Psyllid ID: psy13345

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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------
Protein Sequence
MSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKIEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDMECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEELEEYQKKKDKEAKDKQEKEKIPPHDTSFINELQLSDFKQTLQRNGIDCEFMDGVLICCRGTVAVRRVVLVSTPDMECGFSRDLFFQWCSSPENSIIITNRNRADDSDSNVIVLEGCLSDEYYRVQQLLYDQYAIL
Secondary Structure (PSIPRED)
cHHHHHHHccccccccEEEcccHHHHHHHHHHHHHHHcHHHHHHHHcccccccccccccccccHHHHHcccccEEEEEccccccccHHHHHHHHHccccccEEEEEcccccccHHHHHHHccccccEEEccEEEEEEEHHEEHHHHcccccHHHHHHHHHcccccccccccHHHHHHHHHHHHHccccEEEcccEEEEcccEEEEcccccccccccccccHHHHHHHHccccccccEEEcccccccccccEEEccccccHHHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHcHHHccccEEEEcHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccEEEEHHccccHHHHHcccccEEEEEccccHccccHHHHHHHHccccccEEEEEcccccHHHHHHHHHcccccEEEEEcccEEEcccHEHHHHHHHccHHHHHHHHHHcccccEEEEEccccHHHHHHHHHHHHHHHHHcccEEEEEccEEEEEEEcccccccccccccHHHHHHHccccHHcccHHHHHHcccccccEEEEEccccHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
MSDKLMKSfegarnnpfhfkhVKLCHSLAELAKIEWMSDKLMKSfegarnnpfhfkhVKLCHSLAelakvpspkvvlvstpdmecgfsrdlffqwcsspensiiitnrtspgtLARDLIELGGNRTLTLQVKKRIRLEGEELEEYQKKKDKEAkdkqekekipphdtsfinelqlSDFKQTLQrngidcefmdGVLICCRGTVAVRRVVLVstpdmecgfsrdlffqwcsspensiiitnrnraddsdsnviVLEGCLSDEYYRVQQLLYDQYAIL
Flexible Loop (DISEMBL)
msdklmksfegarnnpfhfkHVKLCHSLAELAKIEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDMECGFSRDLFFQWCSSPENSiiitnrtspGTLARDLIelggnrtltlqvkkrirlegeeleeyqkkkdkeakdkqekekipphdtsfineLQLSDFKQTLQRNGIDCEFMDGVLICCRGTVAVRRVVLVStpdmecgfsRDLFFQWCSSPENSIIItnrnraddsdsNVIVLEGCLSDEYYRVQQLLYDQYAIL
Low Complexity Region (SEG)
MSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKIEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDMECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEELeeyqkkkdkeakdkqekekIPPHDTSFINELQLSDFKQTLQRNGIDCEFMDGVLICCRGTVAVRRVVLVSTPDMECGFSRDLFFQWCSSPENSIIITNRNRADDSDSNVIVLEGCLSDEYYRVQQLLYDQYAIL
Disordered region (IsUnstruct)
***************PFHFKHVKLCHSLAELAKIEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDMECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRI*********************************FINELQLSDFKQTLQRNGIDCEFMDGVLICCRGTVAVRRVVLVSTPDMECGFSRDLFFQWCSSPENSIIITNRNRADDSDSNVIVLEGCLSDEYYRVQQLLYDQYAI*
Disordered Region (DISOPRED)
MSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKIEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDMECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTL*LQVKKRIRLEGEELEEYQKKKDK*************************************CEFMDGVLICCRGTVAVRRV*******MECGFSRDLF**************************IVLEGCLSDEYYRVQQLLYDQYAIL
Disordered Region (DISEMBL)
MSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKIEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDMECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEELEE******************PPHDTSFINELQLSDFKQTLQRNGIDCEFMDGVLICCRGTVAVRRVVLVSTPDMECGFSRDLFFQWCSSPENSIIITNRNRADDSDSNVIVLEGCLSDEYYRVQQLLYDQYAIL
Disordered Region (DISPRO)
MSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKIEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDMECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEELEEYQKKKDKEAKDKQEKEKIPPHDTSFINELQLSDFKQTLQRNGIDCEFMDGVLICCRGTVAVRRVVLVSTPDMECGFSRDLFFQWCSSPENSIIITNRNRADDSDSNVIVLEGCLSDEYYRVQQLLYDQYAIL
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKIEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDMECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRxxxxxxxxxxxxxxxxxxxxxxxxxxxxPPHDTSFINELQLSDFKQTLQRNGIDCEFMDGVLICCRGTVAVRRVVLVSTPDMECGFSRDLFFQWCSSPENSIIITNRNRADDSDSNVIVLEGCLSDEYYRVQQLLYDQYAIL
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	276	2.2.26 [Sep-21-2011]
Q9V3D6	756	Probable cleavage and pol	no	N/A	0.456	0.166	0.592	4e-39
O35218	782	Cleavage and polyadenylat	yes	N/A	0.257	0.090	0.621	4e-39
Q9W799	783	Cleavage and polyadenylat	N/A	N/A	0.257	0.090	0.603	1e-38
Q10568	782	Cleavage and polyadenylat	yes	N/A	0.246	0.086	0.620	3e-38
Q9P2I0	782	Cleavage and polyadenylat	yes	N/A	0.246	0.086	0.620	4e-38
O17403	843	Probable cleavage and pol	yes	N/A	0.456	0.149	0.482	5e-28
A8XUS3	842	Probable cleavage and pol	N/A	N/A	0.456	0.149	0.453	1e-24
Q9LKF9	739	Cleavage and polyadenylat	yes	N/A	0.427	0.159	0.386	9e-19
Q55BS1	784	Cleavage and polyadenylat	yes	N/A	0.456	0.160	0.371	3e-18
Q652P4	738	Cleavage and polyadenylat	yes	N/A	0.467	0.174	0.353	4e-14

>sp|Q9V3D6|CPSF2_DROME Probable cleavage and polyadenylation specificity factor subunit 2 OS=Drosophila melanogaster GN=Cpsf100 PE=1 SV=1

 Score =  162 bits (409), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 77/130 (59%), Positives = 101/130 (77%), Gaps = 4/130 (3%)

Query: 24  LCHSLAELAK--IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPS-PKVVLVST 80
           + +++ E AK  IEWMSDKL K+FEGARNNPF FKH++LCHSLA++ K+P+ PKVVL ST
Sbjct: 272 VSYNVIEFAKSQIEWMSDKLTKAFEGARNNPFQFKHIQLCHSLADVYKLPAGPKVVLAST 331

Query: 81  PDMECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIE-LGGNRTLTLQVKKRIRLEG 139
           PD+E GF+RDLF QW S+  NSII+T RTSPGTLA +L+E     + + L V++R+ LEG
Sbjct: 332 PDLESGFTRDLFVQWASNANNSIILTTRTSPGTLAMELVENCAPGKQIELDVRRRVDLEG 391

Query: 140 EELEEYQKKK 149
            ELEEY + +
Sbjct: 392 AELEEYLRTQ 401

CPSF plays a key role in pre-mRNA 3'-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A)polymerase and other factors to bring about cleavage and poly(A) addition.
Drosophila melanogaster (taxid: 7227)

>sp|O35218|CPSF2_MOUSE Cleavage and polyadenylation specificity factor subunit 2 OS=Mus musculus GN=Cpsf2 PE=1 SV=1

 Score =  161 bits (408), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 69/111 (62%), Positives = 91/111 (81%)

Query: 32  AKIEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDMECGFSRDL 91
           +++EWMSDKLM+ FE  RNNPF F+H+ LCH L++LA+VPSPKVVL S PD+ECGFSRDL
Sbjct: 282 SQVEWMSDKLMRCFEDKRNNPFQFRHLSLCHGLSDLARVPSPKVVLASQPDLECGFSRDL 341

Query: 92  FFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEEL 142
           F QWC  P+NSII+T RT+PGTLAR LI+    +   ++++KR++LEG+EL
Sbjct: 342 FIQWCQDPKNSIILTYRTTPGTLARFLIDNPTEKVTEIELRKRVKLEGKEL 392

Component of the cleavage and polyadenylation specificity factor (CPSF) complex that play a key role in pre-mRNA 3'-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition. Involved in the histone 3' end pre-mRNA processing.

Mus musculus (taxid: 10090)

>sp|Q9W799|CPSF2_XENLA Cleavage and polyadenylation specificity factor subunit 2 OS=Xenopus laevis GN=cpsf2 PE=1 SV=1

 Score =  160 bits (405), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 67/111 (60%), Positives = 91/111 (81%)

Query: 32  AKIEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDMECGFSRDL 91
           +++EWMSDKLM+ FE  RNNPF F+H+ LCH  ++LA+VPSPKVVL S PD+ECGFSR+L
Sbjct: 282 SQVEWMSDKLMRCFEDKRNNPFQFRHLTLCHGYSDLARVPSPKVVLASQPDLECGFSREL 341

Query: 92  FFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEEL 142
           F QWC  P+NS+I+T RT+PGTLAR LI+    R + ++++KR++LEG+EL
Sbjct: 342 FIQWCQDPKNSVILTYRTTPGTLARFLIDHPSERIIDIELRKRVKLEGKEL 392

CPSF plays a key role in pre-mRNA 3'-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition. In X.laevis this subunit seems to be predominantly involved in cytoplasmic polyadenylation reaction. May also be involved in the histone 3'-end pre-mRNA processing.

Xenopus laevis (taxid: 8355)

>sp|Q10568|CPSF2_BOVIN Cleavage and polyadenylation specificity factor subunit 2 OS=Bos taurus GN=CPSF2 PE=1 SV=1

 Score =  159 bits (401), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 67/108 (62%), Positives = 88/108 (81%)

Query: 32  AKIEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDMECGFSRDL 91
           +++EWMSDKLM+ FE  RNNPF F+H+ LCH L++LA+VPSPKVVL S PD+ECGFSRDL
Sbjct: 282 SQVEWMSDKLMRCFEDKRNNPFQFRHLSLCHGLSDLARVPSPKVVLASQPDLECGFSRDL 341

Query: 92  FFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEG 139
           F QWC  P+NSII+T RT+PGTLAR LI+    +   ++++KR++LEG
Sbjct: 342 FIQWCQDPKNSIILTYRTTPGTLARFLIDNPSEKVTEIELRKRVKLEG 389

Component of the cleavage and polyadenylation specificity factor (CPSF) complex that play a key role in pre-mRNA 3'-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition. Involved in the histone 3' end pre-mRNA processing.

Bos taurus (taxid: 9913)

>sp|Q9P2I0|CPSF2_HUMAN Cleavage and polyadenylation specificity factor subunit 2 OS=Homo sapiens GN=CPSF2 PE=1 SV=2

 Score =  158 bits (400), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 67/108 (62%), Positives = 88/108 (81%)

Query: 32  AKIEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDMECGFSRDL 91
           +++EWMSDKLM+ FE  RNNPF F+H+ LCH L++LA+VPSPKVVL S PD+ECGFSRDL
Sbjct: 282 SQVEWMSDKLMRCFEDKRNNPFQFRHLSLCHGLSDLARVPSPKVVLASQPDLECGFSRDL 341

Query: 92  FFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEG 139
           F QWC  P+NSII+T RT+PGTLAR LI+    +   ++++KR++LEG
Sbjct: 342 FIQWCQDPKNSIILTYRTTPGTLARFLIDNPSEKITEIELRKRVKLEG 389

Component of the cleavage and polyadenylation specificity factor (CPSF) complex that play a key role in pre-mRNA 3'-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition. Involved in the histone 3' end pre-mRNA processing.

Homo sapiens (taxid: 9606)

>sp|O17403|CPSF2_CAEEL Probable cleavage and polyadenylation specificity factor subunit 2 OS=Caenorhabditis elegans GN=cpsf-2 PE=3 SV=1

 Score =  125 bits (313), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 67/139 (48%), Positives = 88/139 (63%), Gaps = 13/139 (9%)

Query: 24  LCHSLAELAK--IEWMSDKLMK-SFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVST 80
           +  S+ + AK  +EWM++KL K     AR NPF  KHV LCHS  EL +V SPKVVL S+
Sbjct: 271 VASSVVQFAKSQLEWMNEKLFKYDSSSARYNPFTLKHVTLCHSHQELMRVRSPKVVLCSS 330

Query: 81  PDMECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELG----------GNRTLTLQ 130
            DME GFSR+LF  WCS P N +I+T R +  TLA  L+ +            +R ++L 
Sbjct: 331 QDMESGFSRELFLDWCSDPRNGVILTARPASFTLAAKLVNMAERANDGVLKHEDRLISLV 390

Query: 131 VKKRIRLEGEELEEYQKKK 149
           VKKR+ LEGEEL EY+++K
Sbjct: 391 VKKRVALEGEELLEYKRRK 409

CPSF plays a key role in pre-mRNA 3'-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A)polymerase and other factors to bring about cleavage and poly(A) addition.

Caenorhabditis elegans (taxid: 6239)

>sp|A8XUS3|CPSF2_CAEBR Probable cleavage and polyadenylation specificity factor subunit 2 OS=Caenorhabditis briggsae GN=cpsf-2 PE=3 SV=2

 Score =  114 bits (284), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 63/139 (45%), Positives = 86/139 (61%), Gaps = 13/139 (9%)

Query: 24  LCHSLAELAK--IEWMSDKLMK-SFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVST 80
           +  S+ + AK  +EWM +KL +     AR NPF  K+V L HS  EL K+ SPKVVL S+
Sbjct: 271 VASSVVQFAKSQLEWMDEKLFRYDSSSARYNPFTLKNVNLVHSHLELIKIRSPKVVLCSS 330

Query: 81  PDMECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELG----------GNRTLTLQ 130
            DME GFSR+LF  WC+   N +I+T R +  TLA  L+EL            ++ L+L 
Sbjct: 331 QDMETGFSRELFLDWCADQRNGVILTARPASFTLAARLVELAERANDGVLRNEDKHLSLL 390

Query: 131 VKKRIRLEGEELEEYQKKK 149
           V+KR+ LEGEEL EY+++K
Sbjct: 391 VRKRVPLEGEELLEYKRRK 409

CPSF plays a key role in pre-mRNA 3'-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A)polymerase and other factors to bring about cleavage and poly(A) addition.

Caenorhabditis briggsae (taxid: 6238)

>sp|Q9LKF9|CPSF2_ARATH Cleavage and polyadenylation specificity factor subunit 2 OS=Arabidopsis thaliana GN=CPSF100 PE=1 SV=2

 Score = 94.4 bits (233), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 46/119 (38%), Positives = 72/119 (60%), Gaps = 1/119 (0%)

Query: 34  IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVP-SPKVVLVSTPDMECGFSRDLF 92
           +EWMSD + KSFE +R+N F  +HV L  +  +L   P  PKVVL S   +E GF+R++F
Sbjct: 281 LEWMSDSISKSFETSRDNAFLLRHVTLLINKTDLDNAPPGPKVVLASMASLEAGFAREIF 340

Query: 93  FQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEELEEYQKKKDK 151
            +W + P N ++ T     GTLAR L      + + + + KR+ L GEEL  Y++++++
Sbjct: 341 VEWANDPRNLVLFTETGQFGTLARMLQSAPPPKFVKVTMSKRVPLAGEELIAYEEEQNR 399

CPSF plays a key role in pre-mRNA 3'-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A)polymerase and other factors to bring about cleavage and poly(A) addition.

Arabidopsis thaliana (taxid: 3702)

>sp|Q55BS1|CPSF2_DICDI Cleavage and polyadenylation specificity factor subunit 2 OS=Dictyostelium discoideum GN=cpsf2 PE=3 SV=1

 Score = 92.4 bits (228), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 49/132 (37%), Positives = 80/132 (60%), Gaps = 6/132 (4%)

Query: 32  AKIEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVP-SPKVVLVSTPDMECGFSRD 90
           +++E+MS      FE    NPF FKH+K+  SL EL ++P + KV+L S+ D+E GFSR+
Sbjct: 285 SQLEFMSSTASVKFEQNIENPFSFKHIKILSSLEELQELPDTNKVILTSSQDLETGFSRE 344

Query: 91  LFFQWCSSPENSIIITNRTSPGTLARDLIEL-----GGNRTLTLQVKKRIRLEGEELEEY 145
           LF QWCS P+  I+ T +    +LA  LI+      G  + + +    R+ L G+EL +Y
Sbjct: 345 LFIQWCSDPKTLILFTQKIPKDSLADKLIKQYSTPNGRGKCIEIVQGSRVPLTGDELLQY 404

Query: 146 QKKKDKEAKDKQ 157
           + ++ K+ ++K+
Sbjct: 405 EMEQAKQREEKR 416

Component of the cleavage and polyadenylation specificity factor (CPSF) complex that play a key role in pre-mRNA 3'-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition.

Dictyostelium discoideum (taxid: 44689)

>sp|Q652P4|CPSF2_ORYSJ Cleavage and polyadenylation specificity factor subunit 2 OS=Oryza sativa subsp. japonica GN=Os09g0569400 PE=2 SV=1

 Score = 78.6 bits (192), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 46/130 (35%), Positives = 75/130 (57%), Gaps = 1/130 (0%)

Query: 34  IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVP-SPKVVLVSTPDMECGFSRDLF 92
           +EWM+D + KSFE  R+N F  K V    +  EL K+  +PKVVL S   +E GFS D+F
Sbjct: 280 LEWMNDSISKSFEHTRDNAFLLKCVTQIINKDELEKLGDAPKVVLASMASLEVGFSHDIF 339

Query: 93  FQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEELEEYQKKKDKE 152
               +  +N ++ T +   GTLAR L      + + + + KRI L G+EL+ Y++++++ 
Sbjct: 340 VDMANEAKNLVLFTEKGQFGTLARMLQVDPPPKAVKVTMSKRIPLVGDELKAYEEEQERI 399

Query: 153 AKDKQEKEKI 162
            K++  K  +
Sbjct: 400 KKEEALKASL 409

CPSF plays a key role in pre-mRNA 3'-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A)polymerase and other factors to bring about cleavage and poly(A) addition.

