Citrus Sinensis ID: 017048

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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-------38
Protein Sequence
MGGGGRVEVVSSKGCSRLFLGSVPSLRRLRGGVQSFESMSPASSSLASDSVLPANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHISADLARQVGMMLENIQNGIAREEINGGNVPEDAQSCKNKISQEKRQQTVNLAKNGVRSRRSRRMQIRLAVKMLMNITHLCFLMRKRMARIQKLHLQI
Secondary Structure (PSIPRED)
ccccccEEEEcccccccccccccccHHHHccccccccccccccccccccccccccccccccEEEEccccHHHHHHHHHHHHHHccEEcccccccccEEEEEccccHHHHHHHHHccccccEEEcccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEcccccHHHHHHHHHHHHHcccEEEcccccccccEEEEcccHHHHHHHHcccccccHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHccccHHHHccccccccccccccccccHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccccEEEEEEcccccEEEEcccccccccccccccccccccccccccccccccccccccEEEEEEccccHHHHHHHHHHHHHHcccEccccccccEEEEEEcccccHHHHHHHHccccccEEEcHHHHHHHHHccccccHHHccccccccccccccccHHccccccccccccccccccccccccccccccHHcccHHHHccccEEEEcccccHHHHHHHHHHHHccccEEEEEEEEcccEEEEEEEcHHHHHHHccccccccHHHHHHHHHHcccccEEEEcHHHHHHHHHHHHHHcccccccEEcccccccccccccccccHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MGGGGRVEVVSskgcsrlflgsvpslrrlrggvqsfesmspassslasdsvlpanapfsGLVICVTGLSKEARKQVMEATErlggqyspdlhpqctHLVVQSFGGRKFEHALkhgsrnglYIVTLGWFVDSVRRNVRLSESLYTVksidehgmhLDKLNRLvgfagtensclpagiyeakqfnatgkherdsnrsmnstlsgcsmyvdsDVSEELRNKVFEAATNEGATLVNQWFVGcgasyvvceedsvqkymghsnnlvTPVWVLKTAKEKHVQRLVHISADLARQVGMMLENIQNGiareeinggnvpedaQSCKNKISQEKRQQTVNLAKNGVRSRRSRRMQIRLAVKMLMNITHLCFLMRKRMARIQKLHLQI
Flexible Loop (DISEMBL)
mggggrvevvsskgcsrlflgsvpslRRLRGGVQSFESMSPASSSLASDSVLPANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYtvksidehgmhLDKLNRLVGFAGTENSCLPAGIYEAKQFnatgkherdsnrsmnstLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHISADLARQVGMMLENIQNGIAREEINGGNVPEDAQSCKNkisqekrqqtvnlakngvrsrrsrrMQIRLAVKMLMNITHLCFLMRKRMARIQKLHLQI
Low Complexity Region (SEG)
MGGGGRVEVVSSKGCSRLFLGSVPSLRRLRGGVQsfesmspassslasdsVLPANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHISADLARQVGMMLENIQNGIAREEINGGNVPEDAQSCKNKISQEKRQQTVNLAKNGVrsrrsrrMQIRLAVKMLMNITHLCFLMRKRMARIQKLHLQI
Disordered region (IsUnstruct)
**************CSRLFLGS********************************NAPFSGLVICVTGLSK*************GGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQF***********************YV*******LRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHISADLARQVGMMLENIQNGIA********************************************QIRLAVKMLMNITHLCFLMRKRMARIQ******
Disordered Region (DISOPRED)
****GR********CS***LGSVPSLRRLRGG*******************LPANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTV***********************************************************MYVDSDVS************NEGATLVNQWFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHISADLARQ************************************************************LAVKMLMNITHLCFLMRKRMARI*******
Disordered Region (DISEMBL)
*********VSSKGCSRLFLGSVPSLRRLRGGVQS*************DSVLPANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNA*************STLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHISADLARQVGMMLENIQNGIAREEINGGNVPEDAQSCKNKISQEKRQQTVNLA*********RRMQIRLAVKMLMNITHLCFLMRKRMARIQKLHLQI
Disordered Region (DISPRO)
****GRVEVVSSKGCSRLFLGSV***************************VLPANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKS**********************************F*ATGKHER*SNRSMNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHISADLARQVGMMLENIQNGIARE**************KNKISQEKRQQTVNLAKNGVRSRRSRRMQIRLAVKMLMNITHLCFLMRKRMARIQKLHLQI
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGGGGRVEVVSSKGCSRLFLGSVPSLRRLRGGVQSFESMSPASSSLASDSVLPANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHISADLARQVGMMLENIQNGIAREEINGGNVPEDAQSCKNKISQEKRQQTVNLAKNGVRSRRSRRMQIRLAVKMLMNITHLCFLMRKRMARIQKLHLQI
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	378	2.2.26 [Sep-21-2011]
Q6ZQF0	1515	DNA topoisomerase 2-bindi	yes	no	0.251	0.062	0.41	1e-10
Q92547	1522	DNA topoisomerase 2-bindi	yes	no	0.235	0.058	0.404	4e-10
Q800K6	1513	DNA topoisomerase 2-bindi	N/A	no	0.563	0.140	0.257	6e-09
Q7ZZY3	1513	DNA topoisomerase 2-bindi	N/A	no	0.563	0.140	0.257	2e-08
Q90WJ3	1256	PAX-interacting protein 1	N/A	no	0.219	0.066	0.348	3e-07
Q6NZQ4	1056	PAX-interacting protein 1	no	no	0.232	0.083	0.340	1e-06
Q6ZW49	1069	PAX-interacting protein 1	no	no	0.219	0.077	0.337	2e-06
A0JNA8	984	PAX-interacting protein 1	no	no	0.232	0.089	0.340	4e-06
Q9H8V3	914	Protein ECT2 OS=Homo sapi	no	no	0.216	0.089	0.333	4e-06
Q07139	913	Protein ECT2 OS=Mus muscu	no	no	0.216	0.089	0.311	2e-05

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

 Score = 67.4 bits (163), 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 = 66.2 bits (160), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 38/94 (40%), Positives = 52/94 (55%), Gaps = 5/94 (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 RNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDE 150
           R  ++ VT  WF DS+ +     ES+Y  +   E
Sbjct: 256 RWNVHCVTTQWFFDSIEKGFCQDESIYKTEPRPE 289

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 = 62.0 bits (149), Expect = 6e-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 = 60.8 bits (146), Expect = 2e-08,   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 = 56.6 bits (135), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 30/86 (34%), Positives = 46/86 (53%), Gaps = 3/86 (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 NGLYIVTLGWFVDSVRRNVRLSESLY 143
             + IVT  W +DSV    +  E+LY
Sbjct: 158 --IKIVTPDWVLDSVSEKTKKDEALY 181

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

 Score = 53.9 bits (128), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 29/86 (33%), Positives = 42/86 (48%), Gaps = 3/86 (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 NGLYIVTLGWFVDSVRRNVRLSESLY 143
             + IVT  W +D V    +  E+ Y
Sbjct: 156 ASIKIVTPDWVLDCVSEKTKKDEAFY 181

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

 Score = 52.8 bits (125), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 30/90 (33%), Positives = 44/90 (48%), Gaps = 8/90 (8%)

Query: 56  APFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQS--FGGRKFEHALK 113
            PF   ++   G S E +  + E TE  GG+Y P    +CTHLVV+        FE + K
Sbjct: 269 PPFQDCILSFLGFSDEEKTNMEEMTEMQGGKYLPLGDERCTHLVVEENIVKDLPFEPSKK 328

Query: 114 HGSRNGLYIVTLGWFVDSVRRNVRLSESLY 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|Q07139|ECT2_MOUSE Protein ECT2 OS=Mus musculus GN=Ect2 PE=1 SV=2

 Score = 50.8 bits (120), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 28/90 (31%), Positives = 44/90 (48%), Gaps = 8/90 (8%)

Query: 56  APFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQ--SFGGRKFEHALK 113
            PF   ++   G S E +  + E TE  GG Y P    +CTHL+V+  +     FE + K
Sbjct: 269 PPFQDCILSFLGFSDEEKHSMEEMTEMQGGSYLPVGDERCTHLIVEENTVKDLPFEPSKK 328

Query: 114 HGSRNGLYIVTLGWFVDSVRRNVRLSESLY 143
                 L++V   WF  S++ + R  E++Y
Sbjct: 329 ------LFVVKQEWFWGSIQMDARAGETMY 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.

Mus musculus (taxid: 10090)

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	378
255550221	556	topbp1, putative [Ricinus communis] gi|2	0.891	0.606	0.679	1e-137
359476287	546	PREDICTED: uncharacterized protein LOC10	0.883	0.611	0.676	1e-132
359476289	551	PREDICTED: uncharacterized protein LOC10	0.883	0.606	0.663	1e-129
147855443	565	hypothetical protein VITISV_022337 [Viti	0.883	0.591	0.641	1e-128
356509851	542	PREDICTED: uncharacterized protein LOC10	0.896	0.625	0.611	1e-117
356518187	541	PREDICTED: uncharacterized protein LOC10	0.896	0.626	0.616	1e-114
357465905	570	DNA topoisomerase 2-binding protein [Med	0.857	0.568	0.614	1e-112
449452943	553	PREDICTED: uncharacterized protein LOC10	0.902	0.616	0.576	1e-108
388494050	529	unknown [Lotus japonicus]	0.880	0.629	0.606	1e-106
115479373	548	Os09g0440200 [Oryza sativa Japonica Grou	0.883	0.609	0.525	6e-94

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

 Score =  493 bits (1268), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 240/353 (67%), Positives = 293/353 (83%), Gaps = 16/353 (4%)

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 ENIQNGIAREEINGGNVPEDAQSCKNKISQEKRQQTVNLAKNGVRSRRSRRMQ 346
           EN QNG A +EIN G+ P D ++ ++++S  +RQ  VN AKN VRSRR RRMQ
Sbjct: 309 ENFQNGSAEQEINTGSAPLDVRNLRSQVSYGQRQHIVNFAKNAVRSRRGRRMQ 361

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 =  476 bits (1225), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 234/346 (67%), Positives = 284/346 (82%), Gaps = 12/346 (3%)

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 AREEINGGNVPEDAQSCKNKISQEKRQQTVNLAKNGVRSRRSRRMQ 346
             EE+N  N P+D    + K S E+RQ+ V+LAK GVR+RR+R MQ
Sbjct: 305 ELEEMNRENGPQDTPCPRKKASHEERQEIVSLAKAGVRNRRARYMQ 350

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 =  468 bits (1203), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 233/351 (66%), Positives = 283/351 (80%), Gaps = 17/351 (4%)

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 IQNGIAREEINGGNVPEDAQSCKNKISQEKRQQTVNLAKNGVRSRRSRRMQ 346
           +QNGI  EE+N  N P+D    + K S E+RQ+ V+LAK GVR+RR+R MQ
Sbjct: 305 VQNGIELEEMNRENGPQDTPCPRKKASHEERQEIVSLAKAGVRNRRARYMQ 355

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 =  464 bits (1193), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 234/365 (64%), Positives = 284/365 (77%), Gaps = 31/365 (8%)

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 SRRMQ 346
           +R MQ
Sbjct: 365 ARYMQ 369

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 =  428 bits (1101), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 216/353 (61%), Positives = 268/353 (75%), Gaps = 14/353 (3%)

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 ENIQNGIAREEINGGNVPEDAQSCKNKISQEKRQQTVNLAKNGVRSRRSRRMQ 346
           E+I NGI+ +E+    V  +    ++++  E+RQQ VN AKNGVRSRR RRMQ
Sbjct: 294 EDIHNGISGKEVIKQKVLNNLLDTESEVGYEERQQIVNSAKNGVRSRRGRRMQ 346

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 =  417 bits (1073), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 217/352 (61%), Positives = 270/352 (76%), Gaps = 13/352 (3%)

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 NIQNGIAREEINGGNVPEDAQSCKNKISQEKRQQTVNLAKNGVRSRRSRRMQ 346
           +I N I+ +E+    V  +    ++++S E+RQQ VN AKNGVR+RR RRMQ
Sbjct: 294 DIHNDISGKEVIKQKVLNNLPDTESEVSYEERQQIVNSAKNGVRNRRGRRMQ 345

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 =  412 bits (1058), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 212/345 (61%), Positives = 260/345 (75%), Gaps = 21/345 (6%)

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 REEINGGNVPEDAQSCKNKISQEKRQQTVNLAKNGVRSRRSRRMQ 346
            +EI    V +D Q  K++I  ++RQQ VN AKNGVRSRR RRMQ
Sbjct: 297 -KEIVKQKVHDDLQGSKSEIGCKERQQIVNSAKNGVRSRRGRRMQ 340

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  396 bits (1018), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 207/359 (57%), Positives = 255/359 (71%), Gaps = 18/359 (5%)

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  VICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQ---------SFGGRKFEHAL 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 QVGMMLENIQNGIAREEINGGNVPEDAQSCKNKISQEKRQQTVNLAKNGVRSRRSRRMQ 346
           Q+   LE++      E  N     ED ++ ++K +Q +R+QT++ AK GVR RR+ RMQ
Sbjct: 301 QISSTLEDLCAENFTEAKN--RQQEDTRTSRSKTTQAEREQTISNAKLGVRKRRACRMQ 357

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  392 bits (1007), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 210/346 (60%), Positives = 255/346 (73%), Gaps = 13/346 (3%)

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 AREEINGGNVPEDAQSCKNKISQEKRQQTVNLAKNGVRSRRSRRMQ 346
           + +E+    V  D Q  K+++S ++RQQ VN AK GVR+RR RRMQ
Sbjct: 288 SGKEVIKQKVHGDLQGSKSEVSYKERQQIVNSAKIGVRNRRGRRMQ 333

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115479373|ref|NP_001063280.1| Os09g0440200 [Oryza sativa Japonica Group] gi|51091406|dbj|BAD36149.1| unknown protein [Oryza sativa Japonica Group] gi|113631513|dbj|BAF25194.1| Os09g0440200 [Oryza sativa Japonica Group]

 Score =  350 bits (899), Expect = 6e-94,   Method: Compositional matrix adjust.
 Identities = 186/354 (52%), Positives = 243/354 (68%), Gaps = 20/354 (5%)

Query: 7   VEVVSSKGCSRLFLGSVPSLRRLRGGVQSFESMSPASSSLASDSVLPANAPFSGLVICVT 66
           VEVV S+GCSRL L   P ++       S  S S        D     + PF+GLVICVT
Sbjct: 6   VEVVVSRGCSRLVL---PGMQPSSASAASSSSFSRGGHGGGGDRRPLPDGPFAGLVICVT 62

Query: 67  GLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLG 126
           GLSKEAR QV EATER+GG+YS  LHP+CTHLVVQSF GRKFEHA+KHG++NGL++VTLG
Sbjct: 63  GLSKEARTQVKEATERMGGEYSGSLHPKCTHLVVQSFAGRKFEHAVKHGAKNGLFVVTLG 122

Query: 127 WFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQF-NAT 185
           W VD VRR++RL ESLY++K+I E+GM L + NRLVG   + NSCLP  +++ K F + T
Sbjct: 123 WLVDCVRRSMRLDESLYSIKNIGENGMPLGEFNRLVGAPVSGNSCLPPMMFQEKTFSDTT 182

Query: 186 GKHERDSNRSMNS----TLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGAS 241
            KH   ++R  +       +  S+Y+D  +S E+R KV +AAT EGA L++ WF+GC A+
Sbjct: 183 EKHRLQTSRKEHDHDEFLFTNDSIYIDPGISGEMRKKVSDAATREGAKLLDHWFIGCHAT 242

Query: 242 YVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHISADLARQVGMMLENIQNGIA 301
           YVVCE+ SV++Y+GHS+N+VTP+W+LKTAKEK +QRLVH+S+DLARQV  +LEN Q    
Sbjct: 243 YVVCEDASVKRYVGHSDNIVTPLWILKTAKEKGLQRLVHLSSDLARQVATILENAQTFQE 302

Query: 302 REEINGGNVPE---------DAQSCKNKISQEKRQQTVNLAKNGVRSRRSRRMQ 346
             +I  G+VP            Q   ++I QE RQ+ V +AK  VR RR+RRMQ
Sbjct: 303 NRKI--GDVPSVNSNSSGVPSTQGEIDEIHQE-RQKFVEVAKKNVRDRRARRMQ 353

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

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	378
TAIR|locus:2097149	502	AT3G43930 "AT3G43930" [Arabido	0.743	0.559	0.506	2.4e-67
TAIR|locus:2057711	470	AT2G26270 "AT2G26270" [Arabido	0.621	0.5	0.489	1.9e-58
UNIPROTKB|E1BSJ5	508	TOPBP1 "Uncharacterized protei	0.227	0.169	0.417	2.9e-09
RGD|1562949	1516	Topbp1 "topoisomerase (DNA) II	0.515	0.128	0.272	1.6e-08
TAIR|locus:2031412	972	MEI1 "AT1G77320" [Arabidopsis	0.227	0.088	0.404	1.7e-08
UNIPROTKB|G3X684	1524	TOPBP1 "Uncharacterized protei	0.550	0.136	0.285	5.7e-08
UNIPROTKB|Q92547	1522	TOPBP1 "DNA topoisomerase 2-bi	0.362	0.090	0.333	8.4e-08
MGI|MGI:1920018	1515	Topbp1 "topoisomerase (DNA) II	0.227	0.056	0.417	1.3e-07
UNIPROTKB|Q800K6	1513	topbp1-A "DNA topoisomerase 2-	0.224	0.056	0.366	2.2e-07
UNIPROTKB|F1P482	1062	PAXIP1 "Uncharacterized protei	0.219	0.078	0.360	5.2e-05

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

 Score = 684 (245.8 bits), Expect = 2.4e-67, P = 2.4e-67
 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

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

 Score = 600 (216.3 bits), Expect = 1.9e-58, P = 1.9e-58
 Identities = 122/249 (48%), Positives = 174/249 (69%)

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 XXXXXXXMQ 346
                    MQ
Sbjct:   267 RRRRARHMQ 275

GO:0003674 "molecular_function" evidence=ND

GO:0005576 "extracellular region" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 168 (64.2 bits), Expect = 2.9e-09, Sum P(2) = 2.9e-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

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

 Score = 164 (62.8 bits), Expect = 1.6e-08, P = 1.6e-08
 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

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

 Score = 163 (62.4 bits), Expect = 1.7e-08, Sum P(2) = 1.7e-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 = 5.7e-08, P = 5.7e-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

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

 Score = 161 (61.7 bits), Expect = 8.4e-08, Sum P(2) = 8.4e-08
 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 = 1.3e-07, Sum P(2) = 1.3e-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 = 2.2e-07, Sum P(2) = 2.2e-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 = 5.2e-05, Sum P(2) = 5.2e-05
 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

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00032303001 SubName- Full=Chromosome chr4 scaffold_6, whole genome shotgun sequence; (531 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	378
pfam12738	63	pfam12738, PTCB-BRCT, twin BRCT domain	5e-13
pfam00533	77	pfam00533, BRCT, BRCA1 C Terminus (BRCT) domain	6e-13
smart00292	78	smart00292, BRCT, breast cancer carboxy-terminal d	1e-11
cd00027	72	cd00027, BRCT, Breast Cancer Suppressor Protein (B	3e-11
TIGR00575	652	TIGR00575, dnlj, DNA ligase, NAD-dependent	0.001

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

 Score = 63.0 bits (154), Expect = 5e-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 = 63.2 bits (154), Expect = 6e-13
 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 = 59.7 bits (145), Expect = 1e-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 = 58.1 bits (141), Expect = 3e-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	378
PF12738	63	PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2W	99.56
PF00533	78	BRCT: BRCA1 C Terminus (BRCT) domain; InterPro: IP	99.54
KOG1929	811	consensus Nucleotide excision repair factor NEF2,	99.5
smart00292	80	BRCT breast cancer carboxy-terminal domain.	99.34
KOG3524	850	consensus Predicted guanine nucleotide exchange fa	99.3
cd00027	72	BRCT Breast Cancer Suppressor Protein (BRCA1), car	99.3
KOG3226	508	consensus DNA repair protein [Replication, recombi	99.22
PF00533	78	BRCT: BRCA1 C Terminus (BRCT) domain; InterPro: IP	99.21
KOG1929	811	consensus Nucleotide excision repair factor NEF2,	99.15
KOG0966	881	consensus ATP-dependent DNA ligase IV [Replication	99.14
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	99.03
smart00292	80	BRCT breast cancer carboxy-terminal domain.	99.02
cd00027	72	BRCT Breast Cancer Suppressor Protein (BRCA1), car	98.84
PLN03122	815	Poly [ADP-ribose] polymerase; Provisional	98.66
PLN03123	981	poly [ADP-ribose] polymerase; Provisional	98.62
KOG3548	1176	consensus DNA damage checkpoint protein RHP9/CRB2/	98.56
PF12738	63	PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2W	98.55
KOG3226	508	consensus DNA repair protein [Replication, recombi	98.06
PRK14350	669	ligA NAD-dependent DNA ligase LigA; Provisional	98.06
KOG2043	896	consensus Signaling protein SWIFT and related BRCT	97.99
PRK06063	313	DNA polymerase III subunit epsilon; Provisional	97.95
PRK06195	309	DNA polymerase III subunit epsilon; Validated	97.87
PRK07956	665	ligA NAD-dependent DNA ligase LigA; Validated	97.85
PRK14351	689	ligA NAD-dependent DNA ligase LigA; Provisional	97.81
COG0272	667	Lig NAD-dependent DNA ligase (contains BRCT domain	97.79
TIGR00575	652	dnlj DNA ligase, NAD-dependent. The member of this	97.73
KOG2481	570	consensus Protein required for normal rRNA process	97.55
COG5163	591	NOP7 Protein required for biogenesis of the 60S ri	97.43
KOG3524	850	consensus Predicted guanine nucleotide exchange fa	97.41
KOG0966	881	consensus ATP-dependent DNA ligase IV [Replication	97.36
PLN03122	815	Poly [ADP-ribose] polymerase; Provisional	97.32
KOG2093	1016	consensus Translesion DNA polymerase - REV1 deoxyc	97.23
PLN03123	981	poly [ADP-ribose] polymerase; Provisional	97.03
KOG2481	570	consensus Protein required for normal rRNA process	96.96
KOG0323	635	consensus TFIIF-interacting CTD phosphatases, incl	96.78
COG5163	591	NOP7 Protein required for biogenesis of the 60S ri	96.52
COG5275	276	BRCT domain type II [General function prediction o	96.21
KOG2043	896	consensus Signaling protein SWIFT and related BRCT	95.85
PRK14350	669	ligA NAD-dependent DNA ligase LigA; Provisional	94.73
PRK06063	313	DNA polymerase III subunit epsilon; Provisional	93.91
PRK06195	309	DNA polymerase III subunit epsilon; Validated	93.51
PRK07956	665	ligA NAD-dependent DNA ligase LigA; Validated	93.5
COG0272	667	Lig NAD-dependent DNA ligase (contains BRCT domain	93.24
PRK14351	689	ligA NAD-dependent DNA ligase LigA; Provisional	93.17
TIGR00575	652	dnlj DNA ligase, NAD-dependent. The member of this	92.16
KOG3548	1176	consensus DNA damage checkpoint protein RHP9/CRB2/	91.65
PRK05601	377	DNA polymerase III subunit epsilon; Validated	85.41

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

Probab=99.56  E-value=7.6e-16  Score=115.62  Aligned_cols=63  Identities=40%  Similarity=0.721  Sum_probs=55.2

