Psyllid ID: psy8716

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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-
Protein Sequence
MDQLFEVSFSPLAATGKAMSQELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKGSGCNVCTHPTCGQALLSTGIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTENNCDCVQFTSNDK
Secondary Structure (PSIPRED)
cccccEEEEEccccccccccccccccccccEEEEEEccccccEEEEcccccccccccccccccccccccccccccHHccccccccccccccEEEEEccccccEEEEccccccEEEcccccEEEEccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccHEEEEccccccccccccccccccccccEEEEEEccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccEEEEcccccccEEEEEccccEEEEEccccEEEEEcccccccHEEEEcccc
Coil and Loop (DISEMBL)
mdqlfevsfsplaaTGKAMSQelkcpiddFELLCWSmgnkgksyilcpycynnppyrdmkkgsgcnvcthptcgqaLLSTGIASCLQCEGgvlvldlssapkwkiccnkcdiiihvfpdaqkvqvctenncdcvqftsndk
Flexible Loop (DISEMBL)
MDQLFEVSFSPLAATGKAMSQELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKGSGCNVCTHPTCGQALLSTGIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTENNCDCvqftsndk
Low Complexity Region (SEG)
MDQLFEVSFSPLAATGKAMSQELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKGSGCNVCTHPTCGQALLSTGIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTENNCDCVQFTSNDK
Disordered region (IsUnstruct)
********************QELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKGSGCNVCTHPTCGQALLSTGIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTENNCDCVQF*****
Disordered Region (DISOPRED)
*DQLFEVSFSP*********QELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPY********CNVCTHPTCGQALLSTGIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTENNCDCVQFT****
Disordered Region (DISEMBL)
MDQLFEVSFSPLAATGKAMSQELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKGSGCNVCTHPTCGQALLSTGIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTENNCDCVQFTSNDK
Disordered Region (DISPRO)
***LFEVSFSPLAATGKAMSQELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKGSGCNVCTHPTCGQALLSTGIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTENNCDCVQFTS***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDQLFEVSFSPLAATGKAMSQELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKGSGCNVCTHPTCGQALLSTGIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTENNCDCVQFTSNDK
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	141	2.2.26 [Sep-21-2011]
O95985	862	DNA topoisomerase 3-beta-	yes	N/A	0.914	0.149	0.482	1e-42
Q9Z321	862	DNA topoisomerase 3-beta-	yes	N/A	0.950	0.155	0.474	1e-42
O96651	875	DNA topoisomerase 3-beta	yes	N/A	0.886	0.142	0.447	1e-33

>sp|O95985|TOP3B_HUMAN DNA topoisomerase 3-beta-1 OS=Homo sapiens GN=TOP3B PE=1 SV=1

 Score =  171 bits (433), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 81/168 (48%), Positives = 104/168 (61%), Gaps = 39/168 (23%)

Query: 1   MDQLFEVSFSPLAATGKAMSQ--------------------------------------- 21
           MD+L EVSFSPLAATGK +S+                                       
Sbjct: 603 MDELMEVSFSPLAATGKPLSRCGKCHRFMKYIQAKPSRLHCSHCDETYTLPQNGTIKLYK 662

Query: 22  ELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKGSGCNVCTHPTCGQALLSTG 81
           EL+CP+DDFEL+ WS G++GKSY LCPYCYN+PP+RDMKKG GCN CTHP+C  +L   G
Sbjct: 663 ELRCPLDDFELVLWSSGSRGKSYPLCPYCYNHPPFRDMKKGMGCNECTHPSCQHSLSMLG 722

Query: 82  IASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTEN 129
           I  C++CE GVLVLD +S PKWK+ CNKC+++ H F +A +V+V  + 
Sbjct: 723 IGQCVECESGVLVLDPTSGPKWKVACNKCNVVAHCFENAHRVRVSADT 770

Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone (By similarity). Possesses negatively supercoiled DNA relaxing activity.
Homo sapiens (taxid: 9606)
EC: 5EC: .EC: 9EC: 9EC: .EC: 1EC: .EC: 2

>sp|Q9Z321|TOP3B_MOUSE DNA topoisomerase 3-beta-1 OS=Mus musculus GN=Top3b PE=2 SV=1

 Score =  171 bits (433), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 83/175 (47%), Positives = 106/175 (60%), Gaps = 41/175 (23%)

Query: 1   MDQLFEVSFSPLAATGKAMSQ--------------------------------------- 21
           MD+L EVSFSPLAATGK +S+                                       
Sbjct: 603 MDELMEVSFSPLAATGKPLSRCGKCHRFMKYIQAKPSRLHCSHCDETYTLPQNGTIKLYK 662

Query: 22  ELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKGSGCNVCTHPTCGQALLSTG 81
           EL+CP+DDFEL+ WS G++GKSY LCPYCYN+PP+RDMKKG GCN CTHPTC  +L   G
Sbjct: 663 ELRCPLDDFELVLWSSGSRGKSYPLCPYCYNHPPFRDMKKGMGCNECTHPTCQHSLSMLG 722

Query: 82  IASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTE--NNCDCV 134
           I  C++CE GVLVLD +S PKWK+ CN C+++ H F +A +V+V  +  N C+  
Sbjct: 723 IGQCVECENGVLVLDPTSGPKWKVACNTCNVVAHCFENAHRVRVSADTCNTCEAA 777

Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone (By similarity). Possesses negatively supercoiled DNA relaxing activity.

Mus musculus (taxid: 10090)

EC: 5

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: .

EC: 2

>sp|O96651|TOP3B_DROME DNA topoisomerase 3-beta OS=Drosophila melanogaster GN=Top3beta PE=2 SV=2

 Score =  141 bits (355), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 73/163 (44%), Positives = 93/163 (57%), Gaps = 38/163 (23%)

Query: 1   MDQLFEVSFSPLAATGKAMSQ--------------------------------------E 22
           MD LFEVSFSPLA +GKA S+                                      E
Sbjct: 598 MDALFEVSFSPLAESGKAHSRCGKCRRYMKYIQTKPARLHCSHCDETYALPIGNVKVYRE 657

Query: 23  LKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKGSGCNVCTHPTCGQALLSTGI 82
            KCP+DDF+LL +S G KG+SY  CPYCYN+PP+ DM    GCN CT+  C  +L + GI
Sbjct: 658 FKCPLDDFDLLAFSTGVKGRSYPFCPYCYNHPPFSDMPHLGGCNTCTNANCPHSLNTLGI 717

Query: 83  ASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQV 125
           +SC++C  GVLVLD + AP WK+ CN+CD+II+ F  A K+ V
Sbjct: 718 SSCVECPTGVLVLDCTLAPTWKLGCNRCDVIINCFKGATKITV 760

Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone (By similarity). Weakly relaxes negative supercoils and displays a distinct preference for binding single-stranded DNA.

Drosophila melanogaster (taxid: 7227)

EC: 5

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: .

EC: 2

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	141
156551898	852	PREDICTED: DNA topoisomerase 3-beta-1-li	0.943	0.156	0.531	6e-46
350424370	851	PREDICTED: DNA topoisomerase 3-beta-1-li	0.936	0.155	0.543	2e-45
340722711	851	PREDICTED: DNA topoisomerase 3-beta-1-li	0.936	0.155	0.543	2e-45
193591899	854	PREDICTED: DNA topoisomerase 3-beta-1-li	0.943	0.155	0.529	3e-45
328697671	853	PREDICTED: DNA topoisomerase 3-beta-1-li	0.943	0.155	0.529	4e-45
332027377	848	DNA topoisomerase 3-beta-1 [Acromyrmex e	0.936	0.155	0.537	4e-45
383857261	851	PREDICTED: DNA topoisomerase 3-beta-1-li	0.936	0.155	0.543	5e-45
307203099	851	DNA topoisomerase 3-beta-1 [Harpegnathos	0.936	0.155	0.543	5e-45
307184245	851	DNA topoisomerase 3-beta-1 [Camponotus f	0.936	0.155	0.537	9e-45
380025214	851	PREDICTED: DNA topoisomerase 3-beta-1 [A	0.936	0.155	0.537	1e-44

>gi|156551898|ref|XP_001606777.1| PREDICTED: DNA topoisomerase 3-beta-1-like [Nasonia vitripennis]

 Score =  188 bits (478), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 92/173 (53%), Positives = 111/173 (64%), Gaps = 40/173 (23%)

Query: 1   MDQLFEVSFSPLAATGKAMSQ--------------------------------------- 21
           MDQLFEVSFSPL+A+GK+ S+                                       
Sbjct: 601 MDQLFEVSFSPLSASGKSHSRCGKCRRYMKYIQTKPSRLHCAHCNETYNLPQNGNIRIYK 660

