Citrus Sinensis ID: 012081

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-
Protein Sequence
MGGGGRVEVVSSKGCSRLFLGSVPSLRRLRGGVQSFESMSPASSSLASDSVLPANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHISADLARQVGMMLENIQNGIAREEINGGNVPEDAQSCKNKISQEKRQQTVNLAKNGVRSRRSRRMQTCQTPIRPLTPSSLLDSICWSISEPTSTASIYTDSFSGEDVNEHHPSVFFDAEADGKDSEASFANLTRMLTESEKSELIFKNHFLTILFPVDRFAEMGPSSRTYFSDNGFTCLQVLDYIYEFYQV
Secondary Structure (PSIPRED)
cccccEEEEEEcccccccccccHHHHHHHHcccccccccccccccccccccccccccccccEEEEccccHHHHHHHHHHHHHHccEEcccccccccEEEEEccccHHHHHHHHHccccccEEEcHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccHHHHHHHHHHHHHcccEEEcccccccccEEEEEccHHHHHHHHccccEEcHHHHHHHHHHHccHHHccccHHHHHHHHHHHHccccccHHHHHcccccccccccccccccHHHHHHHHHHHHcccccccccccccccccccccccccccccccEEcccccccccccccccccccccccccccccccccccccccHHccccccccccccccHHHHccccEEEEcccHHHHHccccccccccccccHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccccEEEEEEcccccEEEEcccccccccccccccccccccccccccccccccccccccEEEEEEccccHHHHHHHHHHHHHHccccccccccccEEEEEEcccccHHHHHHHHcccccEEEEEHHHHHHHHHcccccccHHEEEccccccccccccccccccccccccccccHHHcccccHHHHHcccccccccccHcccccEEEEcccccHHHHHHHHHHHHccccEEEEEEEEccccEEEEEccHHHHHHHccccccccHHHHHHHHHHccccEEEEEcHHHHHHHHHHHHHHcccccccEccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHcEEEEEccccccEEEEEEcccccccccccccEEEEccccccccccccccccccccccHHHHHHEcccEEEEEccHHHHHcccccccccccccccHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MGGGGRVEVVSskgcsrlflgsvpslrrlrggvqsfesmspassslasdsvlpanapfsGLVICVTGLSKEARKQVMEATErlggqyspdlhpqctHLVVQSFGGRKFEHALkhgsrnglYIVTLGWFVDSVRRNVRLSESLYTVksidehgmhLDKLNRLvgfagtensclpagiyeakqfnatgkherdsnrsmnstlsgcsmyvdsDVSEELRNKVFEAATNEGATLVNQWFVGcgasyvvceedsvqkymghsnnlvTPVWVLKTAKEKHVQRLVHISADLARQVGMMLENIQNGiareeinggnvpedaQSCKNKISQEKRQQTVNLAkngvrsrrsrrmqtcqtpirpltpsslldsicwsiseptstasiytdsfsgedvnehhpsvffdaeadgkdseASFANLTRMLTESEKSELIFKnhfltilfpvdrfaemgpssrtyfsdngftCLQVLDYIYEFYQV
Flexible Loop (DISEMBL)
mggggrvevvsskgcsrlflgsvpslRRLRGGVQSFESMSPASSSLASDSVLPANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYtvksidehgmhLDKLNRLVGFAGTENSCLPAGIYEAKQFnatgkherdsnrsmnstLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHISADLARQVGMMLENIQNGIAREEINGGNVPEDAQSCKNkisqekrqqtvnlakngvrsrrsrrmqtcqtpirpltpssllDSICWSISEPTSTASIYTDSFSGEDVNEHHPSVFFDAEADGKDSEASFANLTRMLTESEKSELIFKNHFLTILFPVDRFAEMGPSSRTYFSDNGFTCLQVLDYIYEFYQV
Low Complexity Region (SEG)
MGGGGRVEVVSSKGCSRLFLGSVPSLRRLRGGVQsfesmspassslasdsVLPANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHISADLARQVGMMLENIQNGIAREEINGGNVPEDAQSCKNKISQEKRQQTVNLAKNGVRSRRSRRMQTCQTPIRPLTPSSLLDSICWSISEPTSTASIYTDSFSGEDVNEHHPSVFFDAEADGKDSEASFANLTRMLTESEKSELIFKNHFLTILFPVDRFAEMGPSSRTYFSDNGFTCLQVLDYIYEFYQV
Disordered region (IsUnstruct)
**************CSRLFLGS********************************NAPFSGLVICVTGLSK*************GGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQF***********************YV*******LRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHISADLARQVGMMLENIQNGIA*********************************************************SLLDSICWSISE******IY********************************************ELIFKNHFLTILFPVDRFAEMGPSSRTYFSDNGFTCLQVLDYIYEFY**
Disordered Region (DISOPRED)
****GRV*VVSSKGCSRLFLGSVPSLRRLRGG*****************SVLPANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTV***********************************************************MYVDSDV************TNEGATLVNQWFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHISADLARQVG**********************************************************************LDSICWSISE*****************************************************LIFKNHFLTILFPVDRFAEMGPSSRTYFSDNGFTCLQVLDYIYEFYQV
Disordered Region (DISEMBL)
*********VSSKGCSRLFLGSVPSLRRLRGGVQS*************DSVLPANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNA*************STLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHISADLARQVGMMLENIQNGIAREEINGGNVPEDAQSCKNKISQEKRQQTVNLA**************CQTPIRPLTPSSLLDSICWSISEPTSTASIYTDSFSGEDVNEHHPSVFFDAEADGKDSEASFANLTRMLTESEKSELIFKNHFLTILFPVDRFAEMGPSSRTYFSDNGFTCLQVLDYIYEFYQV
Disordered Region (DISPRO)
****GRVEVVSSKGCSRLFLGSV***************************VLPANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSI**********NRLVGFAGTENSCLPAGIYEAKQFN*T**HERDSNRSMNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHISADLARQVGMMLENIQN******************************TVNLAKNGVRSRR**RMQTCQTPIRPLTPSSLLDSICWSISEPTSTASIYTDSFS***************E*******************SEKSELIFKNHFLTILFPVDRFAEMGPSSRTYFSDNGFTCLQVLDYIYEFYQV
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGGGGRVEVVSSKGCSRLFLGSVPSLRRLRGGVQSFESMSPASSSLASDSVLPANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHISADLARQVGMMLENIQNGIAREEINGGNVPEDAQSCKNKISQEKRQQTVNLAKNGVRSRRSRRMQTCQTPIRPLTPSSLLDSICWSISEPTSTASIYTDSFSGEDVNEHHPSVFFDAEADGKDSEASFANLTRMLTESEKSELIFKNHFLTILFPVDRFAEMGPSSRTYFSDNGFTCLQVLDYIYEFYQV
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	471	2.2.26 [Sep-21-2011]
Q6ZQF0	1515	DNA topoisomerase 2-bindi	yes	no	0.201	0.062	0.41	1e-10
Q92547	1522	DNA topoisomerase 2-bindi	yes	no	0.174	0.053	0.425	4e-10
Q800K6	1513	DNA topoisomerase 2-bindi	N/A	no	0.452	0.140	0.257	4e-09
Q7ZZY3	1513	DNA topoisomerase 2-bindi	N/A	no	0.452	0.140	0.257	9e-09
Q90WJ3	1256	PAX-interacting protein 1	N/A	no	0.186	0.070	0.340	2e-07
Q6NZQ4	1056	PAX-interacting protein 1	no	no	0.186	0.083	0.340	2e-06
A0JNA8	984	PAX-interacting protein 1	no	no	0.186	0.089	0.340	4e-06
Q6ZW49	1069	PAX-interacting protein 1	no	no	0.186	0.082	0.329	5e-06
Q9H8V3	914	Protein ECT2 OS=Homo sapi	no	no	0.171	0.088	0.337	1e-05
P32372	648	S-M checkpoint control pr	yes	no	0.167	0.121	0.289	2e-05

>sp|Q6ZQF0|TOPB1_MOUSE DNA topoisomerase 2-binding protein 1 OS=Mus musculus GN=Topbp1 PE=1 SV=2

 Score = 68.6 bits (166), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 41/100 (41%), Positives = 56/100 (56%), Gaps = 5/100 (5%)

Query: 58  FSGLVICVTGLSKEARKQVMEATERLGGQYSPDLH-PQCTHLVVQSFGGRKFEHALKHGS 116
           F G +ICVTGL+   RK V + T + GGQY   L   +CTHL+VQ   G+K+E A     
Sbjct: 200 FLGCIICVTGLNGIHRKTVQQLTAKHGGQYMGQLKMNECTHLIVQEPKGQKYECA----R 255

Query: 117 RNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLD 156
           R  ++ VTL WF DS+ +     ES+Y  ++  E  M  D
Sbjct: 256 RWNVHCVTLQWFHDSIEKGFCQDESIYKAETRVEAKMVPD 295

Required for DNA replication. Plays a role in the rescue of stalled replication forks and checkpoint control. Binds double-stranded DNA breaks and nicks as well as single-stranded DNA. Recruits the SWI/SNF chromatin remodeling complex to E2F1-responsive promoters. Down-regulates E2F1 activity and inhibits E2F1-dependent apoptosis during G1/S transition and after DNA damage. Induces a large increase in the kinase activity of ATR (By similarity). May play a role in spermatogenesis.
Mus musculus (taxid: 10090)

>sp|Q92547|TOPB1_HUMAN DNA topoisomerase 2-binding protein 1 OS=Homo sapiens GN=TOPBP1 PE=1 SV=3

 Score = 66.6 bits (161), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 37/87 (42%), Positives = 50/87 (57%), Gaps = 5/87 (5%)

Query: 58  FSGLVICVTGLSKEARKQVMEATERLGGQYSPDLH-PQCTHLVVQSFGGRKFEHALKHGS 116
           F G +ICVTGL    RK+V + T + GGQY   L   +CTHL+VQ   G+K+E A     
Sbjct: 200 FLGCIICVTGLCGLDRKEVQQLTVKHGGQYMGQLKMNECTHLIVQEPKGQKYECA----K 255

Query: 117 RNGLYIVTLGWFVDSVRRNVRLSESLY 143
           R  ++ VT  WF DS+ +     ES+Y
Sbjct: 256 RWNVHCVTTQWFFDSIEKGFCQDESIY 282

Required for DNA replication. Plays a role in the rescue of stalled replication forks and checkpoint control. Binds double-stranded DNA breaks and nicks as well as single-stranded DNA. Recruits the SWI/SNF chromatin remodeling complex to E2F1-responsive promoters. Down-regulates E2F1 activity and inhibits E2F1-dependent apoptosis during G1/S transition and after DNA damage. Induces a large increase in the kinase activity of ATR.

Homo sapiens (taxid: 9606)

>sp|Q800K6|TOB1A_XENLA DNA topoisomerase 2-binding protein 1-A OS=Xenopus laevis GN=topbp1-A PE=1 SV=2

 Score = 63.2 bits (152), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 63/245 (25%), Positives = 108/245 (44%), Gaps = 32/245 (13%)

Query: 58  FSGLVICVTGLSKEARKQVMEATERLGGQYSPDLH-PQCTHLVVQSFGGRKFEHALKHGS 116
           F G  ICVTGLS   RK+V   T   GG+Y+  L   + THL+VQ   G+K+E A K   
Sbjct: 199 FRGCTICVTGLSSLDRKEVQRLTALHGGEYTGQLKMNESTHLIVQEAKGQKYECARKW-- 256

Query: 117 RNGLYIVTLGWFVDSVRRNVRLSESLY------TVKSIDEHGMHL---DKLNRLVGFAGT 167
              ++ +++ WF DS+ +     E++Y      T+KS+ +         K N    +  +
Sbjct: 257 --NVHCISVQWFFDSIEKGFCQDETMYKIEPASTIKSVPDTSTPTGGNSKPNSRTLYDVS 314

Query: 168 ENSCLPAGIYEAKQFNATGKHERD------------SNRSMNSTLSGCSMYVDSDVSEEL 215
           + S +         FN+      D            S ++ +  L GC +Y+      +L
Sbjct: 315 QISNISTSCVNESAFNSAMASRLDPPADTLENLDISSLQAPDDLLDGCRIYLCGFGGRKL 374

Query: 216 RNKVFEAATNEGATLVNQWFVGCGASYVVCEED-SVQKYMG---HSNNLVTPVWVLKTAK 271
            +K+ +   N G    NQ   G     +V E D  +++++    H   ++T  W+L +  
Sbjct: 375 -DKLRKLINNGGGVRFNQ-LTGDVTHIIVGETDEELKQFLNKTQHRPYVLTVKWLLDSFA 432

Query: 272 EKHVQ 276
           + H+Q
Sbjct: 433 KGHLQ 437

Has dual roles in initiation of DNA replication, and regulation of checkpoint responses. Required for DNA replication initiation but not for the formation of pre-replicative complexes or the elongation stages. Necessary for the loading of replication factors onto chromatin, including gemc1, cdc45, DNA polymerases and components of the GINS complex such as ginsl/sld5. Binds chromatin in both S-phase cyclin-dependent kinase (S-CDK)-independent and S-CDK-dependent modes. Chromatin binding is required for the action of S-CDK, which in turn triggers the formation of preinitiation complexes of DNA replication. Its role in checkpoint activation is independent of the DNA replication role. In response to DNA damage, triggers the recruitment of checkpoint signaling proteins on chromatin, which activate the chek1 signaling pathway and block S-phase progression. Increases the kinase activity of atr to numerous substrates, and is required for the phosphorylation of Rad1.

Xenopus laevis (taxid: 8355)

>sp|Q7ZZY3|TOB1B_XENLA DNA topoisomerase 2-binding protein 1-B OS=Xenopus laevis GN=topbp1-B PE=2 SV=1

 Score = 62.0 bits (149), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 63/245 (25%), Positives = 108/245 (44%), Gaps = 32/245 (13%)

Query: 58  FSGLVICVTGLSKEARKQVMEATERLGGQYSPDLH-PQCTHLVVQSFGGRKFEHALKHGS 116
           F G  ICVTGLS   RK+V   T   GG+Y+  L   + THL+VQ   G+K+E A K   
Sbjct: 199 FRGCTICVTGLSSLDRKEVQRLTALHGGEYTGQLKMNESTHLIVQEAKGQKYECARKW-- 256

Query: 117 RNGLYIVTLGWFVDSVRRNVRLSESLY------TVKSIDEHGMHL---DKLNRLVGFAGT 167
              ++ +++ WF DS+ +     E++Y      T+KS+ +         K N    +  +
Sbjct: 257 --IVHCISVQWFFDSIEKGFCQDETMYKIEPASTIKSVPDTSTPTGGNSKPNSRTLYDVS 314

Query: 168 ENSCLPAGIYEAKQFNATGKHERD------------SNRSMNSTLSGCSMYVDSDVSEEL 215
           + S +         FN+      D            S ++ +  L GC +Y+      +L
Sbjct: 315 QISNISTSCVNESAFNSAMASRLDPPADTLENLDISSLQAPDDLLDGCRIYLCGFGGRKL 374

Query: 216 RNKVFEAATNEGATLVNQWFVGCGASYVVCEED-SVQKYMG---HSNNLVTPVWVLKTAK 271
            +K+ +   N G    NQ   G     +V E D  +++++    H   ++T  W+L +  
Sbjct: 375 -DKLRKLINNGGGVRFNQ-LTGDVTHIIVGETDEELKQFLNKTQHRPYVLTVKWLLDSFA 432

Query: 272 EKHVQ 276
           + H+Q
Sbjct: 433 KGHLQ 437

Has dual roles in initiation of DNA replication, and regulation of checkpoint responses. Required for DNA replication initiation but not for the formation of pre-replicative complexes or the elongation stages. Necessary for the loading of replication factors onto chromatin, including gemc1, cdc45, DNA polymerases and components of the GINS complex such as ginsl/sld5. Binds chromatin in both S-phase cyclin-dependent kinase (S-CDK)-independent and S-CDK-dependent modes. Chromatin binding is required for the action of S-CDK, which in turn triggers the formation of preinitiation complexes of DNA replication. Its role in checkpoint activation is independent of the DNA replication role. In response to DNA damage, triggers the recruitment of checkpoint signaling proteins on chromatin, which activate the chek1 signaling pathway and block S-phase progression. Increases the kinase activity of atr to numerous substrates, and is required for the phosphorylation of Rad1.

Xenopus laevis (taxid: 8355)

>sp|Q90WJ3|PAXI1_XENLA PAX-interacting protein 1 OS=Xenopus laevis GN=paxip1 PE=1 SV=1

 Score = 57.4 bits (137), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 31/91 (34%), Positives = 48/91 (52%), Gaps = 3/91 (3%)

Query: 58  FSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSR 117
           F G+  C++ +S + R  +   T   GG     L+ +CTHL+V    G K+E+A + GS 
Sbjct: 99  FFGVTACLSQVSPDDRNSLWALTTFYGGDCQLSLNKKCTHLIVPEPKGNKYEYAFQRGS- 157

Query: 118 NGLYIVTLGWFVDSVRRNVRLSESLYTVKSI 148
             + IVT  W +DSV    +  E+LY  + I
Sbjct: 158 --IKIVTPDWVLDSVSEKTKKDEALYHPRLI 186

Involved in DNA damage response. Promotes ubiquitination of PCNA following UV irradiation and may regulate recruitment of polymerase eta and rad51 to chromatin after DNA damage. May function as transcriptional cofactor in TGF beta signaling. Accentuates smad2-dependent transcription.

Xenopus laevis (taxid: 8355)

>sp|Q6NZQ4|PAXI1_MOUSE PAX-interacting protein 1 OS=Mus musculus GN=Paxip1 PE=1 SV=1

 Score = 54.3 bits (129), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 31/91 (34%), Positives = 45/91 (49%), Gaps = 3/91 (3%)

Query: 58  FSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSR 117
           F GL  C++ +S E R  +       GG    +L+ +CTHL+V    G K+E A+K   R
Sbjct: 99  FFGLTACLSQVSSEDRSALWALVTFHGGSCQLNLNKKCTHLIVPEPKGEKYERAVK---R 155

Query: 118 NGLYIVTLGWFVDSVRRNVRLSESLYTVKSI 148
             + IVT  W +D V    R  E+ Y  + I
Sbjct: 156 TSIKIVTPDWVLDCVSEKRRKDEAFYHPRLI 186

Involved in DNA damage response and in transcriptional regulation through histone methyltransferase (HMT) complexes. Plays a role in early development. In DNA damage response is required for cell survival after ionizing radiation. In vitro shown to be involved in the homologous recombination mechanism for the repair of double-strand breaks (DSBs). Its localization to DNA damage foci requires Rnf8 and Ube2n. Recruits Tp53bp1 to DNA damage foci and, at least in particular repair processes, effective DNA damage response appears to require the association with Tp53bp1 phosphorylated by Atm. Together with Tp53bp1 regulates Atm association. Recruits Pa1 to sites of DNA damage and the Pa1:Paxip1 complex is required for cell survival in response to DNA damage; the function is probbaly independent of MLL-containing histone methyltransferase (HMT) complexes. Promotes ubiquitination of PCNA following UV irradiation and may regulate recruitment of polymerase eta and Rad51 to chromatin after DNA damage. Proposed to be involved in transcriptional regulation by linking MLL-containing histone methyltransferase (HMT) complexes to gene promoters by interacting with promoter-bound transcription factors such as Pax2. Associates with gene promoters that are known to be regulated by Mll2. During immunoglobulin class switching in activated B-cells is involved in trimethylation of histone H3 at 'Lys-4' and in transcription initiation of downstream switch regions at the immunoglobulin heavy-chain (Igh) locus; this function appears to involve the recruitment of MLL-containing HMT complexes.

Mus musculus (taxid: 10090)

>sp|A0JNA8|PAXI1_BOVIN PAX-interacting protein 1 OS=Bos taurus GN=PAXIP1 PE=2 SV=1

 Score = 53.1 bits (126), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 31/91 (34%), Positives = 46/91 (50%), Gaps = 3/91 (3%)

Query: 58  FSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSR 117
           F G+  C++ +S E R  +       GG    +L+ +CTHLVV    G K+E AL+   R
Sbjct: 99  FFGITACLSQVSPEDRSALWAMLTFHGGGCQLNLNRKCTHLVVPEPKGEKYECALR---R 155

Query: 118 NGLYIVTLGWFVDSVRRNVRLSESLYTVKSI 148
             + IVT  W +D +    R  E+LY  + I
Sbjct: 156 ASIKIVTPDWVLDCISEKTRKDEALYHPRLI 186

Involved in DNA damage response and in transcriptional regulation through histone methyltransferase (HMT) complexes. Plays a role in early development. In DNA damage response is required for cell survival after ionizing radiation. In vitro shown to be involved in the homologous recombination mechanism for the repair of double-strand breaks (DSBs). Its localization to DNA damage foci requires RNF8 and UBE2N. Recruits TP53BP1 to DNA damage foci and, at least in particular repair processes, effective DNA damage response appears to require the association with TP53BP1 phosphorylated by ATM. Together with TP53BP1 regulates ATM association. Recruits PA1 to sites of DNA damage and the PA1:PAXIP1 complex is required for cell survival in response to DNA damage; the function is probbaly independent of MLL-containing histone methyltransferase (HMT) complexes. Promotes ubiquitination of PCNA following UV irradiation and may regulate recruitment of polymerase eta and RAD51 to chromatin after DNA damage. Proposed to be involved in transcriptional regulation by linking MLL-containing histone methyltransferase (HMT) complexes to gene promoters by interacting with promoter-bound transcription factors such as PAX2. Associates with gene promoters that are known to be regulated by MLL2. During immunoglobulin class switching in activated B-cells is involved in trimethylation of histone H3 at 'Lys-4' and in transcription initiation of downstream switch regions at the immunoglobulin heavy-chain (Igh) locus; this function appears to involve the recruitment of MLL-containing HMT complexes.

Bos taurus (taxid: 9913)

>sp|Q6ZW49|PAXI1_HUMAN PAX-interacting protein 1 OS=Homo sapiens GN=PAXIP1 PE=1 SV=2

 Score = 53.1 bits (126), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 30/91 (32%), Positives = 44/91 (48%), Gaps = 3/91 (3%)

Query: 58  FSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSR 117
           F G+  C++ +S E R  +       GG     L+ +CTHL+V    G K+E ALK   R
Sbjct: 99  FFGITACLSQVSSEDRSALWALVTFYGGDCQLTLNKKCTHLIVPEPKGEKYECALK---R 155

Query: 118 NGLYIVTLGWFVDSVRRNVRLSESLYTVKSI 148
             + IVT  W +D V    +  E+ Y  + I
Sbjct: 156 ASIKIVTPDWVLDCVSEKTKKDEAFYHPRLI 186

Involved in DNA damage response and in transcriptional regulation through histone methyltransferase (HMT) complexes. Plays a role in early development. In DNA damage response is required for cell survival after ionizing radiation. In vitro shown to be involved in the homologous recombination mechanism for the repair of double-strand breaks (DSBs). Its localization to DNA damage foci requires RNF8 and UBE2N. Recruits TP53BP1 to DNA damage foci and, at least in particular repair processes, effective DNA damage response appears to require the association with TP53BP1 phosphorylated by ATM at 'Ser-25'. Together with TP53BP1 regulates ATM association. Recruits PA1 to sites of DNA damage and the PA1:PAXIP1 complex is required for cell survival in response to DNA damage; the function is probbaly independent of MLL-containing histone methyltransferase (HMT) complexes. Promotes ubiquitination of PCNA following UV irradiation and may regulate recruitment of polymerase eta and RAD51 to chromatin after DNA damage. Proposed to be involved in transcriptional regulation by linking MLL-containing histone methyltransferase (HMT) complexes to gene promoters by interacting with promoter-bound transcription factors such as PAX2. Associates with gene promoters that are known to be regulated by MLL2. During immunoglobulin class switching in activated B-cells is involved in trimethylation of histone H3 at 'Lys-4' and in transcription initiation of downstream switch regions at the immunoglobulin heavy-chain (Igh) locus; this function appears to involve the recruitment of MLL-containing HMT complexes.

Homo sapiens (taxid: 9606)

>sp|Q9H8V3|ECT2_HUMAN Protein ECT2 OS=Homo sapiens GN=ECT2 PE=1 SV=4

 Score = 52.0 bits (123), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 30/89 (33%), Positives = 44/89 (49%), Gaps = 8/89 (8%)

Query: 57  PFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQS--FGGRKFEHALKH 114
           PF   ++   G S E +  + E TE  GG+Y P    +CTHLVV+        FE + K 
Sbjct: 270 PFQDCILSFLGFSDEEKTNMEEMTEMQGGKYLPLGDERCTHLVVEENIVKDLPFEPSKK- 328

Query: 115 GSRNGLYIVTLGWFVDSVRRNVRLSESLY 143
                LY+V   WF  S++ + R  E++Y
Sbjct: 329 -----LYVVKQEWFWGSIQMDARAGETMY 352

Guanine nucleotide exchange factor (GEF) that catalyzes the exchange of GDP for GTP. Promotes guanine nucleotide exchange on the Rho family members of small GTPases, like RHOA, RHOC, RAC1 and CDC42. Required for signal transduction pathways involved in the regulation of cytokinesis. Component of the centralspindlin complex that serves as a microtubule-dependent and Rho-mediated signaling required for the myosin contractile ring formation during the cell cycle cytokinesis. Regulates the translocation of RHOA from the central spindle to the equatorial region. Plays a role in the control of mitotic spindle assembly; regulates the activation of CDC42 in metaphase for the process of spindle fibers attachment to kinetochores before chromosome congression. Involved in the regulation of epithelial cell polarity; participates in the formation of epithelial tight junctions in a polarity complex PARD3-PARD6-protein kinase PRKCQ-dependent manner. Plays a role in the regulation of neurite outgrowth. Inhibits phenobarbital (PB)-induced NR1I3 nuclear translocation. Stimulates the activity of RAC1 through its association with the oncogenic PARD6A-PRKCI complex in cancer cells, thereby acting to coordinately drive tumor cell proliferation and invasion. Also stimulates genotoxic stress-induced RHOB activity in breast cancer cells leading to their cell death.

Homo sapiens (taxid: 9606)

>sp|P32372|RAD4_SCHPO S-M checkpoint control protein rad4 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rad4 PE=1 SV=2

 Score = 51.2 bits (121), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/83 (28%), Positives = 43/83 (51%), Gaps = 4/83 (4%)

Query: 63  ICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYI 122
           +C+T + +  R ++     + GG + PDL    THL+  +  GRK+E+ALK      + +
Sbjct: 107 VCLTNIGQPERSRIENYVLKHGGTFCPDLTRDVTHLIAGTSSGRKYEYALKW----KINV 162

Query: 123 VTLGWFVDSVRRNVRLSESLYTV 145
           V + W   S++RN  L    + +
Sbjct: 163 VCVEWLWQSIQRNAVLEPQYFQL 185

Essential component for DNA replication and also the checkpoint control system which couples S and M phases. May directly or indirectly interact with chromatin proteins to form the complex required for the initiation and/or progression of DNA synthesis.

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

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	471
255550221	556	topbp1, putative [Ricinus communis] gi|2	0.976	0.827	0.733	0.0
359476287	546	PREDICTED: uncharacterized protein LOC10	0.972	0.838	0.712	0.0
359476289	551	PREDICTED: uncharacterized protein LOC10	0.972	0.831	0.703	0.0
147855443	565	hypothetical protein VITISV_022337 [Viti	0.972	0.810	0.683	0.0
356509851	542	PREDICTED: uncharacterized protein LOC10	0.983	0.854	0.660	1e-180
356518187	541	PREDICTED: uncharacterized protein LOC10	0.983	0.855	0.672	1e-179
357465905	570	DNA topoisomerase 2-binding protein [Med	0.951	0.785	0.663	1e-177
388494050	529	unknown [Lotus japonicus]	0.970	0.863	0.657	1e-169
449452943	553	PREDICTED: uncharacterized protein LOC10	0.987	0.840	0.633	1e-166
296081736	463	unnamed protein product [Vitis vinifera]	0.783	0.796	0.712	1e-157

>gi|255550221|ref|XP_002516161.1| topbp1, putative [Ricinus communis] gi|223544647|gb|EEF46163.1| topbp1, putative [Ricinus communis]

 Score =  726 bits (1875), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 350/477 (73%), Positives = 411/477 (86%), Gaps = 17/477 (3%)

Query: 6   RVEVVSSKGCSRLFLG---SVPSLRRLRGGVQSFESMSPASSSLASDSVLP-ANAPFSGL 61
           +VEV++SKGCSRLF+G   S+PS R    G+QSFE MSP ++S+ S++VL  +  PFSGL
Sbjct: 13  KVEVINSKGCSRLFVGLSSSIPSFR----GLQSFEPMSPTTASIGSEAVLVRSTGPFSGL 68

Query: 62  VICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQ---SFGGRKFEHALKHGSRN 118
           VICVTGLS+EARKQVMEATERLGG+YSP+LHP CTHLVVQ    FGGRKFEHALKHGS+N
Sbjct: 69  VICVTGLSREARKQVMEATERLGGRYSPNLHPHCTHLVVQISFYFGGRKFEHALKHGSKN 128

Query: 119 GLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYE 178
           GL++VT+GWFVDSVRRNVRLSESLY+VKS+ E  + LD LNRLVG  GTENSCLP GI +
Sbjct: 129 GLFVVTIGWFVDSVRRNVRLSESLYSVKSVGETDVRLDDLNRLVGINGTENSCLPVGIND 188

Query: 179 AKQFNAT-GKHER----DSNRSMNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQ 233
           AK+F+A  G H+R     SNR+++STLSG SM++DS++S+ELRNKV+EAA  EGAT ++Q
Sbjct: 189 AKKFDAIEGLHKRLSARSSNRNIDSTLSGSSMFIDSEISDELRNKVYEAAIREGATFLDQ 248

Query: 234 WFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHISADLARQVGMML 293
           WF+GC AS+VVCE  SVQ+Y+GHSNNLVTP+WVLKTAKEK+ QRLVH+SADLARQVGMML
Sbjct: 249 WFIGCSASHVVCEGASVQRYLGHSNNLVTPLWVLKTAKEKNAQRLVHLSADLARQVGMML 308

Query: 294 ENIQNGIAREEINGGNVPEDAQSCKNKISQEKRQQTVNLAKNGVRSRRSRRMQTCQTPIR 353
           EN QNG A +EIN G+ P D ++ ++++S  +RQ  VN AKN VRSRR RRMQTCQTPIR
Sbjct: 309 ENFQNGSAEQEINTGSAPLDVRNLRSQVSYGQRQHIVNFAKNAVRSRRGRRMQTCQTPIR 368

Query: 354 PLTPSSLLDSICWSISEPTSTASIYTDSFSGEDVNEHHPSVFFDAEADGKDSEASFANLT 413
           P+TPSSLLDSICWSISEPTSTASIYTDSFS EDV+E HPSVFFDA+ DGKDSEASFANLT
Sbjct: 369 PITPSSLLDSICWSISEPTSTASIYTDSFSSEDVSE-HPSVFFDAKGDGKDSEASFANLT 427

Query: 414 RMLTESEKSELIFKNHFLTILFPVDRFAEMGPSSRTYFSDNGFTCLQVLDYIYEFYQ 470
           R LTESEK+ELIFKNHFLTILFPVDRF+EMGPSSRT+F +NGFTC+QVLDYIY FYQ
Sbjct: 428 RALTESEKTELIFKNHFLTILFPVDRFSEMGPSSRTFFGENGFTCIQVLDYIYTFYQ 484

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359476287|ref|XP_003631811.1| PREDICTED: uncharacterized protein LOC100262753 isoform 2 [Vitis vinifera]

 Score =  690 bits (1781), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 335/470 (71%), Positives = 395/470 (84%), Gaps = 12/470 (2%)

Query: 7   VEVVSSKGCSRLFLGSVPSLRRLRGGVQSFESMSPASSSLASDSVLPANAPFSGLVICVT 66
           VEV+SSKGCSRL +G   SL  +RG +++FE MSPASSS+       +N PFSGLVICVT
Sbjct: 11  VEVISSKGCSRLLVGISSSLPPMRG-LKTFEPMSPASSSVGR-----SNGPFSGLVICVT 64

Query: 67  GLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLG 126
           GLSKEARKQVM+A ERLGGQYSP+LHPQCTHLVVQSFGGRK +HALKHGS+NGL++VTLG
Sbjct: 65  GLSKEARKQVMDAAERLGGQYSPNLHPQCTHLVVQSFGGRKLDHALKHGSKNGLFVVTLG 124

Query: 127 WFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYE-AKQFNAT 185
           WFVDSVRRNVRLSESLY VK++ E+G+ +D+LNRL+GF+G ENSCLPAG++E AKQ   T
Sbjct: 125 WFVDSVRRNVRLSESLYYVKNVGENGVRMDELNRLIGFSGAENSCLPAGMFENAKQSVMT 184

Query: 186 GKHE-----RDSNRSMNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGA 240
                    R+S RS++STLSG SM++DSD+S ELRNKV EAA   GA LV+QWFVGC A
Sbjct: 185 EDPHLWFSGRESKRSVDSTLSGHSMFIDSDISAELRNKVVEAAARGGAMLVDQWFVGCNA 244

Query: 241 SYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHISADLARQVGMMLENIQNGI 300
           +YVVCE  S+Q+Y+GHSNNLVTP+W+LKTAKE++ QRLVH+SADLARQVGM+LEN+QNGI
Sbjct: 245 NYVVCEGPSIQRYLGHSNNLVTPLWILKTAKERYAQRLVHMSADLARQVGMVLENVQNGI 304

Query: 301 AREEINGGNVPEDAQSCKNKISQEKRQQTVNLAKNGVRSRRSRRMQTCQTPIRPLTPSSL 360
             EE+N  N P+D    + K S E+RQ+ V+LAK GVR+RR+R MQTCQTPIRP+ PSSL
Sbjct: 305 ELEEMNRENGPQDTPCPRKKASHEERQEIVSLAKAGVRNRRARYMQTCQTPIRPINPSSL 364

Query: 361 LDSICWSISEPTSTASIYTDSFSGEDVNEHHPSVFFDAEADGKDSEASFANLTRMLTESE 420
           LDSICWSISEPTSTASIYT+S S  DV+EH  SVFFDA+ DGK+SEASFAN +R+LTESE
Sbjct: 365 LDSICWSISEPTSTASIYTESSSVGDVSEHQTSVFFDAKGDGKESEASFANFSRLLTESE 424

Query: 421 KSELIFKNHFLTILFPVDRFAEMGPSSRTYFSDNGFTCLQVLDYIYEFYQ 470
           K+ELIFK HFLTIL PVDRFAEMGPSSRT+FS  GFTCLQVLD+IY FYQ
Sbjct: 425 KAELIFKGHFLTILLPVDRFAEMGPSSRTFFSSKGFTCLQVLDHIYAFYQ 474

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359476289|ref|XP_002282127.2| PREDICTED: uncharacterized protein LOC100262753 isoform 1 [Vitis vinifera]

 Score =  682 bits (1759), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 334/475 (70%), Positives = 394/475 (82%), Gaps = 17/475 (3%)

Query: 7   VEVVSSKGCSRLFLGSVPSLRRLRGGVQSFESMSPASSSLASDSVLPANAPFSGLVICVT 66
           VEV+SSKGCSRL +G   SL  +RG +++FE MSPASSS+       +N PFSGLVICVT
Sbjct: 11  VEVISSKGCSRLLVGISSSLPPMRG-LKTFEPMSPASSSVGR-----SNGPFSGLVICVT 64

Query: 67  GLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQS-----FGGRKFEHALKHGSRNGLY 121
           GLSKEARKQVM+A ERLGGQYSP+LHPQCTHLVVQ      FGGRK +HALKHGS+NGL+
Sbjct: 65  GLSKEARKQVMDAAERLGGQYSPNLHPQCTHLVVQISFNLIFGGRKLDHALKHGSKNGLF 124

Query: 122 IVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYE-AK 180
           +VTLGWFVDSVRRNVRLSESLY VK++ E+G+ +D+LNRL+GF+G ENSCLPAG++E AK
Sbjct: 125 VVTLGWFVDSVRRNVRLSESLYYVKNVGENGVRMDELNRLIGFSGAENSCLPAGMFENAK 184

Query: 181 QFNATGKHE-----RDSNRSMNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWF 235
           Q   T         R+S RS++STLSG SM++DSD+S ELRNKV EAA   GA LV+QWF
Sbjct: 185 QSVMTEDPHLWFSGRESKRSVDSTLSGHSMFIDSDISAELRNKVVEAAARGGAMLVDQWF 244

Query: 236 VGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHISADLARQVGMMLEN 295
           VGC A+YVVCE  S+Q+Y+GHSNNLVTP+W+LKTAKE++ QRLVH+SADLARQVGM+LEN
Sbjct: 245 VGCNANYVVCEGPSIQRYLGHSNNLVTPLWILKTAKERYAQRLVHMSADLARQVGMVLEN 304

Query: 296 IQNGIAREEINGGNVPEDAQSCKNKISQEKRQQTVNLAKNGVRSRRSRRMQTCQTPIRPL 355
           +QNGI  EE+N  N P+D    + K S E+RQ+ V+LAK GVR+RR+R MQTCQTPIRP+
Sbjct: 305 VQNGIELEEMNRENGPQDTPCPRKKASHEERQEIVSLAKAGVRNRRARYMQTCQTPIRPI 364

Query: 356 TPSSLLDSICWSISEPTSTASIYTDSFSGEDVNEHHPSVFFDAEADGKDSEASFANLTRM 415
            PSSLLDSICWSISEPTSTASIYT+S S  DV+EH  SVFFDA+ DGK+SEASFAN +R+
Sbjct: 365 NPSSLLDSICWSISEPTSTASIYTESSSVGDVSEHQTSVFFDAKGDGKESEASFANFSRL 424

Query: 416 LTESEKSELIFKNHFLTILFPVDRFAEMGPSSRTYFSDNGFTCLQVLDYIYEFYQ 470
           LTESEK+ELIFK HFLTIL PVDRFAEMGPSSRT+FS  GFTCLQVLD+IY FYQ
Sbjct: 425 LTESEKAELIFKGHFLTILLPVDRFAEMGPSSRTFFSSKGFTCLQVLDHIYAFYQ 479

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147855443|emb|CAN79610.1| hypothetical protein VITISV_022337 [Vitis vinifera]

 Score =  675 bits (1741), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 334/489 (68%), Positives = 394/489 (80%), Gaps = 31/489 (6%)

Query: 7   VEVVSSKGCSRLFLGSVPSLRRLRGGVQSFESMSPASSSLASDSVLPANAPFSGLVICVT 66
           VEV+SSKGCSRL +G   SL  +RG +++FE MSPASSS+       +N PFSGLVICVT
Sbjct: 11  VEVISSKGCSRLLVGISSSLPPMRG-LKTFEPMSPASSSVGR-----SNGPFSGLVICVT 64

Query: 67  GLSKEARKQVMEATERLGGQYSPDLHPQCTHLVV-------------------QSFGGRK 107
           GLSKEARKQVM+ATERLGGQYSP+LHPQCTHLVV                    SFGGRK
Sbjct: 65  GLSKEARKQVMDATERLGGQYSPNLHPQCTHLVVFYDFMLCFETLSCGLFNTFYSFGGRK 124

Query: 108 FEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGT 167
            +HALKHGS+NGL++VTLGWFVDSVRRNVRLSESLY VK++ E+G+ +D+LNRL+GF+G 
Sbjct: 125 LDHALKHGSKNGLFVVTLGWFVDSVRRNVRLSESLYYVKNVGENGVRMDELNRLIGFSGA 184

Query: 168 ENSCLPAGIYE-AKQFNATGKHE-----RDSNRSMNSTLSGCSMYVDSDVSEELRNKVFE 221
           ENSCLPAG++E AKQ   T         R+S RS++STLSG SM++DSD+S ELRNKV E
Sbjct: 185 ENSCLPAGMFENAKQSVMTEDPHLWFSGRESKRSVDSTLSGHSMFIDSDISAELRNKVVE 244

Query: 222 AATNEGATLVNQWFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHI 281
           AA   GA LV+QWFVGC A+YVVCE  S+Q+Y+GHSNNLVTP+W+LKTAKE++ QRLVH+
Sbjct: 245 AAARGGAMLVDQWFVGCNANYVVCEGPSIQRYLGHSNNLVTPLWILKTAKERYAQRLVHM 304

Query: 282 SADLARQVGMMLENIQNGIAREEINGGNVPEDAQSCKNKISQEKRQQTVNLAKNGVRSRR 341
           SADLARQVGM+LEN+QNGI  EE+N  N P+D    + K S E+RQ+ V+LAK GVR+RR
Sbjct: 305 SADLARQVGMVLENVQNGIELEEMNRENGPQDTPCPRKKASHEERQEIVSLAKAGVRNRR 364

Query: 342 SRRMQTCQTPIRPLTPSSLLDSICWSISEPTSTASIYTDSFSGEDVNEHHPSVFFDAEAD 401
           +R MQTCQTPIRP+ PSSLLDSICWSISEPTSTASIYT+S S  DV+EH  SVFFDA+ D
Sbjct: 365 ARYMQTCQTPIRPINPSSLLDSICWSISEPTSTASIYTESSSVGDVSEHQTSVFFDAKGD 424

Query: 402 GKDSEASFANLTRMLTESEKSELIFKNHFLTILFPVDRFAEMGPSSRTYFSDNGFTCLQV 461
           GK+SEASFAN +R+LTESEK+ELIFK HFLTIL P DRFAEMGPSSRT+FS  GFTCLQV
Sbjct: 425 GKESEASFANFSRLLTESEKAELIFKGHFLTILLPXDRFAEMGPSSRTFFSSKGFTCLQV 484

Query: 462 LDYIYEFYQ 470
           LD+IY FYQ
Sbjct: 485 LDHIYAFYQ 493

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356509851|ref|XP_003523658.1| PREDICTED: uncharacterized protein LOC100807358 [Glycine max]

 Score =  636 bits (1640), Expect = e-180,   Method: Compositional matrix adjust.
 Identities = 315/477 (66%), Positives = 379/477 (79%), Gaps = 14/477 (2%)

Query: 1   MGGGGRVEVVSSKGCSRLFLGSVPSLRRLRGGVQSFESMSPASSSLASDSVLPANAPFSG 60
           MGG GRVEVVS KGCSRLF  S+PS R    G+Q  E MSPASS L    V  +  PF+G
Sbjct: 1   MGGDGRVEVVSGKGCSRLFSSSLPSFR----GLQPLEPMSPASSPL---QVPSSTTPFAG 53

Query: 61  LVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQ---SFGGRKFEHALKHGSR 117
           LVICVTGLSKEAR QVMEAT+RLGGQYSP+LHP+CTHLVVQ   SFGGRKFEHALKHG++
Sbjct: 54  LVICVTGLSKEARNQVMEATDRLGGQYSPNLHPRCTHLVVQISFSFGGRKFEHALKHGAK 113

Query: 118 NGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIY 177
           NGL++VTLGWFVDSVR++VRLSES Y VKS  ++  HL+    L  +   ENSCLPA I 
Sbjct: 114 NGLFVVTLGWFVDSVRKSVRLSESHYRVKSYGDNNTHLEDFRLLPEYTNAENSCLPARIL 173

Query: 178 EAKQFNATGKHER----DSNRSMNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQ 233
           + KQ  +  + +R    +S R+++STLSGCS+YVD  +S ELRNKV E A+ EGA+LV Q
Sbjct: 174 QTKQAISVEELQRFTGRESIRNLDSTLSGCSIYVDPGISSELRNKVIETASREGASLVEQ 233

Query: 234 WFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHISADLARQVGMML 293
           WFVGC  S+VV E  S+Q+Y+G+S+ L+TP+WVLKTAKEK+V+RLV +S DLA+QVG+ML
Sbjct: 234 WFVGCNVSHVVTEGTSIQRYLGYSSYLITPLWVLKTAKEKYVRRLVRMSVDLAKQVGLML 293

Query: 294 ENIQNGIAREEINGGNVPEDAQSCKNKISQEKRQQTVNLAKNGVRSRRSRRMQTCQTPIR 353
           E+I NGI+ +E+    V  +    ++++  E+RQQ VN AKNGVRSRR RRMQTCQTPIR
Sbjct: 294 EDIHNGISGKEVIKQKVLNNLLDTESEVGYEERQQIVNSAKNGVRSRRGRRMQTCQTPIR 353

Query: 354 PLTPSSLLDSICWSISEPTSTASIYTDSFSGEDVNEHHPSVFFDAEADGKDSEASFANLT 413
           P+TP++LLDSICWSISE TS ASIYTDSFS ED +E+H S+FF A+ DGKDSEASF+N T
Sbjct: 354 PITPNNLLDSICWSISESTSAASIYTDSFSVEDPSENHTSIFFYAKGDGKDSEASFSNST 413

Query: 414 RMLTESEKSELIFKNHFLTILFPVDRFAEMGPSSRTYFSDNGFTCLQVLDYIYEFYQ 470
           R LTESEKSELIFKN FLTILFP+DRFAEMGPSSRT+FS NGF CLQVLD+I+ FYQ
Sbjct: 414 RPLTESEKSELIFKNPFLTILFPIDRFAEMGPSSRTFFSHNGFRCLQVLDHIHAFYQ 470

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356518187|ref|XP_003527763.1| PREDICTED: uncharacterized protein LOC100815253 [Glycine max]

 Score =  635 bits (1638), Expect = e-179,   Method: Compositional matrix adjust.
 Identities = 320/476 (67%), Positives = 384/476 (80%), Gaps = 13/476 (2%)

Query: 1   MGGGGRVEVVSSKGCSRLFLGSVPSLRRLRGGVQSFESMSPASSSLASDSVLPANAPFSG 60
           MGG GRVEVVS KGCSRLF  S+PS R    G+Q  E MSPASS L    V  + APF+G
Sbjct: 1   MGGDGRVEVVSGKGCSRLFSSSIPSFR----GLQPLEPMSPASSPL---QVPSSTAPFAG 53

Query: 61  LVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQ--SFGGRKFEHALKHGSRN 118
           LVICVTGLSKEAR QVMEATERLGGQYSP+LHPQCTHLVVQ  SFGGRKFEHALKHG++N
Sbjct: 54  LVICVTGLSKEARNQVMEATERLGGQYSPNLHPQCTHLVVQIYSFGGRKFEHALKHGAKN 113

Query: 119 GLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYE 178
           GL++VTLGWFVDSVR+ VRLSES Y VKS  ++   L+    L  +   ENSC PA I++
Sbjct: 114 GLFVVTLGWFVDSVRKTVRLSESHYRVKSYGDNNTRLEDFRLLPEYRNAENSCFPARIHQ 173

Query: 179 AKQFNATGKHER----DSNRSMNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQW 234
           + Q N+  + +R    +SNR+ +STLSGCS+YVD  +S ELRNKV E A+ EGA+LV QW
Sbjct: 174 SNQANSVEELQRFTGRESNRNSDSTLSGCSIYVDPGISSELRNKVIETASREGASLVEQW 233

Query: 235 FVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHISADLARQVGMMLE 294
           FVGC  S+VV E  S+Q+Y+G+S+NL+TP+W+LKTAKEK+V++LVH+S DLA+QVG+MLE
Sbjct: 234 FVGCSVSHVVTEGTSIQRYLGYSSNLITPLWILKTAKEKYVRKLVHMSVDLAKQVGLMLE 293

Query: 295 NIQNGIAREEINGGNVPEDAQSCKNKISQEKRQQTVNLAKNGVRSRRSRRMQTCQTPIRP 354
           +I N I+ +E+    V  +    ++++S E+RQQ VN AKNGVR+RR RRMQTCQTPIRP
Sbjct: 294 DIHNDISGKEVIKQKVLNNLPDTESEVSYEERQQIVNSAKNGVRNRRGRRMQTCQTPIRP 353

Query: 355 LTPSSLLDSICWSISEPTSTASIYTDSFSGEDVNEHHPSVFFDAEADGKDSEASFANLTR 414
           +TP++LLDSICWSISEPTSTASIYTDSFS ED +E+H S+FFDA+ DGKDSEASF+N TR
Sbjct: 354 ITPNNLLDSICWSISEPTSTASIYTDSFSVEDPSENHTSIFFDAKGDGKDSEASFSNSTR 413

Query: 415 MLTESEKSELIFKNHFLTILFPVDRFAEMGPSSRTYFSDNGFTCLQVLDYIYEFYQ 470
            LTESEKSELIFKNHFLTIL P+DRFAEMGPSSRT+FS NGFTCLQVLD+I  FYQ
Sbjct: 414 PLTESEKSELIFKNHFLTILLPIDRFAEMGPSSRTFFSHNGFTCLQVLDHIRAFYQ 469

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357465905|ref|XP_003603237.1| DNA topoisomerase 2-binding protein [Medicago truncatula] gi|355492285|gb|AES73488.1| DNA topoisomerase 2-binding protein [Medicago truncatula]

 Score =  626 bits (1614), Expect = e-177,   Method: Compositional matrix adjust.
 Identities = 311/469 (66%), Positives = 374/469 (79%), Gaps = 21/469 (4%)

Query: 6   RVEVVSSKGCSRLFLGSVPSLRRLRGGVQSFESMSPASSSLASDSVLPANAPFSGLVICV 65
           RVEVVS KGCSRLF  S+ +L       Q  + MSP SSS      LP+NAPF+GLVICV
Sbjct: 13  RVEVVSGKGCSRLFSSSIRNL-------QPLDQMSPVSSS----PQLPSNAPFAGLVICV 61

Query: 66  TGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTL 125
           TGLSKEAR QVMEATERLGGQYSP+LHPQCTHLV  SFGGRKFEHALKHG++NGL++VTL
Sbjct: 62  TGLSKEARNQVMEATERLGGQYSPNLHPQCTHLV-HSFGGRKFEHALKHGTKNGLFVVTL 120

Query: 126 GWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNAT 185
           GWFVDSVR+NVRL+ESLY++KS  ++ M LD    L G+    N CLPA I+E K  +  
Sbjct: 121 GWFVDSVRKNVRLTESLYSLKSYGDNDMKLDDFRLLPGYTNAGN-CLPARIHEIKHTHHA 179

Query: 186 GKHER----DSNRSMNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGAS 241
            +  R    +SNRS++S+LSGCS+YVD  +S EL+NKV E A+ EGA+L +QWFVGC  S
Sbjct: 180 EEFRRFSGAESNRSLDSSLSGCSIYVDPGISSELQNKVAETASREGASLADQWFVGCNVS 239

Query: 242 YVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHISADLARQVGMMLENIQNGIA 301
           +VV E  S+Q+Y+G+S+NL+TPVW+LKTAKEK VQRLV +S DLARQVG+ML++I     
Sbjct: 240 HVVTEGTSIQRYLGYSSNLITPVWILKTAKEKQVQRLVSMSVDLARQVGLMLDDISG--- 296

Query: 302 REEINGGNVPEDAQSCKNKISQEKRQQTVNLAKNGVRSRRSRRMQTCQTPIRPLTPSSLL 361
            +EI    V +D Q  K++I  ++RQQ VN AKNGVRSRR RRMQTCQTPIRP+TP++LL
Sbjct: 297 -KEIVKQKVHDDLQGSKSEIGCKERQQIVNSAKNGVRSRRGRRMQTCQTPIRPITPNNLL 355

Query: 362 DSICWSISEPTSTASIYTDSFSGEDVNEHHPSVFFDAEADGKDSEASFANLTRMLTESEK 421
           DSICWSISE TSTASIYTDSFS ED +E+H S+FFDA+ DGKDS+ASF++ TR LTESEK
Sbjct: 356 DSICWSISEATSTASIYTDSFSAEDPSENHTSIFFDAKGDGKDSDASFSHSTRPLTESEK 415

Query: 422 SELIFKNHFLTILFPVDRFAEMGPSSRTYFSDNGFTCLQVLDYIYEFYQ 470
           SELIFKNHFLTILFPVDRF+E+GPS+RT FS NGFTCLQVLD+I+ FYQ
Sbjct: 416 SELIFKNHFLTILFPVDRFSEIGPSTRTLFSHNGFTCLQVLDHIHAFYQ 464

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388494050|gb|AFK35091.1| unknown [Lotus japonicus]

 Score =  602 bits (1553), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 309/470 (65%), Positives = 368/470 (78%), Gaps = 13/470 (2%)

Query: 1   MGGGGRVEVVSSKGCSRLFLGSVPSLRRLRGGVQSFESMSPASSSLASDSVLPANAPFSG 60
           MGG G VEVV  KGCSRLF  S         G+Q  E +SPASSS        ++APF+G
Sbjct: 1   MGGDGIVEVVGGKGCSRLFSSSFR-------GLQPMEPVSPASSSSRVR----SSAPFAG 49

Query: 61  LVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGL 120
           LVICVTGLSKE R QV EATERLGGQYS +LHPQCTHLVVQSFGGRK EHALKHG++NGL
Sbjct: 50  LVICVTGLSKETRNQVREATERLGGQYSSNLHPQCTHLVVQSFGGRKLEHALKHGAKNGL 109

Query: 121 YIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAK 180
            + TLGWFVDSVR+NVRL+ES Y+VKS  ++ M LD    L  +   EN CLPA I+E K
Sbjct: 110 LVATLGWFVDSVRKNVRLTESHYSVKSYGDNNMRLDDFKLLTRYTEAENYCLPARIHETK 169

Query: 181 QFNATGKHERDSNRSMNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGA 240
             ++  + +R S R   STLSGCS+YVD  +S EL  KV E A+ EGA LV QWFVGC  
Sbjct: 170 HAHSVEEIQRFSGR--ESTLSGCSIYVDPGISSELCTKVVETASREGARLVEQWFVGCNV 227

Query: 241 SYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHISADLARQVGMMLENIQNGI 300
           S+VV E  S+Q+Y+G+S+NLVTP+W+LKTAKEK+VQRLVH+SADLA+QVG+MLE+I NGI
Sbjct: 228 SHVVTEGTSIQRYLGYSSNLVTPLWILKTAKEKNVQRLVHMSADLAKQVGLMLEDINNGI 287

Query: 301 AREEINGGNVPEDAQSCKNKISQEKRQQTVNLAKNGVRSRRSRRMQTCQTPIRPLTPSSL 360
           + +E+    V  D Q  K+++S ++RQQ VN AK GVR+RR RRMQTCQTPIRP+TP++L
Sbjct: 288 SGKEVIKQKVHGDLQGSKSEVSYKERQQIVNSAKIGVRNRRGRRMQTCQTPIRPITPNNL 347

Query: 361 LDSICWSISEPTSTASIYTDSFSGEDVNEHHPSVFFDAEADGKDSEASFANLTRMLTESE 420
           LDSI WSISEPTSTASIYTDSFS ED +E+  S+FF+++ DGKDSEASFAN TR LTESE
Sbjct: 348 LDSISWSISEPTSTASIYTDSFSVEDPSENCNSIFFESKGDGKDSEASFANSTRPLTESE 407

Query: 421 KSELIFKNHFLTILFPVDRFAEMGPSSRTYFSDNGFTCLQVLDYIYEFYQ 470
           KSELIFKNHFLTILFP+DRF+EMGPSSRT+FS +GFTCLQVLD+I  FYQ
Sbjct: 408 KSELIFKNHFLTILFPIDRFSEMGPSSRTFFSHSGFTCLQVLDHIQAFYQ 457

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449452943|ref|XP_004144218.1| PREDICTED: uncharacterized protein LOC101211759 [Cucumis sativus]

 Score =  592 bits (1527), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 306/483 (63%), Positives = 365/483 (75%), Gaps = 18/483 (3%)

Query: 3   GGGRVEVVSSKGCSRLFLGSVPSLRRLRGGVQSFESMSPASSSLASDSV-LPANAPFSGL 61
           GGG VEVVSSKGCSRL  G    L  L GG+Q  ESMS AS S  S+ V +    PF+GL
Sbjct: 2   GGGTVEVVSSKGCSRLLFGFSSPLSSL-GGLQQLESMSLASPSSRSEPVKVRLAGPFTGL 60

Query: 62  VICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQS---------FGGRKFEHAL 112
           VICVTGLSKEARKQV EATERLGGQYSP+LHPQCTHLVVQ           GGRKFEHA 
Sbjct: 61  VICVTGLSKEARKQVKEATERLGGQYSPNLHPQCTHLVVQISLDIFNLFFLGGRKFEHAF 120

Query: 113 KHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCL 172
           KHGSRNGL++V+LGWFVDSVRRNVRLSESLYT+KS+ E+   LD+L  L G  G  NSCL
Sbjct: 121 KHGSRNGLFVVSLGWFVDSVRRNVRLSESLYTIKSLGENSGRLDELKHLAGSGGDGNSCL 180

Query: 173 PAGIYEAKQFNATGKHE-----RDSNRSMNSTLSGCSMYVDSDVSEELRNKVFEAATNEG 227
           P GI+  +Q +  G  +     +D +R M+S LSG SMY+D+D+S ELR+KV EAA   G
Sbjct: 181 PVGIHGVEQNDTIGDSQLSFSKKDRDRRMDSNLSGQSMYIDTDISPELRHKVIEAAKGVG 240

Query: 228 ATLVNQWFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHISADLAR 287
           A+LV+ WF GC  ++VVCE  S+ +Y+G S+NLVTP+W+LKT  EK  QRL+H+SADLAR
Sbjct: 241 ASLVDHWFAGCSTNHVVCERTSIHRYLGQSSNLVTPLWILKTVTEKRAQRLIHMSADLAR 300

Query: 288 QVGMMLENIQNGIAREEINGGNVPEDAQSCKNKISQEKRQQTVNLAKNGVRSRRSRRMQT 347
           Q+   LE++      E  N     ED ++ ++K +Q +R+QT++ AK GVR RR+ RMQT
Sbjct: 301 QISSTLEDLCAENFTEAKN--RQQEDTRTSRSKTTQAEREQTISNAKLGVRKRRACRMQT 358

Query: 348 CQTPIRPLTPSSLLDSICWSISEPTSTASIYTDSFSGEDVNEHHPSVFFDAEADGKDSEA 407
           CQ PIRPLTPSSLLDSICWSISEP+S+ASIYTDSFS E V+EHH   FFDA  DGK+SEA
Sbjct: 359 CQNPIRPLTPSSLLDSICWSISEPSSSASIYTDSFSSEGVSEHHTPEFFDATGDGKESEA 418

Query: 408 SFANLTRMLTESEKSELIFKNHFLTILFPVDRFAEMGPSSRTYFSDNGFTCLQVLDYIYE 467
           SF+NLTR L+ESEKSE++FKNH+LTILFPVDRF EMGPSSRTYFS  GFTC Q+LD+IY 
Sbjct: 419 SFSNLTRPLSESEKSEVVFKNHYLTILFPVDRFFEMGPSSRTYFSYKGFTCFQILDHIYT 478

Query: 468 FYQ 470
           FYQ
Sbjct: 479 FYQ 481

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296081736|emb|CBI20741.3| unnamed protein product [Vitis vinifera]

 Score =  559 bits (1441), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 267/375 (71%), Positives = 317/375 (84%), Gaps = 6/375 (1%)

Query: 102 SFGGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRL 161
           SFGGRK +HALKHGS+NGL++VTLGWFVDSVRRNVRLSESLY VK++ E+G+ +D+LNRL
Sbjct: 17  SFGGRKLDHALKHGSKNGLFVVTLGWFVDSVRRNVRLSESLYYVKNVGENGVRMDELNRL 76

Query: 162 VGFAGTENSCLPAGIYE-AKQFNATGKHE-----RDSNRSMNSTLSGCSMYVDSDVSEEL 215
           +GF+G ENSCLPAG++E AKQ   T         R+S RS++STLSG SM++DSD+S EL
Sbjct: 77  IGFSGAENSCLPAGMFENAKQSVMTEDPHLWFSGRESKRSVDSTLSGHSMFIDSDISAEL 136

Query: 216 RNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHV 275
           RNKV EAA   GA LV+QWFVGC A+YVVCE  S+Q+Y+GHSNNLVTP+W+LKTAKE++ 
Sbjct: 137 RNKVVEAAARGGAMLVDQWFVGCNANYVVCEGPSIQRYLGHSNNLVTPLWILKTAKERYA 196

Query: 276 QRLVHISADLARQVGMMLENIQNGIAREEINGGNVPEDAQSCKNKISQEKRQQTVNLAKN 335
           QRLVH+SADLARQVGM+LEN+QNGI  EE+N  N P+D    + K S E+RQ+ V+LAK 
Sbjct: 197 QRLVHMSADLARQVGMVLENVQNGIELEEMNRENGPQDTPCPRKKASHEERQEIVSLAKA 256

Query: 336 GVRSRRSRRMQTCQTPIRPLTPSSLLDSICWSISEPTSTASIYTDSFSGEDVNEHHPSVF 395
           GVR+RR+R MQTCQTPIRP+ PSSLLDSICWSISEPTSTASIYT+S S  DV+EH  SVF
Sbjct: 257 GVRNRRARYMQTCQTPIRPINPSSLLDSICWSISEPTSTASIYTESSSVGDVSEHQTSVF 316

Query: 396 FDAEADGKDSEASFANLTRMLTESEKSELIFKNHFLTILFPVDRFAEMGPSSRTYFSDNG 455
           FDA+ DGK+SEASFAN +R+LTESEK+ELIFK HFLTIL PVDRFAEMGPSSRT+FS  G
Sbjct: 317 FDAKGDGKESEASFANFSRLLTESEKAELIFKGHFLTILLPVDRFAEMGPSSRTFFSSKG 376

Query: 456 FTCLQVLDYIYEFYQ 470
           FTCLQVLD+IY FYQ
Sbjct: 377 FTCLQVLDHIYAFYQ 391

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	471
TAIR|locus:2057711	470	AT2G26270 "AT2G26270" [Arabido	0.760	0.761	0.560	1.5e-106
TAIR|locus:2097149	502	AT3G43930 "AT3G43930" [Arabido	0.596	0.559	0.506	7.3e-105
UNIPROTKB|E1BSJ5	508	TOPBP1 "Uncharacterized protei	0.182	0.169	0.417	9e-09
TAIR|locus:2031412	972	MEI1 "AT1G77320" [Arabidopsis	0.182	0.088	0.404	5.1e-08
UNIPROTKB|G3X684	1524	TOPBP1 "Uncharacterized protei	0.441	0.136	0.285	9.8e-08
RGD|1562949	1516	Topbp1 "topoisomerase (DNA) II	0.414	0.128	0.272	2.3e-07
UNIPROTKB|Q92547	1522	TOPBP1 "DNA topoisomerase 2-bi	0.290	0.090	0.333	2.4e-07
MGI|MGI:1920018	1515	Topbp1 "topoisomerase (DNA) II	0.182	0.056	0.417	3.8e-07
UNIPROTKB|Q800K6	1513	topbp1-A "DNA topoisomerase 2-	0.180	0.056	0.366	5.8e-07
UNIPROTKB|F1P482	1062	PAXIP1 "Uncharacterized protei	0.176	0.078	0.360	0.00012