Q ss_pred             eEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCchhhHhhhhcCCCceEEEEeeh
Q 017048           61 LVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGW  127 (378)
Q Consensus        61 ~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~W  127 (378)
                      ++||+||+++.++..|.++++.+||.|..+++.++|||||....+.||+.|.+    +|++||+|+|
T Consensus         1 ~~i~~sg~~~~~~~~l~~~i~~~Gg~~~~~lt~~~THLI~~~~~~~K~~~A~~----~gi~vV~~~W   63 (63)
T PF12738_consen    1 VVICFSGFSGKERSQLRKLIEALGGKYSKDLTKKTTHLICSSPEGKKYRKAKE----WGIPVVSPDW   63 (63)
T ss_dssp             -EEEEEEB-TTTCCHHHHHHHCTT-EEESSSSTT-SEEEEES--HHHHHHHHH----CTSEEEEHHH
T ss_pred             CEEEECCCCHHHHHHHHHHHHHCCCEEeccccCCceEEEEeCCCcHHHHHHHH----CCCcEECCCC
Confidence            58999999999999999999999999999999999999999999999999998    5899999999

>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=99.54  E-value=6.4e-15  Score=113.77  Aligned_cols=75  Identities=25%  Similarity=0.567  Sum_probs=70.0

Q ss_pred             CCCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeee--cCchhhHhhhhcCCCceEEEEeehhhhh
Q 017048           54 ANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSF--GGRKFEHALKHGSRNGLYIVTLGWFVDS  131 (378)
Q Consensus        54 ~~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~--~~~Ky~~A~k~~~~~gi~IV~~~Wl~dc  131 (378)
                      +.++|+|+.||+++++..+++.+.++|+.+||++...+++.+||||+...  .+.|+..|..    .+++||+++||.||
T Consensus         2 ~~~~F~g~~f~i~~~~~~~~~~l~~~i~~~GG~v~~~~~~~~thvI~~~~~~~~~k~~~~~~----~~i~iV~~~Wi~~c   77 (78)
T PF00533_consen    2 KPKIFEGCTFCISGFDSDEREELEQLIKKHGGTVSNSFSKKTTHVIVGNPNKRTKKYKAAIA----NGIPIVSPDWIEDC   77 (78)
T ss_dssp             STTTTTTEEEEESSTSSSHHHHHHHHHHHTTEEEESSSSTTSSEEEESSSHCCCHHHHHHHH----TTSEEEETHHHHHH
T ss_pred             CCCCCCCEEEEEccCCCCCHHHHHHHHHHcCCEEEeecccCcEEEEeCCCCCccHHHHHHHH----CCCeEecHHHHHHh
Confidence            57899999999999999999999999999999999999999999999887  7888888887    69999999999999


Q ss_pred             h
Q 017048          132 V  132 (378)
Q Consensus       132 i  132 (378)
                      +
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=99.50  E-value=3.9e-14  Score=151.49  Aligned_cols=174  Identities=18%  Similarity=0.266  Sum_probs=144.0

Q ss_pred             CCCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCchhhHhhhhcCCCceEEEEeehhhhhhh
Q 017048           54 ANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVR  133 (378)
Q Consensus        54 ~~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci~  133 (378)
                      ...+|.|+.||.+|+++..+..|...+..+||.+...+++.|||||+.+..+.||..|..    .+++|++.+|+...+.
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            578999999999999999999999999999999999999999999999999999966654    6999999999999887


Q ss_pred             cccccccceeeeeccCccCcccccccccccccCCCccccccchhhhhhhhccCCCccccccccCccccccceeecchhhH
Q 017048          134 RNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVSE  213 (378)
Q Consensus       134 ~g~~l~e~~Y~~~~~~~~~~~~d~~~~l~~~s~~e~s~lp~~i~E~~~s~~~e~~~~~~~~~~~~lF~G~~fyl~~gfs~  213 (378)
                      .+..-.|..+. ..      ..+                                     ......|.|+.|++ .||+.
T Consensus        82 ~~~~~~e~~~~-~~------l~~-------------------------------------~~~~p~~~~~~Vc~-tgl~~  116 (811)
T KOG1929|consen   82 LWLLNKEIRLL-DP------LRD-------------------------------------TMKCPGFFGLKVCL-TGLSG  116 (811)
T ss_pred             HhhhhccCccC-cc------chh-------------------------------------hhcCCcccceEEEe-cccch
Confidence            77540111111 00      000                                     01246899999999 89999


Q ss_pred             HHHHHHHHHHhhccceeeeeeeeccCCceEEecccch-hhh---hcCCCCccchhhHHhhhhHhhhhhH
Q 017048          214 ELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSV-QKY---MGHSNNLVTPVWVLKTAKEKHVQRL  278 (378)
Q Consensus       214 ~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~s~-~~~---l~~~~~IVt~~WI~dcik~~~~qr~  278 (378)
                      .++..++.+|..+||+....  +...+.+++..+... .+|   +.+++++|+.+|+.+|+..+..+..
T Consensus       117 ~eK~ei~~~v~k~gg~~~~~--L~s~v~~~~~~~~~~~~kYe~al~wn~~v~~~~w~~~s~~~~~~~~~  183 (811)
T KOG1929|consen  117 DEKSEIKILVPKHGGTLHRS--LSSDVNSLKILPEVKTEKYEQALKWNIPVVSDDWLFDSIEKTAVLET  183 (811)
T ss_pred             HHHHHHHHHhhhcccEEehh--hhhhhheeeeccccchHHHHHHHhhCCccccHHHHhhhhcccccccc
Confidence            99999999999999999999  688888888876433 666   6799999999999999999887654

>smart00292 BRCT breast cancer carboxy-terminal domain

Probab=99.34  E-value=8.6e-13  Score=100.62  Aligned_cols=76  Identities=34%  Similarity=0.570  Sum_probs=66.2

Q ss_pred             CCccceEEEEcc-cCHHHHHHHHHHHHHhcCccCCCCCC-ccceEEEeeecCchh--hHhhhhcCCCceEEEEeehhhhh
Q 017048           56 APFSGLVICVTG-LSKEARKQVMEATERLGGQYSPDLHP-QCTHLVVQSFGGRKF--EHALKHGSRNGLYIVTLGWFVDS  131 (378)
Q Consensus        56 ~~F~g~~I~vsG-~~~~~r~~L~~lI~~~GG~~~~~lt~-~~THLI~~~~~~~Ky--~~A~k~~~~~gi~IV~~~Wl~dc  131 (378)
                      ++|+|+.||++| +....+..+.+++..+||++...++. ++||+|+.+....+.  ..|..    .+++||+++||.||
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 999999988766553  44443    68999999999999


Q ss_pred             hhcc
Q 017048          132 VRRN  135 (378)
Q Consensus       132 i~~g  135 (378)
                      ++.+
T Consensus        77 ~~~~   80 (80)
T smart00292       77 LKAG   80 (80)
T ss_pred             HHCc
Confidence            9764

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

Probab=99.30  E-value=1.8e-12  Score=133.84  Aligned_cols=168  Identities=17%  Similarity=0.295  Sum_probs=134.6

Q ss_pred             CCCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCchhhHhhhhcCCCceEEEEeehhhhhhh
Q 017048           54 ANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVR  133 (378)
Q Consensus        54 ~~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci~  133 (378)
                      .+-+|.|++.|+||+-+.+. .+-.+++.|||.+..+++..+||+|+....++||..|+-     +.+++.|+||..|++
T Consensus       115 y~~~m~~vvlcfTg~rkk~e-~lv~lvh~mgg~irkd~nsktthli~n~s~gek~~~a~t-----~~~~~rp~wv~~aw~  188 (850)
T KOG3524|consen  115 YCELMKDVVMCFTGERKKKE-ELVDLVHYMGGSIRKDTNSKTTHLIANKVEGEKQSIALV-----GVPTMRPDWVTEAWK  188 (850)
T ss_pred             cchhhcCceeeeeccchhhH-HHHHHHHHhcceeEeeeccCceEEEeecccceEEEEEee-----ccceechHhhhhhhc
Confidence            46789999999999987555 899999999999999999999999999999999999885     699999999999987


Q ss_pred             cccccccceeeeeccCccCcccccccccccccCCCccccccchhhhhhhhccCCCccccccccCccccccceeecchhhH
Q 017048          134 RNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVSE  213 (378)
Q Consensus       134 ~g~~l~e~~Y~~~~~~~~~~~~d~~~~l~~~s~~e~s~lp~~i~E~~~s~~~e~~~~~~~~~~~~lF~G~~fyl~~gfs~  213 (378)
                      ...++   .|.+.....                            .             ..+....|.|+.|+| .||+.
T Consensus       189 ~rn~~---yfda~~~~f----------------------------~-------------d~hrl~~feg~~~~f-~gF~~  223 (850)
T KOG3524|consen  189 HRNDS---YFDAMEPCF----------------------------V-------------DKHRLGVFEGLSLFF-HGFKQ  223 (850)
T ss_pred             Ccchh---hhhhhccch----------------------------h-------------hhhccccccCCeEee-cCCcH
Confidence            54322   222221100                            0             011236799999999 89999


Q ss_pred             HHHHHHHHHHhhccceeeeeeeeccCCceEEecccchhhh---hcCCCCccchhhHHhhhhHhhh
Q 017048          214 ELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKY---MGHSNNLVTPVWVLKTAKEKHV  275 (378)
Q Consensus       214 ~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~s~~~~---l~~~~~IVt~~WI~dcik~~~~  275 (378)
                      ++.+.+.+..+..||++...   +..+||||++++...-.   .+....+|..+|.+=+|-.|.+
T Consensus       224 ee~~~m~~sle~~gg~~a~~---d~~cthvvv~e~~~~~~p~~~s~~~~~vk~ewfw~siq~g~~  285 (850)
T KOG3524|consen  224 EEIDDMLRSLENTGGKLAPS---DTLCTHVVVNEDNDEVEPLAVSSNQVHVKKEWFWVSIQRGCC  285 (850)
T ss_pred             HHHHHHHHHHHhcCCcccCC---CCCceeEeecCCccccccccccccceeecccceEEEEecchh
Confidence            99999999999999999985   89999999998543322   3456678899999988887744

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

Probab=99.30  E-value=2e-12  Score=96.36  Aligned_cols=70  Identities=36%  Similarity=0.607  Sum_probs=62.6

Q ss_pred             ceEEEEcccC-HHHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCch-hhHhhhhcCCCceEEEEeehhhhhhh
Q 017048           60 GLVICVTGLS-KEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRK-FEHALKHGSRNGLYIVTLGWFVDSVR  133 (378)
Q Consensus        60 g~~I~vsG~~-~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~K-y~~A~k~~~~~gi~IV~~~Wl~dci~  133 (378)
                      |+.|+++|.. +.++..|++++..+||++...++..+||||+......+ +..|..    .+++||+++||.||++
T Consensus         1 ~~~~~i~g~~~~~~~~~l~~~i~~~Gg~v~~~~~~~~thvI~~~~~~~~~~~~~~~----~~~~iV~~~Wi~~~~~   72 (72)
T cd00027           1 GLTFVITGDLPSEERDELKELIEKLGGKVTSSVSKKTTHVIVGSDAGPKKLLKAIK----LGIPIVTPEWLLDCLK   72 (72)
T ss_pred             CCEEEEEecCCCcCHHHHHHHHHHcCCEEeccccCCceEEEECCCCCchHHHHHHH----cCCeEecHHHHHHHhC
Confidence            6889999998 88999999999999999999999999999998876665 666665    6999999999999974

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.

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

Probab=99.22  E-value=6.9e-12  Score=121.60  Aligned_cols=91  Identities=22%  Similarity=0.376  Sum_probs=85.7

Q ss_pred             CCCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCchhhHhhhhcCCCceEEEEeehhhhhhh
Q 017048           54 ANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVR  133 (378)
Q Consensus        54 ~~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci~  133 (378)
                      -.++++|++|.++||-+.+|..|+.....+|++|..+.+..+|||||..+.+.||.+..-    +|-.||+.+||.+|..
T Consensus       314 l~klL~GVV~VlSGfqNP~Rs~LRskAl~LGAkY~pDW~~gsThLICAF~NTPKy~QV~g----~Gg~IV~keWI~~Cy~  389 (508)
T KOG3226|consen  314 LSKLLEGVVFVLSGFQNPERSTLRSKALTLGAKYQPDWNAGSTHLICAFPNTPKYRQVEG----NGGTIVSKEWITECYA  389 (508)
T ss_pred             HHHhhhceEEEEecccCchHHHHHHHHHhhcccccCCcCCCceeEEEecCCCcchhhccc----CCceEeeHHHHHHHHH
Confidence            467899999999999999999999999999999999999999999999999999998775    6889999999999999


Q ss_pred             cccccccceeeeecc
Q 017048          134 RNVRLSESLYTVKSI  148 (378)
Q Consensus       134 ~g~~l~e~~Y~~~~~  148 (378)
                      ..++||...|.+...
T Consensus       390 ~kk~lp~rrYlm~~~  404 (508)
T KOG3226|consen  390 QKKLLPIRRYLMHAG  404 (508)
T ss_pred             HHhhccHHHHHhcCC
Confidence            999999999998764

>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=99.21  E-value=1.1e-11  Score=95.55  Aligned_cols=71  Identities=18%  Similarity=0.421  Sum_probs=62.3

Q ss_pred             CccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEeccc--chhhh---hcCCCCccchhhHHhhh
Q 017048          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED--SVQKY---MGHSNNLVTPVWVLKTA  270 (378)
Q Consensus       197 ~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~--s~~~~---l~~~~~IVt~~WI~dci  270 (378)
                      ..+|+|+.||+ .+++...++.|.++|+.+||++.+.  ....+||+|++..  ...++   ...++.||+++||.||+
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 8888888999999999999999988  6999999999874  33333   56899999999999997

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=99.15  E-value=3.6e-11  Score=128.98  Aligned_cols=191  Identities=17%  Similarity=0.167  Sum_probs=134.4

Q ss_pred             cCCCcc--cCCCCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeeec-CchhhHhhhhcCCCceEE
Q 017048           46 LASDSV--LPANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFG-GRKFEHALKHGSRNGLYI  122 (378)
Q Consensus        46 ~~~~~~--~~~~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~-~~Ky~~A~k~~~~~gi~I  122 (378)
                      ++++|.  ....+.|.|+.||+|||...++.++..+|..|||++...++..++|++..... +.||+.|++    |+++|
T Consensus        90 ~~~~~l~~~~~~p~~~~~~Vc~tgl~~~eK~ei~~~v~k~gg~~~~~L~s~v~~~~~~~~~~~~kYe~al~----wn~~v  165 (811)
T KOG1929|consen   90 RLLDPLRDTMKCPGFFGLKVCLTGLSGDEKSEIKILVPKHGGTLHRSLSSDVNSLKILPEVKTEKYEQALK----WNIPV  165 (811)
T ss_pred             ccCccchhhhcCCcccceEEEecccchHHHHHHHHHhhhcccEEehhhhhhhheeeeccccchHHHHHHHh----hCCcc
Confidence            455552  34788999999999999999999999999999999999999888888876654 499999998    58999


Q ss_pred             EEeehhhhhhhcccccccceeeeeccCccCcccccccccccccCCCccccccchhhhh-hhhccCCCccccccccCcccc
Q 017048          123 VTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAK-QFNATGKHERDSNRSMNSTLS  201 (378)
Q Consensus       123 V~~~Wl~dci~~g~~l~e~~Y~~~~~~~~~~~~d~~~~l~~~s~~e~s~lp~~i~E~~-~s~~~e~~~~~~~~~~~~lF~  201 (378)
                      |+.+|+++|+..+..+++..|++....+.-..+... .   .......+.....+... .+......+....+....+..
T Consensus       166 ~~~~w~~~s~~~~~~~~~~~~e~~~~~~~is~~~~~-~---~~~~~~~~~s~t~~~~~~~~~~~~n~~~~p~~a~~~~~~  241 (811)
T KOG1929|consen  166 VSDDWLFDSIEKTAVLETKPYEGAPVAEAISGPIGS-T---LPKEILDGDSRTANDTWSTSKVVTNIKVLPFQAKIGNLD  241 (811)
T ss_pred             ccHHHHhhhhcccccccccccccccccceeccCCcc-c---cccccccccchhhhccccchhcccccccchhhhhccccc
Confidence            999999999999999999999987732211111000 0   00000000000000000 000001111122233344789


Q ss_pred             ccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEecc
Q 017048          202 GCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEE  247 (378)
Q Consensus       202 G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~  247 (378)
                      +|.+|+ .+++...+..|.+.++.+||.....  ....++|++.+.
T Consensus       242 ~c~v~~-s~~~~~~~s~l~r~~~~g~~~~~~e--~~e~~st~l~~~  284 (811)
T KOG1929|consen  242 DCLVET-SGTTSRNRSALSRLSNNGGSLRFLE--RLEETSTSLLGD  284 (811)
T ss_pred             cceeee-cCCcccchhHhHHhhhcccceeecc--cCccccchhhcc
Confidence            999999 7888888999999999999999988  478889998876

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

Probab=99.14  E-value=4.8e-11  Score=125.37  Aligned_cols=212  Identities=20%  Similarity=0.260  Sum_probs=125.1

Q ss_pred             CCCCCccceEEEE-cccCH-HHHHHHHHHHHHhcCccCCCCCCccceEEE--eeecCchhhHhhhhcCCCceEEEEeehh
Q 017048           53 PANAPFSGLVICV-TGLSK-EARKQVMEATERLGGQYSPDLHPQCTHLVV--QSFGGRKFEHALKHGSRNGLYIVTLGWF  128 (378)
Q Consensus        53 ~~~~~F~g~~I~v-sG~~~-~~r~~L~~lI~~~GG~~~~~lt~~~THLI~--~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl  128 (378)
                      ....+|.|+.||+ +|.+. ..+..++++|.++||.+..++.+..||+|+  +...+.+-..|++    +++.||+|+||
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            4678999999999 67765 458999999999999999999998999996  3333444444554    59999999999


Q ss_pred             hhhhhcccccccceeeeeccCccCcc-----cccccccc----c-------ccCCCccc--cccchhhhhhhhccCCCcc
Q 017048          129 VDSVRRNVRLSESLYTVKSIDEHGMH-----LDKLNRLV----G-------FAGTENSC--LPAGIYEAKQFNATGKHER  190 (378)
Q Consensus       129 ~dci~~g~~l~e~~Y~~~~~~~~~~~-----~d~~~~l~----~-------~s~~e~s~--lp~~i~E~~~s~~~e~~~~  190 (378)
                      .||+...++++..++.+-...+....     .|.+..++    +       ++...+|.  +|...        .-+...
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            99999999888766655443221110     11111111    0       00000000  00000        000000


Q ss_pred             ccccccCccccccc-eeecch-hhHHHHHHHHHHHhhccceeeeee----eeccCCceEEecc--c---ch---hhh-hc
Q 017048          191 DSNRSMNSTLSGCS-MYVDSD-VSEELRNKVFEAATNEGATLVNQW----FVGCGASYVVCEE--D---SV---QKY-MG  255 (378)
Q Consensus       191 ~~~~~~~~lF~G~~-fyl~~g-fs~~~~~~L~~lI~~~GG~vv~~~----~~~~~vTHVV~~~--~---s~---~~~-l~  255 (378)
                      .+.+. ..+|..++ ||.... ++. +-....-.++.+||.+++.-    +....+||+|+..  .   +.   ++. +-
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 23333333 333222 222 23344556888899999763    1345679999873  1   11   122 11


Q ss_pred             CCCCccchhhHHhhhhHhhhhhH
Q 017048          256 HSNNLVTPVWVLKTAKEKHVQRL  278 (378)
Q Consensus       256 ~~~~IVt~~WI~dcik~~~~qr~  278 (378)
                      ..-+||.|.|+.+|+.++.++..
T Consensus       855 ~~rkv~~~~wv~~s~~~~~~~~e  877 (881)
T KOG0966|consen  855 IKRKVVAPSWVDHSINENCLLPE  877 (881)
T ss_pred             ccccccCHHHHHHhhcccccCcc
Confidence            12289999999999998876654

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

Probab=99.03  E-value=6.2e-10  Score=116.72  Aligned_cols=179  Identities=18%  Similarity=0.232  Sum_probs=129.4

Q ss_pred             ceEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeee------cCchhhHhhhhcCCCceEEEEeehhhhhhh
Q 017048           60 GLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSF------GGRKFEHALKHGSRNGLYIVTLGWFVDSVR  133 (378)
Q Consensus        60 g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~------~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci~  133 (378)
                      -.+.+++|.++.++..+.+..+.   +.+.+....+||+|++..      .+.||..++    ..|.||++++|+..|++
T Consensus       478 k~~~~~s~l~p~ek~~v~~~a~~---t~~k~~~~~~thvi~~~~~~g~c~rTlk~~~gi----l~gkwi~~~~w~~~s~k  550 (684)
T KOG4362|consen  478 KLVLLVSGLTPSEKQLVEKFAVD---TISKFWIEPVTHVIASTDLEGACLRTLKVLMGI----LRGKWILSYDWVLASLK  550 (684)
T ss_pred             ceeeeeccCCcchHHHHHHHHHH---HHhhccCCCceeeeeecccccchhhhHHHHHHh----hcCceeeeHHHHHHHHH
Confidence            36778899999999999988888   888888899999999765      345555444    47999999999999999


Q ss_pred             cccccccceeeeeccCccCcccccccccccccCCCccccccchhhhhhhhccCCCccccccccCccccccceeecchhhH
Q 017048          134 RNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVSE  213 (378)
Q Consensus       134 ~g~~l~e~~Y~~~~~~~~~~~~d~~~~l~~~s~~e~s~lp~~i~E~~~s~~~e~~~~~~~~~~~~lF~G~~fyl~~gfs~  213 (378)
                      .+++++|.+|++.-+.......-.-.+                             .........||.|..||+...|+.
T Consensus       551 ~~~~~~eepfEl~~d~~~~~~~~~~~~-----------------------------~~a~s~~~kLf~gl~~~~~g~fs~  601 (684)
T KOG4362|consen  551 LRKWVSEEPFELQIDVPGAREGPKEKR-----------------------------LRAESYKPKLFEGLKFYFVGDFSN  601 (684)
T ss_pred             hcCCCCCCCeeEeecccCcccCccccc-----------------------------ccccccCcchhcCCcceeeccccc
Confidence            999999999999765332211000000                             011123478999999999888988


Q ss_pred             HHHHHHHHHHhhccceeeeeee---eccCC-ceEEecc----c--------chhhh-hcCCCCccchhhHHhhhhHhh
Q 017048          214 ELRNKVFEAATNEGATLVNQWF---VGCGA-SYVVCEE----D--------SVQKY-MGHSNNLVTPVWVLKTAKEKH  274 (378)
Q Consensus       214 ~~~~~L~~lI~~~GG~vv~~~~---~~~~v-THVV~~~----~--------s~~~~-l~~~~~IVt~~WI~dcik~~~  274 (378)
                      .-.++|+.++...||++...-.   .+..+ |.++...    +        ....+ ...+...|+..|++|++.-+.
T Consensus       602 ~p~~~l~~l~~~~gg~~l~~~~~~~~~~k~s~~~~~~~~~~~~~~~~~k~~~~ea~~~s~~a~~~~~~wvl~s~a~~~  679 (684)
T KOG4362|consen  602 PPKEQLQELVHLAGGTILQVPRVAYSDKKKSTIVVLSEKPVLDSILWQKVNDAEALALSQRARAVSSSWVLDSIAGYQ  679 (684)
T ss_pred             CcHHHHHHHHhhcCcceeeccCcccccccccceeEeecccCCCchhhhhhccHHHHHHhcCCCccchhhhhcchhcee
Confidence            7789999999999999986421   22333 3333322    1        12222 457889999999999997543

>smart00292 BRCT breast cancer carboxy-terminal domain

Probab=99.02  E-value=2.6e-10  Score=86.79  Aligned_cols=73  Identities=14%  Similarity=0.205  Sum_probs=60.3

Q ss_pred             cccccceeecchhhHHHHHHHHHHHhhccceeeeeeeecc-CCceEEecccch-----hhhhcCCCCccchhhHHhhhhH
Q 017048          199 TLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGC-GASYVVCEEDSV-----QKYMGHSNNLVTPVWVLKTAKE  272 (378)
Q Consensus       199 lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~-~vTHVV~~~~s~-----~~~l~~~~~IVt~~WI~dcik~  272 (378)
                      +|+|+.||+...+....++.+.+++..+||++...  ... .+||+|+.+...     ......++.||+++||.||+++
T Consensus         2 ~f~g~~~~~~g~~~~~~~~~l~~~i~~~Gg~~~~~--~~~~~~thvi~~~~~~~~~~~~~~~~~~~~iV~~~Wi~~~~~~   79 (80)
T smart00292        2 LFKGKVFVITGKFDKNERDELKELIEALGGKVTSS--LSSKTTTHVIVGSPEGGKLELLLAIALGIPIVTEDWLLDCLKA   79 (80)
T ss_pred             ccCCeEEEEeCCCCCccHHHHHHHHHHcCCEEecc--cCccceeEEEEcCCCCccHHHHHHHHcCCCCccHHHHHHHHHC
Confidence            79999999953377788999999999999999998  455 899999987432     2224688999999999999976


Q ss_pred             h
Q 017048          273 K  273 (378)
Q Consensus       273 ~  273 (378)
                      +
T Consensus        80 ~   80 (80)
T smart00292       80 G   80 (80)
T ss_pred             c
Confidence            3

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

Probab=98.84  E-value=2.6e-09  Score=79.32  Aligned_cols=67  Identities=22%  Similarity=0.321  Sum_probs=54.6

Q ss_pred             ccceeecchhh-HHHHHHHHHHHhhccceeeeeeeeccCCceEEecccch----hhhhcCCCCccchhhHHhhhh
Q 017048          202 GCSMYVDSDVS-EELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSV----QKYMGHSNNLVTPVWVLKTAK  271 (378)
Q Consensus       202 G~~fyl~~gfs-~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~s~----~~~l~~~~~IVt~~WI~dcik  271 (378)
                      |+.||+ .+.. ...+..|+++++.+||++.+.  ....+||+|+.....    ......++.||++.||.||++
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            678999 4544 667889999999999999998  578999999987332    233568899999999999984

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.

