchhHHHHHHHhhccCcCcHHHHHHHHHHHH-----HHHHhhhcCCChHHHHHHHHhh
Q 035754          274 VANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQ-----QHLAALRVMKYGSNVYKWTTAS  330 (335)
Q Consensus       274 l~~~~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~-----~~~~~L~~~~~gs~v~~~l~~~  330 (335)
                      |++|+||++|++++++.++.      ++.++.++.     +.+..|+.++||.+|+++++..
T Consensus       239 Ls~~k~gs~Vvek~l~~~~~------~~~ii~ell~~~~~~~l~~L~~d~~gnyViq~~l~~  294 (333)
T 3bwt_A          239 LSIHKFGSNVIEKILKTAIV------SEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDI  294 (333)
T ss_dssp             HHTSTTHHHHHHHHHTSHHH------HHHHHHHHHHTTHHHHHHHHHTSTTHHHHHHHHHHH
T ss_pred             HHcccHHHHHHHHHHcccch------hHHHHHHHHhccCchHHHHHHcCChHHHHHHHHHHh
Confidence            99999999999999986543      456777765     5789999999999999999854

>3v71_A PUF (pumilio/FBF) domain-containing protein 7, CO transcript evidence; PUF repeats, RNA binding protein-RNA complex; HET: EPE; 2.90A {Caenorhabditis elegans}

Probab=100.00  E-value=2.8e-42  Score=316.23  Aligned_cols=282  Identities=16%  Similarity=0.163  Sum_probs=249.8

Q ss_pred             HHHH--HhhHHhhccCccchHHHHHHhhhcCHHH-HHHHHHHHhcccchhhhhhccccCcHHHHHHHhhhcCChhHHHHH
Q 035754           43 FWVV--SGFTFELMSGQYGRFVFGKFIESCNESQ-LALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHV  119 (335)
Q Consensus        43 ~~e~--~~~~~~L~~~~~gs~v~q~ll~~~~~~~-~~~i~~~l~~~~~~~~~l~~~~~gs~vlq~ll~~~~~~~~~~~~i  119 (335)
                      ++++  .|++.+++.|++||+++|+.++.+++++ +..+++++....+++.+|+.|+||++|+|++++. +..++...++
T Consensus        13 L~~~~~~G~i~~~a~Dq~Gsr~lQ~~l~~~~~~~~~~~if~~l~e~~~~~~~L~~d~~Gn~vvQklle~-~~~~~~~~li   91 (382)
T 3v71_A           13 LEDVLLNGQLIDFAIDPSGVKFLEANYPLDSEDQIRKAVFEKFTESTTLFVGLCHSRNGNFIVQKLVEL-ATPAEQRELL   91 (382)
T ss_dssp             HHHHHHTTCHHHHHHSHHHHHHHHHTSCSCTTCHHHHHHHHHHHSCHHHHHHHHSSTTHHHHHHHHHHT-CCHHHHHHHH
T ss_pred             HHHHhhCCCEehhccCCcccHHHHHHcccCChHHHHHHHHHHHHhhHHHHHHHhcCcHHHHHHHHHHHh-CCHHHHHHHH
Confidence            5566  6999999999999999999999987654 6788898864446889999999999999999998 5544555556


Q ss_pred             HHHHHHhhhhhhcCCCccHHHHHHhhcCCcchhHHHHHHHHH-hHHHhhcCCCccHHHHHHHhccChHHHHHHHHHHH--
Q 035754          120 MSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALE-HCLYLACHEQGCINLNNFIDNMKGSRRKQILHLIS--  196 (335)
Q Consensus       120 ~~~l~~~~~~l~~d~~g~~vvq~~l~~~~~~~~~~l~~~~~~-~~~~l~~~~~g~~vlq~~l~~~~~~~~~~l~~~l~--  196 (335)
                      .+.+.+++..++.|.+|++|+|++++.++.+++..+++.+.+ ++..++.|++|++|+|++++..+++.+..|++.+.  
T Consensus        92 ~~~l~g~v~~Ls~~~~G~rvvQk~ie~~~~~~~~~li~eL~~~~~~~L~~D~~GnhVIQk~le~~~~~~~~~Ii~~~~~~  171 (382)
T 3v71_A           92 RQMIDGGLLAMCKDKFACRVVQLALQKFDHSNVFQLIQELSTFDLAAMCTDQISIHVIQRVVKQLPVDMWTFFVHFLSSG  171 (382)
T ss_dssp             HHHHHTCHHHHHTSTTHHHHHHHHHHHSCHHHHHHHHHHHHTSCHHHHHHSTTTHHHHHHHHTTSCTTTSHHHHHHHHST
T ss_pred             HHHhcchHHHHHhCccchHHHHHHHHHCCHHHHHHHHHHhcccchHHHhcCcccccHHHHHHHHCCHHHHHHHHHHHhcc
Confidence            565789999999999999999999999999999999999998 89999999999999999999999999999999987  