Oryza sativa subsp. japonica (taxid: 39947)

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	276
345480428	739	PREDICTED: probable cleavage and polyade	0.492	0.184	0.741	3e-54
332028657	737	Putative cleavage and polyadenylation sp	0.492	0.184	0.712	1e-52
340713940	737	PREDICTED: probable cleavage and polyade	0.492	0.184	0.712	2e-52
328780437	730	PREDICTED: probable cleavage and polyade	0.492	0.186	0.712	2e-52
350400562	737	PREDICTED: probable cleavage and polyade	0.492	0.184	0.712	2e-52
380025109	737	PREDICTED: probable cleavage and polyade	0.492	0.184	0.712	2e-52
307189918	737	Probable cleavage and polyadenylation sp	0.492	0.184	0.705	4e-52
322783252	737	hypothetical protein SINV_80021 [Solenop	0.492	0.184	0.705	2e-51
383852782	737	PREDICTED: probable cleavage and polyade	0.492	0.184	0.705	2e-51
270010824	733	hypothetical protein TcasGA2_TC014506 [T	0.456	0.171	0.710	4e-48

>gi|345480428|ref|XP_001601407.2| PREDICTED: probable cleavage and polyadenylation specificity factor subunit 2-like [Nasonia vitripennis]

 Score =  218 bits (554), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 103/139 (74%), Positives = 122/139 (87%), Gaps = 3/139 (2%)

Query: 24  LCHSLAELAK--IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTP 81
           + +++ E AK  IEWMSDKLMKSFEGARNNPF FKH++LCHS+AEL +VPSPKVVL STP
Sbjct: 272 VSYNVVEFAKSQIEWMSDKLMKSFEGARNNPFQFKHLQLCHSMAELNQVPSPKVVLASTP 331

Query: 82  DMECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEE 141
           DMECGFSRDLF QWCS+P+NSIIIT+RTSPGTLARDL+E GGNR +TL++KK++RLEG E
Sbjct: 332 DMECGFSRDLFLQWCSNPQNSIIITSRTSPGTLARDLVENGGNRNITLEIKKKVRLEGAE 391

Query: 142 LEEYQKK-KDKEAKDKQEK 159
           LEEY KK K K+ + KQEK
Sbjct: 392 LEEYMKKEKVKQEQLKQEK 410

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332028657|gb|EGI68691.1| Putative cleavage and polyadenylation specificity factor subunit 2 [Acromyrmex echinatior]

 Score =  212 bits (540), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 99/139 (71%), Positives = 123/139 (88%), Gaps = 3/139 (2%)

Query: 24  LCHSLAELAK--IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTP 81
           + +++ E AK  IEWMSDKLM+SFEGARNNPF FKH++LCHS+AEL +VPSPKVVL STP
Sbjct: 272 VSYNVVEFAKSQIEWMSDKLMRSFEGARNNPFQFKHLQLCHSMAELNQVPSPKVVLASTP 331

Query: 82  DMECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEE 141
           DMECGFSR+LF QWCS+P+NSII+T+RTSPGTLARDL+E GGNR +TL+VK+R++LEG E
Sbjct: 332 DMECGFSRELFLQWCSNPQNSIILTSRTSPGTLARDLVEKGGNRNITLEVKRRVKLEGIE 391

Query: 142 LEEYQKK-KDKEAKDKQEK 159
           LEEYQK+ K K+ + KQE+
Sbjct: 392 LEEYQKREKLKQEQLKQEQ 410

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340713940|ref|XP_003395491.1| PREDICTED: probable cleavage and polyadenylation specificity factor subunit 2-like isoform 1 [Bombus terrestris] gi|340713942|ref|XP_003395492.1| PREDICTED: probable cleavage and polyadenylation specificity factor subunit 2-like isoform 2 [Bombus terrestris]

 Score =  211 bits (538), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 99/139 (71%), Positives = 122/139 (87%), Gaps = 3/139 (2%)

Query: 24  LCHSLAELAK--IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTP 81
           + +++ E AK  IEWMSDKLM+SFEGARNNPF FKH++LCHS+AEL +VPSPKVVL STP
Sbjct: 272 VSYNVVEFAKSQIEWMSDKLMRSFEGARNNPFQFKHLQLCHSMAELNQVPSPKVVLASTP 331

Query: 82  DMECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEE 141
           DMECGFSR+LF QWC +P+NSII+T+RTSPGTLARDL+E GGNR +TL+VK+RI+LEG E
Sbjct: 332 DMECGFSRELFLQWCGNPQNSIILTSRTSPGTLARDLVEKGGNRNITLEVKRRIKLEGLE 391

Query: 142 LEEYQKK-KDKEAKDKQEK 159
           LEEYQ+K K K+ + KQE+
Sbjct: 392 LEEYQRKEKLKQEQLKQEQ 410

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328780437|ref|XP_394940.3| PREDICTED: probable cleavage and polyadenylation specificity factor subunit 2 [Apis mellifera]

 Score =  211 bits (538), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 99/139 (71%), Positives = 122/139 (87%), Gaps = 3/139 (2%)

Query: 24  LCHSLAELAK--IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTP 81
           + +++ E AK  IEWMSDKLM+SFEGARNNPF FKH++LCHS+AEL +VPSPKVVL STP
Sbjct: 272 VSYNVVEFAKSQIEWMSDKLMRSFEGARNNPFQFKHLQLCHSMAELNQVPSPKVVLASTP 331

Query: 82  DMECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEE 141
           DMECGFSR+LF QWC +P+NSII+T+RTSPGTLARDL+E GGNR +TL+VK+RI+LEG E
Sbjct: 332 DMECGFSRELFLQWCGNPQNSIILTSRTSPGTLARDLVEKGGNRNITLEVKRRIKLEGLE 391

Query: 142 LEEYQKK-KDKEAKDKQEK 159
           LEEYQ+K K K+ + KQE+
Sbjct: 392 LEEYQRKEKLKQEQLKQEQ 410

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350400562|ref|XP_003485880.1| PREDICTED: probable cleavage and polyadenylation specificity factor subunit 2-like [Bombus impatiens]

 Score =  211 bits (538), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 99/139 (71%), Positives = 122/139 (87%), Gaps = 3/139 (2%)

Query: 24  LCHSLAELAK--IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTP 81
           + +++ E AK  IEWMSDKLM+SFEGARNNPF FKH++LCHS+AEL +VPSPKVVL STP
Sbjct: 272 VSYNVVEFAKSQIEWMSDKLMRSFEGARNNPFQFKHLQLCHSMAELNQVPSPKVVLASTP 331

Query: 82  DMECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEE 141
           DMECGFSR+LF QWC +P+NSII+T+RTSPGTLARDL+E GGNR +TL+VK+RI+LEG E
Sbjct: 332 DMECGFSRELFLQWCGNPQNSIILTSRTSPGTLARDLVEKGGNRNITLEVKRRIKLEGLE 391

Query: 142 LEEYQKK-KDKEAKDKQEK 159
           LEEYQ+K K K+ + KQE+
Sbjct: 392 LEEYQRKEKLKQEQLKQEQ 410

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380025109|ref|XP_003696322.1| PREDICTED: probable cleavage and polyadenylation specificity factor subunit 2-like [Apis florea]

 Score =  211 bits (538), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 99/139 (71%), Positives = 122/139 (87%), Gaps = 3/139 (2%)

Query: 24  LCHSLAELAK--IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTP 81
           + +++ E AK  IEWMSDKLM+SFEGARNNPF FKH++LCHS+AEL +VPSPKVVL STP
Sbjct: 272 VSYNVVEFAKSQIEWMSDKLMRSFEGARNNPFQFKHLQLCHSMAELNQVPSPKVVLASTP 331

Query: 82  DMECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEE 141
           DMECGFSR+LF QWC +P+NSII+T+RTSPGTLARDL+E GGNR +TL+VK+RI+LEG E
Sbjct: 332 DMECGFSRELFLQWCGNPQNSIILTSRTSPGTLARDLVEKGGNRNITLEVKRRIKLEGLE 391

Query: 142 LEEYQKK-KDKEAKDKQEK 159
           LEEYQ+K K K+ + KQE+
Sbjct: 392 LEEYQRKEKLKQEQLKQEQ 410

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307189918|gb|EFN74154.1| Probable cleavage and polyadenylation specificity factor subunit 2 [Camponotus floridanus]

 Score =  210 bits (535), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 98/139 (70%), Positives = 121/139 (87%), Gaps = 3/139 (2%)

Query: 24  LCHSLAELAK--IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTP 81
           + +++ E AK  IEWMSDKLM+SFEGARNNPF FKH++LCHS+ EL +VPSPKVVL STP
Sbjct: 272 VSYNVVEFAKSQIEWMSDKLMRSFEGARNNPFQFKHLQLCHSMVELNQVPSPKVVLASTP 331

Query: 82  DMECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEE 141
           DMECGFSR+LF QWC++P+NSIIIT+RTSPGTLARDL+E GGNR +TL VK+R++LEG E
Sbjct: 332 DMECGFSRELFLQWCTNPQNSIIITSRTSPGTLARDLVEKGGNRNITLDVKRRVKLEGIE 391

Query: 142 LEEYQKK-KDKEAKDKQEK 159
           LEEYQK+ K K+ + KQE+
Sbjct: 392 LEEYQKREKLKQEQMKQEQ 410

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322783252|gb|EFZ10838.1| hypothetical protein SINV_80021 [Solenopsis invicta]

 Score =  208 bits (530), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 98/139 (70%), Positives = 121/139 (87%), Gaps = 3/139 (2%)

Query: 24  LCHSLAELAK--IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTP 81
           + +++ E AK  IEWMSDKLM+SFEGARNNPF FKH++LCHS+AEL +VPSPKVVL STP
Sbjct: 272 VSYNVVEFAKSQIEWMSDKLMRSFEGARNNPFQFKHLQLCHSMAELNQVPSPKVVLASTP 331

Query: 82  DMECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEE 141
           DMECGFSR+LF QWCS+ +NSII+T+RTSPGTLARDL+E GGNR +TL VK+R++LEG E
Sbjct: 332 DMECGFSRELFLQWCSNTQNSIILTSRTSPGTLARDLVEKGGNRNITLDVKRRVKLEGIE 391

Query: 142 LEEYQKK-KDKEAKDKQEK 159
           LEEYQK+ K K+ + KQE+
Sbjct: 392 LEEYQKREKLKQEQMKQEQ 410

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383852782|ref|XP_003701904.1| PREDICTED: probable cleavage and polyadenylation specificity factor subunit 2-like [Megachile rotundata]

 Score =  208 bits (530), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 98/139 (70%), Positives = 121/139 (87%), Gaps = 3/139 (2%)

Query: 24  LCHSLAELAK--IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTP 81
           + +++ E AK  IEWMSDKLM+SFEGARNNPF FKH++LCHS+AEL +VPSPKVVL STP
Sbjct: 272 VSYNVVEFAKSQIEWMSDKLMRSFEGARNNPFQFKHLQLCHSMAELNQVPSPKVVLASTP 331

Query: 82  DMECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEE 141
           DMECGFSR+LF QWC + +NSII+T+RTSPGTLARDL+E GGNR +TL+VK+RI+LEG E
Sbjct: 332 DMECGFSRELFLQWCGNSQNSIILTSRTSPGTLARDLVEKGGNRNITLEVKRRIKLEGLE 391

Query: 142 LEEYQKK-KDKEAKDKQEK 159
           LEEYQ+K K K+ + KQE+
Sbjct: 392 LEEYQRKEKLKQEQLKQEQ 410

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270010824|gb|EFA07272.1| hypothetical protein TcasGA2_TC014506 [Tribolium castaneum]

 Score =  197 bits (501), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 91/128 (71%), Positives = 108/128 (84%), Gaps = 2/128 (1%)

Query: 24  LCHSLAELAK--IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTP 81
           + +++ E AK  IEWMSDKLM+SFEGARNNPF FKH++LCHSL EL KV SPKVVL S+P
Sbjct: 272 VSYNVVEFAKSQIEWMSDKLMRSFEGARNNPFQFKHLQLCHSLHELQKVSSPKVVLASSP 331

Query: 82  DMECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEE 141
           DME GFSR+LF QWCS+P NSIIIT RTSPGTLARDL++ GGNR + L VK+R++LEG E
Sbjct: 332 DMESGFSRELFLQWCSNPNNSIIITTRTSPGTLARDLVDNGGNRQIDLVVKRRVKLEGSE 391

Query: 142 LEEYQKKK 149
           LEEYQK +
Sbjct: 392 LEEYQKSQ 399

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

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	276
ZFIN|ZDB-GENE-040718-79	790	cpsf2 "cleavage and polyadenyl	0.423	0.148	0.596	2.1e-54
FB|FBgn0027873	756	Cpsf100 "Cleavage and polyaden	0.423	0.154	0.611	1.3e-47
UNIPROTKB|Q10568	782	CPSF2 "Cleavage and polyadenyl	0.423	0.149	0.596	2.1e-47
RGD|1309687	782	Cpsf2 "cleavage and polyadenyl	0.423	0.149	0.596	2.1e-47
UNIPROTKB|E2R496	782	CPSF2 "Uncharacterized protein	0.423	0.149	0.596	2.6e-47
UNIPROTKB|Q9P2I0	782	CPSF2 "Cleavage and polyadenyl	0.423	0.149	0.596	2.6e-47
MGI|MGI:1861601	782	Cpsf2 "cleavage and polyadenyl	0.423	0.149	0.596	3.4e-47
UNIPROTKB|F1NMN0	782	CPSF2 "Uncharacterized protein	0.423	0.149	0.588	5.6e-47
UNIPROTKB|Q9W799	783	cpsf2 "Cleavage and polyadenyl	0.423	0.149	0.579	1.2e-46
UNIPROTKB|F1SD85	385	CPSF2 "Uncharacterized protein	0.384	0.275	0.601	3.2e-33

ZFIN|ZDB-GENE-040718-79 cpsf2 "cleavage and polyadenylation specific factor 2" [Danio rerio (taxid:7955)]

 Score = 392 (143.0 bits), Expect = 2.1e-54, Sum P(3) = 2.1e-54
 Identities = 71/119 (59%), Positives = 94/119 (78%)

Query:    26 HSLAELAK--IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDM 83
             +++ E +K  +EWMSDKLM+ FE  RNNPF F+H+ LCHSL++LA+VPSPKVVL S PD+
Sbjct:   274 YNVVEFSKSQVEWMSDKLMRCFEDKRNNPFQFRHLSLCHSLSDLARVPSPKVVLCSQPDL 333

Query:    84 ECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEEL 142
             E GFSR+LF QWC   +NS+I+T RT+PGTLAR LI+  G + + L+++KR RLEG EL
Sbjct:   334 ESGFSRELFIQWCQDAKNSVILTYRTTPGTLARYLIDNPGEKRIELEIRKRCRLEGREL 392

GO:0006378 "mRNA polyadenylation" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0006379 "mRNA cleavage" evidence=IEA

GO:0005847 "mRNA cleavage and polyadenylation specificity factor complex" evidence=IEA

FB|FBgn0027873 Cpsf100 "Cleavage and polyadenylation specificity factor 100" [Drosophila melanogaster (taxid:7227)]

 Score = 382 (139.5 bits), Expect = 1.3e-47, Sum P(2) = 1.3e-47
 Identities = 74/121 (61%), Positives = 95/121 (78%)

Query:    26 HSLAELAK--IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPS-PKVVLVSTPD 82
             +++ E AK  IEWMSDKL K+FEGARNNPF FKH++LCHSLA++ K+P+ PKVVL STPD
Sbjct:   274 YNVIEFAKSQIEWMSDKLTKAFEGARNNPFQFKHIQLCHSLADVYKLPAGPKVVLASTPD 333

Query:    83 MECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIE-LGGNRTLTLQVKKRIRLEGEE 141
             +E GF+RDLF QW S+  NSII+T RTSPGTLA +L+E     + + L V++R+ LEG E
Sbjct:   334 LESGFTRDLFVQWASNANNSIILTTRTSPGTLAMELVENCAPGKQIELDVRRRVDLEGAE 393

Query:   142 L 142
             L
Sbjct:   394 L 394

GO:0006379 "mRNA cleavage" evidence=ISS;NAS

GO:0005847 "mRNA cleavage and polyadenylation specificity factor complex" evidence=ISS

GO:0006378 "mRNA polyadenylation" evidence=ISS;IMP;NAS

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

GO:0016787 "hydrolase activity" evidence=IEA

GO:0006398 "histone mRNA 3'-end processing" evidence=IMP

GO:0022008 "neurogenesis" evidence=IMP

UNIPROTKB|Q10568 CPSF2 "Cleavage and polyadenylation specificity factor subunit 2" [Bos taurus (taxid:9913)]

 Score = 402 (146.6 bits), Expect = 2.1e-47, Sum P(2) = 2.1e-47
 Identities = 71/119 (59%), Positives = 95/119 (79%)