>PLN03122 Poly [ADP-ribose] polymerase; Provisional

Probab=98.66  E-value=1.6e-08  Score=109.59  Aligned_cols=89  Identities=25%  Similarity=0.455  Sum_probs=78.4

Q ss_pred             CCCCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeeec-----CchhhHhhhhcCCCceEEEEeeh
Q 017048           53 PANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFG-----GRKFEHALKHGSRNGLYIVTLGW  127 (378)
Q Consensus        53 ~~~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~-----~~Ky~~A~k~~~~~gi~IV~~~W  127 (378)
                      ...++|.|++|++||..+..|.+++++|+.+||+++..+ ..+||+|+....     +.|+..|.+    .||+||+.+|
T Consensus       185 ~~~kpL~G~~fviTGtl~~sr~elK~~Ie~~GGkvsssV-s~~T~lIvt~~ev~k~gsSKlkkAk~----lgIpIVsEd~  259 (815)
T PLN03122        185 APGKPFSGMMISLSGRLSRTHQYWKKDIEKHGGKVANSV-EGVTCLVVSPAERERGGSSKIAEAME----RGIPVVREAW  259 (815)
T ss_pred             ccCCCcCCcEEEEeCCCCCCHHHHHHHHHHcCCEEcccc-ccceEEEEcCccccccCccHHHHHHH----cCCcCccHHH
Confidence            466789999999999876689999999999999999999 567888886643     378999987    6999999999


Q ss_pred             hhhhhhcccccccceeeee
Q 017048          128 FVDSVRRNVRLSESLYTVK  146 (378)
Q Consensus       128 l~dci~~g~~l~e~~Y~~~  146 (378)
                      |.+|++.++.+++..|.+.
T Consensus       260 L~d~i~~~k~~~~~~y~l~  278 (815)
T PLN03122        260 LIDSIEKQEAQPLEAYDVV  278 (815)
T ss_pred             HHHHHhcCCcccchhhhhc
Confidence            9999999999999999885

>PLN03123 poly [ADP-ribose] polymerase; Provisional

Probab=98.62  E-value=2.4e-08  Score=110.24  Aligned_cols=91  Identities=20%  Similarity=0.303  Sum_probs=79.4

Q ss_pred             CCCCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeee---cCchhhHhhhhcCCCceEEEEeehhh
Q 017048           53 PANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSF---GGRKFEHALKHGSRNGLYIVTLGWFV  129 (378)
Q Consensus        53 ~~~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~---~~~Ky~~A~k~~~~~gi~IV~~~Wl~  129 (378)
                      ...++|.|+.|+++|-.+....++++.|+.+||+|+..++..+||||+...   .+.|+..|.+    .+++||+.+||.
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 SESEFLGDLKVSIVGASKEKVTEWKAKIEEAGGVFHATVKKDTNCLVVCGELDDEDAEMRKARR----MKIPIVREDYLV  464 (981)
T ss_pred             ccCCCcCCeEEEEecCCCCcHHHHHHHHHhcCCEEeeeccCCceEEEccHHhhhcchHHHHHHh----cCCCcccHHHHH
Confidence            467899999999999877777899999999999999999999999999753   4566777776    589999999999


Q ss_pred             hhhhcccccccceeeeec
Q 017048          130 DSVRRNVRLSESLYTVKS  147 (378)
Q Consensus       130 dci~~g~~l~e~~Y~~~~  147 (378)
                      ||+..+.++|+..|.+..
T Consensus       465 ds~~~~~~~p~~~y~~~~  482 (981)
T PLN03123        465 DCFKKKKKLPFDKYKLEA  482 (981)
T ss_pred             HHHhccccCcchhhhhcc
Confidence            999999999999887653

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

Probab=98.56  E-value=5.5e-08  Score=103.77  Aligned_cols=195  Identities=18%  Similarity=0.163  Sum_probs=110.1

Q ss_pred             CCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCC-CCC-------------------------ccceEEEee-ecCch
Q 017048           55 NAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPD-LHP-------------------------QCTHLVVQS-FGGRK  107 (378)
Q Consensus        55 ~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~-lt~-------------------------~~THLI~~~-~~~~K  107 (378)
                      ..+|.||+|.+|+... ++++....++.+||.+... |..                         .--.||+.. ..+.|
T Consensus       923 kniFd~cvF~lTsa~~-sd~~~r~s~e~~gg~vle~gl~~~Fn~p~~g~~~~lr~Ln~~q~~ks~~qalLIsdth~Rt~K 1001 (1176)
T KOG3548|consen  923 KNIFDGCVFMLTSANR-SDSASRPSMEKHGGLVLEKGLMNLFNTPFKGGGIVLRQLNSFQERKSNYQALLISDTHYRTHK 1001 (1176)
T ss_pred             cchhcceeEEEecccc-chhhhhhhhhccCChhhhccccccccccccCCcchHHhhhHHhhhccccceeEeehhhhHHHH
Confidence            4799999999999763 2233445555578765433 111                         012334422 26789


Q ss_pred             hhHhhhhcCCCceEEEEeehhhhhhhcccccccceeeeeccCccCcccccccccccccCCCccccccchh-hhhhhhccC
Q 017048          108 FEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIY-EAKQFNATG  186 (378)
Q Consensus       108 y~~A~k~~~~~gi~IV~~~Wl~dci~~g~~l~e~~Y~~~~~~~~~~~~d~~~~l~~~s~~e~s~lp~~i~-E~~~s~~~e  186 (378)
                      |..|+.    .|||.|++.||.+|+++++++|..+|.+.......  .|             +-+..++. ....    +
T Consensus      1002 YLeaLA----~giPcVh~~fI~aC~e~nr~Vdy~~YLLpsGyS~r--ld-------------s~l~~~i~~fn~~----~ 1058 (1176)
T KOG3548|consen 1002 YLEALA----RGIPCVHNTFIQACGEQNRCVDYTDYLLPSGYSIR--LD-------------SQLMPAIEPFNPS----E 1058 (1176)
T ss_pred             HHHHHH----cCCCcccHHHHHHHHhccccccchhhcccCccccc--cc-------------cccccCccccCch----h
Confidence            999997    69999999999999999999999999987632110  00             00000110 0000    0


Q ss_pred             CCccccccccCccccccceeecchhhHHHHHHHHHHHhhccceeeeeeee---ccCC------ceEEecc--cchhhhh-
Q 017048          187 KHERDSNRSMNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFV---GCGA------SYVVCEE--DSVQKYM-  254 (378)
Q Consensus       187 ~~~~~~~~~~~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~---~~~v------THVV~~~--~s~~~~l-  254 (378)
                      .+...-....+.+|.-..++..++  ....+.....+..+|+-+++....   +.+.      -|++++.  ++.-+|+ 
T Consensus      1059 nLkd~~l~vk~~l~~~~v~q~gp~--~~f~e~~~e~le~G~aa~vd~~hada~~~D~~l~~fdvvl~d~~~~~svmk~ad 1136 (1176)
T KOG3548|consen 1059 NLKDTTLYVKSTLSAREVTQTGPG--GTFIEIWKEILELGGAAVVDGYHADAETLDETLLKFDVVLVDGTFRDSVMKYAD 1136 (1176)
T ss_pred             hccceeeEeeccccceeEEEecCC--cchHHHHHHHHHhhchheecccccccccccccccceeEEEecCccHHHHHHHHH
Confidence            000000001133333323333222  344566777888888888876321   1111      1222222  3444553 


Q ss_pred             cCCCCccchhhHHhhhhHhhh
Q 017048          255 GHSNNLVTPVWVLKTAKEKHV  275 (378)
Q Consensus       255 ~~~~~IVt~~WI~dcik~~~~  275 (378)
                      .-+.++|+++||.+||-.|+.
T Consensus      1137 ~l~~pvvs~EWvIQtiI~~~~ 1157 (1176)
T KOG3548|consen 1137 TLGAPVVSSEWVIQTIILGKA 1157 (1176)
T ss_pred             HhCCCccChhHhheeeecccc
Confidence            357999999999999987753

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

Probab=98.55  E-value=2.1e-08  Score=74.94  Aligned_cols=60  Identities=17%  Similarity=0.304  Sum_probs=47.7

Q ss_pred             cceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEecccchhhh---hcCCCCccchhh
Q 017048          203 CSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKY---MGHSNNLVTPVW  265 (378)
Q Consensus       203 ~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~s~~~~---l~~~~~IVt~~W  265 (378)
                      ++|++ +||++.+++.|.++++.+||++.+.  +..++||+|+.....++|   ...+++||+++|
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            35777 7898888999999999999999999  599999999988666666   567899999999

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

Probab=98.06  E-value=2.9e-06  Score=83.07  Aligned_cols=83  Identities=19%  Similarity=0.414  Sum_probs=72.2

Q ss_pred             cCccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEecccchhhh---hcCCCCccchhhHHhhhhH
Q 017048          196 MNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKY---MGHSNNLVTPVWVLKTAKE  272 (378)
Q Consensus       196 ~~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~s~~~~---l~~~~~IVt~~WI~dcik~  272 (378)
                      .+.|++|..|.| +||..+.|..|+..+..+|+++-.+|  +.++||+||.-....+|   .+.+-.||+-+||++|...
T Consensus       314 l~klL~GVV~Vl-SGfqNP~Rs~LRskAl~LGAkY~pDW--~~gsThLICAF~NTPKy~QV~g~Gg~IV~keWI~~Cy~~  390 (508)
T KOG3226|consen  314 LSKLLEGVVFVL-SGFQNPERSTLRSKALTLGAKYQPDW--NAGSTHLICAFPNTPKYRQVEGNGGTIVSKEWITECYAQ  390 (508)
T ss_pred             HHHhhhceEEEE-ecccCchHHHHHHHHHhhcccccCCc--CCCceeEEEecCCCcchhhcccCCceEeeHHHHHHHHHH
Confidence            368999999999 89999999999999999999999998  99999999987655566   5678899999999999999


Q ss_pred             hhhhhHHhh
Q 017048          273 KHVQRLVHI  281 (378)
Q Consensus       273 ~~~qr~~~~  281 (378)
                      +++...-.|
T Consensus       391 kk~lp~rrY  399 (508)
T KOG3226|consen  391 KKLLPIRRY  399 (508)
T ss_pred             HhhccHHHH
Confidence            887655444

>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=98.06  E-value=3.2e-06  Score=90.61  Aligned_cols=74  Identities=22%  Similarity=0.282  Sum_probs=66.9

Q ss_pred             CCCccceEEEEccc-CHHHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCchhhHhhhhcCCCceEEEEeehhhhhh
Q 017048           55 NAPFSGLVICVTGL-SKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSV  132 (378)
Q Consensus        55 ~~~F~g~~I~vsG~-~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci  132 (378)
                      ..+|.|.+|||||. +...|.+++++|+.+||+++..++++|++||++...|.|.++|.+    .||+|++.+.+.+-+
T Consensus       591 ~~~l~gktfV~TG~l~~~~R~e~~~lie~~Ggkv~ssVSkktd~LV~G~~aGsKl~KA~~----LGI~Ii~e~~f~~~l  665 (669)
T PRK14350        591 NSFLFGKKFCITGSFNGYSRSVLIDKLTKKGAIFNTCVTKYLDFLLVGEKAGLKLKKANN----LGIKIMSLFDIKSYV  665 (669)
T ss_pred             CCccCCcEEEEecccCCCCHHHHHHHHHHcCCEEeccccCCCcEEEECCCCCchHHHHHH----cCCEEecHHHHHHHh
Confidence            45799999999995 457899999999999999999999999999999888999999998    699999999887644

>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=97.99  E-value=3.2e-06  Score=92.77  Aligned_cols=137  Identities=23%  Similarity=0.387  Sum_probs=97.2

Q ss_pred             eEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeee-cCchhhHhhhhcCCCceEEEEeehhhhhhhcccccc
Q 017048           61 LVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSF-GGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLS  139 (378)
Q Consensus        61 ~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~-~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci~~g~~l~  139 (378)
                      +.+.++++.+  ...++..++.+||.+.... .++||+|+... .+.|+..|+.    .|++||+++||.+|++.|.++|
T Consensus       660 ~~~lfs~~~~--~~~~k~~~k~lg~s~~ss~-~e~Th~i~~rirRT~k~Leai~----~G~~ivT~~wL~s~~k~g~~~d  732 (896)
T KOG2043|consen  660 IEVLFSDKND--GKNYKLAKKFLGGSVASSD-SEATHFIADRIRRTLKFLEAIS----SGKPLVTPQWLVSSLKSGEKLD  732 (896)
T ss_pred             eeeeeeeccC--chhhhhHHhhccceeeccc-ccceeeeehhhhccHHHHhhhc----cCCcccchHHHHHHhhcccccc
Confidence            4455566543  3347888899998888777 47899999754 6788888886    6999999999999999999999


Q ss_pred             cceeeeeccCccCcccccccccccccCCCccccccchhhhhhhhccCCCccccccccCccccccceeecchhhHHHHHHH
Q 017048          140 ESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVSEELRNKV  219 (378)
Q Consensus       140 e~~Y~~~~~~~~~~~~d~~~~l~~~s~~e~s~lp~~i~E~~~s~~~e~~~~~~~~~~~~lF~G~~fyl~~gfs~~~~~~L  219 (378)
                      +..|.+.+..... +   |    +.      ++-..+.            +.  .. ..+|.|..||+.+++.+ ....+
T Consensus       733 ek~yil~D~ekEk-~---~----gf------~l~ssl~------------RA--r~-~plL~g~~v~vtp~v~p-~~~~v  782 (896)
T KOG2043|consen  733 EKPYILHDEEKEK-E---F----GF------RLKSSLL------------RA--RA-DPLLEGINVHVTPSVTP-SPKTV  782 (896)
T ss_pred             CccccccCHHHHh-c---c----Cc------chhhHHH------------Hh--hc-chhhcCceEEecccccc-Ccchh
Confidence            9999987642110 0   0    00      0000000            00  01 37899999999766654 35679


Q ss_pred             HHHHhhccceeeeee
Q 017048          220 FEAATNEGATLVNQW  234 (378)
Q Consensus       220 ~~lI~~~GG~vv~~~  234 (378)
                      .++|+..||.++...
T Consensus       783 ~eiie~~ggnvv~~~  797 (896)
T KOG2043|consen  783 VEIIEISGGNVVSDS  797 (896)
T ss_pred             HHHHhhcCcceeccc
Confidence            999999999999874

>PRK06063 DNA polymerase III subunit epsilon; Provisional

Probab=97.95  E-value=7.1e-06  Score=80.76  Aligned_cols=73  Identities=15%  Similarity=0.209  Sum_probs=64.7

Q ss_pred             CCccceEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeeecC--chhhHhhhhcCCCceEEEEeehhhhhh
Q 017048           56 APFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGG--RKFEHALKHGSRNGLYIVTLGWFVDSV  132 (378)
Q Consensus        56 ~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~--~Ky~~A~k~~~~~gi~IV~~~Wl~dci  132 (378)
                      ++|.|.+|+|||-....|.+++++|+.+||++...+++++++||+++..+  .|..+|.+    .||+|++.+=+.+-+
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 PLVQGMRVALSAEVSRTHEELVERILHAGLAYSDSVDRDTSLVVCNDPAPEQGKGYHARQ----LGVPVLDEAAFLELL  305 (313)
T ss_pred             cccCCCEEEEecCCCCCHHHHHHHHHHcCCEecCccccCccEEEECCCCCcccHHHHHHH----cCCccccHHHHHHHH
Confidence            45799999999976679999999999999999999999999999998766  79999987    699999987766544

>PRK06195 DNA polymerase III subunit epsilon; Validated

Probab=97.87  E-value=1.9e-05  Score=77.62  Aligned_cols=78  Identities=21%  Similarity=0.261  Sum_probs=63.9

Q ss_pred             CCCccceEEEEcccC-HHHHHHHHHHHHHhcCccCCCCCCccceEEEeee---------cCchhhHhhhh-cCCCceEEE
Q 017048           55 NAPFSGLVICVTGLS-KEARKQVMEATERLGGQYSPDLHPQCTHLVVQSF---------GGRKFEHALKH-GSRNGLYIV  123 (378)
Q Consensus        55 ~~~F~g~~I~vsG~~-~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~---------~~~Ky~~A~k~-~~~~gi~IV  123 (378)
                      ..+|.|.+|||||-. .-.|.+++++|+.+||++..+++++|++||++..         .+.|.++|.+. ....+|+|+
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            457999999999975 5789999999999999999999999999999853         46799999763 112489999


Q ss_pred             Eeehhhhhh
Q 017048          124 TLGWFVDSV  132 (378)
Q Consensus       124 ~~~Wl~dci  132 (378)
                      +.+=+++-+
T Consensus       298 ~E~~f~~l~  306 (309)
T PRK06195        298 NEEEFLQKC  306 (309)
T ss_pred             cHHHHHHHH
Confidence            877555543

>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated

Probab=97.85  E-value=1.4e-05  Score=86.08  Aligned_cols=75  Identities=20%  Similarity=0.293  Sum_probs=67.6

Q ss_pred             CCccceEEEEcccCH-HHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCchhhHhhhhcCCCceEEEEeehhhhhhhc
Q 017048           56 APFSGLVICVTGLSK-EARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVRR  134 (378)
Q Consensus        56 ~~F~g~~I~vsG~~~-~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci~~  134 (378)
                      .+|.|.+|||||... ..|.+++++|+.+||.++..++++|++||++...|.|..+|.+    .||+|++.+-+.+.+..
T Consensus       589 ~~~~g~~~v~TG~l~~~~R~e~~~~i~~~G~~v~~sVs~kt~~lv~G~~~gsK~~kA~~----lgI~ii~E~~f~~~l~~  664 (665)
T PRK07956        589 VDLAGKTVVLTGTLEQLSRDEAKEKLEALGAKVSGSVSKKTDLVVAGEAAGSKLAKAQE----LGIEVLDEEEFLRLLGE  664 (665)
T ss_pred             CCccccEEEEeCCCCCCCHHHHHHHHHHcCCEEeCcccCCCCEEEECCCCChHHHHHHH----cCCeEEcHHHHHHHHhc
Confidence            459999999999864 5899999999999999999999999999999888899999998    69999999988876643

>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=97.81  E-value=1.7e-05  Score=85.43  Aligned_cols=76  Identities=22%  Similarity=0.238  Sum_probs=67.9

Q ss_pred             CCCccceEEEEcccCH-HHHHHHHHHHHHhcCccCCCCCCccceEEEeeecC-chhhHhhhhcCCCceEEEEeehhhhhh
Q 017048           55 NAPFSGLVICVTGLSK-EARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGG-RKFEHALKHGSRNGLYIVTLGWFVDSV  132 (378)
Q Consensus        55 ~~~F~g~~I~vsG~~~-~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~-~Ky~~A~k~~~~~gi~IV~~~Wl~dci  132 (378)
                      ..+|.|.+|||||... -+|.+++++|+.+||++..+++++|++||++...| .|..+|.+    .||+|++.+-|.+-+
T Consensus       607 ~~~l~g~~~v~TG~l~~~~R~~~~~~i~~~Gg~v~~sVs~kt~~Lv~G~~~g~sKl~kA~~----lgi~ii~E~~f~~ll  682 (689)
T PRK14351        607 GDALDGLTFVFTGSLSGYTRSEAQELVEAHGGNATGSVSGNTDYLVVGENPGQSKRDDAEA----NDVPTLDEEEFEELL  682 (689)
T ss_pred             CCCCCCcEEEEccCCCCCCHHHHHHHHHHcCCEEcCCcCCCccEEEEcCCCChhHHHHHHH----CCCeEecHHHHHHHH
Confidence            4579999999999864 58999999999999999999999999999998777 79999987    699999999888766


Q ss_pred             hc
Q 017048          133 RR  134 (378)
Q Consensus       133 ~~  134 (378)
                      +.
T Consensus       683 ~~  684 (689)
T PRK14351        683 AE  684 (689)
T ss_pred             Hh
Confidence            53

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

Probab=97.79  E-value=1.7e-05  Score=83.87  Aligned_cols=72  Identities=22%  Similarity=0.308  Sum_probs=66.6

Q ss_pred             CCccceEEEEcccC-HHHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCchhhHhhhhcCCCceEEEEeehhhhh
Q 017048           56 APFSGLVICVTGLS-KEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDS  131 (378)
Q Consensus        56 ~~F~g~~I~vsG~~-~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~dc  131 (378)
                      .+|.|.+|++||.- .-.|.+.+++++.+||+++.++++++++||++...|.|+.+|.+    .||+|++.+++..-
T Consensus       593 ~~l~gkt~V~TGtL~~~sR~eak~~le~lGakv~~SVSkktD~vvaG~~aGSKl~kA~e----Lgv~i~~E~~~~~l  665 (667)
T COG0272         593 SPLAGKTFVLTGTLEGMSRDEAKALLEALGAKVSGSVSKKTDYVVAGENAGSKLAKAQE----LGVKIIDEEEFLAL  665 (667)
T ss_pred             cccCCCEEEEeccCCCCCHHHHHHHHHHcCCEEeceecccccEEEEcCCCChHHHHHHH----cCCeEecHHHHHHh
Confidence            88999999999975 48999999999999999999999999999999999999999998    69999999887653

>TIGR00575 dnlj DNA ligase, NAD-dependent

Probab=97.73  E-value=2.7e-05  Score=83.71  Aligned_cols=69  Identities=22%  Similarity=0.361  Sum_probs=62.2

Q ss_pred             CCCccceEEEEcccC-HHHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCchhhHhhhhcCCCceEEEEeeh
Q 017048           55 NAPFSGLVICVTGLS-KEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGW  127 (378)
Q Consensus        55 ~~~F~g~~I~vsG~~-~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~W  127 (378)
                      ..+|.|.+|||||.. ...|.+++++|+.+||+++.++++++++||++...|.|+++|.+    .||+|++.+.
T Consensus       582 ~~~l~gk~~v~TG~l~~~~R~~~~~~i~~~G~~v~~sVs~kt~~lv~G~~~gsKl~kA~~----lgi~ii~E~~  651 (652)
T TIGR00575       582 GSPLAGKTFVLTGTLSQMSRDEAKELLENLGGKVASSVSKKTDYVIAGEKAGSKLAKAQE----LGIPIINEEE  651 (652)
T ss_pred             CCCccCcEEEEeccCCCCCHHHHHHHHHHcCCEEeCCcCCCccEEEECCCCChHHHHHHH----cCCcEechhh
Confidence            457999999999975 46899999999999999999999999999999888889999998    6999988654

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.