Query: 22  ELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKG-SGCNVCTHPTCGQALLST 80
           ELKCP+DDFELL +S G +GKSY  CPYC+NNPP+RDMKKG SGCN CTHPTC   L S 
Sbjct: 661 ELKCPLDDFELLSYSTGTRGKSYTFCPYCFNNPPFRDMKKGLSGCNACTHPTCPHGLNSN 720

Query: 81  GIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTENNCDC 133
           G++SCL+CE G+LVLD S+APKWK+ CN+CD+IIH+F DA KV V  +  CDC
Sbjct: 721 GLSSCLECESGILVLDPSAAPKWKLVCNRCDVIIHLFADAHKVMVEADEVCDC 773

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350424370|ref|XP_003493773.1| PREDICTED: DNA topoisomerase 3-beta-1-like [Bombus impatiens]

 Score =  186 bits (473), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 94/173 (54%), Positives = 111/173 (64%), Gaps = 41/173 (23%)

Query: 1   MDQLFEVSFSPLAATGKAMSQ--------------------------------------- 21
           MDQLFEVSFSPL+A+GKA S+                                       
Sbjct: 601 MDQLFEVSFSPLSASGKAHSRCGKCRRYMKYIQTKPSRMHCAHCNETYNLPQNGNIRIYK 660

Query: 22  ELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKG-SGCNVCTHPTCGQALLST 80
           ELKCP+DDFELL WS G +GKSY  CPYCYNNPP+RDMKKG SGCN CTHPTC   + S 
Sbjct: 661 ELKCPLDDFELLSWSTGARGKSYTFCPYCYNNPPFRDMKKGMSGCNSCTHPTCPHGMNSN 720

Query: 81  GIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTENNCDC 133
           G++SCL+C  G+LVLD S+APKWK+ CN+CD+IIH+F +A KV V TE  CDC
Sbjct: 721 GLSSCLECNAGILVLDPSAAPKWKLVCNRCDVIIHLFENAHKVTVDTE-VCDC 772

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340722711|ref|XP_003399746.1| PREDICTED: DNA topoisomerase 3-beta-1-like [Bombus terrestris]

 Score =  186 bits (473), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 94/173 (54%), Positives = 111/173 (64%), Gaps = 41/173 (23%)

Query: 1   MDQLFEVSFSPLAATGKAMSQ--------------------------------------- 21
           MDQLFEVSFSPL+A+GKA S+                                       
Sbjct: 601 MDQLFEVSFSPLSASGKAHSRCGKCRRYMKYIQTKPSRMHCAHCNETYNLPQNGNIRIYK 660

Query: 22  ELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKG-SGCNVCTHPTCGQALLST 80
           ELKCP+DDFELL WS G +GKSY  CPYCYNNPP+RDMKKG SGCN CTHPTC   + S 
Sbjct: 661 ELKCPLDDFELLSWSTGARGKSYTFCPYCYNNPPFRDMKKGMSGCNSCTHPTCPHGMNSN 720

Query: 81  GIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTENNCDC 133
           G++SCL+C  G+LVLD S+APKWK+ CN+CD+IIH+F +A KV V TE  CDC
Sbjct: 721 GLSSCLECNAGILVLDPSAAPKWKLVCNRCDVIIHLFENAHKVTVDTE-VCDC 772

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193591899|ref|XP_001951574.1| PREDICTED: DNA topoisomerase 3-beta-1-like isoform 1 [Acyrthosiphon pisum]

 Score =  186 bits (471), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 91/172 (52%), Positives = 105/172 (61%), Gaps = 39/172 (22%)

Query: 1   MDQLFEVSFSPLAATGKAMSQ--------------------------------------- 21
           MD LFEVSF+ LAA+GKA+S+                                       
Sbjct: 602 MDSLFEVSFTTLAASGKALSRCGKCRRYMKLIIAKPSRLHCSHCDETYNLPQNGNIRIYK 661

Query: 22  ELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKGSGCNVCTHPTCGQALLSTG 81
           ELKCP+DDFEL+ WS GNKG+SY LCPYCYN P +RDMKK SGCN+C HPTC Q     G
Sbjct: 662 ELKCPLDDFELVTWSTGNKGRSYPLCPYCYNQPAFRDMKKHSGCNLCLHPTCPQGFYVNG 721

Query: 82  IASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTENNCDC 133
           IASCLQC+ GVLVLD SS PKWK+ CNKCD+I H+F DA K+ V     CDC
Sbjct: 722 IASCLQCDNGVLVLDPSSGPKWKVGCNKCDVIFHLFEDAHKITVEESKECDC 773

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328697671|ref|XP_003240406.1| PREDICTED: DNA topoisomerase 3-beta-1-like isoform 2 [Acyrthosiphon pisum]

 Score =  186 bits (471), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 91/172 (52%), Positives = 105/172 (61%), Gaps = 39/172 (22%)

Query: 1   MDQLFEVSFSPLAATGKAMSQ--------------------------------------- 21
           MD LFEVSF+ LAA+GKA+S+                                       
Sbjct: 601 MDSLFEVSFTTLAASGKALSRCGKCRRYMKLIIAKPSRLHCSHCDETYNLPQNGNIRIYK 660

Query: 22  ELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKGSGCNVCTHPTCGQALLSTG 81
           ELKCP+DDFEL+ WS GNKG+SY LCPYCYN P +RDMKK SGCN+C HPTC Q     G
Sbjct: 661 ELKCPLDDFELVTWSTGNKGRSYPLCPYCYNQPAFRDMKKHSGCNLCLHPTCPQGFYVNG 720

Query: 82  IASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTENNCDC 133
           IASCLQC+ GVLVLD SS PKWK+ CNKCD+I H+F DA K+ V     CDC
Sbjct: 721 IASCLQCDNGVLVLDPSSGPKWKVGCNKCDVIFHLFEDAHKITVEESKECDC 772

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332027377|gb|EGI67460.1| DNA topoisomerase 3-beta-1 [Acromyrmex echinatior]

 Score =  185 bits (470), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 93/173 (53%), Positives = 112/173 (64%), Gaps = 41/173 (23%)

Query: 1   MDQLFEVSFSPLAATGKAMSQ--------------------------------------- 21
           MDQLFEVSFSPL+A+GKA S+                                       
Sbjct: 598 MDQLFEVSFSPLSASGKAHSRCGKCRRYMKYIQTKPSRMHCAHCNETYNLPQNGNIRIYK 657

Query: 22  ELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKG-SGCNVCTHPTCGQALLST 80
           ELKCP+DDFELL WS G +GKSY  CPYCYNNPP+RDMKKG SGCN CTHPTC   + S 
Sbjct: 658 ELKCPLDDFELLSWSTGTRGKSYTFCPYCYNNPPFRDMKKGMSGCNSCTHPTCPHGMNSN 717

Query: 81  GIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTENNCDC 133
           G++SCL+C+ G+LVLD S+APKWK+ CN+CD+IIH+F +A KV V T+  CDC
Sbjct: 718 GLSSCLECDLGILVLDPSAAPKWKLGCNRCDVIIHLFENAHKVTVDTD-TCDC 769

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383857261|ref|XP_003704123.1| PREDICTED: DNA topoisomerase 3-beta-1-like [Megachile rotundata]

 Score =  185 bits (470), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 94/173 (54%), Positives = 112/173 (64%), Gaps = 41/173 (23%)

Query: 1   MDQLFEVSFSPLAATGKAMSQ--------------------------------------- 21
           MDQLFEVSFSPL+A+GKA S+                                       
Sbjct: 601 MDQLFEVSFSPLSASGKAHSRCGKCRRYMKYIQTKPSRMHCAHCNETYNLPQNGNIRIYK 660

Query: 22  ELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKG-SGCNVCTHPTCGQALLST 80
           ELKCP+DDFELL WS G +GKSY  CPYCYNNPP+RDMKKG SGCN CTHPTC   + S 
Sbjct: 661 ELKCPLDDFELLSWSTGARGKSYTFCPYCYNNPPFRDMKKGTSGCNSCTHPTCPHGMNSN 720

Query: 81  GIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTENNCDC 133
           GI+SCL+C+ G+LVLD S+APKWK+ CN+CD+IIH+F +A KV V T+  CDC
Sbjct: 721 GISSCLECDTGILVLDPSAAPKWKLGCNRCDVIIHLFENAHKVTVDTD-VCDC 772

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307203099|gb|EFN82279.1| DNA topoisomerase 3-beta-1 [Harpegnathos saltator]

 Score =  185 bits (469), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 94/173 (54%), Positives = 113/173 (65%), Gaps = 41/173 (23%)