Q ss_pred             HhHHhhhcCCChhHHHHHhhccCChhh-----------HHHHHHHHHHhHHHhccCcchhHHHHHHHhcCCc--H--HHH
Q 035754          197 VNAASLSRHRSGNYVVQHVLSLEDPFL-----------IDAICFALRGHYVDLSLTKCGSFVVQKCLKYQNA--V--HYI  261 (335)
Q Consensus       197 ~~~~~l~~d~~G~~viq~~l~~~~~~~-----------~~~i~~~l~~~~~~l~~~~~gS~vve~~l~~~~~--~--~~i  261 (335)
                      +++..++.|+||++|+|++++.++++.           ...+++.+.++...|+.|+||++|+|++++.++.  .  ..|
T Consensus       172 ~~~~~la~h~~Gc~VlQ~~le~~~~~~k~~~~~~r~~~l~~l~~~I~~~~~~L~~d~~GNyVIQ~iL~~~~~~e~~r~~i  251 (382)
T 3v71_A          172 DSLMAVCQDKYGCRLVQQVIDRLAENPKLPCFKFRIQLLHSLMTCIVRNCYRLSSNEFANYVIQYVIKSSGIMEMYRDTI  251 (382)
T ss_dssp             THHHHHHHSTTHHHHHHHHHHHHTCCSSSTTHHHHHHHHHHHHHHHHTTHHHHHTSTTTHHHHHHHHTCCSTHHHHHHHH
T ss_pred             cchHhHhcCchhhHHHHHHHHhCCHhhhhhhhhHHHHHHHHHHHHHHHHHHHHhhCccccHHHHHHHhcCCCcHHHHHHH
Confidence            699999999999999999999876542           2356778888999999999999999999999764  2  678


Q ss_pred             HHH-HhChhhHHhhhcCcchhHHHHHHHhhccCcCcHHHHHHHHHHHHH-----------HHHhhhcCCChHHHHHHHHh
Q 035754          262 IEE-LLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQ-----------HLAALRVMKYGSNVYKWTTA  329 (335)
Q Consensus       262 ~~~-l~~~~~~~~l~~~~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~-----------~~~~L~~~~~gs~v~~~l~~  329 (335)
                      +.+ +.+  ++..|++|+|||+|++++|..+++    .+++.+++++.+           .+..|..++||.+|+++++.
T Consensus       252 i~~~l~~--~~~~Ls~~k~gS~Vvek~l~~~~~----~~r~~ii~el~~~~~~~~~~~~~~l~~l~~D~ygNyVvQ~~L~  325 (382)
T 3v71_A          252 IDKCLLR--NLLSMSQDKYASHVIEGAFLFAPP----ALLHEMMEEIFSGYVKDVESNRDALDILLFHQYGNYVVQQMIS  325 (382)
T ss_dssp             HHHTTTT--CHHHHTTSTTHHHHHHHHHHHCCH----HHHHHHHHHHCC--CCCSSSCCCHHHHHHTCTTHHHHHHHHHH
T ss_pred             HHHHHHH--HHHHHhcCchHhHHHHHHHHhCCH----HHHHHHHHHHHhhccccccccchHHHHHHCCCCccHHHHHHHH
Confidence            875 777  999999999999999999999998    899999999974           78899999999999999986


Q ss_pred             hC
Q 035754          330 SH  331 (335)
Q Consensus       330 ~~  331 (335)
                      ..
T Consensus       326 ~~  327 (382)
T 3v71_A          326 IC  327 (382)
T ss_dssp             HH
T ss_pred             Hc
Confidence            53

>3k62_A FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding factor, PUF, RNA-binding specificity, base flipping, base stacking; 1.90A {Caenorhabditis elegans} PDB: 3k5y_A 3k5z_A 3k61_A 3k5q_A 3k64_A 3qg9_A 3v6y_A 3v74_A 3qgc_A 3qgb_A

Probab=100.00  E-value=2.4e-40  Score=305.37  Aligned_cols=276  Identities=14%  Similarity=0.200  Sum_probs=248.0