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

Probab=97.55  E-value=4.6e-05  Score=77.65  Aligned_cols=81  Identities=14%  Similarity=0.220  Sum_probs=59.6

Q ss_pred             CccccccceeecchhhHHHHHHHHHHHhhccceeeeee------e--eccCCceEEecccchhhhhcCCCCccchhhHHh
Q 017048          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQW------F--VGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLK  268 (378)
Q Consensus       197 ~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~------~--~~~~vTHVV~~~~s~~~~l~~~~~IVt~~WI~d  268 (378)
                      ..+|+|+.||+...++   ++.|.=+|+++||.|.-..      +  .++.+||=|++.+..+.-.. +-.-|.|+||.|
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---RESLEFIIRSFGGKVSWDPLGIGATYDESDERITHQIVDRPGQQTSVI-GRTYVQPQWVFD  400 (570)
T ss_pred             HHHhhcceeeeeccCc---hHHHHHHHHHcCCceecCccCCCCcccccccceeeeeecccCccceee-eeeeecchhhhh
Confidence            6899999999976665   5668889999999998651      1  24567999998755433211 234688999999


Q ss_pred             hhhHhhhhhHHhh
Q 017048          269 TAKEKHVQRLVHI  281 (378)
Q Consensus       269 cik~~~~qr~~~~  281 (378)
                      |+.++.+...-.|
T Consensus       401 svNar~llpt~~Y  413 (570)
T KOG2481|consen  401 SVNARLLLPTEKY  413 (570)
T ss_pred             hccchhhccHhhh
Confidence            9999987655444

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

Probab=97.43  E-value=6.5e-05  Score=74.40  Aligned_cols=81  Identities=12%  Similarity=0.276  Sum_probs=59.2

Q ss_pred             CccccccceeecchhhHHHHHHHHHHHhhccceeeeeee---------eccCCceEEecccchhhhhcCCCCccchhhHH
Q 017048          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWF---------VGCGASYVVCEEDSVQKYMGHSNNLVTPVWVL  267 (378)
Q Consensus       197 ~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~---------~~~~vTHVV~~~~s~~~~l~~~~~IVt~~WI~  267 (378)
                      .++|+|++||++..++.   +.|.=+|.++||.|+.+.-         .+..+||-||+.+-++.-. .+..-|.|+||.
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            57999999999755553   4577789999999987631         4567899999875443222 244568899999


Q ss_pred             hhhhHhhhhhHHhh
Q 017048          268 KTAKEKHVQRLVHI  281 (378)
Q Consensus       268 dcik~~~~qr~~~~  281 (378)
                      |||..|.+-+.-.|
T Consensus       424 DsiNkG~l~~~~~Y  437 (591)
T COG5163         424 DSINKGKLACVENY  437 (591)
T ss_pred             hhhccccchhhhhc
Confidence            99999987654333

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

Probab=97.41  E-value=0.00017  Score=75.80  Aligned_cols=91  Identities=24%  Similarity=0.367  Sum_probs=76.3

Q ss_pred             CCCCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCchhhHhhhhcCCCceEEEEeehhhhhh
Q 017048           53 PANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSV  132 (378)
Q Consensus        53 ~~~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci  132 (378)
                      ....+|+|+.|+|-||.+++...+....+..||.+.. -...|||||+.+....---.+.    .....+|..+|+|-++
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-SDTLCTHVVVNEDNDEVEPLAV----SSNQVHVKKEWFWVSI  280 (850)
T ss_pred             hccccccCCeEeecCCcHHHHHHHHHHHHhcCCcccC-CCCCceeEeecCCccccccccc----cccceeecccceEEEE
Confidence            4688999999999999999999999999999999999 4478999999665433222223    2577899999999999


Q ss_pred             hcccccccceeeeecc
Q 017048          133 RRNVRLSESLYTVKSI  148 (378)
Q Consensus       133 ~~g~~l~e~~Y~~~~~  148 (378)
                      ..|.+..|..|.+...
T Consensus       281 q~g~~a~e~~yl~~~~  296 (850)
T KOG3524|consen  281 QRGCCAIEDNYLLPTG  296 (850)
T ss_pred             ecchhccccceecccc
Confidence            9999999999988664

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

Probab=97.36  E-value=0.00053  Score=73.30  Aligned_cols=80  Identities=21%  Similarity=0.407  Sum_probs=63.6

Q ss_pred             cCccccccceeecchhhHHH-HHHHHHHHhhccceeeeeeeeccCCceEEec--ccc-hhhh--hcCCCCccchhhHHhh
Q 017048          196 MNSTLSGCSMYVDSDVSEEL-RNKVFEAATNEGATLVNQWFVGCGASYVVCE--EDS-VQKY--MGHSNNLVTPVWVLKT  269 (378)
Q Consensus       196 ~~~lF~G~~fyl~~gfs~~~-~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~--~~s-~~~~--l~~~~~IVt~~WI~dc  269 (378)
                      ...+|+|..||+.+|.+... +..|+++|..+||.++..  +..+.+++|+-  ..+ ..++  +.....||.|.|++||
T Consensus       630 ~s~if~gl~f~Vlsgt~~~~tk~~le~~ivenGG~iv~n--v~p~~~~ci~~a~~et~~vk~~~~~~~cdVl~p~Wlldc  707 (881)
T KOG0966|consen  630 ISNIFDGLEFCVLSGTSETHTKAKLEEIIVENGGKIVQN--VGPSDTLCIATAGKETTRVKAQAIKRSCDVLKPAWLLDC  707 (881)
T ss_pred             hhhhhcCeeEEEecCCcccccHHHHHHHHHHcCCEEEEc--CCCCCcceEEeccccchHHHHHHHhccCceeeHHHHHHH
Confidence            37899999999988776544 688999999999999998  57778998863  222 2222  5678999999999999


Q ss_pred             hhHhhhhh
Q 017048          270 AKEKHVQR  277 (378)
Q Consensus       270 ik~~~~qr  277 (378)
                      .+...++.
T Consensus       708 c~~~~l~p  715 (881)
T KOG0966|consen  708 CKKQRLLP  715 (881)
T ss_pred             Hhhhhccc
Confidence            99987543

>PLN03122 Poly [ADP-ribose] polymerase; Provisional

Probab=97.32  E-value=0.00022  Score=77.96  Aligned_cols=83  Identities=16%  Similarity=0.274  Sum_probs=66.3

Q ss_pred             cCccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEecccc--------hhhhhcCCCCccchhhHH
Q 017048          196 MNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDS--------VQKYMGHSNNLVTPVWVL  267 (378)
Q Consensus       196 ~~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~s--------~~~~l~~~~~IVt~~WI~  267 (378)
                      ....|.|++|.|...|+. .++.++.+|+.+||+++++  + +.+||+|+.+..        +++....+++||+.+||.
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            356799999999655654 6788999999999999998  4 778888886522        333445689999999999


Q ss_pred             hhhhHhhhhhHHhhh
Q 017048          268 KTAKEKHVQRLVHIS  282 (378)
Q Consensus       268 dcik~~~~qr~~~~s  282 (378)
                      +|++.+..+.+..|.
T Consensus       262 d~i~~~k~~~~~~y~  276 (815)
T PLN03122        262 DSIEKQEAQPLEAYD  276 (815)
T ss_pred             HHHhcCCcccchhhh
Confidence            999999887776653

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

Probab=97.23  E-value=0.00012  Score=78.62  Aligned_cols=89  Identities=12%  Similarity=0.232  Sum_probs=71.3

Q ss_pred             CCCCCccceEEEEcccCHHHHHHHHHHHHHhcCccC-CCCCCccceEEEeeecCchhhHhhhhcCCCceEEEEeehhhhh
Q 017048           53 PANAPFSGLVICVTGLSKEARKQVMEATERLGGQYS-PDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDS  131 (378)
Q Consensus        53 ~~~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~-~~lt~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~dc  131 (378)
                      .....|.|+.||+.|...+...+++..-..+||.+. .+....+||+|+......+....      ..-...+++|+.+|
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            578899999999999999888899999999999988 56667899999977643333211      23356889999999


Q ss_pred             hhcccccccceeeeec
Q 017048          132 VRRNVRLSESLYTVKS  147 (378)
Q Consensus       132 i~~g~~l~e~~Y~~~~  147 (378)
                      .+.+..+.-.+|....
T Consensus       117 ~~~~~~~~~~~~~~~t  132 (1016)
T KOG2093|consen  117 CENGMDVGYYPYQLYT  132 (1016)
T ss_pred             HhccCccccccceeec
Confidence            9999998877777654

>PLN03123 poly [ADP-ribose] polymerase; Provisional

Probab=97.03  E-value=0.00065  Score=75.77  Aligned_cols=82  Identities=11%  Similarity=0.064  Sum_probs=63.6

Q ss_pred             CccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEeccc------chhhhhcCCCCccchhhHHhhh
Q 017048          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED------SVQKYMGHSNNLVTPVWVLKTA  270 (378)
Q Consensus       197 ~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~------s~~~~l~~~~~IVt~~WI~dci  270 (378)
                      ...|.|+.|.+...|+. ....+++.|+.+||++...  +...+||+|+..+      ..++....+++||+.+||.||+
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 SEFLGDLKVSIVGASKE-KVTEWKAKIEEAGGVFHAT--VKKDTNCLVVCGELDDEDAEMRKARRMKIPIVREDYLVDCF  467 (981)
T ss_pred             CCCcCCeEEEEecCCCC-cHHHHHHHHHhcCCEEeee--ccCCceEEEccHHhhhcchHHHHHHhcCCCcccHHHHHHHH
Confidence            46799999999655654 3478999999999999998  7889999999861      1222334579999999999999


Q ss_pred             hHhhhhhHHhh
Q 017048          271 KEKHVQRLVHI  281 (378)
Q Consensus       271 k~~~~qr~~~~  281 (378)
                      +.+..++...|
T Consensus       468 ~~~~~~p~~~y  478 (981)
T PLN03123        468 KKKKKLPFDKY  478 (981)
T ss_pred             hccccCcchhh
Confidence            98865554443

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

Probab=96.96  E-value=0.00062  Score=69.60  Aligned_cols=83  Identities=25%  Similarity=0.302  Sum_probs=63.4

Q ss_pred             CCCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCCC----------CCccceEEEeeec-CchhhHhhhhcCCCceEE
Q 017048           54 ANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDL----------HPQCTHLVVQSFG-GRKFEHALKHGSRNGLYI  122 (378)
Q Consensus        54 ~~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~l----------t~~~THLI~~~~~-~~Ky~~A~k~~~~~gi~I  122 (378)
                      ...+|+|++|.++.--+  ++.|.-+|...||.++-+-          +...||=|+..+. ..+|         .|-.-
T Consensus       324 ~kslF~glkFfl~reVP--resL~fiI~s~GG~V~wd~~~~g~~~~~~d~~ITH~IvDrP~~~~~v---------~gR~Y  392 (570)
T KOG2481|consen  324 HKSLFSGLKFFLNREVP--RESLEFIIRSFGGKVSWDPLGIGATYDESDERITHQIVDRPGQQTSV---------IGRTY  392 (570)
T ss_pred             HHHHhhcceeeeeccCc--hHHHHHHHHHcCCceecCccCCCCcccccccceeeeeecccCcccee---------eeeee
Confidence            45699999999986543  3458889999999987662          1234888886652 2333         25667


Q ss_pred             EEeehhhhhhhcccccccceeeeec
Q 017048          123 VTLGWFVDSVRRNVRLSESLYTVKS  147 (378)
Q Consensus       123 V~~~Wl~dci~~g~~l~e~~Y~~~~  147 (378)
                      |-|+||+||+.++.++|...|.+..
T Consensus       393 vQPQWvfDsvNar~llpt~~Y~~G~  417 (570)
T KOG2481|consen  393 VQPQWVFDSVNARLLLPTEKYFPGK  417 (570)
T ss_pred             ecchhhhhhccchhhccHhhhCCCc
Confidence            9999999999999999999999865

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

Probab=96.78  E-value=0.00045  Score=73.25  Aligned_cols=93  Identities=20%  Similarity=0.381  Sum_probs=79.3

Q ss_pred             CCCCccceEEEEcccCH----HHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCchhhHhhhhcCCCceEEEEeehhh
Q 017048           54 ANAPFSGLVICVTGLSK----EARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFV  129 (378)
Q Consensus        54 ~~~~F~g~~I~vsG~~~----~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~  129 (378)
                      ....+.|+.+.++|+.+    .++..+-.....+|.....+++..+||+|+.++.+.|...|...   ..++||++.|+|
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            55688999999999743    45566777778899999999999999999999999998888763   459999999999


Q ss_pred             hhhhcccccccceeeeeccC
Q 017048          130 DSVRRNVRLSESLYTVKSID  149 (378)
Q Consensus       130 dci~~g~~l~e~~Y~~~~~~  149 (378)
                      .|..++..++|..|.+....
T Consensus       515 ~~~e~w~~v~ek~~~l~~~~  534 (635)
T KOG0323|consen  515 RSLEKWGKVEEKLEPLDDDQ  534 (635)
T ss_pred             HHHHHhcchhcccccccccc
Confidence            99999999999999887643

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

Probab=96.52  E-value=0.0016  Score=64.88  Aligned_cols=83  Identities=18%  Similarity=0.239  Sum_probs=64.1

Q ss_pred             CCCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCC-----------CCCccceEEEeeec-CchhhHhhhhcCCCceE
Q 017048           54 ANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPD-----------LHPQCTHLVVQSFG-GRKFEHALKHGSRNGLY  121 (378)
Q Consensus        54 ~~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~-----------lt~~~THLI~~~~~-~~Ky~~A~k~~~~~gi~  121 (378)
                      ...+|.|++|+++.--+.  .-|+-+|...||.+...           ++..+||-||..+- ..|+         .|..
T Consensus       347 ~~slFS~f~FyisreVp~--dsLefiilscGG~V~~~p~~~~i~~~~~vD~~vth~i~drp~~~~kv---------egrt  415 (591)
T COG5163         347 LKSLFSGFKFYISREVPG--DSLEFIILSCGGSVVGSPCEADIHVSEKVDEKVTHQIVDRPVMKNKV---------EGRT  415 (591)
T ss_pred             hhhhhhceEEEEeccccc--hHHHHHHHHcCCcccCchhhccCCchhhccchhhhhhccchhhhhhh---------ccee
Confidence            467999999999875432  23788899999987543           44578998986652 2333         2777


Q ss_pred             EEEeehhhhhhhcccccccceeeeec
Q 017048          122 IVTLGWFVDSVRRNVRLSESLYTVKS  147 (378)
Q Consensus       122 IV~~~Wl~dci~~g~~l~e~~Y~~~~  147 (378)
                      -|.|+||+||+..|.+.+...|.+..
T Consensus       416 YiQPQw~fDsiNkG~l~~~~~Y~~G~  441 (591)
T COG5163         416 YIQPQWLFDSINKGKLACVENYCVGK  441 (591)
T ss_pred             eechHHHHhhhccccchhhhhccccc
Confidence            89999999999999999999998865

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

Probab=96.21  E-value=0.0054  Score=56.54  Aligned_cols=74  Identities=19%  Similarity=0.162  Sum_probs=61.6

Q ss_pred             CCCCCccceEEEEcccCH-HHHHHHHHHHHHhcCccCCCCCCccceEEEeeec-CchhhHhhhhcCCCceEEEEeehhhh
Q 017048           53 PANAPFSGLVICVTGLSK-EARKQVMEATERLGGQYSPDLHPQCTHLVVQSFG-GRKFEHALKHGSRNGLYIVTLGWFVD  130 (378)
Q Consensus        53 ~~~~~F~g~~I~vsG~~~-~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~-~~Ky~~A~k~~~~~gi~IV~~~Wl~d  130 (378)
                      .....+.|++|.|+|..+ -+|.+-+.+|..+||.++...+..+|+||.++.. ..|.+.+.+    .+|+.+..+=|..
T Consensus       152 g~~~cL~G~~fVfTG~l~TlsR~~a~~lvk~yGgrvT~~pSskTtflvlGdnaGP~K~ekiKq----lkIkaidEegf~~  227 (276)
T COG5275         152 GERECLKGKVFVFTGDLKTLSRDDAKTLVKVYGGRVTAVPSSKTTFLVLGDNAGPSKMEKIKQ----LKIKAIDEEGFDS  227 (276)
T ss_pred             CCcccccccEEEEecccccccchhHHHHHHHhCCeeecccccceeEEEecCCCChHHHHHHHH----hCCccccHHHHHH
Confidence            567789999999999876 7899999999999999999999999999998764 467777776    5888876555433

>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=95.85  E-value=0.0059  Score=67.62  Aligned_cols=62  Identities=16%  Similarity=0.251  Sum_probs=50.1

Q ss_pred             HHHHHHHhhccceeeeeeeeccCCceEEecc-cchhhh---hcCCCCccchhhHHhhhhHhhhhhHHhh
Q 017048          217 NKVFEAATNEGATLVNQWFVGCGASYVVCEE-DSVQKY---MGHSNNLVTPVWVLKTAKEKHVQRLVHI  281 (378)
Q Consensus       217 ~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~-~s~~~~---l~~~~~IVt~~WI~dcik~~~~qr~~~~  281 (378)
                      ..+++.+++.||.+.++   ...+||+|+.. ....++   ++.++.||++.||.+|++.|.+.....|
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            34788899999999998   78899999986 222233   5788999999999999999988766554

>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=94.73  E-value=0.033  Score=60.29  Aligned_cols=72  Identities=15%  Similarity=0.149  Sum_probs=58.0

Q ss_pred             CccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEeccc---chhhhhcCCCCccchhhHHhhh
Q 017048          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED---SVQKYMGHSNNLVTPVWVLKTA  270 (378)
Q Consensus       197 ~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~---s~~~~l~~~~~IVt~~WI~dci  270 (378)
                      ...|.|.+|.|...|+.-.|+.++++|+.+||++.++  +..++++||++..   ++++.-..++.|++.+.+++-+
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            3569999999965676656899999999999999999  8999999999862   3444445678999888877643

>PRK06063 DNA polymerase III subunit epsilon; Provisional

Probab=93.91  E-value=0.081  Score=52.17  Aligned_cols=68  Identities=16%  Similarity=0.234  Sum_probs=53.5

Q ss_pred             ccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEeccc-----chhhhhcCCCCccchhhHHh
Q 017048          198 STLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED-----SVQKYMGHSNNLVTPVWVLK  268 (378)
Q Consensus       198 ~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~-----s~~~~l~~~~~IVt~~WI~d  268 (378)
                      .+|.|.+|.|...++ ..|+.++++|+.+||++.++  ++.++++||+.+.     ++++....++.|++..=+++
T Consensus       231 ~l~~g~~~v~TG~l~-~~R~e~~~~~~~~G~~v~~s--Vs~~t~~lv~g~~~~~ssK~~kA~~~gi~ii~e~~f~~  303 (313)
T PRK06063        231 PLVQGMRVALSAEVS-RTHEELVERILHAGLAYSDS--VDRDTSLVVCNDPAPEQGKGYHARQLGVPVLDEAAFLE  303 (313)
T ss_pred             cccCCCEEEEecCCC-CCHHHHHHHHHHcCCEecCc--cccCccEEEECCCCCcccHHHHHHHcCCccccHHHHHH
Confidence            578999999966676 46889999999999999999  7999999999852     23444456788887654444

>PRK06195 DNA polymerase III subunit epsilon; Validated

Probab=93.51  E-value=0.068  Score=52.54  Aligned_cols=49  Identities=12%  Similarity=0.162  Sum_probs=42.4

Q ss_pred             CccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEecc
Q 017048          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEE  247 (378)
Q Consensus       197 ~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~  247 (378)
                      ...|.|.+|.|...|..-.|+.++++|+..||++.++  ++.+++++|++.
T Consensus       218 ~~~l~g~~~vfTG~l~~~~R~~~~~~~~~~Gg~v~~s--Vs~~t~~lV~G~  266 (309)
T PRK06195        218 FTAFKEEVVVFTGGLASMTRDEAMILVRRLGGTVGSS--VTKKTTYLVTNT  266 (309)
T ss_pred             CccccCCEEEEccccCCCCHHHHHHHHHHhCCEecCC--cccCceEEEECC
Confidence            3469999999966675556888999999999999999  799999999984

>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated

Probab=93.50  E-value=0.07  Score=57.85  Aligned_cols=73  Identities=18%  Similarity=0.171  Sum_probs=58.0

Q ss_pred             ccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEeccc---chhhhhcCCCCccchhhHHhhhhH
Q 017048          198 STLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED---SVQKYMGHSNNLVTPVWVLKTAKE  272 (378)
Q Consensus       198 ~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~---s~~~~l~~~~~IVt~~WI~dcik~  272 (378)
                      ..|.|.+|+|...++.-.|+.++++|+..||++.++  ++.++++||++..   .+++....++.|++.+-+++.+.+
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            349999999955565446889999999999999999  7999999999863   344445568999998888776643

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

Probab=93.24  E-value=0.088  Score=56.33  Aligned_cols=70  Identities=19%  Similarity=0.207  Sum_probs=57.9

Q ss_pred             ccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEeccc---chhhhhcCCCCccchhhHHhh
Q 017048          198 STLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED---SVQKYMGHSNNLVTPVWVLKT  269 (378)
Q Consensus       198 ~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~---s~~~~l~~~~~IVt~~WI~dc  269 (378)
                      ..|.|.+|.|...++.-.|+..+.+++..||+|.++  +..++++||++++   .+++...-++.|.+.+++++-
T Consensus       593 ~~l~gkt~V~TGtL~~~sR~eak~~le~lGakv~~S--VSkktD~vvaG~~aGSKl~kA~eLgv~i~~E~~~~~l  665 (667)
T COG0272         593 SPLAGKTFVLTGTLEGMSRDEAKALLEALGAKVSGS--VSKKTDYVVAGENAGSKLAKAQELGVKIIDEEEFLAL  665 (667)
T ss_pred             cccCCCEEEEeccCCCCCHHHHHHHHHHcCCEEece--ecccccEEEEcCCCChHHHHHHHcCCeEecHHHHHHh
Confidence            789999999976677666888999999999999999  7999999999873   344545678999998887653

>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=93.17  E-value=0.1  Score=56.81  Aligned_cols=74  Identities=15%  Similarity=0.163  Sum_probs=59.0

Q ss_pred             CccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEeccc----chhhhhcCCCCccchhhHHhhhhH
Q 017048          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED----SVQKYMGHSNNLVTPVWVLKTAKE  272 (378)
Q Consensus       197 ~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~----s~~~~l~~~~~IVt~~WI~dcik~  272 (378)
                      ...|.|.+|+|...+..-.|+.++++|+..||++.++  +..+++++|++..    .+++.-..++.|++.+-+.+-+++
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            4569999999965565446888999999999999999  7999999999862    233444568899998888876654

>TIGR00575 dnlj DNA ligase, NAD-dependent

Probab=92.16  E-value=0.13  Score=55.79  Aligned_cols=66  Identities=20%  Similarity=0.271  Sum_probs=51.7

Q ss_pred             CccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEeccc---chhhhhcCCCCccchh
Q 017048          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED---SVQKYMGHSNNLVTPV  264 (378)
Q Consensus       197 ~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~---s~~~~l~~~~~IVt~~  264 (378)
                      ...|.|.+|+|...++.-.|+.++++|+.+||++.++  +..+++++|++..   .+++....++.|++.+
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            3569999999955566556888999999999999999  7999999999863   3444445677777654

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.