Query: 1   MDQLFEVSFSPLAATGKAMSQ--------------------------------------- 21
           MDQLFEVSFSPL+A+GKA S+                                       
Sbjct: 601 MDQLFEVSFSPLSASGKAHSRCGKCRRYMKYIQTKPSRMHCAHCNETYNLPQNGNIRIYK 660

Query: 22  ELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKG-SGCNVCTHPTCGQALLST 80
           ELKCP+DDFELL WS G +GKSY  CPYCYNNPP+RDMKKG SGCN CTHPTC   + ST
Sbjct: 661 ELKCPLDDFELLSWSTGARGKSYTFCPYCYNNPPFRDMKKGMSGCNSCTHPTCPHGMNST 720

Query: 81  GIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTENNCDC 133
           G++SCL+C+ G+LVLD S+APKWK+ CN+CD+IIH+F +A KV V T+  CDC
Sbjct: 721 GLSSCLECDLGILVLDPSAAPKWKLGCNRCDVIIHLFENAHKVTVDTD-VCDC 772

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307184245|gb|EFN70718.1| DNA topoisomerase 3-beta-1 [Camponotus floridanus]

 Score =  184 bits (468), Expect = 9e-45,   Method: Compositional matrix adjust.
 Identities = 93/173 (53%), Positives = 112/173 (64%), Gaps = 41/173 (23%)

Query: 1   MDQLFEVSFSPLAATGKAMSQ--------------------------------------- 21
           MDQLFEVSFSPL+A+GKA S+                                       
Sbjct: 601 MDQLFEVSFSPLSASGKAHSRCGKCRRYMKYIQTKPSRMHCAHCNETYNLPQNGNIRIYK 660

Query: 22  ELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKG-SGCNVCTHPTCGQALLST 80
           ELKCP+DDFELL WS G +GKSY  CPYCYNNPP+RDMKKG SGCN CTHPTC   + S 
Sbjct: 661 ELKCPLDDFELLSWSTGARGKSYTFCPYCYNNPPFRDMKKGMSGCNSCTHPTCPHGMNSN 720

Query: 81  GIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTENNCDC 133
           G++SCL+C+ G+LVLD S+APKWK+ CN+CD+IIH+F +A KV V T+  CDC
Sbjct: 721 GLSSCLECDLGILVLDPSAAPKWKLGCNRCDVIIHLFENAHKVTVDTD-TCDC 772

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380025214|ref|XP_003696372.1| PREDICTED: DNA topoisomerase 3-beta-1 [Apis florea]

 Score =  184 bits (467), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 93/173 (53%), Positives = 111/173 (64%), Gaps = 41/173 (23%)

Query: 1   MDQLFEVSFSPLAATGKAMSQ--------------------------------------- 21
           MDQLFEVSFSPL+A+GKA S+                                       
Sbjct: 601 MDQLFEVSFSPLSASGKAHSRCGKCRRYMKYIQTKPSRMHCAHCNETYNLPQNGNIRIYK 660

Query: 22  ELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKG-SGCNVCTHPTCGQALLST 80
           ELKCP+DDFELL WS G +GKS+  CPYCYNNPP+RDMKKG SGCN CTHPTC   + S 
Sbjct: 661 ELKCPLDDFELLSWSTGTRGKSFTFCPYCYNNPPFRDMKKGISGCNSCTHPTCPHGMNSN 720

Query: 81  GIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTENNCDC 133
           GI+SCL+C  G+LVLD S+APKWK+ CN+CD+IIH+F +A KV V TE  C+C
Sbjct: 721 GISSCLECNAGILVLDPSAAPKWKLGCNRCDVIIHLFENAHKVTVDTE-VCEC 772

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

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	141
UNIPROTKB|Q5ZK71	862	TOP3B "DNA topoisomerase" [Gal	0.787	0.128	0.625	5.2e-46
UNIPROTKB|E1BQG8	863	TOP3B "DNA topoisomerase" [Gal	0.787	0.128	0.625	5.2e-46
MGI|MGI:1333803	862	Top3b "topoisomerase (DNA) III	0.794	0.129	0.587	8.2e-45
RGD|1309468	862	Top3b "topoisomerase (DNA) III	0.794	0.129	0.587	1.1e-44
UNIPROTKB|O95985	862	TOP3B "DNA topoisomerase 3-bet	0.801	0.131	0.584	1.4e-44
ZFIN|ZDB-GENE-070705-37	862	top3b "topoisomerase (DNA) III	0.787	0.128	0.580	2.2e-44
UNIPROTKB|E2R770	862	TOP3B "DNA topoisomerase" [Can	0.801	0.131	0.584	6.1e-44
UNIPROTKB|F1RL05	859	TOP3B "DNA topoisomerase" [Sus	0.801	0.131	0.566	7.7e-44
FB|FBgn0026015	875	Top3beta "Topoisomerase 3beta"	0.794	0.128	0.526	3.1e-36
WB|WBGene00012995	869	Y48C3A.14 [Caenorhabditis eleg	0.801	0.130	0.435	3.8e-26

UNIPROTKB|Q5ZK71 TOP3B "DNA topoisomerase" [Gallus gallus (taxid:9031)]

 Score = 430 (156.4 bits), Expect = 5.2e-46, Sum P(2) = 5.2e-46
 Identities = 70/112 (62%), Positives = 89/112 (79%)

Query:    21 QELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKGSGCNVCTHPTCGQALLST 80
             +EL+CP+DDFEL+ WS G++GKSY LCPYCYN+PP+RDMKKG GCN CTHPTC  +L   
Sbjct:   662 KELRCPLDDFELVLWSSGSRGKSYPLCPYCYNHPPFRDMKKGMGCNECTHPTCQHSLSML 721

Query:    81 GIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTENNCD 132
             GI  C++CE GVLVLD +S PKWK+ CNKC++I+H F +A KV+V  E  C+
Sbjct:   722 GIGQCVECENGVLVLDSTSGPKWKMACNKCNVIVHFFENAHKVRVSPET-CE 772

GO:0005694 "chromosome" evidence=IEA

GO:0006265 "DNA topological change" evidence=IEA

GO:0003917 "DNA topoisomerase type I activity" evidence=IEA

UNIPROTKB|E1BQG8 TOP3B "DNA topoisomerase" [Gallus gallus (taxid:9031)]

 Score = 430 (156.4 bits), Expect = 5.2e-46, Sum P(2) = 5.2e-46
 Identities = 70/112 (62%), Positives = 89/112 (79%)

Query:    21 QELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKGSGCNVCTHPTCGQALLST 80
             +EL+CP+DDFEL+ WS G++GKSY LCPYCYN+PP+RDMKKG GCN CTHPTC  +L   
Sbjct:   663 KELRCPLDDFELVLWSSGSRGKSYPLCPYCYNHPPFRDMKKGMGCNECTHPTCQHSLSML 722

Query:    81 GIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTENNCD 132
             GI  C++CE GVLVLD +S PKWK+ CNKC++I+H F +A KV+V  E  C+
Sbjct:   723 GIGQCVECENGVLVLDSTSGPKWKMACNKCNVIVHFFENAHKVRVSPET-CE 773

GO:0006265 "DNA topological change" evidence=IEA

GO:0000793 "condensed chromosome" evidence=IEA

GO:0007059 "chromosome segregation" evidence=IEA

GO:0003917 "DNA topoisomerase type I activity" evidence=IEA

MGI|MGI:1333803 Top3b "topoisomerase (DNA) III beta" [Mus musculus (taxid:10090)]

 Score = 419 (152.6 bits), Expect = 8.2e-45, Sum P(2) = 8.2e-45
 Identities = 67/114 (58%), Positives = 88/114 (77%)

Query:    21 QELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKGSGCNVCTHPTCGQALLST 80
             +EL+CP+DDFEL+ WS G++GKSY LCPYCYN+PP+RDMKKG GCN CTHPTC  +L   
Sbjct:   662 KELRCPLDDFELVLWSSGSRGKSYPLCPYCYNHPPFRDMKKGMGCNECTHPTCQHSLSML 721

Query:    81 GIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTE--NNCD 132
             GI  C++CE GVLVLD +S PKWK+ CN C+++ H F +A +V+V  +  N C+
Sbjct:   722 GIGQCVECENGVLVLDPTSGPKWKVACNTCNVVAHCFENAHRVRVSADTCNTCE 775

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000793 "condensed chromosome" evidence=IDA

GO:0003677 "DNA binding" evidence=IEA

GO:0003916 "DNA topoisomerase activity" evidence=IEA

GO:0003917 "DNA topoisomerase type I activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

GO:0006265 "DNA topological change" evidence=IEA

GO:0007059 "chromosome segregation" evidence=IMP

GO:0016853 "isomerase activity" evidence=IEA

RGD|1309468 Top3b "topoisomerase (DNA) III beta" [Rattus norvegicus (taxid:10116)]