TAIR|locus:2057711 AT2G26270 "AT2G26270" [Arabidopsis thaliana (taxid:3702)]

 Score = 1054 (376.1 bits), Expect = 1.5e-106, P = 1.5e-106
 Identities = 209/373 (56%), Positives = 277/373 (74%)

Query:   105 GRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGF 164
             GRKFEH LKHG+RNGL++VT+GWFVDSV+RN R+SESLY VK + ++    D+L+R+   
Sbjct:    34 GRKFEHTLKHGARNGLFVVTIGWFVDSVKRNFRMSESLYNVKQLRQNCEKGDELSRVFDL 93

Query:   165 AGTENSCLPAGIYEAKQFNATGKHER------DSNRSMNSTLSGCSMYVDSDVSEELRNK 218
                E  C P  I +A  F  + K+ +      +S  S++ +L+   MYVDSD+S+ELR K
Sbjct:    94 ---ETICRPRQI-QAVHFGTSTKNHQVSSSGTESGTSVDMSLADHCMYVDSDISDELRLK 149

Query:   219 VFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRL 278
             V + A  +GA +++ WF+GC AS+VVCE  S+Q+Y+GH+  +V+P+WVLKT  EKH QRL
Sbjct:   150 VLKVAGEQGAKVIDSWFIGCNASFVVCEGASIQRYLGHAKTIVSPLWVLKTV-EKHRQRL 208

Query:   279 VHISADLARQVGMMLENIQNGIAREEING-GNVPEDAQSCKNKISQEKRQQTVNLAKNGV 337
             VH+S DLARQ+G+MLEN ++G A E+I+G GN  E  +S    +S+++R++TVN+AK GV
Sbjct:   209 VHMSPDLARQLGLMLENFEDGAANEKISGQGNSQEAFKS--RSLSKQERKETVNIAKTGV 266

Query:   338 RSRRSRRMQTCQTPIRPLTPSSLLDSICWSISEPTSTASIYTDSFSGEDVNEHHPSVFFD 397
             R RR+R MQTCQ PIR +T  SLLD+ICW+ISE  S A+I+TDS S  D++E  PSV  D
Sbjct:   267 RRRRARHMQTCQNPIRRITQYSLLDNICWTISEAASAATIFTDS-SSRDISEPQPSVVQD 325

Query:   398 AEADGKDSEASFANLTRMLTESEKSELIFKNHFLTILFPVDRFAEMGPSSRTYFSDNGFT 457
                 G D  ASF+N TR LTESEK+E+IFK+ FLTIL+P DRF+EMGPSSRTYFSD+GFT
Sbjct:   326 GIDKGLDPVASFSNSTRALTESEKTEVIFKDSFLTILYPADRFSEMGPSSRTYFSDSGFT 385

Query:   458 CLQVLDYIYEFYQ 470
             CLQ+LDYIY FYQ
Sbjct:   386 CLQILDYIYRFYQ 398

GO:0003674 "molecular_function" evidence=ND

GO:0005576 "extracellular region" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2097149 AT3G43930 "AT3G43930" [Arabidopsis thaliana (taxid:3702)]

 Score = 684 (245.8 bits), Expect = 7.3e-105, Sum P(2) = 7.3e-105
 Identities = 150/296 (50%), Positives = 191/296 (64%)

Query:     1 MGGGGRVEVVSSKGCSRLFLGSVPSLRRLRGGVQXXXXXXXXXXXXXXXXVLPANAPFSG 60
             M G  R EV+ +K CS+L +   PSLR  R                    V  ++ PFSG
Sbjct:     1 MEGVRRAEVIDTKRCSKLRVDFTPSLRGSRISEPFSPATTTTTTSRFHPPVR-SDGPFSG 59

Query:    61 LVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGL 120
             L+ICVTGLSKEARKQV EATERLGG+YS  LH  CTHLVVQ++ GRKFEHALKHG R  L
Sbjct:    60 LIICVTGLSKEARKQVKEATERLGGEYSALLHSLCTHLVVQNYDGRKFEHALKHGRRETL 119

Query:   121 YIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAK 180
             YIVTLGWFVDSV RNV+LSES Y VK+ +E  ++ D L  +  +A  E      G+   +
Sbjct:   120 YIVTLGWFVDSVCRNVKLSESFYAVKNPEETKVNEDGLKSV--YA-VEKLHRGGGV---Q 173

Query:   181 QFNATGKHERDSNRSMNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGA 240
                 TG        S +  LSG S+++D+D+SEE+R +V + A   GA L+ QWF+GC A
Sbjct:   174 GIEVTG--------SKDLALSGYSVFIDADISEEVRRQVSQVAVEGGAKLMTQWFIGCNA 225

Query:   241 SYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHISADLARQVGMMLENI 296
             S+VVCE  SV +Y+GHS+NLVTP+W+ KT +EK  Q LV +S DLAR +  M+EN+
Sbjct:   226 SHVVCEGGSVLRYLGHSSNLVTPLWLQKTLEEKPTQNLVQMSDDLARDLRTMIENL 281

GO:0003674 "molecular_function" evidence=ND

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|E1BSJ5 TOPBP1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 168 (64.2 bits), Expect = 9.0e-09, Sum P(2) = 9.0e-09
 Identities = 38/91 (41%), Positives = 52/91 (57%)

Query:    58 FSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHP-QCTHLVVQSFGGRKFEHALKHGS 116
             F G  ICVTGLS   RK+V   T   GGQYS  L   +CTHL+VQ   G+K+E A K   
Sbjct:   199 FLGCTICVTGLSSSDRKEVQRLTAEHGGQYSGQLKMNECTHLIVQEPKGQKYECAKKWN- 257

Query:   117 RNGLYIVTLGWFVDSVRRNVRLSESLYTVKS 147
                ++ V + WF DS+ +     E++Y ++S
Sbjct:   258 ---VHCVPVQWFSDSIEKGFCQDETMYKIES 285

GO:0000794 "condensed nuclear chromosome" evidence=IEA

GO:0001673 "male germ cell nucleus" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0010212 "response to ionizing radiation" evidence=IEA

GO:0016605 "PML body" evidence=IEA

TAIR|locus:2031412 MEI1 "AT1G77320" [Arabidopsis thaliana (taxid:3702)]

 Score = 163 (62.4 bits), Expect = 5.1e-08, Sum P(2) = 5.1e-08
 Identities = 36/89 (40%), Positives = 49/89 (55%)

Query:    57 PFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGS 116
             PFSGL ICVT +  + RK + +     GG YS +L   CTHL+  +  G K++ A K G 
Sbjct:   184 PFSGLTICVTRIPADERKGMEKVISEYGGSYSAELTKSCTHLIADAAEGDKYKVARKWGH 243

Query:   117 RNGLYIVTLGWFVDSVRRNVRLSESLYTV 145
                + IVT  WF  S+ + V L+E  Y V
Sbjct:   244 ---IQIVTRKWFQQSIDKKVCLNEESYPV 269

GO:0003713 "transcription coactivator activity" evidence=ISS

GO:0005622 "intracellular" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0007131 "reciprocal meiotic recombination" evidence=TAS

GO:0007140 "male meiosis" evidence=IMP

GO:0006974 "response to DNA damage stimulus" evidence=ISS

GO:0007143 "female meiosis" evidence=IMP

UNIPROTKB|G3X684 TOPBP1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 159 (61.0 bits), Expect = 9.8e-08, P = 9.8e-08
 Identities = 67/235 (28%), Positives = 104/235 (44%)

Query:    58 FSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHP-QCTHLVVQS---FGGRKFEHALK 113
             F G +ICVTGL    RK V + T + GGQY   L   +CTHL+VQ      G+K+E A  
Sbjct:   200 FLGCIICVTGLCTLDRKSVQQLTVKHGGQYMGQLKMNECTHLIVQEPKDIIGQKYECA-- 257

Query:   114 HGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLP 173
                R  ++ VT  WF DSV +     ES+Y  +   E    +   +   G   T +S   
Sbjct:   258 --KRWNVHCVTTQWFFDSVEKGFCQDESIYKTEPRSE-AKSMPDTSTPTGQINTIDSRTL 314

Query:   174 AGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDS-DVS-----EELRN--KVFEAATN 225
             + +      NA+  +E   N S+NS L      +++ D+S     E+L +  +++    N
Sbjct:   315 SDVSHISNINASCINESICN-SVNSKLEPTIENLENLDISAFQAPEDLLDGCRIYLCGFN 373

Query:   226 -----EGATLVNQWFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHV 275
                  +   L+N    G G  +    ED     +G  ++ +   W  K+A   HV
Sbjct:   374 GRKLDKLRRLINS---GGGVRFNQLNEDVTHVIVGDDDDELKQFWD-KSAHRPHV 424

GO:0016605 "PML body" evidence=IEA

GO:0010212 "response to ionizing radiation" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0001673 "male germ cell nucleus" evidence=IEA

GO:0000794 "condensed nuclear chromosome" evidence=IEA

RGD|1562949 Topbp1 "topoisomerase (DNA) II binding protein 1" [Rattus norvegicus (taxid:10116)]

 Score = 164 (62.8 bits), Expect = 2.3e-07, Sum P(2) = 2.3e-07
 Identities = 61/224 (27%), Positives = 104/224 (46%)

Query:    58 FSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHP-QCTHLVVQSFGGRKFEHALKHGS 116
             F G +ICVTGL+   RK V + T + GGQY   L   +CTHL+VQ   G+K+E A     
Sbjct:   200 FLGCIICVTGLNGIHRKTVQQLTAKHGGQYMGQLKMNECTHLIVQEPKGQKYECA----R 255

Query:   117 RNGLYIVTLGWFVDSVRRNVRLSESLY------TVKSIDE-------HGMHLDKLNRLVG 163
             R  ++ VTL WF DS+ +     ES+Y       VK++ +        G    +L  +  
Sbjct:   256 RWNVHCVTLQWFHDSIEKGFCQDESIYKAEPRAAVKTVPDTSTPTAQSGTEYHRLADVSH 315

Query:   164 FAGTENSCLPAGIYEA--KQFNATGKHERDSNRSM----NSTLSGCSMYVDSDVSEELRN 217
              +    SC+   ++ +   +   T ++  + + SM       L GC +Y+      +L +
Sbjct:   316 ISNINGSCVNETMFGSTTSKLECTLENLENLDISMFQAPEDLLDGCRIYLCGFSGRKL-D 374

Query:   218 KVFEAATNEGATLVNQWFVGCGASYVVCE--EDSVQKYMGHSNN 259
             K+     + G    NQ  +    ++V+    ED V+++   S++
Sbjct:   375 KLRRLINSGGGVRFNQ--LNEDVTHVIMGDYEDDVRQFWSKSSH 416

GO:0000794 "condensed nuclear chromosome" evidence=ISO

GO:0001673 "male germ cell nucleus" evidence=ISO

GO:0005694 "chromosome" evidence=ISO

GO:0006974 "response to DNA damage stimulus" evidence=ISO

GO:0010212 "response to ionizing radiation" evidence=ISO

GO:0016605 "PML body" evidence=ISO

UNIPROTKB|Q92547 TOPBP1 "DNA topoisomerase 2-binding protein 1" [Homo sapiens (taxid:9606)]

 Score = 161 (61.7 bits), Expect = 2.4e-07, Sum P(2) = 2.4e-07
 Identities = 48/144 (33%), Positives = 69/144 (47%)

Query:    58 FSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHP-QCTHLVVQSFGGRKFEHALKHGS 116
             F G +ICVTGL    RK+V + T + GGQY   L   +CTHL+VQ   G+K+E A     
Sbjct:   200 FLGCIICVTGLCGLDRKEVQQLTVKHGGQYMGQLKMNECTHLIVQEPKGQKYECA----K 255

Query:   117 RNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGI 176
             R  ++ VT  WF DS+ +     ES+Y  +   E    +   +       T +S   + +
Sbjct:   256 RWNVHCVTTQWFFDSIEKGFCQDESIYKTEPRPE-AKTMPNSSTPTSQINTIDSRTLSDV 314

Query:   177 YEAKQFNATGKHERDSNRSMNSTL 200
                   NA+   E   N S+NS L
Sbjct:   315 SNISNINASCVSESICN-SLNSKL 337

GO:0003677 "DNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0000794 "condensed nuclear chromosome" evidence=IEA

GO:0001673 "male germ cell nucleus" evidence=IEA

GO:0000922 "spindle pole" evidence=IEA

GO:0005815 "microtubule organizing center" evidence=IEA

GO:0006281 "DNA repair" evidence=NAS

GO:0006974 "response to DNA damage stimulus" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0010212 "response to ionizing radiation" evidence=IDA

GO:0016605 "PML body" evidence=IDA

GO:0005694 "chromosome" evidence=IDA

GO:0005634 "nucleus" evidence=TAS

GO:0006259 "DNA metabolic process" evidence=TAS

GO:0008022 "protein C-terminus binding" evidence=TAS

MGI|MGI:1920018 Topbp1 "topoisomerase (DNA) II binding protein 1" [Mus musculus (taxid:10090)]

 Score = 163 (62.4 bits), Expect = 3.8e-07, Sum P(2) = 3.8e-07
 Identities = 38/91 (41%), Positives = 53/91 (58%)

Query:    58 FSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHP-QCTHLVVQSFGGRKFEHALKHGS 116
             F G +ICVTGL+   RK V + T + GGQY   L   +CTHL+VQ   G+K+E A     
Sbjct:   200 FLGCIICVTGLNGIHRKTVQQLTAKHGGQYMGQLKMNECTHLIVQEPKGQKYECA----R 255

Query:   117 RNGLYIVTLGWFVDSVRRNVRLSESLYTVKS 147
             R  ++ VTL WF DS+ +     ES+Y  ++
Sbjct:   256 RWNVHCVTLQWFHDSIEKGFCQDESIYKAET 286

GO:0000794 "condensed nuclear chromosome" evidence=IDA

GO:0001673 "male germ cell nucleus" evidence=IDA

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005694 "chromosome" evidence=ISO;IDA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005856 "cytoskeleton" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=ISO

GO:0007131 "reciprocal meiotic recombination" evidence=ISA

GO:0010212 "response to ionizing radiation" evidence=ISO

GO:0016605 "PML body" evidence=ISO

UNIPROTKB|Q800K6 topbp1-A "DNA topoisomerase 2-binding protein 1-A" [Xenopus laevis (taxid:8355)]

 Score = 148 (57.2 bits), Expect = 5.8e-07, Sum P(2) = 5.8e-07
 Identities = 33/90 (36%), Positives = 51/90 (56%)

Query:    58 FSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHP-QCTHLVVQSFGGRKFEHALKHGS 116
             F G  ICVTGLS   RK+V   T   GG+Y+  L   + THL+VQ   G+K+E A K   
Sbjct:   199 FRGCTICVTGLSSLDRKEVQRLTALHGGEYTGQLKMNESTHLIVQEAKGQKYECARKWN- 257

Query:   117 RNGLYIVTLGWFVDSVRRNVRLSESLYTVK 146
                ++ +++ WF DS+ +     E++Y ++
Sbjct:   258 ---VHCISVQWFFDSIEKGFCQDETMYKIE 284

GO:0000076 "DNA replication checkpoint" evidence=IMP

GO:0000785 "chromatin" evidence=IDA

GO:0003682 "chromatin binding" evidence=IMP;IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0006270 "DNA replication initiation" evidence=IMP

GO:0006974 "response to DNA damage stimulus" evidence=IMP

GO:0019900 "kinase binding" evidence=IPI

GO:0030174 "regulation of DNA-dependent DNA replication initiation" evidence=IMP

GO:0033138 "positive regulation of peptidyl-serine phosphorylation" evidence=IDA

GO:0035563 "positive regulation of chromatin binding" evidence=IMP

GO:0045860 "positive regulation of protein kinase activity" evidence=IDA

GO:0071163 "DNA replication preinitiation complex assembly" evidence=IMP

GO:0071165 "GINS complex assembly" evidence=IMP

GO:0071168 "protein localization to chromatin" evidence=IMP

GO:0005656 "pre-replicative complex" evidence=IMP

GO:0006267 "pre-replicative complex assembly" evidence=IMP

GO:0006271 "DNA strand elongation involved in DNA replication" evidence=IMP

UNIPROTKB|F1P482 PAXIP1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 127 (49.8 bits), Expect = 0.00012, Sum P(2) = 0.00012
 Identities = 31/86 (36%), Positives = 44/86 (51%)

Query:    58 FSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSR 117
             F G+  C++ +S E R  +       GG    +L+ +CTHL+V    G K+E A KH S 
Sbjct:   104 FFGVTACLSQVSSEDRNTLWALITFYGGNCQLNLNKKCTHLIVPEPKGEKYECACKHDS- 162

Query:   118 NGLYIVTLGWFVDSVRRNVRLSESLY 143
               + IVT  W VDSV    +  E+ Y
Sbjct:   163 --IKIVTPEWVVDSVADKAKKEETPY 186

GO:0000416 "positive regulation of histone H3-K36 methylation" evidence=IEA

GO:0001570 "vasculogenesis" evidence=IEA

GO:0010212 "response to ionizing radiation" evidence=IEA

GO:0030330 "DNA damage response, signal transduction by p53 class mediator" evidence=IEA

GO:0031398 "positive regulation of protein ubiquitination" evidence=IEA

GO:0035066 "positive regulation of histone acetylation" evidence=IEA

GO:0035097 "histone methyltransferase complex" evidence=IEA

GO:0043542 "endothelial cell migration" evidence=IEA

GO:0045830 "positive regulation of isotype switching" evidence=IEA

GO:0051568 "histone H3-K4 methylation" evidence=IEA

GO:0051571 "positive regulation of histone H3-K4 methylation" evidence=IEA

GO:0060261 "positive regulation of transcription initiation from RNA polymerase II promoter" evidence=IEA

GO:0060612 "adipose tissue development" evidence=IEA

GO:0060717 "chorion development" 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 Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	471
pfam12738	63	pfam12738, PTCB-BRCT, twin BRCT domain	2e-13
pfam00533	77	pfam00533, BRCT, BRCA1 C Terminus (BRCT) domain	1e-12
smart00292	78	smart00292, BRCT, breast cancer carboxy-terminal d	2e-11
cd00027	72	cd00027, BRCT, Breast Cancer Suppressor Protein (B	4e-11
TIGR00575	652	TIGR00575, dnlj, DNA ligase, NAD-dependent	0.001

>gnl|CDD|193214 pfam12738, PTCB-BRCT, twin BRCT domain

 Score = 64.5 bits (158), Expect = 2e-13
 Identities = 27/67 (40%), Positives = 39/67 (58%), Gaps = 4/67 (5%)

Query: 61  LVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGL 120
           LVICV+G S + RK + +  E LG +YS DL  + THL+ +   G K+E A K     G+
Sbjct: 1   LVICVSGYSGDDRKYLQKLIEALGAEYSKDLTKKVTHLICKRGEGEKYEKAKK----WGI 56

Query: 121 YIVTLGW 127
            +V+  W
Sbjct: 57  PVVSHLW 63

This is a BRCT domain that appears in duplicate in most member sequences. BRCT domains are peptide- and phosphopeptide-binding modules. BRCT domains are present in a number of proteins involved in DNA checkpoint controls and DNA repair. Length = 63

>gnl|CDD|215978 pfam00533, BRCT, BRCA1 C Terminus (BRCT) domain

 Score = 62.8 bits (153), Expect = 1e-12
 Identities = 24/77 (31%), Positives = 37/77 (48%), Gaps = 5/77 (6%)

Query: 57  PFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSF-GGRKFEHALKHG 115
            F G    +TGL    R+++ E  E+LGG+ +  L  + TH++V    G  K   A+  G
Sbjct: 5   LFKGKTFVITGLDSLEREELEELIEKLGGKVTDSLSKKTTHVIVGENAGTLKLLKAIALG 64

Query: 116 SRNGLYIVTLGWFVDSV 132
                 IVT  W +D +
Sbjct: 65  IP----IVTEEWLLDCI 77

The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers. BRCT domains are often found as tandem-repeat pairs. Structures of the BRCA1 BRCT domains revealed a basis for a widely utilised head-to-tail BRCT-BRCT oligomerisation mode. This conserved tandem BRCT architecture facilitates formation of the canonical BRCT phospho-peptide interaction cleft at a groove between the BRCT domains. Disease associated missense and nonsense mutations in the BRCA1 BRCT domains disrupt peptide binding by directly occluding this peptide binding groove, or by disrupting key conserved BRCT core folding determinants. Length = 77

>gnl|CDD|214602 smart00292, BRCT, breast cancer carboxy-terminal domain

 Score = 59.3 bits (144), Expect = 2e-11
 Identities = 25/78 (32%), Positives = 35/78 (44%), Gaps = 4/78 (5%)

Query: 57  PFSGLVICVTG-LSKEARKQVMEATERLGGQYSPDLH-PQCTHLVVQSFGGRKFEHALKH 114
            F G    +TG   KE R ++ E  E LGG+ +  L     TH++V S  G K E     
Sbjct: 3   LFKGKTFYITGSFDKEERDELKELIEALGGKVTSSLSSKTTTHVIVGSPEGGKLELLK-- 60

Query: 115 GSRNGLYIVTLGWFVDSV 132
               G+ IV   W +D +
Sbjct: 61  AIALGIPIVKEEWLLDCL 78

Length = 78

>gnl|CDD|237994 cd00027, BRCT, Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain

 Score = 58.5 bits (142), Expect = 4e-11
 Identities = 25/75 (33%), Positives = 40/75 (53%), Gaps = 4/75 (5%)

Query: 60  GLVICVTG-LSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRN 118
           GL   +TG L  E R ++ E  E+LGG+ +  +  + TH++V S  G K    L    + 
Sbjct: 1   GLTFVITGDLPSEERDELKELIEKLGGKVTSSVSKKTTHVIVGSDAGPKK---LLKAIKL 57

Query: 119 GLYIVTLGWFVDSVR 133
           G+ IVT  W +D ++
Sbjct: 58  GIPIVTPEWLLDCLK 72

The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks. Length = 72

>gnl|CDD|233030 TIGR00575, dnlj, DNA ligase, NAD-dependent

 Score = 40.7 bits (96), Expect = 0.001
 Identities = 21/92 (22%), Positives = 41/92 (44%), Gaps = 9/92 (9%)

Query: 26  LRRLRG-GVQSFESMSPASSSLASDSVLPANAPFSGLVICVTG-LSKEARKQVMEATERL 83
           +++L   GV+        ++ LA        +P +G    +TG LS+ +R +  E  E L
Sbjct: 559 IKKLEELGVEMESLPEKVNAELA-------GSPLAGKTFVLTGTLSQMSRDEAKELLENL 611

Query: 84  GGQYSPDLHPQCTHLVVQSFGGRKFEHALKHG 115
           GG+ +  +  +  +++     G K   A + G
Sbjct: 612 GGKVASSVSKKTDYVIAGEKAGSKLAKAQELG 643

All proteins in this family with known functions are NAD-dependent DNA ligases. Functions of these proteins include DNA repair, DNA replication, and DNA recombination. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed [DNA metabolism, DNA replication, recombination, and repair]. Length = 652

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	471
PF12738	63	PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2W	99.57
KOG1929	811	consensus Nucleotide excision repair factor NEF2,	99.56
PF00533	78	BRCT: BRCA1 C Terminus (BRCT) domain; InterPro: IP	99.53
KOG1929	811	consensus Nucleotide excision repair factor NEF2,	99.35
smart00292	80	BRCT breast cancer carboxy-terminal domain.	99.33
cd00027	72	BRCT Breast Cancer Suppressor Protein (BRCA1), car	99.3
KOG0966	881	consensus ATP-dependent DNA ligase IV [Replication	99.29
KOG3524	850	consensus Predicted guanine nucleotide exchange fa	99.29
PF00533	78	BRCT: BRCA1 C Terminus (BRCT) domain; InterPro: IP	99.23
KOG3226	508	consensus DNA repair protein [Replication, recombi	99.17
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	99.06
smart00292	80	BRCT breast cancer carboxy-terminal domain.	99.04
cd00027	72	BRCT Breast Cancer Suppressor Protein (BRCA1), car	98.89
KOG3548	1176	consensus DNA damage checkpoint protein RHP9/CRB2/	98.67
PLN03122	815	Poly [ADP-ribose] polymerase; Provisional	98.63
PF12738	63	PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2W	98.6
PLN03123	981	poly [ADP-ribose] polymerase; Provisional	98.56
KOG3226	508	consensus DNA repair protein [Replication, recombi	98.15
PRK14350	669	ligA NAD-dependent DNA ligase LigA; Provisional	98.0
PRK06063	313	DNA polymerase III subunit epsilon; Provisional	97.93
PRK06195	309	DNA polymerase III subunit epsilon; Validated	97.91
KOG2043	896	consensus Signaling protein SWIFT and related BRCT	97.89
KOG2481	570	consensus Protein required for normal rRNA process	97.87
COG0272	667	Lig NAD-dependent DNA ligase (contains BRCT domain	97.87
PRK07956	665	ligA NAD-dependent DNA ligase LigA; Validated	97.83
PRK14351	689	ligA NAD-dependent DNA ligase LigA; Provisional	97.8
TIGR00575	652	dnlj DNA ligase, NAD-dependent. The member of this	97.74
COG5163	591	NOP7 Protein required for biogenesis of the 60S ri	97.67
PLN03122	815	Poly [ADP-ribose] polymerase; Provisional	97.47
PLN03123	981	poly [ADP-ribose] polymerase; Provisional	97.26
KOG2093	1016	consensus Translesion DNA polymerase - REV1 deoxyc	97.08
KOG0966	881	consensus ATP-dependent DNA ligase IV [Replication	97.04
COG5275	276	BRCT domain type II [General function prediction o	96.52
KOG0323	635	consensus TFIIF-interacting CTD phosphatases, incl	96.32
KOG3524	850	consensus Predicted guanine nucleotide exchange fa	96.27
KOG2481	570	consensus Protein required for normal rRNA process	95.68
KOG2043	896	consensus Signaling protein SWIFT and related BRCT	95.33
PRK14350	669	ligA NAD-dependent DNA ligase LigA; Provisional	94.46
PRK06063	313	DNA polymerase III subunit epsilon; Provisional	94.22
PRK06195	309	DNA polymerase III subunit epsilon; Validated	94.2
KOG3548	1176	consensus DNA damage checkpoint protein RHP9/CRB2/	94.2
PRK07956	665	ligA NAD-dependent DNA ligase LigA; Validated	94.06
COG5163	591	NOP7 Protein required for biogenesis of the 60S ri	93.95
PRK14351	689	ligA NAD-dependent DNA ligase LigA; Provisional	93.44
COG0272	667	Lig NAD-dependent DNA ligase (contains BRCT domain	91.91
TIGR00575	652	dnlj DNA ligase, NAD-dependent. The member of this	91.79
PRK05601	377	DNA polymerase III subunit epsilon; Validated	86.64
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	81.93

>PF12738 PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2WT8_C 3EF1_A 3EF0_A

Probab=99.57  E-value=2.1e-15  Score=117.64  Aligned_cols=63  Identities=40%  Similarity=0.736  Sum_probs=55.7

Q ss_pred             cEEEEeCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHHHHHHHhcCCCCCceEecchH
Q 012081           61 LVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGW  127 (471)
Q Consensus        61 lvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~W  127 (471)
                      ++||+|||.+.+|..|.++|+.|||.|..+|++++|||||....++||+.|.+|    +++||+++|
T Consensus         1 ~~i~~sg~~~~~~~~l~~~i~~~Gg~~~~~lt~~~THLI~~~~~~~K~~~A~~~----gi~vV~~~W   63 (63)
T PF12738_consen    1 VVICFSGFSGKERSQLRKLIEALGGKYSKDLTKKTTHLICSSPEGKKYRKAKEW----GIPVVSPDW   63 (63)
T ss_dssp             -EEEEEEB-TTTCCHHHHHHHCTT-EEESSSSTT-SEEEEES--HHHHHHHHHC----TSEEEEHHH
T ss_pred             CEEEECCCCHHHHHHHHHHHHHCCCEEeccccCCceEEEEeCCCcHHHHHHHHC----CCcEECCCC
Confidence            589999999999999999999999999999999999999999999999999998    799999999

>KOG1929 consensus Nucleotide excision repair factor NEF2, RAD4/CUT5 component [Replication, recombination and repair]

Probab=99.56  E-value=2.1e-14  Score=159.46  Aligned_cols=178  Identities=17%  Similarity=0.255  Sum_probs=147.1

Q ss_pred             CCCCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHHHHHHHhcCCCCCceEecchHHHHHHH
Q 012081           54 ANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVR  133 (471)
Q Consensus        54 ~~~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~Dcik  133 (471)
                      .+++|+|+.||.||+.+..++.|.+.+..+||.|...++++|||||+......||..|..    .+++|++..|+...+.
T Consensus         6 ~~~~~~~v~~~~t~i~p~~~~~l~~~~~~~Gg~~~~~~t~~~thli~~~~~s~~~~~a~~----~~~~~~~~~wi~~~~d   81 (811)
T KOG1929|consen    6 YSKPMSGVTFSPTGINPIKREELSKKFIKLGGIDFKDFTPSVTHLIVGSVTSSKYAAAHR----FDIKVLDSSWIDYIYD   81 (811)
T ss_pred             cCcccCCceeccCcCCHHHHHHHHHHHHhcCceeeeccCCcCceeecccccccchhhhhc----CCCceecchHHHHHHH
Confidence            568999999999999999999999999999999999999999999999999999955544    5999999999999888


Q ss_pred             cccCCCCCccccccccccCcchhhhhcccCCcCCCCCCCCcccchhhccccccccccccccCCCCCCCCcEEEEeCCCCH
Q 012081          134 RNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVSE  213 (471)
Q Consensus       134 ~g~~lde~~Y~l~~~~e~~~~~~~~~~L~~~s~~e~~~lp~~I~es~~s~s~E~ld~~~~~~~~~lF~G~~Iyl~~gfs~  213 (471)
                      .+.. . ..-.+.+.            +.+     .                         .....|.||.|++ .||+.
T Consensus        82 ~~~~-~-~e~~~~~~------------l~~-----~-------------------------~~~p~~~~~~Vc~-tgl~~  116 (811)
T KOG1929|consen   82 LWLL-N-KEIRLLDP------------LRD-----T-------------------------MKCPGFFGLKVCL-TGLSG  116 (811)
T ss_pred             Hhhh-h-ccCccCcc------------chh-----h-------------------------hcCCcccceEEEe-cccch
Confidence            7765 2 21111100            000     0                         0135789999999 99999


Q ss_pred             HHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCchH-HHH---hcCCCceechhHHHHHHhhCCcCccCCcC
Q 012081          214 ELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSV-QKY---MGHSNNLVTPVWVLKTAKEKHVQRLVHIS  282 (471)
Q Consensus       214 ~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~s~-~k~---l~~~~~IVs~~WL~dcik~g~lqp~~~ys  282 (471)
                      .++..+..+|..+||+....  +...+.|+++.+... .+|   +.++++||+.+|+++|+.++..++...|-
T Consensus       117 ~eK~ei~~~v~k~gg~~~~~--L~s~v~~~~~~~~~~~~kYe~al~wn~~v~~~~w~~~s~~~~~~~~~~~~e  187 (811)
T KOG1929|consen  117 DEKSEIKILVPKHGGTLHRS--LSSDVNSLKILPEVKTEKYEQALKWNIPVVSDDWLFDSIEKTAVLETKPYE  187 (811)
T ss_pred             HHHHHHHHHhhhcccEEehh--hhhhhheeeeccccchHHHHHHHhhCCccccHHHHhhhhcccccccccccc
Confidence            99999999999999999999  688888888777433 454   57999999999999999999998876664

>PF00533 BRCT: BRCA1 C Terminus (BRCT) domain; InterPro: IPR001357 The BRCT domain (after the C_terminal domain of a breast cancer susceptibility protein) is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage [], for example as found in the breast cancer DNA-repair protein BRCA1

Probab=99.53  E-value=4.5e-14  Score=112.93  Aligned_cols=75  Identities=24%  Similarity=0.555  Sum_probs=70.8

Q ss_pred             CCCCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecC--CCHHHHHHHhcCCCCCceEecchHHHHH
Q 012081           54 ANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSF--GGRKFEHALKHGSRNGLYIVTLGWFVDS  131 (471)
Q Consensus        54 ~~~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~--~g~Ky~~A~k~~~~~gi~IV~p~WI~Dc  131 (471)
                      +.++|+|+.||++++...+|+.|.++|+.+||++...+++.+||||+...  ...||..|...    +++||+++||.||
T Consensus         2 ~~~~F~g~~f~i~~~~~~~~~~l~~~i~~~GG~v~~~~~~~~thvI~~~~~~~~~k~~~~~~~----~i~iV~~~Wi~~c   77 (78)
T PF00533_consen    2 KPKIFEGCTFCISGFDSDEREELEQLIKKHGGTVSNSFSKKTTHVIVGNPNKRTKKYKAAIAN----GIPIVSPDWIEDC   77 (78)
T ss_dssp             STTTTTTEEEEESSTSSSHHHHHHHHHHHTTEEEESSSSTTSSEEEESSSHCCCHHHHHHHHT----TSEEEETHHHHHH
T ss_pred             CCCCCCCEEEEEccCCCCCHHHHHHHHHHcCCEEEeecccCcEEEEeCCCCCccHHHHHHHHC----CCeEecHHHHHHh
Confidence            45899999999999999999999999999999999999999999999988  78899999985    8999999999999


Q ss_pred             H
Q 012081          132 V  132 (471)
Q Consensus       132 i  132 (471)
                      +
T Consensus        78 i   78 (78)
T PF00533_consen   78 I   78 (78)
T ss_dssp             H
T ss_pred             C
Confidence            6

The domain is an approximately 100 amino acid tandem repeat, which appears to act as a phospho-protein binding domain []. A chitin biosynthesis protein from yeast also seems to belong to this group. ; GO: 0005622 intracellular; PDB: 3L46_A 3AL3_A 3AL2_A 1WF6_A 3II6_X 2NTE_B 3FA2_A 2R1Z_A 2COK_A 2K7F_A ....

>KOG1929 consensus Nucleotide excision repair factor NEF2, RAD4/CUT5 component [Replication, recombination and repair]

Probab=99.35  E-value=2.6e-12  Score=142.92  Aligned_cols=233  Identities=16%  Similarity=0.140  Sum_probs=155.8

Q ss_pred             CCceEEEecCCcceeeccCccch--------hhhccccccccccC--CC-CCCCCcC-CC--CCCCCCCCCcEEEEeCCC
Q 012081            4 GGRVEVVSSKGCSRLFLGSVPSL--------RRLRGGVQSFESMS--PA-SSSLASD-SV--LPANAPFSGLVICVTGLS   69 (471)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~s~~~~--------r~~~~~lq~~~~~~--~~-~s~~~~~-~~--~~~~~iF~GlvI~vTG~~   69 (471)
                      ||++--+.+..|+||+.-+..+.        -.+...-+|.+..-  .. ...+..+ |.  ...++.|.|+.||+|||.
T Consensus        36 Gg~~~~~~t~~~thli~~~~~s~~~~~a~~~~~~~~~~~wi~~~~d~~~~~~e~~~~~~l~~~~~~p~~~~~~Vc~tgl~  115 (811)
T KOG1929|consen   36 GGIDFKDFTPSVTHLIVGSVTSSKYAAAHRFDIKVLDSSWIDYIYDLWLLNKEIRLLDPLRDTMKCPGFFGLKVCLTGLS  115 (811)
T ss_pred             CceeeeccCCcCceeecccccccchhhhhcCCCceecchHHHHHHHHhhhhccCccCccchhhhcCCcccceEEEecccc
Confidence            45555677888888864443222        22223333333211  11 1333333 31  345689999999999999


Q ss_pred             hhhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCC-HHHHHHHhcCCCCCceEecchHHHHHHHcccCCCCCccccccc
Q 012081           70 KEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGG-RKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSI  148 (471)
Q Consensus        70 ~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g-~Ky~~A~k~~~~~gi~IV~p~WI~Dcik~g~~lde~~Y~l~~~  148 (471)
                      .++|.++..+|.+|||++...|..+++|+++..... +||+.|++|    +++||+.+|+++|+.++..++.+.|++...
T Consensus       116 ~~eK~ei~~~v~k~gg~~~~~L~s~v~~~~~~~~~~~~kYe~al~w----n~~v~~~~w~~~s~~~~~~~~~~~~e~~~~  191 (811)
T KOG1929|consen  116 GDEKSEIKILVPKHGGTLHRSLSSDVNSLKILPEVKTEKYEQALKW----NIPVVSDDWLFDSIEKTAVLETKPYEGAPV  191 (811)
T ss_pred             hHHHHHHHHHhhhcccEEehhhhhhhheeeeccccchHHHHHHHhh----CCccccHHHHhhhhcccccccccccccccc
Confidence            999999999999999999999999888888877655 999999999    899999999999999999999999999863


Q ss_pred             cccCcchhhhhcccCCcCCCCCCCCcccchhhc-cccccccccccccCCCCCCCCcEEEEeCCCCHHHHHHHHHHHHhCC
Q 012081          149 DEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQ-FNATGKHERDSNRSMNSTLSGCSMYVDSDVSEELRNKVFEAATNEG  227 (471)
Q Consensus       149 ~e~~~~~~~~~~L~~~s~~e~~~lp~~I~es~~-s~s~E~ld~~~~~~~~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~G  227 (471)
                      .+....+....    +......+.....+.... ...+.+.+.........+..+|.+|+ .|++...+..|.++++.+|
T Consensus       192 ~~~is~~~~~~----~~~~~~~~~s~t~~~~~~~~~~~~n~~~~p~~a~~~~~~~c~v~~-s~~~~~~~s~l~r~~~~g~  266 (811)
T KOG1929|consen  192 AEAISGPIGST----LPKEILDGDSRTANDTWSTSKVVTNIKVLPFQAKIGNLDDCLVET-SGTTSRNRSALSRLSNNGG  266 (811)
T ss_pred             cceeccCCccc----cccccccccchhhhccccchhcccccccchhhhhccccccceeee-cCCcccchhHhHHhhhccc
Confidence            33221110000    000000000000000000 00011122222223344789999999 9999999999999999999


Q ss_pred             CEEEccccCCCCceEEEEcC
Q 012081          228 ATLVNQWFVGCGASYVVCEE  247 (471)
Q Consensus       228 G~v~d~~~~~~~vTHVVv~~  247 (471)
                      |...+.  ....++|++.++
T Consensus       267 ~~~~~e--~~e~~st~l~~~  284 (811)
T KOG1929|consen  267 SLRFLE--RLEETSTSLLGD  284 (811)
T ss_pred             ceeecc--cCccccchhhcc
Confidence            999888  588889999877

>smart00292 BRCT breast cancer carboxy-terminal domain

Probab=99.33  E-value=4e-12  Score=100.24  Aligned_cols=76  Identities=34%  Similarity=0.570  Sum_probs=67.0

Q ss_pred             CCCCCcEEEEeC-CChhhHHHHHHHHHHcCCEEcccCCC-CceEEEEecCCCHH--HHHHHhcCCCCCceEecchHHHHH
Q 012081           56 APFSGLVICVTG-LSKEARKQVMEATERLGGQYSPDLHP-QCTHLVVQSFGGRK--FEHALKHGSRNGLYIVTLGWFVDS  131 (471)
Q Consensus        56 ~iF~GlvI~vTG-~~~~er~~L~~lI~~~GG~~~~~l~~-~~THLV~~~~~g~K--y~~A~k~~~~~gi~IV~p~WI~Dc  131 (471)
                      ++|+|+.||++| +....+..+.++|..+||++...++. ++||+|+.+....+  +..|..    .+++||+++||.||
T Consensus         1 ~~f~g~~~~~~g~~~~~~~~~l~~~i~~~Gg~~~~~~~~~~~thvi~~~~~~~~~~~~~~~~----~~~~iV~~~Wi~~~   76 (80)
T smart00292        1 KLFKGKVFVITGKFDKNERDELKELIEALGGKVTSSLSSKTTTHVIVGSPEGGKLELLLAIA----LGIPIVTEDWLLDC   76 (80)
T ss_pred             CccCCeEEEEeCCCCCccHHHHHHHHHHcCCEEecccCccceeEEEEcCCCCccHHHHHHHH----cCCCCccHHHHHHH
Confidence            479999999999 77899999999999999999999998 99999999876654  455655    48999999999999


Q ss_pred             HHcc
Q 012081          132 VRRN  135 (471)
Q Consensus       132 ik~g  135 (471)
                      ++.+
T Consensus        77 ~~~~   80 (80)
T smart00292       77 LKAG   80 (80)
T ss_pred             HHCc
Confidence            9864

>cd00027 BRCT Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain

Probab=99.30  E-value=8.3e-12  Score=96.22  Aligned_cols=70  Identities=36%  Similarity=0.612  Sum_probs=63.6

Q ss_pred             CcEEEEeCCC-hhhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHH-HHHHHhcCCCCCceEecchHHHHHHH
Q 012081           60 GLVICVTGLS-KEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRK-FEHALKHGSRNGLYIVTLGWFVDSVR  133 (471)
Q Consensus        60 GlvI~vTG~~-~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~K-y~~A~k~~~~~gi~IV~p~WI~Dcik  133 (471)
                      |+.|+++|.. ..++..|.++|..+||++...++..+||||+......+ +..|..+    +++||+++||.||++
T Consensus         1 ~~~~~i~g~~~~~~~~~l~~~i~~~Gg~v~~~~~~~~thvI~~~~~~~~~~~~~~~~----~~~iV~~~Wi~~~~~   72 (72)
T cd00027           1 GLTFVITGDLPSEERDELKELIEKLGGKVTSSVSKKTTHVIVGSDAGPKKLLKAIKL----GIPIVTPEWLLDCLK   72 (72)
T ss_pred             CCEEEEEecCCCcCHHHHHHHHHHcCCEEeccccCCceEEEECCCCCchHHHHHHHc----CCeEecHHHHHHHhC
Confidence            6889999998 79999999999999999999999999999999887665 7777764    899999999999984

The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks.

>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]

Probab=99.29  E-value=2.2e-11  Score=132.70  Aligned_cols=216  Identities=19%  Similarity=0.227  Sum_probs=131.1

Q ss_pred             CCCCCCCCcEEEEe-CCCh-hhHHHHHHHHHHcCCEEcccCCCCceEEEE--ecCCCHHHHHHHhcCCCCCceEecchHH
Q 012081           53 PANAPFSGLVICVT-GLSK-EARKQVMEATERLGGQYSPDLHPQCTHLVV--QSFGGRKFEHALKHGSRNGLYIVTLGWF  128 (471)
Q Consensus        53 ~~~~iF~GlvI~vT-G~~~-~er~~L~~lI~~~GG~~~~~l~~~~THLV~--~~~~g~Ky~~A~k~~~~~gi~IV~p~WI  128 (471)
                      ....+|.|+.|||- |... ..+..++++|.++||++..++.+..||+|+  +.....+..+|++    +++.||+|.||
T Consensus       629 ~~s~if~gl~f~Vlsgt~~~~tk~~le~~ivenGG~iv~nv~p~~~~ci~~a~~et~~vk~~~~~----~~cdVl~p~Wl  704 (881)
T KOG0966|consen  629 KISNIFDGLEFCVLSGTSETHTKAKLEEIIVENGGKIVQNVGPSDTLCIATAGKETTRVKAQAIK----RSCDVLKPAWL  704 (881)
T ss_pred             chhhhhcCeeEEEecCCcccccHHHHHHHHHHcCCEEEEcCCCCCcceEEeccccchHHHHHHHh----ccCceeeHHHH
Confidence            35689999999994 6666 458999999999999999999999999996  3334444455555    38999999999


Q ss_pred             HHHHHcccCCCCCccccccccccCc---------chhhhh------cccC-CcCCCCCC--CCcccchhhcccccccccc
Q 012081          129 VDSVRRNVRLSESLYTVKSIDEHGM---------HLDKLN------RLVG-FAGTENSC--LPAGIYEAKQFNATGKHER  190 (471)
Q Consensus       129 ~Dcik~g~~lde~~Y~l~~~~e~~~---------~~~~~~------~L~~-~s~~e~~~--lp~~I~es~~s~s~E~ld~  190 (471)
                      +||++..+++++.++.+-.-.+...         ..|.+.      .|.. ++.++.+.  +|...        .-+.+-
T Consensus       705 ldcc~~~~l~p~~P~~~fh~~e~~~~~~a~~~D~~gdSy~~di~l~~l~~~ls~~k~S~ds~~~~~--------~~~~~~  776 (881)
T KOG0966|consen  705 LDCCKKQRLLPWLPRDLFHATEKGREKLAKEVDCLGDSYENDIDLEQLKKVLSGIKKSQDSLPPMG--------ASEKDS  776 (881)
T ss_pred             HHHHhhhhccccccHHHHhhCchHHHHHHHHHhhhcchhhhhccHHHHHHHHhhhhhcccccCchh--------hhhhhc
Confidence            9999999998877655432211100         001111      1111 01111100  00000        000010


Q ss_pred             ccccCCCCCCCCcEEEE-eCC-CCHHHHHHHHHHHHhCCCEEEccc----cCCCCceEEEEcC--ch------HHHHh-c
Q 012081          191 DSNRSMNSTLSGCSMYV-DSD-VSEELRNKVFEAATNEGATLVNQW----FVGCGASYVVCEE--DS------VQKYM-G  255 (471)
Q Consensus       191 ~~~~~~~~lF~G~~Iyl-~~g-fs~~~r~~L~~lI~~~GG~v~d~~----~~~~~vTHVVv~~--~s------~~k~l-~  255 (471)
                      .+.+. ..+|..++++. ..+ ++. +-..+.-.++.+||.+++.-    +...++||+|+..  ++      .++.. .
T Consensus       777 ~e~r~-~~~~~~~~~f~~~~~~~~s-e~~~~~l~~k~~g~~i~~~~~~~~~~~~~~t~~v~~~i~~~h~~~~~~~~~~lt  854 (881)
T KOG0966|consen  777 LERRF-SLFLSSLRMFYVLRRKLSS-EEVIIELKLKNFGGRITDAQSECNNIGAKYTHCVLRCIDEDHEKIKEQKKASLT  854 (881)
T ss_pred             HHHhh-ccccccceeeecccccccH-HHHHHHHHHHHhcceeeeccchhhhcccceeeeeeeecchHHHHHHHHHHHHhc
Confidence            11111 23344444443 222 333 33455566788899998763    2455679999864  11      12221 1


Q ss_pred             CCCceechhHHHHHHhhCCcCccCCcC
Q 012081          256 HSNNLVTPVWVLKTAKEKHVQRLVHIS  282 (471)
Q Consensus       256 ~~~~IVs~~WL~dcik~g~lqp~~~ys  282 (471)
                      ...+||.+.||.+|+.++.++|+..|+
T Consensus       855 ~~rkv~~~~wv~~s~~~~~~~~e~~~~  881 (881)
T KOG0966|consen  855 IKRKVVAPSWVDHSINENCLLPEEDFP  881 (881)
T ss_pred             ccccccCHHHHHHhhcccccCccccCC
Confidence            222999999999999999999998774

>KOG3524 consensus Predicted guanine nucleotide exchange factor (PEBBLE) [Signal transduction mechanisms]

Probab=99.29  E-value=2.7e-12  Score=137.72  Aligned_cols=175  Identities=17%  Similarity=0.263  Sum_probs=139.9

Q ss_pred             CCCCCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHHHHHHHhcCCCCCceEecchHHHHHH
Q 012081           53 PANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSV  132 (471)
Q Consensus        53 ~~~~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~Dci  132 (471)
                      -.+-+|+|++.|+||+...+. .+-.+|+.|||.+..+++..+||+|+....++||..|+-     +.+++.|+||..||
T Consensus       114 ly~~~m~~vvlcfTg~rkk~e-~lv~lvh~mgg~irkd~nsktthli~n~s~gek~~~a~t-----~~~~~rp~wv~~aw  187 (850)
T KOG3524|consen  114 LYCELMKDVVMCFTGERKKKE-ELVDLVHYMGGSIRKDTNSKTTHLIANKVEGEKQSIALV-----GVPTMRPDWVTEAW  187 (850)
T ss_pred             ccchhhcCceeeeeccchhhH-HHHHHHHHhcceeEeeeccCceEEEeecccceEEEEEee-----ccceechHhhhhhh
Confidence            467899999999999998655 899999999999999999999999999999999999976     59999999999999


Q ss_pred             HcccCCCCCccccccccccCcchhhhhcccCCcCCCCCCCCcccchhhccccccccccccccCCCCCCCCcEEEEeCCCC
Q 012081          133 RRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVS  212 (471)
Q Consensus       133 k~g~~lde~~Y~l~~~~e~~~~~~~~~~L~~~s~~e~~~lp~~I~es~~s~s~E~ld~~~~~~~~~lF~G~~Iyl~~gfs  212 (471)
                      +....+   .|.+....        +.                                 ....-..|.|+.|+| .||+
T Consensus       188 ~~rn~~---yfda~~~~--------f~---------------------------------d~hrl~~feg~~~~f-~gF~  222 (850)
T KOG3524|consen  188 KHRNDS---YFDAMEPC--------FV---------------------------------DKHRLGVFEGLSLFF-HGFK  222 (850)
T ss_pred             cCcchh---hhhhhccc--------hh---------------------------------hhhccccccCCeEee-cCCc
Confidence            864322   22221100        00                                 001135799999999 9999


Q ss_pred             HHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCchHHHHh---cCCCceechhHHHHHHhhCCcCccCCc
Q 012081          213 EELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKYM---GHSNNLVTPVWVLKTAKEKHVQRLVHI  281 (471)
Q Consensus       213 ~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~s~~k~l---~~~~~IVs~~WL~dcik~g~lqp~~~y  281 (471)
                      .++...+-+.....||++..+   +..+||||++++......   +....+|..+|++=+|..|..-.+..|
T Consensus       223 ~ee~~~m~~sle~~gg~~a~~---d~~cthvvv~e~~~~~~p~~~s~~~~~vk~ewfw~siq~g~~a~e~~y  291 (850)
T KOG3524|consen  223 QEEIDDMLRSLENTGGKLAPS---DTLCTHVVVNEDNDEVEPLAVSSNQVHVKKEWFWVSIQRGCCAIEDNY  291 (850)
T ss_pred             HHHHHHHHHHHHhcCCcccCC---CCCceeEeecCCccccccccccccceeecccceEEEEecchhccccce
Confidence            999999999999999999986   889999999985433222   456678999999988888765555555

>PF00533 BRCT: BRCA1 C Terminus (BRCT) domain; InterPro: IPR001357 The BRCT domain (after the C_terminal domain of a breast cancer susceptibility protein) is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage [], for example as found in the breast cancer DNA-repair protein BRCA1

Probab=99.23  E-value=2.6e-11  Score=96.91  Aligned_cols=71  Identities=18%  Similarity=0.421  Sum_probs=63.2

Q ss_pred             CCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCc--hHHHH---hcCCCceechhHHHHHH
Q 012081          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED--SVQKY---MGHSNNLVTPVWVLKTA  270 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~--s~~k~---l~~~~~IVs~~WL~dci  270 (471)
                      ..+|+||.||| .+++...++.|.++|+.+||++...  ....+||||+...  ...++   ...+++||+++||.||+
T Consensus         3 ~~~F~g~~f~i-~~~~~~~~~~l~~~i~~~GG~v~~~--~~~~~thvI~~~~~~~~~k~~~~~~~~i~iV~~~Wi~~ci   78 (78)
T PF00533_consen    3 PKIFEGCTFCI-SGFDSDEREELEQLIKKHGGTVSNS--FSKKTTHVIVGNPNKRTKKYKAAIANGIPIVSPDWIEDCI   78 (78)
T ss_dssp             TTTTTTEEEEE-SSTSSSHHHHHHHHHHHTTEEEESS--SSTTSSEEEESSSHCCCHHHHHHHHTTSEEEETHHHHHHH
T ss_pred             CCCCCCEEEEE-ccCCCCCHHHHHHHHHHcCCEEEee--cccCcEEEEeCCCCCccHHHHHHHHCCCeEecHHHHHHhC
Confidence            57999999999 9999999999999999999999998  6999999999875  33333   36899999999999997

The domain is an approximately 100 amino acid tandem repeat, which appears to act as a phospho-protein binding domain []. A chitin biosynthesis protein from yeast also seems to belong to this group. ; GO: 0005622 intracellular; PDB: 3L46_A 3AL3_A 3AL2_A 1WF6_A 3II6_X 2NTE_B 3FA2_A 2R1Z_A 2COK_A 2K7F_A ....

>KOG3226 consensus DNA repair protein [Replication, recombination and repair]

Probab=99.17  E-value=2.2e-11  Score=122.85  Aligned_cols=92  Identities=22%  Similarity=0.370  Sum_probs=86.0

Q ss_pred             CCCCCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHHHHHHHhcCCCCCceEecchHHHHHH
Q 012081           53 PANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSV  132 (471)
Q Consensus        53 ~~~~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~Dci  132 (471)
                      ...++++|+++.++||.+.+|..|+.....||++|..+++..+|||||.-.++.||.+..-    +|-.||+-+||.+|.
T Consensus       313 el~klL~GVV~VlSGfqNP~Rs~LRskAl~LGAkY~pDW~~gsThLICAF~NTPKy~QV~g----~Gg~IV~keWI~~Cy  388 (508)
T KOG3226|consen  313 ELSKLLEGVVFVLSGFQNPERSTLRSKALTLGAKYQPDWNAGSTHLICAFPNTPKYRQVEG----NGGTIVSKEWITECY  388 (508)
T ss_pred             hHHHhhhceEEEEecccCchHHHHHHHHHhhcccccCCcCCCceeEEEecCCCcchhhccc----CCceEeeHHHHHHHH
Confidence            3457999999999999999999999999999999999999999999999999999999876    478999999999999


Q ss_pred             HcccCCCCCccccccc
Q 012081          133 RRNVRLSESLYTVKSI  148 (471)
Q Consensus       133 k~g~~lde~~Y~l~~~  148 (471)
                      +..++||...|.+...
T Consensus       389 ~~kk~lp~rrYlm~~~  404 (508)
T KOG3226|consen  389 AQKKLLPIRRYLMHAG  404 (508)
T ss_pred             HHHhhccHHHHHhcCC
Confidence            9999999999999643

>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]

Probab=99.06  E-value=8.7e-10  Score=120.15  Aligned_cols=186  Identities=18%  Similarity=0.238  Sum_probs=132.8

Q ss_pred             CCCC-CcEEEEeCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecC------CCHHHHHHHhcCCCCCceEecchHH
Q 012081           56 APFS-GLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSF------GGRKFEHALKHGSRNGLYIVTLGWF  128 (471)
Q Consensus        56 ~iF~-GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~------~g~Ky~~A~k~~~~~gi~IV~p~WI  128 (471)
                      .-|+ .++.+++|+++.++..|.+.++.   +...+....+||+|+...      .+.||..++.    +|.||++++|+
T Consensus       473 ~~~~kk~~~~~s~l~p~ek~~v~~~a~~---t~~k~~~~~~thvi~~~~~~g~c~rTlk~~~gil----~gkwi~~~~w~  545 (684)
T KOG4362|consen  473 HRFKKKLVLLVSGLTPSEKQLVEKFAVD---TISKFWIEPVTHVIASTDLEGACLRTLKVLMGIL----RGKWILSYDWV  545 (684)
T ss_pred             cCcccceeeeeccCCcchHHHHHHHHHH---HHhhccCCCceeeeeecccccchhhhHHHHHHhh----cCceeeeHHHH
Confidence            3444 47899999999999999999988   778888889999999876      3466666655    59999999999


Q ss_pred             HHHHHcccCCCCCccccccccccCcchhhhhcccCCcCCCCCCCCcccchhhccccccccccccccCCCCCCCCcEEEEe
Q 012081          129 VDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVD  208 (471)
Q Consensus       129 ~Dcik~g~~lde~~Y~l~~~~e~~~~~~~~~~L~~~s~~e~~~lp~~I~es~~s~s~E~ld~~~~~~~~~lF~G~~Iyl~  208 (471)
                      ..|++.+++++|.+|++..............++.                             .....+.||.|..||+.
T Consensus       546 ~~s~k~~~~~~eepfEl~~d~~~~~~~~~~~~~~-----------------------------a~s~~~kLf~gl~~~~~  596 (684)
T KOG4362|consen  546 LASLKLRKWVSEEPFELQIDVPGAREGPKEKRLR-----------------------------AESYKPKLFEGLKFYFV  596 (684)
T ss_pred             HHHHHhcCCCCCCCeeEeecccCcccCccccccc-----------------------------ccccCcchhcCCcceee
Confidence            9999999999999999974321110000000000                             00113689999999997


Q ss_pred             CCCCHHHHHHHHHHHHhCCCEEEccc---cCCCCceEEEEcC-----c--------hHHHHh-cCCCceechhHHHHHHh
Q 012081          209 SDVSEELRNKVFEAATNEGATLVNQW---FVGCGASYVVCEE-----D--------SVQKYM-GHSNNLVTPVWVLKTAK  271 (471)
Q Consensus       209 ~gfs~~~r~~L~~lI~~~GG~v~d~~---~~~~~vTHVVv~~-----~--------s~~k~l-~~~~~IVs~~WL~dcik  271 (471)
                      ..|+....++|++++...||++...-   ..+.+++-+++-.     .        +...+. ..+...|+..||+|++.
T Consensus       597 g~fs~~p~~~l~~l~~~~gg~~l~~~~~~~~~~k~s~~~~~~~~~~~~~~~~~k~~~~ea~~~s~~a~~~~~~wvl~s~a  676 (684)
T KOG4362|consen  597 GDFSNPPKEQLQELVHLAGGTILQVPRVAYSDKKKSTIVVLSEKPVLDSILWQKVNDAEALALSQRARAVSSSWVLDSIA  676 (684)
T ss_pred             cccccCcHHHHHHHHhhcCcceeeccCcccccccccceeEeecccCCCchhhhhhccHHHHHHhcCCCccchhhhhcchh
Confidence            78999889999999999999987541   1233444444322     0        122222 57889999999999996


Q ss_pred             hCCcCc
Q 012081          272 EKHVQR  277 (471)
Q Consensus       272 ~g~lqp  277 (471)
                      -...+.
T Consensus       677 ~~~~~~  682 (684)
T KOG4362|consen  677 GYQILV  682 (684)
T ss_pred             ceeeee
Confidence            554443

>smart00292 BRCT breast cancer carboxy-terminal domain

Probab=99.04  E-value=5.9e-10  Score=87.74  Aligned_cols=72  Identities=14%  Similarity=0.211  Sum_probs=61.4

Q ss_pred             CCCCcEEEEeCC-CCHHHHHHHHHHHHhCCCEEEccccCCC-CceEEEEcCchH-----HHHhcCCCceechhHHHHHHh
Q 012081          199 TLSGCSMYVDSD-VSEELRNKVFEAATNEGATLVNQWFVGC-GASYVVCEEDSV-----QKYMGHSNNLVTPVWVLKTAK  271 (471)
Q Consensus       199 lF~G~~Iyl~~g-fs~~~r~~L~~lI~~~GG~v~d~~~~~~-~vTHVVv~~~s~-----~k~l~~~~~IVs~~WL~dcik  271 (471)
                      +|+|+.||+ .| +....++.+.+++..+||++...  ... .+||+|+.+...     ..+...+++||+++||.||++
T Consensus         2 ~f~g~~~~~-~g~~~~~~~~~l~~~i~~~Gg~~~~~--~~~~~~thvi~~~~~~~~~~~~~~~~~~~~iV~~~Wi~~~~~   78 (80)
T smart00292        2 LFKGKVFVI-TGKFDKNERDELKELIEALGGKVTSS--LSSKTTTHVIVGSPEGGKLELLLAIALGIPIVTEDWLLDCLK   78 (80)
T ss_pred             ccCCeEEEE-eCCCCCccHHHHHHHHHHcCCEEecc--cCccceeEEEEcCCCCccHHHHHHHHcCCCCccHHHHHHHHH
Confidence            799999999 56 88889999999999999999998  466 899999988432     333468899999999999998


Q ss_pred             hC
Q 012081          272 EK  273 (471)
Q Consensus       272 ~g  273 (471)
                      ++
T Consensus        79 ~~   80 (80)
T smart00292       79 AG   80 (80)
T ss_pred             Cc
Confidence            64

>cd00027 BRCT Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain

Probab=98.89  E-value=4.6e-09  Score=80.71  Aligned_cols=67  Identities=22%  Similarity=0.346  Sum_probs=56.4

Q ss_pred             CcEEEEeCCCC-HHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCch----HHHHhcCCCceechhHHHHHHh
Q 012081          202 GCSMYVDSDVS-EELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDS----VQKYMGHSNNLVTPVWVLKTAK  271 (471)
Q Consensus       202 G~~Iyl~~gfs-~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~s----~~k~l~~~~~IVs~~WL~dcik  271 (471)
                      |+.||+ .|.. ...+..|.+++..+||++.+.  ....+||+|+....    .......+++||+++||.||++
T Consensus         1 ~~~~~i-~g~~~~~~~~~l~~~i~~~Gg~v~~~--~~~~~thvI~~~~~~~~~~~~~~~~~~~iV~~~Wi~~~~~   72 (72)
T cd00027           1 GLTFVI-TGDLPSEERDELKELIEKLGGKVTSS--VSKKTTHVIVGSDAGPKKLLKAIKLGIPIVTPEWLLDCLK   72 (72)
T ss_pred             CCEEEE-EecCCCcCHHHHHHHHHHcCCEEecc--ccCCceEEEECCCCCchHHHHHHHcCCeEecHHHHHHHhC
Confidence            689999 6655 778899999999999999998  57899999998843    3344468999999999999984

The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks.