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

Probab=91.65  E-value=0.14  Score=56.28  Aligned_cols=84  Identities=12%  Similarity=0.261  Sum_probs=53.6

Q ss_pred             CccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeec----c--CCceE-----------------Eeccc--chh
Q 017048          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVG----C--GASYV-----------------VCEED--SVQ  251 (378)
Q Consensus       197 ~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~----~--~vTHV-----------------V~~~~--s~~  251 (378)
                      ..+|.||.|.|...+..  ......-+..+||.+.+..+..    .  +.+.+                 ++.+.  ...
T Consensus       923 kniFd~cvF~lTsa~~s--d~~~r~s~e~~gg~vle~gl~~~Fn~p~~g~~~~lr~Ln~~q~~ks~~qalLIsdth~Rt~ 1000 (1176)
T KOG3548|consen  923 KNIFDGCVFMLTSANRS--DSASRPSMEKHGGLVLEKGLMNLFNTPFKGGGIVLRQLNSFQERKSNYQALLISDTHYRTH 1000 (1176)
T ss_pred             cchhcceeEEEeccccc--hhhhhhhhhccCChhhhccccccccccccCCcchHHhhhHHhhhccccceeEeehhhhHHH
Confidence            38999999999554532  3446667777999999875211    0  11111                 11110  123


Q ss_pred             hh---hcCCCCccchhhHHhhhhHhhhhhHHhhhHhH
Q 017048          252 KY---MGHSNNLVTPVWVLKTAKEKHVQRLVHISADL  285 (378)
Q Consensus       252 ~~---l~~~~~IVt~~WI~dcik~~~~qr~~~~s~dl  285 (378)
                      +|   ++.++..|++.||-+|++.+.+++   |+.+|
T Consensus      1001 KYLeaLA~giPcVh~~fI~aC~e~nr~Vd---y~~YL 1034 (1176)
T KOG3548|consen 1001 KYLEALARGIPCVHNTFIQACGEQNRCVD---YTDYL 1034 (1176)
T ss_pred             HHHHHHHcCCCcccHHHHHHHHhcccccc---chhhc
Confidence            34   578999999999999999985555   55444

>PRK05601 DNA polymerase III subunit epsilon; Validated

Probab=85.41  E-value=0.86  Score=45.94  Aligned_cols=75  Identities=21%  Similarity=0.257  Sum_probs=61.5

Q ss_pred             CCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeeec--CchhhHhhhhcCCCceEEEEeehhhhhh
Q 017048           55 NAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFG--GRKFEHALKHGSRNGLYIVTLGWFVDSV  132 (378)
Q Consensus        55 ~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~--~~Ky~~A~k~~~~~gi~IV~~~Wl~dci  132 (378)
                      .++-+|+.|.|++-...++..|...+...|=.|+..++..+.-|||+...  .-|-.+|..    .|||+++-.=|.+.+
T Consensus       292 ~~lv~Gm~v~~~~e~~~~~d~li~~~~~agL~y~~~~~r~tslvv~n~~~~~~gk~~~a~~----~gipl~~d~~fl~~~  367 (377)
T PRK05601        292 KGLVAGMEVVVAPEITMDPDIIIQAIVRAGLAYSEKLTRQTSVVVCNQTRDLDGKAMHAQR----KGIPLLSDVAFLAAV  367 (377)
T ss_pred             CccccCcEEEEeCCccCCHHHHHHHHHHccchhhhccccceeEEEeCCCCCccchhhhhhh----cCCCccCHHHHHHHH
Confidence            34778999999999888889999999999999999999998888887653  345555554    699999988777766


Q ss_pred             h
Q 017048          133 R  133 (378)
Q Consensus       133 ~  133 (378)
                      .
T Consensus       368 ~  368 (377)
T PRK05601        368 E  368 (377)
T ss_pred             H
Confidence            4

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	378
3olc_X	298	Crystal Structure Of The N-Terminal Region Of Topbp		2e-11
2xnh_A	287	Structure And Function Of The Rad9-Binding Region O		3e-11
2xnk_A	292	Structure And Function Of The Rad9-Binding Region O		3e-11
3l46_A	112	Crystal Structure Of The Second Brct Domain Of Epit		7e-07
2cou_A	109	Solution Structure Of The Second Brct Domain Of Epi		3e-06

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

Iteration: 1
 Score = 66.2 bits (160), 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|2XNH|A Chain A, Structure And Function Of The Rad9-Binding Region Of The Dna Damage Checkpoint Adaptor Topbp1 Length = 287

Iteration: 1
 Score = 66.2 bits (160), Expect = 3e-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 = 66.2 bits (160), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 38/94 (40%), Positives = 52/94 (55%), Gaps = 5/94 (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 RNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDE 150
           R  ++ VT  WF DS+ +     ES+Y  +   E
Sbjct: 258 RWNVHCVTTQWFFDSIEKGFCQDESIYKTEPRPE 291

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 7e-07,   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 = 49.7 bits (117), Expect = 3e-06,   Method: Composition-based stats.
 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	378
2cou_A	109	ECT2 protein; BRCT domain, RHO GTPase, structural	1e-30
3l46_A	112	Protein ECT2; alternative splicing, guanine-nucleo	2e-30
2d8m_A	129	DNA-repair protein XRCC1; parallel beta-sheet, DNA	5e-26
3l3e_A	107	DNA topoisomerase 2-binding protein 1; BRCT domain	7e-23
1t15_A	214	Breast cancer type 1 susceptibility protein; prote	7e-22
3olc_X	298	DNA topoisomerase 2-binding protein 1; BRCT domain	3e-21
3olc_X	298	DNA topoisomerase 2-binding protein 1; BRCT domain	1e-15
1l0b_A	229	BRCA1; TANDEM-BRCT, three-helix bundle, unknown fu	3e-21
2nte_A	210	BARD-1, BRCA1-associated ring domain protein 1; BR	2e-20
1wf6_A	132	Similar to S.pombe -RAD4+/CUT5+product (A40727); B	8e-20
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	8e-17
3al2_A	235	DNA topoisomerase 2-binding protein 1; BRCT domain	2e-14
3sqd_A	219	PAX-interacting protein 1; tandem BRCT domains, ce	4e-12
3pc6_A	104	DNA repair protein XRCC1; BRCT domain, protein:pro	1e-10
3l41_A	220	BRCT-containing protein 1; BRC1, BRCT domain, tand	1e-10
3u3z_A	199	Microcephalin; DNA repair, cell cycle regulation,	2e-10
2etx_A	209	Mediator of DNA damage checkpoint protein 1; tande	5e-09
3ii6_X	263	DNA ligase 4; XRCC4, NHEJ, DNA repair, BRCT, alter	1e-08
3ii6_X	263	DNA ligase 4; XRCC4, NHEJ, DNA repair, BRCT, alter	7e-08
3ef0_A	372	RNA polymerase II subunit A C-terminal domain phos	2e-08
3ef1_A	442	RNA polymerase II subunit A C-terminal domain phos	6e-08
2jw5_A	106	DNA polymerase lambda; BRCT domain, family X polym	3e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-06
1z56_C	264	DNA ligase IV; DNA repair, BRCT, NHEJ, XRCC4, DNA	1e-05
1qzv_F	154	Plant photosystem I: subunit PSAF; photosynthesis,	7e-04

>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 =  112 bits (281), Expect = 1e-30
 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

>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 (280), Expect = 2e-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

>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 =  100 bits (250), Expect = 5e-26
 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 = 7e-22
 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

>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 = 91.7 bits (227), Expect = 3e-21
 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 = 75.9 bits (186), Expect = 1e-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

>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 = 3e-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

>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 = 2e-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 = 83.8 bits (207), Expect = 8e-20
 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 = 75.3 bits (185), 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 = 8e-17
 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 = 71.3 bits (174), Expect = 2e-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 = 64.2 bits (156), Expect = 4e-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

>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 = 57.3 bits (138), Expect = 1e-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

>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 = 1e-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

>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 = 59.0 bits (142), Expect = 2e-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

>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 = 55.0 bits (132), Expect = 5e-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 = 1e-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 = 7e-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 = 54.8 bits (131), Expect = 2e-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 = 53.5 bits (127), Expect = 6e-08
 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 = 47.9 bits (113), Expect = 4e-06
 Identities = 54/408 (13%), Positives = 107/408 (26%), Gaps = 139/408 (34%)

Query: 22  SVPSLR---RLRGGVQSFESMSPAS------------SSLASDSVLPAN--APFSGLVIC 64
           +V  L+   +LR  +     + PA             + +A D  L           +  
Sbjct: 130 NVSRLQPYLKLRQALLE---LRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFW 186

Query: 65  VT-GLSKEARKQVMEATERLGGQYSPDLHPQCTH-----LVVQSFGGRKFEHALKHGSRN 118
           +           V+E  ++L  Q  P+   +  H     L + S               N
Sbjct: 187 LNLKNCNSPE-TVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYEN 245

Query: 119 GLYIVTLGWFVDSVR------------------RNVRLSESL----YTVKSIDEH--GMH 154
            L +      + +V+                  R  ++++ L     T  S+D H   + 
Sbjct: 246 CLLV------LLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLT 299

Query: 155 LDKLNRLVG-FAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVSE 213
            D++  L+  +       LP    E    N                    S+     ++E
Sbjct: 300 PDEVKSLLLKYLDCRPQDLPR---EVLTTNP---------------RR-LSI-----IAE 335

Query: 214 ELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEK 273
            +R+             +  W                     H N        L T  E 
Sbjct: 336 SIRDG------------LATW-----------------DNWKHVNC-----DKLTTIIES 361

Query: 274 HVQRLVHISADLARQVGMMLENIQNGIAREEINGGNVPEDAQSC--KNKISQEKRQQTVN 331
            +  L        R++   L      +        ++P    S    + I  +       
Sbjct: 362 SLNVL---EPAEYRKMFDRL-----SVFPPSA---HIPTILLSLIWFDVIKSDVMVVVNK 410

Query: 332 LAKNGVRSRRSRRMQIRLAVKMLMNITHLCFL-MRKRMARIQKLHLQI 378
           L K  +  ++ +   I +            +L ++ ++     LH  I
Sbjct: 411 LHKYSLVEKQPKESTISI---------PSIYLELKVKLENEYALHRSI 449

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

 Score = 45.3 bits (106), Expect = 1e-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

>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant photosynthetic reaction center, peripheral antenna; HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1 Length = 154

 Score = 38.8 bits (89), Expect = 7e-04
 Identities = 9/33 (27%), Positives = 19/33 (57%), Gaps = 7/33 (21%)

Query: 70  KEARKQVMEATERLGGQYSPDLHPQCTHLVVQS 102
           K+A K+ ++A+ +L   Y+ D  P    L +++
Sbjct: 19  KQALKK-LQASLKL---YADDSAPA---LAIKA 44

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	378
3olc_X	298	DNA topoisomerase 2-binding protein 1; BRCT domain	99.95
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	99.93
1t15_A	214	Breast cancer type 1 susceptibility protein; prote	99.93
2nte_A	210	BARD-1, BRCA1-associated ring domain protein 1; BR	99.93
3u3z_A	199	Microcephalin; DNA repair, cell cycle regulation,	99.92
3sqd_A	219	PAX-interacting protein 1; tandem BRCT domains, ce	99.89
1z56_C	264	DNA ligase IV; DNA repair, BRCT, NHEJ, XRCC4, DNA	99.89
2etx_A	209	Mediator of DNA damage checkpoint protein 1; tande	99.88
1kzy_C	259	Tumor suppressor P53-binding protein 1; tandem-BRC	99.88
3l46_A	112	Protein ECT2; alternative splicing, guanine-nucleo	99.87
3al2_A	235	DNA topoisomerase 2-binding protein 1; BRCT domain	99.87
2cou_A	109	ECT2 protein; BRCT domain, RHO GTPase, structural	99.84
2vxb_A	241	DNA repair protein RHP9; BRCT, nucleus, cell cycle	99.83
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
3l41_A	220	BRCT-containing protein 1; BRC1, BRCT domain, tand	99.76
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	99.73
3olc_X	298	DNA topoisomerase 2-binding protein 1; BRCT domain	99.72
3pa6_A	107	Microcephalin; BRCT domain, cell cycle; HET: MSE;	99.65
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
3ef1_A	442	RNA polymerase II subunit A C-terminal domain phos	99.53
3ef0_A	372	RNA polymerase II subunit A C-terminal domain phos	99.51
2cou_A	109	ECT2 protein; BRCT domain, RHO GTPase, structural	99.46
3l46_A	112	Protein ECT2; alternative splicing, guanine-nucleo	99.45
1wf6_A	132	Similar to S.pombe -RAD4+/CUT5+product (A40727); B	99.43
4id3_A	92	DNA repair protein REV1; BRCT domain, protein bind	99.42
2ebw_A	97	DNA repair protein REV1; A/B/A 3 layers, parallel	99.37
3pc6_A	104	DNA repair protein XRCC1; BRCT domain, protein:pro	99.28
3l3e_A	107	DNA topoisomerase 2-binding protein 1; BRCT domain	99.27
1l7b_A	92	DNA ligase; BRCT, autostructure, structural genomi	99.24
2d8m_A	129	DNA-repair protein XRCC1; parallel beta-sheet, DNA	99.18
2k6g_A	109	Replication factor C subunit 1; protein, BRCT, DNA	99.16
3pc7_A	88	DNA ligase 3; DNA repair, BRCT domain, protein:pro	99.14
2ep8_A	100	Pescadillo homolog 1; A/B/A 3 layers, nucleolus, r	99.13
2ep8_A	100	Pescadillo homolog 1; A/B/A 3 layers, nucleolus, r	99.11
3pa6_A	107	Microcephalin; BRCT domain, cell cycle; HET: MSE;	99.1
3ii6_X	263	DNA ligase 4; XRCC4, NHEJ, DNA repair, BRCT, alter	99.1
2ebu_A	112	Replication factor C subunit 1; A/B/A 3 layers, pa	99.09
2coe_A	120	Deoxynucleotidyltransferase, terminal variant; BRC	99.06
2jw5_A	106	DNA polymerase lambda; BRCT domain, family X polym	99.04
2jw5_A	106	DNA polymerase lambda; BRCT domain, family X polym	99.04
1z56_C	264	DNA ligase IV; DNA repair, BRCT, NHEJ, XRCC4, DNA	99.02
2cok_A	113	Poly [ADP-ribose] polymerase-1; BRCT domain, DNA r	98.96
3pc7_A	88	DNA ligase 3; DNA repair, BRCT domain, protein:pro	98.94
3u3z_A	199	Microcephalin; DNA repair, cell cycle regulation,	98.92
2coe_A	120	Deoxynucleotidyltransferase, terminal variant; BRC	98.87
1t15_A	214	Breast cancer type 1 susceptibility protein; prote	98.86
3sqd_A	219	PAX-interacting protein 1; tandem BRCT domains, ce	98.84
1l0b_A	229	BRCA1; TANDEM-BRCT, three-helix bundle, unknown fu	98.82
2nte_A	210	BARD-1, BRCA1-associated ring domain protein 1; BR	98.72
2dun_A	133	POL MU, DNA polymerase MU; layers A/B/A, parallel	98.65
3al2_A	235	DNA topoisomerase 2-binding protein 1; BRCT domain	98.6
3ef0_A	372	RNA polymerase II subunit A C-terminal domain phos	98.59
1kzy_C	259	Tumor suppressor P53-binding protein 1; tandem-BRC	98.59
2dun_A	133	POL MU, DNA polymerase MU; layers A/B/A, parallel	98.58
2etx_A	209	Mediator of DNA damage checkpoint protein 1; tande	98.57
2vxb_A	241	DNA repair protein RHP9; BRCT, nucleus, cell cycle	98.56
3ef1_A	442	RNA polymerase II subunit A C-terminal domain phos	98.45
3l41_A	220	BRCT-containing protein 1; BRC1, BRCT domain, tand	98.36
1l7b_A	92	DNA ligase; BRCT, autostructure, structural genomi	98.27
1dgs_A	667	DNA ligase; AMP complex, NAD+-dependent; HET: DNA	98.14
3t7k_A	256	RTT107, regulator of TY1 transposition protein 107	98.12
2owo_A	671	DNA ligase; protein-DNA complex, ligase-DNA comple	98.05
2k6g_A	109	Replication factor C subunit 1; protein, BRCT, DNA	97.9
2cok_A	113	Poly [ADP-ribose] polymerase-1; BRCT domain, DNA r	97.82
3huf_A	325	DNA repair and telomere maintenance protein NBS1;	97.78
2ebu_A	112	Replication factor C subunit 1; A/B/A 3 layers, pa	97.77
2l42_A	106	DNA-binding protein RAP1; BRCT domain, protein bin	97.56
2l42_A	106	DNA-binding protein RAP1; BRCT domain, protein bin	97.1
4gns_A	290	Chitin biosynthesis protein CHS5; FN3, BRCT, tetra	95.95
1dgs_A	667	DNA ligase; AMP complex, NAD+-dependent; HET: DNA	95.42
2owo_A	671	DNA ligase; protein-DNA complex, ligase-DNA comple	94.56
3huf_A	325	DNA repair and telomere maintenance protein NBS1;	92.28
3qbz_A	160	DDK kinase regulatory subunit DBF4; FHA domain,RAD	91.56
3oq4_A	134	DBF4, protein DNA52; DDK, BRCT, RAD53, replication	88.47
3qbz_A	160	DDK kinase regulatory subunit DBF4; FHA domain,RAD	86.95
3oq0_A	151	DBF4, protein DNA52; DDK, BRCT, RAD53, replication	86.6
3oq0_A	151	DBF4, protein DNA52; DDK, BRCT, RAD53, replication	85.22
3t7k_A	256	RTT107, regulator of TY1 transposition protein 107	80.37

>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=99.95  E-value=2.5e-28  Score=236.20  Aligned_cols=179  Identities=22%  Similarity=0.317  Sum_probs=152.9

Q ss_pred             CCCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCchhhHhhhhcCCCceEEEEeehhhhhhh
Q 017048           54 ANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVR  133 (378)
Q Consensus        54 ~~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci~  133 (378)
                      ...+|+|++||+||+.+.++..|.++|+.+||+++.++++++||||+....+.||..|.+    .|++||+++||.+|++
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 YNMVMSDVTISCTSLEKEKREEVHKYVQMMGGRVYRDLNVSVTHLIAGEVGSKKYLVAAN----LKKPILLPSWIKTLWE  177 (298)
T ss_dssp             CCCTTTTCEEEEESCCHHHHHHHHHHHHHTTCEECSSCCTTCCEEEESSSCSHHHHHHHH----TTCCEECHHHHHHHHH
T ss_pred             cccccCCeEEEeCCCcHHhHHHHHHHHHHCCCEEecCcCCCeeEEEEeCCCChHHHHHHH----CCCeEeeHHHHHHHHH
Confidence            367999999999999999999999999999999999999999999999999999999997    6999999999999999


Q ss_pred             cccccccceeeeeccCccCcccccccccccccCCCccccccchhhhhhhhccCCCccccccccCccccccceeecchhhH
Q 017048          134 RNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVSE  213 (378)
Q Consensus       134 ~g~~l~e~~Y~~~~~~~~~~~~d~~~~l~~~s~~e~s~lp~~i~E~~~s~~~e~~~~~~~~~~~~lF~G~~fyl~~gfs~  213 (378)
                      .++.++...|.  ..     +.+                                     .....+|+|++|++ +|+.+
T Consensus       178 ~~~~~~~~~~~--~~-----~~~-------------------------------------~~~~~~f~g~~i~~-tG~~~  212 (298)
T 3olc_X          178 KSQEKKITRYT--DI-----NME-------------------------------------DFKCPIFLGCIICV-TGLCG  212 (298)
T ss_dssp             HHHTTCCSSGG--GS-----CGG-------------------------------------GGBCCTTTTCEEEE-CSCCH
T ss_pred             cCCcCCccccc--cc-----ccc-------------------------------------cccccccCCeEEEE-eCCCC
Confidence            99877544331  00     000                                     11246899999999 78888


Q ss_pred             HHHHHHHHHHhhccceeeeeeeec-cCCceEEecccchhhh---hcCCCCccchhhHHhhhhHhhhhhHHhhhH
Q 017048          214 ELRNKVFEAATNEGATLVNQWFVG-CGASYVVCEEDSVQKY---MGHSNNLVTPVWVLKTAKEKHVQRLVHISA  283 (378)
Q Consensus       214 ~~~~~L~~lI~~~GG~vv~~~~~~-~~vTHVV~~~~s~~~~---l~~~~~IVt~~WI~dcik~~~~qr~~~~s~  283 (378)
                      ..++.++++|+.+||++.+.  +. .++||||+......+|   ...+++||+++||+||++.|.+++.-.|..
T Consensus       213 ~~r~~l~~li~~~GG~~~~~--ls~~~~THLI~~~~~g~K~~~A~~~gi~IV~~~Wl~dsi~~g~~lde~~Y~l  284 (298)
T 3olc_X          213 LDRKEVQQLTVKHGGQYMGQ--LKMNECTHLIVQEPKGQKYECAKRWNVHCVTTQWFFDSIEKGFCQDESIYKT  284 (298)
T ss_dssp             HHHHHHHHHHHHTTCEECSS--CCTTTCCEEECSSSCSHHHHHHHHTTCEEECHHHHHHHHHHTSCCCGGGSBS
T ss_pred             ccHHHHHHHHHHcCCEEece--ecCCCceEEEEeCCCchHHHHHHHCCCeEEeHHHHHHHHHCCCCCCchhcCC
Confidence            88999999999999999998  56 7999999987544444   456899999999999999999988877744

>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=6.7e-27  Score=222.39  Aligned_cols=223  Identities=14%  Similarity=0.173  Sum_probs=149.4

Q ss_pred             CCCCCccceEEEE-cccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCchhhHhhhhcCCCceEEEEeehhhhh
Q 017048           53 PANAPFSGLVICV-TGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDS  131 (378)
Q Consensus        53 ~~~~~F~g~~I~v-sG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~dc  131 (378)
                      ...++|+|++||| +|.....+++|+++|..|||++..++++.+||+|+.. .+.|+..++++   ..++||+|+||.||
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-ENIRVKNIILS---NKHDVVKPAWLLEC   81 (263)
T ss_dssp             CCCCTTTTCEEEECCCC--CCHHHHHHHHHHTTCEECSSCCTTEEEEECSS-CCHHHHHHHHS---CSCCEECHHHHHHH
T ss_pred             cCcccCCCeEEEEEcCCCCCCHHHHHHHHHHcCCEEEecCCCCEEEEEeCC-CCHHHHHHHhc---CCCCEeehHHHHHH
Confidence            4688999999998 6887788999999999999999999998888878854 45888888873   24999999999999