 Score = 418 (152.2 bits), Expect = 1.1e-44, Sum P(2) = 1.1e-44
 Identities = 67/114 (58%), Positives = 87/114 (76%)

Query:    21 QELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKGSGCNVCTHPTCGQALLST 80
             +EL+CP+DDFEL+ WS G++GKSY LCPYCYN+PP+RDMKKG GCN CTHPTC  +L   
Sbjct:   662 KELRCPLDDFELVLWSSGSRGKSYPLCPYCYNHPPFRDMKKGMGCNECTHPTCQHSLSML 721

Query:    81 GIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTE--NNCD 132
             GI  C++CE GVLVLD +S PKWK+ CN C ++ H F +A +V+V  +  N C+
Sbjct:   722 GIGQCVECENGVLVLDPTSGPKWKVACNTCSVVAHCFDNAHRVRVSADTCNTCE 775

GO:0000793 "condensed chromosome" evidence=IEA;ISO

GO:0003917 "DNA topoisomerase type I activity" evidence=IEA

GO:0006265 "DNA topological change" evidence=IEA

GO:0007059 "chromosome segregation" evidence=IEA;ISO

UNIPROTKB|O95985 TOP3B "DNA topoisomerase 3-beta-1" [Homo sapiens (taxid:9606)]

 Score = 417 (151.9 bits), Expect = 1.4e-44, Sum P(2) = 1.4e-44
 Identities = 66/113 (58%), Positives = 87/113 (76%)

Query:    21 QELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKGSGCNVCTHPTCGQALLST 80
             +EL+CP+DDFEL+ WS G++GKSY LCPYCYN+PP+RDMKKG GCN CTHP+C  +L   
Sbjct:   662 KELRCPLDDFELVLWSSGSRGKSYPLCPYCYNHPPFRDMKKGMGCNECTHPSCQHSLSML 721

Query:    81 GIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTENNCDC 133
             GI  C++CE GVLVLD +S PKWK+ CNKC+++ H F +A +V+V  +    C
Sbjct:   722 GIGQCVECESGVLVLDPTSGPKWKVACNKCNVVAHCFENAHRVRVSADTCSVC 774

GO:0006265 "DNA topological change" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003917 "DNA topoisomerase type I activity" evidence=IEA

GO:0000793 "condensed chromosome" evidence=IEA

GO:0007059 "chromosome segregation" evidence=IEA

GO:0003677 "DNA binding" evidence=TAS

GO:0003916 "DNA topoisomerase activity" evidence=TAS

GO:0005634 "nucleus" evidence=TAS

ZFIN|ZDB-GENE-070705-37 top3b "topoisomerase (DNA) III beta" [Danio rerio (taxid:7955)]

 Score = 417 (151.9 bits), Expect = 2.2e-44, Sum P(2) = 2.2e-44
 Identities = 65/112 (58%), Positives = 91/112 (81%)

Query:    21 QELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKGSGCNVCTHPTCGQALLST 80
             +ELKCP+D+FEL+ W+ G++GKSY +CPYC++NPP+RDMKKG GCN CTHP+C  +L S 
Sbjct:   663 KELKCPLDEFELVLWTSGSRGKSYPVCPYCFSNPPFRDMKKGMGCNECTHPSCQHSLNSL 722

Query:    81 GIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTENNCD 132
             GI  C++CE GVLV D +S PKW++ CNKC++++H F  A KVQV ++++CD
Sbjct:   723 GIGQCVECETGVLVFDPTSGPKWRMACNKCNVVVHFFEQAHKVQV-SQDSCD 773

GO:0003677 "DNA binding" evidence=IEA

GO:0003916 "DNA topoisomerase activity" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

GO:0006265 "DNA topological change" evidence=IEA

GO:0003917 "DNA topoisomerase type I activity" evidence=IEA

GO:0016853 "isomerase activity" evidence=IEA

UNIPROTKB|E2R770 TOP3B "DNA topoisomerase" [Canis lupus familiaris (taxid:9615)]

 Score = 411 (149.7 bits), Expect = 6.1e-44, Sum P(2) = 6.1e-44
 Identities = 66/113 (58%), Positives = 86/113 (76%)

Query:    21 QELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKGSGCNVCTHPTCGQALLST 80
             +EL+CP+DDFEL+ WS G++GKSY LCPYC N+PP+RDMKKG GCN CTHPTC  +L   
Sbjct:   662 KELRCPLDDFELVLWSSGSRGKSYPLCPYCSNHPPFRDMKKGMGCNECTHPTCQHSLSML 721

Query:    81 GIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTENNCDC 133
             GI  C++CE GVLVLD +S PKWK+ CNKC+++ H F +A +V+V  +    C
Sbjct:   722 GIGQCVECESGVLVLDPTSGPKWKVACNKCNVVAHCFENAYRVRVSADTCPTC 774

GO:0007059 "chromosome segregation" evidence=IEA

GO:0000793 "condensed chromosome" evidence=IEA

GO:0003917 "DNA topoisomerase type I activity" evidence=IEA

GO:0006265 "DNA topological change" evidence=IEA

UNIPROTKB|F1RL05 TOP3B "DNA topoisomerase" [Sus scrofa (taxid:9823)]

 Score = 410 (149.4 bits), Expect = 7.7e-44, Sum P(2) = 7.7e-44
 Identities = 64/113 (56%), Positives = 88/113 (77%)

Query:    21 QELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKGSGCNVCTHPTCGQALLST 80
             +EL+CP+DDFEL+ WS G++GKSY LCPYC N+PP+RDMKKG+GCN CTHPTC  +L   
Sbjct:   662 KELRCPLDDFELVLWSSGSRGKSYPLCPYCSNHPPFRDMKKGTGCNECTHPTCQHSLNML 721

Query:    81 GIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTENNCDC 133
             GI  C++CE GVLVLD +S PKW++ CN+C+++ H F +A +V+V ++    C
Sbjct:   722 GIGQCVECESGVLVLDPTSGPKWRVACNRCNVVAHCFENAHRVRVSSDTCSTC 774

GO:0007059 "chromosome segregation" evidence=IEA

GO:0000793 "condensed chromosome" evidence=IEA

GO:0003917 "DNA topoisomerase type I activity" evidence=IEA

GO:0006265 "DNA topological change" evidence=IEA

FB|FBgn0026015 Top3beta "Topoisomerase 3beta" [Drosophila melanogaster (taxid:7227)]

 Score = 345 (126.5 bits), Expect = 3.1e-36, Sum P(2) = 3.1e-36
 Identities = 60/114 (52%), Positives = 80/114 (70%)

Query:    21 QELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKGSGCNVCTHPTCGQALLST 80
             +E KCP+DDF+LL +S G KG+SY  CPYCYN+PP+ DM    GCN CT+  C  +L + 
Sbjct:   656 REFKCPLDDFDLLAFSTGVKGRSYPFCPYCYNHPPFSDMPHLGGCNTCTNANCPHSLNTL 715

Query:    81 GIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTENNC-DC 133
             GI+SC++C  GVLVLD + AP WK+ CN+CD+II+ F  A K+ V  E  C +C
Sbjct:   716 GISSCVECPTGVLVLDCTLAPTWKLGCNRCDVIINCFKGATKITV-EEAKCQEC 768

GO:0003917 "DNA topoisomerase type I activity" evidence=ISS;NAS

GO:0003916 "DNA topoisomerase activity" evidence=IDA;NAS

GO:0004520 "endodeoxyribonuclease activity" evidence=IDA

GO:0000737 "DNA catabolic process, endonucleolytic" evidence=IDA

GO:0006265 "DNA topological change" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

WB|WBGene00012995 Y48C3A.14 [Caenorhabditis elegans (taxid:6239)]

 Score = 306 (112.8 bits), Expect = 3.8e-26, P = 3.8e-26
 Identities = 51/117 (43%), Positives = 80/117 (68%)

Query:    24 KCPIDDFELLCWS-MGNK-GKSYILCPYCYNNPPYRDMKKGSGCNVCTHPTCGQALLSTG 81
             KCP+DDF+++ +   G K  +++ LCP+C+NNPP+  M +G+GC+ C HP+C  ++ S G
Sbjct:   670 KCPLDDFDVILYQGPGGKLARTFTLCPFCFNNPPFEKMPQGAGCDTCVHPSCQYSISSNG 729

Query:    82 IASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTENNCD-C-VQF 136
             +  CLQ  GGV++LD  S PKW++ CNKC  ++ +F  A KV+V +  +C+ C  QF
Sbjct:   730 VCGCLQDCGGVMLLDTQSHPKWRMTCNKCPSVVGLFEGAIKVKVDSTRSCEQCDAQF 786

GO:0003677 "DNA binding" evidence=IEA

GO:0003917 "DNA topoisomerase type I activity" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