Query:    26 HSLAELAK--IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDM 83
             +++ E +K  +EWMSDKLM+ FE  RNNPF F+H+ LCH L++LA+VPSPKVVL S PD+
Sbjct:   274 YNVVEFSKSQVEWMSDKLMRCFEDKRNNPFQFRHLSLCHGLSDLARVPSPKVVLASQPDL 333

Query:    84 ECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEEL 142
             ECGFSRDLF QWC  P+NSII+T RT+PGTLAR LI+    +   ++++KR++LEG+EL
Sbjct:   334 ECGFSRDLFIQWCQDPKNSIILTYRTTPGTLARFLIDNPSEKVTEIELRKRVKLEGKEL 392

GO:0006398 "histone mRNA 3'-end processing" evidence=ISS

GO:0005847 "mRNA cleavage and polyadenylation specificity factor complex" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0006379 "mRNA cleavage" evidence=IEA

GO:0006378 "mRNA polyadenylation" evidence=IEA

RGD|1309687 Cpsf2 "cleavage and polyadenylation specific factor 2, 100kDa" [Rattus norvegicus (taxid:10116)]

 Score = 402 (146.6 bits), Expect = 2.1e-47, Sum P(2) = 2.1e-47
 Identities = 71/119 (59%), Positives = 95/119 (79%)

Query:    26 HSLAELAK--IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDM 83
             +++ E +K  +EWMSDKLM+ FE  RNNPF F+H+ LCH L++LA+VPSPKVVL S PD+
Sbjct:   274 YNVVEFSKSQVEWMSDKLMRCFEDKRNNPFQFRHLSLCHGLSDLARVPSPKVVLASQPDL 333

Query:    84 ECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEEL 142
             ECGFSRDLF QWC  P+NSII+T RT+PGTLAR LI+    +   ++++KR++LEG+EL
Sbjct:   334 ECGFSRDLFIQWCQDPKNSIILTYRTTPGTLARFLIDNPSEKVTEIELRKRVKLEGKEL 392

GO:0005847 "mRNA cleavage and polyadenylation specificity factor complex" evidence=IEA;ISO

GO:0006378 "mRNA polyadenylation" evidence=IEA

GO:0006379 "mRNA cleavage" evidence=IEA

GO:0006398 "histone mRNA 3'-end processing" evidence=IEA;ISO

GO:0016787 "hydrolase activity" evidence=IEA

UNIPROTKB|E2R496 CPSF2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 401 (146.2 bits), Expect = 2.6e-47, Sum P(2) = 2.6e-47
 Identities = 71/119 (59%), Positives = 95/119 (79%)

Query:    26 HSLAELAK--IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDM 83
             +++ E +K  +EWMSDKLM+ FE  RNNPF F+H+ LCH L++LA+VPSPKVVL S PD+
Sbjct:   274 YNVVEFSKSQVEWMSDKLMRCFEDKRNNPFQFRHLSLCHGLSDLARVPSPKVVLASQPDL 333

Query:    84 ECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEEL 142
             ECGFSRDLF QWC  P+NSII+T RT+PGTLAR LI+    +   ++++KR++LEG+EL
Sbjct:   334 ECGFSRDLFIQWCQDPKNSIILTYRTTPGTLARFLIDNPSEKITEIELRKRVKLEGKEL 392

GO:0006398 "histone mRNA 3'-end processing" evidence=IEA

GO:0005847 "mRNA cleavage and polyadenylation specificity factor complex" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0006379 "mRNA cleavage" evidence=IEA

GO:0006378 "mRNA polyadenylation" evidence=IEA

UNIPROTKB|Q9P2I0 CPSF2 "Cleavage and polyadenylation specificity factor subunit 2" [Homo sapiens (taxid:9606)]

 Score = 401 (146.2 bits), Expect = 2.6e-47, Sum P(2) = 2.6e-47
 Identities = 71/119 (59%), Positives = 95/119 (79%)

Query:    26 HSLAELAK--IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDM 83
             +++ E +K  +EWMSDKLM+ FE  RNNPF F+H+ LCH L++LA+VPSPKVVL S PD+
Sbjct:   274 YNVVEFSKSQVEWMSDKLMRCFEDKRNNPFQFRHLSLCHGLSDLARVPSPKVVLASQPDL 333

Query:    84 ECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEEL 142
             ECGFSRDLF QWC  P+NSII+T RT+PGTLAR LI+    +   ++++KR++LEG+EL
Sbjct:   334 ECGFSRDLFIQWCQDPKNSIILTYRTTPGTLARFLIDNPSEKITEIELRKRVKLEGKEL 392

GO:0006378 "mRNA polyadenylation" evidence=IEA

GO:0006379 "mRNA cleavage" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0006398 "histone mRNA 3'-end processing" evidence=IDA

GO:0005847 "mRNA cleavage and polyadenylation specificity factor complex" evidence=IDA

GO:0000398 "mRNA splicing, via spliceosome" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=TAS

GO:0006369 "termination of RNA polymerase II transcription" evidence=TAS

GO:0006397 "mRNA processing" evidence=TAS

GO:0006406 "mRNA export from nucleus" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0031124 "mRNA 3'-end processing" evidence=TAS

MGI|MGI:1861601 Cpsf2 "cleavage and polyadenylation specific factor 2" [Mus musculus (taxid:10090)]

 Score = 400 (145.9 bits), Expect = 3.4e-47, Sum P(2) = 3.4e-47
 Identities = 71/119 (59%), Positives = 95/119 (79%)

Query:    26 HSLAELAK--IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDM 83
             +++ E +K  +EWMSDKLM+ FE  RNNPF F+H+ LCH L++LA+VPSPKVVL S PD+
Sbjct:   274 YNVVEFSKSQVEWMSDKLMRCFEDKRNNPFQFRHLSLCHGLSDLARVPSPKVVLASQPDL 333

Query:    84 ECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEEL 142
             ECGFSRDLF QWC  P+NSII+T RT+PGTLAR LI+    +   ++++KR++LEG+EL
Sbjct:   334 ECGFSRDLFIQWCQDPKNSIILTYRTTPGTLARFLIDNPTEKVTEIELRKRVKLEGKEL 392

GO:0003674 "molecular_function" evidence=ND

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005847 "mRNA cleavage and polyadenylation specificity factor complex" evidence=ISO;IDA

GO:0006397 "mRNA processing" evidence=IEA

GO:0006398 "histone mRNA 3'-end processing" evidence=ISO

GO:0016787 "hydrolase activity" evidence=IEA

UNIPROTKB|F1NMN0 CPSF2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 398 (145.2 bits), Expect = 5.6e-47, Sum P(2) = 5.6e-47
 Identities = 70/119 (58%), Positives = 96/119 (80%)

Query:    26 HSLAELAK--IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDM 83
             +++ E +K  +EWMSDKLM+ FE  RNNPF F+H+ LCHSL++LA+VPSPKVVL S PD+
Sbjct:   274 YNVVEFSKSQVEWMSDKLMRCFEDKRNNPFQFRHLSLCHSLSDLARVPSPKVVLASQPDL 333

Query:    84 ECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEEL 142
             ECGFSRDLF QWC   +NSII+T RT+PGTLAR LI+    + + +++++R++LEG+EL
Sbjct:   334 ECGFSRDLFIQWCQDSKNSIILTYRTTPGTLARFLIDNPSEKVIDIELRRRVKLEGKEL 392

GO:0006378 "mRNA polyadenylation" evidence=IEA

GO:0006379 "mRNA cleavage" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0005847 "mRNA cleavage and polyadenylation specificity factor complex" evidence=IEA

GO:0006398 "histone mRNA 3'-end processing" evidence=IEA

UNIPROTKB|Q9W799 cpsf2 "Cleavage and polyadenylation specificity factor subunit 2" [Xenopus laevis (taxid:8355)]

 Score = 396 (144.5 bits), Expect = 1.2e-46, Sum P(2) = 1.2e-46
 Identities = 69/119 (57%), Positives = 95/119 (79%)

Query:    26 HSLAELAK--IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDM 83
             +++ E +K  +EWMSDKLM+ FE  RNNPF F+H+ LCH  ++LA+VPSPKVVL S PD+
Sbjct:   274 YNVVEFSKSQVEWMSDKLMRCFEDKRNNPFQFRHLTLCHGYSDLARVPSPKVVLASQPDL 333

Query:    84 ECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEEL 142
             ECGFSR+LF QWC  P+NS+I+T RT+PGTLAR LI+    R + ++++KR++LEG+EL
Sbjct:   334 ECGFSRELFIQWCQDPKNSVILTYRTTPGTLARFLIDHPSERIIDIELRKRVKLEGKEL 392

GO:0005847 "mRNA cleavage and polyadenylation specificity factor complex" evidence=ISS

UNIPROTKB|F1SD85 CPSF2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 362 (132.5 bits), Expect = 3.2e-33, P = 3.2e-33
 Identities = 65/108 (60%), Positives = 84/108 (77%)

Query:    26 HSLAELAK--IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDM 83
             +++ E +K  +EWMSDKLM+ FE  RNNPF F+H+ LCH L++LA+VPSPKVVL S PD+
Sbjct:   274 YNVVEFSKSQVEWMSDKLMRCFEDKRNNPFQFRHLSLCHGLSDLARVPSPKVVLASQPDL 333

Query:    84 ECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQV 131
             ECGFSRDLF QWC  P+NSII+T RT+PGTLAR LI+    +   ++V
Sbjct:   334 ECGFSRDLFIQWCQDPKNSIILTYRTTPGTLARFLIDNPSEKITEIEV 381

GO:0016787 "hydrolase activity" evidence=IEA

GO:0006379 "mRNA cleavage" evidence=IEA

GO:0006378 "mRNA polyadenylation" evidence=IEA

GO:0005847 "mRNA cleavage and polyadenylation specificity factor complex" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	276
smart01027	126	smart01027, Beta-Casp, Beta-Casp domain	6e-24
pfam10996	124	pfam10996, Beta-Casp, Beta-Casp domain	2e-19
pfam13299	152	pfam13299, CPSF100_C, Cleavage and polyadenylation	3e-17
COG1782	637	COG1782, COG1782, Predicted metal-dependent RNase,	2e-05
smart01027	126	smart01027, Beta-Casp, Beta-Casp domain	3e-05
COG1236	427	COG1236, YSH1, Predicted exonuclease of the beta-l	4e-05
pfam10996	124	pfam10996, Beta-Casp, Beta-Casp domain	5e-05

>gnl|CDD|214983 smart01027, Beta-Casp, Beta-Casp domain

 Score = 93.4 bits (233), Expect = 6e-24
 Identities = 34/88 (38%), Positives = 47/88 (53%), Gaps = 4/88 (4%)

Query: 34  IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAE---LAKVPSPKVVLVSTPDMECGFSRD 90
            EWMSD++ K FE    NPF FK++K   SL E   L     PKV++ S+  +  G SR 
Sbjct: 40  PEWMSDEIRKRFE-QGRNPFDFKNLKFVKSLEESKRLNDYKGPKVIIASSGMLTGGRSRH 98

Query: 91  LFFQWCSSPENSIIITNRTSPGTLARDL 118
              +    P N++I+T   + GTL R L
Sbjct: 99  YLKRLAPDPRNTVILTGYQAEGTLGRKL 126

The beta-CASP domain is found C terminal to the beta-lactamase domain in pre-mRNA 3'-end-processing endonuclease. The active site of this enzyme is located at the interface of these two domains. Length = 126

>gnl|CDD|220932 pfam10996, Beta-Casp, Beta-Casp domain

 Score = 81.5 bits (202), Expect = 2e-19
 Identities = 28/86 (32%), Positives = 42/86 (48%), Gaps = 2/86 (2%)

Query: 34  IEWMSDKLMKSFEGARNNPF-HFKHVKLCHSLAELAKVPSPKVVLVSTPDMECGFSRDLF 92
            EW+SD   K F      PF + K V+      EL  +  PKV++ S+  +E G S    
Sbjct: 40  PEWLSDS-AKEFLLRGAFPFDNLKFVRSVDESKELNNLGGPKVIIASSGMLEGGRSLHYL 98

Query: 93  FQWCSSPENSIIITNRTSPGTLARDL 118
            +    P+N++I+T   + GTL R L
Sbjct: 99  KKLAPDPKNTVILTGYQAEGTLGRKL 124

The beta-CASP domain is found C terminal to the beta-lactamase domain in pre-mRNA 3'-end-processing endonuclease. The active site of this enzyme is located at the interface of these two domains. Length = 124

>gnl|CDD|222032 pfam13299, CPSF100_C, Cleavage and polyadenylation factor 2 C-terminal

 Score = 76.1 bits (188), Expect = 3e-17
 Identities = 39/161 (24%), Positives = 54/161 (33%), Gaps = 47/161 (29%)

Query: 120 ELGGNRTLTLQVKKRIRLEGEELEEYQKKKDKEAKDKQ------EKEKIPPHDTSFINEL 173
           E           K     E E      K +     D+              H   FI +L
Sbjct: 32  ESDTPEETETSAKAIETEETETESSDDKLELSPELDELPTLEALTSATRSAHQPLFIGDL 91

Query: 174 QLSDFKQTLQRNGIDCEFM-DGVLICCRGTVAVRRVVLVSTPDMECGFSRDLFFQWCSSP 232
           +L+D K+ L   GI  EF  +G L+ C G VAVR+                         
Sbjct: 92  RLADLKKALASAGIQAEFKGEGTLV-CNGKVAVRK------------------------- 125

Query: 233 ENSIIITNRNRADDSDSNVIVLEGCLSDEYYRVQQLLYDQY 273
                         S +  IV+EG LS  YY V++L+Y+Q 
Sbjct: 126 --------------SATGRIVIEGTLSPSYYEVRKLIYEQL 152

This family lies at the C-terminus of many fungal and plant cleavage and polyadenylation specificity factor subunit 2 proteins. The exact function of the domain is not known, but is likely to function as a binding domain for the protein within the overall CPSF complex. Length = 152

>gnl|CDD|224696 COG1782, COG1782, Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]

 Score = 45.0 bits (107), Expect = 2e-05
 Identities = 23/113 (20%), Positives = 46/113 (40%), Gaps = 13/113 (11%)

Query: 35  EWMSDKLMKSFEGARNNPF---HFKHVKLCHSLAELAKVPSPKVVLVSTPDMECGFSRDL 91
           E+++ +L +       NPF    FK V+      E+ +   P ++L ++  +  G   + 
Sbjct: 460 EYLNKELRERIFHEGENPFLSEIFKRVEGSDERQEIIESDEPAIILATSGMLNGGPVVEY 519

Query: 92  FFQWCSSPENSIIITNRTSPGTLAR---------DLIELGGNRTLTLQVKKRI 135
           F      P+N++I     + GTL R          +    G +T  ++V   +
Sbjct: 520 FKHLAPDPKNTLIFVGYQAEGTLGRRIQSGAKEIPIPGEDG-KTEVIKVNMEV 571

Length = 637

>gnl|CDD|214983 smart01027, Beta-Casp, Beta-Casp domain

 Score = 42.5 bits (101), Expect = 3e-05
 Identities = 9/32 (28%), Positives = 17/32 (53%)

Query: 208 VVLVSTPDMECGFSRDLFFQWCSSPENSIIIT 239
           V++ S+  +  G SR    +    P N++I+T
Sbjct: 83  VIIASSGMLTGGRSRHYLKRLAPDPRNTVILT 114

The beta-CASP domain is found C terminal to the beta-lactamase domain in pre-mRNA 3'-end-processing endonuclease. The active site of this enzyme is located at the interface of these two domains. Length = 126

>gnl|CDD|224157 COG1236, YSH1, Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]

 Score = 44.3 bits (105), Expect = 4e-05
 Identities = 27/111 (24%), Positives = 46/111 (41%), Gaps = 9/111 (8%)

Query: 34  IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDM-ECGFSRDLF 92
           I      L+K  E        F+ V+   +         P VV ++ P M + G SR   
Sbjct: 265 IGLDLPDLLKVAES------RFRFVESRRNSMREGIDKGPAVV-LAAPGMLKGGRSRYYL 317

Query: 93  FQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEELE 143
               S  +N +++    + GTL R L+E GG       ++ +++   EEL+
Sbjct: 318 KHLLSDEKNWVLLPGYQAEGTLGRVLLE-GGTSVHIKGIEIKVKARVEELD 367

Length = 427

>gnl|CDD|220932 pfam10996, Beta-Casp, Beta-Casp domain

 Score = 41.5 bits (98), Expect = 5e-05
 Identities = 9/32 (28%), Positives = 18/32 (56%)

Query: 208 VVLVSTPDMECGFSRDLFFQWCSSPENSIIIT 239
           V++ S+  +E G S     +    P+N++I+T
Sbjct: 81  VIIASSGMLEGGRSLHYLKKLAPDPKNTVILT 112

The beta-CASP domain is found C terminal to the beta-lactamase domain in pre-mRNA 3'-end-processing endonuclease. The active site of this enzyme is located at the interface of these two domains. Length = 124

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	276
2i7t_A	459	Structure Of Human Cpsf-73 Length = 459		5e-09