>KOG3548 consensus DNA damage checkpoint protein RHP9/CRB2/53BP1 [Replication, recombination and repair]

Probab=98.67  E-value=6.3e-08  Score=107.25  Aligned_cols=196  Identities=20%  Similarity=0.204  Sum_probs=114.2

Q ss_pred             CCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEccc-----CCCC---------------------ceEEEEecC-CCHHH
Q 012081           56 APFSGLVICVTGLSKEARKQVMEATERLGGQYSPD-----LHPQ---------------------CTHLVVQSF-GGRKF  108 (471)
Q Consensus        56 ~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~-----l~~~---------------------~THLV~~~~-~g~Ky  108 (471)
                      .+|.||+|.+|+.... +++.+..++.+||.+...     |+..                     --.||+... .+.||
T Consensus       924 niFd~cvF~lTsa~~s-d~~~r~s~e~~gg~vle~gl~~~Fn~p~~g~~~~lr~Ln~~q~~ks~~qalLIsdth~Rt~KY 1002 (1176)
T KOG3548|consen  924 NIFDGCVFMLTSANRS-DSASRPSMEKHGGLVLEKGLMNLFNTPFKGGGIVLRQLNSFQERKSNYQALLISDTHYRTHKY 1002 (1176)
T ss_pred             chhcceeEEEeccccc-hhhhhhhhhccCChhhhccccccccccccCCcchHHhhhHHhhhccccceeEeehhhhHHHHH
Confidence            6999999999997753 345555666677775322     1110                     123455443 46899


Q ss_pred             HHHHhcCCCCCceEecchHHHHHHHcccCCCCCccccccccccCcchhhhhcccCCcCCCCCCCCcccchhhcccccccc
Q 012081          109 EHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKH  188 (471)
Q Consensus       109 ~~A~k~~~~~gi~IV~p~WI~Dcik~g~~lde~~Y~l~~~~e~~~~~~~~~~L~~~s~~e~~~lp~~I~es~~s~s~E~l  188 (471)
                      ..|++.    |||+|++.||.+|+++++++|-.+|.++..-....        -       ..+..+|.-   .+..+++
T Consensus      1003 LeaLA~----giPcVh~~fI~aC~e~nr~Vdy~~YLLpsGyS~rl--------d-------s~l~~~i~~---fn~~~nL 1060 (1176)
T KOG3548|consen 1003 LEALAR----GIPCVHNTFIQACGEQNRCVDYTDYLLPSGYSIRL--------D-------SQLMPAIEP---FNPSENL 1060 (1176)
T ss_pred             HHHHHc----CCCcccHHHHHHHHhccccccchhhcccCcccccc--------c-------cccccCccc---cCchhhc
Confidence            999996    89999999999999999999999999974321110        0       000000000   0000111


Q ss_pred             ccccccCCCCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccC---CCCce----EEEEcC----chHHHHh-cC
Q 012081          189 ERDSNRSMNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFV---GCGAS----YVVCEE----DSVQKYM-GH  256 (471)
Q Consensus       189 d~~~~~~~~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~---~~~vT----HVVv~~----~s~~k~l-~~  256 (471)
                      -...-.. ...+.+..|.+ .|-...-.+.+...+..+|+-+++..+.   +.+.+    -||+.+    .+..+++ .-
T Consensus      1061 kd~~l~v-k~~l~~~~v~q-~gp~~~f~e~~~e~le~G~aa~vd~~hada~~~D~~l~~fdvvl~d~~~~~svmk~ad~l 1138 (1176)
T KOG3548|consen 1061 KDTTLYV-KSTLSAREVTQ-TGPGGTFIEIWKEILELGGAAVVDGYHADAETLDETLLKFDVVLVDGTFRDSVMKYADTL 1138 (1176)
T ss_pred             cceeeEe-eccccceeEEE-ecCCcchHHHHHHHHHhhchheecccccccccccccccceeEEEecCccHHHHHHHHHHh
Confidence            0000000 11233333333 2333445677778888888888877321   11111    133333    3566666 47


Q ss_pred             CCceechhHHHHHHhhCCcC
Q 012081          257 SNNLVTPVWVLKTAKEKHVQ  276 (471)
Q Consensus       257 ~~~IVs~~WL~dcik~g~lq  276 (471)
                      +.++|+++||.+||-.|.-.
T Consensus      1139 ~~pvvs~EWvIQtiI~~~~i 1158 (1176)
T KOG3548|consen 1139 GAPVVSSEWVIQTIILGKAI 1158 (1176)
T ss_pred             CCCccChhHhheeeeccccC
Confidence            89999999999999887643

>PLN03122 Poly [ADP-ribose] polymerase; Provisional

Probab=98.63  E-value=6.9e-08  Score=108.72  Aligned_cols=89  Identities=26%  Similarity=0.480  Sum_probs=78.6

Q ss_pred             CCCCCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecCC----C-HHHHHHHhcCCCCCceEecchH
Q 012081           53 PANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFG----G-RKFEHALKHGSRNGLYIVTLGW  127 (471)
Q Consensus        53 ~~~~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~----g-~Ky~~A~k~~~~~gi~IV~p~W  127 (471)
                      ...++|.|++|++||.....|.+++++|+.+||++...+ ..+||+|+....    + .|++.|.+.    ||+||+.+|
T Consensus       185 ~~~kpL~G~~fviTGtl~~sr~elK~~Ie~~GGkvsssV-s~~T~lIvt~~ev~k~gsSKlkkAk~l----gIpIVsEd~  259 (815)
T PLN03122        185 APGKPFSGMMISLSGRLSRTHQYWKKDIEKHGGKVANSV-EGVTCLVVSPAERERGGSSKIAEAMER----GIPVVREAW  259 (815)
T ss_pred             ccCCCcCCcEEEEeCCCCCCHHHHHHHHHHcCCEEcccc-ccceEEEEcCccccccCccHHHHHHHc----CCcCccHHH
Confidence            455789999999999777799999999999999999999 667788887743    3 799999986    899999999


Q ss_pred             HHHHHHcccCCCCCccccc
Q 012081          128 FVDSVRRNVRLSESLYTVK  146 (471)
Q Consensus       128 I~Dcik~g~~lde~~Y~l~  146 (471)
                      |.+|++.++.+++..|.+.
T Consensus       260 L~d~i~~~k~~~~~~y~l~  278 (815)
T PLN03122        260 LIDSIEKQEAQPLEAYDVV  278 (815)
T ss_pred             HHHHHhcCCcccchhhhhc
Confidence            9999999999999999884

>PF12738 PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2WT8_C 3EF1_A 3EF0_A

Probab=98.60  E-value=3.3e-08  Score=76.90  Aligned_cols=60  Identities=17%  Similarity=0.302  Sum_probs=48.8

Q ss_pred             cEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCchHHHHh---cCCCceechhH
Q 012081          203 CSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKYM---GHSNNLVTPVW  265 (471)
Q Consensus       203 ~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~s~~k~l---~~~~~IVs~~W  265 (471)
                      ++|++ +||++.++..|.++++.+||.+.++  +..++||+|+......||.   .++++||+++|
T Consensus         1 ~~i~~-sg~~~~~~~~l~~~i~~~Gg~~~~~--lt~~~THLI~~~~~~~K~~~A~~~gi~vV~~~W   63 (63)
T PF12738_consen    1 VVICF-SGFSGKERSQLRKLIEALGGKYSKD--LTKKTTHLICSSPEGKKYRKAKEWGIPVVSPDW   63 (63)
T ss_dssp             -EEEE-EEB-TTTCCHHHHHHHCTT-EEESS--SSTT-SEEEEES--HHHHHHHHHCTSEEEEHHH
T ss_pred             CEEEE-CCCCHHHHHHHHHHHHHCCCEEecc--ccCCceEEEEeCCCcHHHHHHHHCCCcEECCCC
Confidence            47888 9999999999999999999999999  6999999999886666554   68899999999

>PLN03123 poly [ADP-ribose] polymerase; Provisional

Probab=98.56  E-value=1.1e-07  Score=109.25  Aligned_cols=90  Identities=20%  Similarity=0.305  Sum_probs=80.8

Q ss_pred             CCCCCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecC---CCHHHHHHHhcCCCCCceEecchHHH
Q 012081           53 PANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSF---GGRKFEHALKHGSRNGLYIVTLGWFV  129 (471)
Q Consensus        53 ~~~~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~---~g~Ky~~A~k~~~~~gi~IV~p~WI~  129 (471)
                      ...++|.|+.|++.|-.+..+.+++++|+.+||+|+..++..+||||+...   .+.|++.|.+.    +|+||+.+||.
T Consensus       389 ~~~~~l~~~~i~i~G~~~~~~~~~k~~Ie~~GG~~s~~v~~~~t~l~tt~e~~k~~~kv~qAk~~----~ipIVsedwL~  464 (981)
T PLN03123        389 SESEFLGDLKVSIVGASKEKVTEWKAKIEEAGGVFHATVKKDTNCLVVCGELDDEDAEMRKARRM----KIPIVREDYLV  464 (981)
T ss_pred             ccCCCcCCeEEEEecCCCCcHHHHHHHHHhcCCEEeeeccCCceEEEccHHhhhcchHHHHHHhc----CCCcccHHHHH
Confidence            455899999999999888888999999999999999999999999999863   46789999885    79999999999


Q ss_pred             HHHHcccCCCCCccccc
Q 012081          130 DSVRRNVRLSESLYTVK  146 (471)
Q Consensus       130 Dcik~g~~lde~~Y~l~  146 (471)
                      ||++.+..+++..|.+.
T Consensus       465 ds~~~~~~~p~~~y~~~  481 (981)
T PLN03123        465 DCFKKKKKLPFDKYKLE  481 (981)
T ss_pred             HHHhccccCcchhhhhc
Confidence            99999999999888774

>KOG3226 consensus DNA repair protein [Replication, recombination and repair]

Probab=98.15  E-value=1.6e-06  Score=88.17  Aligned_cols=82  Identities=20%  Similarity=0.408  Sum_probs=73.8

Q ss_pred             CCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCchHHHH---hcCCCceechhHHHHHHhhC
Q 012081          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKY---MGHSNNLVTPVWVLKTAKEK  273 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~s~~k~---l~~~~~IVs~~WL~dcik~g  273 (471)
                      +.|+.|..|.| +||....|..|+.....+|+++-.+|  +.++||+||.=...-||   .+.+-+||+-+||.+|...+
T Consensus       315 ~klL~GVV~Vl-SGfqNP~Rs~LRskAl~LGAkY~pDW--~~gsThLICAF~NTPKy~QV~g~Gg~IV~keWI~~Cy~~k  391 (508)
T KOG3226|consen  315 SKLLEGVVFVL-SGFQNPERSTLRSKALTLGAKYQPDW--NAGSTHLICAFPNTPKYRQVEGNGGTIVSKEWITECYAQK  391 (508)
T ss_pred             HHhhhceEEEE-ecccCchHHHHHHHHHhhcccccCCc--CCCceeEEEecCCCcchhhcccCCceEeeHHHHHHHHHHH
Confidence            67999999999 99999999999999999999999998  99999999977555555   46888999999999999999


Q ss_pred             CcCccCCc
Q 012081          274 HVQRLVHI  281 (471)
Q Consensus       274 ~lqp~~~y  281 (471)
                      +++|...|
T Consensus       392 k~lp~rrY  399 (508)
T KOG3226|consen  392 KLLPIRRY  399 (508)
T ss_pred             hhccHHHH
Confidence            99997666

>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=98.00  E-value=1.4e-05  Score=89.16  Aligned_cols=74  Identities=22%  Similarity=0.305  Sum_probs=67.4

Q ss_pred             CCCCCCcEEEEeC-CChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHHHHHHHhcCCCCCceEecchHHHHHH
Q 012081           55 NAPFSGLVICVTG-LSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSV  132 (471)
Q Consensus        55 ~~iF~GlvI~vTG-~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~Dci  132 (471)
                      ..+|.|.+||+|| +....|.+++++|+++||++...+++++++||++...|.|+++|.+.    ||+|++.+.+.+-+
T Consensus       591 ~~~l~gktfV~TG~l~~~~R~e~~~lie~~Ggkv~ssVSkktd~LV~G~~aGsKl~KA~~L----GI~Ii~e~~f~~~l  665 (669)
T PRK14350        591 NSFLFGKKFCITGSFNGYSRSVLIDKLTKKGAIFNTCVTKYLDFLLVGEKAGLKLKKANNL----GIKIMSLFDIKSYV  665 (669)
T ss_pred             CCccCCcEEEEecccCCCCHHHHHHHHHHcCCEEeccccCCCcEEEECCCCCchHHHHHHc----CCEEecHHHHHHHh
Confidence            3579999999999 55578999999999999999999999999999999899999999996    89999999887743

>PRK06063 DNA polymerase III subunit epsilon; Provisional

Probab=97.93  E-value=2.4e-05  Score=80.09  Aligned_cols=73  Identities=15%  Similarity=0.214  Sum_probs=65.8

Q ss_pred             CCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCC--HHHHHHHhcCCCCCceEecchHHHHHH
Q 012081           56 APFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGG--RKFEHALKHGSRNGLYIVTLGWFVDSV  132 (471)
Q Consensus        56 ~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g--~Ky~~A~k~~~~~gi~IV~p~WI~Dci  132 (471)
                      ++|.|.+|++||-....|.+++++|+.+||++...+++++++||++...+  .|.++|.+.    ||+|++.+=+.+-+
T Consensus       231 ~l~~g~~~v~TG~l~~~R~e~~~~~~~~G~~v~~sVs~~t~~lv~g~~~~~ssK~~kA~~~----gi~ii~e~~f~~ll  305 (313)
T PRK06063        231 PLVQGMRVALSAEVSRTHEELVERILHAGLAYSDSVDRDTSLVVCNDPAPEQGKGYHARQL----GVPVLDEAAFLELL  305 (313)
T ss_pred             cccCCCEEEEecCCCCCHHHHHHHHHHcCCEecCccccCccEEEECCCCCcccHHHHHHHc----CCccccHHHHHHHH
Confidence            45799999999966689999999999999999999999999999998877  799999996    89999988777655

>PRK06195 DNA polymerase III subunit epsilon; Validated

Probab=97.91  E-value=4.6e-05  Score=77.78  Aligned_cols=79  Identities=20%  Similarity=0.269  Sum_probs=65.0

Q ss_pred             CCCCCCcEEEEeCCC-hhhHHHHHHHHHHcCCEEcccCCCCceEEEEecC---------CCHHHHHHHhcC-CCCCceEe
Q 012081           55 NAPFSGLVICVTGLS-KEARKQVMEATERLGGQYSPDLHPQCTHLVVQSF---------GGRKFEHALKHG-SRNGLYIV  123 (471)
Q Consensus        55 ~~iF~GlvI~vTG~~-~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~---------~g~Ky~~A~k~~-~~~gi~IV  123 (471)
                      ..+|.|.+||+||-. ...|.++.++|+.+||++..++++++++||++..         .+.|+++|.+.. .-.+|+|+
T Consensus       218 ~~~l~g~~~vfTG~l~~~~R~~~~~~~~~~Gg~v~~sVs~~t~~lV~G~~~~~~~~~~~~~~K~~kA~~l~~~g~~i~ii  297 (309)
T PRK06195        218 FTAFKEEVVVFTGGLASMTRDEAMILVRRLGGTVGSSVTKKTTYLVTNTKDIEDLNREEMSNKLKKAIDLKKKGQNIKFL  297 (309)
T ss_pred             CccccCCEEEEccccCCCCHHHHHHHHHHhCCEecCCcccCceEEEECCCcchhhcccCcChHHHHHHHHHhCCCCcEEe
Confidence            357999999999965 5799999999999999999999999999999853         478999998741 01489999


Q ss_pred             cchHHHHHHH
Q 012081          124 TLGWFVDSVR  133 (471)
Q Consensus       124 ~p~WI~Dcik  133 (471)
                      +.+=+.+-++
T Consensus       298 ~E~~f~~l~~  307 (309)
T PRK06195        298 NEEEFLQKCK  307 (309)
T ss_pred             cHHHHHHHHh
Confidence            9876665443

>KOG2043 consensus Signaling protein SWIFT and related BRCT domain proteins [Transcription; Signal transduction mechanisms; Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=97.89  E-value=2e-05  Score=90.00  Aligned_cols=136  Identities=21%  Similarity=0.301  Sum_probs=97.1

Q ss_pred             EEEEeCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecC-CCHHHHHHHhcCCCCCceEecchHHHHHHHcccCCCC
Q 012081           62 VICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSF-GGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSE  140 (471)
Q Consensus        62 vI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~-~g~Ky~~A~k~~~~~gi~IV~p~WI~Dcik~g~~lde  140 (471)
                      .+.++++.  +...++..++.+||.+.... .+.||+|+... .+.|+..|+..    |++||+++||.+|++.|.++|+
T Consensus       661 ~~lfs~~~--~~~~~k~~~k~lg~s~~ss~-~e~Th~i~~rirRT~k~Leai~~----G~~ivT~~wL~s~~k~g~~~de  733 (896)
T KOG2043|consen  661 EVLFSDKN--DGKNYKLAKKFLGGSVASSD-SEATHFIADRIRRTLKFLEAISS----GKPLVTPQWLVSSLKSGEKLDE  733 (896)
T ss_pred             eeeeeecc--CchhhhhHHhhccceeeccc-ccceeeeehhhhccHHHHhhhcc----CCcccchHHHHHHhhccccccC
Confidence            34445543  34467888999998877776 57899999876 57899999885    7899999999999999999999


Q ss_pred             CccccccccccCcchhhhhcccCCcCCCCCCCCcccchhhccccccccccccccCCCCCCCCcEEEEeCCCCHHHHHHHH
Q 012081          141 SLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVSEELRNKVF  220 (471)
Q Consensus       141 ~~Y~l~~~~e~~~~~~~~~~L~~~s~~e~~~lp~~I~es~~s~s~E~ld~~~~~~~~~lF~G~~Iyl~~gfs~~~r~~L~  220 (471)
                      +.|.+.+...-...  .++....+.                          ..+. ..+|.|..||+.+.+.+ ....+-
T Consensus       734 k~yil~D~ekEk~~--gf~l~ssl~--------------------------RAr~-~plL~g~~v~vtp~v~p-~~~~v~  783 (896)
T KOG2043|consen  734 KPYILHDEEKEKEF--GFRLKSSLL--------------------------RARA-DPLLEGINVHVTPSVTP-SPKTVV  783 (896)
T ss_pred             ccccccCHHHHhcc--CcchhhHHH--------------------------Hhhc-chhhcCceEEecccccc-CcchhH
Confidence            99999764311100  000000000                          0001 36899999999665554 457899


Q ss_pred             HHHHhCCCEEEccc
Q 012081          221 EAATNEGATLVNQW  234 (471)
Q Consensus       221 ~lI~~~GG~v~d~~  234 (471)
                      ++|...||.++...
T Consensus       784 eiie~~ggnvv~~~  797 (896)
T KOG2043|consen  784 EIIEISGGNVVSDS  797 (896)
T ss_pred             HHHhhcCcceeccc
Confidence            99999999999873

>KOG2481 consensus Protein required for normal rRNA processing [RNA processing and modification]

Probab=97.87  E-value=8.7e-06  Score=86.02  Aligned_cols=83  Identities=13%  Similarity=0.177  Sum_probs=64.0

Q ss_pred             CCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccc--------cCCCCceEEEEcCchHHHHhcCCCceechhHHHH
Q 012081          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQW--------FVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLK  268 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~--------~~~~~vTHVVv~~~s~~k~l~~~~~IVs~~WL~d  268 (471)
                      ..+|+|+.|||....+   ++.|.-+|+++||.|.-+-        ..++.+||=||..+..+.-. -+...|.|+||+|
T Consensus       325 kslF~glkFfl~reVP---resL~fiI~s~GG~V~wd~~~~g~~~~~~d~~ITH~IvDrP~~~~~v-~gR~YvQPQWvfD  400 (570)
T KOG2481|consen  325 KSLFSGLKFFLNREVP---RESLEFIIRSFGGKVSWDPLGIGATYDESDERITHQIVDRPGQQTSV-IGRTYVQPQWVFD  400 (570)
T ss_pred             HHHhhcceeeeeccCc---hHHHHHHHHHcCCceecCccCCCCcccccccceeeeeecccCcccee-eeeeeecchhhhh
Confidence            6799999999965555   5778999999999998551        12466799999886543322 2455789999999


Q ss_pred             HHhhCCcCccCCcCh
Q 012081          269 TAKEKHVQRLVHISA  283 (471)
Q Consensus       269 cik~g~lqp~~~ys~  283 (471)
                      |++++.++|...|-+
T Consensus       401 svNar~llpt~~Y~~  415 (570)
T KOG2481|consen  401 SVNARLLLPTEKYFP  415 (570)
T ss_pred             hccchhhccHhhhCC
Confidence            999999999888743

>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]

Probab=97.87  E-value=3.3e-05  Score=84.91  Aligned_cols=72  Identities=22%  Similarity=0.314  Sum_probs=67.1

Q ss_pred             CCCCCcEEEEeCCC-hhhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHHHHHHHhcCCCCCceEecchHHHHH
Q 012081           56 APFSGLVICVTGLS-KEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDS  131 (471)
Q Consensus        56 ~iF~GlvI~vTG~~-~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~Dc  131 (471)
                      .+|.|.+|++||-- .-.|.+++++++.+||+++..++++++.||++...|.|+.+|.+.    ||+|++.+++..-
T Consensus       593 ~~l~gkt~V~TGtL~~~sR~eak~~le~lGakv~~SVSkktD~vvaG~~aGSKl~kA~eL----gv~i~~E~~~~~l  665 (667)
T COG0272         593 SPLAGKTFVLTGTLEGMSRDEAKALLEALGAKVSGSVSKKTDYVVAGENAGSKLAKAQEL----GVKIIDEEEFLAL  665 (667)
T ss_pred             cccCCCEEEEeccCCCCCHHHHHHHHHHcCCEEeceecccccEEEEcCCCChHHHHHHHc----CCeEecHHHHHHh
Confidence            78999999999955 489999999999999999999999999999999999999999996    8999999988754

>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated

Probab=97.83  E-value=4.8e-05  Score=85.10  Aligned_cols=75  Identities=20%  Similarity=0.298  Sum_probs=68.6

Q ss_pred             CCCCCcEEEEeCCCh-hhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHHHHHHHhcCCCCCceEecchHHHHHHHc
Q 012081           56 APFSGLVICVTGLSK-EARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVRR  134 (471)
Q Consensus        56 ~iF~GlvI~vTG~~~-~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~Dcik~  134 (471)
                      ..|.|.+||+||... -.|.++.++|+.+||++...+++++++||++...|.|.++|.+.    ||+|++.+-+.+.+..
T Consensus       589 ~~~~g~~~v~TG~l~~~~R~e~~~~i~~~G~~v~~sVs~kt~~lv~G~~~gsK~~kA~~l----gI~ii~E~~f~~~l~~  664 (665)
T PRK07956        589 VDLAGKTVVLTGTLEQLSRDEAKEKLEALGAKVSGSVSKKTDLVVAGEAAGSKLAKAQEL----GIEVLDEEEFLRLLGE  664 (665)
T ss_pred             CCccccEEEEeCCCCCCCHHHHHHHHHHcCCEEeCcccCCCCEEEECCCCChHHHHHHHc----CCeEEcHHHHHHHHhc
Confidence            359999999999775 59999999999999999999999999999999889999999996    8999999999887654

>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=97.80  E-value=6.4e-05  Score=84.28  Aligned_cols=76  Identities=21%  Similarity=0.227  Sum_probs=69.0

Q ss_pred             CCCCCCcEEEEeCCCh-hhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCC-HHHHHHHhcCCCCCceEecchHHHHHH
Q 012081           55 NAPFSGLVICVTGLSK-EARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGG-RKFEHALKHGSRNGLYIVTLGWFVDSV  132 (471)
Q Consensus        55 ~~iF~GlvI~vTG~~~-~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g-~Ky~~A~k~~~~~gi~IV~p~WI~Dci  132 (471)
                      ..+|.|.+||+||... -.|.+++++|+.+||++..++++++++||++...| .|.++|.+.    ||+|++.+-+.+-+
T Consensus       607 ~~~l~g~~~v~TG~l~~~~R~~~~~~i~~~Gg~v~~sVs~kt~~Lv~G~~~g~sKl~kA~~l----gi~ii~E~~f~~ll  682 (689)
T PRK14351        607 GDALDGLTFVFTGSLSGYTRSEAQELVEAHGGNATGSVSGNTDYLVVGENPGQSKRDDAEAN----DVPTLDEEEFEELL  682 (689)
T ss_pred             CCCCCCcEEEEccCCCCCCHHHHHHHHHHcCCEEcCCcCCCccEEEEcCCCChhHHHHHHHC----CCeEecHHHHHHHH
Confidence            4579999999999765 69999999999999999999999999999999888 799999985    89999999998877


Q ss_pred             Hc
Q 012081          133 RR  134 (471)
Q Consensus       133 k~  134 (471)
                      +.
T Consensus       683 ~~  684 (689)
T PRK14351        683 AE  684 (689)
T ss_pred             Hh
Confidence            64

>TIGR00575 dnlj DNA ligase, NAD-dependent

Probab=97.74  E-value=5.7e-05  Score=84.35  Aligned_cols=69  Identities=22%  Similarity=0.359  Sum_probs=62.5

Q ss_pred             CCCCCCcEEEEeCCCh-hhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHHHHHHHhcCCCCCceEecchH
Q 012081           55 NAPFSGLVICVTGLSK-EARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGW  127 (471)
Q Consensus        55 ~~iF~GlvI~vTG~~~-~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~W  127 (471)
                      ..+|.|.+||+||... ..|.+++++|+.+||++..++++++++||++...|.|+++|.+.    ||+|++.+.
T Consensus       582 ~~~l~gk~~v~TG~l~~~~R~~~~~~i~~~G~~v~~sVs~kt~~lv~G~~~gsKl~kA~~l----gi~ii~E~~  651 (652)
T TIGR00575       582 GSPLAGKTFVLTGTLSQMSRDEAKELLENLGGKVASSVSKKTDYVIAGEKAGSKLAKAQEL----GIPIINEEE  651 (652)
T ss_pred             CCCccCcEEEEeccCCCCCHHHHHHHHHHcCCEEeCCcCCCccEEEECCCCChHHHHHHHc----CCcEechhh
Confidence            3579999999999654 78999999999999999999999999999999889999999996    899998653

The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.

>COG5163 NOP7 Protein required for biogenesis of the 60S ribosomal subunit [Translation, ribosomal structure and biogenesis]

Probab=97.67  E-value=3.3e-05  Score=79.49  Aligned_cols=89  Identities=12%  Similarity=0.264  Sum_probs=68.9

Q ss_pred             CCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccc---------cCCCCceEEEEcCchHHHHhcCCCceechhHHH
Q 012081          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQW---------FVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVL  267 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~---------~~~~~vTHVVv~~~s~~k~l~~~~~IVs~~WL~  267 (471)
                      ..+|+|+.||+...++.   ..|+-+|.++||.|+.+-         ..+..+||-||..+-++.-. .+...|.|+||+
T Consensus       348 ~slFS~f~FyisreVp~---dsLefiilscGG~V~~~p~~~~i~~~~~vD~~vth~i~drp~~~~kv-egrtYiQPQw~f  423 (591)
T COG5163         348 KSLFSGFKFYISREVPG---DSLEFIILSCGGSVVGSPCEADIHVSEKVDEKVTHQIVDRPVMKNKV-EGRTYIQPQWLF  423 (591)
T ss_pred             hhhhhceEEEEeccccc---hHHHHHHHHcCCcccCchhhccCCchhhccchhhhhhccchhhhhhh-cceeeechHHHH
Confidence            57999999999655553   568889999999998651         14667899999887654433 356778999999


Q ss_pred             HHHhhCCcCccCCcC--hHHHhhh
Q 012081          268 KTAKEKHVQRLVHIS--ADLARQV  289 (471)
Q Consensus       268 dcik~g~lqp~~~ys--~dl~r~~  289 (471)
                      |||..|.+.+...|.  ..|.+|+
T Consensus       424 DsiNkG~l~~~~~Y~~G~~LPpHl  447 (591)
T COG5163         424 DSINKGKLACVENYCVGKRLPPHL  447 (591)
T ss_pred             hhhccccchhhhhccccccCCCCc
Confidence            999999999998885  3456665

>PLN03122 Poly [ADP-ribose] polymerase; Provisional

Probab=97.47  E-value=0.00028  Score=80.09  Aligned_cols=84  Identities=15%  Similarity=0.271  Sum_probs=69.2

Q ss_pred             CCCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCc--------hHHHHhcCCCceechhHHH
Q 012081          196 MNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED--------SVQKYMGHSNNLVTPVWVL  267 (471)
Q Consensus       196 ~~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~--------s~~k~l~~~~~IVs~~WL~  267 (471)
                      ....|.|+.|.|...|+. .|..++++|..+||++..+  + .++||+|+.+.        .++++...+++||+.+||+
T Consensus       186 ~~kpL~G~~fviTGtl~~-sr~elK~~Ie~~GGkvsss--V-s~~T~lIvt~~ev~k~gsSKlkkAk~lgIpIVsEd~L~  261 (815)
T PLN03122        186 PGKPFSGMMISLSGRLSR-THQYWKKDIEKHGGKVANS--V-EGVTCLVVSPAERERGGSSKIAEAMERGIPVVREAWLI  261 (815)
T ss_pred             cCCCcCCcEEEEeCCCCC-CHHHHHHHHHHcCCEEccc--c-ccceEEEEcCccccccCccHHHHHHHcCCcCccHHHHH
Confidence            356799999999444655 7889999999999999999  4 77889988662        2455567899999999999


Q ss_pred             HHHhhCCcCccCCcCh
Q 012081          268 KTAKEKHVQRLVHISA  283 (471)
Q Consensus       268 dcik~g~lqp~~~ys~  283 (471)
                      +|++.+..+++..|..
T Consensus       262 d~i~~~k~~~~~~y~l  277 (815)
T PLN03122        262 DSIEKQEAQPLEAYDV  277 (815)
T ss_pred             HHHhcCCcccchhhhh
Confidence            9999999999887743

>PLN03123 poly [ADP-ribose] polymerase; Provisional

Probab=97.26  E-value=0.0005  Score=79.66  Aligned_cols=82  Identities=11%  Similarity=0.064  Sum_probs=66.2

Q ss_pred             CCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCc------hHHHHhcCCCceechhHHHHHH
Q 012081          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED------SVQKYMGHSNNLVTPVWVLKTA  270 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~------s~~k~l~~~~~IVs~~WL~dci  270 (471)
                      ...|.|+.|.+...|+ .....+++.|..+||++...  +...+||||+..+      .++++...+++||+.+||.||+
T Consensus       391 ~~~l~~~~i~i~G~~~-~~~~~~k~~Ie~~GG~~s~~--v~~~~t~l~tt~e~~k~~~kv~qAk~~~ipIVsedwL~ds~  467 (981)
T PLN03123        391 SEFLGDLKVSIVGASK-EKVTEWKAKIEEAGGVFHAT--VKKDTNCLVVCGELDDEDAEMRKARRMKIPIVREDYLVDCF  467 (981)
T ss_pred             CCCcCCeEEEEecCCC-CcHHHHHHHHHhcCCEEeee--ccCCceEEEccHHhhhcchHHHHHHhcCCCcccHHHHHHHH
Confidence            5779999999944455 44588999999999999999  6889999998762      2344445689999999999999


Q ss_pred             hhCCcCccCCc
Q 012081          271 KEKHVQRLVHI  281 (471)
Q Consensus       271 k~g~lqp~~~y  281 (471)
                      +.+..+|...|
T Consensus       468 ~~~~~~p~~~y  478 (981)
T PLN03123        468 KKKKKLPFDKY  478 (981)
T ss_pred             hccccCcchhh
Confidence            99987777655

>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]

Probab=97.08  E-value=0.00025  Score=79.27  Aligned_cols=199  Identities=10%  Similarity=0.098  Sum_probs=119.6

Q ss_pred             CCCCCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEc-ccCCCCceEEEEecCCCHHHHHHHhcCCCCCceEecchHHHHH
Q 012081           53 PANAPFSGLVICVTGLSKEARKQVMEATERLGGQYS-PDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDS  131 (471)
Q Consensus        53 ~~~~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~-~~l~~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~Dc  131 (471)
                      .....|+|+-||+.|...+...++++.-.-+||.+. .+....++|+|+......|.+-.      ..=+..+++|+.+|
T Consensus        43 t~~s~fs~is~~~ngs~~e~~nelk~~~~~~t~~~~~~~~rs~T~~ii~~~l~a~~vk~~------~~~~~~~~e~iie~  116 (1016)
T KOG2093|consen   43 TGSSSFSGISISVNGSTDESANELKLQNMFHTGASAASYERSGTENIIAQGLPADLVKGF------TIPKHISIEWIIEC  116 (1016)
T ss_pred             CCcceeeeeeeccCCccccchHHHhhhhhhcccccccccccccceeeecccchHHHhccc------cchhhhcHHHHHHH
Confidence            356899999999999999999999999999999998 55556899999988754443322      23467899999999


Q ss_pred             HHcccCCCCCccccccccccCcchhhhhcccCCcCCCCCCCCcccchhhccccccccccccccCCCCCCCCcEEEEeCCC
Q 012081          132 VRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDV  211 (471)
Q Consensus       132 ik~g~~lde~~Y~l~~~~e~~~~~~~~~~L~~~s~~e~~~lp~~I~es~~s~s~E~ld~~~~~~~~~lF~G~~Iyl~~gf  211 (471)
                      +++++.+.-.+|............     +...   .. +.|..              -.....+..+|.++.|++ .|.
T Consensus       117 ~~~~~~~~~~~~~~~t~~~h~q~~-----~~~~---~~-~~~~D--------------~q~~~~~~ki~~~n~iki-nG~  172 (1016)
T KOG2093|consen  117 CENGMDVGYYPYQLYTGQSHEQAQ-----LAFP---VT-SFPKD--------------QQISSQSSKIFKNNVIKI-NGY  172 (1016)
T ss_pred             HhccCccccccceeeccchhcccc-----cCCC---cc-cCCcc--------------ccccccchhccccceeee-cCC
Confidence            999999888777765433222110     0000   00 00000              000111356899999999 888


Q ss_pred             CHHHHHHHH-HHHHhCCCEEEccccCCCCceEEEEcCchHHHHhcCCCceechhHHHHHHhhCCcCccCCcC
Q 012081          212 SEELRNKVF-EAATNEGATLVNQWFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHIS  282 (471)
Q Consensus       212 s~~~r~~L~-~lI~~~GG~v~d~~~~~~~vTHVVv~~~s~~k~l~~~~~IVs~~WL~dcik~g~lqp~~~ys  282 (471)
                      +.+..-.|. -....+++...+.-...+.++|.+.++.-..++ -.+...++|.|+.+.+..-...+...||
T Consensus       173 ~E~~~~dlepp~gv~~d~~~~~~~~~rd~v~~~l~~~~l~n~~-f~n~~~~sP~~~~~k~~~a~~~~~~~~S  243 (1016)
T KOG2093|consen  173 NEPESLDLEPPSGVLHDKAEDDSTSARDHVDHELAGNLLLNKR-FVNIENTSPDWIVDKELTAHTGTGQNYS  243 (1016)
T ss_pred             CCccccccCCCcccccchhhhhhhhHHHHHHHHhccccccccc-cceeeecCchhhhhhhhhhccCCccccc
Confidence            755431222 111111222222111233344444332100111 1345678899999998876666666665

>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]

Probab=97.04  E-value=0.0012  Score=73.49  Aligned_cols=82  Identities=20%  Similarity=0.377  Sum_probs=66.0

Q ss_pred             CCCCCCcEEEEeCCCCHHH-HHHHHHHHHhCCCEEEccccCCCCceEEEE--cCch-HH--HHhcCCCceechhHHHHHH
Q 012081          197 NSTLSGCSMYVDSDVSEEL-RNKVFEAATNEGATLVNQWFVGCGASYVVC--EEDS-VQ--KYMGHSNNLVTPVWVLKTA  270 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~~-r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv--~~~s-~~--k~l~~~~~IVs~~WL~dci  270 (471)
                      ..+|+|..||+-+|.+... +..|+++|..+||.++.+  +....||.|+  +..+ ..  ..+.....||.|.||+||.
T Consensus       631 s~if~gl~f~Vlsgt~~~~tk~~le~~ivenGG~iv~n--v~p~~~~ci~~a~~et~~vk~~~~~~~cdVl~p~Wlldcc  708 (881)
T KOG0966|consen  631 SNIFDGLEFCVLSGTSETHTKAKLEEIIVENGGKIVQN--VGPSDTLCIATAGKETTRVKAQAIKRSCDVLKPAWLLDCC  708 (881)
T ss_pred             hhhhcCeeEEEecCCcccccHHHHHHHHHHcCCEEEEc--CCCCCcceEEeccccchHHHHHHHhccCceeeHHHHHHHH
Confidence            5789999999977776554 689999999999999998  6777888886  3332 22  2336789999999999999


Q ss_pred             hhCCcCccCC
Q 012081          271 KEKHVQRLVH  280 (471)
Q Consensus       271 k~g~lqp~~~  280 (471)
                      ...+++|..+
T Consensus       709 ~~~~l~p~~P  718 (881)
T KOG0966|consen  709 KKQRLLPWLP  718 (881)
T ss_pred             hhhhcccccc
Confidence            9999888643

>COG5275 BRCT domain type II [General function prediction only]

Probab=96.52  E-value=0.009  Score=57.43  Aligned_cols=78  Identities=19%  Similarity=0.178  Sum_probs=66.4

Q ss_pred             CCCCCCCCCCcEEEEeCCCh-hhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCC-HHHHHHHhcCCCCCceEecchHH
Q 012081           51 VLPANAPFSGLVICVTGLSK-EARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGG-RKFEHALKHGSRNGLYIVTLGWF  128 (471)
Q Consensus        51 ~~~~~~iF~GlvI~vTG~~~-~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g-~Ky~~A~k~~~~~gi~IV~p~WI  128 (471)
                      |......+.|++|.+||... -+|..-..+|..+||+++...+..+|+||.++..| .|.+.+..+    +|+++..+=|
T Consensus       150 peg~~~cL~G~~fVfTG~l~TlsR~~a~~lvk~yGgrvT~~pSskTtflvlGdnaGP~K~ekiKql----kIkaidEegf  225 (276)
T COG5275         150 PEGERECLKGKVFVFTGDLKTLSRDDAKTLVKVYGGRVTAVPSSKTTFLVLGDNAGPSKMEKIKQL----KIKAIDEEGF  225 (276)
T ss_pred             CCCCcccccccEEEEecccccccchhHHHHHHHhCCeeecccccceeEEEecCCCChHHHHHHHHh----CCccccHHHH
Confidence            34566889999999999877 88999999999999999999999999999998866 578888876    8999887766


Q ss_pred             HHHH
Q 012081          129 VDSV  132 (471)
Q Consensus       129 ~Dci  132 (471)
                      ..-|
T Consensus       226 ~~LI  229 (276)
T COG5275         226 DSLI  229 (276)
T ss_pred             HHHH
Confidence            5444

>KOG0323 consensus TFIIF-interacting CTD phosphatases, including NLI-interacting factor [Transcription]

Probab=96.32  E-value=0.0017  Score=71.74  Aligned_cols=93  Identities=20%  Similarity=0.381  Sum_probs=80.2

Q ss_pred             CCCCCCCcEEEEeCCCh----hhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHHHHHHHhcCCCCCceEecchHHH
Q 012081           54 ANAPFSGLVICVTGLSK----EARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFV  129 (471)
Q Consensus        54 ~~~iF~GlvI~vTG~~~----~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~  129 (471)
                      ....++|+.+.++|+.+    .++..+-.....+|....++++..+||+|+.+..+.|..+|...   +.++||++.|++
T Consensus       438 ~~~v~~~~~~vfSg~~P~~~~~~~s~~~~~~~~~g~vs~~~~~~~~th~i~~~~gt~k~~~a~~~---~~~~Vv~~~wl~  514 (635)
T KOG0323|consen  438 RTKVLKGSQIVFSGLHPTGSTDESADILGVAQQLGAVSAPDVSDKTTHLIAANAGTKKVYKAVVS---GSAKVVNAAWLW  514 (635)
T ss_pred             hhHHhhccceeecccccCcCCcchhhhhhhhhcccceecccccchhhhHHhhccCcceeeccccc---cceeEechhHHH
Confidence            45689999999999765    45567777778899999999999999999999999998888775   359999999999


Q ss_pred             HHHHcccCCCCCcccccccc
Q 012081          130 DSVRRNVRLSESLYTVKSID  149 (471)
Q Consensus       130 Dcik~g~~lde~~Y~l~~~~  149 (471)
                      .|+.++..++|..|.+....
T Consensus       515 ~~~e~w~~v~ek~~~l~~~~  534 (635)
T KOG0323|consen  515 RSLEKWGKVEEKLEPLDDDQ  534 (635)
T ss_pred             HHHHHhcchhcccccccccc
Confidence            99999999999999887543

>KOG3524 consensus Predicted guanine nucleotide exchange factor (PEBBLE) [Signal transduction mechanisms]

Probab=96.27  E-value=0.0039  Score=68.55  Aligned_cols=92  Identities=24%  Similarity=0.366  Sum_probs=76.7

Q ss_pred             CCCCCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHHHHHHHhcCCCCCceEecchHHHHHH
Q 012081           53 PANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSV  132 (471)
Q Consensus        53 ~~~~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~Dci  132 (471)
                      .....|.|+.||+-||..++...+....+..||++.. -+..|||||+......---.+..    ....+|..+|++=++
T Consensus       206 hrl~~feg~~~~f~gF~~ee~~~m~~sle~~gg~~a~-~d~~cthvvv~e~~~~~~p~~~s----~~~~~vk~ewfw~si  280 (850)
T KOG3524|consen  206 HRLGVFEGLSLFFHGFKQEEIDDMLRSLENTGGKLAP-SDTLCTHVVVNEDNDEVEPLAVS----SNQVHVKKEWFWVSI  280 (850)
T ss_pred             hccccccCCeEeecCCcHHHHHHHHHHHHhcCCcccC-CCCCceeEeecCCcccccccccc----ccceeecccceEEEE
Confidence            4578999999999999999999999999999999999 45689999998765432222322    367899999999999


Q ss_pred             HcccCCCCCcccccccc
Q 012081          133 RRNVRLSESLYTVKSID  149 (471)
Q Consensus       133 k~g~~lde~~Y~l~~~~  149 (471)
                      .+|.+..|..|.+....
T Consensus       281 q~g~~a~e~~yl~~~~~  297 (850)
T KOG3524|consen  281 QRGCCAIEDNYLLPTGK  297 (850)
T ss_pred             ecchhccccceeccccc
Confidence            99999999999887653

>KOG2481 consensus Protein required for normal rRNA processing [RNA processing and modification]

Probab=95.68  E-value=0.011  Score=63.14  Aligned_cols=81  Identities=26%  Similarity=0.305  Sum_probs=61.8

Q ss_pred             CCCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccC-C---------CCceEEEEecCC-CHHHHHHHhcCCCCCceEe
Q 012081           55 NAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDL-H---------PQCTHLVVQSFG-GRKFEHALKHGSRNGLYIV  123 (471)
Q Consensus        55 ~~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l-~---------~~~THLV~~~~~-g~Ky~~A~k~~~~~gi~IV  123 (471)
                      -.+|+|++|.++.=.+  |+.|.=+|...||.++-+- .         ...||=|+..+. ..+|         .|-.-|
T Consensus       325 kslF~glkFfl~reVP--resL~fiI~s~GG~V~wd~~~~g~~~~~~d~~ITH~IvDrP~~~~~v---------~gR~Yv  393 (570)
T KOG2481|consen  325 KSLFSGLKFFLNREVP--RESLEFIIRSFGGKVSWDPLGIGATYDESDERITHQIVDRPGQQTSV---------IGRTYV  393 (570)
T ss_pred             HHHhhcceeeeeccCc--hHHHHHHHHHcCCceecCccCCCCcccccccceeeeeecccCcccee---------eeeeee
Confidence            3699999999985433  5688889999999987762 1         235898887653 2222         245679


Q ss_pred             cchHHHHHHHcccCCCCCccccc
Q 012081          124 TLGWFVDSVRRNVRLSESLYTVK  146 (471)
Q Consensus       124 ~p~WI~Dcik~g~~lde~~Y~l~  146 (471)
                      -|+||+||+.++.+++...|.+-
T Consensus       394 QPQWvfDsvNar~llpt~~Y~~G  416 (570)
T KOG2481|consen  394 QPQWVFDSVNARLLLPTEKYFPG  416 (570)
T ss_pred             cchhhhhhccchhhccHhhhCCC
Confidence            99999999999999999999874

>KOG2043 consensus Signaling protein SWIFT and related BRCT domain proteins [Transcription; Signal transduction mechanisms; Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=95.33  E-value=0.019  Score=66.24  Aligned_cols=62  Identities=16%  Similarity=0.251  Sum_probs=52.6

Q ss_pred             HHHHHHHHhCCCEEEccccCCCCceEEEEcC-chHHHH---hcCCCceechhHHHHHHhhCCcCccCCc
Q 012081          217 NKVFEAATNEGATLVNQWFVGCGASYVVCEE-DSVQKY---MGHSNNLVTPVWVLKTAKEKHVQRLVHI  281 (471)
Q Consensus       217 ~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~-~s~~k~---l~~~~~IVs~~WL~dcik~g~lqp~~~y  281 (471)
                      ..+.+.++..||.+..+   ...+||+|+.. ....++   ++.++.||+++||.+|++.|.++++..|
T Consensus       671 ~~~k~~~k~lg~s~~ss---~~e~Th~i~~rirRT~k~Leai~~G~~ivT~~wL~s~~k~g~~~dek~y  736 (896)
T KOG2043|consen  671 KNYKLAKKFLGGSVASS---DSEATHFIADRIRRTLKFLEAISSGKPLVTPQWLVSSLKSGEKLDEKPY  736 (896)
T ss_pred             hhhhhHHhhccceeecc---cccceeeeehhhhccHHHHhhhccCCcccchHHHHHHhhccccccCccc
Confidence            44888899999999998   78999999987 333344   3688999999999999999999999887

>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=94.46  E-value=0.1  Score=58.81  Aligned_cols=72  Identities=15%  Similarity=0.149  Sum_probs=60.5

Q ss_pred             CCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCc---hHHHHhcCCCceechhHHHHHH
Q 012081          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED---SVQKYMGHSNNLVTPVWVLKTA  270 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~---s~~k~l~~~~~IVs~~WL~dci  270 (471)
                      ...|.|.+|.|...|+.-.|+.++++|..+||++.++  ...++++||++..   .+.|+...+++|++.+.+++-+
T Consensus       591 ~~~l~gktfV~TG~l~~~~R~e~~~lie~~Ggkv~ss--VSkktd~LV~G~~aGsKl~KA~~LGI~Ii~e~~f~~~l  665 (669)
T PRK14350        591 NSFLFGKKFCITGSFNGYSRSVLIDKLTKKGAIFNTC--VTKYLDFLLVGEKAGLKLKKANNLGIKIMSLFDIKSYV  665 (669)
T ss_pred             CCccCCcEEEEecccCCCCHHHHHHHHHHcCCEEecc--ccCCCcEEEECCCCCchHHHHHHcCCEEecHHHHHHHh
Confidence            3569999999944487777999999999999999999  7999999999863   4666667899999999888744

>PRK06063 DNA polymerase III subunit epsilon; Provisional

Probab=94.22  E-value=0.13  Score=52.70  Aligned_cols=70  Identities=16%  Similarity=0.216  Sum_probs=57.7

Q ss_pred             CCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCc-----hHHHHhcCCCceechhHHHHHH
Q 012081          198 STLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED-----SVQKYMGHSNNLVTPVWVLKTA  270 (471)
Q Consensus       198 ~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~-----s~~k~l~~~~~IVs~~WL~dci  270 (471)
                      .+|.|.+|.|...++ ..|+.+.++|..+||++.++  +..++++||+++.     +.+|+...+++|++.+=+++-+
T Consensus       231 ~l~~g~~~v~TG~l~-~~R~e~~~~~~~~G~~v~~s--Vs~~t~~lv~g~~~~~ssK~~kA~~~gi~ii~e~~f~~ll  305 (313)
T PRK06063        231 PLVQGMRVALSAEVS-RTHEELVERILHAGLAYSDS--VDRDTSLVVCNDPAPEQGKGYHARQLGVPVLDEAAFLELL  305 (313)
T ss_pred             cccCCCEEEEecCCC-CCHHHHHHHHHHcCCEecCc--cccCccEEEECCCCCcccHHHHHHHcCCccccHHHHHHHH
Confidence            468999999955677 57899999999999999999  7999999999862     4566667889999877666654

>PRK06195 DNA polymerase III subunit epsilon; Validated

Probab=94.20  E-value=0.12  Score=52.92  Aligned_cols=73  Identities=14%  Similarity=0.206  Sum_probs=56.0

Q ss_pred             CCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCc------------hHHHHh-----cCCCc
Q 012081          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED------------SVQKYM-----GHSNN  259 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~------------s~~k~l-----~~~~~  259 (471)
                      ...|.|.+|.|...|..-.|+.+.++|+.+||.+.++  +..++++||+++.            +++++.     +.+++
T Consensus       218 ~~~l~g~~~vfTG~l~~~~R~~~~~~~~~~Gg~v~~s--Vs~~t~~lV~G~~~~~~~~~~~~~~K~~kA~~l~~~g~~i~  295 (309)
T PRK06195        218 FTAFKEEVVVFTGGLASMTRDEAMILVRRLGGTVGSS--VTKKTTYLVTNTKDIEDLNREEMSNKLKKAIDLKKKGQNIK  295 (309)
T ss_pred             CccccCCEEEEccccCCCCHHHHHHHHHHhCCEecCC--cccCceEEEECCCcchhhcccCcChHHHHHHHHHhCCCCcE
Confidence            3469999999954576667899999999999999999  7899999999842            244443     34888


Q ss_pred             eechhHHHHHHh
Q 012081          260 LVTPVWVLKTAK  271 (471)
Q Consensus       260 IVs~~WL~dcik  271 (471)
                      |++.+=+++-++
T Consensus       296 ii~E~~f~~l~~  307 (309)
T PRK06195        296 FLNEEEFLQKCK  307 (309)
T ss_pred             EecHHHHHHHHh
Confidence            998665555443

>KOG3548 consensus DNA damage checkpoint protein RHP9/CRB2/53BP1 [Replication, recombination and repair]

Probab=94.20  E-value=0.063  Score=61.06  Aligned_cols=82  Identities=9%  Similarity=0.192  Sum_probs=55.3

Q ss_pred             CCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEE------------------------EEcCc--hH
Q 012081          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYV------------------------VCEED--SV  250 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHV------------------------Vv~~~--s~  250 (471)
                      ..+|.||.|.|...+..  ...++.-+..+||.|.+..+.. -.+|=                        ++.+.  ..
T Consensus       923 kniFd~cvF~lTsa~~s--d~~~r~s~e~~gg~vle~gl~~-~Fn~p~~g~~~~lr~Ln~~q~~ks~~qalLIsdth~Rt  999 (1176)
T KOG3548|consen  923 KNIFDGCVFMLTSANRS--DSASRPSMEKHGGLVLEKGLMN-LFNTPFKGGGIVLRQLNSFQERKSNYQALLISDTHYRT  999 (1176)
T ss_pred             cchhcceeEEEeccccc--hhhhhhhhhccCChhhhccccc-cccccccCCcchHHhhhHHhhhccccceeEeehhhhHH
Confidence            47999999999444433  3456666777999998874222 12221                        11221  23


Q ss_pred             HHHh---cCCCceechhHHHHHHhhCCcCccCCc
Q 012081          251 QKYM---GHSNNLVTPVWVLKTAKEKHVQRLVHI  281 (471)
Q Consensus       251 ~k~l---~~~~~IVs~~WL~dcik~g~lqp~~~y  281 (471)
                      .||+   +.++.+|++.||.+|++.+++++.-+|
T Consensus      1000 ~KYLeaLA~giPcVh~~fI~aC~e~nr~Vdy~~Y 1033 (1176)
T KOG3548|consen 1000 HKYLEALARGIPCVHNTFIQACGEQNRCVDYTDY 1033 (1176)
T ss_pred             HHHHHHHHcCCCcccHHHHHHHHhccccccchhh
Confidence            4554   689999999999999999998885443

>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated

Probab=94.06  E-value=0.13  Score=57.98  Aligned_cols=73  Identities=18%  Similarity=0.171  Sum_probs=60.5

Q ss_pred             CCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCc---hHHHHhcCCCceechhHHHHHHhh
Q 012081          198 STLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED---SVQKYMGHSNNLVTPVWVLKTAKE  272 (471)
Q Consensus       198 ~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~---s~~k~l~~~~~IVs~~WL~dcik~  272 (471)
                      ..|.|.+|+|...++.-.|+.+.++|..+||.+.++  .+.++++||+++.   .++++...+++|++.+-+++.+.+
T Consensus       589 ~~~~g~~~v~TG~l~~~~R~e~~~~i~~~G~~v~~s--Vs~kt~~lv~G~~~gsK~~kA~~lgI~ii~E~~f~~~l~~  664 (665)
T PRK07956        589 VDLAGKTVVLTGTLEQLSRDEAKEKLEALGAKVSGS--VSKKTDLVVAGEAAGSKLAKAQELGIEVLDEEEFLRLLGE  664 (665)
T ss_pred             CCccccEEEEeCCCCCCCHHHHHHHHHHcCCEEeCc--ccCCCCEEEECCCCChHHHHHHHcCCeEEcHHHHHHHHhc
Confidence            359999999944465557899999999999999999  7999999999873   456666789999999999887754

>COG5163 NOP7 Protein required for biogenesis of the 60S ribosomal subunit [Translation, ribosomal structure and biogenesis]

Probab=93.95  E-value=0.051  Score=56.62  Aligned_cols=82  Identities=18%  Similarity=0.241  Sum_probs=61.7

Q ss_pred             CCCCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEccc-----------CCCCceEEEEecCC-CHHHHHHHhcCCCCCce
Q 012081           54 ANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPD-----------LHPQCTHLVVQSFG-GRKFEHALKHGSRNGLY  121 (471)
Q Consensus        54 ~~~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~-----------l~~~~THLV~~~~~-g~Ky~~A~k~~~~~gi~  121 (471)
                      ...+|+|.+|.++.-.+  +.-|+-+|..+||.+...           .+..+||-||..+- ..||         .|..
T Consensus       347 ~~slFS~f~FyisreVp--~dsLefiilscGG~V~~~p~~~~i~~~~~vD~~vth~i~drp~~~~kv---------egrt  415 (591)
T COG5163         347 LKSLFSGFKFYISREVP--GDSLEFIILSCGGSVVGSPCEADIHVSEKVDEKVTHQIVDRPVMKNKV---------EGRT  415 (591)
T ss_pred             hhhhhhceEEEEecccc--chHHHHHHHHcCCcccCchhhccCCchhhccchhhhhhccchhhhhhh---------ccee
Confidence            34799999999986433  336777899999997543           33467888887652 2222         2667


Q ss_pred             EecchHHHHHHHcccCCCCCccccc
Q 012081          122 IVTLGWFVDSVRRNVRLSESLYTVK  146 (471)
Q Consensus       122 IV~p~WI~Dcik~g~~lde~~Y~l~  146 (471)
                      -|.|+||+||+..|.+...+.|.+-
T Consensus       416 YiQPQw~fDsiNkG~l~~~~~Y~~G  440 (591)
T COG5163         416 YIQPQWLFDSINKGKLACVENYCVG  440 (591)
T ss_pred             eechHHHHhhhccccchhhhhcccc
Confidence            8999999999999999999999874

>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=93.44  E-value=0.21  Score=56.55  Aligned_cols=74  Identities=15%  Similarity=0.163  Sum_probs=61.4

Q ss_pred             CCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCc----hHHHHhcCCCceechhHHHHHHhh
Q 012081          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED----SVQKYMGHSNNLVTPVWVLKTAKE  272 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~----s~~k~l~~~~~IVs~~WL~dcik~  272 (471)
                      ...|.|.+|+|...+..-.|+.+.++|..+||++.++  +..++++||+++.    .++++...++.|++.+-+++-+++
T Consensus       607 ~~~l~g~~~v~TG~l~~~~R~~~~~~i~~~Gg~v~~s--Vs~kt~~Lv~G~~~g~sKl~kA~~lgi~ii~E~~f~~ll~~  684 (689)
T PRK14351        607 GDALDGLTFVFTGSLSGYTRSEAQELVEAHGGNATGS--VSGNTDYLVVGENPGQSKRDDAEANDVPTLDEEEFEELLAE  684 (689)
T ss_pred             CCCCCCcEEEEccCCCCCCHHHHHHHHHHcCCEEcCC--cCCCccEEEEcCCCChhHHHHHHHCCCeEecHHHHHHHHHh
Confidence            4579999999944466557899999999999999999  7999999999863    355555689999999999887765

>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]

Probab=91.91  E-value=0.38  Score=53.73  Aligned_cols=71  Identities=18%  Similarity=0.198  Sum_probs=60.0

Q ss_pred             CCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCc---hHHHHhcCCCceechhHHHHHH
Q 012081          198 STLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED---SVQKYMGHSNNLVTPVWVLKTA  270 (471)
Q Consensus       198 ~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~---s~~k~l~~~~~IVs~~WL~dci  270 (471)
                      ..|.|.+|.|...++.-.|+..+.++...||+|..+  ...++++||++++   .+.|+...+++|.+.+++++-+
T Consensus       593 ~~l~gkt~V~TGtL~~~sR~eak~~le~lGakv~~S--VSkktD~vvaG~~aGSKl~kA~eLgv~i~~E~~~~~ll  666 (667)
T COG0272         593 SPLAGKTFVLTGTLEGMSRDEAKALLEALGAKVSGS--VSKKTDYVVAGENAGSKLAKAQELGVKIIDEEEFLALL  666 (667)
T ss_pred             cccCCCEEEEeccCCCCCHHHHHHHHHHcCCEEece--ecccccEEEEcCCCChHHHHHHHcCCeEecHHHHHHhh
Confidence            689999999965688777899999999999999999  6888888888774   4666667899999998887643

>TIGR00575 dnlj DNA ligase, NAD-dependent

Probab=91.79  E-value=0.3  Score=55.07  Aligned_cols=66  Identities=20%  Similarity=0.271  Sum_probs=53.8

Q ss_pred             CCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCc---hHHHHhcCCCceechh
Q 012081          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED---SVQKYMGHSNNLVTPV  264 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~---s~~k~l~~~~~IVs~~  264 (471)
                      ...|.|.+|+|...|+.-.|+.+.++|+.+||++.++  ...++++||+++.   .++++...+++|++.+
T Consensus       582 ~~~l~gk~~v~TG~l~~~~R~~~~~~i~~~G~~v~~s--Vs~kt~~lv~G~~~gsKl~kA~~lgi~ii~E~  650 (652)
T TIGR00575       582 GSPLAGKTFVLTGTLSQMSRDEAKELLENLGGKVASS--VSKKTDYVIAGEKAGSKLAKAQELGIPIINEE  650 (652)
T ss_pred             CCCccCcEEEEeccCCCCCHHHHHHHHHHcCCEEeCC--cCCCccEEEECCCCChHHHHHHHcCCcEechh
Confidence            3569999999944466667899999999999999999  7899999999873   4566666788888754

The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.