GO:0006265 "DNA topological change" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008168 "methyltransferase activity" evidence=IEA

GO:0032259 "methylation" evidence=IEA

GO:0003916 "DNA topoisomerase activity" 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

No hit with e-value below 0.005

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	141
KOG1957|consensus	555		99.96
PRK07219	822	DNA topoisomerase I; Validated	97.88
PF01396	39	zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc	96.46
KOG2906|consensus	105		94.72
COG0551	140	TopA Zn-finger domain associated with topoisomeras	92.06
PRK07220	740	DNA topoisomerase I; Validated	91.65
PRK07219	822	DNA topoisomerase I; Validated	90.83
PRK06319	860	DNA topoisomerase I/SWI domain fusion protein; Val	90.8
PF02150	35	RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I	90.37
smart00661	52	RPOL9 RNA polymerase subunit 9.	89.82
PF14206	78	Cys_rich_CPCC: Cysteine-rich CPCC	87.32
COG0551	140	TopA Zn-finger domain associated with topoisomeras	87.06
PF14803	34	Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.	86.55
PRK14973	936	DNA topoisomerase I; Provisional	86.1
PF05502	483	Dynactin_p62: Dynactin p62 family; InterPro: IPR00	83.67
PRK07220	740	DNA topoisomerase I; Validated	83.39

>KOG1957|consensus

Probab=99.96  E-value=2.4e-30  Score=227.96  Aligned_cols=134  Identities=34%  Similarity=0.697  Sum_probs=127.4

Q ss_pred             CCcccccccccccccCcCCC-------------------------------------CCCcCcCCCceEEEEEeCCCCee
Q psy8716           1 MDQLFEVSFSPLAATGKAMS-------------------------------------QELKCPIDDFELLCWSMGNKGKS   43 (141)
Q Consensus         1 md~Lfe~~Fs~l~~sgkp~s-------------------------------------~e~~CPLd~FeLl~~s~g~~gks   43 (141)
                      +|.|||++|+++|+.|+|||                                     +..+|||++||+++|.+|...++
T Consensus       300 ~D~L~~~s~gtdAgdgpPitpmr~~~R~m~~~dtkRLY~~vCqhf~~tp~~~~~k~it~~k~slgdeqf~lw~~Gk~~~~  379 (555)
T KOG1957|consen  300 GDTLFEASFGTDAGDGPPITPMRKCNRYMKSGDTKRLYCYVCQHFYATPQFKCKKVITTVKCSLGDEQFILWCTGKRLRE  379 (555)
T ss_pred             ccccccccccCcCCCCCCcCcccccccccccccceeecchhhhhheeccCcCceEEEeeeeeccCCeeEEeccCcceecc
Confidence            68999999999999999999                                     77999999999999999999999


Q ss_pred             eecCccCCCCCCcCCCCCCcccccccCCCCccccccceeecCCCCCCceEEEecCCCCceEEEcCCCCeEEEccCCCeeE
Q psy8716          44 YILCPYCYNNPPYRDMKKGSGCNVCTHPTCGQALLSTGIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKV  123 (141)
Q Consensus        44 y~lCP~CyN~PPf~~~~~~~~C~~C~hptC~~S~~~~~V~~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~v~l~~~a~kv  123 (141)
                      |.+||+|||||   +|+.+++|++|+||.|+|||..+||++|.||++++|++|+++ |||+|.||+|+++++-.+.++++
T Consensus       380 ~gft~fm~n~p---~m~wgagcdECthPScq~slSmlgiG~~vEc~~v~Lv~~qTs-PkwylTcnkcisvme~hgigtda  455 (555)
T KOG1957|consen  380 FGFTPFMPNNP---KMPWGAGCDECTHPSCQQSLSMLGIGQCVECESVELVLDQTS-PKWYLTCNKCISVMEKHGIGTDA  455 (555)
T ss_pred             CCccccccCCC---ccccccCCCccCCchHHhhhhcccceeEEEeccEEEEecCCC-CCceeehhhhHHHHHhhccccee
Confidence            99999999999   899999999999999999999999999999998999998877 99999999999999999999999


Q ss_pred             ecCCCCce-eeccceec
Q psy8716         124 QVCTENNC-DCVQFTSN  139 (141)
Q Consensus       124 ~v~~~~~C-~C~a~ll~  139 (141)
                      +|.-+. | -|++.+++
T Consensus       456 sI~Vhi-nsiceRnYv~  471 (555)
T KOG1957|consen  456 SIPVHI-NSICERNYVT  471 (555)
T ss_pred             eEEEee-cchhhhheEe
Confidence            998887 8 89887764

>PRK07219 DNA topoisomerase I; Validated

Probab=97.88  E-value=6.1e-05  Score=71.21  Aligned_cols=100  Identities=21%  Similarity=0.376  Sum_probs=70.7

Q ss_pred             cCcCCCCCCcCcCCCceEEEEEeCCCCeeeecCccCCCCCCcCCCCCCcccccccCCCCccccccceeecCCCCCCceEE
Q psy8716          15 TGKAMSQELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKGSGCNVCTHPTCGQALLSTGIASCLQCEGGVLV   94 (141)
Q Consensus        15 sgkp~s~e~~CPLd~FeLl~~s~g~~gksy~lCP~CyN~PPf~~~~~~~~C~~C~hptC~~S~~~~~V~~C~~C~~G~Lv   94 (141)
                      .|+....+..||.||..++.+..+ ++..|..||.|.++.+++.-                   ...+..||+|+ |.|+
T Consensus       641 ~~~~~~~~~~Cp~CG~~lvk~~~~-r~~~~~~CP~C~~~~~~~~~-------------------~~~~~~CP~Cg-~~l~  699 (822)
T PRK07219        641 TGRIKVLDEVCEKCGLPVIKILRG-KQTFVVGCPDCEAEKEEEDP-------------------DEVIGPCPKCG-GELA  699 (822)
T ss_pred             CCccccccCCCCCCCcceEEEecc-CccccccCCCCCCCcccccc-------------------ccccccCCCCC-CeeE
Confidence            344333467899999999888653 45667889999998875421                   11245899998 7888


Q ss_pred             EecCCCCceEEEcCC---CCeEEEccCCCeeEecCCCCce-eecccee
Q psy8716          95 LDLSSAPKWKICCNK---CDIIIHVFPDAQKVQVCTENNC-DCVQFTS  138 (141)
Q Consensus        95 Ldp~s~pkw~l~Cn~---C~~~v~l~~~a~kv~v~~~~~C-~C~a~ll  138 (141)
                      +......+ ++.|++   |.+...+++.. .+.+++.. | +|+..++
T Consensus       700 ~k~gr~G~-F~~Cs~yp~C~~~~~l~~~~-~~~~~~~~-CpkCg~~l~  744 (822)
T PRK07219        700 IKQLKYGS-FLGCTNYPKCKYTLPLPRRG-KITVTDEK-CPECGLPLL  744 (822)
T ss_pred             EEcCCCCC-eeeCCCCCCCCceeeccccc-ccccccCC-CCCCCCeEE
Confidence            86544444 999985   99999999753 33345666 9 9998765

>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i

Probab=96.46  E-value=0.0049  Score=37.69  Aligned_cols=36  Identities=22%  Similarity=0.485  Sum_probs=29.5

Q ss_pred             eecCCCCCCceEEEecCCCCceEEEcCC---CCeEEEccCC
Q psy8716          82 IASCLQCEGGVLVLDLSSAPKWKICCNK---CDIIIHVFPD  119 (141)
Q Consensus        82 V~~C~~C~~G~LvLdp~s~pkw~l~Cn~---C~~~v~l~~~  119 (141)
                      |..||.|+ +.|++- .+..+.+++|+.   |.++++++++
T Consensus         1 ~~~CP~Cg-~~lv~r-~~k~g~F~~Cs~yP~C~~~~~~~~n   39 (39)
T PF01396_consen    1 VEKCPKCG-GPLVLR-RGKKGKFLGCSNYPECKYTEPLPKN   39 (39)
T ss_pred             CcCCCCCC-ceeEEE-ECCCCCEEECCCCCCcCCeEeCCCC
Confidence            35799999 999994 555669999995   9999999874

e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome

>KOG2906|consensus

Probab=94.72  E-value=0.05  Score=40.25  Aligned_cols=33  Identities=18%  Similarity=0.561  Sum_probs=26.7