Q ss_pred             HhhHHhhccCccchHHHHHHhhhc-CHHHHHHHHHHHhcccchhhhhhccccCcHHHHHHHhhhcCCh-------hHHHH
Q 035754           47 SGFTFELMSGQYGRFVFGKFIESC-NESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLP-------PLLYH  118 (335)
Q Consensus        47 ~~~~~~L~~~~~gs~v~q~ll~~~-~~~~~~~i~~~l~~~~~~~~~l~~~~~gs~vlq~ll~~~~~~~-------~~~~~  118 (335)
                      +|++.+++.|++||+++|+.++.+ +++++..|++++.+..+++.+|+.|+||++|+|++++. + ++       ++...
T Consensus        28 ~G~i~~la~Dq~GsR~lQ~~l~~~~~~e~~~~If~el~~~~~~~~~L~~d~fGNyvvQKlle~-~-~~~~~~~~~~q~~~  105 (412)
T 3k62_A           28 SGDLMKFAVDKTGCQFLEKAVKGSLTSYQKFQLFEQVIGRKDDFLKLSTNIFGNYLVQSVIGI-S-LATNDDGYTKRQEK  105 (412)
T ss_dssp             HTCHHHHHTSHHHHHHHHHHTTSCCCHHHHHHHHHHHSSSHHHHHHHHTSTTHHHHHHHHHHH-H-HHCCSTTHHHHHHH
T ss_pred             CCCcHHHhcCChhHHHHHHHhccCCCHHHHHHHHHHHHhhhhHHHHHHhCcHHHHHHHHHHHh-C-CcccccccHHHHHH
Confidence            699999999999999999999997 89999999999982222489999999999999999998 3 44       56667


Q ss_pred             HHHHHHHhhhhhhcCCCccHHHHHHhhcCCcchhHHHHHHH--HHhHHHhhcCCCccHHHHHHHhccChHHHHHHHHHHH
Q 035754          119 VMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAA--LEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLIS  196 (335)
Q Consensus       119 i~~~l~~~~~~l~~d~~g~~vvq~~l~~~~~~~~~~l~~~~--~~~~~~l~~~~~g~~vlq~~l~~~~~~~~~~l~~~l~  196 (335)
                      +.+.+.+++..++.|++|++|+|++++.++++++..+++.+  .+++..++.|++|++|+|++++..+++.+..|++.+.
T Consensus       106 i~~~l~g~v~~L~~~~~GsrvvQk~le~~~~~~~~~iv~eL~~~~~i~~L~~D~~GNhVIQK~Le~~~~~~~~~I~~~~~  185 (412)
T 3k62_A          106 LKNFISSQMTDMCLDKFACRVIQSSLQNMDLSLACKLVQALPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIVDFVA  185 (412)
T ss_dssp             HHHHHHHTHHHHHHSTTHHHHHHHHHHHSCHHHHHHHHHTSCCSHHHHHHHHCTTTHHHHHHHHHHSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcChhhhHHHHHHHHhCCHHHHHHHHHHHhccccHHHHHhCccccHHHHHHHHhCCHHHHHHHHHHHh
Confidence            78889999999999999999999999999999999999999  6899999999999999999999999999999999987


Q ss_pred             --HhHHhhhcCCChhHHHHHhhccCCh------------hhHH----HHHHHHHHhHHHhccCcchhHHHHHHHhcCCcH
Q 035754          197 --VNAASLSRHRSGNYVVQHVLSLEDP------------FLID----AICFALRGHYVDLSLTKCGSFVVQKCLKYQNAV  258 (335)
Q Consensus       197 --~~~~~l~~d~~G~~viq~~l~~~~~------------~~~~----~i~~~l~~~~~~l~~~~~gS~vve~~l~~~~~~  258 (335)
                        +++.++++|+||++|+|++++..++            +.+.    .+++.+..+...|+.|+||++|+|.+++.+.+.
T Consensus       186 ~~~~~~~la~h~~GcrVvQk~le~~~~~~~~~~~~~~~~~qr~~il~~L~~~I~~~~~~L~~dq~GNyViQ~iL~~g~~~  265 (412)
T 3k62_A          186 TPEHLRQICSDKYGCRVVQTIIEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQHIVSNDDLA  265 (412)
T ss_dssp             SHHHHHHHHTSHHHHHHHHHHHHHTSCSGGGTTSCHHHHHHHHHHHHHHHHHHHHTHHHHHHSTTTHHHHHHHHHCGGGH
T ss_pred             cchhHHHHhcCcchHHHHHHHHHhcCcccccchhhhhhHHHHHHHHHHHHHHHHHHHHHHhhCccccHHHHHHHhcCCch
Confidence              6999999999999999999998763            2333    467777888999999999999999999998764