>PRK05601 DNA polymerase III subunit epsilon; Validated

Probab=86.64  E-value=3.2  Score=43.67  Aligned_cols=75  Identities=23%  Similarity=0.273  Sum_probs=65.3

Q ss_pred             CCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecCC--CHHHHHHHhcCCCCCceEecchHHHHHHH
Q 012081           56 APFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFG--GRKFEHALKHGSRNGLYIVTLGWFVDSVR  133 (471)
Q Consensus        56 ~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~--g~Ky~~A~k~~~~~gi~IV~p~WI~Dcik  133 (471)
                      ++-+|+.|.|++=...++..|.+.+...|=.|+..+++.+.-|||....  .-|-.+|...    |||+|+-.=+++.++
T Consensus       293 ~lv~Gm~v~~~~e~~~~~d~li~~~~~agL~y~~~~~r~tslvv~n~~~~~~gk~~~a~~~----gipl~~d~~fl~~~~  368 (377)
T PRK05601        293 GLVAGMEVVVAPEITMDPDIIIQAIVRAGLAYSEKLTRQTSVVVCNQTRDLDGKAMHAQRK----GIPLLSDVAFLAAVE  368 (377)
T ss_pred             ccccCcEEEEeCCccCCHHHHHHHHHHccchhhhccccceeEEEeCCCCCccchhhhhhhc----CCCccCHHHHHHHHH
Confidence            4778999999999999999999999999999999999999999998764  3577777664    899999998888876


Q ss_pred             c
Q 012081          134 R  134 (471)
Q Consensus       134 ~  134 (471)
                      .
T Consensus       369 ~  369 (377)
T PRK05601        369 R  369 (377)
T ss_pred             H
Confidence            4

>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]

Probab=81.93  E-value=2.6  Score=47.39  Aligned_cols=78  Identities=14%  Similarity=0.082  Sum_probs=58.9

Q ss_pred             CCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCc------hHHHHh---cCCCceechhHHHHHH
Q 012081          200 LSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED------SVQKYM---GHSNNLVTPVWVLKTA  270 (471)
Q Consensus       200 F~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~------s~~k~l---~~~~~IVs~~WL~dci  270 (471)
                      |+-....+-.+.++.+.+.+.+.++.   ++...  ....+||+|..-+      ...+++   ..+..|++..|++.|+
T Consensus       475 ~~kk~~~~~s~l~p~ek~~v~~~a~~---t~~k~--~~~~~thvi~~~~~~g~c~rTlk~~~gil~gkwi~~~~w~~~s~  549 (684)
T KOG4362|consen  475 FKKKLVLLVSGLTPSEKQLVEKFAVD---TISKF--WIEPVTHVIASTDLEGACLRTLKVLMGILRGKWILSYDWVLASL  549 (684)
T ss_pred             cccceeeeeccCCcchHHHHHHHHHH---HHhhc--cCCCceeeeeecccccchhhhHHHHHHhhcCceeeeHHHHHHHH
Confidence            33333444378999988888888877   66655  4889999997542      234443   4889999999999999


Q ss_pred             hhCCcCccCCcC
Q 012081          271 KEKHVQRLVHIS  282 (471)
Q Consensus       271 k~g~lqp~~~ys  282 (471)
                      +.++++++..|.
T Consensus       550 k~~~~~~eepfE  561 (684)
T KOG4362|consen  550 KLRKWVSEEPFE  561 (684)
T ss_pred             HhcCCCCCCCee
Confidence            999999988764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	471
3olc_X	298	Crystal Structure Of The N-Terminal Region Of Topbp		2e-11
2xnk_A	292	Structure And Function Of The Rad9-Binding Region O		2e-11
2xnh_A	287	Structure And Function Of The Rad9-Binding Region O		2e-11
3l46_A	112	Crystal Structure Of The Second Brct Domain Of Epit		2e-06
2cou_A	109	Solution Structure Of The Second Brct Domain Of Epi		2e-06

>pdb|3OLC|X Chain X, Crystal Structure Of The N-Terminal Region Of Topbp1 Length = 298

Iteration: 1
 Score = 67.0 bits (162), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 37/87 (42%), Positives = 50/87 (57%), Gaps = 5/87 (5%)
Query: 58  FSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHP-QCTHLVVQSFGGRKFEHALKHGS 116
           F G +ICVTGL    RK+V + T + GGQY   L   +CTHL+VQ   G+K+E A     
Sbjct: 200 FLGCIICVTGLCGLDRKEVQQLTVKHGGQYXGQLKXNECTHLIVQEPKGQKYECA----K 255
Query: 117 RNGLYIVTLGWFVDSVRRNVRLSESLY 143
           R  ++ VT  WF DS+ +     ES+Y
Sbjct: 256 RWNVHCVTTQWFFDSIEKGFCQDESIY 282

>pdb|2XNK|A Chain A, Structure And Function Of The Rad9-Binding Region Of The Dna Damage Checkpoint Adaptor Topbp1 Length = 292

Iteration: 1
 Score = 67.0 bits (162), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 37/87 (42%), Positives = 50/87 (57%), Gaps = 5/87 (5%)
Query: 58  FSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHP-QCTHLVVQSFGGRKFEHALKHGS 116
           F G +ICVTGL    RK+V + T + GGQY   L   +CTHL+VQ   G+K+E A     
Sbjct: 202 FLGCIICVTGLCGLDRKEVQQLTVKHGGQYXGQLKXNECTHLIVQEPKGQKYECA----K 257
Query: 117 RNGLYIVTLGWFVDSVRRNVRLSESLY 143
           R  ++ VT  WF DS+ +     ES+Y
Sbjct: 258 RWNVHCVTTQWFFDSIEKGFCQDESIY 284

>pdb|2XNH|A Chain A, Structure And Function Of The Rad9-Binding Region Of The Dna Damage Checkpoint Adaptor Topbp1 Length = 287

Iteration: 1
 Score = 67.0 bits (162), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 37/87 (42%), Positives = 50/87 (57%), Gaps = 5/87 (5%)
Query: 58  FSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHP-QCTHLVVQSFGGRKFEHALKHGS 116
           F G +ICVTGL    RK+V + T + GGQY   L   +CTHL+VQ   G+K+E A     
Sbjct: 200 FLGCIICVTGLCGLDRKEVQQLTVKHGGQYXGQLKXNECTHLIVQEPKGQKYECA----K 255
Query: 117 RNGLYIVTLGWFVDSVRRNVRLSESLY 143
           R  ++ VT  WF DS+ +     ES+Y
Sbjct: 256 RWNVHCVTTQWFFDSIEKGFCQDESIY 282

>pdb|3L46|A Chain A, Crystal Structure Of The Second Brct Domain Of Epithelial Cell Transforming 2 (Ect2) Length = 112

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 30/89 (33%), Positives = 44/89 (49%), Gaps = 8/89 (8%)
Query: 57  PFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQS--FGGRKFEHALKH 114
           PF   ++   G S E +  + E TE  GG+Y P    +CTHLVV+        FE + K 
Sbjct: 21  PFQDCILSFLGFSDEEKTNMEEMTEMQGGKYLPLGDERCTHLVVEENIVKDLPFEPSKK- 79
Query: 115 GSRNGLYIVTLGWFVDSVRRNVRLSESLY 143
                LY+V   WF  S++ + R  E++Y
Sbjct: 80  -----LYVVKQEWFWGSIQMDARAGETMY 103

>pdb|2COU|A Chain A, Solution Structure Of The Second Brct Domain Of Epithelial Cell Transforming 2 Length = 109

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/89 (31%), Positives = 44/89 (49%), Gaps = 8/89 (8%)
Query: 57  PFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQ--SFGGRKFEHALKH 114
           PF   ++   G S E +  + E TE  GG Y P    +CTHL+V+  +     FE + K 
Sbjct: 12  PFQDCILSFLGFSDEEKHSMEEMTEMQGGSYLPVGDERCTHLIVEENTVKDLPFEPSKK- 70
Query: 115 GSRNGLYIVTLGWFVDSVRRNVRLSESLY 143
                L++V   WF  S++ + R  E++Y
Sbjct: 71  -----LFVVKQEWFWGSIQMDARAGETMY 94

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	471
3l46_A	112	Protein ECT2; alternative splicing, guanine-nucleo	7e-30
2cou_A	109	ECT2 protein; BRCT domain, RHO GTPase, structural	2e-29
2d8m_A	129	DNA-repair protein XRCC1; parallel beta-sheet, DNA	2e-25
3l3e_A	107	DNA topoisomerase 2-binding protein 1; BRCT domain	2e-22
1t15_A	214	Breast cancer type 1 susceptibility protein; prote	1e-21
1l0b_A	229	BRCA1; TANDEM-BRCT, three-helix bundle, unknown fu	7e-21
3olc_X	298	DNA topoisomerase 2-binding protein 1; BRCT domain	1e-20
3olc_X	298	DNA topoisomerase 2-binding protein 1; BRCT domain	3e-15
2nte_A	210	BARD-1, BRCA1-associated ring domain protein 1; BR	3e-20
1wf6_A	132	Similar to S.pombe -RAD4+/CUT5+product (A40727); B	3e-19
3pa6_A	107	Microcephalin; BRCT domain, cell cycle; HET: MSE;	4e-17
2ebw_A	97	DNA repair protein REV1; A/B/A 3 layers, parallel	2e-16
3al2_A	235	DNA topoisomerase 2-binding protein 1; BRCT domain	4e-14
3sqd_A	219	PAX-interacting protein 1; tandem BRCT domains, ce	5e-12
3u3z_A	199	Microcephalin; DNA repair, cell cycle regulation,	1e-10
3l41_A	220	BRCT-containing protein 1; BRC1, BRCT domain, tand	2e-10
3pc6_A	104	DNA repair protein XRCC1; BRCT domain, protein:pro	2e-10
2etx_A	209	Mediator of DNA damage checkpoint protein 1; tande	4e-09
3ii6_X	263	DNA ligase 4; XRCC4, NHEJ, DNA repair, BRCT, alter	2e-08
3ii6_X	263	DNA ligase 4; XRCC4, NHEJ, DNA repair, BRCT, alter	9e-08
3ef0_A	372	RNA polymerase II subunit A C-terminal domain phos	3e-08
3ef1_A	442	RNA polymerase II subunit A C-terminal domain phos	2e-07
2jw5_A	106	DNA polymerase lambda; BRCT domain, family X polym	3e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-07
1z56_C	264	DNA ligase IV; DNA repair, BRCT, NHEJ, XRCC4, DNA	4e-05

>3l46_A Protein ECT2; alternative splicing, guanine-nucleotide releasing factor, phosphoprotein, polymorphism, proto-oncogene, structural genomics; 1.48A {Homo sapiens} Length = 112

 Score =  111 bits (279), Expect = 7e-30
 Identities = 27/90 (30%), Positives = 42/90 (46%), Gaps = 4/90 (4%)

Query: 57  PFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGS 116
           PF   ++   G S E +  + E TE  GG+Y P    +CTHLVV+    +          
Sbjct: 21  PFQDCILSFLGFSDEEKTNMEEMTEMQGGKYLPLGDERCTHLVVEENIVKDLPFEPS--- 77

Query: 117 RNGLYIVTLGWFVDSVRRNVRLSESLYTVK 146
              LY+V   WF  S++ + R  E++Y  +
Sbjct: 78  -KKLYVVKQEWFWGSIQMDARAGETMYLYE 106

>2cou_A ECT2 protein; BRCT domain, RHO GTPase, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 109

 Score =  110 bits (276), Expect = 2e-29
 Identities = 25/94 (26%), Positives = 42/94 (44%), Gaps = 4/94 (4%)

Query: 57  PFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGS 116
           PF   ++   G S E +  + E TE  GG Y P    +CTHL+V+    +          
Sbjct: 12  PFQDCILSFLGFSDEEKHSMEEMTEMQGGSYLPVGDERCTHLIVEENTVKDLPFEPS--- 68

Query: 117 RNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDE 150
              L++V   WF  S++ + R  E++Y  +  + 
Sbjct: 69  -KKLFVVKQEWFWGSIQMDARAGETMYLYEKANT 101

>2d8m_A DNA-repair protein XRCC1; parallel beta-sheet, DNA ligase III, poly(ADP-ribose) polymerase-1, DNA polymerase beta, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 129

 Score = 99.6 bits (248), Expect = 2e-25
 Identities = 25/113 (22%), Positives = 37/113 (32%), Gaps = 4/113 (3%)

Query: 38  SMSPASSSLASDSVLPANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTH 97
           S S                   G+V+ ++G     R ++ +    LG +Y PD     TH
Sbjct: 3   SGSSGEPRRPRAGPEELGKILQGVVVVLSGFQNPFRSELRDKALELGAKYRPDWTRDSTH 62

Query: 98  LVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDE 150
           L+       K+   L      G  IV   W +D  R   RL    Y +     
Sbjct: 63  LICAFANTPKYSQVLGL----GGRIVRKEWVLDCHRMRRRLPSQRYLMAGPGS 111

>1t15_A Breast cancer type 1 susceptibility protein; protein-peptide complex, antitumor protein; HET: SEP; 1.85A {Homo sapiens} SCOP: c.15.1.3 c.15.1.3 PDB: 1jnx_X* 1t29_A* 1t2v_A* 1y98_A* 3coj_X* 3k0h_A* 3k0k_A* 3pxe_A* 3pxb_A 3pxc_X 1t2u_A 1n5o_X 3pxa_A 3k15_A* 3k16_A* 3pxd_A 2ing_X 1oqa_A Length = 214

 Score = 91.8 bits (227), Expect = 1e-21
 Identities = 31/205 (15%), Positives = 61/205 (29%), Gaps = 16/205 (7%)

Query: 60  GLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALK--HGSR 117
            + + V+GL+ E    V +   +     +  +  + TH+V+++      E  LK   G  
Sbjct: 4   RMSMVVSGLTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIA 63

Query: 118 NGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRL------------VGFA 165
            G ++V+  W   S++    L+E  + V+  D       +  +             +   
Sbjct: 64  GGKWVVSYFWVTQSIKERKMLNEHDFEVRG-DVVNGRNHQGPKRARESQDRKIFRGLEIC 122

Query: 166 GTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVSEELRNKVFEAATN 225
                               G        S         + V    +    N        
Sbjct: 123 CYGPFTNMPTDQLEWMVQLCGASVVKELSSFTLGTGVHPIVVVQPDAWTEDNGFHAIGQM 182

Query: 226 EGATLVN-QWFVGCGASYVVCEEDS 249
             A +V  +W +   A Y   E D+
Sbjct: 183 CEAPVVTREWVLDSVALYQCQELDT 207

>1l0b_A BRCA1; TANDEM-BRCT, three-helix bundle, unknown function; 2.30A {Rattus norvegicus} SCOP: c.15.1.3 c.15.1.3 Length = 229

 Score = 90.2 bits (223), Expect = 7e-21
 Identities = 32/203 (15%), Positives = 66/203 (32%), Gaps = 13/203 (6%)

Query: 60  GLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALK--HGSR 117
            + + V+GL+ +    V +  E+     +  +  + TH+++++      E  LK   G  
Sbjct: 7   DISMVVSGLTPKEVMIVQKFAEKYRLALTDVITEETTHVIIKTDAEFVCERTLKYFLGIA 66

Query: 118 NGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEH-----GMHLDKLNRLVGFAGTENSCL 172
            G +IV+  W + S++    LS   + VK          G    + ++   F G +  C 
Sbjct: 67  GGKWIVSYSWVIKSIQERKLLSVHEFEVKGDVVTGSNHQGPRRSRESQEKLFEGLQIYCC 126

Query: 173 PAGIYEAKQF-----NATGKHERDSNRSMNSTLSGCSMYVDSDVSEELRNKVFEAATNEG 227
                  K          G         +        + +    +    N   +      
Sbjct: 127 EPFTNMPKDELERMLQLCGASVVKELPLLTRDTGAHPIVLVQPSAWTEDNDCPDIGQLCK 186

Query: 228 ATLVN-QWFVGCGASYVVCEEDS 249
             LV   W +   + Y   + D+
Sbjct: 187 GRLVMWDWVLDSISVYRCRDLDA 209

>3olc_X DNA topoisomerase 2-binding protein 1; BRCT domain, DNA repair, RAD9, DNA binding protein; HET: DNA; 2.40A {Homo sapiens} PDB: 2xnk_A* 2xnh_A* Length = 298

 Score = 91.3 bits (226), Expect = 1e-20
 Identities = 37/91 (40%), Positives = 51/91 (56%), Gaps = 5/91 (5%)

Query: 57  PFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHP-QCTHLVVQSFGGRKFEHALKHG 115
            F G +ICVTGL    RK+V + T + GGQY   L   +CTHL+VQ   G+K+E A    
Sbjct: 199 IFLGCIICVTGLCGLDRKEVQQLTVKHGGQYMGQLKMNECTHLIVQEPKGQKYECAK--- 255

Query: 116 SRNGLYIVTLGWFVDSVRRNVRLSESLYTVK 146
            R  ++ VT  WF DS+ +     ES+Y  +
Sbjct: 256 -RWNVHCVTTQWFFDSIEKGFCQDESIYKTE 285

>3olc_X DNA topoisomerase 2-binding protein 1; BRCT domain, DNA repair, RAD9, DNA binding protein; HET: DNA; 2.40A {Homo sapiens} PDB: 2xnk_A* 2xnh_A* Length = 298

 Score = 75.2 bits (184), Expect = 3e-15
 Identities = 33/189 (17%), Positives = 58/189 (30%), Gaps = 26/189 (13%)

Query: 55  NAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKH 114
           N   S + I  T L KE R++V +  + +GG+   DL+   THL+    G +K+  A   
Sbjct: 103 NMVMSDVTISCTSLEKEKREEVHKYVQMMGGRVYRDLNVSVTHLIAGEVGSKKYLVAA-- 160

Query: 115 GSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLV----GFAGTENS 170
                  I+   W      ++            I+            +    G  G +  
Sbjct: 161 --NLKKPILLPSWIKTLWEKSQEKKI--TRYTDINMEDFKCPIFLGCIICVTGLCGLDRK 216

Query: 171 CLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATL 230
            +       +     G       +    T           + +E + + +E A       
Sbjct: 217 EV------QQLTVKHGGQYMGQLKMNECTHL---------IVQEPKGQKYECAKRWNVHC 261

Query: 231 VN-QWFVGC 238
           V  QWF   
Sbjct: 262 VTTQWFFDS 270

>2nte_A BARD-1, BRCA1-associated ring domain protein 1; BRCT, ring finger, zinc-binding protein, ubiquitin LI antitumor protein; 1.90A {Homo sapiens} PDB: 3fa2_A 2r1z_A Length = 210

 Score = 87.9 bits (217), Expect = 3e-20
 Identities = 39/212 (18%), Positives = 63/212 (29%), Gaps = 27/212 (12%)

Query: 61  LVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGL 120
           LV+  +GLS E +K + E    L  +   +     TH+VV     +     +  G  NG 
Sbjct: 3   LVLIGSGLSSEQQKMLSELAVILKAKKYTEFDSTVTHVVVPGDAVQSTLKCM-LGILNGC 61

Query: 121 YIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAG------TENSCLPA 174
           +I+   W    +RR V   E  Y +           +      F G            P 
Sbjct: 62  WILKFEWVKACLRRKVCEQEEKYEIPEGPRRSRLNREQLLPKLFDGCYFYLWGTFKHHPK 121

Query: 175 GIYE----------------AKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVSEELRNK 218
                                        +    +   +S    C+ Y+   + E+L N 
Sbjct: 122 DNLIKLVTAGGGQILSRKPKPDSDVTQTINTVAYHARPDSDQRFCTQYI---IYEDLCNY 178

Query: 219 VFEAATNEGATLVN-QWFVGCGASYVVCEEDS 249
             E             WF+ C  S+ +   DS
Sbjct: 179 HPERVRQGKVWKAPSSWFIDCVMSFELLPLDS 210

>1wf6_A Similar to S.pombe -RAD4+/CUT5+product (A40727); BRCT, topoisomerase II binding protein, checkpoint; NMR {Homo sapiens} SCOP: c.15.1.5 Length = 132

 Score = 83.0 bits (205), Expect = 3e-19
 Identities = 23/112 (20%), Positives = 39/112 (34%), Gaps = 5/112 (4%)

Query: 38  SMSPASSSLASDSVLPANAP---FSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQ 94
            + P   +L +  V    AP     G  I + G S     ++       GG     L+  
Sbjct: 18  KLEPTLENLENLDVSAFQAPEDLLDGCRIYLCGFSGRKLDKLRRLINSGGGVRFNQLNED 77

Query: 95  CTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVK 146
            TH++V  +     +   K   R   ++V   W ++   +   LSE  Y   
Sbjct: 78  VTHVIVGDYDDELKQFWNKSAHR--PHVVGAKWLLECFSKGYMLSEEPYIHS 127

>3pa6_A Microcephalin; BRCT domain, cell cycle; HET: MSE; 1.50A {Homo sapiens} PDB: 3ktf_A* 2wt8_A* Length = 107

 Score = 76.1 bits (187), Expect = 4e-17
 Identities = 19/100 (19%), Positives = 37/100 (37%), Gaps = 8/100 (8%)

Query: 56  APFSGLVICVTGLSKE----ARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHA 111
                +V  V   S        K        +G + S   + Q TH++ +      ++ A
Sbjct: 6   PILKDVVAYVEVWSSNGTENYSKTFTTQLVDMGAKVSKTFNKQVTHVIFKDGYQSTWDKA 65

Query: 112 LKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEH 151
            K     G+ +V++ W          + ESL+   +++EH
Sbjct: 66  QKR----GVKLVSVLWVEKCRTAGAHIDESLFPAANMNEH 101

>2ebw_A DNA repair protein REV1; A/B/A 3 layers, parallel beta-sheet, DNA replication, translession synthesis, TLS, DNA polymerase zeta, PCNA; HET: DNA; NMR {Homo sapiens} Length = 97

 Score = 74.1 bits (182), Expect = 2e-16
 Identities = 21/103 (20%), Positives = 42/103 (40%), Gaps = 8/103 (7%)

Query: 47  ASDSVLPANAP-FSGLVICVTGLSKEARKQVMEATERLGGQYSPDL-HPQCTHLVVQSFG 104
            S      ++  FSG+ I V G +  + +++ +     GGQY       + TH++  +  
Sbjct: 1   GSSGSSGTSSTIFSGVAIYVNGYTDPSAEELRKLMMLHGGQYHVYYSRSKTTHIIATNLP 60

Query: 105 GRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKS 147
             K +         G  ++   W V+S++    LS   Y + +
Sbjct: 61  NAKIKEL------KGEKVIRPEWIVESIKAGRLLSYIPYQLYT 97

>3al2_A DNA topoisomerase 2-binding protein 1; BRCT domain, protein binding, DNA binding protein; HET: DNA MSE; 2.00A {Homo sapiens} PDB: 3al3_A* Length = 235

 Score = 70.6 bits (172), Expect = 4e-14
 Identities = 17/94 (18%), Positives = 33/94 (35%), Gaps = 7/94 (7%)

Query: 53  PANAPFSGLVICVTGLSKEARKQVMEATERLGGQY--SPDLHPQCTHLVVQSFG-GRKFE 109
           P  +     +  ++ L+ + R       E+LGG         P CTH+VV       K+ 
Sbjct: 2   PLGSLKKQYIFQLSSLNPQERIDYCHLIEKLGGLVIEKQCFDPTCTHIVVGHPLRNEKYL 61

Query: 110 HALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLY 143
            ++      G +++   +          + E  Y
Sbjct: 62  ASV----AAGKWVLHRSYLEACRTAGHFVQEEDY 91

>3sqd_A PAX-interacting protein 1; tandem BRCT domains, cell cycle; HET: SEP; 2.15A {Homo sapiens} Length = 219

 Score = 64.6 bits (157), Expect = 5e-12
 Identities = 21/92 (22%), Positives = 35/92 (38%), Gaps = 6/92 (6%)

Query: 56  APFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGG-RKFEHALKH 114
            P     +  TG      +Q ++    LGG+ +     +CTHL+        KF  A+  
Sbjct: 12  TPELTPFVLFTGFEPVQVQQYIKKLYILGGEVAESAQ-KCTHLIASKVTRTVKFLTAISV 70

Query: 115 GSRNGLYIVTLGWFVDSVRRNVRLSESLYTVK 146
                 +IVT  W  +  R    + E  Y ++
Sbjct: 71  ----VKHIVTPEWLEECFRCQKFIDEQNYILR 98

>3u3z_A Microcephalin; DNA repair, cell cycle regulation, cell cycle; HET: SEP PTR; 1.50A {Homo sapiens} PDB: 3szm_A* 3t1n_A* 3sht_A 3shv_A* Length = 199

 Score = 59.8 bits (144), Expect = 1e-10
 Identities = 14/95 (14%), Positives = 36/95 (37%), Gaps = 6/95 (6%)

Query: 62  VICVTGLSKEARKQVMEATERLGG-QYSPDLHPQCTHLVVQSFG-GRKFEHALKHGSRNG 119
            + +T +  E +  V++  ++L G   +PD+    TH++             +      G
Sbjct: 13  TLVMTSMPSEKQNVVIQVVDKLKGFSIAPDVCETTTHVLSGKPLRTLNVLLGIAR----G 68

Query: 120 LYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMH 154
            ++++  W + S+     +SE  + +         
Sbjct: 69  CWVLSYDWVLWSLELGHWISEEPFELSHHFPAAPL 103

>3l41_A BRCT-containing protein 1; BRC1, BRCT domain, tandem BRCT repeat, phosphoserine binding domain, DNA repair, cell division, mitosis; HET: SEP; 1.45A {Schizosaccharomyces pombe} PDB: 3l40_A* Length = 220

 Score = 59.6 bits (144), Expect = 2e-10
 Identities = 18/105 (17%), Positives = 38/105 (36%), Gaps = 9/105 (8%)

Query: 57  PFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGG-RKFEHALKHG 115
               + I  TG  K+     ++   +L    + +    CTHL+        KF  ++ +G
Sbjct: 5   ASKRVYITFTGYDKKPSIDNLK---KLDMSITSNPSK-CTHLIAPRILRTSKFLCSIPYG 60

Query: 116 SRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNR 160
                 +VT+ W    ++ +  + E  Y +   ++       L  
Sbjct: 61  ----PCVVTMDWINSCLKTHEIVDEEPYLLNDPEKELELGCTLES 101

>3pc6_A DNA repair protein XRCC1; BRCT domain, protein:protein interactions, DNA L III-alpha BRCT2 domain, DNA binding protein; HET: DNA; 1.90A {Mus musculus} PDB: 3pc8_A* 3qvg_B* 1cdz_A Length = 104

 Score = 56.5 bits (136), Expect = 2e-10
 Identities = 18/98 (18%), Positives = 31/98 (31%), Gaps = 3/98 (3%)

Query: 58  FSGLVICVTG-LSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGS 116
           F G    + G    + R++++       G+    ++ +   ++        FE AL    
Sbjct: 8   FEGKHFFLYGEFPGDERRRLIRYVTAFNGELEDYMNERVQFVITAQEWDPNFEEALMENP 67

Query: 117 RNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMH 154
              L  V   W      +   L   LY V     H  H
Sbjct: 68  S--LAFVRPRWIYSCNEKQKLLPHQLYGVVPQAHHHHH 103

>2etx_A Mediator of DNA damage checkpoint protein 1; tandem BRCT domains histone gamma-H2AX, cell cycle; 1.33A {Homo sapiens} PDB: 2azm_A* 3k05_A* 2ado_A Length = 209

 Score = 55.4 bits (133), Expect = 4e-09
 Identities = 38/214 (17%), Positives = 64/214 (29%), Gaps = 49/214 (22%)

Query: 62  VICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFG-GRKFEHALKHGSRNGL 120
            +  TG+     ++ +     LGG  +     + +HLV        KF  AL      G+
Sbjct: 14  KVLFTGVVDARGERAVL---ALGGSLAGSAA-EASHLVTDRIRRTVKFLCALGR----GI 65

Query: 121 YIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAK 180
            I++L W   S +    L    Y V   D                              K
Sbjct: 66  PILSLDWLHQSRKAGFFLPPDEYVVT--DPEQ--------------------------EK 97

Query: 181 QFNATGKHERDSNRSMNSTLSGCSMYVDSDVS---EELRNKVFEAATNEGATLVNQWFVG 237
            F  + +      R     L G  +YV   V     ++  ++       G T +      
Sbjct: 98  NFGFSLQDALSRARERR-LLEGYEIYVTPGVQPPPPQMG-EIISCC---GGTYLPSMPRS 152

Query: 238 CGASYVV--CEEDS--VQKYMGHSNNLVTPVWVL 267
                VV  C +D       +     L++P ++L
Sbjct: 153 YKPQRVVITCPQDFPHCSIPLRVGLPLLSPEFLL 186

>3ii6_X DNA ligase 4; XRCC4, NHEJ, DNA repair, BRCT, alternative splicing, coiled coil, DNA damage, DNA recombination, isopeptide bond, nucleus; HET: DNA; 2.40A {Homo sapiens} PDB: 2e2w_A* Length = 263

 Score = 54.2 bits (129), Expect = 2e-08
 Identities = 10/63 (15%), Positives = 23/63 (36%), Gaps = 1/63 (1%)

Query: 84  GGQYSPDLHPQCTHLVVQSFGGRKFEHA-LKHGSRNGLYIVTLGWFVDSVRRNVRLSESL 142
           G +    L    +H+++     R  +    +   +    I+   W  DS+ +     E+ 
Sbjct: 201 GAKVVSCLAEGVSHVIIGEDHSRVADFKAFRRTFKRKFKILKESWVTDSIDKCELQEENQ 260

Query: 143 YTV 145
           Y +
Sbjct: 261 YLI 263

>3ii6_X DNA ligase 4; XRCC4, NHEJ, DNA repair, BRCT, alternative splicing, coiled coil, DNA damage, DNA recombination, isopeptide bond, nucleus; HET: DNA; 2.40A {Homo sapiens} PDB: 2e2w_A* Length = 263

 Score = 52.2 bits (124), Expect = 9e-08
 Identities = 29/250 (11%), Positives = 70/250 (28%), Gaps = 35/250 (14%)

Query: 58  FSGLVICV-TGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGS 116
           F  +  CV +G   + +  +       GG    +  P  T+ V+      + ++ +    
Sbjct: 11  FEDVEFCVMSGTDSQPKPDLENRIAEFGGYIVQNPGP-DTYCVIAGSENIRVKNIILSNK 69

Query: 117 RNGLYIVTLGWFVDSVRRNVRLSESLYTVKSI---------DEHGMHLDKLNRLVGFAGT 167
            +   +V   W ++  +    +      +  +          E+  + D           
Sbjct: 70  HD---VVKPAWLLECFKTKSFVPWQPRFMIHMCPSTKEHFAREYDCYGDSYFIDTDLNQL 126

Query: 168 ENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVSEELRNKVFEAATNEG 227
           +           +          D     +   S  SM+    V  +    + + +T   
Sbjct: 127 KEVFSGIKNSNEQTPEEMASLIADLEYRYSWDCSPLSMFRRHTVYLDSYAVINDLSTKNE 186

Query: 228 AT---LVNQWFVGCGA----------SYVVCEED--------SVQKYMGHSNNLVTPVWV 266
            T   +        GA          S+V+  ED        + ++       ++   WV
Sbjct: 187 GTRLAIKALELRFHGAKVVSCLAEGVSHVIIGEDHSRVADFKAFRRTFKRKFKILKESWV 246

Query: 267 LKTAKEKHVQ 276
             +  +  +Q
Sbjct: 247 TDSIDKCELQ 256

>3ef0_A RNA polymerase II subunit A C-terminal domain phosphatase; CTD, FCPH, BRCT, hydrolase, ALF4, transition state analog, cobalt, magnesium; 2.10A {Schizosaccharomyces pombe} Length = 372

 Score = 54.4 bits (130), Expect = 3e-08
 Identities = 19/92 (20%), Positives = 34/92 (36%), Gaps = 7/92 (7%)

Query: 58  FSGLVICVTGLS----KEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALK 113
             G  +  +G+           + +     G +   D     THL+       K + A+ 
Sbjct: 283 LKGCRLLFSGVIPLGVDVLSSDIAKWAMSFGAEVVLDFSVPPTHLIAAKIRTEKVKKAVS 342

Query: 114 HGSRNGLYIVTLGWFVDSVRRNVRLSESLYTV 145
            G    + +V L W  +S+ +  RL ES Y +
Sbjct: 343 MG---NIKVVKLNWLTESLSQWKRLPESDYLL 371

>3ef1_A RNA polymerase II subunit A C-terminal domain phosphatase; CTD, FCPH, BRCT, hydrolase, BEF3, acylphosphate analog, cobalt, magnesium; HET: BFD; 2.15A {Schizosaccharomyces pombe} Length = 442

 Score = 52.3 bits (124), Expect = 2e-07
 Identities = 19/92 (20%), Positives = 34/92 (36%), Gaps = 7/92 (7%)

Query: 58  FSGLVICVTGL----SKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALK 113
             G  +  +G+           + +     G +   D     THL+       K + A+ 
Sbjct: 353 LKGCRLLFSGVIPLGVDVLSSDIAKWAMSFGAEVVLDFSVPPTHLIAAKIRTEKVKKAVS 412

Query: 114 HGSRNGLYIVTLGWFVDSVRRNVRLSESLYTV 145
            G    + +V L W  +S+ +  RL ES Y +
Sbjct: 413 MG---NIKVVKLNWLTESLSQWKRLPESDYLL 441

>2jw5_A DNA polymerase lambda; BRCT domain, family X polymerase, nonhomologous END joining (NHEJ), DNA damage, DNA repair, DNA replication, DNA synthesis; HET: DNA; NMR {Homo sapiens} Length = 106

 Score = 47.7 bits (113), Expect = 3e-07
 Identities = 21/104 (20%), Positives = 36/104 (34%), Gaps = 4/104 (3%)

Query: 47  ASDSVLPANAPFSGLVICV--TGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSF- 103
            S+S   A    S L   V  TG+ +   +   +   + GGQ  P   P  TH+VV    
Sbjct: 1   GSNSGEEAEEWLSSLRAHVVRTGIGRARAELFEKQIVQHGGQLCPAQGPGVTHIVVDEGM 60

Query: 104 -GGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVK 146
              R            G  +V   W    ++    +  + +++ 
Sbjct: 61  DYERALRLLRLPQLPPGAQLVKSAWLSLCLQERRLVDVAGFSIF 104

>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 = 51.8 bits (123), Expect = 4e-07
 Identities = 79/526 (15%), Positives = 149/526 (28%), Gaps = 158/526 (30%)

Query: 8   EVVSSKGCSRLFLGSVPSLRRLRGGVQSFESMSPASSSLASDSVLPANAPFSGLVICVTG 67
            ++S +    + + S  ++        +  S          + VL  N  F      ++ 
Sbjct: 44  SILSKEEIDHI-IMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKF-----LMSP 97

Query: 68  LSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGR-----KFEHALKHG---SRNG 119
           +  E R+  M         Y             Q F        +    L+      R  
Sbjct: 98  IKTEQRQPSMMTRM-----YIEQRDRLYN--DNQVFAKYNVSRLQPYLKLRQALLELRPA 150

Query: 120 LYIVTLG-------WFVDSVRRNVRLSESLY------TVKSIDEHGMHLDKLNRLVGFAG 166
             ++  G       W    V  + ++   +        +K+ +     L+ L +L     
Sbjct: 151 KNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKL----- 205

Query: 167 TENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVSEELRNKVFEAATNE 226
                    +Y+    N T + +  SN  +              +  ELR  + ++   E
Sbjct: 206 ---------LYQIDP-NWTSRSDHSSNIKLRI----------HSIQAELRR-LLKSKPYE 244

Query: 227 GATLV--NQWFVGCGASYVVCEEDSVQKYMGHSNNLVTP-----VWVLKTAKEKHVQRLV 279
              LV  N           V    +   +      L+T         L  A   H+  L 
Sbjct: 245 NCLLVLLN-----------VQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHI-SLD 292

Query: 280 HIS--------------------ADLARQ--------VGMMLENIQNGIAR----EEING 307
           H S                     DL R+        + ++ E+I++G+A     + +N 
Sbjct: 293 HHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNC 352

Query: 308 GNVPEDAQSCKNKIS-QEKRQQTVNLA---KNGVRSRRSRRMQTCQTPIRPLTPSSLLDS 363
             +    +S  N +   E R+    L+    +                I    P+ LL S
Sbjct: 353 DKLTTIIESSLNVLEPAEYRKMFDRLSVFPPS--------------AHI----PTILL-S 393

Query: 364 ICWSISEPTSTASIYTDSFSGEDVNE-HHPSVFFDAEADGKDSEASFANLTRMLTESEKS 422
           + W     +    +         VN+ H  S+    E   K+S  S  ++   L    K 
Sbjct: 394 LIWFDVIKSDVMVV---------VNKLHKYSL---VEKQPKESTISIPSIY--LELKVKL 439

Query: 423 ELIFKNHFLTILFPVDRFAEMGPSSRTYFSDNGFTCLQVLDYIYEF 468
           E  +  H    +  VD +     +    F  +      +  Y Y  
Sbjct: 440 ENEYALH--RSI--VDHY-----NIPKTFDSDDLIPPYLDQYFYSH 476

>1z56_C DNA ligase IV; DNA repair, BRCT, NHEJ, XRCC4, DNA ligase, coiled-coil; HET: DNA; 3.92A {Saccharomyces cerevisiae} Length = 264

 Score = 44.1 bits (103), Expect = 4e-05
 Identities = 21/209 (10%), Positives = 51/209 (24%), Gaps = 24/209 (11%)

Query: 58  FSGLVICV-------TGLSKEARKQVMEATERLGGQYS----PDLHPQCTHLVVQSFGGR 106
           F+GL+  V           +  R ++ +     GG+         H      ++      
Sbjct: 6   FAGLLFYVLSDYVTEDTGIRITRAELEKTIVEHGGKLIYNVILKRHSIGDVRLISCKTTT 65

Query: 107 KFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHL-----DKLNRL 161
           + +  +  G      I+   W +D +     +        ++ +    +     D L   
Sbjct: 66  ECKALIDRGYD----ILHPNWVLDCIAYKRLILIEPNYCFNVSQKMRAVAEKRVDCLGDS 121

Query: 162 VGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMN-STLSGCSMYVDSDVSEELRNKVF 220
                +E         +               R       S    YV         + + 
Sbjct: 122 FENDISETKLSSLYKSQLSLPPMGELEIDSEVRRFPLFLFSNRIAYVPRRKISTEDDIIE 181

Query: 221 EAATNEGATLVNQWFVGCGASYVVCEEDS 249
                 G  + +Q  +    + ++     
Sbjct: 182 MKIKLFGGKITDQQSL---CNLIIIPYTD 207

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	471
3olc_X	298	DNA topoisomerase 2-binding protein 1; BRCT domain	99.96
3ii6_X	263	DNA ligase 4; XRCC4, NHEJ, DNA repair, BRCT, alter	99.94
1l0b_A	229	BRCA1; TANDEM-BRCT, three-helix bundle, unknown fu	99.94
2nte_A	210	BARD-1, BRCA1-associated ring domain protein 1; BR	99.94
1t15_A	214	Breast cancer type 1 susceptibility protein; prote	99.94
3u3z_A	199	Microcephalin; DNA repair, cell cycle regulation,	99.93
1kzy_C	259	Tumor suppressor P53-binding protein 1; tandem-BRC	99.9
1z56_C	264	DNA ligase IV; DNA repair, BRCT, NHEJ, XRCC4, DNA	99.9
2etx_A	209	Mediator of DNA damage checkpoint protein 1; tande	99.89
3sqd_A	219	PAX-interacting protein 1; tandem BRCT domains, ce	99.88
3al2_A	235	DNA topoisomerase 2-binding protein 1; BRCT domain	99.87
2vxb_A	241	DNA repair protein RHP9; BRCT, nucleus, cell cycle	99.85
3l46_A	112	Protein ECT2; alternative splicing, guanine-nucleo	99.84
2cou_A	109	ECT2 protein; BRCT domain, RHO GTPase, structural	99.82
3l41_A	220	BRCT-containing protein 1; BRC1, BRCT domain, tand	99.78
3l3e_A	107	DNA topoisomerase 2-binding protein 1; BRCT domain	99.78
2d8m_A	129	DNA-repair protein XRCC1; parallel beta-sheet, DNA	99.77
4id3_A	92	DNA repair protein REV1; BRCT domain, protein bind	99.75
2ebw_A	97	DNA repair protein REV1; A/B/A 3 layers, parallel	99.74
3olc_X	298	DNA topoisomerase 2-binding protein 1; BRCT domain	99.66
3pa6_A	107	Microcephalin; BRCT domain, cell cycle; HET: MSE;	99.66
1wf6_A	132	Similar to S.pombe -RAD4+/CUT5+product (A40727); B	99.6
3pc6_A	104	DNA repair protein XRCC1; BRCT domain, protein:pro	99.59
1wf6_A	132	Similar to S.pombe -RAD4+/CUT5+product (A40727); B	99.58
3ef1_A	442	RNA polymerase II subunit A C-terminal domain phos	99.55
4id3_A	92	DNA repair protein REV1; BRCT domain, protein bind	99.54
3l46_A	112	Protein ECT2; alternative splicing, guanine-nucleo	99.53
3ef0_A	372	RNA polymerase II subunit A C-terminal domain phos	99.53
2cou_A	109	ECT2 protein; BRCT domain, RHO GTPase, structural	99.51
2ebw_A	97	DNA repair protein REV1; A/B/A 3 layers, parallel	99.47
3pc6_A	104	DNA repair protein XRCC1; BRCT domain, protein:pro	99.42
3l3e_A	107	DNA topoisomerase 2-binding protein 1; BRCT domain	99.39
2d8m_A	129	DNA-repair protein XRCC1; parallel beta-sheet, DNA	99.32
3pa6_A	107	Microcephalin; BRCT domain, cell cycle; HET: MSE;	99.27
2ep8_A	100	Pescadillo homolog 1; A/B/A 3 layers, nucleolus, r	99.24
1l7b_A	92	DNA ligase; BRCT, autostructure, structural genomi	99.24
3pc7_A	88	DNA ligase 3; DNA repair, BRCT domain, protein:pro	99.22
2coe_A	120	Deoxynucleotidyltransferase, terminal variant; BRC	99.22
2k6g_A	109	Replication factor C subunit 1; protein, BRCT, DNA	99.16
2ep8_A	100	Pescadillo homolog 1; A/B/A 3 layers, nucleolus, r	99.14
2jw5_A	106	DNA polymerase lambda; BRCT domain, family X polym	99.12
2ebu_A	112	Replication factor C subunit 1; A/B/A 3 layers, pa	99.09
3ii6_X	263	DNA ligase 4; XRCC4, NHEJ, DNA repair, BRCT, alter	99.04
2cok_A	113	Poly [ADP-ribose] polymerase-1; BRCT domain, DNA r	99.01
2jw5_A	106	DNA polymerase lambda; BRCT domain, family X polym	98.97
2nte_A	210	BARD-1, BRCA1-associated ring domain protein 1; BR	98.96
1z56_C	264	DNA ligase IV; DNA repair, BRCT, NHEJ, XRCC4, DNA	98.95
1l0b_A	229	BRCA1; TANDEM-BRCT, three-helix bundle, unknown fu	98.93
1t15_A	214	Breast cancer type 1 susceptibility protein; prote	98.9
3u3z_A	199	Microcephalin; DNA repair, cell cycle regulation,	98.9
3pc7_A	88	DNA ligase 3; DNA repair, BRCT domain, protein:pro	98.86
3sqd_A	219	PAX-interacting protein 1; tandem BRCT domains, ce	98.85
3ef0_A	372	RNA polymerase II subunit A C-terminal domain phos	98.82
3al2_A	235	DNA topoisomerase 2-binding protein 1; BRCT domain	98.82
2coe_A	120	Deoxynucleotidyltransferase, terminal variant; BRC	98.81
2dun_A	133	POL MU, DNA polymerase MU; layers A/B/A, parallel	98.76
1kzy_C	259	Tumor suppressor P53-binding protein 1; tandem-BRC	98.73
2vxb_A	241	DNA repair protein RHP9; BRCT, nucleus, cell cycle	98.72
3ef1_A	442	RNA polymerase II subunit A C-terminal domain phos	98.7
2etx_A	209	Mediator of DNA damage checkpoint protein 1; tande	98.61
2dun_A	133	POL MU, DNA polymerase MU; layers A/B/A, parallel	98.49
3l41_A	220	BRCT-containing protein 1; BRC1, BRCT domain, tand	98.49
1l7b_A	92	DNA ligase; BRCT, autostructure, structural genomi	98.23
3t7k_A	256	RTT107, regulator of TY1 transposition protein 107	98.21
2k6g_A	109	Replication factor C subunit 1; protein, BRCT, DNA	98.03
1dgs_A	667	DNA ligase; AMP complex, NAD+-dependent; HET: DNA	97.96
2cok_A	113	Poly [ADP-ribose] polymerase-1; BRCT domain, DNA r	97.92
2ebu_A	112	Replication factor C subunit 1; A/B/A 3 layers, pa	97.91
2owo_A	671	DNA ligase; protein-DNA complex, ligase-DNA comple	97.86
2l42_A	106	DNA-binding protein RAP1; BRCT domain, protein bin	97.57
3huf_A	325	DNA repair and telomere maintenance protein NBS1;	97.53
2l42_A	106	DNA-binding protein RAP1; BRCT domain, protein bin	97.27
4gns_A	290	Chitin biosynthesis protein CHS5; FN3, BRCT, tetra	96.76
1dgs_A	667	DNA ligase; AMP complex, NAD+-dependent; HET: DNA	94.62
2owo_A	671	DNA ligase; protein-DNA complex, ligase-DNA comple	93.51
3huf_A	325	DNA repair and telomere maintenance protein NBS1;	92.83
4gns_A	290	Chitin biosynthesis protein CHS5; FN3, BRCT, tetra	91.77
3t7k_A	256	RTT107, regulator of TY1 transposition protein 107	90.15
3oq4_A	134	DBF4, protein DNA52; DDK, BRCT, RAD53, replication	89.88
3qbz_A	160	DDK kinase regulatory subunit DBF4; FHA domain,RAD	89.13
3oq0_A	151	DBF4, protein DNA52; DDK, BRCT, RAD53, replication	87.8
3oq0_A	151	DBF4, protein DNA52; DDK, BRCT, RAD53, replication	87.54
3qbz_A	160	DDK kinase regulatory subunit DBF4; FHA domain,RAD	82.2

>3olc_X DNA topoisomerase 2-binding protein 1; BRCT domain, DNA repair, RAD9, DNA binding protein; HET: DNA; 2.40A {Homo sapiens} PDB: 2xnk_A* 2xnh_A*

Probab=99.96  E-value=1.4e-28  Score=246.87  Aligned_cols=180  Identities=21%  Similarity=0.301  Sum_probs=155.9

Q ss_pred             CCCCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHHHHHHHhcCCCCCceEecchHHHHHHH
Q 012081           54 ANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVR  133 (471)
Q Consensus        54 ~~~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~Dcik  133 (471)
                      ...+|+|++||+||+.+++|..|.++|+.+||++..++++++||||+....+.||..|.+.    +++||+++||.+|++
T Consensus       102 y~~~l~g~~~~~tG~~~~~r~~l~~~i~~~GG~v~~~~t~~tTHLI~~~~~t~Ky~~A~~~----gi~IV~~~Wl~~c~~  177 (298)
T 3olc_X          102 YNMVMSDVTISCTSLEKEKREEVHKYVQMMGGRVYRDLNVSVTHLIAGEVGSKKYLVAANL----KKPILLPSWIKTLWE  177 (298)
T ss_dssp             CCCTTTTCEEEEESCCHHHHHHHHHHHHHTTCEECSSCCTTCCEEEESSSCSHHHHHHHHT----TCCEECHHHHHHHHH
T ss_pred             cccccCCeEEEeCCCcHHhHHHHHHHHHHCCCEEecCcCCCeeEEEEeCCCChHHHHHHHC----CCeEeeHHHHHHHHH
Confidence            4679999999999999999999999999999999999999999999999999999999985    899999999999999


Q ss_pred             cccCCCCCccccccccccCcchhhhhcccCCcCCCCCCCCcccchhhccccccccccccccCCCCCCCCcEEEEeCCCCH
Q 012081          134 RNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVSE  213 (471)
Q Consensus       134 ~g~~lde~~Y~l~~~~e~~~~~~~~~~L~~~s~~e~~~lp~~I~es~~s~s~E~ld~~~~~~~~~lF~G~~Iyl~~gfs~  213 (471)
                      .++.++...|.-...          .                                  .....+|+|++|++ +|+..
T Consensus       178 ~~~~~~~~~~~~~~~----------~----------------------------------~~~~~~f~g~~i~~-tG~~~  212 (298)
T 3olc_X          178 KSQEKKITRYTDINM----------E----------------------------------DFKCPIFLGCIICV-TGLCG  212 (298)
T ss_dssp             HHHTTCCSSGGGSCG----------G----------------------------------GGBCCTTTTCEEEE-CSCCH
T ss_pred             cCCcCCccccccccc----------c----------------------------------cccccccCCeEEEE-eCCCC
Confidence            998776544311000          0                                  01146899999999 99999


Q ss_pred             HHHHHHHHHHHhCCCEEEccccCC-CCceEEEEcCchHHHH---hcCCCceechhHHHHHHhhCCcCccCCcChH
Q 012081          214 ELRNKVFEAATNEGATLVNQWFVG-CGASYVVCEEDSVQKY---MGHSNNLVTPVWVLKTAKEKHVQRLVHISAD  284 (471)
Q Consensus       214 ~~r~~L~~lI~~~GG~v~d~~~~~-~~vTHVVv~~~s~~k~---l~~~~~IVs~~WL~dcik~g~lqp~~~ys~d  284 (471)
                      ..|+.|+++|..+||++.++  +. .++||||+......|+   ...+++||+++||+||+++|+++++..|..+
T Consensus       213 ~~r~~l~~li~~~GG~~~~~--ls~~~~THLI~~~~~g~K~~~A~~~gi~IV~~~Wl~dsi~~g~~lde~~Y~l~  285 (298)
T 3olc_X          213 LDRKEVQQLTVKHGGQYMGQ--LKMNECTHLIVQEPKGQKYECAKRWNVHCVTTQWFFDSIEKGFCQDESIYKTE  285 (298)
T ss_dssp             HHHHHHHHHHHHTTCEECSS--CCTTTCCEEECSSSCSHHHHHHHHTTCEEECHHHHHHHHHHTSCCCGGGSBSC
T ss_pred             ccHHHHHHHHHHcCCEEece--ecCCCceEEEEeCCCchHHHHHHHCCCeEEeHHHHHHHHHCCCCCCchhcCCC
Confidence            99999999999999999998  56 7999999988544444   4678999999999999999999999998654

>3ii6_X DNA ligase 4; XRCC4, NHEJ, DNA repair, BRCT, alternative splicing, coiled coil, DNA damage, DNA recombination, isopeptide bond, nucleus; HET: DNA; 2.40A {Homo sapiens} PDB: 2e2w_A*

Probab=99.94  E-value=5.5e-27  Score=231.26  Aligned_cols=218  Identities=14%  Similarity=0.207  Sum_probs=150.4

Q ss_pred             CCCCCCCCcEEEE-eCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHHHHHHHhcCCCCCceEecchHHHHH
Q 012081           53 PANAPFSGLVICV-TGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDS  131 (471)
Q Consensus        53 ~~~~iF~GlvI~v-TG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~Dc  131 (471)
                      ..+++|+|++||| +|.....++.|+++|.+|||++..++++.+||+|+.. .+.|++.+++++   .++||+|+||.||
T Consensus         6 ~~s~lF~G~~f~V~sg~~~~~k~~L~~lI~~~GG~v~~n~~~~t~~iIa~~-~~~k~~~~~~~g---~~~IV~p~Wv~Dc   81 (263)
T 3ii6_X            6 KISNIFEDVEFCVMSGTDSQPKPDLENRIAEFGGYIVQNPGPDTYCVIAGS-ENIRVKNIILSN---KHDVVKPAWLLEC   81 (263)
T ss_dssp             CCCCTTTTCEEEECCCC--CCHHHHHHHHHHTTCEECSSCCTTEEEEECSS-CCHHHHHHHHSC---SCCEECHHHHHHH
T ss_pred             cCcccCCCeEEEEEcCCCCCCHHHHHHHHHHcCCEEEecCCCCEEEEEeCC-CCHHHHHHHhcC---CCCEeehHHHHHH
Confidence            3568999999999 5888889999999999999999999988877778865 459999999862   5999999999999


Q ss_pred             HHcccCCCCCcccccccccc-----Ccch-------------hhhhccc-CCcCCCCCCCCcccchhhccccccccc--c
Q 012081          132 VRRNVRLSESLYTVKSIDEH-----GMHL-------------DKLNRLV-GFAGTENSCLPAGIYEAKQFNATGKHE--R  190 (471)
Q Consensus       132 ik~g~~lde~~Y~l~~~~e~-----~~~~-------------~~~~~L~-~~s~~e~~~lp~~I~es~~s~s~E~ld--~  190 (471)
                      +++++++|.++|.+-...+.     ....             ++++.|. .....+ ...|..     ....+..++  .
T Consensus        82 i~~~~llp~~p~~~~~~~~~~~~~~~~~~D~~GDsy~~~~~~~~l~~ll~~~~~~~-~~~~~~-----~~~~~~~l~~~~  155 (263)
T 3ii6_X           82 FKTKSFVPWQPRFMIHMCPSTKEHFAREYDCYGDSYFIDTDLNQLKEVFSGIKNSN-EQTPEE-----MASLIADLEYRY  155 (263)
T ss_dssp             HHHTSCCCCCGGGEEECCHHHHHHTTTTBCTTSCBSSSCCCHHHHHHHHHSCCCCC-SCCHHH-----HHHHHHHHHHHH
T ss_pred             HhcCCcCCCCHHHHhhCCHHHHHHHHHhccccCCccCCcCCHHHHHHHHHhCcccc-cCCchh-----hHHHHHHHHHhh
Confidence            99999999998876432210     0000             1111110 000000 000000     000000111  1


Q ss_pred             ccccCCCCCCCCcEEEEeC---------CCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCch-----HHHH---
Q 012081          191 DSNRSMNSTLSGCSMYVDS---------DVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDS-----VQKY---  253 (471)
Q Consensus       191 ~~~~~~~~lF~G~~Iyl~~---------gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~s-----~~k~---  253 (471)
                      .....+..+|+||+|||+.         .+.....+.++.+|+.+||++++.  +++.+||||+.++.     ++++   
T Consensus       156 ~~~~~~~~lF~~~~vy~~~~~~~~~~~~~i~~~~l~~~~~~i~~~GG~v~~~--l~~~vTHVVv~~~~~r~~~~~~~~~~  233 (263)
T 3ii6_X          156 SWDCSPLSMFRRHTVYLDSYAVINDLSTKNEGTRLAIKALELRFHGAKVVSC--LAEGVSHVIIGEDHSRVADFKAFRRT  233 (263)
T ss_dssp             TCTTCGGGTTTTCEEEECCBSSTTCGGGBCCSSHHHHHHHHHHHTTCEEESS--CCTTCCEEEECSCCTTHHHHHHHHHT
T ss_pred             cccCCcchhhCCeEEEEecccccCCcccccchhHHHHHHHHHHccCCEEecC--CCCCceEEEECCCCccHHHHHHHHhh
Confidence            1112356899999999942         223334567799999999999999  68899999998631     2222   


Q ss_pred             hcCCCceechhHHHHHHhhCCcCccCCcC
Q 012081          254 MGHSNNLVTPVWVLKTAKEKHVQRLVHIS  282 (471)
Q Consensus       254 l~~~~~IVs~~WL~dcik~g~lqp~~~ys  282 (471)
                      +..+++||+++||.+|+++|+++|+..|.
T Consensus       234 ~~~~~~iV~~~Wv~dci~~~~~l~E~~Y~  262 (263)
T 3ii6_X          234 FKRKFKILKESWVTDSIDKCELQEENQYL  262 (263)
T ss_dssp             CSSCCEEEETHHHHHHHHTTSCCCGGGTB
T ss_pred             cCCCCEEeChHHHHHHHHcCCcCCHhhCC
Confidence            24678999999999999999999998874

>1l0b_A BRCA1; TANDEM-BRCT, three-helix bundle, unknown function; 2.30A {Rattus norvegicus} SCOP: c.15.1.3 c.15.1.3

Probab=99.94  E-value=3.1e-26  Score=219.83  Aligned_cols=192  Identities=18%  Similarity=0.233  Sum_probs=143.3

Q ss_pred             CCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecC------CCHHHHHHHhcCCCCCceEecchHHH
Q 012081           56 APFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSF------GGRKFEHALKHGSRNGLYIVTLGWFV  129 (471)
Q Consensus        56 ~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~------~g~Ky~~A~k~~~~~gi~IV~p~WI~  129 (471)
                      ..+++++||+||+++.++..|.++++.+||.+..+++..|||||+...      .+.||..|+..    |++||+++||.
T Consensus         3 ~~~~~~~i~~sg~~~~~~~~l~~~~~~~G~~~~~~~~~~~THlI~~~~~~~~~~rt~K~~~a~~~----g~~IV~~~Wl~   78 (229)
T 1l0b_A            3 RAERDISMVVSGLTPKEVMIVQKFAEKYRLALTDVITEETTHVIIKTDAEFVCERTLKYFLGIAG----GKWIVSYSWVI   78 (229)
T ss_dssp             CCCCCCEEEEESCCHHHHHHHHHHHHHTTCEECSSCCSSCCEEEECBCTTSEECCCHHHHHHHHT----TCEEEETHHHH
T ss_pred             CCCCCeEEEEcCCCHHHHHHHHHHHHHcCCEEeCCcCCCCCEEEEcCCccccccccHHHHHHHHC----CCcEecHHHHH
Confidence            568899999999999999999999999999999999999999999985      57999999985    89999999999


Q ss_pred             HHHHcccCCCCCccccccccccCcchhhhhcccCCcCCCCCCCCcccchhhccccccccccccccCCCCCCCCcEEEEeC
Q 012081          130 DSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDS  209 (471)
Q Consensus       130 Dcik~g~~lde~~Y~l~~~~e~~~~~~~~~~L~~~s~~e~~~lp~~I~es~~s~s~E~ld~~~~~~~~~lF~G~~Iyl~~  209 (471)
                      ||+++|+++||++|.+.........               ...|.   .             .......+|.|+.||+..
T Consensus        79 ~~~~~~~~~~e~~y~~~~~~~~~~~---------------~~~~~---~-------------~r~~~~~lF~g~~~~~~~  127 (229)
T 1l0b_A           79 KSIQERKLLSVHEFEVKGDVVTGSN---------------HQGPR---R-------------SRESQEKLFEGLQIYCCE  127 (229)
T ss_dssp             HHHTTTSCCCSGGGBCCEETTTCSS---------------SCHHH---H-------------HHHHC--CCTTCEEEECS
T ss_pred             HHHHCCCcCChHHeEeccccccccc---------------cccch---h-------------hhhhhhhhhcCceEEEEe
Confidence            9999999999999998643211000               00000   0             000124699999999955


Q ss_pred             CCCHHHHHHHHHHHHhCCCEEEccccC---CCCceEE-EEcCch------HHHH-hcCCCceechhHHHHHHhhCCcCcc
Q 012081          210 DVSEELRNKVFEAATNEGATLVNQWFV---GCGASYV-VCEEDS------VQKY-MGHSNNLVTPVWVLKTAKEKHVQRL  278 (471)
Q Consensus       210 gfs~~~r~~L~~lI~~~GG~v~d~~~~---~~~vTHV-Vv~~~s------~~k~-l~~~~~IVs~~WL~dcik~g~lqp~  278 (471)
                      .+....++.|.++|+.+||+++.....   ..+.+|+ |+.+..      ++.+ ...+++||+++||+|||.+++++++
T Consensus       128 ~~~~~~~~~l~~li~~~GG~v~~~~~~~~~~~~~~~~vvv~~~~~~~~~~~~~l~~~~~i~iVs~~WlldsI~~~~~~~~  207 (229)
T 1l0b_A          128 PFTNMPKDELERMLQLCGASVVKELPLLTRDTGAHPIVLVQPSAWTEDNDCPDIGQLCKGRLVMWDWVLDSISVYRCRDL  207 (229)
T ss_dssp             CCSSSCHHHHHHHHHHTTCEEECSSSCGGGCCSSCCEEEEC-------------------CEEETHHHHHHHHTTSCCCG
T ss_pred             cCCCCCHHHHHHHHHHCCCEEeCCcccccccCCCceEEEEcCCccchhhhHHHHHHHcCCeEeehhHHHHHHhcCCcCCc
Confidence            576667889999999999999998411   1135774 444321      1212 2467999999999999999999999


Q ss_pred             CCcC
Q 012081          279 VHIS  282 (471)
Q Consensus       279 ~~ys  282 (471)
                      ..|.
T Consensus       208 ~~Y~  211 (229)
T 1l0b_A          208 DAYL  211 (229)
T ss_dssp             GGGB
T ss_pred             cceE
Confidence            8883

>2nte_A BARD-1, BRCA1-associated ring domain protein 1; BRCT, ring finger, zinc-binding protein, ubiquitin LI antitumor protein; 1.90A {Homo sapiens} PDB: 3fa2_A 2r1z_A

Probab=99.94  E-value=2.5e-26  Score=218.40  Aligned_cols=180  Identities=19%  Similarity=0.273  Sum_probs=144.0

Q ss_pred             CcEEEEeCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEec---CCCHHHHHHHhcCCCCCceEecchHHHHHHHccc
Q 012081           60 GLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQS---FGGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNV  136 (471)
Q Consensus        60 GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~---~~g~Ky~~A~k~~~~~gi~IV~p~WI~Dcik~g~  136 (471)
                      |++||+||+.++++..|.+++..+||.+..+++..+||||+..   ..+.||..|+..    |++||+++||.||+++|+
T Consensus         2 ~~vi~~sg~~~~~~~~l~~~~~~~G~~~~~~~~~~~THlV~~~~~~~rt~K~l~a~~~----g~~IV~~~Wl~~c~~~~~   77 (210)
T 2nte_A            2 PLVLIGSGLSSEQQKMLSELAVILKAKKYTEFDSTVTHVVVPGDAVQSTLKCMLGILN----GCWILKFEWVKACLRRKV   77 (210)
T ss_dssp             CCEEEESSCCHHHHHHHHHHHHHTTCEEESSCCTTCCEEEESSSSCCCSHHHHHHHHT----TCEEEETHHHHHHHHHTS
T ss_pred             CEEEEECCCCHHHHHHHHHHHHHcCCEEeCCCCCCCeEEEEcCCCcchHHHHHHHHhc----CCEEecHHHHHHHHHcCC
Confidence            7899999999999999999999999999999999999999987   568999999985    899999999999999999


Q ss_pred             CCCCCccccccccccCcchhhhhcccCCcCCCCCCCCcccchhhccccccccccccccCCCCCCCCcEEEEeCCCCHHHH
Q 012081          137 RLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVSEELR  216 (471)
Q Consensus       137 ~lde~~Y~l~~~~e~~~~~~~~~~L~~~s~~e~~~lp~~I~es~~s~s~E~ld~~~~~~~~~lF~G~~Iyl~~gfs~~~r  216 (471)
                      ++||++|.+......    ...++                                ......+|+|+.||+...+....+
T Consensus        78 ~~~e~~y~~~~~~~~----~r~~~--------------------------------~~~~~~lF~g~~~~l~~~~~~~~~  121 (210)
T 2nte_A           78 CEQEEKYEIPEGPRR----SRLNR--------------------------------EQLLPKLFDGCYFYLWGTFKHHPK  121 (210)
T ss_dssp             CCCGGGTBCTTHHHH----HHHHH--------------------------------HTTCCCTTTTCEEEECSCCSSSCH
T ss_pred             cCChhhccCCCCChh----hhhcc--------------------------------ccccccccCceEEEEeccCCCCCH
Confidence            999999999732100    00000                                001256999999999545777778


Q ss_pred             HHHHHHHHhCCCEEEccccC---------------------CCCceEEEEcCchHH----HHhcCCCceechhHHHHHHh
Q 012081          217 NKVFEAATNEGATLVNQWFV---------------------GCGASYVVCEEDSVQ----KYMGHSNNLVTPVWVLKTAK  271 (471)
Q Consensus       217 ~~L~~lI~~~GG~v~d~~~~---------------------~~~vTHVVv~~~s~~----k~l~~~~~IVs~~WL~dcik  271 (471)
                      +.|+++|+.+||+++...-.                     ...+||.|+..+..+    ++...++.+|+++||+|||.
T Consensus       122 ~~l~~lI~~~GG~v~~~~p~~~~~~~~~~~~v~~~~~~~~~~~~~t~~iv~~~~~~~~~~~~~~~~v~~V~~~Wl~dcI~  201 (210)
T 2nte_A          122 DNLIKLVTAGGGQILSRKPKPDSDVTQTINTVAYHARPDSDQRFCTQYIIYEDLCNYHPERVRQGKVWKAPSSWFIDCVM  201 (210)
T ss_dssp             HHHHHHHHHTTCEEESSCCCGGGCGGGSSCCCCTTSCTTCGGGTCCEEEEECSCSSCCCSCSEETTEEEEEHHHHHHHHH
T ss_pred             HHHHHHHHHCCCEEEecCCCCccccccccceeeeccCCCcccccceEEEEeccccccCHHHHhccCcccccHHHHHHHHH
Confidence            99999999999999963100                     135688888664321    12236678999999999999