Q ss_pred             cCCCCCCceEEEecCCCCceEEEcCCCCeEEEccC
Q psy8716          84 SCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFP  118 (141)
Q Consensus        84 ~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~v~l~~  118 (141)
                      -||.|+ .+|++. ..+.-.+++|+.|+++..+-.
T Consensus         3 FCP~Cg-n~Live-~g~~~~rf~C~tCpY~~~I~~   35 (105)
T KOG2906|consen    3 FCPTCG-NMLIVE-SGESCNRFSCRTCPYVFPISR   35 (105)
T ss_pred             ccCCCC-CEEEEe-cCCeEeeEEcCCCCceeeEee
Confidence            489999 899996 344479999999999887754

>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]

Probab=92.06  E-value=1.4  Score=32.91  Aligned_cols=78  Identities=24%  Similarity=0.399  Sum_probs=50.0

Q ss_pred             CCCcCcCCCceEEEEEeCCCCeeeecC---ccCCCCCCcCCCCCCcccccccCCCCccccccceeecCCCCCCceEEEec
Q psy8716          21 QELKCPIDDFELLCWSMGNKGKSYILC---PYCYNNPPYRDMKKGSGCNVCTHPTCGQALLSTGIASCLQCEGGVLVLDL   97 (141)
Q Consensus        21 ~e~~CPLd~FeLl~~s~g~~gksy~lC---P~CyN~PPf~~~~~~~~C~~C~hptC~~S~~~~~V~~C~~C~~G~LvLdp   97 (141)
                      ...+||.||=+++++.. ..| .|..|   |-|..+|+.                  -.........||+|+.+.|++-.
T Consensus        16 ~~~~Cp~Cg~~m~~~~~-~~g-~f~gCs~yP~C~~~~~~------------------~~~~~~~~~~Cp~C~~~~~~~k~   75 (140)
T COG0551          16 TGQICPKCGKNMVKKFG-KYG-IFLGCSNYPKCDYYEPE------------------KAIAEKTGVKCPKCGKGLLVLKK   75 (140)
T ss_pred             cCccCCcCCCeeEEEEc-cCC-eEEEeCCCCCCCCCccc------------------ccccccCceeCCCCCCCceEEEe
Confidence            45789999999999974 446 66666   333322221                  11223456789999988888865


Q ss_pred             CCCCceEEEcC---CCCeEEEccC
Q psy8716          98 SSAPKWKICCN---KCDIIIHVFP  118 (141)
Q Consensus        98 ~s~pkw~l~Cn---~C~~~v~l~~  118 (141)
                      +...+-++.|+   .|.++.+...
T Consensus        76 ~~~~~~f~~~~~~Pkc~~~~~~~~   99 (140)
T COG0551          76 GRFGKNFLGCSNYPKCRFTEKPKP   99 (140)
T ss_pred             ccCCceEEeecCCCcCceeecCCc
Confidence            55555677777   4666665444

>PRK07220 DNA topoisomerase I; Validated

Probab=91.65  E-value=0.29  Score=46.31  Aligned_cols=54  Identities=19%  Similarity=0.295  Sum_probs=39.9

Q ss_pred             eecCCCCCCceEEEecCCCCceEEEcCC---CCeEEEccCCCeeEecCCCCce-eecccee
Q psy8716          82 IASCLQCEGGVLVLDLSSAPKWKICCNK---CDIIIHVFPDAQKVQVCTENNC-DCVQFTS  138 (141)
Q Consensus        82 V~~C~~C~~G~LvLdp~s~pkw~l~Cn~---C~~~v~l~~~a~kv~v~~~~~C-~C~a~ll  138 (141)
                      +..||.|+ +.|++......++++.|+.   |.+..++|+. .++.+++.. | +||..++
T Consensus       589 ~~~CP~Cg-~~l~~r~~r~g~~f~gCs~yp~C~~~~~l~~~-g~~~~~~~~-Cp~Cg~~~~  646 (740)
T PRK07220        589 IGKCPLCG-SDLMVRRSKRGSRFIGCEGYPECTFSLPLPKS-GQIIVTDKV-CEAHGLNHI  646 (740)
T ss_pred             ccccccCC-CeeeEEecCCCceEEEcCCCCCCCceeeCCCC-CccccCCCC-CCCCCCceE
Confidence            45899998 6677654444478899985   9999999974 345677777 9 9996444

>PRK07219 DNA topoisomerase I; Validated

Probab=90.83  E-value=0.33  Score=46.39  Aligned_cols=55  Identities=20%  Similarity=0.428  Sum_probs=38.7

Q ss_pred             eeecCCCCCCceEEEecCCCCceEEEcCC---CCeEEEccCCCeeEecCCCCce-eecccee
Q psy8716          81 GIASCLQCEGGVLVLDLSSAPKWKICCNK---CDIIIHVFPDAQKVQVCTENNC-DCVQFTS  138 (141)
Q Consensus        81 ~V~~C~~C~~G~LvLdp~s~pkw~l~Cn~---C~~~v~l~~~a~kv~v~~~~~C-~C~a~ll  138 (141)
                      .+..||.|+ +.|++......++++.|..   |.+.++||+.. ++.+.... | .|+..++
T Consensus       601 ~~~~CP~Cg-~~l~~r~~~~g~~F~gCs~yp~C~~t~~lp~~~-~~~~~~~~-Cp~CG~~lv  659 (822)
T PRK07219        601 TIGKCPECG-GDLIIIRTDKGSRFVGCSGYPDCRNTFPLPSTG-RIKVLDEV-CEKCGLPVI  659 (822)
T ss_pred             ccCcCCCCC-CcceeeeccCCceeeecCCCcCCCCeeecCCCC-ccccccCC-CCCCCcceE
Confidence            356799998 5555543333338999976   99999999854 35666666 8 8887654

>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated

Probab=90.80  E-value=1.4  Score=42.59  Aligned_cols=34  Identities=26%  Similarity=0.526  Sum_probs=23.3

Q ss_pred             ecCCC--CCCceEEEecCCCCceEEEcCC---CCeEEEcc
Q psy8716          83 ASCLQ--CEGGVLVLDLSSAPKWKICCNK---CDIIIHVF  117 (141)
Q Consensus        83 ~~C~~--C~~G~LvLdp~s~pkw~l~Cn~---C~~~v~l~  117 (141)
                      -.||+  |+ |-|++....-.+|++.|++   |.++++..
T Consensus       694 ~~CP~~~C~-g~l~~r~gr~G~~f~~Cs~yp~C~~~~~~~  732 (860)
T PRK06319        694 VPCPAIGCT-GHIVKRRSRFNKMFYSCSEYPACSVIGNSI  732 (860)
T ss_pred             CCCCCcCCC-CcEEEEecCCCCeeeccCCCCCCceeeccC
Confidence            37996  67 6677754444578899985   99775433

>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2

Probab=90.37  E-value=0.43  Score=28.51  Aligned_cols=31  Identities=19%  Similarity=0.387  Sum_probs=21.6

Q ss_pred             cCCCCCCceEEEecCCCCceEEEcCCCCeEEEcc
Q psy8716          84 SCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVF  117 (141)
Q Consensus        84 ~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~v~l~  117 (141)
                      -||+|+ ++|+... ...+.+ .|+.|+++..+-
T Consensus         3 FCp~C~-nlL~p~~-~~~~~~-~C~~C~Y~~~~~   33 (35)
T PF02150_consen    3 FCPECG-NLLYPKE-DKEKRV-ACRTCGYEEPIS   33 (35)
T ss_dssp             BETTTT-SBEEEEE-ETTTTE-EESSSS-EEE-S
T ss_pred             eCCCCC-ccceEcC-CCccCc-CCCCCCCccCCC
Confidence            389999 8888753 445555 999999987653

7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=89.82  E-value=0.67  Score=28.70  Aligned_cols=34  Identities=21%  Similarity=0.489  Sum_probs=24.5

Q ss_pred             cCCCCCCceEEEecCCCCceEEEcCCCCeEEEccCC
Q psy8716          84 SCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPD  119 (141)
Q Consensus        84 ~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~v~l~~~  119 (141)
                      -||+|+ .+|... ....+.++.|..|.+...+.+.
T Consensus         2 FCp~Cg-~~l~~~-~~~~~~~~vC~~Cg~~~~~~~~   35 (52)
T smart00661        2 FCPKCG-NMLIPK-EGKEKRRFVCRKCGYEEPIEQK   35 (52)
T ss_pred             CCCCCC-Cccccc-cCCCCCEEECCcCCCeEECCCc
Confidence            388998 666553 2333468999999999888665

>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC

Probab=87.32  E-value=0.4  Score=33.74  Aligned_cols=26  Identities=27%  Similarity=0.664  Sum_probs=21.1