Q ss_pred             hhcccccccceeeeeccCc-----cCcccccccccccccC--CCccccccchh--h----hhhhhccCCCc--ccccccc
Q 017048          132 VRRNVRLSESLYTVKSIDE-----HGMHLDKLNRLVGFAG--TENSCLPAGIY--E----AKQFNATGKHE--RDSNRSM  196 (378)
Q Consensus       132 i~~g~~l~e~~Y~~~~~~~-----~~~~~d~~~~l~~~s~--~e~s~lp~~i~--E----~~~s~~~e~~~--~~~~~~~  196 (378)
                      +++++++|..+|.+-...+     ...+.|.|...+....  .+...+-..+.  +    ...+...+.++  ......+
T Consensus        82 i~~~~llp~~p~~~~~~~~~~~~~~~~~~D~~GDsy~~~~~~~~l~~ll~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  161 (263)
T 3ii6_X           82 FKTKSFVPWQPRFMIHMCPSTKEHFAREYDCYGDSYFIDTDLNQLKEVFSGIKNSNEQTPEEMASLIADLEYRYSWDCSP  161 (263)
T ss_dssp             HHHTSCCCCCGGGEEECCHHHHHHTTTTBCTTSCBSSSCCCHHHHHHHHHSCCCCCSCCHHHHHHHHHHHHHHHTCTTCG
T ss_pred             HhcCCcCCCCHHHHhhCCHHHHHHHHHhccccCCccCCcCCHHHHHHHHHhCcccccCCchhhHHHHHHHHHhhcccCCc
Confidence            9999999988886654322     1123344433321100  00000000000  0    00000000000  1111235


Q ss_pred             Cccccccceeecc---------hhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEecccc-----hhhh---hcCCCC
Q 017048          197 NSTLSGCSMYVDS---------DVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDS-----VQKY---MGHSNN  259 (378)
Q Consensus       197 ~~lF~G~~fyl~~---------gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~s-----~~~~---l~~~~~  259 (378)
                      ..+|+||+|||+.         .++....+.++.+|+++||++++.  +++.+||||+.++.     ++.+   ....++
T Consensus       162 ~~lF~~~~vy~~~~~~~~~~~~~i~~~~l~~~~~~i~~~GG~v~~~--l~~~vTHVVv~~~~~r~~~~~~~~~~~~~~~~  239 (263)
T 3ii6_X          162 LSMFRRHTVYLDSYAVINDLSTKNEGTRLAIKALELRFHGAKVVSC--LAEGVSHVIIGEDHSRVADFKAFRRTFKRKFK  239 (263)
T ss_dssp             GGTTTTCEEEECCBSSTTCGGGBCCSSHHHHHHHHHHHTTCEEESS--CCTTCCEEEECSCCTTHHHHHHHHHTCSSCCE
T ss_pred             chhhCCeEEEEecccccCCcccccchhHHHHHHHHHHccCCEEecC--CCCCceEEEECCCCccHHHHHHHHhhcCCCCE
Confidence            7899999999942         122224456788999999999999  58899999998632     2222   346789


Q ss_pred             ccchhhHHhhhhHhhhhhHHhh
Q 017048          260 LVTPVWVLKTAKEKHVQRLVHI  281 (378)
Q Consensus       260 IVt~~WI~dcik~~~~qr~~~~  281 (378)
                      ||++.||.||+++|.+.+.-.|
T Consensus       240 iV~~~Wv~dci~~~~~l~E~~Y  261 (263)
T 3ii6_X          240 ILKESWVTDSIDKCELQEENQY  261 (263)
T ss_dssp             EEETHHHHHHHHTTSCCCGGGT
T ss_pred             EeChHHHHHHHHcCCcCCHhhC
Confidence            9999999999999988876555

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

Probab=99.93  E-value=8.1e-27  Score=216.22  Aligned_cols=192  Identities=18%  Similarity=0.221  Sum_probs=141.8

Q ss_pred             CCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeee------cCchhhHhhhhcCCCceEEEEeehh
Q 017048           55 NAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSF------GGRKFEHALKHGSRNGLYIVTLGWF  128 (378)
Q Consensus        55 ~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~------~~~Ky~~A~k~~~~~gi~IV~~~Wl  128 (378)
                      ...+++++||+||+++.++..|.+++..+||.++.+++..|||||+...      .+.||..|+.    .|+|||+++||
T Consensus         2 ~~~~~~~~i~~sg~~~~~~~~l~~~~~~~G~~~~~~~~~~~THlI~~~~~~~~~~rt~K~~~a~~----~g~~IV~~~Wl   77 (229)
T 1l0b_A            2 ERAERDISMVVSGLTPKEVMIVQKFAEKYRLALTDVITEETTHVIIKTDAEFVCERTLKYFLGIA----GGKWIVSYSWV   77 (229)
T ss_dssp             -CCCCCCEEEEESCCHHHHHHHHHHHHHTTCEECSSCCSSCCEEEECBCTTSEECCCHHHHHHHH----TTCEEEETHHH
T ss_pred             CCCCCCeEEEEcCCCHHHHHHHHHHHHHcCCEEeCCcCCCCCEEEEcCCccccccccHHHHHHHH----CCCcEecHHHH
Confidence            3578999999999999999999999999999999999999999999875      6889999997    69999999999


Q ss_pred             hhhhhcccccccceeeeeccCccCcccccccccccccCCCccccccchhhhhhhhccCCCccccccccCccccccceeec
Q 017048          129 VDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVD  208 (378)
Q Consensus       129 ~dci~~g~~l~e~~Y~~~~~~~~~~~~d~~~~l~~~s~~e~s~lp~~i~E~~~s~~~e~~~~~~~~~~~~lF~G~~fyl~  208 (378)
                      .||+++|+++||++|.+.........               ...|....                .....+|+|+.||+.
T Consensus        78 ~~~~~~~~~~~e~~y~~~~~~~~~~~---------------~~~~~~~r----------------~~~~~lF~g~~~~~~  126 (229)
T 1l0b_A           78 IKSIQERKLLSVHEFEVKGDVVTGSN---------------HQGPRRSR----------------ESQEKLFEGLQIYCC  126 (229)
T ss_dssp             HHHHTTTSCCCSGGGBCCEETTTCSS---------------SCHHHHHH----------------HHC--CCTTCEEEEC
T ss_pred             HHHHHCCCcCChHHeEeccccccccc---------------cccchhhh----------------hhhhhhhcCceEEEE
Confidence            99999999999999998753221100               00000000                012479999999995


Q ss_pred             chhhHHHHHHHHHHHhhccceeeeeeeec---cCCce-EEecccc------hhhh-hcCCCCccchhhHHhhhhHhhhhh
Q 017048          209 SDVSEELRNKVFEAATNEGATLVNQWFVG---CGASY-VVCEEDS------VQKY-MGHSNNLVTPVWVLKTAKEKHVQR  277 (378)
Q Consensus       209 ~gfs~~~~~~L~~lI~~~GG~vv~~~~~~---~~vTH-VV~~~~s------~~~~-l~~~~~IVt~~WI~dcik~~~~qr  277 (378)
                      ..+....++.|+++|+.+||++++.....   .+.+| ||+.++.      ++.+ ...+++||+++||+|||..+.++.
T Consensus       127 ~~~~~~~~~~l~~li~~~GG~v~~~~~~~~~~~~~~~~vvv~~~~~~~~~~~~~l~~~~~i~iVs~~WlldsI~~~~~~~  206 (229)
T 1l0b_A          127 EPFTNMPKDELERMLQLCGASVVKELPLLTRDTGAHPIVLVQPSAWTEDNDCPDIGQLCKGRLVMWDWVLDSISVYRCRD  206 (229)
T ss_dssp             SCCSSSCHHHHHHHHHHTTCEEECSSSCGGGCCSSCCEEEEC-------------------CEEETHHHHHHHHTTSCCC
T ss_pred             ecCCCCCHHHHHHHHHHCCCEEeCCcccccccCCCceEEEEcCCccchhhhHHHHHHHcCCeEeehhHHHHHHhcCCcCC
Confidence            55655567889999999999999985221   23566 4544321      1222 246799999999999999998888


Q ss_pred             HHhh
Q 017048          278 LVHI  281 (378)
Q Consensus       278 ~~~~  281 (378)
                      .-.|
T Consensus       207 ~~~Y  210 (229)
T 1l0b_A          207 LDAY  210 (229)
T ss_dssp             GGGG
T ss_pred             ccce
Confidence            7666

>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=99.93  E-value=4.5e-26  Score=208.54  Aligned_cols=189  Identities=17%  Similarity=0.194  Sum_probs=142.1

Q ss_pred             cceEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeee------cCchhhHhhhhcCCCceEEEEeehhhhhh
Q 017048           59 SGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSF------GGRKFEHALKHGSRNGLYIVTLGWFVDSV  132 (378)
Q Consensus        59 ~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~------~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci  132 (378)
                      ++++|++||+++.++..|.+++..+||.+..+++..|||||+...      .+.||..|+.    .|++||+++||.||+
T Consensus         3 ~~~~~~~sg~~~~~~~~l~~~~~~~G~~~~~~~~~~~THli~~~~~~~~~~rt~k~~~a~~----~g~~IV~~~Wl~~~~   78 (214)
T 1t15_A            3 KRMSMVVSGLTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIA----GGKWVVSYFWVTQSI   78 (214)
T ss_dssp             -CCEEEEESCCHHHHHHHHHHHHHHTCEECSSCCTTCCEEEECBCTTSEECCBHHHHHHHH----TTCEEEETHHHHHHH
T ss_pred             CcEEEEECCCCHHHHHHHHHHHHHhCCEEeCccCCCCcEEEEeCCcccchhhhHHHHHHHh----cCCEEeCHHHHHHHH
Confidence            589999999999999999999999999999999999999999875      4799999987    599999999999999


Q ss_pred             hcccccccceeeeeccCccCcccccccccccccCCCccccccchhhhhhhhccCCCccccccccCccccccceeecchhh
Q 017048          133 RRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVS  212 (378)
Q Consensus       133 ~~g~~l~e~~Y~~~~~~~~~~~~d~~~~l~~~s~~e~s~lp~~i~E~~~s~~~e~~~~~~~~~~~~lF~G~~fyl~~gfs  212 (378)
                      ++|+++||++|.+...........               -|.+..+               .....+|+|+.||+...+.
T Consensus        79 ~~~~~~~e~~y~~~~~~~~~~~~~---------------~~~~~r~---------------~~~~~lF~g~~~~~~~~~~  128 (214)
T 1t15_A           79 KERKMLNEHDFEVRGDVVNGRNHQ---------------GPKRARE---------------SQDRKIFRGLEICCYGPFT  128 (214)
T ss_dssp             HTTSCCCGGGGBCCEETTTBTTCC---------------HHHHHHT---------------CTTSCTTTTCEEEECSCCS
T ss_pred             HCCCcCChHHeEeecccccccccc---------------chhhHhh---------------cCCCcccCCCEEEEEecCC
Confidence            999999999999875322110000               0000000               0125799999999965565


Q ss_pred             HHHHHHHHHHHhhccceeeeeeeecc--CCce-E-Eecccc------hhhh-hcCCCCccchhhHHhhhhHhhhhhHHhh
Q 017048          213 EELRNKVFEAATNEGATLVNQWFVGC--GASY-V-VCEEDS------VQKY-MGHSNNLVTPVWVLKTAKEKHVQRLVHI  281 (378)
Q Consensus       213 ~~~~~~L~~lI~~~GG~vv~~~~~~~--~vTH-V-V~~~~s------~~~~-l~~~~~IVt~~WI~dcik~~~~qr~~~~  281 (378)
                      ...++.|+++|+.+||++++......  ..+| + |+.++.      .+.+ ...++++|+++||+||+..+.++..-.|
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            55578899999999999998742111  1224 4 343321      1111 3467899999999999999998887666

>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=99.93  E-value=9.4e-27  Score=213.59  Aligned_cols=179  Identities=18%  Similarity=0.257  Sum_probs=140.3

Q ss_pred             ceEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEee---ecCchhhHhhhhcCCCceEEEEeehhhhhhhccc
Q 017048           60 GLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQS---FGGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNV  136 (378)
Q Consensus        60 g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~---~~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci~~g~  136 (378)
                      +++|++||+++.++..|.+++..+||.+..++++.|||||+..   ..+.||..|+.    .|++||+++||.||+++|+
T Consensus         2 ~~vi~~sg~~~~~~~~l~~~~~~~G~~~~~~~~~~~THlV~~~~~~~rt~K~l~a~~----~g~~IV~~~Wl~~c~~~~~   77 (210)
T 2nte_A            2 PLVLIGSGLSSEQQKMLSELAVILKAKKYTEFDSTVTHVVVPGDAVQSTLKCMLGIL----NGCWILKFEWVKACLRRKV   77 (210)
T ss_dssp             CCEEEESSCCHHHHHHHHHHHHHTTCEEESSCCTTCCEEEESSSSCCCSHHHHHHHH----TTCEEEETHHHHHHHHHTS
T ss_pred             CEEEEECCCCHHHHHHHHHHHHHcCCEEeCCCCCCCeEEEEcCCCcchHHHHHHHHh----cCCEEecHHHHHHHHHcCC
Confidence            6899999999999999999999999999999999999999977   57899999987    5999999999999999999


Q ss_pred             ccccceeeeeccCccCcccccccccccccCCCccccccchhhhhhhhccCCCccccccccCccccccceeecchhhHHHH
Q 017048          137 RLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVSEELR  216 (378)
Q Consensus       137 ~l~e~~Y~~~~~~~~~~~~d~~~~l~~~s~~e~s~lp~~i~E~~~s~~~e~~~~~~~~~~~~lF~G~~fyl~~gfs~~~~  216 (378)
                      ++||++|.+...+..       .               +++..              .....+|+|+.||+...+....+
T Consensus        78 ~~~e~~y~~~~~~~~-------~---------------r~~~~--------------~~~~~lF~g~~~~l~~~~~~~~~  121 (210)
T 2nte_A           78 CEQEEKYEIPEGPRR-------S---------------RLNRE--------------QLLPKLFDGCYFYLWGTFKHHPK  121 (210)
T ss_dssp             CCCGGGTBCTTHHHH-------H---------------HHHHH--------------TTCCCTTTTCEEEECSCCSSSCH
T ss_pred             cCChhhccCCCCChh-------h---------------hhccc--------------cccccccCceEEEEeccCCCCCH
Confidence            999999998642100       0               00000              01257999999999555665668


Q ss_pred             HHHHHHHhhccceeeeeeee---------------------ccCCceEEecccchh----hhhcCCCCccchhhHHhhhh
Q 017048          217 NKVFEAATNEGATLVNQWFV---------------------GCGASYVVCEEDSVQ----KYMGHSNNLVTPVWVLKTAK  271 (378)
Q Consensus       217 ~~L~~lI~~~GG~vv~~~~~---------------------~~~vTHVV~~~~s~~----~~l~~~~~IVt~~WI~dcik  271 (378)
                      +.|+++|+.+||++++..+.                     ...+||.|+..+..+    .+...++.+|+++||+|||.
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            88999999999999974321                     134577777653221    12335668999999999999


Q ss_pred             HhhhhhH
Q 017048          272 EKHVQRL  278 (378)
Q Consensus       272 ~~~~qr~  278 (378)
                      .+.++++
T Consensus       202 ~~~llp~  208 (210)
T 2nte_A          202 SFELLPL  208 (210)
T ss_dssp             HTSCCCS
T ss_pred             hCeeccC
Confidence            9887653

>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=99.92  E-value=3.5e-26  Score=208.88  Aligned_cols=182  Identities=16%  Similarity=0.205  Sum_probs=140.9

Q ss_pred             ceEEEEcccCHHHHHHHHHHHHHhcC-ccCCCCCCccceEEEeee-cCchhhHhhhhcCCCceEEEEeehhhhhhhcccc
Q 017048           60 GLVICVTGLSKEARKQVMEATERLGG-QYSPDLHPQCTHLVVQSF-GGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVR  137 (378)
Q Consensus        60 g~~I~vsG~~~~~r~~L~~lI~~~GG-~~~~~lt~~~THLI~~~~-~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci~~g~~  137 (378)
                      ..+|++||++++++..|.++|..+|| .++.+++..|||||+... .+.||..|+.    .|+|||+++||.+|+++|++
T Consensus        11 ~~~~~~sgl~~~~~~~l~~~i~~lgG~~~~~~~~~~~THlv~~~~~rT~K~l~ai~----~g~~Iv~~~Wv~~~~~~g~~   86 (199)
T 3u3z_A           11 TRTLVMTSMPSEKQNVVIQVVDKLKGFSIAPDVCETTTHVLSGKPLRTLNVLLGIA----RGCWVLSYDWVLWSLELGHW   86 (199)
T ss_dssp             CCEEEEESCCHHHHHHHHHHHHHHCSCEEESSCCTTEEEEEESSCCCBHHHHHHHH----TTCEEEETHHHHHHHHHTSC
T ss_pred             CeEEEEcCCCHHHHHHHHHHHHHcCCcEEecCCCCCCeEEEECCCCCCHHHHHHHH----CCCcEEeHHHHHHHhhCCCC
Confidence            46899999999999999999999988 677899999999999875 7899999997    68999999999999999999


Q ss_pred             cccceeeeeccCccCcccccccccccccCCCccccccchhhhhhhhccCCCccccccccCccccccc-eeecchhhHHHH
Q 017048          138 LSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCS-MYVDSDVSEELR  216 (378)
Q Consensus       138 l~e~~Y~~~~~~~~~~~~d~~~~l~~~s~~e~s~lp~~i~E~~~s~~~e~~~~~~~~~~~~lF~G~~-fyl~~gfs~~~~  216 (378)
                      +||++|.+........    ..++               +..          .........+|+|+. ||+ .++....+
T Consensus        87 l~e~~y~~~~~~~~~~----~~rl---------------~r~----------~~~~~~~~~LF~g~~~~~v-~~~~~~~~  136 (199)
T 3u3z_A           87 ISEEPFELSHHFPAAP----LCRS---------------ECH----------LSAGPYRGTLFADQPVMFV-SPASSPPV  136 (199)
T ss_dssp             CCSGGGBCTTTCTHHH----HHHH---------------HHH----------HCSSSCCCCTTTTSCCEEE-CTTCSSCH
T ss_pred             CChhhccccCCccccc----cchh---------------hhh----------hhcccccchhhCCCeEEEE-CCCCCCCH
Confidence            9999999976432110    0000               000          000012358999995 666 55555557


Q ss_pred             HHHHHHHhhccceeeeeeeeccCCceEEecccchhhhhcCCCCccchhhHHhhhhHhhhhhHHhh
Q 017048          217 NKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHVQRLVHI  281 (378)
Q Consensus       217 ~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~s~~~~l~~~~~IVt~~WI~dcik~~~~qr~~~~  281 (378)
                      +.|+++|+.+||+++...   ..++++|++... +  ...++.+|+|+||+|||.++.++++..|
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            889999999999999983   456777765322 1  2356789999999999999999888666

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

Probab=99.89  E-value=8.6e-24  Score=195.82  Aligned_cols=187  Identities=17%  Similarity=0.266  Sum_probs=140.5

Q ss_pred             CCCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeee-cCchhhHhhhhcCCCceEEEEeehhhhhh
Q 017048           54 ANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSF-GGRKFEHALKHGSRNGLYIVTLGWFVDSV  132 (378)
Q Consensus        54 ~~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~-~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci  132 (378)
                      +..|+.|++||+||+.+.++..+.++|..+||.+..+. .+|||||+... .+.||..|+.    .|+|||+++||.+|+
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-QKCTHLIASKVTRTVKFLTAIS----VVKHIVTPEWLEECF   84 (219)
T ss_dssp             CCCGGGCCEEEECSCCHHHHHHHHHHHHHTTCEECSSG-GGCSEEECSSCCCCHHHHHHTT----TCSEEECHHHHHHHH
T ss_pred             ccCCCCCeEEEEeCCChHHHHHHHHHHHHCCCEEeCCC-CCceEEEECCCCCCHHHHHHHH----cCCCEecHHHHHHHH
Confidence            57789999999999999999999999999999999886 89999999876 4569999987    689999999999999


Q ss_pred             hcccccccceeeeeccCccCcccccccccccccCCCccccccchhhhhhhhccCCCccccccccCccccccceeecchhh
Q 017048          133 RRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVS  212 (378)
Q Consensus       133 ~~g~~l~e~~Y~~~~~~~~~~~~d~~~~l~~~s~~e~s~lp~~i~E~~~s~~~e~~~~~~~~~~~~lF~G~~fyl~~gfs  212 (378)
                      ++|+++||++|.+......        ..+++      .+...+...               ....+|+|+.||+.+.+.
T Consensus        85 ~~~~~l~e~~y~l~d~~~e--------~~~~~------~l~~~l~ra---------------~~~~LF~G~~f~it~~~~  135 (219)
T 3sqd_A           85 RCQKFIDEQNYILRDAEAE--------VLFSF------SLEESLKRA---------------HVSPLFKAKYFYITPGIC  135 (219)
T ss_dssp             HHTSCCCSGGGBCCCHHHH--------HHTTC------CHHHHHHHH---------------HHSCTTTTEEEEECTTCS
T ss_pred             HcCCCCChHhccCCCchhh--------hhcCC------ChHHHhhhh---------------ccccccCCcEEEEeCCCC
Confidence            9999999999998753210        00000      000000000               125799999999976665


Q ss_pred             HHHHHHHHHHHhhccceeeeeeeec---------cC-CceEEec-cc---chhhhhcCCCCccchhhHHhhhhHhhh
Q 017048          213 EELRNKVFEAATNEGATLVNQWFVG---------CG-ASYVVCE-ED---SVQKYMGHSNNLVTPVWVLKTAKEKHV  275 (378)
Q Consensus       213 ~~~~~~L~~lI~~~GG~vv~~~~~~---------~~-vTHVV~~-~~---s~~~~l~~~~~IVt~~WI~dcik~~~~  275 (378)
                      +. ++.|+++|+.+||+++...+..         .. ...+|+. +.   ..+.+...++.|++++||++||-.+++
T Consensus       136 ~~-~~~l~~lI~~~GG~v~~~~p~~~~~~~~~~~~~~~~~ivis~~~d~~~~~~~~~~~~~v~s~E~il~~Il~q~l  211 (219)
T 3sqd_A          136 PS-LSTMKAIVECAGGKVLSKQPSFRKLMEHKQNSSLSEIILISCENDLHLCREYFARGIDVHNAEFVLTGVLTQTL  211 (219)
T ss_dssp             SC-HHHHHHHHHHTTCEEESSCCCHHHHHHHHHCTTSCEEEEEECGGGGGGGHHHHHTTCCCEETHHHHHHHHHTCC
T ss_pred             CC-HHHHHHHHHHCCCEEECCCCchHHhhhhhcccCCCCEEEEecccHHHHHHHHHHCCCcEEeHHHHHHHHHheee
Confidence            44 6789999999999999885321         11 2334433 32   234456679999999999999987543

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

Probab=99.89  E-value=9.1e-25  Score=207.08  Aligned_cols=220  Identities=13%  Similarity=0.105  Sum_probs=122.3