Q ss_pred             hCCcCccC
Q 012081          272 EKHVQRLV  279 (471)
Q Consensus       272 ~g~lqp~~  279 (471)
                      ++++||..
T Consensus       202 ~~~llp~~  209 (210)
T 2nte_A          202 SFELLPLD  209 (210)
T ss_dssp             HTSCCCSC
T ss_pred             hCeeccCC
Confidence            99999974

>1t15_A Breast cancer type 1 susceptibility protein; protein-peptide complex, antitumor protein; HET: SEP; 1.85A {Homo sapiens} SCOP: c.15.1.3 c.15.1.3 PDB: 1jnx_X* 1t29_A* 1t2v_A* 1y98_A* 3coj_X* 3k0h_A* 3k0k_A* 3pxe_A* 3pxb_A 3pxc_X 1t2u_A 1n5o_X 3pxa_A 3k15_A* 3k16_A* 3pxd_A 2ing_X 1oqa_A

Probab=99.94  E-value=9.2e-26  Score=213.74  Aligned_cols=190  Identities=16%  Similarity=0.194  Sum_probs=144.7

Q ss_pred             CCcEEEEeCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecC------CCHHHHHHHhcCCCCCceEecchHHHHHH
Q 012081           59 SGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSF------GGRKFEHALKHGSRNGLYIVTLGWFVDSV  132 (471)
Q Consensus        59 ~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~------~g~Ky~~A~k~~~~~gi~IV~p~WI~Dci  132 (471)
                      +|++|++||+.+.++..|.++++.+||.+..+++..+||||+.+.      .+.||..|+..    |++||+++||.||+
T Consensus         3 ~~~~~~~sg~~~~~~~~l~~~~~~~G~~~~~~~~~~~THli~~~~~~~~~~rt~k~~~a~~~----g~~IV~~~Wl~~~~   78 (214)
T 1t15_A            3 KRMSMVVSGLTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAG----GKWVVSYFWVTQSI   78 (214)
T ss_dssp             -CCEEEEESCCHHHHHHHHHHHHHHTCEECSSCCTTCCEEEECBCTTSEECCBHHHHHHHHT----TCEEEETHHHHHHH
T ss_pred             CcEEEEECCCCHHHHHHHHHHHHHhCCEEeCccCCCCcEEEEeCCcccchhhhHHHHHHHhc----CCEEeCHHHHHHHH
Confidence            589999999999999999999999999999999999999999985      47999999985    89999999999999


Q ss_pred             HcccCCCCCccccccccccCcchhhhhcccCCcCCCCCCCCcccchhhccccccccccccccCCCCCCCCcEEEEeCCCC
Q 012081          133 RRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVS  212 (471)
Q Consensus       133 k~g~~lde~~Y~l~~~~e~~~~~~~~~~L~~~s~~e~~~lp~~I~es~~s~s~E~ld~~~~~~~~~lF~G~~Iyl~~gfs  212 (471)
                      ++|+++||++|.+..............                  ...           . .....+|+|+.||+...+.
T Consensus        79 ~~~~~~~e~~y~~~~~~~~~~~~~~~~------------------~~r-----------~-~~~~~lF~g~~~~~~~~~~  128 (214)
T 1t15_A           79 KERKMLNEHDFEVRGDVVNGRNHQGPK------------------RAR-----------E-SQDRKIFRGLEICCYGPFT  128 (214)
T ss_dssp             HTTSCCCGGGGBCCEETTTBTTCCHHH------------------HHH-----------T-CTTSCTTTTCEEEECSCCS
T ss_pred             HCCCcCChHHeEeeccccccccccchh------------------hHh-----------h-cCCCcccCCCEEEEEecCC
Confidence            999999999999874321100000000                  000           0 0125699999999955576


Q ss_pred             HHHHHHHHHHHHhCCCEEEccccCCC---CceEEEEcCchH----HHH----hcCCCceechhHHHHHHhhCCcCccCCc
Q 012081          213 EELRNKVFEAATNEGATLVNQWFVGC---GASYVVCEEDSV----QKY----MGHSNNLVTPVWVLKTAKEKHVQRLVHI  281 (471)
Q Consensus       213 ~~~r~~L~~lI~~~GG~v~d~~~~~~---~vTHVVv~~~s~----~k~----l~~~~~IVs~~WL~dcik~g~lqp~~~y  281 (471)
                      ...++.|.++|+.+||+++.......   ...+||+.+++.    .++    ...++++|+++||+||+.+++++|+..|
T Consensus       129 ~~~~~~l~~li~~~GG~v~~~~~~~~~~~~~~~ivi~~~~~~~~~~~~~~~a~~~~~~iV~~~Wi~dsi~~~~~l~~~~Y  208 (214)
T 1t15_A          129 NMPTDQLEWMVQLCGASVVKELSSFTLGTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTY  208 (214)
T ss_dssp             SSCHHHHHHHHHHTTCEECCSGGGCCCSTTCCEEEEECGGGCSSCGGGGSSTTTCSSCEEEHHHHHHHHHHTSCCCSGGG
T ss_pred             CCCHHHHHHHHHHCCCEEecCccccccCCCCccEEEECCCcccchhhHHHHHHhcCCcEEeccHHHHhHhhcCcCCCcce
Confidence            66688999999999999998731111   123454433211    122    2467899999999999999999999988


Q ss_pred             C
Q 012081          282 S  282 (471)
Q Consensus       282 s  282 (471)
                      .
T Consensus       209 ~  209 (214)
T 1t15_A          209 L  209 (214)
T ss_dssp             B
T ss_pred             e
Confidence            4

>3u3z_A Microcephalin; DNA repair, cell cycle regulation, cell cycle; HET: SEP PTR; 1.50A {Homo sapiens} PDB: 3szm_A* 3t1n_A* 3sht_A 3shv_A*

Probab=99.93  E-value=1.7e-25  Score=211.97  Aligned_cols=182  Identities=16%  Similarity=0.212  Sum_probs=142.5

Q ss_pred             CcEEEEeCCChhhHHHHHHHHHHcCC-EEcccCCCCceEEEEecC-CCHHHHHHHhcCCCCCceEecchHHHHHHHcccC
Q 012081           60 GLVICVTGLSKEARKQVMEATERLGG-QYSPDLHPQCTHLVVQSF-GGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVR  137 (471)
Q Consensus        60 GlvI~vTG~~~~er~~L~~lI~~~GG-~~~~~l~~~~THLV~~~~-~g~Ky~~A~k~~~~~gi~IV~p~WI~Dcik~g~~  137 (471)
                      ..+|++||++.++++.|.++|..+|| .+..+++..|||||+.+. .+.||..|+..    |++||+++||.+|++.|++
T Consensus        11 ~~~~~~sgl~~~~~~~l~~~i~~lgG~~~~~~~~~~~THlv~~~~~rT~K~l~ai~~----g~~Iv~~~Wv~~~~~~g~~   86 (199)
T 3u3z_A           11 TRTLVMTSMPSEKQNVVIQVVDKLKGFSIAPDVCETTTHVLSGKPLRTLNVLLGIAR----GCWVLSYDWVLWSLELGHW   86 (199)
T ss_dssp             CCEEEEESCCHHHHHHHHHHHHHHCSCEEESSCCTTEEEEEESSCCCBHHHHHHHHT----TCEEEETHHHHHHHHHTSC
T ss_pred             CeEEEEcCCCHHHHHHHHHHHHHcCCcEEecCCCCCCeEEEECCCCCCHHHHHHHHC----CCcEEeHHHHHHHhhCCCC
Confidence            46899999999999999999999988 677999999999999885 68999999985    8999999999999999999


Q ss_pred             CCCCccccccccccCcchhhhhcccCCcCCCCCCCCcccchhhccccccccccccccCCCCCCCCcE-EEEeCCCCHHHH
Q 012081          138 LSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCS-MYVDSDVSEELR  216 (471)
Q Consensus       138 lde~~Y~l~~~~e~~~~~~~~~~L~~~s~~e~~~lp~~I~es~~s~s~E~ld~~~~~~~~~lF~G~~-Iyl~~gfs~~~r  216 (471)
                      +||++|.+.+......    ..++.+..                         ........+|+|+. ||+ .++....+
T Consensus        87 l~e~~y~~~~~~~~~~----~~rl~r~~-------------------------~~~~~~~~LF~g~~~~~v-~~~~~~~~  136 (199)
T 3u3z_A           87 ISEEPFELSHHFPAAP----LCRSECHL-------------------------SAGPYRGTLFADQPVMFV-SPASSPPV  136 (199)
T ss_dssp             CCSGGGBCTTTCTHHH----HHHHHHHH-------------------------CSSSCCCCTTTTSCCEEE-CTTCSSCH
T ss_pred             CChhhccccCCccccc----cchhhhhh-------------------------hcccccchhhCCCeEEEE-CCCCCCCH
Confidence            9999999975422110    00110000                         00011257999995 666 77776677


Q ss_pred             HHHHHHHHhCCCEEEccccCCCCceEEEEcCchHHHHhcCCCceechhHHHHHHhhCCcCccCCc
Q 012081          217 NKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHI  281 (471)
Q Consensus       217 ~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~s~~k~l~~~~~IVs~~WL~dcik~g~lqp~~~y  281 (471)
                      +.|.++|+.+||+++...   ..++++|+.... +  ...++++|+++||+|||.++++||...|
T Consensus       137 ~~L~~lI~~~GG~v~~~~---~~~~iiI~~~~~-~--~~~~~~~V~p~Wi~DsI~~~~llp~~~Y  195 (199)
T 3u3z_A          137 AKLCELVHLCGGRVSQVP---RQASIVIGPYSG-K--KKATVKYLSEKWVLDSITQHKVCAPENY  195 (199)
T ss_dssp             HHHHHHHHHTTCCBCSSG---GGCSEEESCCCS-C--CCTTCEEECHHHHHHHHHHTSCCCGGGG
T ss_pred             HHHHHHHHHcCCEEeccC---CCCEEEEeCCch-h--ccCCCcEEChhHHHHHHHcCCcCChHhc
Confidence            999999999999999982   345555543222 1  1367889999999999999999999887

>1kzy_C Tumor suppressor P53-binding protein 1; tandem-BRCT and linker complexed with non-BRCT protein, three-helix bundle, parallel beta sheet; 2.50A {Homo sapiens} SCOP: c.15.1.4 c.15.1.4 PDB: 1gzh_B

Probab=99.90  E-value=1.9e-23  Score=205.60  Aligned_cols=191  Identities=16%  Similarity=0.143  Sum_probs=144.0

Q ss_pred             CCCCCCCCcEEEEeCCChh-----------------------------hHHHHHHHHHHcCCEEcccCCCC------ceE
Q 012081           53 PANAPFSGLVICVTGLSKE-----------------------------ARKQVMEATERLGGQYSPDLHPQ------CTH   97 (471)
Q Consensus        53 ~~~~iF~GlvI~vTG~~~~-----------------------------er~~L~~lI~~~GG~~~~~l~~~------~TH   97 (471)
                      ....+|.|+.|++|+....                             .|.+|+++|+.+||++..+++..      +||
T Consensus        11 ~~~~iF~g~~F~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~l~~~I~~~GG~v~~~~~~~~~~~~~~t~   90 (259)
T 1kzy_C           11 LNKTLFLGYAFLLTMATTSDKLASRSKLPDGPTGSSEEEEEFLEIPPFNKQYTESQLRAGAGYILEDFNEAQCNTAYQCL   90 (259)
T ss_dssp             SSTTTTTTEEEEECCCC---------------------------CCCCCHHHHHHHHHTTTCEECSSCCTTTTTTTCEEE
T ss_pred             CCCcCcCCcEEEEEcccccccccccccccccccccccccccccccCcccHHHHHHHHHHCCCEEecCccccccccCCCeE
Confidence            4678999999999998653                             66899999999999999999854      799


Q ss_pred             EEEec-CCCHHHHHHHhcCCCCCceEecchHHHHHHHcccCCCCCccccccccccCcchhhhhcccCCcCCCCCCCCccc
Q 012081           98 LVVQS-FGGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGI  176 (471)
Q Consensus        98 LV~~~-~~g~Ky~~A~k~~~~~gi~IV~p~WI~Dcik~g~~lde~~Y~l~~~~e~~~~~~~~~~L~~~s~~e~~~lp~~I  176 (471)
                      ||+.. ..+.||..|+..    |++||+++||.||++.++++|+.+|.++.......     .++..             
T Consensus        91 LIa~~~~rt~K~l~ala~----g~~iVs~~Wl~dc~~~~~~l~~~~Y~l~~g~s~~~-----~~~~~-------------  148 (259)
T 1kzy_C           91 LIADQHCRTRKYFLCLAS----GIPCVSHVWVHDSCHANQLQNYRNYLLPAGYSLEE-----QRILD-------------  148 (259)
T ss_dssp             EEESSCCCSHHHHHHHHH----TCCEEETHHHHHHHHHTSCCCGGGSBCCCEEETTT-----TEEEC-------------
T ss_pred             EEcCCCCCcHHHHHHHhc----CCCCccHHHHHHHHHcCCcCCHHHccCCCCccccc-----chhhh-------------
Confidence            99987 467899999886    89999999999999999999999999974211100     00000             


Q ss_pred             chhhccccccccccccccCCCCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccC-------CCCceEEEEcCc-
Q 012081          177 YEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFV-------GCGASYVVCEED-  248 (471)
Q Consensus       177 ~es~~s~s~E~ld~~~~~~~~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~-------~~~vTHVVv~~~-  248 (471)
                                      ......+|+|++|||.....+..++.+..+++.+||+++.....       ....+|||+.+. 
T Consensus       149 ----------------~~~~~~LF~G~~I~i~~~~~~~~~~~~~~Il~~~Ga~vv~~~~s~~~~~d~~~~~~~viv~d~~  212 (259)
T 1kzy_C          149 ----------------WQPRENPFQNLKVLLVSDQQQNFLELWSEILMTGGAASVKQHHSSAHNKDIALGVFDVVVTDPS  212 (259)
T ss_dssp             ----------------CCCCCCTTTTCEEEEEESCTTTTHHHHHHHHHHTTCSEEEEEESSSSCCCSCGGGCSEEEECTT
T ss_pred             ----------------ccccCCCCCCeEEEEecCCCCCHHHHHHHHHHhcCCEEEeccccchhhhhccCCCCeEEEECCC
Confidence                            00125799999999966665445677899999999998877310       113455555431 


Q ss_pred             --h-H-HHHhcCCCceechhHHHHHHhhCCcCccCCc
Q 012081          249 --S-V-QKYMGHSNNLVTPVWVLKTAKEKHVQRLVHI  281 (471)
Q Consensus       249 --s-~-~k~l~~~~~IVs~~WL~dcik~g~lqp~~~y  281 (471)
                        + . +.....+++||+.+||++||..|+++++...
T Consensus       213 ~~~~~~~~a~~~~i~iVs~EWv~~sI~~~~ll~~~~h  249 (259)
T 1kzy_C          213 CPASVLKCAEALQLPVVSQEWVIQCLIVGERIGFKQH  249 (259)
T ss_dssp             CCHHHHHHHHHHTCCEECHHHHHHHHHHTSCCCTTSS
T ss_pred             ChHHHHHHHHhcCCCEecHHHHHHHHHhCCcCCCCcC
Confidence              1 1 2223578999999999999999999998654

>1z56_C DNA ligase IV; DNA repair, BRCT, NHEJ, XRCC4, DNA ligase, coiled-coil; HET: DNA; 3.92A {Saccharomyces cerevisiae}

Probab=99.90  E-value=1.3e-24  Score=213.52  Aligned_cols=219  Identities=12%  Similarity=0.116  Sum_probs=125.1

Q ss_pred             CCCCCCCcEEEE-eCCCh------hhHHHHHHHHHHcCCEEcccCCCC-----ceEEEEecCCCHHHHHHHhcCCCCCce
Q 012081           54 ANAPFSGLVICV-TGLSK------EARKQVMEATERLGGQYSPDLHPQ-----CTHLVVQSFGGRKFEHALKHGSRNGLY  121 (471)
Q Consensus        54 ~~~iF~GlvI~v-TG~~~------~er~~L~~lI~~~GG~~~~~l~~~-----~THLV~~~~~g~Ky~~A~k~~~~~gi~  121 (471)
                      ..++|+|++||| +|+..      ..|+.|+++|.++||++..+....     +||+|+.. .+.|++.+.++    +++
T Consensus         2 ~s~lF~g~~f~v~~~~~~p~~~~~~~~~~L~~li~~~GG~~~~~~~~~t~~~~~~~iI~~~-~t~k~~~~~~~----~~~   76 (264)
T 1z56_C            2 ISNIFAGLLFYVLSDYVTEDTGIRITRAELEKTIVEHGGKLIYNVILKRHSIGDVRLISCK-TTTECKALIDR----GYD   76 (264)
T ss_dssp             -CCCCCTTCCCCSEEEECCCCCSSSSCCCTHHHHHHHHTTSCCCSSCCCCCSSCCEEEECS-CCGGGGGGTTT----TCC
T ss_pred             ccccCCCcEEEEEcCCCCccccccCCHHHHHHHHHHcCCEEeecCCCCccCccceEEEecC-CcHHHHHHHhC----CCC
Confidence            458999999998 56532      478999999999999988765542     36777754 57788777664    699


Q ss_pred             EecchHHHHHHHcccCCCCCccccccccccCcchhhhhcccCCcCCCCCCCCcc---cc----hhhc--ccccccccccc
Q 012081          122 IVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAG---IY----EAKQ--FNATGKHERDS  192 (471)
Q Consensus       122 IV~p~WI~Dcik~g~~lde~~Y~l~~~~e~~~~~~~~~~L~~~s~~e~~~lp~~---I~----es~~--s~s~E~ld~~~  192 (471)
                      ||+|+||.||+++++++|.++|.+-..... +.+ .+..-.+.. ..++..+..   +.    ....  .....+++...
T Consensus        77 vV~p~Wv~dci~~~~llp~~~y~~~~~~~~-~~~-~~~~~~d~~-gdsy~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~  153 (264)
T 1z56_C           77 ILHPNWVLDCIAYKRLILIEPNYCFNVSQK-MRA-VAEKRVDCL-GDSFENDISETKLSSLYKSQLSLPPMGELEIDSEV  153 (264)
T ss_dssp             CBCSSTTHHHHSSCSCCCCCSCBSCCCGGG-THH-HHGGGBCSS-SCBSSSCCCHHHHHHTTSCCSCCCCCCCCSSCCSC
T ss_pred             EEechHHHHHhhcCCCCCCChHHhhcCCHH-HHH-HHHHhcccc-CCccccCCCHHHHHHHHHhcccccchhhhhhhccc
Confidence            999999999999999999999866422111 000 000000000 000000000   00    0000  00011112222


Q ss_pred             ccCCCCCCCCcEEEEeCCC-CHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCc---------hHHHHhcC------
Q 012081          193 NRSMNSTLSGCSMYVDSDV-SEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED---------SVQKYMGH------  256 (471)
Q Consensus       193 ~~~~~~lF~G~~Iyl~~gf-s~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~---------s~~k~l~~------  256 (471)
                      ...+..+|+||+||| .++ ....++.++.+|+.+||++++.  ++..+||||+...         .+++.+..      
T Consensus       154 ~~~~~~lF~g~~~yl-~~~~~~~~~~~l~~~i~~~GG~v~~~--l~~~t~hVV~~~~~~~~~~~~~~~~~~~~~~~~~~~  230 (264)
T 1z56_C          154 RRFPLFLFSNRIAYV-PRRKISTEDDIIEMKIKLFGGKITDQ--QSLCNLIIIPYTDPILRKDCMNEVHEKIKEQIKASD  230 (264)
T ss_dssp             CCCCCC---------------------CHHHHHHHTTSCCCC--SSSCSEEECCCSSTTTHHHHSSHHHHTTTTTTTSSS
T ss_pred             ccCchhhhCCeEEEE-ecCCCchhHHHHHHHHHHcCCEEecc--cCCCEEEEEeCCCccchHHHHHHHHHHHHhhccccc
Confidence            234578999999999 554 3455677899999999999998  5655566666432         13333322      


Q ss_pred             ---C-CceechhHHHHHHhhCCcCccCCcCh
Q 012081          257 ---S-NNLVTPVWVLKTAKEKHVQRLVHISA  283 (471)
Q Consensus       257 ---~-~~IVs~~WL~dcik~g~lqp~~~ys~  283 (471)
                         + ++||+++||.||+++|+++++..|.+
T Consensus       231 ~~~~~~~iV~~~Wv~dci~~~~ll~e~~Y~~  261 (264)
T 1z56_C          231 TIPKIARVVAPEWVDHSINENCQVPEEDFPV  261 (264)
T ss_dssp             SCCCCCEEECTHHHHHHHTTSCCCSSCCC--
T ss_pred             ccCCCCEEecHHHHHHHHHcCCcCCHHHcCC
Confidence               2 59999999999999999999999854

>2etx_A Mediator of DNA damage checkpoint protein 1; tandem BRCT domains histone gamma-H2AX, cell cycle; 1.33A {Homo sapiens} PDB: 2azm_A* 3k05_A* 2ado_A

Probab=99.89  E-value=2.9e-23  Score=197.71  Aligned_cols=187  Identities=21%  Similarity=0.264  Sum_probs=134.7

Q ss_pred             CCCCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecC-CCHHHHHHHhcCCCCCceEecchHHHHHH
Q 012081           54 ANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSF-GGRKFEHALKHGSRNGLYIVTLGWFVDSV  132 (471)
Q Consensus        54 ~~~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~-~g~Ky~~A~k~~~~~gi~IV~p~WI~Dci  132 (471)
                      +.+...+++|++||+.+++   ++++|+.+||.+..+++ +|||||+... .+.||..|+.+    |++||+++||.+|+
T Consensus         6 ~~~~~~~~~v~~sG~~~~~---~~~~i~~lGg~~~~~~~-~~THlI~~~~~rt~K~l~a~~~----g~~IV~~~Wl~~~~   77 (209)
T 2etx_A            6 LNQESTAPKVLFTGVVDAR---GERAVLALGGSLAGSAA-EASHLVTDRIRRTVKFLCALGR----GIPILSLDWLHQSR   77 (209)
T ss_dssp             ------CCEEEECSSCCHH---HHHHHHHTTCEECSSTT-TCSEEECSSCCCSHHHHHHHHH----TCCEECTHHHHHHH
T ss_pred             ccccCCCcEEEEeCCCcHH---HHHHHHHCCCEEeCCCC-CceEEEECCCCCCHHHHHHHhc----CCccccHHHHHHHH
Confidence            5577889999999999754   48999999999999997 4999999876 58999999996    89999999999999


Q ss_pred             HcccCCCCCccccccccccCcchhhhhcccCCcCCCCCCCCcccchhhccccccccccccccCCCCCCCCcEEEEeCCCC
Q 012081          133 RRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVS  212 (471)
Q Consensus       133 k~g~~lde~~Y~l~~~~e~~~~~~~~~~L~~~s~~e~~~lp~~I~es~~s~s~E~ld~~~~~~~~~lF~G~~Iyl~~gfs  212 (471)
                      ++++++||++|.+.+.....        ..+++      +    .+.        +.. .  ....+|.|++||+. +..
T Consensus        78 ~~~~~l~e~~y~~~~~~~~~--------~~~~~------l----~~~--------~~~-a--~~~~lF~g~~~~~~-~~~  127 (209)
T 2etx_A           78 KAGFFLPPDEYVVTDPEQEK--------NFGFS------L----QDA--------LSR-A--RERRLLEGYEIYVT-PGV  127 (209)
T ss_dssp             HHTSCCCSGGGBCCCHHHHH--------HTTCC------H----HHH--------HHH-H--HHSCTTTTCEEEEC-TTC
T ss_pred             HcCCCCChhhccccChhhhh--------hcCCC------H----HHH--------Hhh-h--hhCCCcCCcEEEEe-CCC
Confidence            99999999999986431100        00000      0    000        000 0  01369999999994 443


Q ss_pred             HHHHHHHHHHHHhCCCEEEccccCCCC--ceEEEEcCc-h---HHHHhcCCCceechhHHHHHHhhCCcCccCCc
Q 012081          213 EELRNKVFEAATNEGATLVNQWFVGCG--ASYVVCEED-S---VQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHI  281 (471)
Q Consensus       213 ~~~r~~L~~lI~~~GG~v~d~~~~~~~--vTHVVv~~~-s---~~k~l~~~~~IVs~~WL~dcik~g~lqp~~~y  281 (471)
                      ...++.|.++|+.+||+++..  ....  -+|+|+..+ +   .+.+...++++|+++||++||..+++ ++..|
T Consensus       128 ~~~~~~l~~li~~~GG~v~~~--~~~~~~~~~ivI~~~~d~~~~~~~~~~~i~vvs~eWi~~sI~~q~l-d~e~y  199 (209)
T 2etx_A          128 QPPPPQMGEIISCCGGTYLPS--MPRSYKPQRVVITCPQDFPHCSIPLRVGLPLLSPEFLLTGVLKQEA-KPEAF  199 (209)
T ss_dssp             SSCHHHHHHHHHHTTCEECSS--CCCSCCTTEEEECCGGGGGGCHHHHHHTCCEECTHHHHHHHHHTCC-CGGGG
T ss_pred             CCCHHHHHHHHHHCCCEEECC--CCCCCCCceEEEECcccHHHHHHHHHCCCeEEcHHHHHHHHHhccc-ChHHh
Confidence            334678999999999999987  3332  267777542 2   23344678999999999999998775 55544

>3sqd_A PAX-interacting protein 1; tandem BRCT domains, cell cycle; HET: SEP; 2.15A {Homo sapiens}

Probab=99.88  E-value=4e-22  Score=191.60  Aligned_cols=185  Identities=16%  Similarity=0.275  Sum_probs=141.2

Q ss_pred             CCCCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecC-CCHHHHHHHhcCCCCCceEecchHHHHHH
Q 012081           54 ANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSF-GGRKFEHALKHGSRNGLYIVTLGWFVDSV  132 (471)
Q Consensus        54 ~~~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~-~g~Ky~~A~k~~~~~gi~IV~p~WI~Dci  132 (471)
                      +..++.|++||+||+.+.++..+.++|+.+||.+..+. .+|||||+... .+.||..|+.+    |++||+++||.+|+
T Consensus        10 ~~~~~~~~~i~~SG~~~~~~~~l~~~i~~lGg~v~~~~-~~~THLI~~~~~rT~K~l~A~~~----g~~IVs~~Wl~~c~   84 (219)
T 3sqd_A           10 KLTPELTPFVLFTGFEPVQVQQYIKKLYILGGEVAESA-QKCTHLIASKVTRTVKFLTAISV----VKHIVTPEWLEECF   84 (219)
T ss_dssp             CCCGGGCCEEEECSCCHHHHHHHHHHHHHTTCEECSSG-GGCSEEECSSCCCCHHHHHHTTT----CSEEECHHHHHHHH
T ss_pred             ccCCCCCeEEEEeCCChHHHHHHHHHHHHCCCEEeCCC-CCceEEEECCCCCCHHHHHHHHc----CCCEecHHHHHHHH
Confidence            45789999999999999999999999999999999886 88999999876 45799999986    89999999999999


Q ss_pred             HcccCCCCCccccccccccCcchhhhhcccCCcCCCCCCCCcccchhhccccccccccccccCCCCCCCCcEEEEeCCCC
Q 012081          133 RRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVS  212 (471)
Q Consensus       133 k~g~~lde~~Y~l~~~~e~~~~~~~~~~L~~~s~~e~~~lp~~I~es~~s~s~E~ld~~~~~~~~~lF~G~~Iyl~~gfs  212 (471)
                      ++|+++||++|.+.+.....        ..++.      +...+..             .  ....+|.|+.|||.+++.
T Consensus        85 ~~~~~l~e~~y~l~d~~~e~--------~~~~~------l~~~l~r-------------a--~~~~LF~G~~f~it~~~~  135 (219)
T 3sqd_A           85 RCQKFIDEQNYILRDAEAEV--------LFSFS------LEESLKR-------------A--HVSPLFKAKYFYITPGIC  135 (219)
T ss_dssp             HHTSCCCSGGGBCCCHHHHH--------HTTCC------HHHHHHH-------------H--HHSCTTTTEEEEECTTCS
T ss_pred             HcCCCCChHhccCCCchhhh--------hcCCC------hHHHhhh-------------h--ccccccCCcEEEEeCCCC
Confidence            99999999999997532100        00000      0000000             0  014699999999966665


Q ss_pred             HHHHHHHHHHHHhCCCEEEccccCCC-----------C-ceEEEEcCc-h---HHHHhcCCCceechhHHHHHHhhCCc
Q 012081          213 EELRNKVFEAATNEGATLVNQWFVGC-----------G-ASYVVCEED-S---VQKYMGHSNNLVTPVWVLKTAKEKHV  275 (471)
Q Consensus       213 ~~~r~~L~~lI~~~GG~v~d~~~~~~-----------~-vTHVVv~~~-s---~~k~l~~~~~IVs~~WL~dcik~g~l  275 (471)
                      +. ++.|+++|+.+||+++...  ..           . ...||+..+ +   .+.+...++.|++.+||++||-.+++
T Consensus       136 ~~-~~~l~~lI~~~GG~v~~~~--p~~~~~~~~~~~~~~~~~ivis~~~d~~~~~~~~~~~~~v~s~E~il~~Il~q~l  211 (219)
T 3sqd_A          136 PS-LSTMKAIVECAGGKVLSKQ--PSFRKLMEHKQNSSLSEIILISCENDLHLCREYFARGIDVHNAEFVLTGVLTQTL  211 (219)
T ss_dssp             SC-HHHHHHHHHHTTCEEESSC--CCHHHHHHHHHCTTSCEEEEEECGGGGGGGHHHHHTTCCCEETHHHHHHHHHTCC
T ss_pred             CC-HHHHHHHHHHCCCEEECCC--CchHHhhhhhcccCCCCEEEEecccHHHHHHHHHHCCCcEEeHHHHHHHHHheee
Confidence            54 7899999999999999873  21           1 234454442 2   34555689999999999999998765

>3al2_A DNA topoisomerase 2-binding protein 1; BRCT domain, protein binding, DNA binding protein; HET: DNA MSE; 2.00A {Homo sapiens} PDB: 3al3_A*

Probab=99.87  E-value=2e-21  Score=188.68  Aligned_cols=203  Identities=13%  Similarity=0.176  Sum_probs=143.8

Q ss_pred             CCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcc--cCCCCceEEEEecCC-CHHHHHHHhcCCCCCceEecchHHHHHH
Q 012081           56 APFSGLVICVTGLSKEARKQVMEATERLGGQYSP--DLHPQCTHLVVQSFG-GRKFEHALKHGSRNGLYIVTLGWFVDSV  132 (471)
Q Consensus        56 ~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~--~l~~~~THLV~~~~~-g~Ky~~A~k~~~~~gi~IV~p~WI~Dci  132 (471)
                      +.-++.+|++||++++++..+.++|+.+||.+..  +++.+|||||+.... +.||..|+..    |+|||+++||.+|+
T Consensus         5 ~~~~~~~~~~Sg~~~~~~~~l~~~i~~LGg~~~~~~~~~~~~THlV~~~~~RT~K~l~aia~----G~wIvs~~wl~~s~   80 (235)
T 3al2_A            5 SLKKQYIFQLSSLNPQERIDYCHLIEKLGGLVIEKQCFDPTCTHIVVGHPLRNEKYLASVAA----GKWVLHRSYLEACR   80 (235)
T ss_dssp             ---CCCEEEEESCCHHHHHHHHHHHHHTTCEECCSSSCCTTCCEEEESSCCCSHHHHHHHHT----TCEEECTHHHHHHH
T ss_pred             cCCCCEEEEEcCCCHHHHHHHHHHHHHcCCEEeccCCCCCCCcEEEECCCCCCHHHHHHHHc----CCcCccHHHHHHHH
Confidence            3447899999999999999999999999999976  578999999999874 8999999995    89999999999999


Q ss_pred             HcccCCCCCcccccccccc----CcchhhhhcccCCcCCCCCCCCcccchhhcccccccccccc-ccCCCCCCCCcEEEE
Q 012081          133 RRNVRLSESLYTVKSIDEH----GMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDS-NRSMNSTLSGCSMYV  207 (471)
Q Consensus       133 k~g~~lde~~Y~l~~~~e~----~~~~~~~~~L~~~s~~e~~~lp~~I~es~~s~s~E~ld~~~-~~~~~~lF~G~~Iyl  207 (471)
                      ++|+++||++|++.+....    ...... ..+...        |...        .+.++... ......+|.|++|||
T Consensus        81 ~~g~~l~E~~ye~~~~~~~d~~~~~~~~~-~~l~~a--------~~r~--------R~~l~~~~~~g~~~~lF~g~~v~l  143 (235)
T 3al2_A           81 TAGHFVQEEDYEWGSSSILDVLTGINVQQ-RRLALA--------AMRW--------RKKIQQRQESGIVEGAFSGWKVIL  143 (235)
T ss_dssp             HHTSCCCSGGGBTTSHHHHTTCTTSCHHH-HHHHHH--------HHHH--------HHHHHHHHTTTCCSSTTTTCEEEE
T ss_pred             HcCCCCChhceeecCcchhccccCCChhh-hHHHHH--------HHHH--------HHHHHhcccccccCCCCCCcEEEE
Confidence            9999999999999754211    000000 000000        0000        00000000 000146999999999


Q ss_pred             eCCCCHHHHHHHHHHHHhCCCEEEcccc--CCCCceEEEEcCc---------hHHHHhcCCCceechhHHHHHHhhCCcC
Q 012081          208 DSDVSEELRNKVFEAATNEGATLVNQWF--VGCGASYVVCEED---------SVQKYMGHSNNLVTPVWVLKTAKEKHVQ  276 (471)
Q Consensus       208 ~~gfs~~~r~~L~~lI~~~GG~v~d~~~--~~~~vTHVVv~~~---------s~~k~l~~~~~IVs~~WL~dcik~g~lq  276 (471)
                      ..+  ....+.++++|+++||+|....-  ...+.||+++.-.         .+..+...+++||+++||+|++..+.+.
T Consensus       144 ~~~--~~~~~~l~~ii~agGg~vl~~~~~~~~~~~t~~~vd~~~~~~~~~~~~~~~~~~~~i~~v~~ewlld~i~~~~~~  221 (235)
T 3al2_A          144 HVD--QSREAGFKRLLQSGGAKVLPGHSVPLFKEATHLFSDLNKLKPDDSGVNIAEAAAQNVYCLRTEYIADYLMQESPP  221 (235)
T ss_dssp             ECC--HHHHHHHHHHHHHTTCEECSSCCGGGGGGCSEEEECC--------CCCHHHHHHTTCEEEETHHHHHHHHCSSCC
T ss_pred             ecC--CCcHHHHHHHHHcCCcEEecCCCCCccccCceEEEecccCCccchhHHHHHHHHcCCcEEcHHHHHHHHhcCCCC
Confidence            543  45668899999999999987620  1134689887541         1333345789999999999999998877


Q ss_pred             ccCCc
Q 012081          277 RLVHI  281 (471)
Q Consensus       277 p~~~y  281 (471)
                      +...|
T Consensus       222 ~~~~y  226 (235)
T 3al2_A          222 HVENY  226 (235)
T ss_dssp             CHHHH
T ss_pred             Chhhe
Confidence            76555

>2vxb_A DNA repair protein RHP9; BRCT, nucleus, cell cycle, DNA damage, DNA replication inhibitor, phosphoprotein, checkpoint signalling; HET: DNA; 2.3A {Schizosaccharomyces pombe} PDB: 2vxc_A*

Probab=99.85  E-value=1.4e-20  Score=183.34  Aligned_cols=196  Identities=15%  Similarity=0.134  Sum_probs=137.6

Q ss_pred             CCCCCcEEEEeCC---ChhhHHHHHHHHHHcCCEEccc-----CC--C-------------------CceEEEEecCC-C
Q 012081           56 APFSGLVICVTGL---SKEARKQVMEATERLGGQYSPD-----LH--P-------------------QCTHLVVQSFG-G  105 (471)
Q Consensus        56 ~iF~GlvI~vTG~---~~~er~~L~~lI~~~GG~~~~~-----l~--~-------------------~~THLV~~~~~-g  105 (471)
                      .+|+|+.||++|.   .+..+.+|+++|+++||++..+     ++  .                   ..||||+.... +
T Consensus         1 ~lF~g~~F~ls~~~~~~~~~k~~L~~~I~~~GG~v~~~g~~~lf~~~~~~~~~~~~~~k~~~~~~~~~~t~lia~~~~rt   80 (241)
T 2vxb_A            1 LIFDDCVFAFSGPVHEDAYDRSALETVVQDHGGLVLDTGLRPLFNDPFKSKQKKLRHLKPQKRSKSWNQAFVVSDTFSRK   80 (241)
T ss_dssp             CTTTTEEEEECCCSSTTSSCHHHHHHHHHHTTCEECTTCSGGGBCCSCC----CCCSCCBCGGGGGCSEEEEECSSCCCC
T ss_pred             CCCCCcEEEEecCCCCchhhHHHHHHHHHHCCCEEecCcchhhccCccccccccccccccccccccccceEEEcCCCCCc
Confidence            3799999999998   4578999999999999999886     22  1                   24999999764 7


Q ss_pred             HHHHHHHhcCCCCCceEecchHHHHHHHcccCCCCCccccccccccCcchhhhhcccCCcCCCCCCCCcccchhhccccc
Q 012081          106 RKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNAT  185 (471)
Q Consensus       106 ~Ky~~A~k~~~~~gi~IV~p~WI~Dcik~g~~lde~~Y~l~~~~e~~~~~~~~~~L~~~s~~e~~~lp~~I~es~~s~s~  185 (471)
                      .||.+|+++    |++||+++||.||++.++++|+.+|.++........ ....+..     .+  .+..  .       
T Consensus        81 ~K~~~ala~----gipiV~~~Wi~dc~~~~~~~~~~~ylL~~~~s~~~~-~~~~~~~-----~~--~~~~--~-------  139 (241)
T 2vxb_A           81 VKYLEALAF----NIPCVHPQFIKQCLKMNRVVDFSPYLLASGYSHRLD-CTLSQRI-----EP--FDTT--D-------  139 (241)
T ss_dssp             HHHHHHHHH----TCCEECTHHHHHHHHHTSCCCSGGGBBEEEEETTTT-EEEECCC-----CC--CCTT--S-------
T ss_pred             HHHHHHHHc----CCCEecHHHHHHHHHcCCcCChhhccCCCCcchhcc-chhhccc-----cC--CChh--h-------
Confidence            899999987    899999999999999999999999999743221100 0000000     00  0000  0       


Q ss_pred             cccccccccCCCCCCCCcEEEEeCCCCH------------HHHHHHHHHHHhCCCEE--EccccCCCCceEEEEcCchHH
Q 012081          186 GKHERDSNRSMNSTLSGCSMYVDSDVSE------------ELRNKVFEAATNEGATL--VNQWFVGCGASYVVCEEDSVQ  251 (471)
Q Consensus       186 E~ld~~~~~~~~~lF~G~~Iyl~~gfs~------------~~r~~L~~lI~~~GG~v--~d~~~~~~~vTHVVv~~~s~~  251 (471)
                       .+ .......+.+|.|++|||-.+...            +..+.+..++..+||++  +..  .....+|+|+.+... 
T Consensus       140 -~l-~~~~~~~~~Lf~g~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~i~~~~Ga~~~~v~~--~~~~~~d~v~~~~~~-  214 (241)
T 2vxb_A          140 -SL-YDRLLARKGPLFGKKILFIIPEAKSWQKKIENTEQGQKALAHVYHALALGADVEIRPN--VAHLECDLILTMDGN-  214 (241)
T ss_dssp             -CH-HHHHHHCCCTTTTCEEEECCCC------------CHHHHHHHHHHHHHTTCEEECCSC--CSSCCCSEEECSSSC-
T ss_pred             -HH-HHHHhhcCcCCCCcEEEEEeCCCcccccccccccccchHHHHHHHHHHcCCceecccc--cccCCccEEEECCcc-
Confidence             00 000012367999999999333221            13478999999999999  444  344567777765322 


Q ss_pred             HHhcCCCceechhHHHHHHhhCCcCc
Q 012081          252 KYMGHSNNLVTPVWVLKTAKEKHVQR  277 (471)
Q Consensus       252 k~l~~~~~IVs~~WL~dcik~g~lqp  277 (471)
                      .....+++||+++||.+|+..|++++
T Consensus       215 ~~~~~~~~iV~~eWv~~~i~~g~~l~  240 (241)
T 2vxb_A          215 IVDETNCPVVDPEWIVECLISQSDIS  240 (241)
T ss_dssp             CCSSCSSCEECHHHHHHHHHHTSCTT
T ss_pred             ccccCCCCEecHHHHHHHHHhceecC
Confidence            12357899999999999999999875

>3l46_A Protein ECT2; alternative splicing, guanine-nucleotide releasing factor, phosphoprotein, polymorphism, proto-oncogene, structural genomics; 1.48A {Homo sapiens}

Probab=99.84  E-value=1.1e-21  Score=169.73  Aligned_cols=90  Identities=30%  Similarity=0.541  Sum_probs=86.3

Q ss_pred             CCCCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHHHHHHHhcCCCCCceEecchHHHHHHH
Q 012081           54 ANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVR  133 (471)
Q Consensus        54 ~~~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~Dcik  133 (471)
                      +.++|.|++||++||++++|..|+++|+.+||+|...++++|||||+....+.||+.|.+|    +|+||+++||.||++
T Consensus        18 ~~p~F~g~~Ic~sGf~~~er~~l~~~i~~~GG~~~~~l~~~cTHLV~~~~~~~K~~~A~~~----~i~IVs~eWl~dsi~   93 (112)
T 3l46_A           18 GVPPFQDCILSFLGFSDEEKTNMEEMTEMQGGKYLPLGDERCTHLVVEENIVKDLPFEPSK----KLYVVKQEWFWGSIQ   93 (112)
T ss_dssp             CCCTTTTCEECEESCCHHHHHHHHHHHHHTTCEECCTTCTTCSEEEECTTTBSSCSSCCCS----SCEEEEHHHHHHHHH
T ss_pred             CCCccCCeEEEEeCCCHHHHHHHHHHHHHcCCEECcccCCCceEEEecCCchhhHHHHHHC----CeeEecHHHHHHHHH
Confidence            5689999999999999999999999999999999999999999999999999999999887    899999999999999


Q ss_pred             cccCCCCCcccccc
Q 012081          134 RNVRLSESLYTVKS  147 (471)
Q Consensus       134 ~g~~lde~~Y~l~~  147 (471)
                      .|.++||+.|.+..
T Consensus        94 ~g~~ldE~~Y~~~~  107 (112)
T 3l46_A           94 MDARAGETMYLYEK  107 (112)
T ss_dssp             HTSCCCGGGSBCCC
T ss_pred             cCCccChhhceecc
Confidence            99999999999964

>2cou_A ECT2 protein; BRCT domain, RHO GTPase, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.82  E-value=7.7e-21  Score=163.47  Aligned_cols=90  Identities=28%  Similarity=0.538  Sum_probs=86.2

Q ss_pred             CCCCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHHHHHHHhcCCCCCceEecchHHHHHHH
Q 012081           54 ANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVR  133 (471)
Q Consensus        54 ~~~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~Dcik  133 (471)
                      ..++|+|++||++||+..+|..|.++|+.|||+|...++++|||||+....+.||++|.+|    +++||+++||.||++
T Consensus         9 ~~~~F~g~~i~~sg~~~~~r~~l~~~i~~~GG~~~~~~~~~~THLV~~~~~~~K~~~a~~~----~i~IV~~~Wl~dsi~   84 (109)
T 2cou_A            9 KVPPFQDCILSFLGFSDEEKHSMEEMTEMQGGSYLPVGDERCTHLIVEENTVKDLPFEPSK----KLFVVKQEWFWGSIQ   84 (109)
T ss_dssp             CCCTTTTCBEEEESSCHHHHHHHHHHHHHHTCBCCCTTCTTCSEEEECTTTCSSCSSCCCT----TSEEECHHHHHHHHH
T ss_pred             cCCcCCCeEEEecCCCHHHHHHHHHHHHHcCCEEecccCCCccEEEEeCCccHHHHHHHHC----CCeEecHHHHHHHHH
Confidence            5689999999999999999999999999999999999999999999999999999999887    899999999999999


Q ss_pred             cccCCCCCcccccc
Q 012081          134 RNVRLSESLYTVKS  147 (471)
Q Consensus       134 ~g~~lde~~Y~l~~  147 (471)
                      +|+++||.+|.+..
T Consensus        85 ~g~~ldE~~Y~~~~   98 (109)
T 2cou_A           85 MDARAGETMYLYEK   98 (109)
T ss_dssp             TTSCCCGGGTBCCC
T ss_pred             cCCcCChhccCCCC
Confidence            99999999999864

>3l41_A BRCT-containing protein 1; BRC1, BRCT domain, tandem BRCT repeat, phosphoserine binding domain, DNA repair, cell division, mitosis; HET: SEP; 1.45A {Schizosaccharomyces pombe} PDB: 3l40_A*

Probab=99.78  E-value=1.6e-19  Score=173.69  Aligned_cols=196  Identities=17%  Similarity=0.294  Sum_probs=138.0

Q ss_pred             CCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecC-CCHHHHHHHhcCCCCCceEecchHHHHHHHcc
Q 012081           57 PFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSF-GGRKFEHALKHGSRNGLYIVTLGWFVDSVRRN  135 (471)
Q Consensus        57 iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~-~g~Ky~~A~k~~~~~gi~IV~p~WI~Dcik~g  135 (471)
                      .-+++.|++||+.+.+   +.++|+.+||.+..+++ +|||||+... .+.||..|+.+    |+|||+++||.+|++.|
T Consensus         5 ~~~~~~v~fSG~~~~~---~~~~i~~lGg~v~~~~~-~~THlV~~~~~RT~K~l~Aia~----g~~IVs~~Wl~~~~~~~   76 (220)
T 3l41_A            5 ASKRVYITFTGYDKKP---SIDNLKKLDMSITSNPS-KCTHLIAPRILRTSKFLCSIPY----GPCVVTMDWINSCLKTH   76 (220)
T ss_dssp             --CCEEEEECSCSSCC---CCGGGGGGTEEECSCTT-TCSEEECSSCCCBHHHHHHGGG----CCEEECHHHHHHHHHHT
T ss_pred             ccceEEEEEeccCCCC---CcchHhhcceeeccCch-hhhhhhhhhHhhhcceeecCCC----CCeEEEhHHHHhhhhhh
Confidence            4467899999999865   38999999999999885 6999999876 58999999996    79999999999999999


Q ss_pred             cCCCCCccccccccccCcchhhhhcccCCcCCCCCCCCcccchhhccccccccccccccCCCCCCCCcEEEEeCCCC-HH
Q 012081          136 VRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVS-EE  214 (471)
Q Consensus       136 ~~lde~~Y~l~~~~e~~~~~~~~~~L~~~s~~e~~~lp~~I~es~~s~s~E~ld~~~~~~~~~lF~G~~Iyl~~gfs-~~  214 (471)
                      +++||++|.+.+.....        ..+++      +...+..             .......+|+|+.|||.+.+. ..
T Consensus        77 ~~l~e~~y~l~d~~~e~--------~~~~~------l~~~~~r-------------ar~~~~~LF~G~~f~it~~~~~~p  129 (220)
T 3l41_A           77 EIVDEEPYLLNDPEKEL--------ELGCT------LESALKR-------------ARAQGPSLLEDYVVYLTSKTVAPE  129 (220)
T ss_dssp             SCCCSGGGBCCCHHHHH--------HHTSC------HHHHHHH-------------HHHHCSCTTTTSEEEEETTSSCGG
T ss_pred             hccccCccccCCcHHHh--------hcccc------HHHHHHH-------------HHhcCchhhhheeEEEeccccCCC
Confidence            99999999997532100        00000      0000000             000125799999999976661 33


Q ss_pred             HHHHHHHHHHhCCCEEEccc-cC-------CCCceEEEEcCchHH---HH---h--cCCCceechhHHHHHHhhCCcCcc
Q 012081          215 LRNKVFEAATNEGATLVNQW-FV-------GCGASYVVCEEDSVQ---KY---M--GHSNNLVTPVWVLKTAKEKHVQRL  278 (471)
Q Consensus       215 ~r~~L~~lI~~~GG~v~d~~-~~-------~~~vTHVVv~~~s~~---k~---l--~~~~~IVs~~WL~dcik~g~lqp~  278 (471)
                      .++.|+++|+.+||+++..- +.       ..+-.+||..+++..   ++   .  ...++||+.+||+++|-.+++--.
T Consensus       130 ~~~~l~~iI~~~GG~v~~~p~~~~~~~~~~~~~~~~vis~~~d~~~~~~f~~~~~~~~~~~i~~~e~ll~~il~q~l~~~  209 (220)
T 3l41_A          130 NVPAVISIVKSNGGVCSTLNVYNKRLARHLEDGNVVLITCNEDSHIWTNFLDNASQNKTIFLQNYDWLIKTVLRQEIDVN  209 (220)
T ss_dssp             GHHHHHHHHHHTTCEEEEECSCCHHHHHHHHHCCEEEEECGGGHHHHTTTHHHHTTCTTEEEEEHHHHHHHHHHTCCCTT
T ss_pred             CCceEEEEEecCCcEechhhHHHHHHHHhcccCCEEEEEeCCcchHHHHhhccccccceEEEechhHHHHHHHHHHcCcc
Confidence            47889999999999999810 00       011135554433322   11   1  134569999999999999888777


Q ss_pred             CCcChHHHh
Q 012081          279 VHISADLAR  287 (471)
Q Consensus       279 ~~ys~dl~r  287 (471)
                      .++++..+|
T Consensus       210 ~~~~~~~~~  218 (220)
T 3l41_A          210 DRIADEFAR  218 (220)
T ss_dssp             CCBCGGGSC
T ss_pred             hHHHHHHhh
Confidence            777766554

>2d8m_A DNA-repair protein XRCC1; parallel beta-sheet, DNA ligase III, poly(ADP-ribose) polymerase-1, DNA polymerase beta, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=1.3e-18  Score=153.77  Aligned_cols=91  Identities=25%  Similarity=0.438  Sum_probs=86.4

Q ss_pred             CCCCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHHHHHHHhcCCCCCceEecchHHHHHHH
Q 012081           54 ANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVR  133 (471)
Q Consensus        54 ~~~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~Dcik  133 (471)
                      ...+|.|++||+||+...+|..|+++|+.|||+|..++++.||||||....+.||+.|.++    +|+||+++||.||++
T Consensus        19 ~~~~f~g~~i~itG~~~~~r~~l~~~i~~~Gg~v~~~~s~~~ThLI~~~~~~~K~~~A~~~----gi~IV~~~Wl~d~~~   94 (129)
T 2d8m_A           19 LGKILQGVVVVLSGFQNPFRSELRDKALELGAKYRPDWTRDSTHLICAFANTPKYSQVLGL----GGRIVRKEWVLDCHR   94 (129)
T ss_dssp             HTTTSTTEEEEEESCCTTHHHHHHHHHHHTTEEEESSCCTTCCEEEESSSSCHHHHHHHHH----TCEEEETHHHHHHHH
T ss_pred             ccccCCCeEEEEeCCCcHHHHHHHHHHHHcCCEEeCCcCCCCeEEEecCCCChHHHHHHHC----CCcEecHHHHHHHHH
Confidence            4578999999999999989999999999999999999999999999999999999999997    899999999999999


Q ss_pred             cccCCCCCccccccc
Q 012081          134 RNVRLSESLYTVKSI  148 (471)
Q Consensus       134 ~g~~lde~~Y~l~~~  148 (471)
                      .++++||.+|.+...
T Consensus        95 ~~~~l~e~~Y~l~~~  109 (129)
T 2d8m_A           95 MRRRLPSQRYLMAGP  109 (129)
T ss_dssp             TTSCCCGGGGBCSSS
T ss_pred             hCCcCChHhcccCCC
Confidence            999999999998753

>4id3_A DNA repair protein REV1; BRCT domain, protein binding; HET: DNA; 1.97A {Saccharomyces cerevisiae S288C}

Probab=99.75  E-value=1.9e-18  Score=142.52  Aligned_cols=87  Identities=26%  Similarity=0.367  Sum_probs=77.5

Q ss_pred             CCCCCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccCC--CCceEEEEecCCCHHHHHHHhcCCCCCceEecchHHHH
Q 012081           53 PANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLH--PQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVD  130 (471)
Q Consensus        53 ~~~~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~--~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~D  130 (471)
                      +.+++|+|++||++|+....+..|+++|+.+||++..+++  +.+||||+....+.|+..+      .+++||+|+||.|
T Consensus         3 ~~~~~f~g~~~~i~g~~~~~~~~l~~~i~~~GG~~~~~~~~~~~~THlI~~~~~~~K~~~~------~~~~iV~~~Wi~d   76 (92)
T 4id3_A            3 QSSKIFKNCVIYINGYTKPGRLQLHEMIVLHGGKFLHYLSSKKTVTHIVASNLPLKKRIEF------ANYKVVSPDWIVD   76 (92)
T ss_dssp             ---CTTTTCEEEECSCCSSCHHHHHHHHHHTTCEEESSCCCTTTCCEEECSCCCHHHHHHT------TTSCEECTHHHHH
T ss_pred             ccccccCCEEEEEeCCCCcCHHHHHHHHHHCCCEEEEEecCCCceEEEEecCCCHHHHHHc------CCCCEEcccHHHH
Confidence            5778999999999998877899999999999999999999  7999999999888875443      3799999999999


Q ss_pred             HHHcccCCCCCcccc
Q 012081          131 SVRRNVRLSESLYTV  145 (471)
Q Consensus       131 cik~g~~lde~~Y~l  145 (471)
                      |+++|+++||++|.+
T Consensus        77 ci~~~~~l~e~~Y~l   91 (92)
T 4id3_A           77 SVKEARLLPWQNYSL   91 (92)
T ss_dssp             HHHHTSCCCGGGGBC
T ss_pred             HHHcCCcCChhhccc
Confidence            999999999999986

>2ebw_A DNA repair protein REV1; A/B/A 3 layers, parallel beta-sheet, DNA replication, translession synthesis, TLS, DNA polymerase zeta, PCNA; HET: DNA; NMR {Homo sapiens}

Probab=99.74  E-value=5.4e-18  Score=141.84  Aligned_cols=88  Identities=23%  Similarity=0.398  Sum_probs=80.8

Q ss_pred             CCCCCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccCC-CCceEEEEecCCCHHHHHHHhcCCCCCceEecchHHHHH
Q 012081           53 PANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLH-PQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDS  131 (471)
Q Consensus        53 ~~~~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~-~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~Dc  131 (471)
                      ...++|+|++||++|+...++..|+++|+.|||+|..+++ ..+||||+....+.|++.+.      +++||+|+||.||
T Consensus         8 ~~~~lF~g~~~~isg~~~~~~~~L~~~i~~~GG~~~~~~~~~~~THlI~~~~~~~k~~~~~------~~~iV~p~Wl~dc   81 (97)
T 2ebw_A            8 TSSTIFSGVAIYVNGYTDPSAEELRKLMMLHGGQYHVYYSRSKTTHIIATNLPNAKIKELK------GEKVIRPEWIVES   81 (97)
T ss_dssp             CCCCTTTTCEEEECSSCSSCHHHHHHHHHHTTCEECSSCCSSSCCEEECSCCCTTHHHHTS------SSCCBCTHHHHHH
T ss_pred             CCCCCCCCeEEEEeCCCcccHHHHHHHHHHcCCEEeeecCCCCCEEEEecCCChHHHHHhc------CCCEeChHHHHHH
Confidence            5678999999999999888899999999999999999887 58999999998889987753      6999999999999


Q ss_pred             HHcccCCCCCccccc
Q 012081          132 VRRNVRLSESLYTVK  146 (471)
Q Consensus       132 ik~g~~lde~~Y~l~  146 (471)
                      +++|+++|+++|.+.
T Consensus        82 i~~~~~l~~~~Y~l~   96 (97)
T 2ebw_A           82 IKAGRLLSYIPYQLY   96 (97)
T ss_dssp             HHHTSCCCSGGGBSC
T ss_pred             HHcCCccCchHcEec
Confidence            999999999999873

>3olc_X DNA topoisomerase 2-binding protein 1; BRCT domain, DNA repair, RAD9, DNA binding protein; HET: DNA; 2.40A {Homo sapiens} PDB: 2xnk_A* 2xnh_A*

Probab=99.66  E-value=1.6e-16  Score=159.16  Aligned_cols=93  Identities=39%  Similarity=0.617  Sum_probs=86.9

Q ss_pred             CCCCCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccCC-CCceEEEEecCCCHHHHHHHhcCCCCCceEecchHHHHH
Q 012081           53 PANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLH-PQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDS  131 (471)
Q Consensus        53 ~~~~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~-~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~Dc  131 (471)
                      ...++|+|++||+||+.+.+|..|+++|+.+||+|+.+++ +.|||||+....+.||+.|.+|    ||+||+++||.||
T Consensus       195 ~~~~~f~g~~i~~tG~~~~~r~~l~~li~~~GG~~~~~ls~~~~THLI~~~~~g~K~~~A~~~----gi~IV~~~Wl~ds  270 (298)
T 3olc_X          195 FKCPIFLGCIICVTGLCGLDRKEVQQLTVKHGGQYMGQLKMNECTHLIVQEPKGQKYECAKRW----NVHCVTTQWFFDS  270 (298)
T ss_dssp             GBCCTTTTCEEEECSCCHHHHHHHHHHHHHTTCEECSSCCTTTCCEEECSSSCSHHHHHHHHT----TCEEECHHHHHHH
T ss_pred             ccccccCCeEEEEeCCCCccHHHHHHHHHHcCCEEeceecCCCceEEEEeCCCchHHHHHHHC----CCeEEeHHHHHHH
Confidence            4568999999999999999999999999999999999999 7999999999999999999997    7999999999999


Q ss_pred             HHcccCCCCCcccccccc
Q 012081          132 VRRNVRLSESLYTVKSID  149 (471)
Q Consensus       132 ik~g~~lde~~Y~l~~~~  149 (471)
                      +++|+++||++|.+....
T Consensus       271 i~~g~~lde~~Y~l~~~~  288 (298)
T 3olc_X          271 IEKGFCQDESIYKTEPRP  288 (298)
T ss_dssp             HHHTSCCCGGGSBSCC--
T ss_pred             HHCCCCCCchhcCCCCCc
Confidence            999999999999997543

>3pa6_A Microcephalin; BRCT domain, cell cycle; HET: MSE; 1.50A {Homo sapiens} PDB: 3ktf_A* 2wt8_A*

Probab=99.66  E-value=3e-16  Score=134.50  Aligned_cols=93  Identities=20%  Similarity=0.319  Sum_probs=83.4

Q ss_pred             CCCCCCCcEEEEeCCCh----hhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHHHHHHHhcCCCCCceEecchHHH
Q 012081           54 ANAPFSGLVICVTGLSK----EARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFV  129 (471)
Q Consensus        54 ~~~iF~GlvI~vTG~~~----~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~  129 (471)
                      -.++|+|++++|..+..    ...+.+..++..+||++...+++.+||||+.+..+.||+.|.+|    +++||+++||.
T Consensus         4 ~~p~f~g~vvyvd~~~~~g~~~~s~~l~~~l~~~GA~v~~~l~~~vTHvV~~~~~~~~~~~A~~~----~i~iV~~~Wv~   79 (107)
T 3pa6_A            4 AAPILKDVVAYVEVWSSNGTENYSKTFTTQLVDMGAKVSKTFNKQVTHVIFKDGYQSTWDKAQKR----GVKLVSVLWVE   79 (107)
T ss_dssp             CCCTTTTCEEEEEEBCTTSCCBCHHHHHHHHHHTTCEECSSCCTTCCEEEEESCCHHHHHHHHHH----TCEEECHHHHH
T ss_pred             cccccCCEEEEEeccCCCChhhHHHHHHHHHHHcCCEEecccCCCccEEEEeCCCChHHHHHhcC----CCEEECHHHHH
Confidence            35799999999988763    23578999999999999999999999999999888999999998    79999999999


Q ss_pred             HHHHcccCCCCCccccccccc
Q 012081          130 DSVRRNVRLSESLYTVKSIDE  150 (471)
Q Consensus       130 Dcik~g~~lde~~Y~l~~~~e  150 (471)
                      ||+++|+++||.+|.+....+
T Consensus        80 ~C~~~~~~vdE~~Y~i~~~~~  100 (107)
T 3pa6_A           80 KCRTAGAHIDESLFPAANMNE  100 (107)
T ss_dssp             HHHHHTSCCCGGGSBCCCTTT
T ss_pred             HHHHhCccCChhcccCCCCcc
Confidence            999999999999999875543

>1wf6_A Similar to S.pombe -RAD4+/CUT5+product (A40727); BRCT, topoisomerase II binding protein, checkpoint; NMR {Homo sapiens} SCOP: c.15.1.5

Probab=99.60  E-value=6e-15  Score=130.68  Aligned_cols=92  Identities=18%  Similarity=0.314  Sum_probs=78.4