Q ss_pred             ---HHHHHH-HhChhhHHhhhcCcchhHHHHHHHhhccCcCcHHHHHHHHHHHHH-----------HHHhhhcCCChHHH
Q 035754          259 ---HYIIEE-LLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQ-----------HLAALRVMKYGSNV  323 (335)
Q Consensus       259 ---~~i~~~-l~~~~~~~~l~~~~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~-----------~~~~L~~~~~gs~v  323 (335)
                         ..|+.. +.+  ++..|++|+||++||+++|+.+++    ..+..++++|..           .+..|..++||.+|
T Consensus       266 ~~r~~ii~~~l~~--~~~~LS~~KfgSnVVek~L~~~~~----~~r~~ii~ei~~~~~~~~~~~~~~l~~L~~DqyGNYV  339 (412)
T 3k62_A          266 VYRECIIEKCLMR--NLLSLSQEKFASHVVEKAFLHAPL----ELLAEMMDEIFDGYIPHPDTGKDALDIMMFHQFGNYV  339 (412)
T ss_dssp             HHHHHHHHHHTTT--CHHHHHTSTTHHHHHHHHHHHCCH----HHHHHHHHHHHHSSCCCTTTCCCHHHHHHHSTTHHHH
T ss_pred             hHHHHHHHHHHHH--HHHHHhcccHhHHHHHHHHHhCCH----HHHHHHHHHHHhhccCCccccchHHHHHhcCCchHHH
Confidence               567764 777  999999999999999999999988    899999999985           48889999999999


Q ss_pred             HHHHHhh
Q 035754          324 YKWTTAS  330 (335)
Q Consensus       324 ~~~l~~~  330 (335)
                      +++++.-
T Consensus       340 iQ~~L~~  346 (412)
T 3k62_A          340 VQCMLTI  346 (412)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9999864

>3hjl_A Flagellar motor switch protein FLIG; armadillo repeat motif, superhelix, conformational plasticit repeat, torque generation; 2.40A {Aquifex aeolicus}

Probab=86.72  E-value=13  Score=32.43  Aligned_cols=160  Identities=13%  Similarity=0.027  Sum_probs=67.3

Q ss_pred             CCCHHHHHHHHHHHHhhHHhhccCccchHHHHHHhhh-cCHHHHHHHHHHHhccc--chhhhhhccccCcHHHHHHHhhh
Q 035754           33 SGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIES-CNESQLALIILKITFQD--QLFLLASVDKFGSSSVKKLIKVV  109 (335)
Q Consensus        33 ~~~~e~~~~i~~e~~~~~~~L~~~~~gs~v~q~ll~~-~~~~~~~~i~~~l~~~~--~~~~~l~~~~~gs~vlq~ll~~~  109 (335)
                      .-++++.+.|++||...+..-..-..|+--++.++.. ..++.-..|++.+....  ..|..|.  ......+-.++.. 
T Consensus        51 ~v~~~~~~~Vl~EF~~~~~~~~~i~~gg~~~~~~L~~aLg~~~A~~ll~~i~~~~~~~~~~~L~--~~dp~~la~~i~~-  127 (329)
T 3hjl_A           51 SVPEEEIENIAEELLDEIKKAGIKIKKPEEFIENIKKVIPPTLAEKFRGILELGDAEKILKEIE--KVDSRILASLLKN-  127 (329)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHTTCCCSCHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHHHHH--TSCHHHHHHHHTT-
T ss_pred             CCCHHHHHHHHHHHHHHHHhcCCCCCchHHHHHHHHHhCCHHHHHHHHHHHhccccCCHHHHHH--CCCHHHHHHHHHh-
Confidence            3456677777777766555443322222344444433 33333344444444110  0111111  1233444444443 