Q ss_pred             CCCCccceEEEE-cccCH------HHHHHHHHHHHHhcCccCCCCCCc-----cceEEEeeecCchhhHhhhhcCCCceE
Q 017048           54 ANAPFSGLVICV-TGLSK------EARKQVMEATERLGGQYSPDLHPQ-----CTHLVVQSFGGRKFEHALKHGSRNGLY  121 (378)
Q Consensus        54 ~~~~F~g~~I~v-sG~~~------~~r~~L~~lI~~~GG~~~~~lt~~-----~THLI~~~~~~~Ky~~A~k~~~~~gi~  121 (378)
                      ..++|+|++||| +|..+      ..+++|+.+|..+||++..+....     +||+|+. ..+.|+..+.+    .+++
T Consensus         2 ~s~lF~g~~f~v~~~~~~p~~~~~~~~~~L~~li~~~GG~~~~~~~~~t~~~~~~~iI~~-~~t~k~~~~~~----~~~~   76 (264)
T 1z56_C            2 ISNIFAGLLFYVLSDYVTEDTGIRITRAELEKTIVEHGGKLIYNVILKRHSIGDVRLISC-KTTTECKALID----RGYD   76 (264)
T ss_dssp             -CCCCCTTCCCCSEEEECCCCCSSSSCCCTHHHHHHHHTTSCCCSSCCCCCSSCCEEEEC-SCCGGGGGGTT----TTCC
T ss_pred             ccccCCCcEEEEEcCCCCccccccCCHHHHHHHHHHcCCEEeecCCCCccCccceEEEec-CCcHHHHHHHh----CCCC
Confidence            467999999998 56532      378899999999999998765432     3677774 45778877765    4699


Q ss_pred             EEEeehhhhhhhcccccccceeeeeccCccC-----cccccccccccccCCCccccccchhhhhh--hhccCCCcccccc
Q 017048          122 IVTLGWFVDSVRRNVRLSESLYTVKSIDEHG-----MHLDKLNRLVGFAGTENSCLPAGIYEAKQ--FNATGKHERDSNR  194 (378)
Q Consensus       122 IV~~~Wl~dci~~g~~l~e~~Y~~~~~~~~~-----~~~d~~~~l~~~s~~e~s~lp~~i~E~~~--s~~~e~~~~~~~~  194 (378)
                      ||+|+||.||+++++++|..+|.+....+..     ...|.+...+.. ......+..-+++...  +....+.+.+...
T Consensus        77 vV~p~Wv~dci~~~~llp~~~y~~~~~~~~~~~~~~~~~d~~gdsy~~-~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~  155 (264)
T 1z56_C           77 ILHPNWVLDCIAYKRLILIEPNYCFNVSQKMRAVAEKRVDCLGDSFEN-DISETKLSSLYKSQLSLPPMGELEIDSEVRR  155 (264)
T ss_dssp             CBCSSTTHHHHSSCSCCCCCSCBSCCCGGGTHHHHGGGBCSSSCBSSS-CCCHHHHHHTTSCCSCCCCCCCCSSCCSCCC
T ss_pred             EEechHHHHHhhcCCCCCCChHHhhcCCHHHHHHHHHhccccCCcccc-CCCHHHHHHHHHhcccccchhhhhhhccccc
Confidence            9999999999999999999988664322111     111222111100 0000000000000000  0000011111123


Q ss_pred             ccCccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEecccc---------hhhhhcC---------
Q 017048          195 SMNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDS---------VQKYMGH---------  256 (378)
Q Consensus       195 ~~~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~s---------~~~~l~~---------  256 (378)
                      .+..+|+||+|||+........+.++.+|+++||++++.  ++..+||||+..+.         +++.+..         
T Consensus       156 ~~~~lF~g~~~yl~~~~~~~~~~~l~~~i~~~GG~v~~~--l~~~t~hVV~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  233 (264)
T 1z56_C          156 FPLFLFSNRIAYVPRRKISTEDDIIEMKIKLFGGKITDQ--QSLCNLIIIPYTDPILRKDCMNEVHEKIKEQIKASDTIP  233 (264)
T ss_dssp             CCCC--------------------CHHHHHHHTTSCCCC--SSSCSEEECCCSSTTTHHHHSSHHHHTTTTTTTSSSSCC
T ss_pred             CchhhhCCeEEEEecCCCchhHHHHHHHHHHcCCEEecc--cCCCEEEEEeCCCccchHHHHHHHHHHHHhhcccccccC
Confidence            457899999999943233455667889999999999998  46666666664321         2222221         


Q ss_pred             C-CCccchhhHHhhhhHhhhhhHHhh
Q 017048          257 S-NNLVTPVWVLKTAKEKHVQRLVHI  281 (378)
Q Consensus       257 ~-~~IVt~~WI~dcik~~~~qr~~~~  281 (378)
                      . ++||++.||.||+++|.+...-.|
T Consensus       234 ~~~~iV~~~Wv~dci~~~~ll~e~~Y  259 (264)
T 1z56_C          234 KIARVVAPEWVDHSINENCQVPEEDF  259 (264)
T ss_dssp             CCCEEECTHHHHHHHTTSCCCSSCCC
T ss_pred             CCCEEecHHHHHHHHHcCCcCCHHHc
Confidence            2 489999999999999988765544

>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=99.88  E-value=5.9e-24  Score=195.29  Aligned_cols=184  Identities=21%  Similarity=0.268  Sum_probs=130.3

Q ss_pred             CCCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeee-cCchhhHhhhhcCCCceEEEEeehhhhhh
Q 017048           54 ANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSF-GGRKFEHALKHGSRNGLYIVTLGWFVDSV  132 (378)
Q Consensus        54 ~~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~-~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci  132 (378)
                      +.+...+++|++||+.+.+   ++++|..+||.+..+++ +|||||+... .+.||..|+.    .|+|||+++||.+|+
T Consensus         6 ~~~~~~~~~v~~sG~~~~~---~~~~i~~lGg~~~~~~~-~~THlI~~~~~rt~K~l~a~~----~g~~IV~~~Wl~~~~   77 (209)
T 2etx_A            6 LNQESTAPKVLFTGVVDAR---GERAVLALGGSLAGSAA-EASHLVTDRIRRTVKFLCALG----RGIPILSLDWLHQSR   77 (209)
T ss_dssp             ------CCEEEECSSCCHH---HHHHHHHTTCEECSSTT-TCSEEECSSCCCSHHHHHHHH----HTCCEECTHHHHHHH
T ss_pred             ccccCCCcEEEEeCCCcHH---HHHHHHHCCCEEeCCCC-CceEEEECCCCCCHHHHHHHh----cCCccccHHHHHHHH
Confidence            5677889999999998754   48899999999999997 5999999765 6899999997    589999999999999


Q ss_pred             hcccccccceeeeeccCccCcccccccccccccCCCccccccchhhhhhhhccCCCccccccccCccccccceeecchhh
Q 017048          133 RRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVS  212 (378)
Q Consensus       133 ~~g~~l~e~~Y~~~~~~~~~~~~d~~~~l~~~s~~e~s~lp~~i~E~~~s~~~e~~~~~~~~~~~~lF~G~~fyl~~gfs  212 (378)
                      ++++++||++|.+.+....        ..+++      .+...+..               .....+|+|++||+.+.+.
T Consensus        78 ~~~~~l~e~~y~~~~~~~~--------~~~~~------~l~~~~~~---------------a~~~~lF~g~~~~~~~~~~  128 (209)
T 2etx_A           78 KAGFFLPPDEYVVTDPEQE--------KNFGF------SLQDALSR---------------ARERRLLEGYEIYVTPGVQ  128 (209)
T ss_dssp             HHTSCCCSGGGBCCCHHHH--------HHTTC------CHHHHHHH---------------HHHSCTTTTCEEEECTTCS
T ss_pred             HcCCCCChhhccccChhhh--------hhcCC------CHHHHHhh---------------hhhCCCcCCcEEEEeCCCC
Confidence            9999999999998653110        00000      00000000               0114799999999965444


Q ss_pred             HHHHHHHHHHHhhccceeeeeeeeccCCceEEecc-cc---hhhhhcCCCCccchhhHHhhhhHhhh
Q 017048          213 EELRNKVFEAATNEGATLVNQWFVGCGASYVVCEE-DS---VQKYMGHSNNLVTPVWVLKTAKEKHV  275 (378)
Q Consensus       213 ~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~-~s---~~~~l~~~~~IVt~~WI~dcik~~~~  275 (378)
                      + .++.|+++|+.+||+++...+....-+|+|+.. ..   .+.+...++++|+++||++||..+.+
T Consensus       129 ~-~~~~l~~li~~~GG~v~~~~~~~~~~~~ivI~~~~d~~~~~~~~~~~i~vvs~eWi~~sI~~q~l  194 (209)
T 2etx_A          129 P-PPPQMGEIISCCGGTYLPSMPRSYKPQRVVITCPQDFPHCSIPLRVGLPLLSPEFLLTGVLKQEA  194 (209)
T ss_dssp             S-CHHHHHHHHHHTTCEECSSCCCSCCTTEEEECCGGGGGGCHHHHHHTCCEECTHHHHHHHHHTCC
T ss_pred             C-CHHHHHHHHHHCCCEEECCCCCCCCCceEEEECcccHHHHHHHHHCCCeEEcHHHHHHHHHhccc
Confidence            3 357899999999999998742111125666643 22   22335678999999999999997654

>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=99.88  E-value=5e-23  Score=195.25  Aligned_cols=188  Identities=17%  Similarity=0.151  Sum_probs=139.0

Q ss_pred             CCCCCccceEEEEcccCHH-----------------------------HHHHHHHHHHHhcCccCCCCCCc------cce
Q 017048           53 PANAPFSGLVICVTGLSKE-----------------------------ARKQVMEATERLGGQYSPDLHPQ------CTH   97 (378)
Q Consensus        53 ~~~~~F~g~~I~vsG~~~~-----------------------------~r~~L~~lI~~~GG~~~~~lt~~------~TH   97 (378)
                      ...++|.|+.|++|+.+..                             .+.+|+++|+.+||.+.++++..      +||
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            4678999999999998643                             56799999999999999998854      789


Q ss_pred             EEEee-ecCchhhHhhhhcCCCceEEEEeehhhhhhhcccccccceeeeeccCccCcccccccccccccCCCccccccch
Q 017048           98 LVVQS-FGGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGI  176 (378)
Q Consensus        98 LI~~~-~~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci~~g~~l~e~~Y~~~~~~~~~~~~d~~~~l~~~s~~e~s~lp~~i  176 (378)
                      ||+.. ..+.||..|+.    .|++||+++||.||+++++.+|+.+|.+........     .+...             
T Consensus        91 LIa~~~~rt~K~l~ala----~g~~iVs~~Wl~dc~~~~~~l~~~~Y~l~~g~s~~~-----~~~~~-------------  148 (259)
T 1kzy_C           91 LIADQHCRTRKYFLCLA----SGIPCVSHVWVHDSCHANQLQNYRNYLLPAGYSLEE-----QRILD-------------  148 (259)
T ss_dssp             EEESSCCCSHHHHHHHH----HTCCEEETHHHHHHHHHTSCCCGGGSBCCCEEETTT-----TEEEC-------------
T ss_pred             EEcCCCCCcHHHHHHHh----cCCCCccHHHHHHHHHcCCcCCHHHccCCCCccccc-----chhhh-------------
Confidence            99966 47889999987    599999999999999999999999999865211000     00000             


Q ss_pred             hhhhhhhccCCCccccccccCccccccceeecchhhHHHHHHHHHHHhhccceeeeeeee-------ccCCceEEecc-c
Q 017048          177 YEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFV-------GCGASYVVCEE-D  248 (378)
Q Consensus       177 ~E~~~s~~~e~~~~~~~~~~~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~-------~~~vTHVV~~~-~  248 (378)
                                      ......+|+|++||+.....+...+.+..+++.+||+++.....       ....+|||+.+ .
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                            01125799999999965554334567888999999999987420       11345555533 1


Q ss_pred             ---chh-hhhcCCCCccchhhHHhhhhHhhhhhH
Q 017048          249 ---SVQ-KYMGHSNNLVTPVWVLKTAKEKHVQRL  278 (378)
Q Consensus       249 ---s~~-~~l~~~~~IVt~~WI~dcik~~~~qr~  278 (378)
                         +.. .....+++||+.+||++||..|.++.+
T Consensus       213 ~~~~~~~~a~~~~i~iVs~EWv~~sI~~~~ll~~  246 (259)
T 1kzy_C          213 CPASVLKCAEALQLPVVSQEWVIQCLIVGERIGF  246 (259)
T ss_dssp             CCHHHHHHHHHHTCCEECHHHHHHHHHHTSCCCT
T ss_pred             ChHHHHHHHHhcCCCEecHHHHHHHHHhCCcCCC
Confidence               111 224578999999999999999887654

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

Probab=99.87  E-value=6e-23  Score=170.71  Aligned_cols=91  Identities=30%  Similarity=0.535  Sum_probs=86.2

Q ss_pred             CCCCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCchhhHhhhhcCCCceEEEEeehhhhhh
Q 017048           53 PANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSV  132 (378)
Q Consensus        53 ~~~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci  132 (378)
                      .+.++|.||+||++||++.+|.+|+++|+.+||+|+..++++|||||+..+.+.||..|.+    ++++||+++||+||+
T Consensus        17 ~~~p~F~g~~Ic~sGf~~~er~~l~~~i~~~GG~~~~~l~~~cTHLV~~~~~~~K~~~A~~----~~i~IVs~eWl~dsi   92 (112)
T 3l46_A           17 QGVPPFQDCILSFLGFSDEEKTNMEEMTEMQGGKYLPLGDERCTHLVVEENIVKDLPFEPS----KKLYVVKQEWFWGSI   92 (112)
T ss_dssp             -CCCTTTTCEECEESCCHHHHHHHHHHHHHTTCEECCTTCTTCSEEEECTTTBSSCSSCCC----SSCEEEEHHHHHHHH
T ss_pred             cCCCccCCeEEEEeCCCHHHHHHHHHHHHHcCCEECcccCCCceEEEecCCchhhHHHHHH----CCeeEecHHHHHHHH
Confidence            4688999999999999999999999999999999999999999999999999999998886    699999999999999


Q ss_pred             hcccccccceeeeec
Q 017048          133 RRNVRLSESLYTVKS  147 (378)
Q Consensus       133 ~~g~~l~e~~Y~~~~  147 (378)
                      +.|.++||+.|.+..
T Consensus        93 ~~g~~ldE~~Y~~~~  107 (112)
T 3l46_A           93 QMDARAGETMYLYEK  107 (112)
T ss_dssp             HHTSCCCGGGSBCCC
T ss_pred             HcCCccChhhceecc
Confidence            999999999999865

>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=2.9e-22  Score=187.42  Aligned_cols=204  Identities=12%  Similarity=0.147  Sum_probs=141.9

Q ss_pred             CccceEEEEcccCHHHHHHHHHHHHHhcCccCC--CCCCccceEEEeee-cCchhhHhhhhcCCCceEEEEeehhhhhhh
Q 017048           57 PFSGLVICVTGLSKEARKQVMEATERLGGQYSP--DLHPQCTHLVVQSF-GGRKFEHALKHGSRNGLYIVTLGWFVDSVR  133 (378)
Q Consensus        57 ~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~--~lt~~~THLI~~~~-~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci~  133 (378)
                      .-++.+|++||++++++..+.++|..+||.+..  +++.+|||||+... .+.||..|+.    .|+|||+++||.+|++
T Consensus         6 ~~~~~~~~~Sg~~~~~~~~l~~~i~~LGg~~~~~~~~~~~~THlV~~~~~RT~K~l~aia----~G~wIvs~~wl~~s~~   81 (235)
T 3al2_A            6 LKKQYIFQLSSLNPQERIDYCHLIEKLGGLVIEKQCFDPTCTHIVVGHPLRNEKYLASVA----AGKWVLHRSYLEACRT   81 (235)
T ss_dssp             --CCCEEEEESCCHHHHHHHHHHHHHTTCEECCSSSCCTTCCEEEESSCCCSHHHHHHHH----TTCEEECTHHHHHHHH
T ss_pred             CCCCEEEEEcCCCHHHHHHHHHHHHHcCCEEeccCCCCCCCcEEEECCCCCCHHHHHHHH----cCCcCccHHHHHHHHH
Confidence            346889999999999999999999999999976  57899999999887 5899999997    6999999999999999


Q ss_pred             cccccccceeeeeccCccCccccccccc-ccccCCCccccccchhh-hhhhhccCCCccccccccCccccccceeecchh
Q 017048          134 RNVRLSESLYTVKSIDEHGMHLDKLNRL-VGFAGTENSCLPAGIYE-AKQFNATGKHERDSNRSMNSTLSGCSMYVDSDV  211 (378)
Q Consensus       134 ~g~~l~e~~Y~~~~~~~~~~~~d~~~~l-~~~s~~e~s~lp~~i~E-~~~s~~~e~~~~~~~~~~~~lF~G~~fyl~~gf  211 (378)
                      +|+++||++|++......... ..++.. ..+     ..-|.++.. .....        .......+|+|+.|||..+ 
T Consensus        82 ~g~~l~E~~ye~~~~~~~d~~-~~~~~~~~~l-----~~a~~r~R~~l~~~~--------~~g~~~~lF~g~~v~l~~~-  146 (235)
T 3al2_A           82 AGHFVQEEDYEWGSSSILDVL-TGINVQQRRL-----ALAAMRWRKKIQQRQ--------ESGIVEGAFSGWKVILHVD-  146 (235)
T ss_dssp             HTSCCCSGGGBTTSHHHHTTC-TTSCHHHHHH-----HHHHHHHHHHHHHHH--------TTTCCSSTTTTCEEEEECC-
T ss_pred             cCCCCChhceeecCcchhccc-cCCChhhhHH-----HHHHHHHHHHHHhcc--------cccccCCCCCCcEEEEecC-
Confidence            999999999999764211000 000000 000     000111100 00000        0000147999999999544 


Q ss_pred             hHHHHHHHHHHHhhccceeeeeee--eccCCceEEecccc---------hhhhhcCCCCccchhhHHhhhhHhhhhhHHh
Q 017048          212 SEELRNKVFEAATNEGATLVNQWF--VGCGASYVVCEEDS---------VQKYMGHSNNLVTPVWVLKTAKEKHVQRLVH  280 (378)
Q Consensus       212 s~~~~~~L~~lI~~~GG~vv~~~~--~~~~vTHVV~~~~s---------~~~~l~~~~~IVt~~WI~dcik~~~~qr~~~  280 (378)
                       ....+.++++|+++||+|+...+  ...+.||++++...         +..+...++.+|+++||+|++-.+.+...-.
T Consensus       147 -~~~~~~l~~ii~agGg~vl~~~~~~~~~~~t~~~vd~~~~~~~~~~~~~~~~~~~~i~~v~~ewlld~i~~~~~~~~~~  225 (235)
T 3al2_A          147 -QSREAGFKRLLQSGGAKVLPGHSVPLFKEATHLFSDLNKLKPDDSGVNIAEAAAQNVYCLRTEYIADYLMQESPPHVEN  225 (235)
T ss_dssp             -HHHHHHHHHHHHHTTCEECSSCCGGGGGGCSEEEECC--------CCCHHHHHHTTCEEEETHHHHHHHHCSSCCCHHH
T ss_pred             -CCcHHHHHHHHHcCCcEEecCCCCCccccCceEEEecccCCccchhHHHHHHHHcCCcEEcHHHHHHHHhcCCCCChhh
Confidence             34567899999999999997632  12457898876321         2223457899999999999998876655433

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

Probab=99.84  E-value=8.4e-22  Score=163.20  Aligned_cols=91  Identities=27%  Similarity=0.519  Sum_probs=86.4

Q ss_pred             CCCCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCchhhHhhhhcCCCceEEEEeehhhhhh
Q 017048           53 PANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSV  132 (378)
Q Consensus        53 ~~~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci  132 (378)
                      .+.++|+|++||++||++.+|..|+++|+.+||+|+..++++|||||+....+.||..|.+    ++++||+++||+||+
T Consensus         8 ~~~~~F~g~~i~~sg~~~~~r~~l~~~i~~~GG~~~~~~~~~~THLV~~~~~~~K~~~a~~----~~i~IV~~~Wl~dsi   83 (109)
T 2cou_A            8 FKVPPFQDCILSFLGFSDEEKHSMEEMTEMQGGSYLPVGDERCTHLIVEENTVKDLPFEPS----KKLFVVKQEWFWGSI   83 (109)
T ss_dssp             SCCCTTTTCBEEEESSCHHHHHHHHHHHHHHTCBCCCTTCTTCSEEEECTTTCSSCSSCCC----TTSEEECHHHHHHHH
T ss_pred             ccCCcCCCeEEEecCCCHHHHHHHHHHHHHcCCEEecccCCCccEEEEeCCccHHHHHHHH----CCCeEecHHHHHHHH
Confidence            3688999999999999999999999999999999999999999999999989999998887    689999999999999


Q ss_pred             hcccccccceeeeec
Q 017048          133 RRNVRLSESLYTVKS  147 (378)
Q Consensus       133 ~~g~~l~e~~Y~~~~  147 (378)
                      +.|+++||..|.+..
T Consensus        84 ~~g~~ldE~~Y~~~~   98 (109)
T 2cou_A           84 QMDARAGETMYLYEK   98 (109)
T ss_dssp             HTTSCCCGGGTBCCC
T ss_pred             HcCCcCChhccCCCC
Confidence            999999999999876

>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=99.83  E-value=5.9e-21  Score=179.17  Aligned_cols=195  Identities=15%  Similarity=0.148  Sum_probs=135.1

Q ss_pred             CCccceEEEEccc---CHHHHHHHHHHHHHhcCccCCC-----CC--C-------------------ccceEEEeee-cC
Q 017048           56 APFSGLVICVTGL---SKEARKQVMEATERLGGQYSPD-----LH--P-------------------QCTHLVVQSF-GG  105 (378)
Q Consensus        56 ~~F~g~~I~vsG~---~~~~r~~L~~lI~~~GG~~~~~-----lt--~-------------------~~THLI~~~~-~~  105 (378)
                      .+|+|+.||++|.   ++..+.+|+++|+.+||++..+     ++  .                   ..||||+... .+
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            4899999999998   4578999999999999999886     21  1                   2499999765 48


Q ss_pred             chhhHhhhhcCCCceEEEEeehhhhhhhcccccccceeeeeccCccCcccccccc-cccccCCCccccccchhhhhhhhc
Q 017048          106 RKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNR-LVGFAGTENSCLPAGIYEAKQFNA  184 (378)
Q Consensus       106 ~Ky~~A~k~~~~~gi~IV~~~Wl~dci~~g~~l~e~~Y~~~~~~~~~~~~d~~~~-l~~~s~~e~s~lp~~i~E~~~s~~  184 (378)
                      .||..|+.    +|++||+++||.||+++++.+|+.+|.+......... +..++ +..++. +. .    +.+      
T Consensus        81 ~K~~~ala----~gipiV~~~Wi~dc~~~~~~~~~~~ylL~~~~s~~~~-~~~~~~~~~~~~-~~-~----l~~------  143 (241)
T 2vxb_A           81 VKYLEALA----FNIPCVHPQFIKQCLKMNRVVDFSPYLLASGYSHRLD-CTLSQRIEPFDT-TD-S----LYD------  143 (241)
T ss_dssp             HHHHHHHH----HTCCEECTHHHHHHHHHTSCCCSGGGBBEEEEETTTT-EEEECCCCCCCT-TS-C----HHH------
T ss_pred             HHHHHHHH----cCCCEecHHHHHHHHHcCCcCChhhccCCCCcchhcc-chhhccccCCCh-hh-H----HHH------
Confidence            89999997    5999999999999999999999999998753221100 00000 000000 00 0    000      