Q ss_pred             CcCcCCCceEEEEEeCCCCeeeecCccCC
Q psy8716          23 LKCPIDDFELLCWSMGNKGKSYILCPYCY   51 (141)
Q Consensus        23 ~~CPLd~FeLl~~s~g~~gksy~lCP~Cy   51 (141)
                      ++||-|||..+.-.   .+.+|-+||-||
T Consensus         2 ~~CPCCg~~Tl~~~---~~~~ydIC~VC~   27 (78)
T PF14206_consen    2 YPCPCCGYYTLEER---GEGTYDICPVCF   27 (78)
T ss_pred             ccCCCCCcEEeccC---CCcCceECCCCC
Confidence            57999999887653   345699999998

>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]

Probab=87.06  E-value=0.92  Score=33.90  Aligned_cols=51  Identities=20%  Similarity=0.358  Sum_probs=34.8

Q ss_pred             cceeecCCCCCCceEEEecCCCCceEEEcC---CCCeEEEccCCCeeEecCCCCce-eecc
Q psy8716          79 STGIASCLQCEGGVLVLDLSSAPKWKICCN---KCDIIIHVFPDAQKVQVCTENNC-DCVQ  135 (141)
Q Consensus        79 ~~~V~~C~~C~~G~LvLdp~s~pkw~l~Cn---~C~~~v~l~~~a~kv~v~~~~~C-~C~a  135 (141)
                      ......||.|. +.|++- .+..+|++.|.   .|.+   ++.....+..+..+ | +|+.
T Consensus        14 ~~~~~~Cp~Cg-~~m~~~-~~~~g~f~gCs~yP~C~~---~~~~~~~~~~~~~~-Cp~C~~   68 (140)
T COG0551          14 LKTGQICPKCG-KNMVKK-FGKYGIFLGCSNYPKCDY---YEPEKAIAEKTGVK-CPKCGK   68 (140)
T ss_pred             cccCccCCcCC-CeeEEE-EccCCeEEEeCCCCCCCC---CcccccccccCcee-CCCCCC
Confidence            35677899999 888884 45555999998   4998   33223333445565 9 8995

>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C

Probab=86.55  E-value=1.1  Score=26.83  Aligned_cols=29  Identities=28%  Similarity=0.567  Sum_probs=17.3

Q ss_pred             CCCCCCceEEE-ecCCCCceEEEcCCCCeEE
Q psy8716          85 CLQCEGGVLVL-DLSSAPKWKICCNKCDIII  114 (141)
Q Consensus        85 C~~C~~G~LvL-dp~s~pkw~l~Cn~C~~~v  114 (141)
                      |+.|. +.|.+ -|......|+.|..|.+|-
T Consensus         3 C~~CG-~~l~~~ip~gd~r~R~vC~~Cg~Ih   32 (34)
T PF14803_consen    3 CPQCG-GPLERRIPEGDDRERLVCPACGFIH   32 (34)
T ss_dssp             -TTT---B-EEE--TT-SS-EEEETTTTEEE
T ss_pred             ccccc-ChhhhhcCCCCCccceECCCCCCEE
Confidence            88898 54544 3567889999999999874

>PRK14973 DNA topoisomerase I; Provisional

Probab=86.10  E-value=0.72  Score=45.06  Aligned_cols=51  Identities=20%  Similarity=0.223  Sum_probs=36.6

Q ss_pred             eecCCCCCCceEEEecCCCCceEEEcCC---CCeEEEccCCC-eeEecCCCCce-eecc
Q psy8716          82 IASCLQCEGGVLVLDLSSAPKWKICCNK---CDIIIHVFPDA-QKVQVCTENNC-DCVQ  135 (141)
Q Consensus        82 V~~C~~C~~G~LvLdp~s~pkw~l~Cn~---C~~~v~l~~~a-~kv~v~~~~~C-~C~a  135 (141)
                      ...||.|+ +.|++... ..+-++.|++   |.+.+.|++.. .++.++++. | +||+
T Consensus       588 ~~~CP~CG-~~l~ik~~-k~gkFigCS~Yp~Ck~t~~L~~~~~g~~~~~~~~-Cp~CG~  643 (936)
T PRK14973        588 IGPCPVCG-KDLRIKHI-GSSQFIGCSGYPDCTFNIGLPGTTWGWAIRTDEV-CPIHHL  643 (936)
T ss_pred             cccCCccc-ccceeecc-cCceeEECCCCCCCCccccCCccccccCCCCCCC-CCCCCC
Confidence            46799998 66776533 3344789986   99999998543 345556676 9 9998

>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein

Probab=83.67  E-value=2.1  Score=38.78  Aligned_cols=55  Identities=22%  Similarity=0.556  Sum_probs=35.1

Q ss_pred             eecCccCCCCCCcCCC-CCCcccc-cccCCCCccccccceeecCCCCCCceEEEec-------------CCCCceEEEcC
Q psy8716          44 YILCPYCYNNPPYRDM-KKGSGCN-VCTHPTCGQALLSTGIASCLQCEGGVLVLDL-------------SSAPKWKICCN  108 (141)
Q Consensus        44 y~lCP~CyN~PPf~~~-~~~~~C~-~C~hptC~~S~~~~~V~~C~~C~~G~LvLdp-------------~s~pkw~l~Cn  108 (141)
                      +-.||.|--+-|-... .++.+|. .|.              .||.|. +.|.+-.             ..+..|.|.|+
T Consensus        26 ~~yCp~CL~~~p~~e~~~~~nrC~r~Cf--------------~CP~C~-~~L~~~~~~~~~~~~~~~~~~~~~~~~l~C~   90 (483)
T PF05502_consen   26 SYYCPNCLFEVPSSEARSEKNRCSRNCF--------------DCPICF-SPLSVRASDTPPSPPDPSSDSGGKPYYLSCS   90 (483)
T ss_pred             eeECccccccCChhhheeccceeccccc--------------cCCCCC-CcceeEecccccccccccccCCCCCEEEECC
Confidence            3489999988885432 3455665 555              255666 4333321             23468999999


Q ss_pred             CCCeE
Q psy8716         109 KCDII  113 (141)
Q Consensus       109 ~C~~~  113 (141)
                      .|.+.
T Consensus        91 ~C~Ws   95 (483)
T PF05502_consen   91 YCRWS   95 (483)
T ss_pred             Cceee
Confidence            99874

p62 binds directly to the Arp1 subunit of dynactin [, ].

>PRK07220 DNA topoisomerase I; Validated

Probab=83.39  E-value=4.1  Score=38.68  Aligned_cols=31  Identities=16%  Similarity=0.442  Sum_probs=23.5

Q ss_pred             ecCCCCCCceEEEecCCCCceEEEcCCCCeE
Q psy8716          83 ASCLQCEGGVLVLDLSSAPKWKICCNKCDII  113 (141)
Q Consensus        83 ~~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~  113 (141)
                      ..||.|+.+.+.....+...|++.|..|++.
T Consensus       636 ~~Cp~Cg~~~~k~~~~g~~~~~~~Cp~C~~~  666 (740)
T PRK07220        636 KVCEAHGLNHIRIINGGKRPWDLGCPQCNFI  666 (740)
T ss_pred             CCCCCCCCceEEEEecCCccceeeCCCCCCc
Confidence            4699998677766655545699999889974

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	141
4ayb_P	48	DNA-directed RNA polymerase; transferase, multi-su	93.0
1dl6_A	58	Transcription factor II B (TFIIB); zinc ribbon, ge	87.18
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	87.14
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	81.49
3qt1_I	133	DNA-directed RNA polymerases I, II, and III subun;	80.11

>4ayb_P DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2pmz_P 2wb1_P 2y0s_P 3hkz_P 2waq_P 4b1o_P 4b1p_X

Probab=93.00  E-value=0.046  Score=34.46  Aligned_cols=15  Identities=13%  Similarity=0.642  Sum_probs=13.2

Q ss_pred             CCCcCcCCCceEEEE
Q psy8716          21 QELKCPIDDFELLCW   35 (141)
Q Consensus        21 ~e~~CPLd~FeLl~~   35 (141)
                      .+.+||+|||-++.=
T Consensus        22 P~IrCpyCGyrii~K   36 (48)
T 4ayb_P           22 PGVRCPYCGYKIIFM   36 (48)
T ss_dssp             SSSCCTTTCCSCEEC
T ss_pred             CCcccCccCcEEEEE
Confidence            789999999999864

>1dl6_A Transcription factor II B (TFIIB); zinc ribbon, gene regulation; NMR {Homo sapiens} SCOP: g.41.3.1 PDB: 1rly_A 1ro4_A

Probab=87.18  E-value=0.45  Score=30.30  Aligned_cols=32  Identities=19%  Similarity=0.541  Sum_probs=22.9