Q ss_pred             cCChhHHHHHHHHHHHh----hhhhhcCCCccHHHHHHhhc--CCcchhHHHHHHHHHhHHHh---hc-CCCccHHHHHH
Q 035754          110 AHLPPLLYHVMSALKRL----FKFLMMTKPGSSVILQCLEP--SYNHKNDFIYQAALEHCLYL---AC-HEQGCINLNNF  179 (335)
Q Consensus       110 ~~~~~~~~~i~~~l~~~----~~~l~~d~~g~~vvq~~l~~--~~~~~~~~l~~~~~~~~~~l---~~-~~~g~~vlq~~  179 (335)
                       -+|+....+...+.+.    +...+-+...+-|+.++...  .+|+..+.+-+.+...+...   .. ..-|...+-.+
T Consensus       128 -EhPQtiAlILs~L~p~~AA~vL~~Lp~~~r~ev~~Ria~l~~v~p~~l~~le~~L~~~l~~~~~~~~~~~gG~~~vA~I  206 (329)
T 3hjl_A          128 -EHPQTIALFLSQLSPKKSAEIIQNLPEELKKEVVKRIATLENVNVQYVKELAQILLEEISSLGAKEALKLEGTAVAAEL  206 (329)
T ss_dssp             -SCHHHHHHHHTTSCHHHHHHHHHTSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHHHHHHHHHHHHSCCCCHHHHHHHH
T ss_pred             -CCHHHHHHHHHcCCHHHHHHHHHhCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHhcccccccccccHHHHHHH
Confidence             3444444444333322    22222223333444444333  33333444433333333222   11 23345556666


Q ss_pred             HhccChHHHHHHHHHHH
Q 035754          180 IDNMKGSRRKQILHLIS  196 (335)
Q Consensus       180 l~~~~~~~~~~l~~~l~  196 (335)
                      +...+......++..+.
T Consensus       207 LN~~d~~~e~~il~~L~  223 (329)
T 3hjl_A          207 LNTLDKETRELILQSIG  223 (329)
T ss_dssp             HHHSCHHHHHHHHHHHH
T ss_pred             HhcCChHHHHHHHHHHH
Confidence            66666555555555554

---

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	335
d1m8za_	339	a.118.1.8 (A:) Pumilio 1 {Human (Homo sapiens) [Ta	1e-43
d1m8za_	339	a.118.1.8 (A:) Pumilio 1 {Human (Homo sapiens) [Ta	6e-14
d1m8za_	339	a.118.1.8 (A:) Pumilio 1 {Human (Homo sapiens) [Ta	1e-11

>d1m8za_ a.118.1.8 (A:) Pumilio 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 339

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Pumilio repeat
domain: Pumilio 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  151 bits (382), Expect = 1e-43
 Identities = 71/321 (22%), Positives = 134/321 (41%), Gaps = 16/321 (4%)

Query: 13  DLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNE 72
            +   +QDQ GS+++Q  L          +F  +    ++LM   +G +V  KF E  + 
Sbjct: 25  HIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSL 84

Query: 73  SQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMM 132
            Q   +  +I       L  ++  +G   ++K ++           ++  L       + 
Sbjct: 85  EQKLALAERIRGH---VLSLALQMYGCRVIQKALEF--IPSDQQNEMVRELDGHVLKCVK 139

Query: 133 TKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQIL 192
            + G+ V+ +C+E        FI  A       L+ H  GC  +   +++    +   IL
Sbjct: 140 DQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPIL 199

Query: 193 HLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCL 252
             +  +   L + + GNYV+QHVL    P     I   +RG+ + LS  K  S VV+KC+
Sbjct: 200 EELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCV 259

Query: 253 KYQNAVHY--IIEELL-----NSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVT 305
            + +      +I+E+          +  +  D+Y NYV+Q  +       R    + ++ 
Sbjct: 260 THASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQR----KIVMH 315

Query: 306 KLQQHLAALRVMKYGSNVYKW 326
           K++ H+A LR   YG ++   
Sbjct: 316 KIRPHIATLRKYTYGKHILAK 336

>d1m8za_ a.118.1.8 (A:) Pumilio 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 339

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Pumilio repeat
domain: Pumilio 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.4 bits (169), Expect = 6e-14
 Identities = 49/259 (18%), Positives = 100/259 (38%), Gaps = 12/259 (4%)

Query: 2   QTIAFEHCTNHDLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRF 61
           Q +A        + SLA    G + +Q+ L    S   +++   + G   + +  Q G  
Sbjct: 86  QKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVKDQNGNH 145

Query: 62  VFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMS 121
           V  K IE      L  II    F+ Q+F L++   +G   ++++++     P     ++ 
Sbjct: 146 VVQKCIECVQPQSLQFII--DAFKGQVFALST-HPYGCRVIQRILEHCL--PDQTLPILE 200

Query: 122 ALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFID 181
            L +  + L+  + G+ VI   LE         I      + L L+ H+     +   + 
Sbjct: 201 ELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVT 260

Query: 182 NMKGSRRKQILHLISVNA-------ASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGH 234
           +   + R  ++  +            ++ + +  NYVVQ ++ + +P     +   +R H
Sbjct: 261 HASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPH 320