Q ss_pred             CCCCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHHHHHHHhcCCCCCceEecchHHHHHHH
Q 012081           54 ANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVR  133 (471)
Q Consensus        54 ~~~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~Dcik  133 (471)
                      +..+|+|++|+++|+....+..|+++|..+||++...++..+||||+.+.. .+++.+.+. ...+++||+++||.||++
T Consensus        37 ~~~lF~g~~i~i~G~~~~~~~~L~~~i~~~Gg~v~~~l~~~vTHvI~~~~~-~~~~~~~~~-~~~~~~iV~~~Wv~dsi~  114 (132)
T 1wf6_A           37 PEDLLDGCRIYLCGFSGRKLDKLRRLINSGGGVRFNQLNEDVTHVIVGDYD-DELKQFWNK-SAHRPHVVGAKWLLECFS  114 (132)
T ss_dssp             CTTTTTTCEEEEESCCSHHHHHHHHHHHHTTCEEESSCCSSCCEEEESSCC-SHHHHHHHH-SCCCCCEEEHHHHHHHHH
T ss_pred             cccccCCEEEEEECCChHHHHHHHHHHHHCCCEEeCcCCCCCeEEEECCch-HHHHHHHHh-hCCCCeEechHHHHHHHH
Confidence            458999999999999999999999999999999999999999999998653 344444321 013789999999999999


Q ss_pred             cccCCCCCcccccc
Q 012081          134 RNVRLSESLYTVKS  147 (471)
Q Consensus       134 ~g~~lde~~Y~l~~  147 (471)
                      +|+++||.+|.+..
T Consensus       115 ~~~ll~e~~Y~~~~  128 (132)
T 1wf6_A          115 KGYMLSEEPYIHSG  128 (132)
T ss_dssp             HSSCCCSGGGBCCC
T ss_pred             cCCcCCHhhccCCC
Confidence            99999999998764

>3pc6_A DNA repair protein XRCC1; BRCT domain, protein:protein interactions, DNA L III-alpha BRCT2 domain, DNA binding protein; HET: DNA; 1.90A {Mus musculus} SCOP: c.15.1.1 PDB: 3pc8_A* 3qvg_B* 1cdz_A

Probab=99.59  E-value=6.6e-15  Score=125.44  Aligned_cols=93  Identities=17%  Similarity=0.270  Sum_probs=85.5

Q ss_pred             CCCCCCCCcEEEEeCCC-hhhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHHHHHHHhcCCCCCceEecchHHHHH
Q 012081           53 PANAPFSGLVICVTGLS-KEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDS  131 (471)
Q Consensus        53 ~~~~iF~GlvI~vTG~~-~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~Dc  131 (471)
                      ..+.+|.|++|+++|.. ..+|..|+++|..+||.+...++.++||+|+....+.|++.|++.  ..++.+|+|+||.+|
T Consensus         3 ~Lpd~F~g~~f~l~~~~p~~~r~~l~ryiia~GG~v~~~~~~~vTHvIt~~~~d~~~~~a~~~--~p~~~~V~P~WI~~C   80 (104)
T 3pc6_A            3 ELPDFFEGKHFFLYGEFPGDERRRLIRYVTAFNGELEDYMNERVQFVITAQEWDPNFEEALME--NPSLAFVRPRWIYSC   80 (104)
T ss_dssp             CCCCTTTTCEEEEESCCSTTHHHHHHHHHHHTTCEECSSCCTTCCEEEESSCCCHHHHHHHTT--CTTCEEECHHHHHHH
T ss_pred             CcchhhCCeEEEEcCCCcHHHHHHHHHHHHHcCCEEEcccCCCceEEEeCCCCChhHHHHhhh--CCCCeEEccHHHHHH
Confidence            46789999999999988 589999999999999999999999999999999999999988764  368999999999999


Q ss_pred             HHcccCCCCCcccccc
Q 012081          132 VRRNVRLSESLYTVKS  147 (471)
Q Consensus       132 ik~g~~lde~~Y~l~~  147 (471)
                      +++++++++++|.+..
T Consensus        81 i~~~klvp~~~y~~~~   96 (104)
T 3pc6_A           81 NEKQKLLPHQLYGVVP   96 (104)
T ss_dssp             HHHTSCCCGGGGBCCC
T ss_pred             HhcCccCCcccceecc
Confidence            9999999999999863

>1wf6_A Similar to S.pombe -RAD4+/CUT5+product (A40727); BRCT, topoisomerase II binding protein, checkpoint; NMR {Homo sapiens} SCOP: c.15.1.5

Probab=99.58  E-value=7.1e-15  Score=130.21  Aligned_cols=96  Identities=16%  Similarity=0.281  Sum_probs=81.0

Q ss_pred             ccccccccccCCCCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcC--chHHHHh---cCCCc
Q 012081          185 TGKHERDSNRSMNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEE--DSVQKYM---GHSNN  259 (471)
Q Consensus       185 ~E~ld~~~~~~~~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~--~s~~k~l---~~~~~  259 (471)
                      ++++|......+..+|+||+||| .|+....+..|.++|+.+||++++.  ++..+||||+.+  .++++++   ..+++
T Consensus        26 ~~~~d~~~~~~~~~lF~g~~i~i-~G~~~~~~~~L~~~i~~~Gg~v~~~--l~~~vTHvI~~~~~~~~~~~~~~~~~~~~  102 (132)
T 1wf6_A           26 LENLDVSAFQAPEDLLDGCRIYL-CGFSGRKLDKLRRLINSGGGVRFNQ--LNEDVTHVIVGDYDDELKQFWNKSAHRPH  102 (132)
T ss_dssp             STTCCGGGCCCCTTTTTTCEEEE-ESCCSHHHHHHHHHHHHTTCEEESS--CCSSCCEEEESSCCSHHHHHHHHSCCCCC
T ss_pred             hhhcCcccccccccccCCEEEEE-ECCChHHHHHHHHHHHHCCCEEeCc--CCCCCeEEEECCchHHHHHHHHhhCCCCe
Confidence            34555555555678999999999 7999899999999999999999998  689999999976  3455555   35789


Q ss_pred             eechhHHHHHHhhCCcCccCCcCh
Q 012081          260 LVTPVWVLKTAKEKHVQRLVHISA  283 (471)
Q Consensus       260 IVs~~WL~dcik~g~lqp~~~ys~  283 (471)
                      ||+++||+||+++|+++|+..|.+
T Consensus       103 iV~~~Wv~dsi~~~~ll~e~~Y~~  126 (132)
T 1wf6_A          103 VVGAKWLLECFSKGYMLSEEPYIH  126 (132)
T ss_dssp             EEEHHHHHHHHHHSSCCCSGGGBC
T ss_pred             EechHHHHHHHHcCCcCCHhhccC
Confidence            999999999999999999999853

>3ef1_A RNA polymerase II subunit A C-terminal domain phosphatase; CTD, FCPH, BRCT, hydrolase, BEF3, acylphosphate analog, cobalt, magnesium; HET: BFD; 2.15A {Schizosaccharomyces pombe}

Probab=99.55  E-value=5.8e-15  Score=154.46  Aligned_cols=89  Identities=21%  Similarity=0.357  Sum_probs=83.1

Q ss_pred             CCCCCCCcEEEEeCCChh----hHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHHHHHHHhcCCCCCceEecchHHH
Q 012081           54 ANAPFSGLVICVTGLSKE----ARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFV  129 (471)
Q Consensus        54 ~~~iF~GlvI~vTG~~~~----er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~  129 (471)
                      ..++|.|++||+||+.+.    +|..|.++|+.+||++...+++.||||||....+.||+.|.+++   +|+||+++||.
T Consensus       349 k~~~L~G~~IvfSG~~p~~~~~~r~~l~~~~~~lGa~~~~~vs~~vTHLVa~~~~t~K~~~A~~~g---~IkIVs~~WL~  425 (442)
T 3ef1_A          349 KQKVLKGCRLLFSGVIPLGVDVLSSDIAKWAMSFGAEVVLDFSVPPTHLIAAKIRTEKVKKAVSMG---NIKVVKLNWLT  425 (442)
T ss_dssp             HHTTSTTCEEEEESSSCTTSCSTTSHHHHHHHTTTCEECSSSSSCCSEEEECSCCCHHHHHHHHHS---SSEEEEHHHHH
T ss_pred             hhcccCCcEEEEecccCCCCCccHHHHHHHHHHcCCEEeCCCCCCceEEEeCCCCCHHHHHHHhcC---CCEEEeHHHHH
Confidence            457999999999998752    67899999999999999999999999999999999999999983   79999999999


Q ss_pred             HHHHcccCCCCCcccc
Q 012081          130 DSVRRNVRLSESLYTV  145 (471)
Q Consensus       130 Dcik~g~~lde~~Y~l  145 (471)
                      +|++.|+++||.+|.+
T Consensus       426 dcl~~~krldE~~YlL  441 (442)
T 3ef1_A          426 ESLSQWKRLPESDYLL  441 (442)
T ss_dssp             HHHHHTSCCCGGGTBC
T ss_pred             HHHHcCCcCChhcccc
Confidence            9999999999999986

>4id3_A DNA repair protein REV1; BRCT domain, protein binding; HET: DNA; 1.97A {Saccharomyces cerevisiae S288C}

Probab=99.54  E-value=1.1e-14  Score=119.76  Aligned_cols=83  Identities=16%  Similarity=0.333  Sum_probs=71.6

Q ss_pred             CCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCC--CCceEEEEcCchHHHHh-cCCCceechhHHHHHHhhC
Q 012081          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVG--CGASYVVCEEDSVQKYM-GHSNNLVTPVWVLKTAKEK  273 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~--~~vTHVVv~~~s~~k~l-~~~~~IVs~~WL~dcik~g  273 (471)
                      ..+|+||+||| .|++...+..|+++|+.+||++...  +.  .++||||+......|+. ..+++||+++||+||+++|
T Consensus         5 ~~~f~g~~~~i-~g~~~~~~~~l~~~i~~~GG~~~~~--~~~~~~~THlI~~~~~~~K~~~~~~~~iV~~~Wi~dci~~~   81 (92)
T 4id3_A            5 SKIFKNCVIYI-NGYTKPGRLQLHEMIVLHGGKFLHY--LSSKKTVTHIVASNLPLKKRIEFANYKVVSPDWIVDSVKEA   81 (92)
T ss_dssp             -CTTTTCEEEE-CSCCSSCHHHHHHHHHHTTCEEESS--CCCTTTCCEEECSCCCHHHHHHTTTSCEECTHHHHHHHHHT
T ss_pred             ccccCCEEEEE-eCCCCcCHHHHHHHHHHCCCEEEEE--ecCCCceEEEEecCCCHHHHHHcCCCCEEcccHHHHHHHcC
Confidence            57999999999 8876667889999999999999998  56  79999999886554543 3689999999999999999


Q ss_pred             CcCccCCcC
Q 012081          274 HVQRLVHIS  282 (471)
Q Consensus       274 ~lqp~~~ys  282 (471)
                      +++|+..|.
T Consensus        82 ~~l~e~~Y~   90 (92)
T 4id3_A           82 RLLPWQNYS   90 (92)
T ss_dssp             SCCCGGGGB
T ss_pred             CcCChhhcc
Confidence            999998884

>3l46_A Protein ECT2; alternative splicing, guanine-nucleotide releasing factor, phosphoprotein, polymorphism, proto-oncogene, structural genomics; 1.48A {Homo sapiens}

Probab=99.53  E-value=1.2e-14  Score=125.54  Aligned_cols=84  Identities=13%  Similarity=0.139  Sum_probs=76.5

Q ss_pred             CCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCchHHHHh---cCCCceechhHHHHHHhhC
Q 012081          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKYM---GHSNNLVTPVWVLKTAKEK  273 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~s~~k~l---~~~~~IVs~~WL~dcik~g  273 (471)
                      ...|.||+||+ +||+..+++.|+++|+.+||++...  ++.+|||||+...+.+||.   .++++||+++||+||++.|
T Consensus        19 ~p~F~g~~Ic~-sGf~~~er~~l~~~i~~~GG~~~~~--l~~~cTHLV~~~~~~~K~~~A~~~~i~IVs~eWl~dsi~~g   95 (112)
T 3l46_A           19 VPPFQDCILSF-LGFSDEEKTNMEEMTEMQGGKYLPL--GDERCTHLVVEENIVKDLPFEPSKKLYVVKQEWFWGSIQMD   95 (112)
T ss_dssp             CCTTTTCEECE-ESCCHHHHHHHHHHHHHTTCEECCT--TCTTCSEEEECTTTBSSCSSCCCSSCEEEEHHHHHHHHHHT
T ss_pred             CCccCCeEEEE-eCCCHHHHHHHHHHHHHcCCEECcc--cCCCceEEEecCCchhhHHHHHHCCeeEecHHHHHHHHHcC
Confidence            46899999999 9999999999999999999999998  6999999999986655553   5899999999999999999


Q ss_pred             CcCccCCcCh
Q 012081          274 HVQRLVHISA  283 (471)
Q Consensus       274 ~lqp~~~ys~  283 (471)
                      ..+++..|..
T Consensus        96 ~~ldE~~Y~~  105 (112)
T 3l46_A           96 ARAGETMYLY  105 (112)
T ss_dssp             SCCCGGGSBC
T ss_pred             CccChhhcee
Confidence            9999998854

>3ef0_A RNA polymerase II subunit A C-terminal domain phosphatase; CTD, FCPH, BRCT, hydrolase, ALF4, transition state analog, cobalt, magnesium; 2.10A {Schizosaccharomyces pombe}

Probab=99.53  E-value=1.5e-14  Score=149.01  Aligned_cols=88  Identities=20%  Similarity=0.343  Sum_probs=82.3

Q ss_pred             CCCCCCcEEEEeCCCh----hhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHHHHHHHhcCCCCCceEecchHHHH
Q 012081           55 NAPFSGLVICVTGLSK----EARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVD  130 (471)
Q Consensus        55 ~~iF~GlvI~vTG~~~----~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~D  130 (471)
                      .++|+|++||+||+.+    .++..+.++|+.+||++..++++.||||||....+.||+.|.++   .+|+||+++||.+
T Consensus       280 ~~~L~G~~ivfSG~~~~~~~~~~~~l~~l~~~lGa~v~~~vs~~vTHLVa~~~~t~K~~~A~~~---~~I~IV~~~Wl~~  356 (372)
T 3ef0_A          280 QKVLKGCRLLFSGVIPLGVDVLSSDIAKWAMSFGAEVVLDFSVPPTHLIAAKIRTEKVKKAVSM---GNIKVVKLNWLTE  356 (372)
T ss_dssp             TTTSTTCEEEEESSSCTTSCTTTSHHHHHHHHTTCEEESSSSSCCSEEEECSCCCHHHHHHHHS---SSCCEEEHHHHHH
T ss_pred             hhhcCCcEEEEecccCCCcchhHHHHHHHHHHcCCEEeCcCCCCceEEEEcCCCchHHHHHHhc---CCCEEEcHHHHHH
Confidence            4799999999999874    35789999999999999999999999999999999999999997   3799999999999


Q ss_pred             HHHcccCCCCCcccc
Q 012081          131 SVRRNVRLSESLYTV  145 (471)
Q Consensus       131 cik~g~~lde~~Y~l  145 (471)
                      |++.|+++||.+|.+
T Consensus       357 c~~~~~~vdE~~Y~l  371 (372)
T 3ef0_A          357 SLSQWKRLPESDYLL  371 (372)
T ss_dssp             HHHTTSCCCGGGGBC
T ss_pred             HHHhCCcCChhhcee
Confidence            999999999999986

>2cou_A ECT2 protein; BRCT domain, RHO GTPase, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.51  E-value=1.2e-14  Score=124.80  Aligned_cols=85  Identities=12%  Similarity=0.159  Sum_probs=75.9

Q ss_pred             CCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCchHHHH---hcCCCceechhHHHHHHhhC
Q 012081          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKY---MGHSNNLVTPVWVLKTAKEK  273 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~s~~k~---l~~~~~IVs~~WL~dcik~g  273 (471)
                      ..+|.||+||+ +||+..+++.|.++|+.+||++...  +..++||||+......+|   ..++++||+++||+||++.|
T Consensus        10 ~~~F~g~~i~~-sg~~~~~r~~l~~~i~~~GG~~~~~--~~~~~THLV~~~~~~~K~~~a~~~~i~IV~~~Wl~dsi~~g   86 (109)
T 2cou_A           10 VPPFQDCILSF-LGFSDEEKHSMEEMTEMQGGSYLPV--GDERCTHLIVEENTVKDLPFEPSKKLFVVKQEWFWGSIQMD   86 (109)
T ss_dssp             CCTTTTCBEEE-ESSCHHHHHHHHHHHHHHTCBCCCT--TCTTCSEEEECTTTCSSCSSCCCTTSEEECHHHHHHHHHTT
T ss_pred             CCcCCCeEEEe-cCCCHHHHHHHHHHHHHcCCEEecc--cCCCccEEEEeCCccHHHHHHHHCCCeEecHHHHHHHHHcC
Confidence            56899999999 9999999999999999999999987  799999999987654444   35889999999999999999


Q ss_pred             CcCccCCcChH
Q 012081          274 HVQRLVHISAD  284 (471)
Q Consensus       274 ~lqp~~~ys~d  284 (471)
                      +++++..|...
T Consensus        87 ~~ldE~~Y~~~   97 (109)
T 2cou_A           87 ARAGETMYLYE   97 (109)
T ss_dssp             SCCCGGGTBCC
T ss_pred             CcCChhccCCC
Confidence            99999998543

>2ebw_A DNA repair protein REV1; A/B/A 3 layers, parallel beta-sheet, DNA replication, translession synthesis, TLS, DNA polymerase zeta, PCNA; HET: DNA; NMR {Homo sapiens}

Probab=99.47  E-value=6.8e-14  Score=116.80  Aligned_cols=84  Identities=11%  Similarity=0.255  Sum_probs=70.4

Q ss_pred             CCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCchHHHHh-cCCCceechhHHHHHHhhCCc
Q 012081          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKYM-GHSNNLVTPVWVLKTAKEKHV  275 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~s~~k~l-~~~~~IVs~~WL~dcik~g~l  275 (471)
                      ..+|+|+.||+ .|+....+..|+++|+.+||++...+ ....+||||+......|+. ..+++||+++||+||+++|++
T Consensus        10 ~~lF~g~~~~i-sg~~~~~~~~L~~~i~~~GG~~~~~~-~~~~~THlI~~~~~~~k~~~~~~~~iV~p~Wl~dci~~~~~   87 (97)
T 2ebw_A           10 STIFSGVAIYV-NGYTDPSAEELRKLMMLHGGQYHVYY-SRSKTTHIIATNLPNAKIKELKGEKVIRPEWIVESIKAGRL   87 (97)
T ss_dssp             CCTTTTCEEEE-CSSCSSCHHHHHHHHHHTTCEECSSC-CSSSCCEEECSCCCTTHHHHTSSSCCBCTHHHHHHHHHTSC
T ss_pred             CCCCCCeEEEE-eCCCcccHHHHHHHHHHcCCEEeeec-CCCCCEEEEecCCChHHHHHhcCCCEeChHHHHHHHHcCCc
Confidence            57999999999 88877778999999999999988762 2368999999885433332 138999999999999999999


Q ss_pred             CccCCcC
Q 012081          276 QRLVHIS  282 (471)
Q Consensus       276 qp~~~ys  282 (471)
                      +|+.+|.
T Consensus        88 l~~~~Y~   94 (97)
T 2ebw_A           88 LSYIPYQ   94 (97)
T ss_dssp             CCSGGGB
T ss_pred             cCchHcE
Confidence            9998874

>3pc6_A DNA repair protein XRCC1; BRCT domain, protein:protein interactions, DNA L III-alpha BRCT2 domain, DNA binding protein; HET: DNA; 1.90A {Mus musculus} SCOP: c.15.1.1 PDB: 3pc8_A* 3qvg_B* 1cdz_A

Probab=99.42  E-value=4.9e-13  Score=113.85  Aligned_cols=84  Identities=11%  Similarity=0.241  Sum_probs=70.7

Q ss_pred             CCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCc---hHHHHhc--CCCceechhHHHHHHh
Q 012081          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED---SVQKYMG--HSNNLVTPVWVLKTAK  271 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~---s~~k~l~--~~~~IVs~~WL~dcik  271 (471)
                      +.+|.|++|||+..++..+++.|.++|.++||.+.+.  ++.++||||+..+   +++..+.  .+..+|+|+||++|++
T Consensus         5 pd~F~g~~f~l~~~~p~~~r~~l~ryiia~GG~v~~~--~~~~vTHvIt~~~~d~~~~~a~~~~p~~~~V~P~WI~~Ci~   82 (104)
T 3pc6_A            5 PDFFEGKHFFLYGEFPGDERRRLIRYVTAFNGELEDY--MNERVQFVITAQEWDPNFEEALMENPSLAFVRPRWIYSCNE   82 (104)
T ss_dssp             CCTTTTCEEEEESCCSTTHHHHHHHHHHHTTCEECSS--CCTTCCEEEESSCCCHHHHHHHTTCTTCEEECHHHHHHHHH
T ss_pred             chhhCCeEEEEcCCCcHHHHHHHHHHHHHcCCEEEcc--cCCCceEEEeCCCCChhHHHHhhhCCCCeEEccHHHHHHHh
Confidence            5799999999954554678999999999999998887  6899999999874   4444443  5688999999999999


Q ss_pred             hCCcCccCCcC
Q 012081          272 EKHVQRLVHIS  282 (471)
Q Consensus       272 ~g~lqp~~~ys  282 (471)
                      +++++|+..|-
T Consensus        83 ~~klvp~~~y~   93 (104)
T 3pc6_A           83 KQKLLPHQLYG   93 (104)
T ss_dssp             HTSCCCGGGGB
T ss_pred             cCccCCcccce
Confidence            99999998773

>2d8m_A DNA-repair protein XRCC1; parallel beta-sheet, DNA ligase III, poly(ADP-ribose) polymerase-1, DNA polymerase beta, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.32  E-value=2.3e-12  Score=113.60  Aligned_cols=85  Identities=15%  Similarity=0.252  Sum_probs=74.4

Q ss_pred             CCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCch---HHHHhcCCCceechhHHHHHHhhC
Q 012081          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDS---VQKYMGHSNNLVTPVWVLKTAKEK  273 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~s---~~k~l~~~~~IVs~~WL~dcik~g  273 (471)
                      ..+|.|++|+| +|+....|..|.++|..+||++...  +..++||||+....   ++++...+++||+++||+||++.+
T Consensus        20 ~~~f~g~~i~i-tG~~~~~r~~l~~~i~~~Gg~v~~~--~s~~~ThLI~~~~~~~K~~~A~~~gi~IV~~~Wl~d~~~~~   96 (129)
T 2d8m_A           20 GKILQGVVVVL-SGFQNPFRSELRDKALELGAKYRPD--WTRDSTHLICAFANTPKYSQVLGLGGRIVRKEWVLDCHRMR   96 (129)
T ss_dssp             TTTSTTEEEEE-ESCCTTHHHHHHHHHHHTTEEEESS--CCTTCCEEEESSSSCHHHHHHHHHTCEEEETHHHHHHHHTT
T ss_pred             cccCCCeEEEE-eCCCcHHHHHHHHHHHHcCCEEeCC--cCCCCeEEEecCCCChHHHHHHHCCCcEecHHHHHHHHHhC
Confidence            46899999999 8888778999999999999999998  68899999998753   344446799999999999999999


Q ss_pred             CcCccCCcChH
Q 012081          274 HVQRLVHISAD  284 (471)
Q Consensus       274 ~lqp~~~ys~d  284 (471)
                      +++++..|...
T Consensus        97 ~~l~e~~Y~l~  107 (129)
T 2d8m_A           97 RRLPSQRYLMA  107 (129)
T ss_dssp             SCCCGGGGBCS
T ss_pred             CcCChHhcccC
Confidence            99999988543

>3pa6_A Microcephalin; BRCT domain, cell cycle; HET: MSE; 1.50A {Homo sapiens} PDB: 3ktf_A* 2wt8_A*

Probab=99.27  E-value=3.4e-12  Score=109.29  Aligned_cols=93  Identities=14%  Similarity=0.129  Sum_probs=72.5

Q ss_pred             CCCCCCcEEEEeCCC--CH-HHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCch---HHHHhcCCCceechhHHHHHH
Q 012081          197 NSTLSGCSMYVDSDV--SE-ELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDS---VQKYMGHSNNLVTPVWVLKTA  270 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gf--s~-~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~s---~~k~l~~~~~IVs~~WL~dci  270 (471)
                      ..+|+|+++|++..-  .. ...+.+..+++.+||++++.  +..++||||+.+..   .++....+++||++.||.+|+
T Consensus         5 ~p~f~g~vvyvd~~~~~g~~~~s~~l~~~l~~~GA~v~~~--l~~~vTHvV~~~~~~~~~~~A~~~~i~iV~~~Wv~~C~   82 (107)
T 3pa6_A            5 APILKDVVAYVEVWSSNGTENYSKTFTTQLVDMGAKVSKT--FNKQVTHVIFKDGYQSTWDKAQKRGVKLVSVLWVEKCR   82 (107)
T ss_dssp             CCTTTTCEEEEEEBCTTSCCBCHHHHHHHHHHTTCEECSS--CCTTCCEEEEESCCHHHHHHHHHHTCEEECHHHHHHHH
T ss_pred             ccccCCEEEEEeccCCCChhhHHHHHHHHHHHcCCEEecc--cCCCccEEEEeCCCChHHHHHhcCCCEEECHHHHHHHH
Confidence            458999999995321  11 23467999999999999999  68999999997743   444445789999999999999


Q ss_pred             hhCCcCccCCcChHH-Hhhhhh
Q 012081          271 KEKHVQRLVHISADL-ARQVGM  291 (471)
Q Consensus       271 k~g~lqp~~~ys~dl-~r~~~~  291 (471)
                      ++|+++++..|.... ..++|.
T Consensus        83 ~~~~~vdE~~Y~i~~~~~~~~~  104 (107)
T 3pa6_A           83 TAGAHIDESLFPAANMNEHLSS  104 (107)
T ss_dssp             HHTSCCCGGGSBCCCTTTTC--
T ss_pred             HhCccCChhcccCCCCcccccc
Confidence            999999999997653 355544

>2ep8_A Pescadillo homolog 1; A/B/A 3 layers, nucleolus, ribosome biogenesis, DNA damage, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.24  E-value=8.7e-12  Score=105.44  Aligned_cols=81  Identities=11%  Similarity=0.211  Sum_probs=64.9

Q ss_pred             CCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccc---------cCCCCceEEEEcCchHHHHhcCCCceechhHHH
Q 012081          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQW---------FVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVL  267 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~---------~~~~~vTHVVv~~~s~~k~l~~~~~IVs~~WL~  267 (471)
                      ..+|+|+.|||....+   +..|+.+|+++||.++...         ..+..+||+|++.+..++ ...+..+|+|+||+
T Consensus        10 ~~LF~g~~F~i~~e~p---~~~le~~I~~~GG~v~~~~~~~~g~~~~~~~~~iTh~I~drp~~~~-~~~~r~~VqPqWV~   85 (100)
T 2ep8_A           10 KKLFEGLKFFLNREVP---REALAFIIRSFGGEVSWDKSLCIGATYDVTDSRITHQIVDRPGQQT-SVIGRCYVQPQWVF   85 (100)
T ss_dssp             CCTTSSCEEECCSSSC---HHHHHHHHHHTTCEEECCTTTSSCCCSCTTCTTCCEEECSCTTTSC-CBTTBEEECTHHHH
T ss_pred             HHHcCCcEEEEecCCC---HHHHHHHHHHcCCEEEeccccccCcccccCCCceEEEEecccchhh-hcCCCeEEcchHHH
Confidence            6799999999955444   5778889999999998641         125789999998865433 22445899999999


Q ss_pred             HHHhhCCcCccCCc
Q 012081          268 KTAKEKHVQRLVHI  281 (471)
Q Consensus       268 dcik~g~lqp~~~y  281 (471)
                      ||+++++++|+.+|
T Consensus        86 Dcin~~~lLp~~~Y   99 (100)
T 2ep8_A           86 DSVNARLLLPVAEY   99 (100)
T ss_dssp             HHHHHTSCCCTTTC
T ss_pred             HHHhcCCcCChhhc
Confidence            99999999999887

>1l7b_A DNA ligase; BRCT, autostructure, structural genomics, NESG, PSI, protein structure initiative, northeast structural genomics consortium; HET: DNA; NMR {Thermus thermophilus} SCOP: c.15.1.2

Probab=99.24  E-value=1e-11  Score=103.45  Aligned_cols=77  Identities=23%  Similarity=0.301  Sum_probs=71.7

Q ss_pred             CCCCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHHHHHHHhcCCCCCceEecchHHHHHHH
Q 012081           54 ANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVR  133 (471)
Q Consensus        54 ~~~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~Dcik  133 (471)
                      ...+|.|++||+||.....|.+++++|+.+||++...+++.++|||++...|.|+++|.++    +|+||+.+|+.+++.
T Consensus         4 ~~~~l~G~~~v~TG~l~~~R~e~~~~i~~~Gg~v~~sVskkt~~LV~g~~~gsK~~kA~~l----gI~Ii~E~~f~~~l~   79 (92)
T 1l7b_A            4 GGEALKGLTFVITGELSRPREEVKALLRRLGAKVTDSVSRKTSYLVVGENPGSKLEKARAL----GVPTLTEEELYRLLE   79 (92)
T ss_dssp             CCCSSTTCEEECSTTTTSCHHHHHHHHHHTTCEEESCCSSSCCCBEECSSSSTTHHHHHCS----SSCCEEHHHHHHHHH
T ss_pred             CCCCcCCcEEEEecCCCCCHHHHHHHHHHcCCEEeCcccCCeeEEEeCCCCChHHHHHHHc----CCcEEeHHHHHHHHH
Confidence            4567999999999977669999999999999999999999999999999999999999997    899999999999986


Q ss_pred             c
Q 012081          134 R  134 (471)
Q Consensus       134 ~  134 (471)
                      .
T Consensus        80 ~   80 (92)
T 1l7b_A           80 A   80 (92)
T ss_dssp             H
T ss_pred             h
Confidence            3

>3pc7_A DNA ligase 3; DNA repair, BRCT domain, protein:protein interactions, XRCC1 domain, DNA binding protein; HET: DNA MSE; 1.65A {Homo sapiens} SCOP: c.15.1.2 PDB: 3pc8_C* 1imo_A* 1in1_A* 3qvg_A*

Probab=99.22  E-value=1.4e-11  Score=101.65  Aligned_cols=74  Identities=14%  Similarity=0.263  Sum_probs=62.4

Q ss_pred             CCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCchHHHHhcCCCceechhHHHHHHhhCCcC
Q 012081          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQ  276 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~s~~k~l~~~~~IVs~~WL~dcik~g~lq  276 (471)
                      +.+|.|++|||..+++..  +.|+++|.++||.++... ...++||||+..+     ...+.++|+|+||+||+++|+++
T Consensus        14 pdiFsg~~~~l~~~v~~~--~~l~RyiiAfgG~v~~~~-~~~~vTHvI~~~~-----~~~~~~~V~p~WI~dcI~k~~Ll   85 (88)
T 3pc7_A           14 LDIFTGVRLYLPPSTPDF--SRLRRYFVAFDGDLVQEF-DMTSATHVLGSRD-----KNPAAQQVSPEWIWACIRKRRLV   85 (88)
T ss_dssp             CCCSTTCEECCCTTSTTH--HHHHHHHHHTTCEECCGG-GGGGCSEEESCCT-----TCTTSEEECHHHHHHHHHHTSCC
T ss_pred             ChhhcCeEEEccCCcCch--hhheeeeeecCCEEeccc-CCCcCeEEecCCC-----cCCCCcEEchHHHHHHHhCCccc
Confidence            679999999997677654  789999999999998862 3459999998764     24577899999999999999999


Q ss_pred             cc
Q 012081          277 RL  278 (471)
Q Consensus       277 p~  278 (471)
                      |.
T Consensus        86 ~~   87 (88)
T 3pc7_A           86 AP   87 (88)
T ss_dssp             SC
T ss_pred             CC
Confidence            74

>2coe_A Deoxynucleotidyltransferase, terminal variant; BRCT domain, DNA polymerase, teminal deoxynucleotidyltransferase, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.22  E-value=5.3e-11  Score=103.67  Aligned_cols=84  Identities=12%  Similarity=0.260  Sum_probs=72.0

Q ss_pred             CCCCCCCcEEEEe-CCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCc---hHHHHhc-------CCCceechh
Q 012081          196 MNSTLSGCSMYVD-SDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED---SVQKYMG-------HSNNLVTPV  264 (471)
Q Consensus       196 ~~~lF~G~~Iyl~-~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~---s~~k~l~-------~~~~IVs~~  264 (471)
                      +..+|+|++|||. .++....++.+.++++++||+|++.  +++.+||||+++.   ++.+++.       .+.++|+..
T Consensus        17 p~~~F~g~~iy~v~~~~g~~R~~~l~~l~r~~G~~V~~~--ls~~VTHVVve~~~~~e~~~~l~~~~l~~~~~~~lv~i~   94 (120)
T 2coe_A           17 QDIKFQDLVVFILEKKMGTTRRALLMELARRKGFRVENE--LSDSVTHIVAENNSGSDVLEWLQAQKVQVSSQPELLDVS   94 (120)
T ss_dssp             SCCSCTTCEEEEECTTTCHHHHHHHHHHHHHHTCEECSS--CCTTCCEEEESSCCHHHHHHHHHHCCCCCSSCCEEEEHH
T ss_pred             cccccCCeEEEEeecccchHHHHHHHHHHHHcCCEEeec--cCCCcCEEEecCCCHHHHHHHHhccccccccccEEeecH
Confidence            4789999999994 4678889999999999999999999  6999999999763   3555542       368999999


Q ss_pred             HHHHHHhhCCcCccCCc
Q 012081          265 WVLKTAKEKHVQRLVHI  281 (471)
Q Consensus       265 WL~dcik~g~lqp~~~y  281 (471)
                      ||.+|+++|.++++..+
T Consensus        95 Wl~esmk~g~lv~ee~~  111 (120)
T 2coe_A           95 WLIECIGAGKPVEMTGK  111 (120)
T ss_dssp             HHHHHHHTTSCCCCSSS
T ss_pred             HHHHHHHcCCccCcccc
Confidence            99999999999998654

>2k6g_A Replication factor C subunit 1; protein, BRCT, DNA binding, activator, alternative splicing, ATP-binding, DNA replication, DNA- binding; NMR {Homo sapiens} PDB: 2k7f_A

Probab=99.16  E-value=1.1e-10  Score=100.22  Aligned_cols=79  Identities=23%  Similarity=0.336  Sum_probs=72.3

Q ss_pred             CCCCCCCCcEEEEeCCCh-hhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCC-HHHHHHHhcCCCCCceEecchHHHH
Q 012081           53 PANAPFSGLVICVTGLSK-EARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGG-RKFEHALKHGSRNGLYIVTLGWFVD  130 (471)
Q Consensus        53 ~~~~iF~GlvI~vTG~~~-~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g-~Ky~~A~k~~~~~gi~IV~p~WI~D  130 (471)
                      ....+|.|.+||+||... -.|.+++++|+.+||++...+++.++|||++...+ .|++.|.++    ||+||+.+||.+
T Consensus        28 ~~~~~l~G~~~v~TG~l~~~~R~e~~~~i~~~Gg~v~~sVSkkTd~LV~G~~~g~sK~~kA~~l----gI~Ii~E~~f~~  103 (109)
T 2k6g_A           28 GAENCLEGLIFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGQSKSDKAAAL----GTKIIDEDGLLN  103 (109)
T ss_dssp             CCTTTTTTCEEEEESBCSSCCHHHHHHHHHHTTCEEESSCCTTCCEEEECBCCCHHHHHHHHHH----TCEEECHHHHHH
T ss_pred             CCCCCCCCCEEEEeeeCCCCCHHHHHHHHHHcCCEeeCcccCCceEEEECCCCChHHHHHHHHc----CCeEEeHHHHHH
Confidence            345689999999999775 58999999999999999999999999999999888 899999997    899999999999


Q ss_pred             HHHcc
Q 012081          131 SVRRN  135 (471)
Q Consensus       131 cik~g  135 (471)
                      .+..+
T Consensus       104 ll~~~  108 (109)
T 2k6g_A          104 LIRNL  108 (109)
T ss_dssp             HHHHT
T ss_pred             HHHhC
Confidence            98764

>2ep8_A Pescadillo homolog 1; A/B/A 3 layers, nucleolus, ribosome biogenesis, DNA damage, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.14  E-value=8.4e-11  Score=99.38  Aligned_cols=82  Identities=24%  Similarity=0.310  Sum_probs=67.0

Q ss_pred             CCCCCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEccc-----------CCCCceEEEEecCCCHHHHHHHhcCCCCCce
Q 012081           53 PANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPD-----------LHPQCTHLVVQSFGGRKFEHALKHGSRNGLY  121 (471)
Q Consensus        53 ~~~~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~-----------l~~~~THLV~~~~~g~Ky~~A~k~~~~~gi~  121 (471)
                      ....+|+|++|++.+-  -.|+.|+.+|..+||++..+           .+..+||+|+......+     +   ..+..
T Consensus         8 ~~~~LF~g~~F~i~~e--~p~~~le~~I~~~GG~v~~~~~~~~g~~~~~~~~~iTh~I~drp~~~~-----~---~~~r~   77 (100)
T 2ep8_A            8 KHKKLFEGLKFFLNRE--VPREALAFIIRSFGGEVSWDKSLCIGATYDVTDSRITHQIVDRPGQQT-----S---VIGRC   77 (100)
T ss_dssp             CSCCTTSSCEEECCSS--SCHHHHHHHHHHTTCEEECCTTTSSCCCSCTTCTTCCEEECSCTTTSC-----C---BTTBE
T ss_pred             chHHHcCCcEEEEecC--CCHHHHHHHHHHcCCEEEeccccccCcccccCCCceEEEEecccchhh-----h---cCCCe
Confidence            3568999999999763  35789999999999999875           24689999998764322     1   13679


Q ss_pred             EecchHHHHHHHcccCCCCCccc
Q 012081          122 IVTLGWFVDSVRRNVRLSESLYT  144 (471)
Q Consensus       122 IV~p~WI~Dcik~g~~lde~~Y~  144 (471)
                      +|.|+||.||+.++++||+++|.
T Consensus        78 ~VqPqWV~Dcin~~~lLp~~~Y~  100 (100)
T 2ep8_A           78 YVQPQWVFDSVNARLLLPVAEYF  100 (100)
T ss_dssp             EECTHHHHHHHHHTSCCCTTTCC
T ss_pred             EEcchHHHHHHhcCCcCChhhcC
Confidence            99999999999999999999984

>2jw5_A DNA polymerase lambda; BRCT domain, family X polymerase, nonhomologous END joining (NHEJ), DNA damage, DNA repair, DNA replication, DNA synthesis; HET: DNA; NMR {Homo sapiens}

Probab=99.12  E-value=1.9e-11  Score=104.46  Aligned_cols=85  Identities=16%  Similarity=0.246  Sum_probs=68.0

Q ss_pred             CCCCCCCcEEEEeC-CCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcC----chHHHHh-----cCCCceechhH
Q 012081          196 MNSTLSGCSMYVDS-DVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEE----DSVQKYM-----GHSNNLVTPVW  265 (471)
Q Consensus       196 ~~~lF~G~~Iyl~~-gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~----~s~~k~l-----~~~~~IVs~~W  265 (471)
                      ++.+|+||+|||.+ +.....++.....++.+||++++.  +++++||||+.+    .+..+++     ..+++||+++|
T Consensus         8 ~~~~F~g~~v~~~p~~~~~~r~~i~~~~a~~~Ga~v~~~--~~~~vTHVVvd~~~s~~~~l~~l~~~~l~~~~~iV~~~W   85 (106)
T 2jw5_A            8 AEEWLSSLRAHVVRTGIGRARAELFEKQIVQHGGQLCPA--QGPGVTHIVVDEGMDYERALRLLRLPQLPPGAQLVKSAW   85 (106)
T ss_dssp             GGGCGGGSCCCBCTTTCCSSSTTHHHHHHHHTTCCCCST--TCTTCCEEEECSSSCHHHHHHHTTCSSCCSSCEEEEHHH
T ss_pred             CcCEeCCeEEEEEecCCchHHHHHHHHHHHHcCCEEeec--cCCCccEEEEcCCCCHHHHHHHHhhcccCCCcEEecCch
Confidence            36799999999943 444455677778999999999999  588999999985    2334444     24568999999


Q ss_pred             HHHHHhhCCcCccCCcC
Q 012081          266 VLKTAKEKHVQRLVHIS  282 (471)
Q Consensus       266 L~dcik~g~lqp~~~ys  282 (471)
                      +.||+++++++++..|.
T Consensus        86 v~dci~~~~llde~~y~  102 (106)
T 2jw5_A           86 LSLCLQERRLVDVAGFS  102 (106)
T ss_dssp             HHHHHHTCSCCCGGGTB
T ss_pred             HHHHHhcCcccCccccc
Confidence            99999999999998873

>2ebu_A Replication factor C subunit 1; A/B/A 3 layers, parallel beta-sheet, DNA replication, clamp loader, RFC1, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.09  E-value=4.4e-10  Score=96.81  Aligned_cols=78  Identities=23%  Similarity=0.350  Sum_probs=71.7

Q ss_pred             CCCCCCCCcEEEEeCCCh-hhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCC-HHHHHHHhcCCCCCceEecchHHHH
Q 012081           53 PANAPFSGLVICVTGLSK-EARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGG-RKFEHALKHGSRNGLYIVTLGWFVD  130 (471)
Q Consensus        53 ~~~~iF~GlvI~vTG~~~-~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g-~Ky~~A~k~~~~~gi~IV~p~WI~D  130 (471)
                      ....+|.|++||+||... -.|.+++++|+.+||++...+++.++|||+....+ .|+++|.++    +|+||+.+||.+
T Consensus        18 ~~~~~l~G~~~v~TG~l~~~~R~e~~~~i~~~Ggkv~~sVSkkTd~LV~G~~~g~sKl~KA~~l----gI~IisE~~f~~   93 (112)
T 2ebu_A           18 GAENCLEGLIFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGQSKSDKAAAL----GTKIIDEDGLLN   93 (112)
T ss_dssp             CCSSSSTTCEEEECSCCSSSCHHHHHHHHHHTTCEECSSCCSSCCEEEECSSCCSHHHHHHHHH----TCEEEEHHHHHH
T ss_pred             CCCCCcCCCEEEEeeeCCCCCHHHHHHHHHHcCCEEeccccCCeeEEEecCCCChHHHHHHHHc----CCeEEeHHHHHH
Confidence            344689999999999775 58999999999999999999999999999999888 999999997    899999999999


Q ss_pred             HHHc
Q 012081          131 SVRR  134 (471)
Q Consensus       131 cik~  134 (471)
                      .+..
T Consensus        94 ll~~   97 (112)
T 2ebu_A           94 LIRT   97 (112)
T ss_dssp             HHHH
T ss_pred             HHhh
Confidence            9974

>3ii6_X DNA ligase 4; XRCC4, NHEJ, DNA repair, BRCT, alternative splicing, coiled coil, DNA damage, DNA recombination, isopeptide bond, nucleus; HET: DNA; 2.40A {Homo sapiens} PDB: 2e2w_A*

Probab=99.04  E-value=6.8e-10  Score=109.08  Aligned_cols=92  Identities=12%  Similarity=0.122  Sum_probs=71.3

Q ss_pred             CCCCCCCcEEEEeCCCh----------hhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCC-HHHHHHHhcCCCCCceE
Q 012081           54 ANAPFSGLVICVTGLSK----------EARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGG-RKFEHALKHGSRNGLYI  122 (471)
Q Consensus        54 ~~~iF~GlvI~vTG~~~----------~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g-~Ky~~A~k~~~~~gi~I  122 (471)
                      +..+|+|++|.+.++..          .....++.+|..+||++...++..+||+|+..... .+...+++.....+++|
T Consensus       161 ~~~lF~~~~vy~~~~~~~~~~~~~i~~~~l~~~~~~i~~~GG~v~~~l~~~vTHVVv~~~~~r~~~~~~~~~~~~~~~~i  240 (263)
T 3ii6_X          161 PLSMFRRHTVYLDSYAVINDLSTKNEGTRLAIKALELRFHGAKVVSCLAEGVSHVIIGEDHSRVADFKAFRRTFKRKFKI  240 (263)
T ss_dssp             GGGTTTTCEEEECCBSSTTCGGGBCCSSHHHHHHHHHHHTTCEEESSCCTTCCEEEECSCCTTHHHHHHHHHTCSSCCEE
T ss_pred             cchhhCCeEEEEecccccCCcccccchhHHHHHHHHHHccCCEEecCCCCCceEEEECCCCccHHHHHHHHhhcCCCCEE
Confidence            45799999999977531          13344689999999999999999999999987543 22223333223357899


Q ss_pred             ecchHHHHHHHcccCCCCCcccc
Q 012081          123 VTLGWFVDSVRRNVRLSESLYTV  145 (471)
Q Consensus       123 V~p~WI~Dcik~g~~lde~~Y~l  145 (471)
                      |+++||.||++.|+++||++|.+
T Consensus       241 V~~~Wv~dci~~~~~l~E~~Y~i  263 (263)
T 3ii6_X          241 LKESWVTDSIDKCELQEENQYLI  263 (263)
T ss_dssp             EETHHHHHHHHTTSCCCGGGTBC
T ss_pred             eChHHHHHHHHcCCcCCHhhCCC
Confidence            99999999999999999999964

>2cok_A Poly [ADP-ribose] polymerase-1; BRCT domain, DNA repair, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2le0_A

Probab=99.01  E-value=7.6e-10  Score=95.48  Aligned_cols=84  Identities=15%  Similarity=0.233  Sum_probs=71.2

Q ss_pred             CCCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecC---CCHHHHHHHhcCCCCCceEecchHHH--
Q 012081           55 NAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSF---GGRKFEHALKHGSRNGLYIVTLGWFV--  129 (471)
Q Consensus        55 ~~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~---~g~Ky~~A~k~~~~~gi~IV~p~WI~--  129 (471)
                      ..+|.|++|++||-....|.+++++|+.+||++...+++.++|||+...   .+.|+++|.+.    ||+||+.+||.  
T Consensus         8 ~~~l~G~~~ViTG~l~~~R~e~k~~ie~~Ggkv~~sVskkT~~lV~g~~~e~~gsKl~kA~~l----gI~IvsE~~l~~~   83 (113)
T 2cok_A            8 DKPLSNMKILTLGKLSRNKDEVKAMIEKLGGKLTGTANKASLCISTKKEVEKMNKKMEEVKEA----NIRVVSEDFLQDV   83 (113)
T ss_dssp             CCSSSSCEEEECSCCSSCHHHHHHHHHHTTCEEESCSTTCSEEECCHHHHHHCCHHHHHHHHT----TCCEECTHHHHHH
T ss_pred             CCCcCCCEEEEEecCCCCHHHHHHHHHHCCCEEcCccccCccEEEECCCCCCCChHHHHHHHC----CCcEEeHHHHHHH
Confidence            5679999999999776699999999999999999999999999999943   68999999996    89999999955  


Q ss_pred             --------HHHHcccCCCCCc
Q 012081          130 --------DSVRRNVRLSESL  142 (471)
Q Consensus       130 --------Dcik~g~~lde~~  142 (471)
                              +|++.....|+..
T Consensus        84 ~~~~~~~~~~i~k~~i~~w~~  104 (113)
T 2cok_A           84 SASTKSLQELFLAHILSSWGA  104 (113)
T ss_dssp             HSCCSCHHHHHHHTBCSSCCC
T ss_pred             HhhchhHHHHHHHhcCCCCCC
Confidence                    4555555555443

>2jw5_A DNA polymerase lambda; BRCT domain, family X polymerase, nonhomologous END joining (NHEJ), DNA damage, DNA repair, DNA replication, DNA synthesis; HET: DNA; NMR {Homo sapiens}

Probab=98.97  E-value=4.5e-10  Score=95.82  Aligned_cols=91  Identities=22%  Similarity=0.314  Sum_probs=71.1

Q ss_pred             CCCCCCCcEEEEe--CCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHHHHHHHhc----CCCCCceEecchH
Q 012081           54 ANAPFSGLVICVT--GLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKH----GSRNGLYIVTLGW  127 (471)
Q Consensus        54 ~~~iF~GlvI~vT--G~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~Ky~~A~k~----~~~~gi~IV~p~W  127 (471)
                      +..+|+|++|.+-  +.....++...+.+..+||++...++..+||+|+.+..+  ++..+++    .+..++.||+++|
T Consensus         8 ~~~~F~g~~v~~~p~~~~~~r~~i~~~~a~~~Ga~v~~~~~~~vTHVVvd~~~s--~~~~l~~l~~~~l~~~~~iV~~~W   85 (106)
T 2jw5_A            8 AEEWLSSLRAHVVRTGIGRARAELFEKQIVQHGGQLCPAQGPGVTHIVVDEGMD--YERALRLLRLPQLPPGAQLVKSAW   85 (106)
T ss_dssp             GGGCGGGSCCCBCTTTCCSSSTTHHHHHHHHTTCCCCSTTCTTCCEEEECSSSC--HHHHHHHTTCSSCCSSCEEEEHHH
T ss_pred             CcCEeCCeEEEEEecCCchHHHHHHHHHHHHcCCEEeeccCCCccEEEEcCCCC--HHHHHHHHhhcccCCCcEEecCch
Confidence            5689999999884  433455666677899999999999999999999985433  3333332    1234678999999


Q ss_pred             HHHHHHcccCCCCCccccc
Q 012081          128 FVDSVRRNVRLSESLYTVK  146 (471)
Q Consensus       128 I~Dcik~g~~lde~~Y~l~  146 (471)
                      +.||++.|+++||+.|.+.
T Consensus        86 v~dci~~~~llde~~y~~~  104 (106)
T 2jw5_A           86 LSLCLQERRLVDVAGFSIF  104 (106)
T ss_dssp             HHHHHHTCSCCCGGGTBCS
T ss_pred             HHHHHhcCcccCccccccc
Confidence            9999999999999999764

>2nte_A BARD-1, BRCA1-associated ring domain protein 1; BRCT, ring finger, zinc-binding protein, ubiquitin LI antitumor protein; 1.90A {Homo sapiens} PDB: 3fa2_A 2r1z_A

Probab=98.96  E-value=1.7e-09  Score=102.15  Aligned_cols=132  Identities=14%  Similarity=0.067  Sum_probs=90.7

Q ss_pred             CcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcC---chHHHHh---cCCCceechhHHHHHHhhCCc
Q 012081          202 GCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEE---DSVQKYM---GHSNNLVTPVWVLKTAKEKHV  275 (471)
Q Consensus       202 G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~---~s~~k~l---~~~~~IVs~~WL~dcik~g~l  275 (471)
                      |+.|++ +|++..+++.|.++++.+||.+++.  .+.++||||+..   ....||+   ..++.||+++||.+|+++|++
T Consensus         2 ~~vi~~-sg~~~~~~~~l~~~~~~~G~~~~~~--~~~~~THlV~~~~~~~rt~K~l~a~~~g~~IV~~~Wl~~c~~~~~~   78 (210)
T 2nte_A            2 PLVLIG-SGLSSEQQKMLSELAVILKAKKYTE--FDSTVTHVVVPGDAVQSTLKCMLGILNGCWILKFEWVKACLRRKVC   78 (210)
T ss_dssp             CCEEEE-SSCCHHHHHHHHHHHHHTTCEEESS--CCTTCCEEEESSSSCCCSHHHHHHHHTTCEEEETHHHHHHHHHTSC
T ss_pred             CEEEEE-CCCCHHHHHHHHHHHHHcCCEEeCC--CCCCCeEEEEcCCCcchHHHHHHHHhcCCEEecHHHHHHHHHcCCc
Confidence            578888 9999999999999999999999998  588999999976   3344554   588999999999999999999


Q ss_pred             CccCCcChHHHhhhhhhHhhhcccccccccc-CCCCCCCcccccccccHHHHHHHHHHHhcccccccc
Q 012081          276 QRLVHISADLARQVGMMLENIQNGIAREEIN-GGNVPEDAQSCKNKISQEKRQQTVNLAKNGVRSRRS  342 (471)
Q Consensus       276 qp~~~ys~dl~r~~~~~l~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~r~~~~~~a~~~v~~~~~  342 (471)
                      +++..|...-......+  +..+  ....++ |...-  ..+.-....+++-++||+++...|..+.+
T Consensus        79 ~~e~~y~~~~~~~~~r~--~~~~--~~~~lF~g~~~~--l~~~~~~~~~~~l~~lI~~~GG~v~~~~p  140 (210)
T 2nte_A           79 EQEEKYEIPEGPRRSRL--NREQ--LLPKLFDGCYFY--LWGTFKHHPKDNLIKLVTAGGGQILSRKP  140 (210)
T ss_dssp             CCGGGTBCTTHHHHHHH--HHHT--TCCCTTTTCEEE--ECSCCSSSCHHHHHHHHHHTTCEEESSCC
T ss_pred             CChhhccCCCCChhhhh--cccc--ccccccCceEEE--EeccCCCCCHHHHHHHHHHCCCEEEecCC
Confidence            99998865321111000  0000  011222 11100  00111134688899999998777765554

>1z56_C DNA ligase IV; DNA repair, BRCT, NHEJ, XRCC4, DNA ligase, coiled-coil; HET: DNA; 3.92A {Saccharomyces cerevisiae}

Probab=98.95  E-value=4.5e-10  Score=109.80  Aligned_cols=95  Identities=13%  Similarity=0.113  Sum_probs=52.6

Q ss_pred             CCCCCCCCcEEEEeCCCh-hhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCC--HH----HHHHHhcCC-----CCCc
Q 012081           53 PANAPFSGLVICVTGLSK-EARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGG--RK----FEHALKHGS-----RNGL  120 (471)
Q Consensus        53 ~~~~iF~GlvI~vTG~~~-~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g--~K----y~~A~k~~~-----~~gi  120 (471)
                      .+..+|+|++|++.++.. ..++.++.+|..+||++..+++..+||+|+.....  .+    .+..+..+.     ..++
T Consensus       156 ~~~~lF~g~~~yl~~~~~~~~~~~l~~~i~~~GG~v~~~l~~~t~hVV~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  235 (264)
T 1z56_C          156 FPLFLFSNRIAYVPRRKISTEDDIIEMKIKLFGGKITDQQSLCNLIIIPYTDPILRKDCMNEVHEKIKEQIKASDTIPKI  235 (264)
T ss_dssp             CCCC--------------------CHHHHHHHTTSCCCCSSSCSEEECCCSSTTTHHHHSSHHHHTTTTTTTSSSSCCCC
T ss_pred             CchhhhCCeEEEEecCCCchhHHHHHHHHHHcCCEEecccCCCEEEEEeCCCccchHHHHHHHHHHHHhhcccccccCCC
Confidence            456799999999999754 55567788999999999999987777777754321  22    222211110     0244


Q ss_pred             -eEecchHHHHHHHcccCCCCCcccccc
Q 012081          121 -YIVTLGWFVDSVRRNVRLSESLYTVKS  147 (471)
Q Consensus       121 -~IV~p~WI~Dcik~g~~lde~~Y~l~~  147 (471)
                       +||+++||.||++.|+++||++|.+.+
T Consensus       236 ~~iV~~~Wv~dci~~~~ll~e~~Y~~~~  263 (264)
T 1z56_C          236 ARVVAPEWVDHSINENCQVPEEDFPVVN  263 (264)
T ss_dssp             CEEECTHHHHHHHTTSCCCSSCCC----
T ss_pred             CEEecHHHHHHHHHcCCcCCHHHcCCCC
Confidence             999999999999999999999998754

>1l0b_A BRCA1; TANDEM-BRCT, three-helix bundle, unknown function; 2.30A {Rattus norvegicus} SCOP: c.15.1.3 c.15.1.3

Probab=98.93  E-value=2.2e-09  Score=102.34  Aligned_cols=81  Identities=20%  Similarity=0.250  Sum_probs=71.5

Q ss_pred             CCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCc------hHHHHh---cCCCceechhHHHHH
Q 012081          199 TLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED------SVQKYM---GHSNNLVTPVWVLKT  269 (471)
Q Consensus       199 lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~------s~~k~l---~~~~~IVs~~WL~dc  269 (471)
                      .++++.|++ +|+++.+++.|.++++.+||.+++.  ....+||||+...      ...||+   ..++.||+++||.+|
T Consensus         4 ~~~~~~i~~-sg~~~~~~~~l~~~~~~~G~~~~~~--~~~~~THlI~~~~~~~~~~rt~K~~~a~~~g~~IV~~~Wl~~~   80 (229)
T 1l0b_A            4 AERDISMVV-SGLTPKEVMIVQKFAEKYRLALTDV--ITEETTHVIIKTDAEFVCERTLKYFLGIAGGKWIVSYSWVIKS   80 (229)
T ss_dssp             CCCCCEEEE-ESCCHHHHHHHHHHHHHTTCEECSS--CCSSCCEEEECBCTTSEECCCHHHHHHHHTTCEEEETHHHHHH
T ss_pred             CCCCeEEEE-cCCCHHHHHHHHHHHHHcCCEEeCC--cCCCCCEEEEcCCccccccccHHHHHHHHCCCcEecHHHHHHH
Confidence            578899999 9999999999999999999999998  5889999999864      234554   589999999999999


Q ss_pred             HhhCCcCccCCcC
Q 012081          270 AKEKHVQRLVHIS  282 (471)
Q Consensus       270 ik~g~lqp~~~ys  282 (471)
                      +++|+++++..|.
T Consensus        81 ~~~~~~~~e~~y~   93 (229)
T 1l0b_A           81 IQERKLLSVHEFE   93 (229)
T ss_dssp             HTTTSCCCSGGGB
T ss_pred             HHCCCcCChHHeE
Confidence            9999999998874

>1t15_A Breast cancer type 1 susceptibility protein; protein-peptide complex, antitumor protein; HET: SEP; 1.85A {Homo sapiens} SCOP: c.15.1.3 c.15.1.3 PDB: 1jnx_X* 1t29_A* 1t2v_A* 1y98_A* 3coj_X* 3k0h_A* 3k0k_A* 3pxe_A* 3pxb_A 3pxc_X 1t2u_A 1n5o_X 3pxa_A 3k15_A* 3k16_A* 3pxd_A 2ing_X 1oqa_A

Probab=98.90  E-value=2.1e-09  Score=101.09  Aligned_cols=80  Identities=25%  Similarity=0.291  Sum_probs=69.2

Q ss_pred             CCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCc------hHHHHh---cCCCceechhHHHHHHh
Q 012081          201 SGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED------SVQKYM---GHSNNLVTPVWVLKTAK  271 (471)
Q Consensus       201 ~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~------s~~k~l---~~~~~IVs~~WL~dcik  271 (471)
                      +|+.|++ +|++..+++.|.++++.+||.+.+.  .+.++||||+...      ...||+   ..++.||+++||.||++
T Consensus         3 ~~~~~~~-sg~~~~~~~~l~~~~~~~G~~~~~~--~~~~~THli~~~~~~~~~~rt~k~~~a~~~g~~IV~~~Wl~~~~~   79 (214)
T 1t15_A            3 KRMSMVV-SGLTPEEFMLVYKFARKHHITLTNL--ITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIK   79 (214)
T ss_dssp             -CCEEEE-ESCCHHHHHHHHHHHHHHTCEECSS--CCTTCCEEEECBCTTSEECCBHHHHHHHHTTCEEEETHHHHHHHH
T ss_pred             CcEEEEE-CCCCHHHHHHHHHHHHHhCCEEeCc--cCCCCcEEEEeCCcccchhhhHHHHHHHhcCCEEeCHHHHHHHHH
Confidence            4678888 9999999999999999999999998  5899999999864      234554   58899999999999999


Q ss_pred             hCCcCccCCcCh
Q 012081          272 EKHVQRLVHISA  283 (471)
Q Consensus       272 ~g~lqp~~~ys~  283 (471)
                      +|+++++..|..
T Consensus        80 ~~~~~~e~~y~~   91 (214)
T 1t15_A           80 ERKMLNEHDFEV   91 (214)
T ss_dssp             TTSCCCGGGGBC
T ss_pred             CCCcCChHHeEe
Confidence            999999988753

>3u3z_A Microcephalin; DNA repair, cell cycle regulation, cell cycle; HET: SEP PTR; 1.50A {Homo sapiens} PDB: 3szm_A* 3t1n_A* 3sht_A 3shv_A*

Probab=98.90  E-value=1e-09  Score=103.48  Aligned_cols=82  Identities=18%  Similarity=0.234  Sum_probs=69.0

Q ss_pred             CCCCCCCc-EEEEeCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHHHHHHHhcCCCCCceEecchHHHHHH
Q 012081           54 ANAPFSGL-VICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSV  132 (471)
Q Consensus        54 ~~~iF~Gl-vI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~Dci  132 (471)
                      ..++|+|+ ++|++++....++.|+++|+.+||++..++. .++++|+....      +..    .++++|+|+||.||+
T Consensus       116 ~~~LF~g~~~~~v~~~~~~~~~~L~~lI~~~GG~v~~~~~-~~~iiI~~~~~------~~~----~~~~~V~p~Wi~DsI  184 (199)
T 3u3z_A          116 RGTLFADQPVMFVSPASSPPVAKLCELVHLCGGRVSQVPR-QASIVIGPYSG------KKK----ATVKYLSEKWVLDSI  184 (199)
T ss_dssp             CCCTTTTSCCEEECTTCSSCHHHHHHHHHHTTCCBCSSGG-GCSEEESCCCS------CCC----TTCEEECHHHHHHHH
T ss_pred             cchhhCCCeEEEECCCCCCCHHHHHHHHHHcCCEEeccCC-CCEEEEeCCch------hcc----CCCcEEChhHHHHHH
Confidence            46899999 6899999888899999999999999999984 56777754322      222    489999999999999


Q ss_pred             HcccCCCCCccccc
Q 012081          133 RRNVRLSESLYTVK  146 (471)
Q Consensus       133 k~g~~lde~~Y~l~  146 (471)
                      .+++++|+++|.+.
T Consensus       185 ~~~~llp~~~Y~~~  198 (199)
T 3u3z_A          185 TQHKVCAPENYLLS  198 (199)
T ss_dssp             HHTSCCCGGGGBCC
T ss_pred             HcCCcCChHhccCC
Confidence            99999999999763

>3pc7_A DNA ligase 3; DNA repair, BRCT domain, protein:protein interactions, XRCC1 domain, DNA binding protein; HET: DNA MSE; 1.65A {Homo sapiens} SCOP: c.15.1.2 PDB: 3pc8_C* 1imo_A* 1in1_A* 3qvg_A*