>pdb|2I7T|A Chain A, Structure Of Human Cpsf-73 Length = 459

Iteration: 1
 Score = 58.2 bits (139), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 31/83 (37%), Positives = 44/83 (53%), Gaps = 3/83 (3%)
Query: 37  MSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDMECGFSRDLFFQWC 96
           M+DK+ K      NNPF FKH+    S+     +  P VV+ S   M+ G SR+LF  WC
Sbjct: 289 MNDKIRKQIN--INNPFVFKHISNLKSMDHFDDI-GPSVVMASPGMMQSGLSRELFESWC 345
Query: 97  SSPENSIIITNRTSPGTLARDLI 119
           +   N +II      GTLA+ ++
Sbjct: 346 TDKRNGVIIAGYCVEGTLAKHIM 368

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	276
2i7x_A	717	Protein CFT2; polyadenylation, metallo-B-lactamase	8e-27
3iek_A	431	Ribonuclease TTHA0252; metallo beta lactamase fold	6e-14
2i7t_A	459	Cleavage and polyadenylation specificity factor 73	1e-13
3af5_A	651	Putative uncharacterized protein PH1404; archaeal	3e-13
2xr1_A	640	Cleavage and polyadenylation specificity factor 1	6e-13
2ycb_A	636	Beta-CAsp RNAse, cleavage and polyadenylation spec	1e-12
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-06

>2i7x_A Protein CFT2; polyadenylation, metallo-B-lactamase, PRE-mRNA processing, artemis, V(D)J recombination, double-strand break repair; 2.50A {Saccharomyces cerevisiae} SCOP: d.157.1.10 Length = 717

 Score =  108 bits (270), Expect = 8e-27
 Identities = 28/150 (18%), Positives = 60/150 (40%), Gaps = 23/150 (15%)

Query: 34  IEWMSDKLMKSFEGARN-NPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDMECGFSRDLF 92
           +EW+S  L+K++E   N +PF         +  EL+K P  K+  VS          ++ 
Sbjct: 297 LEWLSPSLLKTWENRNNTSPFEIGSRIKIIAPNELSKYPGSKICFVSEVG---ALINEVI 353

Query: 93  FQWCSSPENSIIITNRTSPGTLARDLI-------------------ELGGNRTLTLQVKK 133
            +  +S + ++I+T  +     + D I                       +  +++   K
Sbjct: 354 IKVGNSEKTTLILTKPSFECASSLDKILEIVEQDERNWKTFPEDGKSFLCDNYISIDTIK 413

Query: 134 RIRLEGEELEEYQKKKDKEAKDKQEKEKIP 163
              L  EE E ++ +  ++ +D+ +K  + 
Sbjct: 414 EEPLSKEETEAFKVQLKEKKRDRNKKILLV 443

>3iek_A Ribonuclease TTHA0252; metallo beta lactamase fold, endonuclease, hydrolase, metal- nuclease, RNA-binding, rRNA processing; HET: FLC; 2.05A {Thermus thermophilus} PDB: 2dkf_A* 3iel_A* 3iem_A* 2zdf_A* 3idz_A* 2zdd_A* 3ie0_A* 2zde_A* 3ie1_A* 2zdw_A* 3a4y_A* 2yvd_A* 3ie2_A* Length = 431

 Score = 70.2 bits (173), Expect = 6e-14
 Identities = 23/114 (20%), Positives = 42/114 (36%), Gaps = 16/114 (14%)

Query: 34  IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAE---LAKVPSPKVVLVSTPDM-ECGFSR 89
           + + S+++   F   +N PF    +++         L + P P VVL +   M   G   
Sbjct: 265 VRYFSEEVQAHFLQGKN-PFRPAGLEVVEHTEASKALNRAPGPMVVL-AGSGMLAGGRIL 322

Query: 90  DLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEELE 143
                  S P N+++       G L  ++I               +R+ GEE+ 
Sbjct: 323 HHLKHGLSDPRNALVFVGYQPQGGLGAEIIA-RP---------PAVRILGEEVP 366

>2i7t_A Cleavage and polyadenylation specificity factor 73 kDa subunit; metallo-B-lactamase, PRE-mRNA processing, artemis, V(D)J recombination; 2.10A {Homo sapiens} SCOP: d.157.1.10 PDB: 2i7v_A Length = 459

 Score = 69.2 bits (170), Expect = 1e-13
 Identities = 33/111 (29%), Positives = 53/111 (47%), Gaps = 14/111 (12%)

Query: 34  IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDM-ECGFSRDLF 92
           +  M+DK+ K      NNPF FKH+    S+        P VV+ ++P M + G SR+LF
Sbjct: 286 VNAMNDKIRKQINI--NNPFVFKHISNLKSMDHF-DDIGPSVVM-ASPGMMQSGLSRELF 341

Query: 93  FQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEELE 143
             WC+   N +II      GTLA+ ++            ++   + G++L 
Sbjct: 342 ESWCTDKRNGVIIAGYCVEGTLAKHIMS-EP--------EEITTMSGQKLP 383

>3af5_A Putative uncharacterized protein PH1404; archaeal CPSF, beta-CAsp family, KH domain, ribonuclease, ME beta-lactamase superfamily, archaea; 2.60A {Pyrococcus horikoshii} PDB: 3af6_A* Length = 651

 Score = 68.5 bits (168), Expect = 3e-13
 Identities = 27/115 (23%), Positives = 46/115 (40%), Gaps = 15/115 (13%)

Query: 34  IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAE---LAKVPSPKVVLVSTPDM-ECGFSR 89
            E++S +L +       NPF  +      +  E   +     P +++ ++  M   G S 
Sbjct: 473 PEYLSRRLREQIFKEGYNPFLSEIFHPVANSRERQDIIDSNEPAIII-ASSGMLVGGPSV 531

Query: 90  DLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEELEE 144
           + F Q    P+NSII  +  + GTL R +   G          + I + GEE   
Sbjct: 532 EYFKQLAPDPKNSIIFVSYQAEGTLGRQVQS-GI---------REIPMVGEEGRT 576

>2xr1_A Cleavage and polyadenylation specificity factor 1 subunit; hydrolase, metallo-beta-lactamase, beta-CAsp, RNA processing; 2.59A {Methanosarcina mazei} Length = 640

 Score = 67.3 bits (165), Expect = 6e-13
 Identities = 22/100 (22%), Positives = 43/100 (43%), Gaps = 7/100 (7%)

Query: 34  IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAE---LAKVPSPKVVLVSTPDM-ECGFSR 89
            E++++ L K       NPF  +  K   S      + + P P V+L +T  M   G   
Sbjct: 462 PEYLNNDLRKLIFQKGQNPFLSECFKPVDSHEARQKIIQNPQPCVIL-ATSGMMNGGPVM 520

Query: 90  DLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTL 129
           + F  +   P N+++     + GT+ R + +  G + + +
Sbjct: 521 EYFKAFAEDPRNTLVFVGYQADGTIGRRIQK--GWKEIPM 558

>2ycb_A Beta-CAsp RNAse, cleavage and polyadenylation specificity factor; hydrolase, KH, metallo-beta-lactamase; 3.10A {Methanothermobacter thermautotrophicusorganism_taxid} Length = 636

 Score = 66.6 bits (163), Expect = 1e-12
 Identities = 27/114 (23%), Positives = 47/114 (41%), Gaps = 14/114 (12%)

Query: 34  IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKV--PSPKVVLVSTPDM-ECGFSRD 90
            E++S  L        +NPF        + + E  ++    P ++L ST  M   G S +
Sbjct: 459 PEYLSKDLRDQIFHMGHNPFISDIFHKVNGMDERREIVEGEPSIIL-STSGMLTGGNSLE 517

Query: 91  LFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEELEE 144
            F   C  P+NS++     + G+L R + + G          K I L+ E+ + 
Sbjct: 518 YFKWLCEDPDNSLVFVGYQAEGSLGRRIQK-G---------WKEIPLKDEDDKM 561

>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 = 48.3 bits (114), Expect = 2e-06
 Identities = 39/319 (12%), Positives = 90/319 (28%), Gaps = 106/319 (33%)

Query: 35  EWMSDKL----------MKSFEGARNN------PFHFKHV-------KLCHSLAELAKVP 71
           +++   +           + +   R+        F   +V       KL  +L EL   P
Sbjct: 92  KFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELR--P 149

Query: 72  SPKVVL---------------VSTPDMECGFSRDLFFQW-----CSSPENSIIITNRTSP 111
           +  V++                 +  ++C     +F  W     C+SPE  + +  +   
Sbjct: 150 AKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIF--WLNLKNCNSPETVLEMLQKL-- 205

Query: 112 GTLARDLIELGGNRTLTLQVKKRIRLEGEELEEYQKKKDKEAKDKQEKEKIPPHDTSFIN 171
                 L ++  N T        I+L    ++   ++  K            P++     
Sbjct: 206 ------LYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKS----------KPYENCL-- 247

Query: 172 ELQLSDF--KQTLQRNGIDCEFMDGVLICCRGT-----VAVRRVVLVSTPDMECGF---- 220
            L L +    +      + C+    +L+  R       ++      +S            
Sbjct: 248 -LVLLNVQNAKAWNAFNLSCK----ILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDE 302

Query: 221 SRDLFFQWCSSPEN--------------SII----ITNRNRAD-----DSDSNVIVLEGC 257
            + L  ++                    SII           D     + D    ++E  
Sbjct: 303 VKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESS 362

Query: 258 LSDEYYRVQQLLYDQYAIL 276
           L+       + ++D+ ++ 
Sbjct: 363 LNVLEPAEYRKMFDRLSVF 381

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	276
3iek_A	431	Ribonuclease TTHA0252; metallo beta lactamase fold	100.0
2i7t_A	459	Cleavage and polyadenylation specificity factor 73	99.98
2xr1_A	640	Cleavage and polyadenylation specificity factor 1	99.96
3af5_A	651	Putative uncharacterized protein PH1404; archaeal	99.96
2ycb_A	636	Beta-CAsp RNAse, cleavage and polyadenylation spec	99.95
2i7x_A	717	Protein CFT2; polyadenylation, metallo-B-lactamase	99.79
3bk2_A	562	RNAse J, metal dependent hydrolase; endoribonuclea	99.28
3zq4_A	555	Ribonuclease J 1, RNAse J1; hydrolase, RNA maturat	99.07
3iek_A	431	Ribonuclease TTHA0252; metallo beta lactamase fold	98.79
2i7t_A	459	Cleavage and polyadenylation specificity factor 73	98.39
2az4_A	429	Hypothetical protein EF2904; structural genomics,	98.14
2xr1_A	640	Cleavage and polyadenylation specificity factor 1	97.81
3af5_A	651	Putative uncharacterized protein PH1404; archaeal	97.8
2ycb_A	636	Beta-CAsp RNAse, cleavage and polyadenylation spec	97.69
2i7x_A	717	Protein CFT2; polyadenylation, metallo-B-lactamase	97.53
3bk2_A	562	RNAse J, metal dependent hydrolase; endoribonuclea	87.94
3zdk_A	336	5' exonuclease apollo; hydrolase; HET: TLA; 2.16A	85.38
4b87_A	367	DNA cross-LINK repair 1A protein; dclre1A, DCLRE,	81.21
3zq4_A	555	Ribonuclease J 1, RNAse J1; hydrolase, RNA maturat	80.3

>3iek_A Ribonuclease TTHA0252; metallo beta lactamase fold, endonuclease, hydrolase, metal- nuclease, RNA-binding, rRNA processing; HET: FLC; 2.05A {Thermus thermophilus} SCOP: d.157.1.10 PDB: 2dkf_A* 3iel_A* 3iem_A* 2zdf_A* 3idz_A* 2zdd_A* 3ie0_A* 2zde_A* 3ie1_A* 2zdw_A* 3a4y_A* 2yvd_A* 3ie2_A*

Probab=100.00  E-value=5.1e-39  Score=309.36  Aligned_cols=187  Identities=14%  Similarity=0.206  Sum_probs=157.9

Q ss_pred             hHHHHHHHhcCCCCCccchhh----hhhhhHHhhc--ccccCHHHHHHHHhccCCCCCCCCceecCCHHH---HhcCCCC
Q psy13345          3 DKLMKSFEGARNNPFHFKHVK----LCHSLAELAK--IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAE---LAKVPSP   73 (276)
Q Consensus         3 ~~L~~l~~~~k~~~i~~~Pi~----~s~~t~~~ak--~ewms~~i~~~~~~~~~nPF~f~~l~~v~s~ee---l~~~~~P   73 (276)
                      |+|..+.+.++.  ++++|||    ++..++.+++  +|||++++++.+. .+.|||.|++++++++.++   +++.++|
T Consensus       230 ell~~l~~~~~~--~~~~pi~~~s~~a~~~~~~~~~~~~~~~~~~~~~~~-~~~~pf~~~~~~~~~~~~~~~~~~~~~~p  306 (431)
T 3iek_A          230 EILYVLYTHGHR--LPRAPIYLDSPMAGRVLSLYPRLVRYFSEEVQAHFL-QGKNPFRPAGLEVVEHTEASKALNRAPGP  306 (431)
T ss_dssp             HHHHHHHHHGGG--SCCCCEEEECHHHHHHHHHGGGGGGGSCHHHHHHHH-TTSCTTCCTTEEECCSHHHHHHHHHSCSS
T ss_pred             HHHHHHHHHHHh--ccCCCEEEeChHHHHHHHHHHHhHHHHHHHHHHHHh-cCCCCCCCCCeEEeCCHHHHHHHhcCCCC
Confidence            444444444433  4456655    4456777777  9999999999886 6789999999999999876   6777899


Q ss_pred             eEEEEeCCCCCcchHHHHHHHhCCCCCCeEEEecCCCCCChhHHHHhccCCceEEEeeceEEeeeh--hhhhhhhhhcCc
Q psy13345         74 KVVLVSTPDMECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEG--EELEEYQKKKDK  151 (276)
Q Consensus        74 ~VIiassgml~~G~s~~~l~~~~~d~~N~Iiltgy~~~gTlgr~L~~~~~~~~i~i~~~~~~~l~~--~el~~fsaHad~  151 (276)
                      ||||||||||++|+|++||++|++||+|+|||||||++||+||+|+++  .++|+| .++.+++++  +.+.+||||||+
T Consensus       307 ~viia~~gm~~~G~~~~~l~~~~~~~~n~ii~~gyq~~gt~g~~l~~~--~~~v~~-~g~~~~v~a~v~~~~~~saHad~  383 (431)
T 3iek_A          307 MVVLAGSGMLAGGRILHHLKHGLSDPRNALVFVGYQPQGGLGAEIIAR--PPAVRI-LGEEVPLRASVHTLGGFSGHAGQ  383 (431)
T ss_dssp             EEEEESCTTSSSSHHHHHHHHHTTCTTCEEEECSCCCTTSHHHHHHTC--CSEEEE-TTEEEECCSEEEECGGGCSSCCH
T ss_pred             eEEEecCCCCCCChHHHHHHHhcCCCCCeEEEECCCCCCChHHHhhcC--CcEEEE-CCEEEEEEEEEEEECCccccCCH
Confidence            999999999999999999999999999999999999999999999987  567999 689999999  566789999999


Q ss_pred             hhhHHHHhhcCCCcceEEeCh-hhHHHHHHHHHHcCCCcccccceeeecCceec
Q psy13345        152 EAKDKQEKEKIPPHDTSFINE-LQLSDFKQTLQRNGIDCEFMDGVLICCRGTVA  204 (276)
Q Consensus       152 ~~l~~~i~~~~p~~v~lvHGE-~~~~~Lk~~L~~~G~~aef~gg~l~~p~~~~~  204 (276)
                      +||++|++..+  +++||||| .++..|++.|.+++.       .+++|.+.++
T Consensus       384 ~~l~~~~~~~~--~v~lvHge~~~~~~l~~~l~~~~~-------~~~~p~~~~~  428 (431)
T 3iek_A          384 DELLDWLQGEP--RVVLVHGEEEKLLALGKLLALRGQ-------EVSLARFGEG  428 (431)
T ss_dssp             HHHHHHHTTCS--EEEEESSCHHHHHHHHHHHHHTTC-------EEEECCTTCC
T ss_pred             HHHHHHHHhCC--eEEEECCCHHHHHHHHHHHHHhCC-------cEEECCCCCE
Confidence            99999999764  89999999 899999999998852       5566666444

>2i7t_A Cleavage and polyadenylation specificity factor 73 kDa subunit; metallo-B-lactamase, PRE-mRNA processing, artemis, V(D)J recombination; 2.10A {Homo sapiens} SCOP: d.157.1.10 PDB: 2i7v_A

Probab=99.98  E-value=6.1e-33  Score=267.94  Aligned_cols=195  Identities=25%  Similarity=0.366  Sum_probs=134.9

Q ss_pred             HHHHHHHhcCCCCCccchhh----hhhhhHHhhc--ccccCHHHHHHHHhccCCCCCCCCceecCCHHHHhcCCCCeEEE
Q psy13345          4 KLMKSFEGARNNPFHFKHVK----LCHSLAELAK--IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVL   77 (276)
Q Consensus         4 ~L~~l~~~~k~~~i~~~Pi~----~s~~t~~~ak--~ewms~~i~~~~~~~~~nPF~f~~l~~v~s~eel~~~~~P~VIi   77 (276)
                      .|+.+|+++.  .++++|||    ++..++.+++  .+||++++++.+.  ..|||.|++++.+.+.+++. ..+|||||
T Consensus       252 ~l~~~~~~~~--~~~~~pi~~~s~~a~~~~~~~~~~~~~~~~~~~~~~~--~~~p~~~~~~~~~~~~~~~~-~~~~~vii  326 (459)
T 2i7t_A          252 ILDEYWQNHP--ELHDIPIYYASSLAKKCMAVYQTYVNAMNDKIRKQIN--INNPFVFKHISNLKSMDHFD-DIGPSVVM  326 (459)
T ss_dssp             HHHHHHHHCG--GGTTSCEEEC-----------------------------------CCSEEECCCTTSSC-CCSSEEEE
T ss_pred             HHHHHHHhcC--CCCCccEEEECHHHHHHHHHHHHHHHHHhHHHHHHhc--ccCCcCCCcceeeCCHHHhc-CCCCeEEE
Confidence            4556666542  23345544    4445666666  9999999998885  57999999999998877764 47899999