Query: 235 YVDLSLTKCGSFVVQKCLK 253
              L     G  ++ K  K
Sbjct: 321 IATLRKYTYGKHILAKLEK 339

>d1m8za_ a.118.1.8 (A:) Pumilio 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 339

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Pumilio repeat
domain: Pumilio 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.5 bits (151), Expect = 1e-11
 Identities = 36/176 (20%), Positives = 67/176 (38%), Gaps = 4/176 (2%)

Query: 149 NHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSG 208
           N   +   +    H +  +  + G   +   ++    + R+ + + I   A  L     G
Sbjct: 12  NRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFG 71

Query: 209 NYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLKYQNAVHYIIEELLNS 268
           NYV+Q            A+   +RGH + L+L   G  V+QK L++  +           
Sbjct: 72  NYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELD 131

Query: 269 DQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNVY 324
             +L+   D+ GN+V+Q  +     Q      Q ++   +  + AL    YG  V 
Sbjct: 132 GHVLKCVKDQNGNHVVQKCIECVQPQSL----QFIIDAFKGQVFALSTHPYGCRVI 183

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	335
d1m8za_	339	Pumilio 1 {Human (Homo sapiens) [TaxId: 9606]}	100.0
d1m8za_	339	Pumilio 1 {Human (Homo sapiens) [TaxId: 9606]}	100.0

>d1m8za_ a.118.1.8 (A:) Pumilio 1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Pumilio repeat
domain: Pumilio 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=2.5e-59  Score=423.98  Aligned_cols=318  Identities=22%  Similarity=0.362  Sum_probs=300.4

Q ss_pred             cccccccccCcchhhhccCchhcHHHHHhhcCCCHHHHHHHHHHHHhhHHhhccCccchHHHHHHhhhcCHHHHHHHHHH
Q 035754            2 QTIAFEHCTNHDLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILK   81 (335)
Q Consensus         2 ~~~~~~~~~~g~~~~la~~~~~s~~lq~~l~~~~~e~~~~i~~e~~~~~~~L~~~~~gs~v~q~ll~~~~~~~~~~i~~~   81 (335)
                      .+++++++. |+++++|+||+|||+||++|+.+++++++.||+++.+++.+|+.|+|||||+|+|+++++++++..|++.
T Consensus        15 ~~~~l~~~~-g~~~~~~~~q~gSr~lQ~~l~~~~~~~~~~I~~~l~~~~~~L~~~~~gn~vvqkll~~~~~~~~~~i~~~   93 (339)
T d1m8za_          15 PNLQLREIA-GHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLEQKLALAER   93 (339)
T ss_dssp             TTCCGGGGT-TCHHHHHTSHHHHHHHHHHHHHCCHHHHHHHHHHHGGGHHHHHTSTTHHHHHHHHHHHSCHHHHHHHHHH
T ss_pred             CCCcHHHHH-hHHHHHhcCchhhHHHHHHHhhCCHHHHHHHHHHHHHHHHHHhhCcccchhHHHHHhhCCHHHHHHHHHH
Confidence            467788886 9999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhcccchhhhhhccccCcHHHHHHHhhhcCChhHHHHHHHHHHHhhhhhhcCCCccHHHHHHhhcCCcchhHHHHHHHHH
Q 035754           82 ITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALE  161 (335)
Q Consensus        82 l~~~~~~~~~l~~~~~gs~vlq~ll~~~~~~~~~~~~i~~~l~~~~~~l~~d~~g~~vvq~~l~~~~~~~~~~l~~~~~~  161 (335)
                      +.   +++.+++.|+|||+|+|++++. +.++.. ..+.+++.+++..++.|++|+||++++++..+++..+.+++.+.+
T Consensus        94 l~---~~~~~L~~~~~gs~Vvq~l~~~-~~~~~~-~~l~~el~~~~~~l~~d~~~~~v~~~~l~~~~~~~~~~i~~~~~~  168 (339)
T d1m8za_          94 IR---GHVLSLALQMYGCRVIQKALEF-IPSDQQ-NEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKG  168 (339)
T ss_dssp             HT---TCHHHHHTSTTHHHHHHHHHHH-SCHHHH-HHHHHTTTTCHHHHHHSTTHHHHHHHHHHHSCGGGGHHHHHHTTT
T ss_pred             HH---hhHHHHhcccccchHHHhhhcc-CCHHHH-HHHHHHHhhhhHHHhcCCCcchHHHHHHHhcCHHHHHHHHHHHHH
Confidence            99   9999999999999999999998 655544 445566999999999999999999999999999999999999999