Probab=98.86  E-value=3.6e-09  Score=87.15  Aligned_cols=75  Identities=12%  Similarity=0.178  Sum_probs=62.5

Q ss_pred             CCCCCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccCCC-CceEEEEecCCCHHHHHHHhcCCCCCceEecchHHHHH
Q 012081           53 PANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHP-QCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDS  131 (471)
Q Consensus        53 ~~~~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~-~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~Dc  131 (471)
                      ..+.+|.|++|.+.+=.++ ...|++.|.++||.+...++. ++||+|+...         +   ..+..+|+|+||+||
T Consensus        12 ~LpdiFsg~~~~l~~~v~~-~~~l~RyiiAfgG~v~~~~~~~~vTHvI~~~~---------~---~~~~~~V~p~WI~dc   78 (88)
T 3pc7_A           12 VLLDIFTGVRLYLPPSTPD-FSRLRRYFVAFDGDLVQEFDMTSATHVLGSRD---------K---NPAAQQVSPEWIWAC   78 (88)
T ss_dssp             CCCCCSTTCEECCCTTSTT-HHHHHHHHHHTTCEECCGGGGGGCSEEESCCT---------T---CTTSEEECHHHHHHH
T ss_pred             cCChhhcCeEEEccCCcCc-hhhheeeeeecCCEEecccCCCcCeEEecCCC---------c---CCCCcEEchHHHHHH
Confidence            4578999999999654333 378899999999999888775 9999997653         2   258999999999999


Q ss_pred             HHcccCCCC
Q 012081          132 VRRNVRLSE  140 (471)
Q Consensus       132 ik~g~~lde  140 (471)
                      ++++++|+.
T Consensus        79 I~k~~Ll~~   87 (88)
T 3pc7_A           79 IRKRRLVAP   87 (88)
T ss_dssp             HHHTSCCSC
T ss_pred             HhCCcccCC
Confidence            999999975

>3sqd_A PAX-interacting protein 1; tandem BRCT domains, cell cycle; HET: SEP; 2.15A {Homo sapiens}

Probab=98.85  E-value=3.8e-09  Score=101.06  Aligned_cols=139  Identities=9%  Similarity=0.009  Sum_probs=93.5

Q ss_pred             CCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCc-hHHHHh---cCCCceechhHHHHHHhhC
Q 012081          198 STLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED-SVQKYM---GHSNNLVTPVWVLKTAKEK  273 (471)
Q Consensus       198 ~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~-s~~k~l---~~~~~IVs~~WL~dcik~g  273 (471)
                      ..+.|++|++ +||++.+++.+.++|+.+||.++++   ..++||||+... ...||+   ..++.||+++||.+|+++|
T Consensus        12 ~~~~~~~i~~-SG~~~~~~~~l~~~i~~lGg~v~~~---~~~~THLI~~~~~rT~K~l~A~~~g~~IVs~~Wl~~c~~~~   87 (219)
T 3sqd_A           12 TPELTPFVLF-TGFEPVQVQQYIKKLYILGGEVAES---AQKCTHLIASKVTRTVKFLTAISVVKHIVTPEWLEECFRCQ   87 (219)
T ss_dssp             CGGGCCEEEE-CSCCHHHHHHHHHHHHHTTCEECSS---GGGCSEEECSSCCCCHHHHHHTTTCSEEECHHHHHHHHHHT
T ss_pred             CCCCCeEEEE-eCCChHHHHHHHHHHHHCCCEEeCC---CCCceEEEECCCCCCHHHHHHHHcCCCEecHHHHHHHHHcC
Confidence            4578999999 9999999999999999999999988   388999999763 233444   6889999999999999999


Q ss_pred             CcCccCCcChHH---HhhhhhhHhhhccccccccccCCCCCCCcccccccccHHHHHHHHHHHhcccccccc
Q 012081          274 HVQRLVHISADL---ARQVGMMLENIQNGIAREEINGGNVPEDAQSCKNKISQEKRQQTVNLAKNGVRSRRS  342 (471)
Q Consensus       274 ~lqp~~~ys~dl---~r~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~a~~~v~~~~~  342 (471)
                      +++++..|....   .+..+.-++..-.......++.+-  .---+.....++++-++||+++...|-.+.+
T Consensus        88 ~~l~e~~y~l~d~~~e~~~~~~l~~~l~ra~~~~LF~G~--~f~it~~~~~~~~~l~~lI~~~GG~v~~~~p  157 (219)
T 3sqd_A           88 KFIDEQNYILRDAEAEVLFSFSLEESLKRAHVSPLFKAK--YFYITPGICPSLSTMKAIVECAGGKVLSKQP  157 (219)
T ss_dssp             SCCCSGGGBCCCHHHHHHTTCCHHHHHHHHHHSCTTTTE--EEEECTTCSSCHHHHHHHHHHTTCEEESSCC
T ss_pred             CCCChHhccCCCchhhhhcCCChHHHhhhhccccccCCc--EEEEeCCCCCCHHHHHHHHHHCCCEEECCCC
Confidence            999999885432   111111111100000011222110  0000111234578999999999877765544

>3ef0_A RNA polymerase II subunit A C-terminal domain phosphatase; CTD, FCPH, BRCT, hydrolase, ALF4, transition state analog, cobalt, magnesium; 2.10A {Schizosaccharomyces pombe}

Probab=98.82  E-value=3.8e-09  Score=108.73  Aligned_cols=83  Identities=17%  Similarity=0.216  Sum_probs=69.7

Q ss_pred             CCCCCCcEEEEeCCCCH----HHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCch---HHHHhcC-CCceechhHHHH
Q 012081          197 NSTLSGCSMYVDSDVSE----ELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDS---VQKYMGH-SNNLVTPVWVLK  268 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~----~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~s---~~k~l~~-~~~IVs~~WL~d  268 (471)
                      ..+|+||+|+| +|+-+    .++..+.+++..+||+++.+  ++.++||||+....   .+++... +++||+++||++
T Consensus       280 ~~~L~G~~ivf-SG~~~~~~~~~~~~l~~l~~~lGa~v~~~--vs~~vTHLVa~~~~t~K~~~A~~~~~I~IV~~~Wl~~  356 (372)
T 3ef0_A          280 QKVLKGCRLLF-SGVIPLGVDVLSSDIAKWAMSFGAEVVLD--FSVPPTHLIAAKIRTEKVKKAVSMGNIKVVKLNWLTE  356 (372)
T ss_dssp             TTTSTTCEEEE-ESSSCTTSCTTTSHHHHHHHHTTCEEESS--SSSCCSEEEECSCCCHHHHHHHHSSSCCEEEHHHHHH
T ss_pred             hhhcCCcEEEE-ecccCCCcchhHHHHHHHHHHcCCEEeCc--CCCCceEEEEcCCCchHHHHHHhcCCCEEEcHHHHHH
Confidence            47999999999 76642    24578999999999999999  68999999998743   3344455 799999999999


Q ss_pred             HHhhCCcCccCCcC
Q 012081          269 TAKEKHVQRLVHIS  282 (471)
Q Consensus       269 cik~g~lqp~~~ys  282 (471)
                      |++.++.+++..|.
T Consensus       357 c~~~~~~vdE~~Y~  370 (372)
T 3ef0_A          357 SLSQWKRLPESDYL  370 (372)
T ss_dssp             HHHTTSCCCGGGGB
T ss_pred             HHHhCCcCChhhce
Confidence            99999999998875

>3al2_A DNA topoisomerase 2-binding protein 1; BRCT domain, protein binding, DNA binding protein; HET: DNA MSE; 2.00A {Homo sapiens} PDB: 3al3_A*

Probab=98.82  E-value=9.2e-09  Score=99.46  Aligned_cols=83  Identities=8%  Similarity=0.083  Sum_probs=70.0

Q ss_pred             CCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCc-hHHHHh---cCCCceechhHHHHHHhhCC
Q 012081          199 TLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED-SVQKYM---GHSNNLVTPVWVLKTAKEKH  274 (471)
Q Consensus       199 lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~-s~~k~l---~~~~~IVs~~WL~dcik~g~  274 (471)
                      .-++.+|.+ +|++.++++.+.++|+.+||.++++...+.+|||||+... ...||+   ..++.||+++||.+|+++|+
T Consensus         6 ~~~~~~~~~-Sg~~~~~~~~l~~~i~~LGg~~~~~~~~~~~~THlV~~~~~RT~K~l~aia~G~wIvs~~wl~~s~~~g~   84 (235)
T 3al2_A            6 LKKQYIFQL-SSLNPQERIDYCHLIEKLGGLVIEKQCFDPTCTHIVVGHPLRNEKYLASVAAGKWVLHRSYLEACRTAGH   84 (235)
T ss_dssp             --CCCEEEE-ESCCHHHHHHHHHHHHHTTCEECCSSSCCTTCCEEEESSCCCSHHHHHHHHTTCEEECTHHHHHHHHHTS
T ss_pred             CCCCEEEEE-cCCCHHHHHHHHHHHHHcCCEEeccCCCCCCCcEEEECCCCCCHHHHHHHHcCCcCccHHHHHHHHHcCC
Confidence            446789999 8999999999999999999999863114789999999884 355555   68999999999999999999


Q ss_pred             cCccCCcC
Q 012081          275 VQRLVHIS  282 (471)
Q Consensus       275 lqp~~~ys  282 (471)
                      ++++..|.
T Consensus        85 ~l~E~~ye   92 (235)
T 3al2_A           85 FVQEEDYE   92 (235)
T ss_dssp             CCCSGGGB
T ss_pred             CCChhcee
Confidence            99998885

>2coe_A Deoxynucleotidyltransferase, terminal variant; BRCT domain, DNA polymerase, teminal deoxynucleotidyltransferase, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.81  E-value=3.6e-08  Score=85.75  Aligned_cols=93  Identities=17%  Similarity=0.289  Sum_probs=71.7

Q ss_pred             CCCCCCCCcEEEEeCC--ChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHHHHHHHhc---CCCCCceEecchH
Q 012081           53 PANAPFSGLVICVTGL--SKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKH---GSRNGLYIVTLGW  127 (471)
Q Consensus        53 ~~~~iF~GlvI~vTG~--~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~Ky~~A~k~---~~~~gi~IV~p~W  127 (471)
                      .+...|.|++|.+..+  ...-++-+.+++..+||++...++..+||+|+.+........-++.   ....+..||+..|
T Consensus        16 ~p~~~F~g~~iy~v~~~~g~~R~~~l~~l~r~~G~~V~~~ls~~VTHVVve~~~~~e~~~~l~~~~l~~~~~~~lv~i~W   95 (120)
T 2coe_A           16 PQDIKFQDLVVFILEKKMGTTRRALLMELARRKGFRVENELSDSVTHIVAENNSGSDVLEWLQAQKVQVSSQPELLDVSW   95 (120)
T ss_dssp             SSCCSCTTCEEEEECTTTCHHHHHHHHHHHHHHTCEECSSCCTTCCEEEESSCCHHHHHHHHHHCCCCCSSCCEEEEHHH
T ss_pred             CcccccCCeEEEEeecccchHHHHHHHHHHHHcCCEEeeccCCCcCEEEecCCCHHHHHHHHhccccccccccEEeecHH
Confidence            4668999999999654  3457788899999999999999999999999974433333332221   1123579999999


Q ss_pred             HHHHHHcccCCCCCcccc
Q 012081          128 FVDSVRRNVRLSESLYTV  145 (471)
Q Consensus       128 I~Dcik~g~~lde~~Y~l  145 (471)
                      |.+|+++|+++||+.|..
T Consensus        96 l~esmk~g~lv~ee~~~~  113 (120)
T 2coe_A           96 LIECIGAGKPVEMTGKHQ  113 (120)
T ss_dssp             HHHHHHTTSCCCCSSSSB
T ss_pred             HHHHHHcCCccCcccceE
Confidence            999999999999966544

>2dun_A POL MU, DNA polymerase MU; layers A/B/A, parallel beta-sheet of 4 strands, non- homologous END jonting, somatic hypermutation, V(D)J recombination; HET: DNA; NMR {Homo sapiens} PDB: 2htf_A*

Probab=98.76  E-value=8.9e-09  Score=90.55  Aligned_cols=82  Identities=15%  Similarity=0.242  Sum_probs=69.4

Q ss_pred             CCCCCCcEEEEeC--CCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCc---hHHHHh----------cCCCcee
Q 012081          197 NSTLSGCSMYVDS--DVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED---SVQKYM----------GHSNNLV  261 (471)
Q Consensus       197 ~~lF~G~~Iyl~~--gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~---s~~k~l----------~~~~~IV  261 (471)
                      ...|.|++||| .  ++....++.|.++++..|++|.+.  +.+.+||||+++.   ++.+||          ..++++|
T Consensus         8 ~~~F~~v~iyi-ve~kmG~sRr~fL~~la~~kGf~v~~~--~S~~VTHVV~E~~s~~~~~~~L~~~~~~l~~~~~~~~lL   84 (133)
T 2dun_A            8 STRFPGVAIYL-VEPRMGRSRRAFLTGLARSKGFRVLDA--CSSEATHVVMEETSAEEAVSWQERRMAAAPPGCTPPALL   84 (133)
T ss_dssp             SCSEEEEEEEE-CHHHHCSHHHHHHHHHHHHHTEEECSS--CCTTCCEEEESSCCHHHHHHHHHHHHHHSCTTCCCCEEE
T ss_pred             ccccCccEEEE-ecCCcCHHHHHHHHHHHHhcCCEeccc--cCCCceEEEecCCCHHHHHHHHHHhhcccCcCCCCcEEe
Confidence            46899999999 4  355668999999999999999999  7999999999774   455555          1557999


Q ss_pred             chhHHHHHHhhCCcCccCCc
Q 012081          262 TPVWVLKTAKEKHVQRLVHI  281 (471)
Q Consensus       262 s~~WL~dcik~g~lqp~~~y  281 (471)
                      ...||.+|+++|+++++..+
T Consensus        85 disWltecm~~g~pV~~e~~  104 (133)
T 2dun_A           85 DISWLTESLGAGQPVPVECR  104 (133)
T ss_dssp             EHHHHHHHHHHTSCCCCCTT
T ss_pred             ccHHHHHHHhcCCcCCcccc
Confidence            99999999999999998643

>1kzy_C Tumor suppressor P53-binding protein 1; tandem-BRCT and linker complexed with non-BRCT protein, three-helix bundle, parallel beta sheet; 2.50A {Homo sapiens} SCOP: c.15.1.4 c.15.1.4 PDB: 1gzh_B

Probab=98.73  E-value=1.6e-08  Score=99.08  Aligned_cols=85  Identities=9%  Similarity=0.195  Sum_probs=67.3

Q ss_pred             CCCCCCcEEEEeCCCCHH-----------------------------HHHHHHHHHHhCCCEEEccccCCC------Cce
Q 012081          197 NSTLSGCSMYVDSDVSEE-----------------------------LRNKVFEAATNEGATLVNQWFVGC------GAS  241 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~-----------------------------~r~~L~~lI~~~GG~v~d~~~~~~------~vT  241 (471)
                      ..+|.|+.|+| ++.+..                             .+..|+++|+.+||+|++++  ..      ..|
T Consensus        13 ~~iF~g~~F~~-t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~l~~~I~~~GG~v~~~~--~~~~~~~~~~t   89 (259)
T 1kzy_C           13 KTLFLGYAFLL-TMATTSDKLASRSKLPDGPTGSSEEEEEFLEIPPFNKQYTESQLRAGAGYILEDF--NEAQCNTAYQC   89 (259)
T ss_dssp             TTTTTTEEEEE-CCCC---------------------------CCCCCHHHHHHHHHTTTCEECSSC--CTTTTTTTCEE
T ss_pred             CcCcCCcEEEE-EcccccccccccccccccccccccccccccccCcccHHHHHHHHHHCCCEEecCc--cccccccCCCe
Confidence            57999999999 766543                             44689999999999999883  32      268


Q ss_pred             EEEEcC-chHHHHh---cCCCceechhHHHHHHhhCCcCccCCcChH
Q 012081          242 YVVCEE-DSVQKYM---GHSNNLVTPVWVLKTAKEKHVQRLVHISAD  284 (471)
Q Consensus       242 HVVv~~-~s~~k~l---~~~~~IVs~~WL~dcik~g~lqp~~~ys~d  284 (471)
                      |+|+.. ....||+   ..++.||++.||.||+++++++++.+|-.+
T Consensus        90 ~LIa~~~~rt~K~l~ala~g~~iVs~~Wl~dc~~~~~~l~~~~Y~l~  136 (259)
T 1kzy_C           90 LLIADQHCRTRKYFLCLASGIPCVSHVWVHDSCHANQLQNYRNYLLP  136 (259)
T ss_dssp             EEEESSCCCSHHHHHHHHHTCCEEETHHHHHHHHHTSCCCGGGSBCC
T ss_pred             EEEcCCCCCcHHHHHHHhcCCCCccHHHHHHHHHcCCcCCHHHccCC
Confidence            999877 2334454   589999999999999999999998887543

>2vxb_A DNA repair protein RHP9; BRCT, nucleus, cell cycle, DNA damage, DNA replication inhibitor, phosphoprotein, checkpoint signalling; HET: DNA; 2.3A {Schizosaccharomyces pombe} PDB: 2vxc_A*

Probab=98.72  E-value=1.4e-08  Score=98.44  Aligned_cols=85  Identities=15%  Similarity=0.207  Sum_probs=66.0

Q ss_pred             CCCCCcEEEEeCC--CCHHHHHHHHHHHHhCCCEEEccc----c-CCC-------------------CceEEEEcCch-H
Q 012081          198 STLSGCSMYVDSD--VSEELRNKVFEAATNEGATLVNQW----F-VGC-------------------GASYVVCEEDS-V  250 (471)
Q Consensus       198 ~lF~G~~Iyl~~g--fs~~~r~~L~~lI~~~GG~v~d~~----~-~~~-------------------~vTHVVv~~~s-~  250 (471)
                      .+|+||.|+|...  ++...+..|.++|+.+||+++++.    | ...                   ..||||+.... .
T Consensus         1 ~lF~g~~F~ls~~~~~~~~~k~~L~~~I~~~GG~v~~~g~~~lf~~~~~~~~~~~~~~k~~~~~~~~~~t~lia~~~~rt   80 (241)
T 2vxb_A            1 LIFDDCVFAFSGPVHEDAYDRSALETVVQDHGGLVLDTGLRPLFNDPFKSKQKKLRHLKPQKRSKSWNQAFVVSDTFSRK   80 (241)
T ss_dssp             CTTTTEEEEECCCSSTTSSCHHHHHHHHHHTTCEECTTCSGGGBCCSCC----CCCSCCBCGGGGGCSEEEEECSSCCCC
T ss_pred             CCCCCcEEEEecCCCCchhhHHHHHHHHHHCCCEEecCcchhhccCccccccccccccccccccccccceEEEcCCCCCc
Confidence            3899999999433  466778899999999999999861    1 111                   34999988632 3


Q ss_pred             HHH---hcCCCceechhHHHHHHhhCCcCccCCcC
Q 012081          251 QKY---MGHSNNLVTPVWVLKTAKEKHVQRLVHIS  282 (471)
Q Consensus       251 ~k~---l~~~~~IVs~~WL~dcik~g~lqp~~~ys  282 (471)
                      .||   +..++.||+++||.||+++++++|...|-
T Consensus        81 ~K~~~ala~gipiV~~~Wi~dc~~~~~~~~~~~yl  115 (241)
T 2vxb_A           81 VKYLEALAFNIPCVHPQFIKQCLKMNRVVDFSPYL  115 (241)
T ss_dssp             HHHHHHHHHTCCEECTHHHHHHHHHTSCCCSGGGB
T ss_pred             HHHHHHHHcCCCEecHHHHHHHHHcCCcCChhhcc
Confidence            444   46899999999999999999999887653

>3ef1_A RNA polymerase II subunit A C-terminal domain phosphatase; CTD, FCPH, BRCT, hydrolase, BEF3, acylphosphate analog, cobalt, magnesium; HET: BFD; 2.15A {Schizosaccharomyces pombe}

Probab=98.70  E-value=1.1e-08  Score=107.05  Aligned_cols=83  Identities=17%  Similarity=0.213  Sum_probs=69.4

Q ss_pred             CCCCCCcEEEEeCCCCHH----HHHHHHHHHHhCCCEEEccccCCCCceEEEEcCch---HHHHhcC-CCceechhHHHH
Q 012081          197 NSTLSGCSMYVDSDVSEE----LRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDS---VQKYMGH-SNNLVTPVWVLK  268 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~----~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~s---~~k~l~~-~~~IVs~~WL~d  268 (471)
                      ..+|.||+|+| +|+-+.    .+..+.++|..+||++..+  ++.++||||+....   .+++... +++||+++||++
T Consensus       350 ~~~L~G~~Ivf-SG~~p~~~~~~r~~l~~~~~~lGa~~~~~--vs~~vTHLVa~~~~t~K~~~A~~~g~IkIVs~~WL~d  426 (442)
T 3ef1_A          350 QKVLKGCRLLF-SGVIPLGVDVLSSDIAKWAMSFGAEVVLD--FSVPPTHLIAAKIRTEKVKKAVSMGNIKVVKLNWLTE  426 (442)
T ss_dssp             HTTSTTCEEEE-ESSSCTTSCSTTSHHHHHHHTTTCEECSS--SSSCCSEEEECSCCCHHHHHHHHHSSSEEEEHHHHHH
T ss_pred             hcccCCcEEEE-ecccCCCCCccHHHHHHHHHHcCCEEeCC--CCCCceEEEeCCCCCHHHHHHHhcCCCEEEeHHHHHH
Confidence            46899999999 775432    4578999999999999999  69999999998754   3333444 699999999999


Q ss_pred             HHhhCCcCccCCcC
Q 012081          269 TAKEKHVQRLVHIS  282 (471)
Q Consensus       269 cik~g~lqp~~~ys  282 (471)
                      |++.++.+++..|.
T Consensus       427 cl~~~krldE~~Yl  440 (442)
T 3ef1_A          427 SLSQWKRLPESDYL  440 (442)
T ss_dssp             HHHHTSCCCGGGTB
T ss_pred             HHHcCCcCChhccc
Confidence            99999999998875

>2etx_A Mediator of DNA damage checkpoint protein 1; tandem BRCT domains histone gamma-H2AX, cell cycle; 1.33A {Homo sapiens} PDB: 2azm_A* 3k05_A* 2ado_A

Probab=98.61  E-value=8.2e-08  Score=90.82  Aligned_cols=88  Identities=17%  Similarity=0.234  Sum_probs=72.2

Q ss_pred             CCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccCCCC--ceEEEEecC-CCHHHHHHHhcCCCCCceEecchHHHHHH
Q 012081           56 APFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQ--CTHLVVQSF-GGRKFEHALKHGSRNGLYIVTLGWFVDSV  132 (471)
Q Consensus        56 ~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~--~THLV~~~~-~g~Ky~~A~k~~~~~gi~IV~p~WI~Dci  132 (471)
                      ++|+|+.|++++.....++.|.++|+.+||++...+.+.  .+|+|+... ...++..+.++    +++||+++||.+|+
T Consensus       114 ~lF~g~~~~~~~~~~~~~~~l~~li~~~GG~v~~~~~~~~~~~~ivI~~~~d~~~~~~~~~~----~i~vvs~eWi~~sI  189 (209)
T 2etx_A          114 RLLEGYEIYVTPGVQPPPPQMGEIISCCGGTYLPSMPRSYKPQRVVITCPQDFPHCSIPLRV----GLPLLSPEFLLTGV  189 (209)
T ss_dssp             CTTTTCEEEECTTCSSCHHHHHHHHHHTTCEECSSCCCSCCTTEEEECCGGGGGGCHHHHHH----TCCEECTHHHHHHH
T ss_pred             CCcCCcEEEEeCCCCCCHHHHHHHHHHCCCEEECCCCCCCCCceEEEECcccHHHHHHHHHC----CCeEEcHHHHHHHH
Confidence            799999999999887788999999999999999888753  256666433 34567777776    79999999999999


Q ss_pred             HcccCCCCCccccccc
Q 012081          133 RRNVRLSESLYTVKSI  148 (471)
Q Consensus       133 k~g~~lde~~Y~l~~~  148 (471)
                      ...+ +|++.|.+...
T Consensus       190 ~~q~-ld~e~y~l~~~  204 (209)
T 2etx_A          190 LKQE-AKPEAFVLSPL  204 (209)
T ss_dssp             HHTC-CCGGGGBCCTT
T ss_pred             Hhcc-cChHHheecCC
Confidence            9866 59999988643

>2dun_A POL MU, DNA polymerase MU; layers A/B/A, parallel beta-sheet of 4 strands, non- homologous END jonting, somatic hypermutation, V(D)J recombination; HET: DNA; NMR {Homo sapiens} PDB: 2htf_A*

Probab=98.49  E-value=2e-07  Score=81.97  Aligned_cols=90  Identities=12%  Similarity=0.226  Sum_probs=71.6

Q ss_pred             CCCCCCCCcEEEEeC--CChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHHHHHHHhcC---------CCCCce
Q 012081           53 PANAPFSGLVICVTG--LSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHG---------SRNGLY  121 (471)
Q Consensus        53 ~~~~iF~GlvI~vTG--~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~Ky~~A~k~~---------~~~gi~  121 (471)
                      .+...|.|++|.+..  +...-|+-|.+++.++|+++...+++.+||+|+.+...+   .+++|.         ...+..
T Consensus         6 ~~~~~F~~v~iyive~kmG~sRr~fL~~la~~kGf~v~~~~S~~VTHVV~E~~s~~---~~~~~L~~~~~~l~~~~~~~~   82 (133)
T 2dun_A            6 SGSTRFPGVAIYLVEPRMGRSRRAFLTGLARSKGFRVLDACSSEATHVVMEETSAE---EAVSWQERRMAAAPPGCTPPA   82 (133)
T ss_dssp             CSSCSEEEEEEEECHHHHCSHHHHHHHHHHHHHTEEECSSCCTTCCEEEESSCCHH---HHHHHHHHHHHHSCTTCCCCE
T ss_pred             CCccccCccEEEEecCCcCHHHHHHHHHHHHhcCCEeccccCCCceEEEecCCCHH---HHHHHHHHhhcccCcCCCCcE
Confidence            355889999999985  444688999999999999999999999999999554432   233321         124678


Q ss_pred             EecchHHHHHHHcccCCCCCcccc
Q 012081          122 IVTLGWFVDSVRRNVRLSESLYTV  145 (471)
Q Consensus       122 IV~p~WI~Dcik~g~~lde~~Y~l  145 (471)
                      +|+..|+.+|++.|+.+|++.+..
T Consensus        83 lLdisWltecm~~g~pV~~e~~~~  106 (133)
T 2dun_A           83 LLDISWLTESLGAGQPVPVECRHR  106 (133)
T ss_dssp             EEEHHHHHHHHHHTSCCCCCTTTS
T ss_pred             EeccHHHHHHHhcCCcCCcccceE
Confidence            999999999999999999865544

>3l41_A BRCT-containing protein 1; BRC1, BRCT domain, tandem BRCT repeat, phosphoserine binding domain, DNA repair, cell division, mitosis; HET: SEP; 1.45A {Schizosaccharomyces pombe} PDB: 3l40_A*

Probab=98.49  E-value=5.6e-08  Score=93.13  Aligned_cols=131  Identities=9%  Similarity=0.060  Sum_probs=85.0

Q ss_pred             CCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCc-hHHHHh---cCCCceechhHHHHHHhhCCc
Q 012081          200 LSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED-SVQKYM---GHSNNLVTPVWVLKTAKEKHV  275 (471)
Q Consensus       200 F~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~-s~~k~l---~~~~~IVs~~WL~dcik~g~l  275 (471)
                      -.+.+|.| +|+++.+   +.++|+.+||.++++   ..++||||+... ...|++   ..+++||+++||.+|+++|.+
T Consensus         6 ~~~~~v~f-SG~~~~~---~~~~i~~lGg~v~~~---~~~~THlV~~~~~RT~K~l~Aia~g~~IVs~~Wl~~~~~~~~~   78 (220)
T 3l41_A            6 SKRVYITF-TGYDKKP---SIDNLKKLDMSITSN---PSKCTHLIAPRILRTSKFLCSIPYGPCVVTMDWINSCLKTHEI   78 (220)
T ss_dssp             -CCEEEEE-CSCSSCC---CCGGGGGGTEEECSC---TTTCSEEECSSCCCBHHHHHHGGGCCEEECHHHHHHHHHHTSC
T ss_pred             cceEEEEE-eccCCCC---CcchHhhcceeeccC---chhhhhhhhhhHhhhcceeecCCCCCeEEEhHHHHhhhhhhhc
Confidence            35678999 8998764   389999999999998   357999999873 344444   689999999999999999999


Q ss_pred             CccCCcChH---HHhhhhhhHhh-hccccc-cccccCCCCCCCcccccc--cccHHHHHHHHHHHhccccc
Q 012081          276 QRLVHISAD---LARQVGMMLEN-IQNGIA-REEINGGNVPEDAQSCKN--KISQEKRQQTVNLAKNGVRS  339 (471)
Q Consensus       276 qp~~~ys~d---l~r~~~~~l~~-~~~~~~-~~~~~~~~~~~~~~~~~~--~~~~~~r~~~~~~a~~~v~~  339 (471)
                      +++.+|...   .....+.-+++ ++...+ ...++.+---.-  +...  ..+.++-++||+++..-|-.
T Consensus        79 l~e~~y~l~d~~~e~~~~~~l~~~~~rar~~~~~LF~G~~f~i--t~~~~~~p~~~~l~~iI~~~GG~v~~  147 (220)
T 3l41_A           79 VDEEPYLLNDPEKELELGCTLESALKRARAQGPSLLEDYVVYL--TSKTVAPENVPAVISIVKSNGGVCST  147 (220)
T ss_dssp             CCSGGGBCCCHHHHHHHTSCHHHHHHHHHHHCSCTTTTSEEEE--ETTSSCGGGHHHHHHHHHHTTCEEEE
T ss_pred             cccCccccCCcHHHhhccccHHHHHHHHHhcCchhhhheeEEE--eccccCCCCCceEEEEEecCCcEech
Confidence            999999532   12222211111 111000 122221110000  1111  34678999999999877765

>1l7b_A DNA ligase; BRCT, autostructure, structural genomics, NESG, PSI, protein structure initiative, northeast structural genomics consortium; HET: DNA; NMR {Thermus thermophilus} SCOP: c.15.1.2

Probab=98.23  E-value=2.4e-06  Score=70.86  Aligned_cols=73  Identities=19%  Similarity=0.255  Sum_probs=62.6

Q ss_pred             CCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCc---hHHHHhcCCCceechhHHHHHHhh
Q 012081          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED---SVQKYMGHSNNLVTPVWVLKTAKE  272 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~---s~~k~l~~~~~IVs~~WL~dcik~  272 (471)
                      ...|.|++|+|...++. .|+.+..+|..+||.+..+  +..+++|||+++.   .++++...+++||+.+|+++++..
T Consensus         5 ~~~l~G~~~v~TG~l~~-~R~e~~~~i~~~Gg~v~~s--Vskkt~~LV~g~~~gsK~~kA~~lgI~Ii~E~~f~~~l~~   80 (92)
T 1l7b_A            5 GEALKGLTFVITGELSR-PREEVKALLRRLGAKVTDS--VSRKTSYLVVGENPGSKLEKARALGVPTLTEEELYRLLEA   80 (92)
T ss_dssp             CCSSTTCEEECSTTTTS-CHHHHHHHHHHTTCEEESC--CSSSCCCBEECSSSSTTHHHHHCSSSCCEEHHHHHHHHHH
T ss_pred             CCCcCCcEEEEecCCCC-CHHHHHHHHHHcCCEEeCc--ccCCeeEEEeCCCCChHHHHHHHcCCcEEeHHHHHHHHHh
Confidence            46799999999434555 8999999999999999999  7899999999874   466666789999999999999864

>3t7k_A RTT107, regulator of TY1 transposition protein 107; BRCT, DNA repair, phospho-peptide, protein binding; HET: SEP; 2.03A {Saccharomyces cerevisiae} PDB: 3t7j_A* 3t7i_A

Probab=98.21  E-value=9.5e-06  Score=78.42  Aligned_cols=175  Identities=11%  Similarity=0.154  Sum_probs=116.6

Q ss_pred             CCcEEEEeCCC-hh-hHHHHHHHHHHcCCEEcccCC--CCceEEEEecC-CCHHHHHHHhcCCCCCceEecchHHHHHHH
Q 012081           59 SGLVICVTGLS-KE-ARKQVMEATERLGGQYSPDLH--PQCTHLVVQSF-GGRKFEHALKHGSRNGLYIVTLGWFVDSVR  133 (471)
Q Consensus        59 ~GlvI~vTG~~-~~-er~~L~~lI~~~GG~~~~~l~--~~~THLV~~~~-~g~Ky~~A~k~~~~~gi~IV~p~WI~Dcik  133 (471)
                      -.+.+++||+. .. +..+ .+....+|=++.++.+  ..|+||||+.. .+.||..|+..+  +--.||+|+||.+|++
T Consensus        21 ~~i~ai~TGc~~~~~~~~D-~~~Lr~LGI~Iv~d~~~~~~~n~LiAPkilRT~KFL~sLa~~--P~~~il~p~FI~~~Lk   97 (256)
T 3t7k_A           21 YDLKAVCTGCFHDGFNEVD-IEILNQLGIKIFDNIKETDKLNCIFAPKILRTEKFLKSLSFE--PLKFALKPEFIIDLLK   97 (256)
T ss_dssp             CCEEEEESSSCSSCCCHHH-HHHHHHTTEEECSSCCGGGCCCEEECSSCCCBHHHHHHTTST--TCCEEECTHHHHHHHH
T ss_pred             eeEEEEecCCcccccCHHH-HHHHHHcCeEEEecCcccCCCCEEEcCchhhHHHHHHHhccC--ccceEeCHHHHHHHHH
Confidence            57889999998 31 1222 3455688999999986  37999999986 689999999853  2236999999999998


Q ss_pred             c---cc------CCCCCccccccccccCcchhhhhcccCCcCCCCCCCCcccchhhccccccccccccccCCCCCCCCc-
Q 012081          134 R---NV------RLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGC-  203 (471)
Q Consensus       134 ~---g~------~lde~~Y~l~~~~e~~~~~~~~~~L~~~s~~e~~~lp~~I~es~~s~s~E~ld~~~~~~~~~lF~G~-  203 (471)
                      .   |+      .++.++|.+++....        .+   .                          .....+.+|.|+ 
T Consensus        98 ~ih~~~~~~~~~~l~~~dY~L~d~~~E--------~l---~--------------------------r~~~~gkLf~~~~  140 (256)
T 3t7k_A           98 QIHSKKDKLSQININLFDYEINGINES--------II---S--------------------------KTKLPTKVFERAN  140 (256)
T ss_dssp             HHC-------CCCCCSSTTBCTTCCHH--------HH---H--------------------------HTTSSSCHHHHTT
T ss_pred             HhhcCCcccccccCChhhccCCCcchh--------HH---h--------------------------hhccccccccCCc
Confidence            8   77      777888887643210        00   0                          011236899998 


Q ss_pred             --EEEEeCCCCHHHHHHHHHHHHhCCCEE---Ecc-ccCC--------------CCceEEEEcCc-----hHHHHh---c
Q 012081          204 --SMYVDSDVSEELRNKVFEAATNEGATL---VNQ-WFVG--------------CGASYVVCEED-----SVQKYM---G  255 (471)
Q Consensus       204 --~Iyl~~gfs~~~r~~L~~lI~~~GG~v---~d~-~~~~--------------~~vTHVVv~~~-----s~~k~l---~  255 (471)
                        +|++..++..- .+.++.+++.+||.=   ... .+..              ....+|++...     .+++.+   .
T Consensus       141 I~ciNls~dI~GG-~e~issIleahG~~~~~~l~~~~~~~~dl~~n~~~~~~~~~~~~~ILia~K~~q~k~Fkk~~~~~~  219 (256)
T 3t7k_A          141 IRCINLVNDIPGG-VDTIGSVLKAHGIEKINVLRSKKCTFEDIIPNDVSKQENGGIFKYVLIVTKASQVKKFTKLINDRD  219 (256)
T ss_dssp             CCEEEEETTCTTC-HHHHHHHHHHTTCCEEEEECTTTCCGGGCCCCC--------CCSEEEECSCHHHHHHHHHHHHHHS
T ss_pred             ceeeeeccCCCCC-HHHHHHHHHHcCCceeeecccccccHHHhhhccccccccCCCCCEEEEEccHHHHHHHHHHhhccc
Confidence              66666666643 367899999999952   222 1111              12347776552     234444   1


Q ss_pred             --CCCceechhHHHHHHhhCC
Q 012081          256 --HSNNLVTPVWVLKTAKEKH  274 (471)
Q Consensus       256 --~~~~IVs~~WL~dcik~g~  274 (471)
                        ...-+|.=.|..+||=...
T Consensus       220 ~n~~~lvveWdWCVksIF~le  240 (256)
T 3t7k_A          220 KNETILIVEWNWCVESIFHLN  240 (256)
T ss_dssp             TTSCEEEECHHHHHHHHHTTS
T ss_pred             ccceEEEEEcHHHHHHHhhee
Confidence              4567999999999996543

>2k6g_A Replication factor C subunit 1; protein, BRCT, DNA binding, activator, alternative splicing, ATP-binding, DNA replication, DNA- binding; NMR {Homo sapiens} PDB: 2k7f_A

Probab=98.03  E-value=1.2e-05  Score=68.72  Aligned_cols=75  Identities=13%  Similarity=0.181  Sum_probs=62.5

Q ss_pred             CCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCc----hHHHHhcCCCceechhHHHHHHhh
Q 012081          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED----SVQKYMGHSNNLVTPVWVLKTAKE  272 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~----s~~k~l~~~~~IVs~~WL~dcik~  272 (471)
                      ...|.|.+|.|...++.-.|+.+.++|..+||.|..+  +..+++|||+++.    .++++...+++||+.+|+++.+..
T Consensus        30 ~~~l~G~~~v~TG~l~~~~R~e~~~~i~~~Gg~v~~s--VSkkTd~LV~G~~~g~sK~~kA~~lgI~Ii~E~~f~~ll~~  107 (109)
T 2k6g_A           30 ENCLEGLIFVITGVLESIERDEAKSLIERYGGKVTGN--VSKKTNYLVMGRDSGQSKSDKAAALGTKIIDEDGLLNLIRN  107 (109)
T ss_dssp             TTTTTTCEEEEESBCSSCCHHHHHHHHHHTTCEEESS--CCTTCCEEEECBCCCHHHHHHHHHHTCEEECHHHHHHHHHH
T ss_pred             CCCCCCCEEEEeeeCCCCCHHHHHHHHHHcCCEeeCc--ccCCceEEEECCCCChHHHHHHHHcCCeEEeHHHHHHHHHh
Confidence            4579999999944465546889999999999999999  7899999999884    345555689999999999999976


Q ss_pred             C
Q 012081          273 K  273 (471)
Q Consensus       273 g  273 (471)
                      +
T Consensus       108 ~  108 (109)
T 2k6g_A          108 L  108 (109)
T ss_dssp             T
T ss_pred             C
Confidence            5

>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2 PDB: 1v9p_A*

Probab=97.96  E-value=1.1e-06  Score=96.40  Aligned_cols=77  Identities=26%  Similarity=0.337  Sum_probs=0.0

Q ss_pred             CCCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHHHHHHHhcCCCCCceEecchHHHHHHHc
Q 012081           55 NAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVRR  134 (471)
Q Consensus        55 ~~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~Dcik~  134 (471)
                      ..+|.|++|++||.....|.+++++|+.+||++...+++++++||++...|.|+++|.+.    ||+||+.+|+.+.+..
T Consensus       585 ~~~l~G~~~v~TG~l~~~R~e~~~~i~~~Ggkv~~sVSkkTd~lV~G~~~gsKl~KA~~l----gI~Ii~E~~f~~~l~~  660 (667)
T 1dgs_A          585 SDLLSGLTFVLTGELSRPREEVKALLGRLGAKVTDSVSRKTSYLVVGENPGSKLEKARAL----GVAVLTEEEFWRFLKE  660 (667)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccccCCCEEEEeCCCCCCHHHHHHHHHHcCCEEcCcccCCeeEEEECCCCChHHHHHHHC----CCeEEeHHHHHHHHhc
Confidence            357999999999976659999999999999999999999999999999999999999986    8999999999999875


Q ss_pred             c
Q 012081          135 N  135 (471)
Q Consensus       135 g  135 (471)
                      +
T Consensus       661 ~  661 (667)
T 1dgs_A          661 K  661 (667)
T ss_dssp             -
T ss_pred             C
Confidence            4

>2cok_A Poly [ADP-ribose] polymerase-1; BRCT domain, DNA repair, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2le0_A

Probab=97.92  E-value=3.3e-05  Score=66.36  Aligned_cols=71  Identities=10%  Similarity=0.152  Sum_probs=58.1

Q ss_pred             CCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcC------chHHHHhcCCCceechhHHHHHH
Q 012081          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEE------DSVQKYMGHSNNLVTPVWVLKTA  270 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~------~s~~k~l~~~~~IVs~~WL~dci  270 (471)
                      ...|.|++|.|...++. .|+.+.++|..+||++..+  +..+++|||+.+      ..++++...+++||+.+||.++.
T Consensus         8 ~~~l~G~~~ViTG~l~~-~R~e~k~~ie~~Ggkv~~s--VskkT~~lV~g~~~e~~gsKl~kA~~lgI~IvsE~~l~~~~   84 (113)
T 2cok_A            8 DKPLSNMKILTLGKLSR-NKDEVKAMIEKLGGKLTGT--ANKASLCISTKKEVEKMNKKMEEVKEANIRVVSEDFLQDVS   84 (113)
T ss_dssp             CCSSSSCEEEECSCCSS-CHHHHHHHHHHTTCEEESC--STTCSEEECCHHHHHHCCHHHHHHHHTTCCEECTHHHHHHH
T ss_pred             CCCcCCCEEEEEecCCC-CHHHHHHHHHHCCCEEcCc--cccCccEEEECCCCCCCChHHHHHHHCCCcEEeHHHHHHHH
Confidence            45799999999555765 7899999999999999999  788999999983      23566667899999999954443

>2ebu_A Replication factor C subunit 1; A/B/A 3 layers, parallel beta-sheet, DNA replication, clamp loader, RFC1, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.91  E-value=2.3e-05  Score=67.24  Aligned_cols=75  Identities=13%  Similarity=0.179  Sum_probs=62.4

Q ss_pred             CCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCc----hHHHHhcCCCceechhHHHHHHhh
Q 012081          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED----SVQKYMGHSNNLVTPVWVLKTAKE  272 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~----s~~k~l~~~~~IVs~~WL~dcik~  272 (471)
                      ...|.|++|.|...|+.-.|+.++++|..+||+|..+  +..+++|||+++.    .++++...+++||+.+|+++.+..
T Consensus        20 ~~~l~G~~~v~TG~l~~~~R~e~~~~i~~~Ggkv~~s--VSkkTd~LV~G~~~g~sKl~KA~~lgI~IisE~~f~~ll~~   97 (112)
T 2ebu_A           20 ENCLEGLIFVITGVLESIERDEAKSLIERYGGKVTGN--VSKKTNYLVMGRDSGQSKSDKAAALGTKIIDEDGLLNLIRT   97 (112)
T ss_dssp             SSSSTTCEEEECSCCSSSCHHHHHHHHHHTTCEECSS--CCSSCCEEEECSSCCSHHHHHHHHHTCEEEEHHHHHHHHHH
T ss_pred             CCCcCCCEEEEeeeCCCCCHHHHHHHHHHcCCEEecc--ccCCeeEEEecCCCChHHHHHHHHcCCeEEeHHHHHHHHhh
Confidence            3579999999944455556899999999999999999  7899999999884    345555789999999999999975


Q ss_pred             C
Q 012081          273 K  273 (471)
Q Consensus       273 g  273 (471)
                      +
T Consensus        98 ~   98 (112)
T 2ebu_A           98 M   98 (112)
T ss_dssp             S
T ss_pred             C
Confidence            4

>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli}

Probab=97.86  E-value=2e-06  Score=94.37  Aligned_cols=75  Identities=16%  Similarity=0.305  Sum_probs=0.0

Q ss_pred             CCCCCCcEEEEeCCCh-hhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHHHHHHHhcCCCCCceEecchHHHHHHH
Q 012081           55 NAPFSGLVICVTGLSK-EARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVR  133 (471)
Q Consensus        55 ~~iF~GlvI~vTG~~~-~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~Dcik  133 (471)
                      ..+|.|++|++||... -.|.+++++|+.+||++...+++++++||++...|.|+++|.+.    ||+||+.+|+.+.+.
T Consensus       595 ~~~l~G~~~v~TG~l~~~~R~e~~~~i~~~Ggkv~~sVSkkTd~lV~G~~~gsKl~KA~~l----gI~Ii~E~~f~~~l~  670 (671)
T 2owo_A          595 DSPFAGKTVVLTGSLSQMSRDDAKARLVELGAKVAGSVSKKTDLVIAGEAAGSKLAKAQEL----GIEVIDEAEMLRLLG  670 (671)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CCcccCcEEEEcCCCCCCCHHHHHHHHHHcCCEEeCcccCceeEEEECCCCChHHHHHHHC----CCcEEcHHHHHHHhc
Confidence            4579999999999776 48999999999999999999999999999999999999999986    899999999988764

>2l42_A DNA-binding protein RAP1; BRCT domain, protein binding; NMR {Saccharomyces cerevisiae}

Probab=97.57  E-value=5e-05  Score=63.07  Aligned_cols=82  Identities=16%  Similarity=0.203  Sum_probs=65.9

Q ss_pred             CCCCCCCcEEEEeCCCh-----hhHHHHHHHHHHcCCEEcccCCCCc--eEEEEecCCCHHHHHHHhcCCCCCceEecch
Q 012081           54 ANAPFSGLVICVTGLSK-----EARKQVMEATERLGGQYSPDLHPQC--THLVVQSFGGRKFEHALKHGSRNGLYIVTLG  126 (471)
Q Consensus        54 ~~~iF~GlvI~vTG~~~-----~er~~L~~lI~~~GG~~~~~l~~~~--THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~  126 (471)
                      ...+|+|+.|.+.--+.     .+.++|+++|..+||.+...+.++.  .+.|++....            .+++.|+|.
T Consensus         8 ~~~vF~g~~Fyin~d~~a~ds~~d~d~L~~lI~~nGG~Vl~~lP~~s~~~~yVVSpyN~------------t~LpTVtpT   75 (106)
T 2l42_A            8 SGPPLSNMKFYLNRDADAHDSLNDIDQLARLIRANGGEVLDSKPRESKENVFIVSPYNH------------TNLPTVTPT   75 (106)
T ss_dssp             SSCSSCCCCBEECCSSSCSSCSSTHHHHHHHHHTTTSCCCEECCCCCSSCCCCBCTTCC------------CSSSBCCTT
T ss_pred             cCccccCcEEEEcCCCccchhhhHHHHHHHHHHhcCcEEhhhCcccccCCeEEEeCCCC------------CCCccccHH
Confidence            45789999999964222     5789999999999999999987633  3555544322            268999999


Q ss_pred             HHHHHHHcccCCCCCcccccc
Q 012081          127 WFVDSVRRNVRLSESLYTVKS  147 (471)
Q Consensus       127 WI~Dcik~g~~lde~~Y~l~~  147 (471)
                      +|.+|+.++.+|+-.+|.++.
T Consensus        76 YI~aC~~~nTLLnv~~YLvp~   96 (106)
T 2l42_A           76 YIKACCQSNSLLNMENYLVPY   96 (106)
T ss_dssp             HHHHHHHSTTSCGGGGCCBCS
T ss_pred             HHHHHHhcCceecccccccCc
Confidence            999999999999999999974

>3huf_A DNA repair and telomere maintenance protein NBS1; NBS1, FHA domain, BRCT domain, phosphoprotein binding, phosp binding, DNA repair; HET: DNA TPO; 2.15A {Schizosaccharomyces pombe} PDB: 3hue_A* 3i0m_A* 3i0n_A*

Probab=97.53  E-value=0.00055  Score=68.42  Aligned_cols=178  Identities=13%  Similarity=0.052  Sum_probs=99.8

Q ss_pred             CCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccC-CCCceEEEEecCCC----HHHHHHHhcCCCCCceEecchHHHHHH
Q 012081           58 FSGLVICVTGLSKEARKQVMEATERLGGQYSPDL-HPQCTHLVVQSFGG----RKFEHALKHGSRNGLYIVTLGWFVDSV  132 (471)
Q Consensus        58 F~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l-~~~~THLV~~~~~g----~Ky~~A~k~~~~~gi~IV~p~WI~Dci  132 (471)
                      +.-+++|++  +.+.+..+.+.++.+||++. ++ ...|||||+.+..+    .|...|+-    ++++||+++||.+..
T Consensus       113 W~P~Vl~~S--ske~~~~L~~~L~~LGik~v-~~~~detTHlVm~krnT~KvTvK~L~ALI----~gkPIV~~~Fl~al~  185 (325)
T 3huf_A          113 WRSMCIQFD--NPEMLSQWASNLNLLGIPTG-LRDSDATTHFVMNRQAGSSITVGTMYAFL----KKTVIIDDSYLQYLS  185 (325)
T ss_dssp             ECCCCEEES--CHHHHHHHHHHHHTTTCCEE-SSCCTTCCEEECCCCCSSCCCHHHHHHHH----TTCEEECHHHHHHHT
T ss_pred             EeeeEEEec--CHHHHHHHHHHHHHcCCEEE-EccCCCEEEEEEeccccccchHHHHHHHH----CCCcEecHHHHHHHH
Confidence            455667773  23467779999999999999 66 56899999986544    45888876    489999999999875


Q ss_pred             HcccCCCCCccccccccccCcchhhhhcccCCcCCCCCCCCcccchhhccccccccccccccCCCCCCCCcEEEEeCCCC
Q 012081          133 RRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVS  212 (471)
Q Consensus       133 k~g~~lde~~Y~l~~~~e~~~~~~~~~~L~~~s~~e~~~lp~~I~es~~s~s~E~ld~~~~~~~~~lF~G~~Iyl~~gfs  212 (471)
                      +..+-.-+..=.+++..+.      .+.+.  .+.|....    ....+               ..-|.|.++++ .+-+
T Consensus       186 ~~e~~~~~~~~~wPdp~df------lP~i~--~g~Ep~~~----~~~~~---------------~~~~~~~~~~~-~~~~  237 (325)
T 3huf_A          186 TVKESVIEDASLMPDALEC------FKNII--KNNDQFPS----SPEDC---------------INSLEGFSCAM-LNTS  237 (325)
T ss_dssp             TCTTCCCCTTSSHHHHHHH------HHHHH--TTCTTCCS----CHHHH---------------TTTTTTCEEEE-ETCC
T ss_pred             HhhhhhhhcccCCCChHHc------CCCCC--CCCCCCCC----CHHHh---------------hcccCceEEEE-EcCc
Confidence            4321110000011100000      00000  00000000    01111               34689988888 3333


Q ss_pred             HHHHHHHHHHHHhCCCEEEccc-------cCCCCceEEEEcCch--HHHH-hcCCCceechhHHHHHHhhCC
Q 012081          213 EELRNKVFEAATNEGATLVNQW-------FVGCGASYVVCEEDS--VQKY-MGHSNNLVTPVWVLKTAKEKH  274 (471)
Q Consensus       213 ~~~r~~L~~lI~~~GG~v~d~~-------~~~~~vTHVVv~~~s--~~k~-l~~~~~IVs~~WL~dcik~g~  274 (471)
                      .    .+.-++...|=.+..-+       .+-++..+||..+.-  ..+. ...++.+.+.+=+++-+-+..
T Consensus       238 ~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  305 (325)
T 3huf_A          238 S----ESHHLLELLGLRISTFMSLGDIDKELISKTDFVVLNNAVYDSEKISFPEGIFCLTIEQLWKIIIERN  305 (325)
T ss_dssp             H----HHHHHHHHTTCEEEEEC------CCSSSSCSEEEEC-------------CCCEEEHHHHHHHHHSSS
T ss_pred             h----hhhHHHHHhcceeeeeeecccchHhhhccccEEEEcccccccccccCCcceEEEEHHHHHHHHhhcc
Confidence            2    35566777787776532       134566677776631  1221 256788888888888776644

>2l42_A DNA-binding protein RAP1; BRCT domain, protein binding; NMR {Saccharomyces cerevisiae}

Probab=97.27  E-value=0.00016  Score=60.13  Aligned_cols=79  Identities=13%  Similarity=0.209  Sum_probs=59.7

Q ss_pred             CCCCCCcEEEEeCCC----CHHHHHHHHHHHHhCCCEEEccccCCCCc--eEEEEcCchHHHHhcCCCceechhHHHHHH
Q 012081          197 NSTLSGCSMYVDSDV----SEELRNKVFEAATNEGATLVNQWFVGCGA--SYVVCEEDSVQKYMGHSNNLVTPVWVLKTA  270 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gf----s~~~r~~L~~lI~~~GG~v~d~~~~~~~v--THVVv~~~s~~k~l~~~~~IVs~~WL~dci  270 (471)
                      ...|.|+.|||..+-    +....+.|.++|+.+||+|+..+  ..+.  .+.||++     |-......|+|.+|..|+
T Consensus         9 ~~vF~g~~Fyin~d~~a~ds~~d~d~L~~lI~~nGG~Vl~~l--P~~s~~~~yVVSp-----yN~t~LpTVtpTYI~aC~   81 (106)
T 2l42_A            9 GPPLSNMKFYLNRDADAHDSLNDIDQLARLIRANGGEVLDSK--PRESKENVFIVSP-----YNHTNLPTVTPTYIKACC   81 (106)
T ss_dssp             SCSSCCCCBEECCSSSCSSCSSTHHHHHHHHHTTTSCCCEEC--CCCCSSCCCCBCT-----TCCCSSSBCCTTHHHHHH
T ss_pred             CccccCcEEEEcCCCccchhhhHHHHHHHHHHhcCcEEhhhC--cccccCCeEEEeC-----CCCCCCccccHHHHHHHH
Confidence            568999999996431    22356889999999999999883  3332  2444443     223467899999999999


Q ss_pred             hhCCcCccCCcC
Q 012081          271 KEKHVQRLVHIS  282 (471)
Q Consensus       271 k~g~lqp~~~ys  282 (471)
                      .++.|+++.+|=
T Consensus        82 ~~nTLLnv~~YL   93 (106)
T 2l42_A           82 QSNSLLNMENYL   93 (106)
T ss_dssp             HSTTSCGGGGCC
T ss_pred             hcCceecccccc
Confidence            999999998884

>4gns_A Chitin biosynthesis protein CHS5; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=96.76  E-value=0.0055  Score=56.04  Aligned_cols=89  Identities=16%  Similarity=0.260  Sum_probs=67.8

Q ss_pred             CCCCCCCcEEEEeCCCh---hhHHHHHHHHHHcCCEEccc-CCCCceEEEEecCC----CHHHHHHHhcCCCCCceEecc
Q 012081           54 ANAPFSGLVICVTGLSK---EARKQVMEATERLGGQYSPD-LHPQCTHLVVQSFG----GRKFEHALKHGSRNGLYIVTL  125 (471)
Q Consensus        54 ~~~iF~GlvI~vTG~~~---~er~~L~~lI~~~GG~~~~~-l~~~~THLV~~~~~----g~Ky~~A~k~~~~~gi~IV~p  125 (471)
                      +-.-+.|+.+|+.-+++   ..--+|.+.....|+.-.+. +--++||.||.+.+    .+....|..    ++|+||.|
T Consensus       158 kmtdmsgitvclgpldplkeisdlqisqclshigarplqrhvaidtthfvcndldneesneelirakh----nnipivrp  233 (290)
T 4gns_A          158 KMTDMSGITVCLGPLDPLKEISDLQISQCLSHIGARPLQRHVAIDTTHFVCNDLDNEESNEELIRAKH----NNIPIVRP  233 (290)
T ss_dssp             CTTCCTTCCEEECCCCGGGTCCHHHHHHHHHHTTCCCCBSSCCTTCCEEECSCCTTCTTCHHHHHHHH----TTCCEECT
T ss_pred             ccccccCceEEecCCChhhhhhhccHHHHHHHhCCchhhheeeeecceeeecCCCcccchHHHHhhhc----cCCCccCH
Confidence            34567899999988876   34567888899999885544 43589999999864    345555554    59999999


Q ss_pred             hHHHHHHHcccCCCCCccccc
Q 012081          126 GWFVDSVRRNVRLSESLYTVK  146 (471)
Q Consensus       126 ~WI~Dcik~g~~lde~~Y~l~  146 (471)
                      +|+..|--..+.+.-..|.+.
T Consensus       234 ewvracevekrivgvrgfyld  254 (290)
T 4gns_A          234 EWVRACEVEKRIVGVRGFYLD  254 (290)
T ss_dssp             HHHHHHHHTTSCCCSGGGBTT
T ss_pred             HHHHHHhhhheeeeeeeEEEc
Confidence            999999988888777766664

>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2 PDB: 1v9p_A*

Probab=94.62  E-value=0.0059  Score=67.00  Aligned_cols=74  Identities=24%  Similarity=0.287  Sum_probs=0.0

Q ss_pred             CCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCc---hHHHHhcCCCceechhHHHHHHhhC
Q 012081          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED---SVQKYMGHSNNLVTPVWVLKTAKEK  273 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~---s~~k~l~~~~~IVs~~WL~dcik~g  273 (471)
                      ...|.|++|.|...++. .|+.++++|..+||++..+  ...++++||+++.   .++|+...+++|++.+|+++.+..+
T Consensus       585 ~~~l~G~~~v~TG~l~~-~R~e~~~~i~~~Ggkv~~s--VSkkTd~lV~G~~~gsKl~KA~~lgI~Ii~E~~f~~~l~~~  661 (667)
T 1dgs_A          585 SDLLSGLTFVLTGELSR-PREEVKALLGRLGAKVTDS--VSRKTSYLVVGENPGSKLEKARALGVAVLTEEEFWRFLKEK  661 (667)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccccCCCEEEEeCCCCC-CHHHHHHHHHHcCCEEcCc--ccCCeeEEEECCCCChHHHHHHHCCCeEEeHHHHHHHHhcC
Confidence            45799999999444666 8999999999999999999  7889999999874   3455556899999999999999765

>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli}

Probab=93.51  E-value=0.013  Score=64.27  Aligned_cols=73  Identities=15%  Similarity=0.197  Sum_probs=0.0

Q ss_pred             CCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCc---hHHHHhcCCCceechhHHHHHHh
Q 012081          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED---SVQKYMGHSNNLVTPVWVLKTAK  271 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~---s~~k~l~~~~~IVs~~WL~dcik  271 (471)
                      ...|.|++|.|...++.-.|+.++++|..+||++..+  ...++++||+++.   .++|+...+++|++.+|+++.+.
T Consensus       595 ~~~l~G~~~v~TG~l~~~~R~e~~~~i~~~Ggkv~~s--VSkkTd~lV~G~~~gsKl~KA~~lgI~Ii~E~~f~~~l~  670 (671)
T 2owo_A          595 DSPFAGKTVVLTGSLSQMSRDDAKARLVELGAKVAGS--VSKKTDLVIAGEAAGSKLAKAQELGIEVIDEAEMLRLLG  670 (671)
T ss_dssp             ------------------------------------------------------------------------------
T ss_pred             CCcccCcEEEEcCCCCCCCHHHHHHHHHHcCCEEeCc--ccCceeEEEECCCCChHHHHHHHCCCcEEcHHHHHHHhc
Confidence            4579999999944465557899999999999999999  7889999999874   34555568999999999998764

>3huf_A DNA repair and telomere maintenance protein NBS1; NBS1, FHA domain, BRCT domain, phosphoprotein binding, phosp binding, DNA repair; HET: DNA TPO; 2.15A {Schizosaccharomyces pombe} PDB: 3hue_A* 3i0m_A* 3i0n_A*

Probab=92.83  E-value=0.26  Score=49.22  Aligned_cols=86  Identities=6%  Similarity=-0.016  Sum_probs=59.5

Q ss_pred             CCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCc---h----HHHHhcCCCceechhHHHHHHhh-
Q 012081          201 SGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED---S----VQKYMGHSNNLVTPVWVLKTAKE-  272 (471)
Q Consensus       201 ~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~---s----~~k~l~~~~~IVs~~WL~dcik~-  272 (471)
                      .-..+++ +  +.+.+..|++.+...||.++ +| ....+||||+...   .    ...++-.+.+||+++||....+. 
T Consensus       114 ~P~Vl~~-S--ske~~~~L~~~L~~LGik~v-~~-~~detTHlVm~krnT~KvTvK~L~ALI~gkPIV~~~Fl~al~~~e  188 (325)
T 3huf_A          114 RSMCIQF-D--NPEMLSQWASNLNLLGIPTG-LR-DSDATTHFVMNRQAGSSITVGTMYAFLKKTVIIDDSYLQYLSTVK  188 (325)
T ss_dssp             CCCCEEE-S--CHHHHHHHHHHHHTTTCCEE-SS-CCTTCCEEECCCCCSSCCCHHHHHHHHTTCEEECHHHHHHHTTCT
T ss_pred             eeeEEEe-c--CHHHHHHHHHHHHHcCCEEE-Ec-cCCCEEEEEEeccccccchHHHHHHHHCCCcEecHHHHHHHHHhh
Confidence            3345555 3  34466779999999999999 75 5777999999752   2    33344579999999999987632 


Q ss_pred             -CCcCccCCcChHHHhhhhhh
Q 012081          273 -KHVQRLVHISADLARQVGMM  292 (471)
Q Consensus       273 -g~lqp~~~ys~dl~r~~~~~  292 (471)
                       ..++. ..-.++...++|-+
T Consensus       189 ~~~~~~-~~~wPdp~dflP~i  208 (325)
T 3huf_A          189 ESVIED-ASLMPDALECFKNI  208 (325)
T ss_dssp             TCCCCT-TSSHHHHHHHHHHH
T ss_pred             hhhhhc-ccCCCChHHcCCCC
Confidence             22222 23456777888775

>4gns_A Chitin biosynthesis protein CHS5; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=91.77  E-value=0.25  Score=45.22  Aligned_cols=89  Identities=16%  Similarity=0.278  Sum_probs=61.6