Q ss_pred             EeCCCCCcchHHHHHHHhCCCCCCeEEEecCCCCCChhHHHHhccCCceEEEeeceEEeeeh-hhhhhhhhhcCchhhHH
Q psy13345         78 VSTPDMECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEG-EELEEYQKKKDKEAKDK  156 (276)
Q Consensus        78 assgml~~G~s~~~l~~~~~d~~N~Iiltgy~~~gTlgr~L~~~~~~~~i~i~~~~~~~l~~-~el~~fsaHad~~~l~~  156 (276)
                      |+||||++|++++||++|++|++|+|+|||||++||+||+|++++  +.+....++.+++++ .+...||+|||+++|++
T Consensus       327 a~~gm~~~g~~~~~l~~~~~~~~~~ii~~gy~~~gt~g~~l~~~~--~~~~~~~g~~~~~~~~v~~~~~S~Had~~~l~~  404 (459)
T 2i7t_A          327 ASPGMMQSGLSRELFESWCTDKRNGVIIAGYCVEGTLAKHIMSEP--EEITTMSGQKLPLKMSVDYISFSAHTDYQQTSE  404 (459)
T ss_dssp             ESCTTCSSHHHHHHHHHHTTCTTCEEEECSCCCTTSHHHHHTTCC--SEEECTTSCEEECCSEEEECCCSCCCCHHHHHH
T ss_pred             EcCcccCCCHHHHHHHHHcCCCCCeEEEEecCCCCChHHHHhhCC--ceeeeeCCcEEEEEEEEEEeeecccCCHHHHHH
Confidence            999999999999999999999999999999999999999999873  455543678888888 45558999999999999


Q ss_pred             HHhhcCCCcceEEeCh-hhHHHHHHHHHHc-CCCcccccceeeecCceeccc
Q psy13345        157 QEKEKIPPHDTSFINE-LQLSDFKQTLQRN-GIDCEFMDGVLICCRGTVAVR  206 (276)
Q Consensus       157 ~i~~~~p~~v~lvHGE-~~~~~Lk~~L~~~-G~~aef~gg~l~~p~~~~~i~  206 (276)
                      |++...|+++++|||| .++..|++.|.++ +.+.+ .+-.+++|.+.+++.
T Consensus       405 ~i~~~~p~~v~~vHGe~~~~~~~~~~l~~~~~~~~~-~~~~~~~p~~~~~~~  455 (459)
T 2i7t_A          405 FIRALKPPHVILVHGEQNEMARLKAALIREYEDNDE-VHIEVHNPRNTEAVT  455 (459)
T ss_dssp             HHHHHCCSEEEEESSCHHHHHHHHHHHHHHHSSCTT-CCCEEECCCTTCCEE
T ss_pred             HHHhcCCCeEEEeCCCHHHHHHHHHHHHHHhccccc-cCceEEeCCCCCEEE
Confidence            9999999999999999 8889999999875 43322 245678888766553

>2xr1_A Cleavage and polyadenylation specificity factor 1 subunit; hydrolase, metallo-beta-lactamase, beta-CAsp, RNA processing; 2.59A {Methanosarcina mazei}

Probab=99.96  E-value=1.4e-29  Score=254.65  Aligned_cols=193  Identities=17%  Similarity=0.202  Sum_probs=146.4

Q ss_pred             hHHHHHHHhcCCCCCccchhhhhhhh----HHhhc-ccccCHHHHHHHHhccCCCCCCCCceecCCHHHHhcC---CCCe
Q psy13345          3 DKLMKSFEGARNNPFHFKHVKLCHSL----AELAK-IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKV---PSPK   74 (276)
Q Consensus         3 ~~L~~l~~~~k~~~i~~~Pi~~s~~t----~~~ak-~ewms~~i~~~~~~~~~nPF~f~~l~~v~s~eel~~~---~~P~   74 (276)
                      |+|..+.+.++.+.++++|||+++++    ..|.+ ++||++.+++.+..++.+||.+++++.+++.++..++   ++|+
T Consensus       426 ell~~l~~~~~~~~~~~~~V~~dg~a~~~~~~~~~~~~~l~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~  505 (640)
T 2xr1_A          426 EVMIVLEESIRKGLIPEVPVYLDGMIWEATAIHATHPEYLNNDLRKLIFQKGQNPFLSECFKPVDSHEARQKIIQNPQPC  505 (640)
T ss_dssp             HHHHHHHHHHHHTSSCCCCEEEESSHHHHHHHHHHCGGGSCHHHHHHC------CTTCTTEEEEC-CHHHHHC----CCC
T ss_pred             HHHHHHHHHHHhCCCCCCcEEEEhHHHHHHHHHHHhHhhhcHHHHHHHHhcccCcccCCceEEeCCHHHHHHHhcCCCCe
Confidence            56666666666667778898887753    34555 9999999998876567899999999999876554332   6899


Q ss_pred             EEEEeCCCCCcchHHHHHHHhCCCCCCeEEEecCCCCCChhHHHHhccCCceEEEe--ece--EEeeeh--hhhhhhhhh
Q psy13345         75 VVLVSTPDMECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQ--VKK--RIRLEG--EELEEYQKK  148 (276)
Q Consensus        75 VIiassgml~~G~s~~~l~~~~~d~~N~Iiltgy~~~gTlgr~L~~~~~~~~i~i~--~~~--~~~l~~--~el~~fsaH  148 (276)
                      |||||+|||+||+++++|++|++|++|+|||||||++||+||+|.++.  ..|.+-  .|.  .+++++  ..+.+||+|
T Consensus       506 vIiat~gm~~gg~~~~~l~~~~~~~~~~vi~sg~~~~gt~gr~l~~g~--~~i~~~~~~G~~~~v~v~~~v~~i~g~SgH  583 (640)
T 2xr1_A          506 VILATSGMMNGGPVMEYFKAFAEDPRNTLVFVGYQADGTIGRRIQKGW--KEIPMTGKNGSTEMLKMNMEVQVVDGFSGH  583 (640)
T ss_dssp             EEEESCTTSSSSHHHHHHHHHSSCTTCEEEECSCCCTTCHHHHHHTTC--CC-----------CCCCCSEEEECCCCSCS
T ss_pred             EEEeCCCccCCChHHHHHHHhhCCCCCEEEEecCCCCCCHHHHHhhcc--ceeeeeccCCCceEEeeeEEEEEEcccccc
Confidence            999999999999999999999999999999999999999999998873  335541  255  566666  344459999


Q ss_pred             cCchhhHHHHhhcC--CCcceEEeCh-hhHHHHHHHHHHc-CCCcccccceeeecCceec
Q psy13345        149 KDKEAKDKQEKEKI--PPHDTSFINE-LQLSDFKQTLQRN-GIDCEFMDGVLICCRGTVA  204 (276)
Q Consensus       149 ad~~~l~~~i~~~~--p~~v~lvHGE-~~~~~Lk~~L~~~-G~~aef~gg~l~~p~~~~~  204 (276)
                      ||+++|++|++.++  |+++++|||| ..+..|++.+.++ |+       .+++|.|.+.
T Consensus       584 ad~~eL~~~i~~~~~~P~~vi~vHGe~~~~~~~a~~~~~~~g~-------~~~~p~~g~~  636 (640)
T 2xr1_A          584 SDRRQLMEYVKRMQPRPERVFTEHGDEKACVDLASSVYKKLKI-------ETRALTNLET  636 (640)
T ss_dssp             CCHHHHHHHHHTCBSCCSEEEEESSCHHHHHHHHHHHHHHHCC-------EEEECCTTCE
T ss_pred             CCHHHHHHHHHHhccCCCEEEEECCCHHHHHHHHHHHHHHcCC-------eEEeCCCCCE
Confidence            99999999999987  9999999999 7889999999654 54       4556666543

>3af5_A Putative uncharacterized protein PH1404; archaeal CPSF, beta-CAsp family, KH domain, ribonuclease, ME beta-lactamase superfamily, archaea; 2.60A {Pyrococcus horikoshii} PDB: 3af6_A*

Probab=99.96  E-value=7.5e-29  Score=249.78  Aligned_cols=193  Identities=19%  Similarity=0.218  Sum_probs=156.0

Q ss_pred             hHHHHHHHhcCCCCCccchhhhhhh----hHHhhc-ccccCHHHHHHHHhccCCCCCCCCceecCCHHH---HhcCCCCe
Q psy13345          3 DKLMKSFEGARNNPFHFKHVKLCHS----LAELAK-IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAE---LAKVPSPK   74 (276)
Q Consensus         3 ~~L~~l~~~~k~~~i~~~Pi~~s~~----t~~~ak-~ewms~~i~~~~~~~~~nPF~f~~l~~v~s~ee---l~~~~~P~   74 (276)
                      |+|..+.+.++.+.++ +|||++++    +..|.+ ++||++.+++.+..++.+||.+++++.+++.++   ++..++|+
T Consensus       438 ell~~l~~~~~~~~l~-~~I~~dg~a~~~~~~~~~~~~~l~~~~~~~~~~~~~~~f~~~~~~~v~~~~~~~~~~~~~~~~  516 (651)
T 3af5_A          438 EVMMVLEEYARIGGIE-VPIYLDGMIWEATAIHTAYPEYLSRRLREQIFKEGYNPFLSEIFHPVANSRERQDIIDSNEPA  516 (651)
T ss_dssp             HHHHHHHHHHTTTCCC-SCEEEESSHHHHHHHHHTCGGGSCHHHHHHTTTSSCCSTTCTTEEECCSHHHHHHHHHSCSCE
T ss_pred             HHHHHHHHhhhhcCCC-CcEEEechHHHHHHHHHHhHHhcCHHHHHHHHhccCCCccCCceEEcCCHHHHHHHhcCCCCE
Confidence            5666666666666666 88888765    334556 999999999887667789999999999997655   33337899


Q ss_pred             EEEEeCCCCCcchHHHHHHHhCCCCCCeEEEecCCCCCChhHHHHhccCCceEEEe--ece--EEeeeh--hhhhhhhhh
Q psy13345         75 VVLVSTPDMECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQ--VKK--RIRLEG--EELEEYQKK  148 (276)
Q Consensus        75 VIiassgml~~G~s~~~l~~~~~d~~N~Iiltgy~~~gTlgr~L~~~~~~~~i~i~--~~~--~~~l~~--~el~~fsaH  148 (276)
                      |||||+|||+||+++++|++|++|++|+|||||||++||+||+|.++  ...+.+-  .|.  .+++++  ..+.+||+|
T Consensus       517 vIia~~gm~~gg~~~~~l~~~~~~~~~~vi~sg~~~~gt~gr~l~~g--~~~i~~~~~~G~~~~v~v~~~v~~i~g~SgH  594 (651)
T 3af5_A          517 IIIASSGMLVGGPSVEYFKQLAPDPKNSIIFVSYQAEGTLGRQVQSG--IREIPMVGEEGRTEVIKVNMEVHTIDGFSGH  594 (651)
T ss_dssp             EEEESCTTSSSSHHHHHHHHHTTCTTCEEEECSCCCTTCHHHHHHHT--CSEEEEECGGGCEEEEECCSEEEECGGGCSS
T ss_pred             EEEECCCCCCCCHHHHHHHHHhCCCCCEEEEeCCCCCCcHHHHHHhc--cceeeehhcCCCceEEEeEEEEEEcCcccCc
Confidence            99999999999999999999999999999999999999999999987  3346652  355  777776  345559999


Q ss_pred             cCchhhHHHHhhcC--CCcceEEeCh-hhHHHHHHHHHHc-CCCcccccceeeecCceecc
Q psy13345        149 KDKEAKDKQEKEKI--PPHDTSFINE-LQLSDFKQTLQRN-GIDCEFMDGVLICCRGTVAV  205 (276)
Q Consensus       149 ad~~~l~~~i~~~~--p~~v~lvHGE-~~~~~Lk~~L~~~-G~~aef~gg~l~~p~~~~~i  205 (276)
                      ||+++|++|++.++  |+++++|||| ..+..|++.+.++ |+       .+++|.+.+.+
T Consensus       595 ad~~eL~~~i~~~~~~P~~vi~vHGe~~~~~~la~~~~~~~g~-------~~~~p~~g~~~  648 (651)
T 3af5_A          595 ADRRELMNYVAKVRPRPERIITVHGEPQKCLDLATSIHRKFGI-------STRAPNNLDTI  648 (651)
T ss_dssp             CCHHHHHHHHHHCBSCCSEEEEESSCHHHHHHHHHHHHHHHCC-------EEECCCTTCEE
T ss_pred             CCHHHHHHHHHHhhcCCCEEEEEcCCHHHHHHHHHHHHHhcCC-------eEEECCCCCEE
Confidence            99999999999988  9999999999 7789999998654 54       35566665443

>2ycb_A Beta-CAsp RNAse, cleavage and polyadenylation specificity factor; hydrolase, KH, metallo-beta-lactamase; 3.10A {Methanothermobacter thermautotrophicusorganism_taxid}

Probab=99.95  E-value=2.6e-28  Score=245.22  Aligned_cols=194  Identities=17%  Similarity=0.199  Sum_probs=155.7

Q ss_pred             hHHHHHHHhcCCCCCccchhhhhhhh----HHhhc-ccccCHHHHHHHHhccCCCCCCCCceecCCHHHHhcC--CCCeE
Q psy13345          3 DKLMKSFEGARNNPFHFKHVKLCHSL----AELAK-IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKV--PSPKV   75 (276)
Q Consensus         3 ~~L~~l~~~~k~~~i~~~Pi~~s~~t----~~~ak-~ewms~~i~~~~~~~~~nPF~f~~l~~v~s~eel~~~--~~P~V   75 (276)
                      |+|..+.+.++.+.++++|||+++++    ..|.+ ++||+..+++.+..++.+||.+++++.+.+.++..++  ++|+|
T Consensus       423 ell~~l~~~~~~~~~~~~~V~~dg~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~l~~~~~~v  502 (636)
T 2ycb_A          423 ELMIVLEEYIRTGIIDEVPVYIDGMIWEANAIHTARPEYLSKDLRDQIFHMGHNPFISDIFHKVNGMDERREIVEGEPSI  502 (636)
T ss_dssp             HHHHHHHHHHHTTSSCCCCEEEEHHHHHHHHHHHHSGGGSCHHHHHHHHTTCCCGGGCTTEEEECCHHHHHHHHHSSSCE
T ss_pred             HHHHHHHHHHHhCCCCCCeEEEehHHHHHHHHHHHhHHhhCHHHHHHHHhccCCcccCCceEEeCCHHHHHHhccCCCEE
Confidence            55555555566667778898887763    33555 9999999998887677899999999999876554332  68999


Q ss_pred             EEEeCCCCCcchHHHHHHHhCCCCCCeEEEecCCCCCChhHHHHhccCCceEEEe--ece--EEeeeh--hhhhhhhhhc
Q psy13345         76 VLVSTPDMECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQ--VKK--RIRLEG--EELEEYQKKK  149 (276)
Q Consensus        76 Iiassgml~~G~s~~~l~~~~~d~~N~Iiltgy~~~gTlgr~L~~~~~~~~i~i~--~~~--~~~l~~--~el~~fsaHa  149 (276)
                      ||||+|||+||+++++|++|++|++|+|||||||++||+||+|.++  ...+.+-  .|.  .+++++  ..+.+||+||
T Consensus       503 Iiat~gm~~gg~~~~~l~~~~~~~~~~vi~sg~~~~Gt~gr~l~~g--~~~i~~~~~~G~~~~v~v~~~v~~i~~~SgHa  580 (636)
T 2ycb_A          503 ILSTSGMLTGGNSLEYFKWLCEDPDNSLVFVGYQAEGSLGRRIQKG--WKEIPLKDEDDKMRVYNVRMNIKTIEGFSGHS  580 (636)
T ss_dssp             EEESCSSSSSHHHHHHHHHHTTCTTSEEEECSCCCSSSHHHHHHTT--CCEEEEECSSSCEEEEECCSEEEECCSCCSSC
T ss_pred             EEecCCccCCChHHHHHHHHhCCCCCEEEEecCCCCCCHHHHhhcC--CceeeeeccCCceeEEEeEEEEEEECCcceeC
Confidence            9999999999999999999999999999999999999999999876  3446552  355  777776  3344599999


Q ss_pred             CchhhHHHHhhcC--CCcceEEeCh-hhHHHHHHHHHHc-CCCcccccceeeecCceecc
Q psy13345        150 DKEAKDKQEKEKI--PPHDTSFINE-LQLSDFKQTLQRN-GIDCEFMDGVLICCRGTVAV  205 (276)
Q Consensus       150 d~~~l~~~i~~~~--p~~v~lvHGE-~~~~~Lk~~L~~~-G~~aef~gg~l~~p~~~~~i  205 (276)
                      |+++|++|++.++  |+++++|||| ..+..|++.+.++ |+       .+++|.|.+.+
T Consensus       581 d~~eL~~~i~~~~~~Pk~vi~vHGe~~~~~~~a~~~~~~~g~-------~~~~p~~g~~~  633 (636)
T 2ycb_A          581 DRRQLMEYVKRISPKPEKILLCHGDNYKTLDLASSIYRTYRI-------ETKTPLNLETV  633 (636)
T ss_dssp             CHHHHHHHHHSCSSCCSEEEEESSCHHHHHHHHHHHHHHHCC-------EEECCCTTCEE
T ss_pred             CHHHHHHHHHHhccCCCEEEEECCCHHHHHHHHHHHHHHcCC-------cEEeCCCCCEE
Confidence            9999999999988  9999999999 7788999999654 54       35566664443