Q ss_pred             hHHHhhcCCCccHHHHHHHhccChHHHHHHHHHHHHhHHhhhcCCChhHHHHHhhccCChhhHHHHHHHHHHhHHHhccC
Q 035754          162 HCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLT  241 (335)
Q Consensus       162 ~~~~l~~~~~g~~vlq~~l~~~~~~~~~~l~~~l~~~~~~l~~d~~G~~viq~~l~~~~~~~~~~i~~~l~~~~~~l~~~  241 (335)
                      ++..++.|++||+++|++++.++++++..+++.+.+++..|+.|++|||++|+++++++++.++.+++.+.+++.+++++
T Consensus       169 ~~~~l~~~~~g~~vlq~~l~~~~~~~~~~l~~~l~~~~~~L~~~~~G~~vvq~~l~~~~~~~~~~i~~~l~~~~~~l~~~  248 (339)
T d1m8za_         169 QVFALSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQH  248 (339)
T ss_dssp             THHHHHTSTTHHHHHHHHHHHSCHHHHHHHHHHHHHTHHHHTTSTTHHHHHHHHHHHSCHHHHHHHHHHHTTCHHHHHTS
T ss_pred             HHHHHHhCcchhHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHcCCHHHHHHHHHHHHhhHHHHHcc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cchhHHHHHHHhcCCcH--HHHHHHHhC-----hhhHHhhhcCcchhHHHHHHHhhccCcCcHHHHHHHHHHHHHHHHhh
Q 035754          242 KCGSFVVQKCLKYQNAV--HYIIEELLN-----SDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTKLQQHLAAL  314 (335)
Q Consensus       242 ~~gS~vve~~l~~~~~~--~~i~~~l~~-----~~~~~~l~~~~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~~~~~L  314 (335)
                      ++||+|+|+|+..+++.  +.++.++..     .+.+..|++|+|||||||++|+.+++    .+++.+++.+.+++.+|
T Consensus       249 k~gS~vve~~l~~~~~~~~~~~~~~l~~~~~~~~~~l~~L~~d~~gn~Viq~~l~~~~~----~~~~~i~~~l~~~~~~L  324 (339)
T d1m8za_         249 KFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEP----GQRKIVMHKIRPHIATL  324 (339)
T ss_dssp             TTHHHHHHHHHHHSCHHHHHHHHHHHHHCEETTEEHHHHHHTSTTHHHHHHHHHHHSCH----HHHHHHHHTTGGGHHHH
T ss_pred             hhHHHHHHHHHHhCCHHHHHHHHHHHHhcccCchHHHHHHHcCCcccHHHHHHHHhCCH----HHHHHHHHHHHHHHHHH
Confidence            99999999999999988  777777753     34799999999999999999999998    89999999999999999


Q ss_pred             hcCCChHHHHHHHHh
Q 035754          315 RVMKYGSNVYKWTTA  329 (335)
Q Consensus       315 ~~~~~gs~v~~~l~~  329 (335)
                      ..++||++|+.+|.+
T Consensus       325 ~~~~~G~~v~~~l~~  339 (339)
T d1m8za_         325 RKYTYGKHILAKLEK  339 (339)
T ss_dssp             TTSSTHHHHHHHHC-
T ss_pred             hcCCcHHHHHHHHhC
Confidence            999999999999853

>d1m8za_ a.118.1.8 (A:) Pumilio 1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Pumilio repeat
domain: Pumilio 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.5e-41  Score=306.71  Aligned_cols=279  Identities=18%  Similarity=0.207  Sum_probs=263.7

Q ss_pred             HHHHHHhhHHhhccCccchHHHHHHhhhcCHHHHHHHHHHHhcccchhhhhhccccCcHHHHHHHhhhcCChhHHHHHHH
Q 035754           42 LFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMS  121 (335)
Q Consensus        42 i~~e~~~~~~~L~~~~~gs~v~q~ll~~~~~~~~~~i~~~l~~~~~~~~~l~~~~~gs~vlq~ll~~~~~~~~~~~~i~~  121 (335)
                      .++++.|++.+++.|++||+++|.+++.++++++..|++++.   +++.+|+.|+||++|+|++++.  +++++...+.+
T Consensus        18 ~l~~~~g~~~~~~~~q~gSr~lQ~~l~~~~~~~~~~I~~~l~---~~~~~L~~~~~gn~vvqkll~~--~~~~~~~~i~~   92 (339)
T d1m8za_          18 QLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEIL---QAAYQLMVDVFGNYVIQKFFEF--GSLEQKLALAE   92 (339)
T ss_dssp             CGGGGTTCHHHHHTSHHHHHHHHHHHHHCCHHHHHHHHHHHG---GGHHHHHTSTTHHHHHHHHHHH--SCHHHHHHHHH
T ss_pred             cHHHHHhHHHHHhcCchhhHHHHHHHhhCCHHHHHHHHHHHH---HHHHHHhhCcccchhHHHHHhh--CCHHHHHHHHH
Confidence            356778999999999999999999999999999999999999   9999999999999999999998  56788888888