Q ss_pred             CCCCCCcEEEEeCCCCHH---HHHHHHHHHHhCCCEEEccccCCCCceEEEEcC---c----hHHHHhcCCCceechhHH
Q 012081          197 NSTLSGCSMYVDSDVSEE---LRNKVFEAATNEGATLVNQWFVGCGASYVVCEE---D----SVQKYMGHSNNLVTPVWV  266 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~---~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~---~----s~~k~l~~~~~IVs~~WL  266 (471)
                      ..-++|.++|+ ..+++-   .--++.+-+.--|+.-.... ..-+.||.||.+   +    ++.+.-..++.||.|+|+
T Consensus       159 mtdmsgitvcl-gpldplkeisdlqisqclshigarplqrh-vaidtthfvcndldneesneelirakhnnipivrpewv  236 (290)
T 4gns_A          159 MTDMSGITVCL-GPLDPLKEISDLQISQCLSHIGARPLQRH-VAIDTTHFVCNDLDNEESNEELIRAKHNNIPIVRPEWV  236 (290)
T ss_dssp             TTCCTTCCEEE-CCCCGGGTCCHHHHHHHHHHTTCCCCBSS-CCTTCCEEECSCCTTCTTCHHHHHHHHTTCCEECTHHH
T ss_pred             cccccCceEEe-cCCChhhhhhhccHHHHHHHhCCchhhhe-eeeecceeeecCCCcccchHHHHhhhccCCCccCHHHH
Confidence            44578999999 433321   11345666777788755442 566789999977   1    233333588999999999


Q ss_pred             HHHHhhCCcCccCCcChHHHh
Q 012081          267 LKTAKEKHVQRLVHISADLAR  287 (471)
Q Consensus       267 ~dcik~g~lqp~~~ys~dl~r  287 (471)
                      -.|--++.++-+-.+..|..+
T Consensus       237 racevekrivgvrgfyldadq  257 (290)
T 4gns_A          237 RACEVEKRIVGVRGFYLDADQ  257 (290)
T ss_dssp             HHHHHTTSCCCSGGGBTTSCG
T ss_pred             HHHhhhheeeeeeeEEEcccH
Confidence            999999988887777666544

>3t7k_A RTT107, regulator of TY1 transposition protein 107; BRCT, DNA repair, phospho-peptide, protein binding; HET: SEP; 2.03A {Saccharomyces cerevisiae} PDB: 3t7j_A* 3t7i_A

Probab=90.15  E-value=0.35  Score=46.71  Aligned_cols=73  Identities=11%  Similarity=0.149  Sum_probs=49.7

Q ss_pred             cEEEEeCCCC-----HHHHHHHHHHHHhCCCEEEccccCC--CCceEEEEcCc-hHHHHh---cCCCc--eechhHHHHH
Q 012081          203 CSMYVDSDVS-----EELRNKVFEAATNEGATLVNQWFVG--CGASYVVCEED-SVQKYM---GHSNN--LVTPVWVLKT  269 (471)
Q Consensus       203 ~~Iyl~~gfs-----~~~r~~L~~lI~~~GG~v~d~~~~~--~~vTHVVv~~~-s~~k~l---~~~~~--IVs~~WL~dc  269 (471)
                      ++..+ +|+.     ...+    +.++..|=.+++.  .+  ..++||+.+.- ...||+   +.++-  +|+|.||.+|
T Consensus        23 i~ai~-TGc~~~~~~~~D~----~~Lr~LGI~Iv~d--~~~~~~~n~LiAPkilRT~KFL~sLa~~P~~~il~p~FI~~~   95 (256)
T 3t7k_A           23 LKAVC-TGCFHDGFNEVDI----EILNQLGIKIFDN--IKETDKLNCIFAPKILRTEKFLKSLSFEPLKFALKPEFIIDL   95 (256)
T ss_dssp             EEEEE-SSSCSSCCCHHHH----HHHHHTTEEECSS--CCGGGCCCEEECSSCCCBHHHHHHTTSTTCCEEECTHHHHHH
T ss_pred             EEEEe-cCCcccccCHHHH----HHHHHcCeEEEec--CcccCCCCEEEcCchhhHHHHHHHhccCccceEeCHHHHHHH
Confidence            45555 5554     4444    4455668888887  33  48999999882 344554   66664  9999999999


Q ss_pred             Hhh---CC------cCccCCcC
Q 012081          270 AKE---KH------VQRLVHIS  282 (471)
Q Consensus       270 ik~---g~------lqp~~~ys  282 (471)
                      ++.   |+      +++..+|.
T Consensus        96 Lk~ih~~~~~~~~~~l~~~dY~  117 (256)
T 3t7k_A           96 LKQIHSKKDKLSQININLFDYE  117 (256)
T ss_dssp             HHHHC-------CCCCCSSTTB
T ss_pred             HHHhhcCCcccccccCChhhcc
Confidence            998   77      77777776

>3oq4_A DBF4, protein DNA52; DDK, BRCT, RAD53, replication checkpoint, FHA domain, regula subunit of DDK, CDC7, phosphorylation, nuclear; 2.40A {Saccharomyces cerevisiae}

Probab=89.88  E-value=0.57  Score=40.95  Aligned_cols=59  Identities=12%  Similarity=0.059  Sum_probs=47.9

Q ss_pred             hHHHHHHHHHHcCCEEcccCCCCceEEEEecCCC--------HHHHHHHhcCCCCCceEecchHHHHHHHc
Q 012081           72 ARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGG--------RKFEHALKHGSRNGLYIVTLGWFVDSVRR  134 (471)
Q Consensus        72 er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g--------~Ky~~A~k~~~~~gi~IV~p~WI~Dcik~  134 (471)
                      .++.|++.+..+||++.+-++..+||+|+.....        +=...|.+.    +++|-+.+=+..-++.
T Consensus        31 ~~~llk~~f~~LGa~I~~FFd~~VTiiITrR~~~~~~~~p~~DIL~rAr~~----~mKIWs~EKl~RfL~~   97 (134)
T 3oq4_A           31 RRDLLKRGFLTLGAQITQFFDTTVTIVITRRSVENIYLLKDTDILSRAKKN----YMKVWSYEKAARFLKN   97 (134)
T ss_dssp             HHHHHHHHHHHTTCEEESSCCTTCCEEEESSCGGGGGGSCTTSHHHHHHHT----TCEEEEHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCEEeeecCCceEEEEeCCcCcccccCCcchHHHHHHHc----CCeeeeHHHHHHHHHh
Confidence            5678899999999999999999999999987632        224667775    8999998888766665

>3qbz_A DDK kinase regulatory subunit DBF4; FHA domain,RAD53, replication checkpoint, cell cycle; 2.69A {Saccharomyces cerevisiae}

Probab=89.13  E-value=0.72  Score=41.45  Aligned_cols=74  Identities=11%  Similarity=0.009  Sum_probs=55.4

Q ss_pred             CCCC-CcEEEEeCCChh------------hHHHHHHHHHHcCCEEcccCCCCceEEEEecCCC--------HHHHHHHhc
Q 012081           56 APFS-GLVICVTGLSKE------------ARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGG--------RKFEHALKH  114 (471)
Q Consensus        56 ~iF~-GlvI~vTG~~~~------------er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g--------~Ky~~A~k~  114 (471)
                      ++|. +.+|.+-+...+            .+..+++.+..+|+++.+-++.++||||+.....        +-+..|.+.
T Consensus        57 kifk~~~vfYFDt~~~~~~~~~~k~kl~K~~~llkr~f~~LGA~I~~FFd~~VTiVIT~R~i~~~~~~~~~Dil~~A~~~  136 (160)
T 3qbz_A           57 KIMKRDSRIYFDITDDVEMNTYNKSKMDKRRDLLKRGFLTLGAQITQFFDTTVTIVITRRSVENIYLLKDTDILSRAKKN  136 (160)
T ss_dssp             HHHHHHCEEEECCCCSSCCCHHHHHHHHHHHHHHHHHHHTTTCEEESSCCTTCCEEEESSCSSCGGGSCTTSHHHHHHHT
T ss_pred             HhCccCcEEEecCCChhhhhHHHHHHHHHHHHHHHHHHHHcCCEeeeeccCCeEEEEecCcCcccccCCchhHHHHHHHc
Confidence            5787 799999877643            1244667888999999999999999999988632        236667663


Q ss_pred             CCCCCceEecchHHHHHHH
Q 012081          115 GSRNGLYIVTLGWFVDSVR  133 (471)
Q Consensus       115 ~~~~gi~IV~p~WI~Dcik  133 (471)
                          +++|-+.+=+..-++
T Consensus       137 ----~mKVW~yeK~~RFLk  151 (160)
T 3qbz_A          137 ----YMKVWSYEKAARFLK  151 (160)
T ss_dssp             ----TCEEEEHHHHHHHHH
T ss_pred             ----CceecchHHHHHHHH
Confidence                789988776655554

>3oq0_A DBF4, protein DNA52; DDK, BRCT, RAD53, replication checkpoint, FHA domain, regula subunit of DDK, CDC7, phosphorylation, nuclear; 2.70A {Saccharomyces cerevisiae}

Probab=87.80  E-value=2.2  Score=38.03  Aligned_cols=74  Identities=11%  Similarity=0.108  Sum_probs=48.7

Q ss_pred             CCCC-CCcEEEEeCC-C---CH-------HHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCc--h---------HHHH
Q 012081          197 NSTL-SGCSMYVDSD-V---SE-------ELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED--S---------VQKY  253 (471)
Q Consensus       197 ~~lF-~G~~Iyl~~g-f---s~-------~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~--s---------~~k~  253 (471)
                      ..++ ++..||||.. .   +.       ..++.|++.+...||+|..=  ++.+|||||+..+  .         +.++
T Consensus        18 rkIM~r~s~iYFdt~~~~~~~~~~~~~l~k~~~llkk~f~~LGa~I~~F--Fd~~VTiIITrR~~~~~~~yp~~DIL~rA   95 (151)
T 3oq0_A           18 GSHMKRDSRIYFDITDDVEMNTYNKSKMDKRRDLLKRGFLTLGAQITQF--FDTTVTIVITRRSVENIYLLKDTDILSRA   95 (151)
T ss_dssp             ---CCCCCEEEECCCCSSCCCHHHHHHHHHHHHHHHHHHHHHTCEEESS--CCTTCCEEEESSCGGGGGGSCTTSHHHHH
T ss_pred             HHHhccCCEEEEeCCCcchhhHHHHHHHHHHHHHHHHHHHHcCCEEeee--cCCceEEEEeCCcCcccccCCcchHHHHH
Confidence            4567 7889999743 2   21       23456778889999999986  7999999999773  1         2333


Q ss_pred             hcCCCceechhHHHHHHhh
Q 012081          254 MGHSNNLVTPVWVLKTAKE  272 (471)
Q Consensus       254 l~~~~~IVs~~WL~dcik~  272 (471)
                      ...+.+|=+.+=+..-++.
T Consensus        96 r~~~mKIWs~EKl~RfL~~  114 (151)
T 3oq0_A           96 KKNYMKVWSYEKAARFLKN  114 (151)
T ss_dssp             HHTTCEEEEHHHHHHHHHT
T ss_pred             HHcCCeeecHHHHHHHHHh
Confidence            3456777666666555543

>3oq0_A DBF4, protein DNA52; DDK, BRCT, RAD53, replication checkpoint, FHA domain, regula subunit of DDK, CDC7, phosphorylation, nuclear; 2.70A {Saccharomyces cerevisiae}

Probab=87.54  E-value=1.4  Score=39.21  Aligned_cols=75  Identities=11%  Similarity=0.032  Sum_probs=54.9

Q ss_pred             CCC-CCcEEEEeCC--Ch----------hhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCC--------HHHHHHHhc
Q 012081           56 APF-SGLVICVTGL--SK----------EARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGG--------RKFEHALKH  114 (471)
Q Consensus        56 ~iF-~GlvI~vTG~--~~----------~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g--------~Ky~~A~k~  114 (471)
                      +|+ .+.+|.+-+-  ..          ..++.|++.+..+||++.+-|+..+||+|+.....        +=...|.+.
T Consensus        19 kIM~r~s~iYFdt~~~~~~~~~~~~~l~k~~~llkk~f~~LGa~I~~FFd~~VTiIITrR~~~~~~~yp~~DIL~rAr~~   98 (151)
T 3oq0_A           19 SHMKRDSRIYFDITDDVEMNTYNKSKMDKRRDLLKRGFLTLGAQITQFFDTTVTIVITRRSVENIYLLKDTDILSRAKKN   98 (151)
T ss_dssp             --CCCCCEEEECCCCSSCCCHHHHHHHHHHHHHHHHHHHHHTCEEESSCCTTCCEEEESSCGGGGGGSCTTSHHHHHHHT
T ss_pred             HHhccCCEEEEeCCCcchhhHHHHHHHHHHHHHHHHHHHHcCCEEeeecCCceEEEEeCCcCcccccCCcchHHHHHHHc
Confidence            567 6777777532  21          13466789999999999999999999999987632        234567775


Q ss_pred             CCCCCceEecchHHHHHHHc
Q 012081          115 GSRNGLYIVTLGWFVDSVRR  134 (471)
Q Consensus       115 ~~~~gi~IV~p~WI~Dcik~  134 (471)
                          +++|-+.+=+..-++.
T Consensus        99 ----~mKIWs~EKl~RfL~~  114 (151)
T 3oq0_A           99 ----YMKVWSYEKAARFLKN  114 (151)
T ss_dssp             ----TCEEEEHHHHHHHHHT
T ss_pred             ----CCeeecHHHHHHHHHh
Confidence                8999998888776665

>3qbz_A DDK kinase regulatory subunit DBF4; FHA domain,RAD53, replication checkpoint, cell cycle; 2.69A {Saccharomyces cerevisiae}

Probab=82.20  E-value=1  Score=40.50  Aligned_cols=49  Identities=12%  Similarity=0.165  Sum_probs=36.0

Q ss_pred             CCCCC-CcEEEEeCCC----CHH-------HHHHHHHHHHhCCCEEEccccCCCCceEEEEcC
Q 012081          197 NSTLS-GCSMYVDSDV----SEE-------LRNKVFEAATNEGATLVNQWFVGCGASYVVCEE  247 (471)
Q Consensus       197 ~~lF~-G~~Iyl~~gf----s~~-------~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~  247 (471)
                      ..+|. ++.||||+.-    +..       .++.|++.+...||.+..-  ++.+|||||+..
T Consensus        56 Rkifk~~~vfYFDt~~~~~~~~~~k~kl~K~~~llkr~f~~LGA~I~~F--Fd~~VTiVIT~R  116 (160)
T 3qbz_A           56 KKIMKRDSRIYFDITDDVEMNTYNKSKMDKRRDLLKRGFLTLGAQITQF--FDTTVTIVITRR  116 (160)
T ss_dssp             HHHHHHHCEEEECCCCSSCCCHHHHHHHHHHHHHHHHHHHTTTCEEESS--CCTTCCEEEESS
T ss_pred             HHhCccCcEEEecCCChhhhhHHHHHHHHHHHHHHHHHHHHcCCEeeee--ccCCeEEEEecC
Confidence            35787 8999997432    111       1234557788999999986  799999999976

---

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	471
d1t15a1	109	c.15.1.3 (A:1649-1757) Breast cancer associated pr	7e-17
d1wf6a_	132	c.15.1.5 (A:) DNA topoisomerase II binding protein	3e-13
d1cdza_	96	c.15.1.1 (A:) DNA-repair protein XRCC1 {Human (Hom	5e-13
d1t15a2	102	c.15.1.3 (A:1758-1859) Breast cancer associated pr	8e-11
d1l7ba_	92	c.15.1.2 (A:) NAD+-dependent DNA ligase, domain 4	9e-08
d1in1a_	88	c.15.1.2 (A:) DNA ligase III alpha {Human (Homo sa	3e-04

>d1t15a1 c.15.1.3 (A:1649-1757) Breast cancer associated protein, BRCA1 {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: BRCT domain
domain: Breast cancer associated protein, BRCA1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 74.0 bits (181), Expect = 7e-17
 Identities = 21/102 (20%), Positives = 44/102 (43%), Gaps = 2/102 (1%)

Query: 61  LVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALK--HGSRN 118
           + + V+GL+ E    V +   +     +  +  + TH+V+++      E  LK   G   
Sbjct: 2   MSMVVSGLTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAG 61

Query: 119 GLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNR 160
           G ++V+  W   S++    L+E  + V+    +G +     R
Sbjct: 62  GKWVVSYFWVTQSIKERKMLNEHDFEVRGDVVNGRNHQGPKR 103

>d1wf6a_ c.15.1.5 (A:) DNA topoisomerase II binding protein 1, TopBP1 {Human (Homo sapiens) [TaxId: 9606]} Length = 132

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: DNA topoisomerase II binding protein 1, TopBP1
domain: DNA topoisomerase II binding protein 1, TopBP1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.8 bits (157), Expect = 3e-13
 Identities = 22/109 (20%), Positives = 38/109 (34%), Gaps = 5/109 (4%)

Query: 41  PASSSLASDSVLPANAP---FSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTH 97
           P   +L +  V    AP     G  I + G S     ++       GG     L+   TH
Sbjct: 21  PTLENLENLDVSAFQAPEDLLDGCRIYLCGFSGRKLDKLRRLINSGGGVRFNQLNEDVTH 80

Query: 98  LVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVK 146
           ++V  +     +   K    +  ++V   W ++   +   LSE  Y   
Sbjct: 81  VIVGDYDDELKQFWNKS--AHRPHVVGAKWLLECFSKGYMLSEEPYIHS 127

>d1cdza_ c.15.1.1 (A:) DNA-repair protein XRCC1 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: DNA-repair protein XRCC1
domain: DNA-repair protein XRCC1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.8 bits (152), Expect = 5e-13
 Identities = 14/89 (15%), Positives = 26/89 (29%), Gaps = 3/89 (3%)

Query: 58  FSGLVICVTG-LSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGS 116
           F G    + G    + R++++       G+    +  +   ++        FE       
Sbjct: 6   FQGKHFFLYGEFPGDERRKLIRYVTAFNGELEDYMSDRVQFVITAQEWDPSFEE--ALMD 63

Query: 117 RNGLYIVTLGWFVDSVRRNVRLSESLYTV 145
              L  V   W      +   L   LY V
Sbjct: 64  NPSLAFVRPRWIYSCNEKQKLLPHQLYGV 92

>d1t15a2 c.15.1.3 (A:1758-1859) Breast cancer associated protein, BRCA1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: BRCT domain
domain: Breast cancer associated protein, BRCA1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.4 bits (135), Expect = 8e-11
 Identities = 21/98 (21%), Positives = 30/98 (30%), Gaps = 7/98 (7%)

Query: 58  FSGLVICVTG-LSKEARKQVMEATERLGGQYSPDLH------PQCTHLVVQSFGGRKFEH 110
           F GL IC  G  +     Q+    +  G     +L            +VVQ     +   
Sbjct: 4   FRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTLGTGVHPIVVVQPDAWTEDNG 63

Query: 111 ALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSI 148
               G      +VT  W +DSV          Y +  I
Sbjct: 64  FHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQI 101

>d1l7ba_ c.15.1.2 (A:) NAD+-dependent DNA ligase, domain 4 {Thermus thermophilus [TaxId: 274]} Length = 92

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: DNA ligase
domain: NAD+-dependent DNA ligase, domain 4
species: Thermus thermophilus [TaxId: 274]

 Score = 47.8 bits (114), Expect = 9e-08
 Identities = 18/80 (22%), Positives = 29/80 (36%), Gaps = 4/80 (5%)

Query: 54  ANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALK 113
                 GL   +TG     R++V     RLG + +  +  + ++LVV    G K E A  
Sbjct: 4   GGEALKGLTFVITGELSRPREEVKALLRRLGAKVTDSVSRKTSYLVVGENPGSKLEKARA 63

Query: 114 HGSRNGLYIVTLGWFVDSVR 133
            G       +T       + 
Sbjct: 64  LGVP----TLTEEELYRLLE 79

>d1in1a_ c.15.1.2 (A:) DNA ligase III alpha {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: DNA ligase
domain: DNA ligase III alpha
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.6 bits (87), Expect = 3e-04
 Identities = 8/83 (9%), Positives = 24/83 (28%), Gaps = 14/83 (16%)

Query: 58  FSGLVICVTGLSKEARKQVMEATERLGGQYSPDLH-PQCTHLVVQSFGGRKFEHALKHGS 116
           F+G+ + +   + +  +          G    +      TH++         +       
Sbjct: 17  FTGVRLYLPPSTPDFSRLRRYFVA-FDGDLVQEFDMTSATHVLGSRDKNPAAQ------- 68

Query: 117 RNGLYIVTLGWFVDSVRRNVRLS 139
                 V+  W    +R+   ++
Sbjct: 69  -----QVSPEWIWACIRKRRLVA 86

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	471
d1cdza_	96	DNA-repair protein XRCC1 {Human (Homo sapiens) [Ta	99.74
d1wf6a_	132	DNA topoisomerase II binding protein 1, TopBP1 {Hu	99.72
d1t15a1	109	Breast cancer associated protein, BRCA1 {Human (Ho	99.67
d1t15a2	102	Breast cancer associated protein, BRCA1 {Human (Ho	99.6
d1wf6a_	132	DNA topoisomerase II binding protein 1, TopBP1 {Hu	99.6
d1cdza_	96	DNA-repair protein XRCC1 {Human (Homo sapiens) [Ta	99.55
d1in1a_	88	DNA ligase III alpha {Human (Homo sapiens) [TaxId:	99.34
d1l7ba_	92	NAD+-dependent DNA ligase, domain 4 {Thermus therm	99.3
d1t15a2	102	Breast cancer associated protein, BRCA1 {Human (Ho	99.28
d1in1a_	88	DNA ligase III alpha {Human (Homo sapiens) [TaxId:	99.24
d1kzyc1	153	53BP1 {Human (Homo sapiens) [TaxId: 9606]}	99.23
d1t15a1	109	Breast cancer associated protein, BRCA1 {Human (Ho	99.19
d1l7ba_	92	NAD+-dependent DNA ligase, domain 4 {Thermus therm	98.32
d1l0ba2	97	Breast cancer associated protein, BRCA1 {Rat (Ratt	98.15
d1kzyc1	153	53BP1 {Human (Homo sapiens) [TaxId: 9606]}	98.13
d1l0ba2	97	Breast cancer associated protein, BRCA1 {Rat (Ratt	97.98
d1kzyc2	106	53BP1 {Human (Homo sapiens) [TaxId: 9606]}	97.49
d1kzyc2	106	53BP1 {Human (Homo sapiens) [TaxId: 9606]}	96.62

>d1cdza_ c.15.1.1 (A:) DNA-repair protein XRCC1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: DNA-repair protein XRCC1
domain: DNA-repair protein XRCC1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=3.5e-18  Score=140.22  Aligned_cols=90  Identities=18%  Similarity=0.305  Sum_probs=83.7

Q ss_pred             CCCCCCcEEEEeC-CChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHHHHHHHhcCCCCCceEecchHHHHHHH
Q 012081           55 NAPFSGLVICVTG-LSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVR  133 (471)
Q Consensus        55 ~~iF~GlvI~vTG-~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~Dcik  133 (471)
                      +.+|+|++|+++| ++..+|..|+++|.++||++...++.++||+|+....+.+|+.+.++.  .+++||+++||.||++
T Consensus         3 pd~F~g~~f~v~g~~~~~~~~~l~~~i~~~GG~v~~~~~~~~THvI~~~~~~~~~~~~~~~~--~~i~iV~~~Wl~dc~~   80 (96)
T d1cdza_           3 PDFFQGKHFFLYGEFPGDERRKLIRYVTAFNGELEDYMSDRVQFVITAQEWDPSFEEALMDN--PSLAFVRPRWIYSCNE   80 (96)
T ss_dssp             CCTTTTCEEEECSCCCTHHHHHHHHHHHHTTCEECSSCSTTCSEEECSSCCCHHHHHHHTTC--TTCEEECTHHHHHHHT
T ss_pred             ccccCCcEEEEeCCCCHHHHHHHHHHHHHhCCEEeccCCCCceEEEEccCCcceeeehhhhC--CCCeEEEEhHHHHHHH
Confidence            4799999999998 778899999999999999999999999999999999999999998752  5899999999999999


Q ss_pred             cccCCCCCccccc
Q 012081          134 RNVRLSESLYTVK  146 (471)
Q Consensus       134 ~g~~lde~~Y~l~  146 (471)
                      +++++|+++|.+.
T Consensus        81 ~~~~lp~~~Y~i~   93 (96)
T d1cdza_          81 KQKLLPHQLYGVV   93 (96)
T ss_dssp             TTSCCCGGGGBCC
T ss_pred             cCCcCCchhcEec
Confidence            9999999999873

>d1wf6a_ c.15.1.5 (A:) DNA topoisomerase II binding protein 1, TopBP1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: DNA topoisomerase II binding protein 1, TopBP1
domain: DNA topoisomerase II binding protein 1, TopBP1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=1.4e-17  Score=145.28  Aligned_cols=93  Identities=18%  Similarity=0.266  Sum_probs=83.9

Q ss_pred             CCCCCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHHHHHHHhcCCCCCceEecchHHHHHH
Q 012081           53 PANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSV  132 (471)
Q Consensus        53 ~~~~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~Dci  132 (471)
                      .+..+|+|++|+++||+..++..|.++|..+||++...++.+|||||+......+++.+.+.  ..+++||+++||.||+
T Consensus        36 ~~~~~f~G~~i~isGf~~~~~~~l~~~i~~~GG~~~~~~~~~vTHvIv~~~~~~~~~~~~~~--~~~i~iV~~~Wl~~c~  113 (132)
T d1wf6a_          36 APEDLLDGCRIYLCGFSGRKLDKLRRLINSGGGVRFNQLNEDVTHVIVGDYDDELKQFWNKS--AHRPHVVGAKWLLECF  113 (132)
T ss_dssp             CCTTTTTTCEEEEESCCSHHHHHHHHHHHHTTCEEESSCCSSCCEEEESSCCSHHHHHHHHS--CCCCCEEEHHHHHHHH
T ss_pred             CchhhhCCeEEEEeeCCCHHHHHHHHHHHHcCCEEecccCCCceEEEecCCCccHHHHHHHh--cCCCCcCCHHHHHHHH
Confidence            45578999999999999999999999999999999999999999999999888887765442  2479999999999999


Q ss_pred             HcccCCCCCcccccc
Q 012081          133 RRNVRLSESLYTVKS  147 (471)
Q Consensus       133 k~g~~lde~~Y~l~~  147 (471)
                      ++++++|+++|.+..
T Consensus       114 ~~~~~l~~~~Y~~~~  128 (132)
T d1wf6a_         114 SKGYMLSEEPYIHSG  128 (132)
T ss_dssp             HHSSCCCSGGGBCCC
T ss_pred             HcCCcCCHHhCcCCC
Confidence            999999999999864

>d1t15a1 c.15.1.3 (A:1649-1757) Breast cancer associated protein, BRCA1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: BRCT domain
domain: Breast cancer associated protein, BRCA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=1.1e-16  Score=135.27  Aligned_cols=85  Identities=19%  Similarity=0.283  Sum_probs=78.4

Q ss_pred             cEEEEeCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecCC------CHHHHHHHhcCCCCCceEecchHHHHHHHc
Q 012081           61 LVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFG------GRKFEHALKHGSRNGLYIVTLGWFVDSVRR  134 (471)
Q Consensus        61 lvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~------g~Ky~~A~k~~~~~gi~IV~p~WI~Dcik~  134 (471)
                      ++|++||+++++++.|.++|+.|||+|...++++|||||+....      +.||..|+.+    |++||+++||.||++.
T Consensus         2 ~~i~~SGl~~~e~~~l~~~i~~~Gg~~~~~~~~~~THlI~~~~~~~~~~rt~K~l~a~~~----g~~IV~~~Wl~~c~~~   77 (109)
T d1t15a1           2 MSMVVSGLTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAG----GKWVVSYFWVTQSIKE   77 (109)
T ss_dssp             CEEEEESCCHHHHHHHHHHHHHHTCEECSSCCTTCCEEEECBCTTSEECCBHHHHHHHHT----TCEEEETHHHHHHHHT
T ss_pred             EEEEECCCCHHHHHHHHHHHHHcCCEEEeEecCCccEEEEecCcchhhHhhHHHHHHHHC----CCccccHHHHHHHHHh
Confidence            68999999999999999999999999999999999999997643      5799999986    8999999999999999


Q ss_pred             ccCCCCCcccccccc
Q 012081          135 NVRLSESLYTVKSID  149 (471)
Q Consensus       135 g~~lde~~Y~l~~~~  149 (471)
                      ++++||.+|.+....
T Consensus        78 ~~~l~e~~y~v~~~~   92 (109)
T d1t15a1          78 RKMLNEHDFEVRGDV   92 (109)
T ss_dssp             TSCCCGGGGBCCEET
T ss_pred             CCcCCchheEEeccc
Confidence            999999999987543

>d1t15a2 c.15.1.3 (A:1758-1859) Breast cancer associated protein, BRCA1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: BRCT domain
domain: Breast cancer associated protein, BRCA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=4.4e-16  Score=128.13  Aligned_cols=88  Identities=20%  Similarity=0.222  Sum_probs=74.6

Q ss_pred             CCCCCcEEEEeC-CChhhHHHHHHHHHHcCCEEcccCC-----CCceEEEEecCC-----CHHHHHHHhcCCCCCceEec
Q 012081           56 APFSGLVICVTG-LSKEARKQVMEATERLGGQYSPDLH-----PQCTHLVVQSFG-----GRKFEHALKHGSRNGLYIVT  124 (471)
Q Consensus        56 ~iF~GlvI~vTG-~~~~er~~L~~lI~~~GG~~~~~l~-----~~~THLV~~~~~-----g~Ky~~A~k~~~~~gi~IV~  124 (471)
                      ++|+|+.||++| |+..++.+|+++|+.+||+++..+.     ..+||+++....     ..++..|..+    +++||+
T Consensus         2 kiF~g~~i~~~g~~~~~~~~~L~~li~~~GG~v~~~~~~~~~~~~~t~~~i~~~~~~~~~~~~~~~~~~~----~i~iV~   77 (102)
T d1t15a2           2 KIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTLGTGVHPIVVVQPDAWTEDNGFHAIGQMC----EAPVVT   77 (102)
T ss_dssp             CTTTTCEEEECSCCSSSCHHHHHHHHHHTTCEECCSGGGCCCSTTCCEEEEECGGGCSSCGGGGSSTTTC----SSCEEE
T ss_pred             CCCCCcEEEEeCCCCCcCHHHHHHHHHHhCCEEeeccccccccccccchheecccccchhhHHHHHHHhC----CCcEEe
Confidence            689999999999 7888999999999999999987664     367898887643     3455555554    899999


Q ss_pred             chHHHHHHHcccCCCCCcccccc
Q 012081          125 LGWFVDSVRRNVRLSESLYTVKS  147 (471)
Q Consensus       125 p~WI~Dcik~g~~lde~~Y~l~~  147 (471)
                      ++||+||+.+++++|+++|.++.
T Consensus        78 ~~Wl~dsi~~~~~lp~~~Yll~~  100 (102)
T d1t15a2          78 REWVLDSVALYQCQELDTYLIPQ  100 (102)
T ss_dssp             HHHHHHHHHHTSCCCSGGGBCCC
T ss_pred             eHHHHHHHHhCCcCCchhccCCC
Confidence            99999999999999999999863

>d1wf6a_ c.15.1.5 (A:) DNA topoisomerase II binding protein 1, TopBP1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: DNA topoisomerase II binding protein 1, TopBP1
domain: DNA topoisomerase II binding protein 1, TopBP1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=1.4e-15  Score=132.49  Aligned_cols=95  Identities=15%  Similarity=0.247  Sum_probs=79.7

Q ss_pred             cccccccccCCCCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCchHH--HHh---cCCCce
Q 012081          186 GKHERDSNRSMNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQ--KYM---GHSNNL  260 (471)
Q Consensus       186 E~ld~~~~~~~~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~s~~--k~l---~~~~~I  260 (471)
                      +++|......+..+|+||+||| .||+..+++.|.++|..+||++.+.  ++.++||||+......  +++   ..+++|
T Consensus        27 ~~~d~~~~~~~~~~f~G~~i~i-sGf~~~~~~~l~~~i~~~GG~~~~~--~~~~vTHvIv~~~~~~~~~~~~~~~~~i~i  103 (132)
T d1wf6a_          27 ENLDVSAFQAPEDLLDGCRIYL-CGFSGRKLDKLRRLINSGGGVRFNQ--LNEDVTHVIVGDYDDELKQFWNKSAHRPHV  103 (132)
T ss_dssp             TTCCGGGCCCCTTTTTTCEEEE-ESCCSHHHHHHHHHHHHTTCEEESS--CCSSCCEEEESSCCSHHHHHHHHSCCCCCE
T ss_pred             hcCChhhhcCchhhhCCeEEEE-eeCCCHHHHHHHHHHHHcCCEEecc--cCCCceEEEecCCCccHHHHHHHhcCCCCc
Confidence            3445444455678999999999 8999999999999999999999998  6999999999874322  222   477899


Q ss_pred             echhHHHHHHhhCCcCccCCcCh
Q 012081          261 VTPVWVLKTAKEKHVQRLVHISA  283 (471)
Q Consensus       261 Vs~~WL~dcik~g~lqp~~~ys~  283 (471)
                      |+++||++|+++++++|+..|-+
T Consensus       104 V~~~Wl~~c~~~~~~l~~~~Y~~  126 (132)
T d1wf6a_         104 VGAKWLLECFSKGYMLSEEPYIH  126 (132)
T ss_dssp             EEHHHHHHHHHHSSCCCSGGGBC
T ss_pred             CCHHHHHHHHHcCCcCCHHhCcC
Confidence            99999999999999999998854

>d1cdza_ c.15.1.1 (A:) DNA-repair protein XRCC1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: DNA-repair protein XRCC1
domain: DNA-repair protein XRCC1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=4.9e-15  Score=121.10  Aligned_cols=84  Identities=12%  Similarity=0.241  Sum_probs=72.1

Q ss_pred             CCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCch---HHHHh--cCCCceechhHHHHHHh
Q 012081          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDS---VQKYM--GHSNNLVTPVWVLKTAK  271 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~s---~~k~l--~~~~~IVs~~WL~dcik  271 (471)
                      +.+|+|++||+..+++..+++.|.++|.++||++.+.  ++.++||||+....   .+...  ..++.||+++||.||++
T Consensus         3 pd~F~g~~f~v~g~~~~~~~~~l~~~i~~~GG~v~~~--~~~~~THvI~~~~~~~~~~~~~~~~~~i~iV~~~Wl~dc~~   80 (96)
T d1cdza_           3 PDFFQGKHFFLYGEFPGDERRKLIRYVTAFNGELEDY--MSDRVQFVITAQEWDPSFEEALMDNPSLAFVRPRWIYSCNE   80 (96)
T ss_dssp             CCTTTTCEEEECSCCCTHHHHHHHHHHHHTTCEECSS--CSTTCSEEECSSCCCHHHHHHHTTCTTCEEECTHHHHHHHT
T ss_pred             ccccCCcEEEEeCCCCHHHHHHHHHHHHHhCCEEecc--CCCCceEEEEccCCcceeeehhhhCCCCeEEEEhHHHHHHH
Confidence            4699999999954599999999999999999999988  69999999997743   22233  35788999999999999


Q ss_pred             hCCcCccCCcC
Q 012081          272 EKHVQRLVHIS  282 (471)
Q Consensus       272 ~g~lqp~~~ys  282 (471)
                      +++++|+.+|-
T Consensus        81 ~~~~lp~~~Y~   91 (96)
T d1cdza_          81 KQKLLPHQLYG   91 (96)
T ss_dssp             TTSCCCGGGGB
T ss_pred             cCCcCCchhcE
Confidence            99999998884

>d1in1a_ c.15.1.2 (A:) DNA ligase III alpha {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: DNA ligase
domain: DNA ligase III alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.34  E-value=3.8e-13  Score=109.26  Aligned_cols=74  Identities=11%  Similarity=0.151  Sum_probs=64.7

Q ss_pred             CCCCCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccCCC-CceEEEEecCCCHHHHHHHhcCCCCCceEecchHHHHH
Q 012081           53 PANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHP-QCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDS  131 (471)
Q Consensus        53 ~~~~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~-~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~Dc  131 (471)
                      ..+.+|+|++|++.+.. .++..|+++|.++||.+..++++ .+||+|+.+...            .+++||+|+||.||
T Consensus        12 ~l~diF~G~~~~i~~~~-p~~~~L~r~i~a~GG~~~~~~~~~~vTHvI~~~~~~------------~~~~iV~p~Wi~dc   78 (88)
T d1in1a_          12 VLLDIFTGVRLYLPPST-PDFSRLRRYFVAFDGDLVQEFDMTSATHVLGSRDKN------------PAAQQVSPEWIWAC   78 (88)
T ss_dssp             CCCSSSTTCBCCCCTTS-TTHHHHHHHHHHHTCBCCCTTCCTTCCCEESCCTTC------------TTSCEECHHHHHHH
T ss_pred             chhhHhCCeEEEECCCC-CCHHHHHHHHHHhCCEEeeeccCCCceEEEEcCCCC------------CCcEEEehHHHHHH
Confidence            46799999999998866 46889999999999999999886 699999986533            35789999999999


Q ss_pred             HHcccCCC
Q 012081          132 VRRNVRLS  139 (471)
Q Consensus       132 ik~g~~ld  139 (471)
                      ++++++||
T Consensus        79 i~~~~lLP   86 (88)
T d1in1a_          79 IRKRRLVA   86 (88)
T ss_dssp             HHHTSCCC
T ss_pred             HHcCCcCC
Confidence            99999986

>d1l7ba_ c.15.1.2 (A:) NAD+-dependent DNA ligase, domain 4 {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: DNA ligase
domain: NAD+-dependent DNA ligase, domain 4
species: Thermus thermophilus [TaxId: 274]

Probab=99.30  E-value=2.1e-12  Score=105.68  Aligned_cols=80  Identities=23%  Similarity=0.289  Sum_probs=74.4

Q ss_pred             CCCCCCCCcEEEEeCCChhhHHHHHHHHHHcCCEEcccCCCCceEEEEecCCCHHHHHHHhcCCCCCceEecchHHHHHH
Q 012081           53 PANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSV  132 (471)
Q Consensus        53 ~~~~iF~GlvI~vTG~~~~er~~L~~lI~~~GG~~~~~l~~~~THLV~~~~~g~Ky~~A~k~~~~~gi~IV~p~WI~Dci  132 (471)
                      ....+|.|.+||+||.....|.+++++|+.+||++...+++.++|||+++..+.|++.|.++    +|+||+.+|+.+.+
T Consensus         3 ~~~~~l~G~~iv~TG~~~~~R~e~~~~i~~~Gg~v~~sVs~~t~~LV~g~~~g~K~~kA~~~----gI~IisE~~f~~~l   78 (92)
T d1l7ba_           3 KGGEALKGLTFVITGELSRPREEVKALLRRLGAKVTDSVSRKTSYLVVGENPGSKLEKARAL----GVPTLTEEELYRLL   78 (92)
T ss_dssp             CCCCSSTTCEEECSTTTTSCHHHHHHHHHHTTCEEESCCSSSCCCBEECSSSSTTHHHHHCS----SSCCEEHHHHHHHH
T ss_pred             CCCCCcCCCEEEEeCCccCCHHHHHHHHHHhCCEEcCccccceeEEEECCCCCcHHHHHHHc----CCcEecHHHHHHHH
Confidence            35689999999999988889999999999999999999999999999999899999999997    89999999999999


Q ss_pred             Hccc
Q 012081          133 RRNV  136 (471)
Q Consensus       133 k~g~  136 (471)
                      +...
T Consensus        79 ~~~~   82 (92)
T d1l7ba_          79 EART   82 (92)
T ss_dssp             HHHH
T ss_pred             HhCC
Confidence            8644

>d1t15a2 c.15.1.3 (A:1758-1859) Breast cancer associated protein, BRCA1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: BRCT domain
domain: Breast cancer associated protein, BRCA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.28  E-value=2.2e-12  Score=105.50  Aligned_cols=84  Identities=17%  Similarity=0.152  Sum_probs=67.1

Q ss_pred             CCCCCcEEEEeCC-CCHHHHHHHHHHHHhCCCEEEcccc---CCCCceEEEEcCc-----hHHHH---hcCCCceechhH
Q 012081          198 STLSGCSMYVDSD-VSEELRNKVFEAATNEGATLVNQWF---VGCGASYVVCEED-----SVQKY---MGHSNNLVTPVW  265 (471)
Q Consensus       198 ~lF~G~~Iyl~~g-fs~~~r~~L~~lI~~~GG~v~d~~~---~~~~vTHVVv~~~-----s~~k~---l~~~~~IVs~~W  265 (471)
                      .+|+|+.||+ .| |+...++.|.++|+.+||+++....   ....+||+++...     ...++   ...+++||+++|
T Consensus         2 kiF~g~~i~~-~g~~~~~~~~~L~~li~~~GG~v~~~~~~~~~~~~~t~~~i~~~~~~~~~~~~~~~~~~~~i~iV~~~W   80 (102)
T d1t15a2           2 KIFRGLEICC-YGPFTNMPTDQLEWMVQLCGASVVKELSSFTLGTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREW   80 (102)
T ss_dssp             CTTTTCEEEE-CSCCSSSCHHHHHHHHHHTTCEECCSGGGCCCSTTCCEEEEECGGGCSSCGGGGSSTTTCSSCEEEHHH
T ss_pred             CCCCCcEEEE-eCCCCCcCHHHHHHHHHHhCCEEeeccccccccccccchheecccccchhhHHHHHHHhCCCcEEeeHH
Confidence            4899999999 65 8888889999999999999987631   2346788887552     11222   246899999999


Q ss_pred             HHHHHhhCCcCccCCcC
Q 012081          266 VLKTAKEKHVQRLVHIS  282 (471)
Q Consensus       266 L~dcik~g~lqp~~~ys  282 (471)
                      |+||+.+++++|+..|-
T Consensus        81 l~dsi~~~~~lp~~~Yl   97 (102)
T d1t15a2          81 VLDSVALYQCQELDTYL   97 (102)
T ss_dssp             HHHHHHHTSCCCSGGGB
T ss_pred             HHHHHHhCCcCCchhcc
Confidence            99999999999999884

>d1in1a_ c.15.1.2 (A:) DNA ligase III alpha {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: DNA ligase
domain: DNA ligase III alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.24  E-value=7.5e-13  Score=107.46  Aligned_cols=74  Identities=14%  Similarity=0.239  Sum_probs=60.9

Q ss_pred             CCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCchHHHHhcCCCceechhHHHHHHhhCCcC
Q 012081          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQ  276 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~s~~k~l~~~~~IVs~~WL~dcik~g~lq  276 (471)
                      ..+|+|++||| .+..+ .++.|+++|.++||+++... ....+||||+....     ..+.++|+|+||+||+++++++
T Consensus        14 ~diF~G~~~~i-~~~~p-~~~~L~r~i~a~GG~~~~~~-~~~~vTHvI~~~~~-----~~~~~iV~p~Wi~dci~~~~lL   85 (88)
T d1in1a_          14 LDIFTGVRLYL-PPSTP-DFSRLRRYFVAFDGDLVQEF-DMTSATHVLGSRDK-----NPAAQQVSPEWIWACIRKRRLV   85 (88)
T ss_dssp             CSSSTTCBCCC-CTTST-THHHHHHHHHHHTCBCCCTT-CCTTCCCEESCCTT-----CTTSCEECHHHHHHHHHHTSCC
T ss_pred             hhHhCCeEEEE-CCCCC-CHHHHHHHHHHhCCEEeeec-cCCCceEEEEcCCC-----CCCcEEEehHHHHHHHHcCCcC
Confidence            67999999999 55443 46789999999999998773 34579999997642     2456899999999999999999


Q ss_pred             cc
Q 012081          277 RL  278 (471)
Q Consensus       277 p~  278 (471)
                      |.
T Consensus        86 Pp   87 (88)
T d1in1a_          86 AP   87 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            74

>d1kzyc1 c.15.1.4 (C:1714-1866) 53BP1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: 53BP1
domain: 53BP1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.23  E-value=1.7e-11  Score=109.21  Aligned_cols=91  Identities=18%  Similarity=0.170  Sum_probs=76.8

Q ss_pred             CCCCCCCCcEEEEeCCCh-----------------------------hhHHHHHHHHHHcCCEEcccCCC------CceE
Q 012081           53 PANAPFSGLVICVTGLSK-----------------------------EARKQVMEATERLGGQYSPDLHP------QCTH   97 (471)
Q Consensus        53 ~~~~iF~GlvI~vTG~~~-----------------------------~er~~L~~lI~~~GG~~~~~l~~------~~TH   97 (471)
                      ....+|.|+.|++|+.+.                             ..+......|+.+||.....++.      .++|
T Consensus        11 ~~~~lF~g~~F~lT~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~p~~~~~~~~~i~~~gg~v~~~~~~~~~~~~~~~~   90 (153)
T d1kzyc1          11 LNKTLFLGYAFLLTMATTSDKLASRSKLPDGPTGSSEEEEEFLEIPPFNKQYTESQLRAGAGYILEDFNEAQCNTAYQCL   90 (153)
T ss_dssp             SSTTTTTTEEEEECCCC---------------------------CCCCCHHHHHHHHHTTTCEECSSCCTTTTTTTCEEE
T ss_pred             CchhhhCCCEEEEecCCCchhhhhhhhcccccCCCccccccccccCccchhhhhhhhhhcCCeEeeccccccccccceEE
Confidence            556899999999997532                             13456677999999999887762      4678


Q ss_pred             EEEecC-CCHHHHHHHhcCCCCCceEecchHHHHHHHcccCCCCCcccccc
Q 012081           98 LVVQSF-GGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKS  147 (471)
Q Consensus        98 LV~~~~-~g~Ky~~A~k~~~~~gi~IV~p~WI~Dcik~g~~lde~~Y~l~~  147 (471)
                      ||+.+. .+.||.+|+++    |++||++.||.||++.|+++||.+|.++.
T Consensus        91 LIa~~~~RT~Kyl~Ala~----g~piv~~~Wi~~c~~~~~~ld~~~YlLpa  137 (153)
T d1kzyc1          91 LIADQHCRTRKYFLCLAS----GIPCVSHVWVHDSCHANQLQNYRNYLLPA  137 (153)
T ss_dssp             EEESSCCCSHHHHHHHHH----TCCEEETHHHHHHHHHTSCCCGGGSBCCC
T ss_pred             EecCCCCchHHHHHHHcc----CCcEEcHHHHHHHHHcCCcCChHHccCCC
Confidence            999887 58999999998    89999999999999999999999999863

>d1t15a1 c.15.1.3 (A:1649-1757) Breast cancer associated protein, BRCA1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: BRCT domain
domain: Breast cancer associated protein, BRCA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.19  E-value=1.5e-11  Score=103.00  Aligned_cols=78  Identities=26%  Similarity=0.308  Sum_probs=67.7

Q ss_pred             cEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCch------HHHHh---cCCCceechhHHHHHHhhC
Q 012081          203 CSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDS------VQKYM---GHSNNLVTPVWVLKTAKEK  273 (471)
Q Consensus       203 ~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~s------~~k~l---~~~~~IVs~~WL~dcik~g  273 (471)
                      .+|++ +|+++++++.|.++|+.+||++.+.  ++.++||||+....      ..||+   ..+++||+++||.+|++++
T Consensus         2 ~~i~~-SGl~~~e~~~l~~~i~~~Gg~~~~~--~~~~~THlI~~~~~~~~~~rt~K~l~a~~~g~~IV~~~Wl~~c~~~~   78 (109)
T d1t15a1           2 MSMVV-SGLTPEEFMLVYKFARKHHITLTNL--ITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKER   78 (109)
T ss_dssp             CEEEE-ESCCHHHHHHHHHHHHHHTCEECSS--CCTTCCEEEECBCTTSEECCBHHHHHHHHTTCEEEETHHHHHHHHTT
T ss_pred             EEEEE-CCCCHHHHHHHHHHHHHcCCEEEeE--ecCCccEEEEecCcchhhHhhHHHHHHHHCCCccccHHHHHHHHHhC
Confidence            36778 8999999999999999999999999  69999999996521      23444   5899999999999999999


Q ss_pred             CcCccCCcCh
Q 012081          274 HVQRLVHISA  283 (471)
Q Consensus       274 ~lqp~~~ys~  283 (471)
                      .++|+..|.+
T Consensus        79 ~~l~e~~y~v   88 (109)
T d1t15a1          79 KMLNEHDFEV   88 (109)
T ss_dssp             SCCCGGGGBC
T ss_pred             CcCCchheEE
Confidence            9999998853

>d1l7ba_ c.15.1.2 (A:) NAD+-dependent DNA ligase, domain 4 {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: DNA ligase
domain: NAD+-dependent DNA ligase, domain 4
species: Thermus thermophilus [TaxId: 274]

Probab=98.32  E-value=5e-07  Score=73.04  Aligned_cols=79  Identities=16%  Similarity=0.205  Sum_probs=65.8

Q ss_pred             CCCCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEccccCCCCceEEEEcCc---hHHHHhcCCCceechhHHHHHHhhC
Q 012081          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED---SVQKYMGHSNNLVTPVWVLKTAKEK  273 (471)
Q Consensus       197 ~~lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~~~~~vTHVVv~~~---s~~k~l~~~~~IVs~~WL~dcik~g  273 (471)
                      +..|.|++|+| +|+-...|+.+..+|..+||.+.++  +..+++|+|+++.   .++++...+++||+.+|+++.++..
T Consensus         5 ~~~l~G~~iv~-TG~~~~~R~e~~~~i~~~Gg~v~~s--Vs~~t~~LV~g~~~g~K~~kA~~~gI~IisE~~f~~~l~~~   81 (92)
T d1l7ba_           5 GEALKGLTFVI-TGELSRPREEVKALLRRLGAKVTDS--VSRKTSYLVVGENPGSKLEKARALGVPTLTEEELYRLLEAR   81 (92)
T ss_dssp             CCSSTTCEEEC-STTTTSCHHHHHHHHHHTTCEEESC--CSSSCCCBEECSSSSTTHHHHHCSSSCCEEHHHHHHHHHHH
T ss_pred             CCCcCCCEEEE-eCCccCCHHHHHHHHHHhCCEEcCc--cccceeEEEECCCCCcHHHHHHHcCCcEecHHHHHHHHHhC
Confidence            56899999999 6643457899999999999999999  7999999999773   4666778999999999999999875


Q ss_pred             CcCcc
Q 012081          274 HVQRL  278 (471)
Q Consensus       274 ~lqp~  278 (471)
                      .-.+.
T Consensus        82 ~~~~~   86 (92)
T d1l7ba_          82 TGKKA   86 (92)
T ss_dssp             HCSCS
T ss_pred             CCCCH
Confidence            43333

>d1l0ba2 c.15.1.3 (A:1705-1801) Breast cancer associated protein, BRCA1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: BRCT domain
domain: Breast cancer associated protein, BRCA1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=98.15  E-value=1.3e-06  Score=70.17  Aligned_cols=84  Identities=17%  Similarity=0.158  Sum_probs=58.0

Q ss_pred             CCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEcccc---CCCCceE-EEEcCc---hHHHHh----cCCCceechhHHH
Q 012081          199 TLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWF---VGCGASY-VVCEED---SVQKYM----GHSNNLVTPVWVL  267 (471)
Q Consensus       199 lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~---~~~~vTH-VVv~~~---s~~k~l----~~~~~IVs~~WL~  267 (471)
                      +|+|.-||+-..|+.-.++.|..++..+||+|+.+..   .+.+.+- ||++++   +...|-    ..+..+|+-+|++
T Consensus         1 lf~~~~icc~gpFt~mt~d~Le~mv~lCGAsVvk~~~~l~~~~~~~~viVvqpda~t~~~~~~~i~~~~~~~vVtreWvL   80 (97)
T d1l0ba2           1 LFEGLQIYCCEPFTNMPKDELERMLQLCGASVVKELPLLTRDTGAHPIVLVQPSAWTEDNDCPDIGQLCKGRLVMWDWVL   80 (97)
T ss_dssp             CCTTCEEEECSCCSSSCHHHHHHHHHHTTCEEECSSSCGGGCCSSCCEEEEC-------------------CEEETHHHH
T ss_pred             CCCCceEEEEccccCCCHHHHHHHHHHcCceeecChhhcCCCCCCeeEEEEcCCccccccccHHHHHhccccEEehhHhh
Confidence            6899999996668877789999999999999998741   1222233 444442   223332    3678899999999


Q ss_pred             HHHhhCCcCccCCcC
Q 012081          268 KTAKEKHVQRLVHIS  282 (471)
Q Consensus       268 dcik~g~lqp~~~ys  282 (471)
                      |||.....|++..|-
T Consensus        81 DSIA~Y~~Q~l~~YL   95 (97)
T d1l0ba2          81 DSISVYRCRDLDAYL   95 (97)
T ss_dssp             HHHHTTSCCCGGGGB
T ss_pred             hhhhheeeeehHhhh
Confidence            999999999987763

>d1kzyc1 c.15.1.4 (C:1714-1866) 53BP1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: 53BP1
domain: 53BP1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.13  E-value=2.2e-06  Score=75.43  Aligned_cols=66  Identities=11%  Similarity=0.204  Sum_probs=51.6

Q ss_pred             HHHHHHHHhCCCEEEcccc----CCCCceEEEEcCc-hHHHHh---cCCCceechhHHHHHHhhCCcCccCCcC
Q 012081          217 NKVFEAATNEGATLVNQWF----VGCGASYVVCEED-SVQKYM---GHSNNLVTPVWVLKTAKEKHVQRLVHIS  282 (471)
Q Consensus       217 ~~L~~lI~~~GG~v~d~~~----~~~~vTHVVv~~~-s~~k~l---~~~~~IVs~~WL~dcik~g~lqp~~~ys  282 (471)
                      ..+...|..+||.+.+.+.    ....++|||++.. ...||+   ..+++||+++||.||+++|+++++..|-
T Consensus        61 ~~~~~~i~~~gg~v~~~~~~~~~~~~~~~~LIa~~~~RT~Kyl~Ala~g~piv~~~Wi~~c~~~~~~ld~~~Yl  134 (153)
T d1kzyc1          61 QYTESQLRAGAGYILEDFNEAQCNTAYQCLLIADQHCRTRKYFLCLASGIPCVSHVWVHDSCHANQLQNYRNYL  134 (153)
T ss_dssp             HHHHHHHHTTTCEECSSCCTTTTTTTCEEEEEESSCCCSHHHHHHHHHTCCEEETHHHHHHHHHTSCCCGGGSB
T ss_pred             hhhhhhhhhcCCeEeeccccccccccceEEEecCCCCchHHHHHHHccCCcEEcHHHHHHHHHcCCcCChHHcc
Confidence            3567789999999988631    1234568888773 355665   6899999999999999999999998874

>d1l0ba2 c.15.1.3 (A:1705-1801) Breast cancer associated protein, BRCA1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: BRCT domain
domain: Breast cancer associated protein, BRCA1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.98  E-value=1e-05  Score=64.86  Aligned_cols=86  Identities=16%  Similarity=0.191  Sum_probs=59.1

Q ss_pred             CCCCcEEEEeC-CChhhHHHHHHHHHHcCCEEcccCCC----CceE-EEEecCC----CHHHHHHHhcCCCCCceEecch
Q 012081           57 PFSGLVICVTG-LSKEARKQVMEATERLGGQYSPDLHP----QCTH-LVVQSFG----GRKFEHALKHGSRNGLYIVTLG  126 (471)
Q Consensus        57 iF~GlvI~vTG-~~~~er~~L~~lI~~~GG~~~~~l~~----~~TH-LV~~~~~----g~Ky~~A~k~~~~~gi~IV~p~  126 (471)
                      +|+|..||+-| |+.-.+.+|+.|++..||.+.+.+.-    ..+| +|+-.++    ..-|....+   +.+.++|+.+
T Consensus         1 lf~~~~icc~gpFt~mt~d~Le~mv~lCGAsVvk~~~~l~~~~~~~~viVvqpda~t~~~~~~~i~~---~~~~~vVtre   77 (97)
T d1l0ba2           1 LFEGLQIYCCEPFTNMPKDELERMLQLCGASVVKELPLLTRDTGAHPIVLVQPSAWTEDNDCPDIGQ---LCKGRLVMWD   77 (97)
T ss_dssp             CCTTCEEEECSCCSSSCHHHHHHHHHHTTCEEECSSSCGGGCCSSCCEEEEC----------------------CEEETH
T ss_pred             CCCCceEEEEccccCCCHHHHHHHHHHcCceeecChhhcCCCCCCeeEEEEcCCccccccccHHHHH---hccccEEehh
Confidence            69999999998 77789999999999999999988762    2333 4444432    233432211   2478999999


Q ss_pred             HHHHHHHcccCCCCCcccc
Q 012081          127 WFVDSVRRNVRLSESLYTV  145 (471)
Q Consensus       127 WI~Dcik~g~~lde~~Y~l  145 (471)
                      |+.||++.=+..+.+.|.+
T Consensus        78 WvLDSIA~Y~~Q~l~~YL~   96 (97)
T d1l0ba2          78 WVLDSISVYRCRDLDAYLV   96 (97)
T ss_dssp             HHHHHHHTTSCCCGGGGBC
T ss_pred             HhhhhhhheeeeehHhhhc
Confidence            9999999988888777765

>d1kzyc2 c.15.1.4 (C:1867-1972) 53BP1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: 53BP1
domain: 53BP1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.49  E-value=9.6e-05  Score=60.30  Aligned_cols=81  Identities=19%  Similarity=0.124  Sum_probs=59.3

Q ss_pred             CCCCcEEEEeCCCCHHHHHHHHHHHHhCCCEEEcccc--------CCCCceEEEEcC---chHHHHh-cCCCceechhHH
Q 012081          199 TLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWF--------VGCGASYVVCEE---DSVQKYM-GHSNNLVTPVWV  266 (471)
Q Consensus       199 lF~G~~Iyl~~gfs~~~r~~L~~lI~~~GG~v~d~~~--------~~~~vTHVVv~~---~s~~k~l-~~~~~IVs~~WL  266 (471)
                      .|.|+++++-+.-+..-++.++.++..+||+++....        ....++-+|+++   +++.+.. ..++++|+.+||
T Consensus         2 pF~~l~vl~vs~~~~~F~e~Ws~IL~~~Ga~vV~~~~~~~~~sd~~~~~~DVvvTD~scp~~vl~~a~~~~ipvVS~EWV   81 (106)
T d1kzyc2           2 PFQNLKVLLVSDQQQNFLELWSEILMTGGAASVKQHHSSAHNKDIALGVFDVVVTDPSCPASVLKCAEALQLPVVSQEWV   81 (106)
T ss_dssp             TTTTCEEEEEESCTTTTHHHHHHHHHHTTCSEEEEEESSSSCCCSCGGGCSEEEECTTCCHHHHHHHHHHTCCEECHHHH
T ss_pred             CCcceEEEEEecccccHHHHHHHHHHhCCceEeeccccchhhccCccccccEEEeCCCCCHHHHHHHHHcCCcEeeHHHH
Confidence            6999999985554555578899999999998876521        011345566655   2444443 479999999999


Q ss_pred             HHHHhhCCcCccC
Q 012081          267 LKTAKEKHVQRLV  279 (471)
Q Consensus       267 ~dcik~g~lqp~~  279 (471)
                      .+|+-.|+.++..
T Consensus        82 IQsLI~G~~~~~d   94 (106)
T d1kzyc2          82 IQCLIVGERIGFK   94 (106)
T ss_dssp             HHHHHHTSCCCTT
T ss_pred             HHHHHccCcCCCC
Confidence            9999999988754

>d1kzyc2 c.15.1.4 (C:1867-1972) 53BP1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: 53BP1
domain: 53BP1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.62  E-value=0.0044  Score=50.19  Aligned_cols=82  Identities=13%  Similarity=0.088  Sum_probs=56.3

Q ss_pred             CCCCCcEEEEeCCCh-hhHHHHHHHHHHcCCEEcccC----------CCCceEEEEecCCCH-HHHHHHhcCCCCCceEe
Q 012081           56 APFSGLVICVTGLSK-EARKQVMEATERLGGQYSPDL----------HPQCTHLVVQSFGGR-KFEHALKHGSRNGLYIV  123 (471)
Q Consensus        56 ~iF~GlvI~vTG~~~-~er~~L~~lI~~~GG~~~~~l----------~~~~THLV~~~~~g~-Ky~~A~k~~~~~gi~IV  123 (471)
                      .||+|+.+.+.+-.. .=++....++...||.....+          ...++.+|+....+. -.+.|..+    |++||
T Consensus         1 npF~~l~vl~vs~~~~~F~e~Ws~IL~~~Ga~vV~~~~~~~~~sd~~~~~~DVvvTD~scp~~vl~~a~~~----~ipvV   76 (106)
T d1kzyc2           1 NPFQNLKVLLVSDQQQNFLELWSEILMTGGAASVKQHHSSAHNKDIALGVFDVVVTDPSCPASVLKCAEAL----QLPVV   76 (106)
T ss_dssp             CTTTTCEEEEEESCTTTTHHHHHHHHHHTTCSEEEEEESSSSCCCSCGGGCSEEEECTTCCHHHHHHHHHH----TCCEE
T ss_pred             CCCcceEEEEEecccccHHHHHHHHHHhCCceEeeccccchhhccCccccccEEEeCCCCCHHHHHHHHHc----CCcEe
Confidence            479998776644333 335666777777777553321          125788888877654 34445555    79999


Q ss_pred             cchHHHHHHHcccCCCCC
Q 012081          124 TLGWFVDSVRRNVRLSES  141 (471)
Q Consensus       124 ~p~WI~Dcik~g~~lde~  141 (471)
                      +.+|+.+|+-.|++++.+
T Consensus        77 S~EWVIQsLI~G~~~~~d   94 (106)
T d1kzyc2          77 SQEWVIQCLIVGERIGFK   94 (106)
T ss_dssp             CHHHHHHHHHHTSCCCTT
T ss_pred             eHHHHHHHHHccCcCCCC
Confidence            999999999999998743