>2i7x_A Protein CFT2; polyadenylation, metallo-B-lactamase, PRE-mRNA processing, artemis, V(D)J recombination, double-strand break repair; 2.50A {Saccharomyces cerevisiae} SCOP: d.157.1.10

Probab=99.79  E-value=1.9e-19  Score=183.15  Aligned_cols=138  Identities=23%  Similarity=0.373  Sum_probs=104.5

Q ss_pred             HHHH-HhcCCCCCccchhhhhh----hhHHhhc--ccccCHHHHHHHHhccC--CCCC-CCCceecCCHHHHhcCCCCeE
Q psy13345          6 MKSF-EGARNNPFHFKHVKLCH----SLAELAK--IEWMSDKLMKSFEGARN--NPFH-FKHVKLCHSLAELAKVPSPKV   75 (276)
Q Consensus         6 ~~l~-~~~k~~~i~~~Pi~~s~----~t~~~ak--~ewms~~i~~~~~~~~~--nPF~-f~~l~~v~s~eel~~~~~P~V   75 (276)
                      ..+| ++.+.+.+++.|||+.+    +++.+++  ++||++++.+.+.. +.  +||. |+++++ .+.++|+++++|||
T Consensus       262 ~~~~~~~~~~~~~~~~pI~l~g~~a~~~~~i~~~~~e~l~~~~~~~~~~-~~~~~pf~~~~~l~~-~~~~~l~~~~~p~V  339 (717)
T 2i7x_A          262 HELLFESTKINAHTQVPVLILSYARGRTLTYAKSMLEWLSPSLLKTWEN-RNNTSPFEIGSRIKI-IAPNELSKYPGSKI  339 (717)
T ss_dssp             HHHHTTC-------CCCEEEECTTTTHHHHHHHTCGGGSCHHHHHHHHS-SSSCCTTCCTTTEEE-CCGGGGGGCCSCEE
T ss_pred             HHhhhhhhccccCCCceEEEECHHHHHHHHHHHHHHHHhChHHHHHHhc-ccccCCccccccCcc-CCHHHHhhCCCCEE
Confidence            3444 33345566667766654    4677777  79999999888863 33  5999 899998 77888999888998


Q ss_pred             EEEeCCCCCcchHHHHHHHhCCCCCCeEEEecCCC-CCChhHHHHhc------------------cCCceEEEeeceEEe
Q psy13345         76 VLVSTPDMECGFSRDLFFQWCSSPENSIIITNRTS-PGTLARDLIEL------------------GGNRTLTLQVKKRIR  136 (276)
Q Consensus        76 Iiassgml~~G~s~~~l~~~~~d~~N~Iiltgy~~-~gTlgr~L~~~------------------~~~~~i~i~~~~~~~  136 (276)
                      |+||.   +||+++++|++||+||+|+|||||||+ +||+||+|+++                  +.++.++++..+++|
T Consensus       340 I~aSG---~gG~~~~~L~~~a~~~~n~VIf~g~~~p~gTlgr~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  416 (717)
T 2i7x_A          340 CFVSE---VGALINEVIIKVGNSEKTTLILTKPSFECASSLDKILEIVEQDERNWKTFPEDGKSFLCDNYISIDTIKEEP  416 (717)
T ss_dssp             EEEES---CHHHHHHHHHHHSSCTTEEEEECSSCCTTCHHHHHHHHHHHTCC--------CCCCEECCEEEEEEEEEEEE
T ss_pred             EEECC---CCHHHHHHHHHHcCCCcCEEEEEcCCCCCCChHHHHHhhhhhhcccccccccccccccCCceEEEEEeeecc
Confidence            88765   899999999999999999999999999 69999999985                  223689999999999


Q ss_pred             eehhhhhhhhhh
Q psy13345        137 LEGEELEEYQKK  148 (276)
Q Consensus       137 l~~~el~~fsaH  148 (276)
                      |.++||..|.+.
T Consensus       417 L~g~EL~~y~~~  428 (717)
T 2i7x_A          417 LSKEETEAFKVQ  428 (717)
T ss_dssp             SCSCCC------
T ss_pred             CCHHHHHHHHHH
Confidence            999999999764

>3bk2_A RNAse J, metal dependent hydrolase; endoribonuclease, exoribonuclease, metallo-beta-lactamase; HET: U5P; 2.10A {Thermus thermophilus} PDB: 3bk1_A* 3t3o_A* 3t3n_A*

Probab=99.28  E-value=4.6e-12  Score=125.47  Aligned_cols=118  Identities=13%  Similarity=0.105  Sum_probs=81.0

Q ss_pred             CHHHHhcCCCCeEEEEeCCCCCcchHHHHHHHhCC--------CCCCeEEEecCCCCCChhHH--HHhccCCceEEEeec
Q psy13345         63 SLAELAKVPSPKVVLVSTPDMECGFSRDLFFQWCS--------SPENSIIITNRTSPGTLARD--LIELGGNRTLTLQVK  132 (276)
Q Consensus        63 s~eel~~~~~P~VIiassgml~~G~s~~~l~~~~~--------d~~N~Iiltgy~~~gTlgr~--L~~~~~~~~i~i~~~  132 (276)
                      +.+++++.+.+++||.++|+. |++ ...+.+++.        +++|+|||+|||.+||.++.  +.+.-....+++   
T Consensus       296 ~~~~~~~~~~~~~vi~~tg~~-ge~-~~~l~ria~~~h~~~~~~~~~~vi~s~~~~~G~~~~~~~~~~~l~~~g~~v---  370 (562)
T 3bk2_A          296 TLEEVKDLPDHQVLILATGSQ-GQP-MSVLHRLAFEGHAKMAIKPGDTVILSSSPIPGNEEAVNRVINRLYALGAYV---  370 (562)
T ss_dssp             CTGGGTTSCGGGEEEEECCTT-SCS-HHHHHHHHTTCCSSCCCCTTCEEEECSCCCTTCHHHHHHHHHHHHHTTCEE---
T ss_pred             CHHHHhcCCCCCEEEEEcCCC-chh-HHHHHhhhhcccccccCCCCCEEEEECCCCCCCeEehhhhcCceeeCCCEE---
Confidence            345777776655444444543 443 335777764        89999999999999997753  222100000111   


Q ss_pred             eEEeeehhhhhhhhhhcCchhhHHHHhhcCCCcceEEeCh-hhHHHHHHHHHHcCCC
Q psy13345        133 KRIRLEGEELEEYQKKKDKEAKDKQEKEKIPPHDTSFINE-LQLSDFKQTLQRNGID  188 (276)
Q Consensus       133 ~~~~l~~~el~~fsaHad~~~l~~~i~~~~p~~v~lvHGE-~~~~~Lk~~L~~~G~~  188 (276)
                        +.. ..+-..||+|||+++|+.|++.++|++++.|||| ..+..+++.+.+.|++
T Consensus       371 --~~~-~~~~i~~SgHa~~~eL~~~i~~~~Pk~vipvHGe~~~~~~~~~~~~~~g~~  424 (562)
T 3bk2_A          371 --LYP-PTYKVHASGHASQEELKLILNLTTPRFFLPWHGEVRHQMNFKWLAESMSRP  424 (562)
T ss_dssp             --ECT-TTSSSCCCSSCCHHHHHHHHHHHCCSEEEEESBCHHHHHHHHHHHHTSSSC
T ss_pred             --EEc-cCCceEEeCCCCHHHHHHHHHhcCCCEEEEEcCCHHHHHHHHHHHHHcCCC
Confidence              111 1233579999999999999999999999999999 7788899877777874

>3zq4_A Ribonuclease J 1, RNAse J1; hydrolase, RNA maturation; 3.00A {Bacillus subtilis}

Probab=99.07  E-value=1.7e-10  Score=114.19  Aligned_cols=126  Identities=10%  Similarity=0.070  Sum_probs=92.1

Q ss_pred             CCCCCceecCCHHHHhcCCC-CeEEEEeCCCCCcchHHHHHHHhCCCCCC--------eEEEecCCCCCChhH--HHHhc
Q psy13345         53 FHFKHVKLCHSLAELAKVPS-PKVVLVSTPDMECGFSRDLFFQWCSSPEN--------SIIITNRTSPGTLAR--DLIEL  121 (276)
Q Consensus        53 F~f~~l~~v~s~eel~~~~~-P~VIiassgml~~G~s~~~l~~~~~d~~N--------~Iiltgy~~~gTlgr--~L~~~  121 (276)
                      +.++...+++ .+++++++. +.||++|++   .|..+.+|.+++.++.|        +|||+|||.+|+.++  ++.+.
T Consensus       272 l~~p~~~~v~-~~~~~~~~~~~~vii~tgs---qGe~~~~L~r~a~~~~~~~~~~~~d~vi~s~~~ipGne~~~~~~~~~  347 (555)
T 3zq4_A          272 INCPKNTFIE-HNEINRMPANKVTILCTGS---QGEPMAALSRIANGTHRQISINPGDTVVFSSSPIPGNTISVSRTINQ  347 (555)
T ss_dssp             CCCCGGGEEC-GGGTTTSCGGGEEEEECCT---TCCTTSHHHHHHSSCCSSCCCCTTCEEEECSCCCTTCHHHHHHHHHH
T ss_pred             ccCCcccEeC-HHHHhhCCCCCEEEEeCCC---CchHHHHHHHHhcCCCCccccCCCCEEEEECCCCCCcHHHHHHHHHH
Confidence            3444444554 667877654 566677766   67779999999999888        999999999999743  23322


Q ss_pred             cCCceEEEeeceEEeeehhhhhhhhhhcCchhhHHHHhhcCCCcceEEeCh-hhHHHHHHHHHHcCCC
Q psy13345        122 GGNRTLTLQVKKRIRLEGEELEEYQKKKDKEAKDKQEKEKIPPHDTSFINE-LQLSDFKQTLQRNGID  188 (276)
Q Consensus       122 ~~~~~i~i~~~~~~~l~~~el~~fsaHad~~~l~~~i~~~~p~~v~lvHGE-~~~~~Lk~~L~~~G~~  188 (276)
                      -      .+.+-++.-...+...||+||++++|+.|++.++|+.++.|||| ..+..+++...+.|++
T Consensus       348 l------~~~g~~v~~~~~~~~h~SgHa~~~eL~~~~~~~~Pk~~ipvHGe~~~~~~~~~~a~~~G~~  409 (555)
T 3zq4_A          348 L------YRAGAEVIHGPLNDIHTSGHGGQEEQKLMLRLIKPKFFMPIHGEYRMQKMHVKLATDCGIP  409 (555)
T ss_dssp             H------HHTTCEEECSSSSCCCCCSSCCHHHHHHHHHHSCEEEEEEESBCHHHHHHHHHHHHHTTCC
T ss_pred             H------HHCCCEEEecCCcceEEeCCCCHHHHHHHHHHhCCCEEEEcCCCHHHHHHHHHHHHHcCCC
Confidence            0      00122222122456789999999999999999999999999999 7788888877777885

>3iek_A Ribonuclease TTHA0252; metallo beta lactamase fold, endonuclease, hydrolase, metal- nuclease, RNA-binding, rRNA processing; HET: FLC; 2.05A {Thermus thermophilus} SCOP: d.157.1.10 PDB: 2dkf_A* 3iel_A* 3iem_A* 2zdf_A* 3idz_A* 2zdd_A* 3ie0_A* 2zde_A* 3ie1_A* 2zdw_A* 3a4y_A* 2yvd_A* 3ie2_A*

Probab=98.79  E-value=1.4e-09  Score=104.14  Aligned_cols=50  Identities=16%  Similarity=0.161  Sum_probs=47.2

Q ss_pred             eccceeEEeeCCcccccchhhhhhhhcCCCCCeEEEeccCCCCCccccee
Q psy13345        203 VAVRRVVLVSTPDMECGFSRDLFFQWCSSPENSIIITNRNRADDSDSNVI  252 (276)
Q Consensus       203 ~~i~~v~~~~~~~~~~g~sr~lf~~~~~~~~n~~~~~~~~~~~~~~~~~~  252 (276)
                      ..-||||+|+++|+++|.++..|.+||.||||.||||||.++||+||+++
T Consensus       303 ~~~p~viia~~gm~~~G~~~~~l~~~~~~~~n~ii~~gyq~~gt~g~~l~  352 (431)
T 3iek_A          303 APGPMVVLAGSGMLAGGRILHHLKHGLSDPRNALVFVGYQPQGGLGAEII  352 (431)
T ss_dssp             SCSSEEEEESCTTSSSSHHHHHHHHHTTCTTCEEEECSCCCTTSHHHHHH
T ss_pred             CCCCeEEEecCCCCCCChHHHHHHHhcCCCCCeEEEECCCCCCChHHHhh
Confidence            35699999999999999999999999999999999999999999998765

>2i7t_A Cleavage and polyadenylation specificity factor 73 kDa subunit; metallo-B-lactamase, PRE-mRNA processing, artemis, V(D)J recombination; 2.10A {Homo sapiens} SCOP: d.157.1.10 PDB: 2i7v_A

Probab=98.39  E-value=8.4e-08  Score=92.07  Aligned_cols=50  Identities=28%  Similarity=0.492  Sum_probs=46.7

Q ss_pred             eccceeEEeeCCcccccchhhhhhhhcCCCCCeEEEeccCCCCCccccee
Q psy13345        203 VAVRRVVLVSTPDMECGFSRDLFFQWCSSPENSIIITNRNRADDSDSNVI  252 (276)
Q Consensus       203 ~~i~~v~~~~~~~~~~g~sr~lf~~~~~~~~n~~~~~~~~~~~~~~~~~~  252 (276)
                      ..-||||+|+++|+++|.+|.+|.+||.||+|.|+||||..+||++|+++
T Consensus       319 ~~~~~viia~~gm~~~g~~~~~l~~~~~~~~~~ii~~gy~~~gt~g~~l~  368 (459)
T 2i7t_A          319 DIGPSVVMASPGMMQSGLSRELFESWCTDKRNGVIIAGYCVEGTLAKHIM  368 (459)
T ss_dssp             CCSSEEEEESCTTCSSHHHHHHHHHHTTCTTCEEEECSCCCTTSHHHHHT
T ss_pred             CCCCeEEEEcCcccCCCHHHHHHHHHcCCCCCeEEEEecCCCCChHHHHh
Confidence            45799999999999999999999999999999999999999999997654

>2az4_A Hypothetical protein EF2904; structural genomics, PSI, protein STR initiative, midwest center for structural genomics, MCSG, U function; 2.00A {Enterococcus faecalis} SCOP: d.157.1.10

Probab=98.14  E-value=1.3e-06  Score=82.66  Aligned_cols=89  Identities=13%  Similarity=0.015  Sum_probs=63.8

Q ss_pred             cCCHHHHhcCCCCeEEEEeCCCCCcchHHHHHHHhCCCCCCeEEEecCCCCCCh---hHHHHhccCCceEEEeeceEEee
Q psy13345         61 CHSLAELAKVPSPKVVLVSTPDMECGFSRDLFFQWCSSPENSIIITNRTSPGTL---ARDLIELGGNRTLTLQVKKRIRL  137 (276)
Q Consensus        61 v~s~eel~~~~~P~VIiassgml~~G~s~~~l~~~~~d~~N~Iiltgy~~~gTl---gr~L~~~~~~~~i~i~~~~~~~l  137 (276)
                      +.+.+++++.++++||+    |  +|.  ++  ++  .+.++|||++++.+|+.   ++++.+.-.....++     .  
T Consensus       315 ~~~~~~~~~~~~~~ii~----~--~~~--~~--~l--~~~~~vi~s~~~~~g~~~~~~~~~~~~~~~~~~~v-----~--  375 (429)
T 2az4_A          315 EIPYDTLLKDKTDYLWQ----V--VNQ--FD--NL--QEGSLYIHSDAQPLGDFDPQYRVFLDLLAKKDITF-----V--  375 (429)
T ss_dssp             BCCHHHHHHCSSSEEEE----C--CSC--GG--GS--CTTCEEEEESCSSCSTTSHHHHHHHHHHHHTTCEE-----E--
T ss_pred             eecHHHHhhCCCcEEEE----e--cCc--HH--hh--CCCCEEEEeCCCCCcccchHHHHHHHHHHhCCCEE-----E--
Confidence            44567888888887766    3  444  22  33  34599999999999984   666665310001122     1  


Q ss_pred             ehhhhhhhhhhcCchhhHHHHhhcCCCcceEEeCh
Q psy13345        138 EGEELEEYQKKKDKEAKDKQEKEKIPPHDTSFINE  172 (276)
Q Consensus       138 ~~~el~~fsaHad~~~l~~~i~~~~p~~v~lvHGE  172 (276)
                         .+ .||+|||+++|+.|++.++|++++.||||
T Consensus       376 ---~i-~~SgHa~~~eL~~~~~~~~Pk~~ipvHGe  406 (429)
T 2az4_A          376 ---RL-ACSGHAIPEDLDKIIALIEPQVLVPIHTL  406 (429)
T ss_dssp             ---EC-CCCSSCCHHHHHHHHHHHCCSEEEEESCS
T ss_pred             ---EE-eecCCCCHHHHHHHHHhhCCCEEEECCCC
Confidence               22 49999999999999999999999999999