Q ss_pred             HHHHhhhhhhcCCCccHHHHHHhhcCCcchhHHHHHHHHHhHHHhhcCCCccHHHHHHHhccChHHHHHHHHHHHHhHHh
Q 035754          122 ALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAAS  201 (335)
Q Consensus       122 ~l~~~~~~l~~d~~g~~vvq~~l~~~~~~~~~~l~~~~~~~~~~l~~~~~g~~vlq~~l~~~~~~~~~~l~~~l~~~~~~  201 (335)
                      .+.+++..++.|++|++|+|++++..+.+....+++.+.+++..++.|++|++|++++++..+++....+++.+.+.+..
T Consensus        93 ~l~~~~~~L~~~~~gs~Vvq~l~~~~~~~~~~~l~~el~~~~~~l~~d~~~~~v~~~~l~~~~~~~~~~i~~~~~~~~~~  172 (339)
T d1m8za_          93 RIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFA  172 (339)
T ss_dssp             HHTTCHHHHHTSTTHHHHHHHHHHHSCHHHHHHHHHTTTTCHHHHHHSTTHHHHHHHHHHHSCGGGGHHHHHHTTTTHHH
T ss_pred             HHHhhHHHHhcccccchHHHhhhccCCHHHHHHHHHHHhhhhHHHhcCCCcchHHHHHHHhcCHHHHHHHHHHHHHHHHH
Confidence            89999999999999999999999999889999999999999999999999999999999999888899999999999999


Q ss_pred             hhcCCChhHHHHHhhccCChhhHHHHHHHHHHhHHHhccCcchhHHHHHHHhcCCcH--HHHHHHHhChhhHHhhhcCcc
Q 035754          202 LSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLKYQNAV--HYIIEELLNSDQILQVANDKY  279 (335)
Q Consensus       202 l~~d~~G~~viq~~l~~~~~~~~~~i~~~l~~~~~~l~~~~~gS~vve~~l~~~~~~--~~i~~~l~~~~~~~~l~~~~~  279 (335)
                      ++++++|++++|.+++..+++.+..+++.+.+++..|+.+++|++|++.+++.++++  +.+++.|.+  ++.+|+.|+|
T Consensus       173 l~~~~~g~~vlq~~l~~~~~~~~~~l~~~l~~~~~~L~~~~~G~~vvq~~l~~~~~~~~~~i~~~l~~--~~~~l~~~k~  250 (339)
T d1m8za_         173 LSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRG--NVLVLSQHKF  250 (339)
T ss_dssp             HHTSTTHHHHHHHHHHHSCHHHHHHHHHHHHHTHHHHTTSTTHHHHHHHHHHHSCHHHHHHHHHHHTT--CHHHHHTSTT
T ss_pred             HHhCcchhHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHcCCHHHHHHHHHHHHh--hHHHHHcchh
Confidence            999999999999999999999999999999999999999999999999999999888  889999999  9999999999


Q ss_pred             hhHHHHHHHhhccCcCcHHHHHHHHHHHHH-------HHHhhhcCCChHHHHHHHHhhC
Q 035754          280 GNYVIQTALAETMRQDRLSVHQRLVTKLQQ-------HLAALRVMKYGSNVYKWTTASH  331 (335)
Q Consensus       280 g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~-------~~~~L~~~~~gs~v~~~l~~~~  331 (335)
                      |++|+++++..+++    +.+..++.++..       .+..|+.++||++|+++++...
T Consensus       251 gS~vve~~l~~~~~----~~~~~~~~~l~~~~~~~~~~l~~L~~d~~gn~Viq~~l~~~  305 (339)
T d1m8za_         251 ASNVVEKCVTHASR----TERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVA  305 (339)
T ss_dssp             HHHHHHHHHHHSCH----HHHHHHHHHHHHCEETTEEHHHHHHTSTTHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHhCCH----HHHHHHHHHHHhcccCchHHHHHHHcCCcccHHHHHHHHhC
Confidence            99999999999988    888888888753       5889999999999999998754