Q ss_pred             ceeecCCCCCCceEEEecCCCCceEEEcCCCCeEE
Q psy8716          80 TGIASCLQCEGGVLVLDLSSAPKWKICCNKCDIII  114 (141)
Q Consensus        80 ~~V~~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~v  114 (141)
                      +.+..||+|++..|+.|...+-   +.|..|.++|
T Consensus         9 l~~~~Cp~C~~~~lv~D~~~ge---~vC~~CGlVl   40 (58)
T 1dl6_A            9 LPRVTCPNHPDAILVEDYRAGD---MICPECGLVV   40 (58)
T ss_dssp             CSCCSBTTBSSSCCEECSSSCC---EECTTTCCEE
T ss_pred             cccccCcCCCCCceeEeCCCCe---EEeCCCCCEE
Confidence            4455788887546888765443   8888888877

>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1

Probab=87.14  E-value=0.37  Score=29.26  Aligned_cols=30  Identities=33%  Similarity=0.749  Sum_probs=23.2

Q ss_pred             eecCCCCCCceEEEecCCCCceEEEcCCCCeEE
Q psy8716          82 IASCLQCEGGVLVLDLSSAPKWKICCNKCDIII  114 (141)
Q Consensus        82 V~~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~v  114 (141)
                      +..||.|++..|+.|+..+   .|.|..|..++
T Consensus         5 ~~~CP~C~~~~l~~d~~~g---elvC~~CG~v~   34 (50)
T 1pft_A            5 QKVCPACESAELIYDPERG---EIVCAKCGYVI   34 (50)
T ss_dssp             CCSCTTTSCCCEEEETTTT---EEEESSSCCBC
T ss_pred             cEeCcCCCCcceEEcCCCC---eEECcccCCcc
Confidence            4579999833899997543   49999998876

>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=81.49  E-value=1.5  Score=31.03  Aligned_cols=35  Identities=17%  Similarity=0.468  Sum_probs=26.3

Q ss_pred             eecCCCCCCceEEEecCC-CCceEEEcCCCCeEEEcc
Q psy8716          82 IASCLQCEGGVLVLDLSS-APKWKICCNKCDIIIHVF  117 (141)
Q Consensus        82 V~~C~~C~~G~LvLdp~s-~pkw~l~Cn~C~~~v~l~  117 (141)
                      ..-||+|+ ++|.+.... ..+-++.|+.|+++..+-
T Consensus         4 m~FCp~Cg-n~L~~~~~~~~~~~~~~C~~C~y~~~~~   39 (113)
T 3h0g_I            4 FQYCIECN-NMLYPREDKVDRVLRLACRNCDYSEIAA   39 (113)
T ss_dssp             CCCCSSSC-CCCEECCCTTTCCCCEECSSSCCEECCS
T ss_pred             ceeCcCCC-CEeeEcccCCCCeeEEECCCCCCeEEcC
Confidence            34599999 888885432 467899999999987654

>3qt1_I DNA-directed RNA polymerases I, II, and III subun; transferase-transcription complex, RNA polymerase II, transc elongation; 4.30A {Saccharomyces cerevisiae}

Probab=80.11  E-value=0.53  Score=34.78  Aligned_cols=40  Identities=15%  Similarity=0.268  Sum_probs=28.3

Q ss_pred             cccceeecCCCCCCceEEEecC-CCCceEEEcCCCCeEEEcc
Q psy8716          77 LLSTGIASCLQCEGGVLVLDLS-SAPKWKICCNKCDIIIHVF  117 (141)
Q Consensus        77 ~~~~~V~~C~~C~~G~LvLdp~-s~pkw~l~Cn~C~~~v~l~  117 (141)
                      ++..++--||+|+ ++|+.... ...+-++.|++|++...+.
T Consensus        19 ~~~~~~~FCPeCg-NmL~pked~~~~~l~~~CrtCgY~~~~~   59 (133)
T 3qt1_I           19 SHMTTFRFCRDCN-NMLYPREDKENNRLLFECRTCSYVEEAG   59 (133)
T ss_dssp             ---CCCCBCTTTC-CBCBCCBCTTTCCBCCBCSSSCCBCCCS
T ss_pred             ccccCCeeCCCCC-CEeeECccCCCceeEEECCCCCCcEEcC
Confidence            4567788899999 88888542 2357889999999866543

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	141
d1k3xa3	40	Endonuclease VIII {Escherichia coli [TaxId: 562]}	85.49
d1pfta_	50	Transcription initiation factor TFIIB, N-terminal	85.39
d2jnea1	71	Hypothetical protein YfgJ {Escherichia coli [TaxId	82.56
d1dl6a_	58	Transcription initiation factor TFIIB, N-terminal	80.73

>d1k3xa3 g.39.1.8 (A:223-262) Endonuclease VIII {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: C-terminal, Zn-finger domain of MutM-like DNA repair proteins
domain: Endonuclease VIII
species: Escherichia coli [TaxId: 562]

Probab=85.49  E-value=0.51  Score=26.76  Aligned_cols=30  Identities=13%  Similarity=0.314  Sum_probs=25.5

Q ss_pred             CCCcCcCCCceEEEEEeCCCCeeeecCccCCC
Q psy8716          21 QELKCPIDDFELLCWSMGNKGKSYILCPYCYN   52 (141)
Q Consensus        21 ~e~~CPLd~FeLl~~s~g~~gksy~lCP~CyN   52 (141)
                      .+..||.|+-.+..+..  .|++...||.|-|
T Consensus        11 ~g~pC~~C~~~I~~~~~--~gR~t~~Cp~CQ~   40 (40)
T d1k3xa3          11 DGEPCERCGSIIEKTTL--SSRPFYWCPGCQH   40 (40)
T ss_dssp             TTSBCTTTCCBCEEEEE--TTEEEEECTTTCC
T ss_pred             CCCccCcCCCEEEEEEE--CCCCCEEChhhCC
Confidence            45789999999998886  4899999999965

>d1pfta_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIB, N-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=85.39  E-value=0.32  Score=28.86  Aligned_cols=28  Identities=36%  Similarity=0.829  Sum_probs=22.2

Q ss_pred             cCCCCCCceEEEecCCCCceEEEcCCCCeEE
Q psy8716          84 SCLQCEGGVLVLDLSSAPKWKICCNKCDIII  114 (141)
Q Consensus        84 ~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~v  114 (141)
                      .||+|++..|+.|..++   -+.|+.|-+++
T Consensus         7 ~Cp~Cgs~~iv~D~~~G---e~vC~~CG~Vi   34 (50)
T d1pfta_           7 VCPACESAELIYDPERG---EIVCAKCGYVI   34 (50)
T ss_dssp             SCTTTSCCCEEEETTTT---EEEESSSCCBC
T ss_pred             cCcCCCCCcEEEECCCC---eEecccCCcEe
Confidence            58899877888886554   78899998776

>d2jnea1 g.41.18.1 (A:1-71) Hypothetical protein YfgJ {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Rubredoxin-like
superfamily: YfgJ-like
family: YfgJ-like
domain: Hypothetical protein YfgJ
species: Escherichia coli [TaxId: 562]

Probab=82.56  E-value=1.1  Score=28.65  Aligned_cols=34  Identities=24%  Similarity=0.338  Sum_probs=23.4

Q ss_pred             ceeecCCCCCCceEEEecCCCCceEEEcCCCCeEEE
Q psy8716          80 TGIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIH  115 (141)
Q Consensus        80 ~~V~~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~v~  115 (141)
                      .-++.||+|....-+|..=++-.  ..||.|+=+|.
T Consensus        29 ~~~a~CPdC~~~Le~LkACGAvd--YFC~~cn~LiS   62 (71)
T d2jnea1          29 EMKALCPDCHQPLQVLKACGAVD--YFCQHGHGLIS   62 (71)
T ss_dssp             EEEEECTTTCSBCEEEEETTEEE--EEETTTTEEEC
T ss_pred             eeEEeCCccccHHHHHHhccchh--hhhccCCceeE
Confidence            44677999987788886544433  45888886654

>d1dl6a_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIB, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.73  E-value=0.64  Score=28.30  Aligned_cols=32  Identities=19%  Similarity=0.541  Sum_probs=21.3

Q ss_pred             ceeecCCCCCCceEEEecCCCCceEEEcCCCCeEE
Q psy8716          80 TGIASCLQCEGGVLVLDLSSAPKWKICCNKCDIII  114 (141)
Q Consensus        80 ~~V~~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~v  114 (141)
                      +.-..||+|++..|+.|...+-   +.|+.|.+++
T Consensus         9 ~~~~~Cp~Cgs~~ii~D~~~Ge---~vC~~CG~Vl   40 (58)
T d1dl6a_           9 LPRVTCPNHPDAILVEDYRAGD---MICPECGLVV   40 (58)
T ss_dssp             CSCCSBTTBSSSCCEECSSSCC---EECTTTCCEE
T ss_pred             ccccCCCCCCCCCEEEECCCCc---EecccCCCEe
Confidence            3445677887667777754433   7788888776