>2xr1_A Cleavage and polyadenylation specificity factor 1 subunit; hydrolase, metallo-beta-lactamase, beta-CAsp, RNA processing; 2.59A {Methanosarcina mazei}

Probab=97.81  E-value=7.2e-06  Score=82.29  Aligned_cols=48  Identities=15%  Similarity=0.274  Sum_probs=44.8

Q ss_pred             ccceeEEeeCCcccccchhhhhhhhcCCCCCeEEEeccCCCCCcccce
Q psy13345        204 AVRRVVLVSTPDMECGFSRDLFFQWCSSPENSIIITNRNRADDSDSNV  251 (276)
Q Consensus       204 ~i~~v~~~~~~~~~~g~sr~lf~~~~~~~~n~~~~~~~~~~~~~~~~~  251 (276)
                      .-|+||+|+++|+++|.++..|.+||.||+|.|+||||..+||++|++
T Consensus       502 ~~~~vIiat~gm~~gg~~~~~l~~~~~~~~~~vi~sg~~~~gt~gr~l  549 (640)
T 2xr1_A          502 PQPCVILATSGMMNGGPVMEYFKAFAEDPRNTLVFVGYQADGTIGRRI  549 (640)
T ss_dssp             -CCCEEEESCTTSSSSHHHHHHHHHSSCTTCEEEECSCCCTTCHHHHH
T ss_pred             CCCeEEEeCCCccCCChHHHHHHHhhCCCCCEEEEecCCCCCCHHHHH
Confidence            568999999999999999999999999999999999999999999863

>3af5_A Putative uncharacterized protein PH1404; archaeal CPSF, beta-CAsp family, KH domain, ribonuclease, ME beta-lactamase superfamily, archaea; 2.60A {Pyrococcus horikoshii} PDB: 3af6_A*

Probab=97.80  E-value=7.9e-06  Score=82.09  Aligned_cols=48  Identities=23%  Similarity=0.288  Sum_probs=45.1

Q ss_pred             ccceeEEeeCCcccccchhhhhhhhcCCCCCeEEEeccCCCCCcccce
Q psy13345        204 AVRRVVLVSTPDMECGFSRDLFFQWCSSPENSIIITNRNRADDSDSNV  251 (276)
Q Consensus       204 ~i~~v~~~~~~~~~~g~sr~lf~~~~~~~~n~~~~~~~~~~~~~~~~~  251 (276)
                      .-|+||+|+++|+++|.++..|.+||.||+|.|+||||..+||+++++
T Consensus       513 ~~~~vIia~~gm~~gg~~~~~l~~~~~~~~~~vi~sg~~~~gt~gr~l  560 (651)
T 3af5_A          513 NEPAIIIASSGMLVGGPSVEYFKQLAPDPKNSIIFVSYQAEGTLGRQV  560 (651)
T ss_dssp             CSCEEEEESCTTSSSSHHHHHHHHHTTCTTCEEEECSCCCTTCHHHHH
T ss_pred             CCCEEEEECCCCCCCCHHHHHHHHHhCCCCCEEEEeCCCCCCcHHHHH
Confidence            458999999999999999999999999999999999999999988763

>2ycb_A Beta-CAsp RNAse, cleavage and polyadenylation specificity factor; hydrolase, KH, metallo-beta-lactamase; 3.10A {Methanothermobacter thermautotrophicusorganism_taxid}

Probab=97.69  E-value=1.3e-05  Score=80.26  Aligned_cols=47  Identities=17%  Similarity=0.321  Sum_probs=44.5

Q ss_pred             ccceeEEeeCCcccccchhhhhhhhcCCCCCeEEEeccCCCCCcccc
Q psy13345        204 AVRRVVLVSTPDMECGFSRDLFFQWCSSPENSIIITNRNRADDSDSN  250 (276)
Q Consensus       204 ~i~~v~~~~~~~~~~g~sr~lf~~~~~~~~n~~~~~~~~~~~~~~~~  250 (276)
                      .-|+||+++++|+++|.++..|.+||.||+|.|+||||..+||++++
T Consensus       498 ~~~~vIiat~gm~~gg~~~~~l~~~~~~~~~~vi~sg~~~~Gt~gr~  544 (636)
T 2ycb_A          498 GEPSIILSTSGMLTGGNSLEYFKWLCEDPDNSLVFVGYQAEGSLGRR  544 (636)
T ss_dssp             SSSCEEEESCSSSSSHHHHHHHHHHTTCTTSEEEECSCCCSSSHHHH
T ss_pred             CCCEEEEecCCccCCChHHHHHHHHhCCCCCEEEEecCCCCCCHHHH
Confidence            45899999999999999999999999999999999999999998875

>2i7x_A Protein CFT2; polyadenylation, metallo-B-lactamase, PRE-mRNA processing, artemis, V(D)J recombination, double-strand break repair; 2.50A {Saccharomyces cerevisiae} SCOP: d.157.1.10

Probab=97.53  E-value=1.8e-05  Score=80.45  Aligned_cols=47  Identities=13%  Similarity=0.217  Sum_probs=42.0

Q ss_pred             ccceeEEeeCCcccccchhhhhhhhcCCCCCeEEEeccCC-CCCcccceee
Q psy13345        204 AVRRVVLVSTPDMECGFSRDLFFQWCSSPENSIIITNRNR-ADDSDSNVIV  253 (276)
Q Consensus       204 ~i~~v~~~~~~~~~~g~sr~lf~~~~~~~~n~~~~~~~~~-~~~~~~~~~~  253 (276)
                      +-|+||+||+   ++|.++.+|.+||.||+|.||||||.. +||++|+++.
T Consensus       335 ~~p~VI~aSG---~gG~~~~~L~~~a~~~~n~VIf~g~~~p~gTlgr~l~~  382 (717)
T 2i7x_A          335 PGSKICFVSE---VGALINEVIIKVGNSEKTTLILTKPSFECASSLDKILE  382 (717)
T ss_dssp             CSCEEEEEES---CHHHHHHHHHHHSSCTTEEEEECSSCCTTCHHHHHHHH
T ss_pred             CCCEEEEECC---CCHHHHHHHHHHcCCCcCEEEEEcCCCCCCChHHHHHh
Confidence            4578888876   889999999999999999999999999 7999987753

>3bk2_A RNAse J, metal dependent hydrolase; endoribonuclease, exoribonuclease, metallo-beta-lactamase; HET: U5P; 2.10A {Thermus thermophilus} PDB: 3bk1_A* 3t3o_A* 3t3n_A*

Probab=87.94  E-value=1  Score=44.06  Aligned_cols=41  Identities=10%  Similarity=0.321  Sum_probs=28.2

Q ss_pred             ceeEEeeCCcccccchhhhhhhhcC--------CCCCeEEEeccCCCCCccc
Q psy13345        206 RRVVLVSTPDMECGFSRDLFFQWCS--------SPENSIIITNRNRADDSDS  249 (276)
Q Consensus       206 ~~v~~~~~~~~~~g~sr~lf~~~~~--------~~~n~~~~~~~~~~~~~~~  249 (276)
                      +.|+++| ++.  |-....|-+||.        +|+|.|+|+|+..+||.++
T Consensus       307 ~~vi~~t-g~~--ge~~~~l~ria~~~h~~~~~~~~~~vi~s~~~~~G~~~~  355 (562)
T 3bk2_A          307 QVLILAT-GSQ--GQPMSVLHRLAFEGHAKMAIKPGDTVILSSSPIPGNEEA  355 (562)
T ss_dssp             GEEEEEC-CTT--SCSHHHHHHHHTTCCSSCCCCTTCEEEECSCCCTTCHHH
T ss_pred             CEEEEEc-CCC--chhHHHHHhhhhcccccccCCCCCEEEEECCCCCCCeEe
Confidence            3455555 442  444445666654        8999999999999999653

>3zdk_A 5' exonuclease apollo; hydrolase; HET: TLA; 2.16A {Homo sapiens}

Probab=85.38  E-value=0.23  Score=45.63  Aligned_cols=32  Identities=6%  Similarity=0.005  Sum_probs=29.4

Q ss_pred             hhhhhhhcCchhhHHHHhhcCCCcceEEe-Chh
Q psy13345        142 LEEYQKKKDKEAKDKQEKEKIPPHDTSFI-NEL  173 (276)
Q Consensus       142 l~~fsaHad~~~l~~~i~~~~p~~v~lvH-GE~  173 (276)
                      ..-||+|+++.||+.|++-++|+.++-+| ||.
T Consensus       271 ~vh~S~Ha~~~EL~~~~~~~~P~~~iPvh~ge~  303 (336)
T 3zdk_A          271 VIPYSDHSSYSELRAFVAALKPCQVVPIVSRRP  303 (336)
T ss_dssp             EECCCSSCBHHHHHHHHHHHCCSCEEESCTTSC
T ss_pred             eeEecCCCCHHHHHHHHHHhCCCEEEEEECCcC
Confidence            35589999999999999999999999999 993

>4b87_A DNA cross-LINK repair 1A protein; dclre1A, DCLRE, interstrand crosslink repair, hydrolase, NIT mustard, cancer, chemotherapy, PSO2 homolog,; HET: DNA; 2.16A {Homo sapiens}

Probab=81.21  E-value=0.81  Score=42.46  Aligned_cols=43  Identities=12%  Similarity=0.102  Sum_probs=32.7

Q ss_pred             hhhhhcCchhhHHHHhhcCCCcceEEeC--h-h---hH-HHHHHHHHHcC
Q psy13345        144 EYQKKKDKEAKDKQEKEKIPPHDTSFIN--E-L---QL-SDFKQTLQRNG  186 (276)
Q Consensus       144 ~fsaHad~~~l~~~i~~~~p~~v~lvHG--E-~---~~-~~Lk~~L~~~G  186 (276)
                      -||+|+...||.+|++.++|++++-.|+  . .   +| ..|+.+..+.|
T Consensus       317 pySeHss~~EL~~fv~~l~p~~iiptv~~~~~~~~~~m~~~~~~w~~~~~  366 (367)
T 4b87_A          317 PYSEHSSYLEMKRFVQWLKPQKIIPTVNVGTWKSRSTMEKYFREWKLEAG  366 (367)
T ss_dssp             CCCSSCCHHHHHHHHHHHCCSEEEECSSCSSHHHHHHHHHHHHHHHHHHC
T ss_pred             eccCCCCHHHHHHHHHhcCCCeEECeecCCCHHHHHHHHHHHHHHHhhcC
Confidence            4899999999999999999999998884  2 2   23 34555555543

>3zq4_A Ribonuclease J 1, RNAse J1; hydrolase, RNA maturation; 3.00A {Bacillus subtilis}

Probab=80.30  E-value=4.2  Score=39.70  Aligned_cols=98  Identities=6%  Similarity=0.073  Sum_probs=54.6

Q ss_pred             hhhhcCchh-hHHHHhhcCCCcceEEeChhhHHHHHHHHHHcCCCcccccceeeecCce--eccceeEEeeCCcccccch
Q psy13345        145 YQKKKDKEA-KDKQEKEKIPPHDTSFINELQLSDFKQTLQRNGIDCEFMDGVLICCRGT--VAVRRVVLVSTPDMECGFS  221 (276)
Q Consensus       145 fsaHad~~~-l~~~i~~~~p~~v~lvHGE~~~~~Lk~~L~~~G~~aef~gg~l~~p~~~--~~i~~v~~~~~~~~~~g~s  221 (276)
                      |+.|-++-| ++..+++.  ...+.++|. .+...-+...+.|+= .++...++.++..  .+-.++|+.++++  .|-.
T Consensus       231 fasnv~R~q~il~~a~~~--gr~v~v~gr-s~~~~~~~~~~~g~l-~~p~~~~v~~~~~~~~~~~~~vii~tgs--qGe~  304 (555)
T 3zq4_A          231 FASNIHRLQQVIEAAVQN--GRKVAVFGR-SMESAIEIGQTLGYI-NCPKNTFIEHNEINRMPANKVTILCTGS--QGEP  304 (555)
T ss_dssp             CTTCHHHHHHHHHHHHTT--TCEEEEESH-HHHHHHHHHHGGGSC-CCCGGGEECGGGTTTSCGGGEEEEECCT--TCCT
T ss_pred             ChhHHHHHHHHHHHHHHH--CCEEEEeCH-HHHHHHHHHHHcCCc-cCCcccEeCHHHHhhCCCCCEEEEeCCC--CchH
Confidence            665555543 44444332  234667885 233333333444421 1222333333322  2223455455555  5667


Q ss_pred             hhhhhhhcCCCCC--------eEEEeccCCCCCcc
Q psy13345        222 RDLFFQWCSSPEN--------SIIITNRNRADDSD  248 (276)
Q Consensus       222 r~lf~~~~~~~~n--------~~~~~~~~~~~~~~  248 (276)
                      +.-|-+||.+++|        +|+|+++..+|+..
T Consensus       305 ~~~L~r~a~~~~~~~~~~~~d~vi~s~~~ipGne~  339 (555)
T 3zq4_A          305 MAALSRIANGTHRQISINPGDTVVFSSSPIPGNTI  339 (555)
T ss_dssp             TSHHHHHHSSCCSSCCCCTTCEEEECSCCCTTCHH
T ss_pred             HHHHHHHhcCCCCccccCCCCEEEEECCCCCCcHH
Confidence            8889999999887        99999999999764

---

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	276
d2i7xa1	514	d.157.1.10 (A:1-422,A:626-717) Cleavage factor two	1e-14

>d2i7xa1 d.157.1.10 (A:1-422,A:626-717) Cleavage factor two protein 2, CFT2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 514

class: Alpha and beta proteins (a+b)
fold: Metallo-hydrolase/oxidoreductase
superfamily: Metallo-hydrolase/oxidoreductase
family: beta-CASP RNA-metabolising hydrolases
domain: Cleavage factor two protein 2, CFT2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 71.4 bits (174), Expect = 1e-14
 Identities = 23/128 (17%), Positives = 49/128 (38%), Gaps = 4/128 (3%)

Query: 34  IEWMSDKLMKSFEGARN-NPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDMECGFSRDLF 92
           +EW+S  L+K++E   N +PF         +  EL+K P  K+  VS          ++ 
Sbjct: 297 LEWLSPSLLKTWENRNNTSPFEIGSRIKIIAPNELSKYPGSKICFVSEVG---ALINEVI 353

Query: 93  FQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEELEEYQKKKDKE 152
            +  +S + ++I+T  +     + D I     +            +    + Y      +
Sbjct: 354 IKVGNSEKTTLILTKPSFECASSLDKILEIVEQDERNWKTFPEDGKSFLCDNYISIDTIK 413

Query: 153 AKDKQEKE 160
            +   ++E
Sbjct: 414 EEPLSKEE 421

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	276
d2i7xa1	514	Cleavage factor two protein 2, CFT2 {Baker's yeast	99.95
d2dkfa1	431	Putative RNA-degradation protein TTHA0252 {Thermus	99.92
d2i7ta1	451	Cleavage and polyadenylation specificity factor su	99.68
d2i7xa1	514	Cleavage factor two protein 2, CFT2 {Baker's yeast	97.41
d2dkfa1	431	Putative RNA-degradation protein TTHA0252 {Thermus	97.21
d2i7ta1	451	Cleavage and polyadenylation specificity factor su	91.29

>d2i7xa1 d.157.1.10 (A:1-422,A:626-717) Cleavage factor two protein 2, CFT2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Metallo-hydrolase/oxidoreductase
superfamily: Metallo-hydrolase/oxidoreductase
family: beta-CASP RNA-metabolising hydrolases
domain: Cleavage factor two protein 2, CFT2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.95  E-value=1.8e-28  Score=238.32  Aligned_cols=191  Identities=16%  Similarity=0.193  Sum_probs=149.9

Q ss_pred             HHHHHHHhcC-CCCCccchhhhhh----hhHHhhc--ccccCHHHHHHHHh-ccCCCCCCCCceecCCHHHHhcCCCCeE
Q psy13345          4 KLMKSFEGAR-NNPFHFKHVKLCH----SLAELAK--IEWMSDKLMKSFEG-ARNNPFHFKHVKLCHSLAELAKVPSPKV   75 (276)
Q Consensus         4 ~L~~l~~~~k-~~~i~~~Pi~~s~----~t~~~ak--~ewms~~i~~~~~~-~~~nPF~f~~l~~v~s~eel~~~~~P~V   75 (276)
                      +|..+|...+ .+.+.++|||+.+    +++.+++  +|||++++++.++. .+.+||+|++++.+.+.+++.+.++|||
T Consensus       260 ~l~~~~~~~~~~~~~~~~pI~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~pf~~~~~~~i~~~~~l~~~~~p~V  339 (514)
T d2i7xa1         260 QVHELLFESTKINAHTQVPVLILSYARGRTLTYAKSMLEWLSPSLLKTWENRNNTSPFEIGSRIKIIAPNELSKYPGSKI  339 (514)
T ss_dssp             HHHHHHTTC-------CCCEEEECTTTTHHHHHHHTCGGGSCHHHHHHHHSSSSCCTTCCTTTEEECCGGGGGGCCSCEE
T ss_pred             HHHHHHHHHHhhccCCCceEEEEChHHHHHHHHHHHhHhhcCHHHHHHHhhhcCCCchhccCceeccCHHHHHhccCCcE
Confidence            3445555443 3456778876544    4677777  99999999999874 3458999999999999999999999999


Q ss_pred             EEEeCCCCCcchHHHHHHHhCCCCCCeEEEe--cCCCCCChhHHHHhccC-----------------CceEEEe------
Q psy13345         76 VLVSTPDMECGFSRDLFFQWCSSPENSIIIT--NRTSPGTLARDLIELGG-----------------NRTLTLQ------  130 (276)
Q Consensus        76 Iiassgml~~G~s~~~l~~~~~d~~N~Iilt--gy~~~gTlgr~L~~~~~-----------------~~~i~i~------  130 (276)
                      ||||+||   |+++++|++|++||+|+|+||  |||.++|+|+.+.....                 ...+++.      
T Consensus       340 Iiat~~~---G~~~~~l~~~a~d~~n~Vi~t~~g~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~  416 (514)
T d2i7xa1         340 CFVSEVG---ALINEVIIKVGNSEKTTLILTKPSFECASSLDKILEIVEQDERNWKTFPEDGKSFLCDNYISIDTIKEEP  416 (514)
T ss_dssp             EEEESCH---HHHHHHHHHHSSCTTEEEEECSSCCTTCHHHHHHHHHHHTCC--------CCCCEECCEEEEEEEEEEEE
T ss_pred             EEEcCCC---chHHHHHHHHhcCCCCEEEEecCCCcccccHHHHHhhhhhhccccccccccccccccCcceeeccccccc
Confidence            9999987   899999999999999999999  99999999999874210                 1111111      


Q ss_pred             -------------------------eceEEeeeh-hhhhhhhhhcCchhhHHHHhhcCCCcceEEeCh-hhHHHHHHHHH
Q psy13345        131 -------------------------VKKRIRLEG-EELEEYQKKKDKEAKDKQEKEKIPPHDTSFINE-LQLSDFKQTLQ  183 (276)
Q Consensus       131 -------------------------~~~~~~l~~-~el~~fsaHad~~~l~~~i~~~~p~~v~lvHGE-~~~~~Lk~~L~  183 (276)
                                               .+..+++++ ++...||+|||+++|++|++.++|+++++|||| ..+++|++.|+
T Consensus       417 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~i~~SgHad~~el~~~~~~~~P~~vvlvHGe~~~~~~~a~~l~  496 (514)
T d2i7xa1         417 LSKEETNFDNLDYLKIDKTLSKRTISTVNVQLKCSVVILNLQSLVDQRSASIIWPSLKSRKIVLSAPKQIQNEEITAKLI  496 (514)
T ss_dssp             SCSCCCCCSCCGGGSCSSCCEEEEEEEEEEEECSEEEECCCCCSCCHHHHHHHGGGSCCSEEEECSCGGGSCHHHHHHHH
T ss_pred             ccccccCcccccccccccccceeecccceEEEEEEEEEEEeeecCCHHHHHHHHHhhCCCEEEEeCCCHHHHHHHHHHHH
Confidence                                     234567777 666789999999999999999999999999999 78999999999


Q ss_pred             HcCCCcccccceeeecCceec
Q psy13345        184 RNGIDCEFMDGVLICCRGTVA  204 (276)
Q Consensus       184 ~~G~~aef~gg~l~~p~~~~~  204 (276)
                      +.|+       .+++|++...
T Consensus       497 ~~g~-------~v~~p~~g~~  510 (514)
T d2i7xa1         497 KKNI-------EVVNMPLNKI  510 (514)
T ss_dssp             HTTC-------EEEECCSSCC
T ss_pred             HCCC-------eEEecCCCCE
Confidence            8864       4666665443

>d2dkfa1 d.157.1.10 (A:1-431) Putative RNA-degradation protein TTHA0252 {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Metallo-hydrolase/oxidoreductase
superfamily: Metallo-hydrolase/oxidoreductase
family: beta-CASP RNA-metabolising hydrolases
domain: Putative RNA-degradation protein TTHA0252
species: Thermus thermophilus [TaxId: 274]

Probab=99.92  E-value=4.3e-25  Score=207.78  Aligned_cols=189  Identities=16%  Similarity=0.229  Sum_probs=153.7

Q ss_pred             chHHHHHHHhcCCCCCccchhhhh----hhhHHhhc--ccccCHHHHHHHHhccCCCCCCCCceecCCHHH---HhcCCC
Q psy13345          2 SDKLMKSFEGARNNPFHFKHVKLC----HSLAELAK--IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAE---LAKVPS   72 (276)
Q Consensus         2 ~~~L~~l~~~~k~~~i~~~Pi~~s----~~t~~~ak--~ewms~~i~~~~~~~~~nPF~f~~l~~v~s~ee---l~~~~~   72 (276)
                      .|+|..+++..+..+  ..|||+.    ...+.+++  .+|++++++..+. ...+||.+.++....+...   +...++
T Consensus       229 qeil~~l~~~~~~~~--~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~  305 (431)
T d2dkfa1         229 QEILYVLYTHGHRLP--RAPIYLDSPMAGRVLSLYPRLVRYFSEEVQAHFL-QGKNPFRPAGLEVVEHTEASKALNRAPG  305 (431)
T ss_dssp             HHHHHHHHTTTTSSC--CCCEEEECHHHHHHHHHGGGGGGGSCHHHHHHHH-TTCCTTSCTTBCCCCSHHHHHHHHHCCS
T ss_pred             HHHHHHHHHhccccC--CccEEEechhHHHHHHHHHhhhhhcCHHHHhhhh-cccCccccccccccCCHHHHHHHHhCCC
Confidence            366777776665543  4565444    34566666  9999999999887 5779999999988877543   667789


Q ss_pred             CeEEEEeCCCCCcchHHHHHHHhCCCCCCeEEEecCCCCCChhHHHHhccCCceEEEeeceEEeeeh--hhhhhhhhhcC
Q psy13345         73 PKVVLVSTPDMECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEG--EELEEYQKKKD  150 (276)
Q Consensus        73 P~VIiassgml~~G~s~~~l~~~~~d~~N~Iiltgy~~~gTlgr~L~~~~~~~~i~i~~~~~~~l~~--~el~~fsaHad  150 (276)
                      |+|+++++||+.+|++..+++.++.|++|+|||||||++||+|++|+++  ...+++ .++.+++++  +.+..||+|||
T Consensus       306 ~~vii~~~~~~~~~~~~~~~~~~~~~~~n~vi~tg~~~~gt~g~~l~~~--~~~~~~-~~~~~~~~~~v~~~~~~SgHa~  382 (431)
T d2dkfa1         306 PMVVLAGSGMLAGGRILHHLKHGLSDPRNALVFVGYQPQGGLGAEIIAR--PPAVRI-LGEEVPLRASVHTLGGFSGHAG  382 (431)
T ss_dssp             SEEEEEECTTSSSSTHHHHHHSSSSSTTCEEEESSCCCTTSTTHHHHTC--CSEEEE-TTEEEECCSEEEECTTSCSSCC
T ss_pred             CceeeccccccccchHHHHHHHhccCCccceeeeeccCCCcHHHHHhcc--CCeEEE-cCcEEEEeeEEEECCcccCCCC
Confidence            9999999999999999999999999999999999999999999999986  445777 678888876  56667999999


Q ss_pred             chhhHHHHhhcCCCcceEEeCh-hhHHHHHHHHHHcCCCcccccceeeecCceecc
Q psy13345        151 KEAKDKQEKEKIPPHDTSFINE-LQLSDFKQTLQRNGIDCEFMDGVLICCRGTVAV  205 (276)
Q Consensus       151 ~~~l~~~i~~~~p~~v~lvHGE-~~~~~Lk~~L~~~G~~aef~gg~l~~p~~~~~i  205 (276)
                      ++||++|++  .|+++++|||| ..+.+|++.+++.|++       +++|+|.++|
T Consensus       383 ~~eL~~~i~--~~~~vi~vHGe~~~~~~~a~~~~~~g~~-------v~~~~nG~~v  429 (431)
T d2dkfa1         383 QDELLDWLQ--GEPRVVLVHGEEEKLLALGKLLALRGQE-------VSLARFGEGV  429 (431)
T ss_dssp             HHHHHHHHT--TCSCEEEESSCHHHHHHHHHHHHTTTCC-------EECCBTTBCE
T ss_pred             HHHHHHHHh--cCCeEEEEcCCHHHHHHHHHHHHhcCCc-------EEEcCCCCEE
Confidence            999999997  47789999999 7788999999888753       4456665544

>d2i7ta1 d.157.1.10 (A:9-459) Cleavage and polyadenylation specificity factor subunit 3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Metallo-hydrolase/oxidoreductase
superfamily: Metallo-hydrolase/oxidoreductase
family: beta-CASP RNA-metabolising hydrolases
domain: Cleavage and polyadenylation specificity factor subunit 3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=7.9e-17  Score=149.28  Aligned_cols=174  Identities=26%  Similarity=0.388  Sum_probs=120.2

Q ss_pred             hHHhhc--ccccCHHHHHHHHhccCCCCCCCCceecCCHHHHhcCCCCeEEEEeCCCCCcchHHHHHHHhCCCCCCeEEE
Q psy13345         28 LAELAK--IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDMECGFSRDLFFQWCSSPENSIII  105 (276)
Q Consensus        28 t~~~ak--~ewms~~i~~~~~~~~~nPF~f~~l~~v~s~eel~~~~~P~VIiassgml~~G~s~~~l~~~~~d~~N~Iil  105 (276)
                      ...++.  .+||++++...+.  ...++.+.++....+..+.. ...|+||+++++++..|.++.+++.++.+++++|++
T Consensus       270 ~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~-~~~~~vv~~~~~~~~~~~~~~~~~~~~~~~~~~v~~  346 (451)
T d2i7ta1         270 CMAVYQTYVNAMNDKIRKQIN--INNPFVFKHISNLKSMDHFD-DIGPSVVMASPGMMQSGLSRELFESWCTDKRNGVII  346 (451)
T ss_dssp             -----------------------------CCSEEECCCTTSSC-CCSSEEEEESCTTCSSHHHHHHHHHHTTCTTCEEEE
T ss_pred             HHHHHHhhhhhhCHHHHHHhh--ccCcccccceeeeeeecccc-ccCceEEEeCccccccchhhhhhhhhccCCCCEEEe
Confidence            444555  9999999988763  45777778877776644433 367999999999999999999999999999999999


Q ss_pred             ecCCCCCChhHHHHhccCCceEEEeeceEEeeeh-hhhhhhhhhcCchhhHHHHhhcCCCcceEEeCh-hhHHHHHHHHH
Q psy13345        106 TNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEG-EELEEYQKKKDKEAKDKQEKEKIPPHDTSFINE-LQLSDFKQTLQ  183 (276)
Q Consensus       106 tgy~~~gTlgr~L~~~~~~~~i~i~~~~~~~l~~-~el~~fsaHad~~~l~~~i~~~~p~~v~lvHGE-~~~~~Lk~~L~  183 (276)
                      ++++..+|.++.+....  ..+.-..+..+++.+ .....||+|+++++|.+|++.++|++++.+||| ..+.++++.|.
T Consensus       347 ~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~i~~v~~SgHss~~eL~~~i~~i~Pk~vipvHGe~~~~~~~~~~l~  424 (451)
T d2i7ta1         347 AGYCVEGTLAKHIMSEP--EEITTMSGQKLPLKMSVDYISFSAHTDYQQTSEFIRALKPPHVILVHGEQNEMARLKAALI  424 (451)
T ss_dssp             CSCCCTTSHHHHHTTCC--SEEECTTSCEEECCSEEEECCCSCCCCHHHHHHHHHHHCCSEEEEESSCHHHHHHHHHHHH
T ss_pred             ccccccCcHHhhhhccc--ceeEeecCcEEeeeeEEEEEeecCCCCHHHHHHHHHHhCCCEEEEEcCCHHHHHHHHHHHH
Confidence            99999999999998752  233222455666655 444679999999999999999999999999999 77899999998


Q ss_pred             HcCCCcccccceeeecCceeccc
Q psy13345        184 RNGIDCEFMDGVLICCRGTVAVR  206 (276)
Q Consensus       184 ~~G~~aef~gg~l~~p~~~~~i~  206 (276)
                      +++......+..+++|+|.+++.
T Consensus       425 ~~~~~~~~~~~~v~~p~nG~~~~  447 (451)
T d2i7ta1         425 REYEDNDEVHIEVHNPRNTEAVT  447 (451)
T ss_dssp             HHHSSCTTCCCEEECCCTTCCEE
T ss_pred             HhhccccccCceEEeCCCCCEEE
Confidence            76444334466788888876543

>d2i7xa1 d.157.1.10 (A:1-422,A:626-717) Cleavage factor two protein 2, CFT2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Metallo-hydrolase/oxidoreductase
superfamily: Metallo-hydrolase/oxidoreductase
family: beta-CASP RNA-metabolising hydrolases
domain: Cleavage factor two protein 2, CFT2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.41  E-value=1.5e-05  Score=75.48  Aligned_cols=46  Identities=15%  Similarity=0.227  Sum_probs=41.8

Q ss_pred             eccceeEEeeCCcccccchhhhhhhhcCCCCCeEEEe--ccCCCCCcccce
Q psy13345        203 VAVRRVVLVSTPDMECGFSRDLFFQWCSSPENSIIIT--NRNRADDSDSNV  251 (276)
Q Consensus       203 ~~i~~v~~~~~~~~~~g~sr~lf~~~~~~~~n~~~~~--~~~~~~~~~~~~  251 (276)
                      .+-||||+||+++   |.++++|.+||.||||.|+||  ||..++|+++.+
T Consensus       334 ~~~p~VIiat~~~---G~~~~~l~~~a~d~~n~Vi~t~~g~~~~~t~~~~~  381 (514)
T d2i7xa1         334 YPGSKICFVSEVG---ALINEVIIKVGNSEKTTLILTKPSFECASSLDKIL  381 (514)
T ss_dssp             CCSCEEEEEESCH---HHHHHHHHHHSSCTTEEEEECSSCCTTCHHHHHHH
T ss_pred             ccCCcEEEEcCCC---chHHHHHHHHhcCCCCEEEEecCCCcccccHHHHH
Confidence            4678999999875   999999999999999999999  999999999754

>d2dkfa1 d.157.1.10 (A:1-431) Putative RNA-degradation protein TTHA0252 {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Metallo-hydrolase/oxidoreductase
superfamily: Metallo-hydrolase/oxidoreductase
family: beta-CASP RNA-metabolising hydrolases
domain: Putative RNA-degradation protein TTHA0252
species: Thermus thermophilus [TaxId: 274]

Probab=97.21  E-value=7.1e-05  Score=68.18  Aligned_cols=50  Identities=16%  Similarity=0.161  Sum_probs=45.7

Q ss_pred             eccceeEEeeCCcccccchhhhhhhhcCCCCCeEEEeccCCCCCccccee
Q psy13345        203 VAVRRVVLVSTPDMECGFSRDLFFQWCSSPENSIIITNRNRADDSDSNVI  252 (276)
Q Consensus       203 ~~i~~v~~~~~~~~~~g~sr~lf~~~~~~~~n~~~~~~~~~~~~~~~~~~  252 (276)
                      .+-++|+++++++++.|.++..|..|+.||+|.||||||+.+||.++.++
T Consensus       303 ~~~~~vii~~~~~~~~~~~~~~~~~~~~~~~n~vi~tg~~~~gt~g~~l~  352 (431)
T d2dkfa1         303 APGPMVVLAGSGMLAGGRILHHLKHGLSDPRNALVFVGYQPQGGLGAEII  352 (431)
T ss_dssp             CCSSEEEEEECTTSSSSTHHHHHHSSSSSTTCEEEESSCCCTTSTTHHHH
T ss_pred             CCCCceeeccccccccchHHHHHHHhccCCccceeeeeccCCCcHHHHHh
Confidence            45678999999999999999999999999999999999999999986553

>d2i7ta1 d.157.1.10 (A:9-459) Cleavage and polyadenylation specificity factor subunit 3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Metallo-hydrolase/oxidoreductase
superfamily: Metallo-hydrolase/oxidoreductase
family: beta-CASP RNA-metabolising hydrolases
domain: Cleavage and polyadenylation specificity factor subunit 3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.29  E-value=0.046  Score=48.18  Aligned_cols=49  Identities=29%  Similarity=0.485  Sum_probs=44.6

Q ss_pred             eccceeEEeeCCcccccchhhhhhhhcCCCCCeEEEeccCCCCCcccce
Q psy13345        203 VAVRRVVLVSTPDMECGFSRDLFFQWCSSPENSIIITNRNRADDSDSNV  251 (276)
Q Consensus       203 ~~i~~v~~~~~~~~~~g~sr~lf~~~~~~~~n~~~~~~~~~~~~~~~~~  251 (276)
                      ..-++|+++.++.+..|.++.++..|+.++++.+++++....++.++.+
T Consensus       311 ~~~~~vv~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~  359 (451)
T d2i7ta1         311 DIGPSVVMASPGMMQSGLSRELFESWCTDKRNGVIIAGYCVEGTLAKHI  359 (451)
T ss_dssp             CCSSEEEEESCTTCSSHHHHHHHHHHTTCTTCEEEECSCCCTTSHHHHH
T ss_pred             ccCceEEEeCccccccchhhhhhhhhccCCCCEEEeccccccCcHHhhh
Confidence            4568899999999999999999999999999999999999999977543