Q ss_pred             cCCCccccccccCccccccceeecchhhH------------HHHHHHHHHHhhcccee--eeeeeeccCCceEEecccch
Q 017048          185 TGKHERDSNRSMNSTLSGCSMYVDSDVSE------------ELRNKVFEAATNEGATL--VNQWFVGCGASYVVCEEDSV  250 (378)
Q Consensus       185 ~e~~~~~~~~~~~~lF~G~~fyl~~gfs~------------~~~~~L~~lI~~~GG~v--v~~~~~~~~vTHVV~~~~s~  250 (378)
                             .....+.+|.|++||+-.+...            +..+.+..+++++||++  +..  .+...+|+|+..++.
T Consensus       144 -------~~~~~~~Lf~g~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~i~~~~Ga~~~~v~~--~~~~~~d~v~~~~~~  214 (241)
T 2vxb_A          144 -------RLLARKGPLFGKKILFIIPEAKSWQKKIENTEQGQKALAHVYHALALGADVEIRPN--VAHLECDLILTMDGN  214 (241)
T ss_dssp             -------HHHHCCCTTTTCEEEECCCC------------CHHHHHHHHHHHHHTTCEEECCSC--CSSCCCSEEECSSSC
T ss_pred             -------HHhhcCcCCCCcEEEEEeCCCcccccccccccccchHHHHHHHHHHcCCceecccc--cccCCccEEEECCcc
Confidence                   0012368999999998433211            12477888999999999  433  344567777764322


Q ss_pred             hhhhcCCCCccchhhHHhhhhHhhhhh
Q 017048          251 QKYMGHSNNLVTPVWVLKTAKEKHVQR  277 (378)
Q Consensus       251 ~~~l~~~~~IVt~~WI~dcik~~~~qr  277 (378)
                       .....+++||+++||.+|+..|.++.
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             12457899999999999999987653

>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=2.1e-19  Score=153.01  Aligned_cols=93  Identities=25%  Similarity=0.423  Sum_probs=87.0

Q ss_pred             CCCCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCchhhHhhhhcCCCceEEEEeehhhhhh
Q 017048           53 PANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSV  132 (378)
Q Consensus        53 ~~~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci  132 (378)
                      +...+|.|++||+||+...+|.+|+++|+.+||+|..++++.||||||....+.||..|.+    ++++||+++||+||+
T Consensus        18 ~~~~~f~g~~i~itG~~~~~r~~l~~~i~~~Gg~v~~~~s~~~ThLI~~~~~~~K~~~A~~----~gi~IV~~~Wl~d~~   93 (129)
T 2d8m_A           18 ELGKILQGVVVVLSGFQNPFRSELRDKALELGAKYRPDWTRDSTHLICAFANTPKYSQVLG----LGGRIVRKEWVLDCH   93 (129)
T ss_dssp             HHTTTSTTEEEEEESCCTTHHHHHHHHHHHTTEEEESSCCTTCCEEEESSSSCHHHHHHHH----HTCEEEETHHHHHHH
T ss_pred             CccccCCCeEEEEeCCCcHHHHHHHHHHHHcCCEEeCCcCCCCeEEEecCCCChHHHHHHH----CCCcEecHHHHHHHH
Confidence            3567899999999999988999999999999999999999999999999999999999998    599999999999999


Q ss_pred             hcccccccceeeeeccC
Q 017048          133 RRNVRLSESLYTVKSID  149 (378)
Q Consensus       133 ~~g~~l~e~~Y~~~~~~  149 (378)
                      ++++++||..|.+....
T Consensus        94 ~~~~~l~e~~Y~l~~~~  110 (129)
T 2d8m_A           94 RMRRRLPSQRYLMAGPG  110 (129)
T ss_dssp             HTTSCCCGGGGBCSSSS
T ss_pred             HhCCcCChHhcccCCCC
Confidence            99999999999987653

>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=99.76  E-value=8.7e-20  Score=168.99  Aligned_cols=183  Identities=17%  Similarity=0.306  Sum_probs=129.2

Q ss_pred             CccceEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeee-cCchhhHhhhhcCCCceEEEEeehhhhhhhcc
Q 017048           57 PFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSF-GGRKFEHALKHGSRNGLYIVTLGWFVDSVRRN  135 (378)
Q Consensus        57 ~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~-~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci~~g  135 (378)
                      .-+++.|++||+.+.+   ..+++..+||.+..+++ +|||||+... .+.||..|+.    .|+|||+++||.+|+++|
T Consensus         5 ~~~~~~v~fSG~~~~~---~~~~i~~lGg~v~~~~~-~~THlV~~~~~RT~K~l~Aia----~g~~IVs~~Wl~~~~~~~   76 (220)
T 3l41_A            5 ASKRVYITFTGYDKKP---SIDNLKKLDMSITSNPS-KCTHLIAPRILRTSKFLCSIP----YGPCVVTMDWINSCLKTH   76 (220)
T ss_dssp             --CCEEEEECSCSSCC---CCGGGGGGTEEECSCTT-TCSEEECSSCCCBHHHHHHGG----GCCEEECHHHHHHHHHHT
T ss_pred             ccceEEEEEeccCCCC---CcchHhhcceeeccCch-hhhhhhhhhHhhhcceeecCC----CCCeEEEhHHHHhhhhhh
Confidence            3457899999998754   38999999999999985 6999999876 6999999997    589999999999999999


Q ss_pred             cccccceeeeeccCccCcccccccccccccCCCccccccchhhhhhhhccCCCccccccccCccccccceeecchh--hH
Q 017048          136 VRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCSMYVDSDV--SE  213 (378)
Q Consensus       136 ~~l~e~~Y~~~~~~~~~~~~d~~~~l~~~s~~e~s~lp~~i~E~~~s~~~e~~~~~~~~~~~~lF~G~~fyl~~gf--s~  213 (378)
                      +++||++|.+.+....        ..+++      .+...+..             .......+|+|+.||+.+.+  .+
T Consensus        77 ~~l~e~~y~l~d~~~e--------~~~~~------~l~~~~~r-------------ar~~~~~LF~G~~f~it~~~~~~p  129 (220)
T 3l41_A           77 EIVDEEPYLLNDPEKE--------LELGC------TLESALKR-------------ARAQGPSLLEDYVVYLTSKTVAPE  129 (220)
T ss_dssp             SCCCSGGGBCCCHHHH--------HHHTS------CHHHHHHH-------------HHHHCSCTTTTSEEEEETTSSCGG
T ss_pred             hccccCccccCCcHHH--------hhccc------cHHHHHHH-------------HHhcCchhhhheeEEEeccccCCC
Confidence            9999999998753110        00000      00000000             00112589999999997766  43


Q ss_pred             HHHHHHHHHHhhccceeeeeeee---------ccCCceEEecccch---hhh---h--cCCCCccchhhHHhhhhHhhhh
Q 017048          214 ELRNKVFEAATNEGATLVNQWFV---------GCGASYVVCEEDSV---QKY---M--GHSNNLVTPVWVLKTAKEKHVQ  276 (378)
Q Consensus       214 ~~~~~L~~lI~~~GG~vv~~~~~---------~~~vTHVV~~~~s~---~~~---l--~~~~~IVt~~WI~dcik~~~~q  276 (378)
                       .++.|+.+|+.+||+++. .|.         .++-.+||..+...   ..|   .  ...+.||+++||+++|-.+++.
T Consensus       130 -~~~~l~~iI~~~GG~v~~-~p~~~~~~~~~~~~~~~~vis~~~d~~~~~~f~~~~~~~~~~~i~~~e~ll~~il~q~l~  207 (220)
T 3l41_A          130 -NVPAVISIVKSNGGVCST-LNVYNKRLARHLEDGNVVLITCNEDSHIWTNFLDNASQNKTIFLQNYDWLIKTVLRQEID  207 (220)
T ss_dssp             -GHHHHHHHHHHTTCEEEE-ECSCCHHHHHHHHHCCEEEEECGGGHHHHTTTHHHHTTCTTEEEEEHHHHHHHHHHTCCC
T ss_pred             -CCceEEEEEecCCcEech-hhHHHHHHHHhcccCCEEEEEeCCcchHHHHhhccccccceEEEechhHHHHHHHHHHcC
Confidence             367899999999999998 210         01224555554322   222   1  1345699999999999876553

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

Probab=99.75  E-value=1.9e-19  Score=143.41  Aligned_cols=87  Identities=26%  Similarity=0.367  Sum_probs=76.3

Q ss_pred             CCCCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCCCC--CccceEEEeeecCchhhHhhhhcCCCceEEEEeehhhh
Q 017048           53 PANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLH--PQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVD  130 (378)
Q Consensus        53 ~~~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt--~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~d  130 (378)
                      +...+|+|++||++|+....+..|+++|+.+||++..+++  +.+||||+....+.|+..+      .+++||+|+||+|
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            5788999999999998766789999999999999999999  8999999988877775432      4899999999999


Q ss_pred             hhhcccccccceeee
Q 017048          131 SVRRNVRLSESLYTV  145 (378)
Q Consensus       131 ci~~g~~l~e~~Y~~  145 (378)
                      |+++|+++||++|.+
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=99.73  E-value=6.7e-19  Score=142.09  Aligned_cols=87  Identities=23%  Similarity=0.410  Sum_probs=79.4

Q ss_pred             CCCCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCCCC-CccceEEEeeecCchhhHhhhhcCCCceEEEEeehhhhh
Q 017048           53 PANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLH-PQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDS  131 (378)
Q Consensus        53 ~~~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt-~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~dc  131 (378)
                      +..++|+|++||++|+...++..|+++|..+||+|..+++ ..+||||+....+.|+..+.      +++||+|+||+||
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            5678999999999999877799999999999999999887 68999999988888887643      7999999999999


Q ss_pred             hhcccccccceeee
Q 017048          132 VRRNVRLSESLYTV  145 (378)
Q Consensus       132 i~~g~~l~e~~Y~~  145 (378)
                      +++|+++|+++|.+
T Consensus        82 i~~~~~l~~~~Y~l   95 (97)
T 2ebw_A           82 IKAGRLLSYIPYQL   95 (97)
T ss_dssp             HHHTSCCCSGGGBS
T ss_pred             HHcCCccCchHcEe
Confidence            99999999999986

>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=99.72  E-value=1.8e-18  Score=167.07  Aligned_cols=133  Identities=31%  Similarity=0.424  Sum_probs=104.6

Q ss_pred             ccccccccccCCc---c-----hhhccccccccccCCcccccc------CCCcccCCCCCccceEEEEcccCHHHHHHHH
Q 017048           12 SKGCSRLFLGSVP---S-----LRRLRGGVQSFESMSPASSSL------ASDSVLPANAPFSGLVICVTGLSKEARKQVM   77 (378)
Q Consensus        12 ~~~~~~~~~~~~~---~-----~r~~~~~~q~~~~~~~~~s~~------~~~~~~~~~~~F~g~~I~vsG~~~~~r~~L~   77 (378)
                      +..+++|++++..   |     ..+.....+|+.........+      .......+.++|+|++||+||+.+.+|.+|+
T Consensus       140 t~~tTHLI~~~~~t~Ky~~A~~~gi~IV~~~Wl~~c~~~~~~~~~~~~~~~~~~~~~~~~f~g~~i~~tG~~~~~r~~l~  219 (298)
T 3olc_X          140 NVSVTHLIAGEVGSKKYLVAANLKKPILLPSWIKTLWEKSQEKKITRYTDINMEDFKCPIFLGCIICVTGLCGLDRKEVQ  219 (298)
T ss_dssp             CTTCCEEEESSSCSHHHHHHHHTTCCEECHHHHHHHHHHHHTTCCSSGGGSCGGGGBCCTTTTCEEEECSCCHHHHHHHH
T ss_pred             CCCeeEEEEeCCCChHHHHHHHCCCeEeeHHHHHHHHHcCCcCCcccccccccccccccccCCeEEEEeCCCCccHHHHH
Confidence            5689999876431   1     234445566666422111000      0001225788999999999999999999999


Q ss_pred             HHHHHhcCccCCCCC-CccceEEEeeecCchhhHhhhhcCCCceEEEEeehhhhhhhcccccccceeeeecc
Q 017048           78 EATERLGGQYSPDLH-PQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSI  148 (378)
Q Consensus        78 ~lI~~~GG~~~~~lt-~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci~~g~~l~e~~Y~~~~~  148 (378)
                      ++|+.+||+|+.+++ ++|||||+..+.+.||..|.+    +|++||+++||+||+++|+++||+.|.+...
T Consensus       220 ~li~~~GG~~~~~ls~~~~THLI~~~~~g~K~~~A~~----~gi~IV~~~Wl~dsi~~g~~lde~~Y~l~~~  287 (298)
T 3olc_X          220 QLTVKHGGQYMGQLKMNECTHLIVQEPKGQKYECAKR----WNVHCVTTQWFFDSIEKGFCQDESIYKTEPR  287 (298)
T ss_dssp             HHHHHTTCEECSSCCTTTCCEEECSSSCSHHHHHHHH----TTCEEECHHHHHHHHHHTSCCCGGGSBSCC-
T ss_pred             HHHHHcCCEEeceecCCCceEEEEeCCCchHHHHHHH----CCCeEEeHHHHHHHHHCCCCCCchhcCCCCC
Confidence            999999999999999 899999999999999999987    5899999999999999999999999998764

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

Probab=99.65  E-value=6.1e-17  Score=133.45  Aligned_cols=92  Identities=20%  Similarity=0.313  Sum_probs=81.6

Q ss_pred             CCCccceEEEEcccCH----HHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCchhhHhhhhcCCCceEEEEeehhhh
Q 017048           55 NAPFSGLVICVTGLSK----EARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVD  130 (378)
Q Consensus        55 ~~~F~g~~I~vsG~~~----~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~d  130 (378)
                      .++|+|++++|.+...    .....+..++..+||++...+++.+||||+.+..+.||+.|.+    ++++||+++||.|
T Consensus         5 ~p~f~g~vvyvd~~~~~g~~~~s~~l~~~l~~~GA~v~~~l~~~vTHvV~~~~~~~~~~~A~~----~~i~iV~~~Wv~~   80 (107)
T 3pa6_A            5 APILKDVVAYVEVWSSNGTENYSKTFTTQLVDMGAKVSKTFNKQVTHVIFKDGYQSTWDKAQK----RGVKLVSVLWVEK   80 (107)
T ss_dssp             CCTTTTCEEEEEEBCTTSCCBCHHHHHHHHHHTTCEECSSCCTTCCEEEEESCCHHHHHHHHH----HTCEEECHHHHHH
T ss_pred             ccccCCEEEEEeccCCCChhhHHHHHHHHHHHcCCEEecccCCCccEEEEeCCCChHHHHHhc----CCCEEECHHHHHH
Confidence            5699999999988752    1346799999999999999999999999999888889999988    4899999999999


Q ss_pred             hhhcccccccceeeeeccCc
Q 017048          131 SVRRNVRLSESLYTVKSIDE  150 (378)
Q Consensus       131 ci~~g~~l~e~~Y~~~~~~~  150 (378)
                      |+++|+++||+.|.+..+.+
T Consensus        81 C~~~~~~vdE~~Y~i~~~~~  100 (107)
T 3pa6_A           81 CRTAGAHIDESLFPAANMNE  100 (107)
T ss_dssp             HHHHTSCCCGGGSBCCCTTT
T ss_pred             HHHhCccCChhcccCCCCcc
Confidence            99999999999999876543

>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=9.5e-16  Score=130.82  Aligned_cols=93  Identities=18%  Similarity=0.312  Sum_probs=78.8

Q ss_pred             CCCCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCchhhHhhhhcCCCceEEEEeehhhhhh
Q 017048           53 PANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSV  132 (378)
Q Consensus        53 ~~~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci  132 (378)
                      .+..+|+||+|+++|+....+..|..+|..+||++...++..+||||+.++ ..++..+... ...+++||+++||+||+
T Consensus        36 ~~~~lF~g~~i~i~G~~~~~~~~L~~~i~~~Gg~v~~~l~~~vTHvI~~~~-~~~~~~~~~~-~~~~~~iV~~~Wv~dsi  113 (132)
T 1wf6_A           36 APEDLLDGCRIYLCGFSGRKLDKLRRLINSGGGVRFNQLNEDVTHVIVGDY-DDELKQFWNK-SAHRPHVVGAKWLLECF  113 (132)
T ss_dssp             CCTTTTTTCEEEEESCCSHHHHHHHHHHHHTTCEEESSCCSSCCEEEESSC-CSHHHHHHHH-SCCCCCEEEHHHHHHHH
T ss_pred             ccccccCCEEEEEECCChHHHHHHHHHHHHCCCEEeCcCCCCCeEEEECCc-hHHHHHHHHh-hCCCCeEechHHHHHHH
Confidence            356899999999999998999999999999999999999999999999764 3344444321 12478999999999999


Q ss_pred             hcccccccceeeeec
Q 017048          133 RRNVRLSESLYTVKS  147 (378)
Q Consensus       133 ~~g~~l~e~~Y~~~~  147 (378)
                      ++|+++||..|.+..
T Consensus       114 ~~~~ll~e~~Y~~~~  128 (132)
T 1wf6_A          114 SKGYMLSEEPYIHSG  128 (132)
T ss_dssp             HHSSCCCSGGGBCCC
T ss_pred             HcCCcCCHhhccCCC
Confidence            999999999998754

>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=1.2e-15  Score=124.91  Aligned_cols=92  Identities=17%  Similarity=0.274  Sum_probs=83.8

Q ss_pred             CCCCccceEEEEcccC-HHHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCchhhHhhhhcCCCceEEEEeehhhhhh
Q 017048           54 ANAPFSGLVICVTGLS-KEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSV  132 (378)
Q Consensus        54 ~~~~F~g~~I~vsG~~-~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci  132 (378)
                      -+.+|.|++|+++|.. +.++..|+++|..+||.+..+++.++||+|+..+.+.+++.|.+.  ..++.+|+|+||++|+
T Consensus         4 Lpd~F~g~~f~l~~~~p~~~r~~l~ryiia~GG~v~~~~~~~vTHvIt~~~~d~~~~~a~~~--~p~~~~V~P~WI~~Ci   81 (104)
T 3pc6_A            4 LPDFFEGKHFFLYGEFPGDERRRLIRYVTAFNGELEDYMNERVQFVITAQEWDPNFEEALME--NPSLAFVRPRWIYSCN   81 (104)
T ss_dssp             CCCTTTTCEEEEESCCSTTHHHHHHHHHHHTTCEECSSCCTTCCEEEESSCCCHHHHHHHTT--CTTCEEECHHHHHHHH
T ss_pred             cchhhCCeEEEEcCCCcHHHHHHHHHHHHHcCCEEEcccCCCceEEEeCCCCChhHHHHhhh--CCCCeEEccHHHHHHH
Confidence            4679999999999987 689999999999999999999999999999998888899887752  3589999999999999


Q ss_pred             hcccccccceeeeec
Q 017048          133 RRNVRLSESLYTVKS  147 (378)
Q Consensus       133 ~~g~~l~e~~Y~~~~  147 (378)
                      ++++++|+.+|.+..
T Consensus        82 ~~~klvp~~~y~~~~   96 (104)
T 3pc6_A           82 EKQKLLPHQLYGVVP   96 (104)
T ss_dssp             HHTSCCCGGGGBCCC
T ss_pred             hcCccCCcccceecc
Confidence            999999999999865

>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=99.53  E-value=2.1e-15  Score=151.95  Aligned_cols=89  Identities=21%  Similarity=0.360  Sum_probs=82.3

Q ss_pred             CCCCccceEEEEcccCH----HHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCchhhHhhhhcCCCceEEEEeehhh
Q 017048           54 ANAPFSGLVICVTGLSK----EARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFV  129 (378)
Q Consensus        54 ~~~~F~g~~I~vsG~~~----~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~  129 (378)
                      +.++|.||+|||||+.+    .++..|..+++.+||+|+..++++||||||+...+.||..|.+++   +|+||+++||+
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            56799999999999864    257899999999999999999999999999999999999999852   69999999999


Q ss_pred             hhhhcccccccceeee
Q 017048          130 DSVRRNVRLSESLYTV  145 (378)
Q Consensus       130 dci~~g~~l~e~~Y~~  145 (378)
                      +|++.|+++||..|.+
T Consensus       426 dcl~~~krldE~~YlL  441 (442)
T 3ef1_A          426 ESLSQWKRLPESDYLL  441 (442)
T ss_dssp             HHHHHTSCCCGGGTBC
T ss_pred             HHHHcCCcCChhcccc
Confidence            9999999999999975

>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=99.51  E-value=3.6e-15  Score=147.95  Aligned_cols=89  Identities=20%  Similarity=0.337  Sum_probs=81.7

Q ss_pred             CCCCccceEEEEcccCH----HHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCchhhHhhhhcCCCceEEEEeehhh
Q 017048           54 ANAPFSGLVICVTGLSK----EARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFV  129 (378)
Q Consensus        54 ~~~~F~g~~I~vsG~~~----~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~  129 (378)
                      ..++|.||+||+||+.+    .++..+.+++..+||+++.+++++||||||+...+.||..|.++   .||+||+++||+
T Consensus       279 k~~~L~G~~ivfSG~~~~~~~~~~~~l~~l~~~lGa~v~~~vs~~vTHLVa~~~~t~K~~~A~~~---~~I~IV~~~Wl~  355 (372)
T 3ef0_A          279 KQKVLKGCRLLFSGVIPLGVDVLSSDIAKWAMSFGAEVVLDFSVPPTHLIAAKIRTEKVKKAVSM---GNIKVVKLNWLT  355 (372)
T ss_dssp             HTTTSTTCEEEEESSSCTTSCTTTSHHHHHHHHTTCEEESSSSSCCSEEEECSCCCHHHHHHHHS---SSCCEEEHHHHH
T ss_pred             HhhhcCCcEEEEecccCCCcchhHHHHHHHHHHcCCEEeCcCCCCceEEEEcCCCchHHHHHHhc---CCCEEEcHHHHH
Confidence            35799999999999963    35689999999999999999999999999999999999999984   389999999999


Q ss_pred             hhhhcccccccceeee
Q 017048          130 DSVRRNVRLSESLYTV  145 (378)
Q Consensus       130 dci~~g~~l~e~~Y~~  145 (378)
                      +|++.|+++||+.|.+
T Consensus       356 ~c~~~~~~vdE~~Y~l  371 (372)
T 3ef0_A          356 ESLSQWKRLPESDYLL  371 (372)
T ss_dssp             HHHHTTSCCCGGGGBC
T ss_pred             HHHHhCCcCChhhcee
Confidence            9999999999999975

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

Probab=99.46  E-value=3.2e-14  Score=117.43  Aligned_cols=84  Identities=12%  Similarity=0.154  Sum_probs=73.7

Q ss_pred             cCccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEecccchhhh---hcCCCCccchhhHHhhhhH
Q 017048          196 MNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKY---MGHSNNLVTPVWVLKTAKE  272 (378)
Q Consensus       196 ~~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~s~~~~---l~~~~~IVt~~WI~dcik~  272 (378)
                      +..+|+||+||+ .||++.++..|.++|+.+||++...  ++..+||||+.....++|   ...+++||+++||+||++.
T Consensus         9 ~~~~F~g~~i~~-sg~~~~~r~~l~~~i~~~GG~~~~~--~~~~~THLV~~~~~~~K~~~a~~~~i~IV~~~Wl~dsi~~   85 (109)
T 2cou_A            9 KVPPFQDCILSF-LGFSDEEKHSMEEMTEMQGGSYLPV--GDERCTHLIVEENTVKDLPFEPSKKLFVVKQEWFWGSIQM   85 (109)
T ss_dssp             CCCTTTTCBEEE-ESSCHHHHHHHHHHHHHHTCBCCCT--TCTTCSEEEECTTTCSSCSSCCCTTSEEECHHHHHHHHHT
T ss_pred             cCCcCCCeEEEe-cCCCHHHHHHHHHHHHHcCCEEecc--cCCCccEEEEeCCccHHHHHHHHCCCeEecHHHHHHHHHc
Confidence            457899999999 7999999999999999999999987  699999999987555544   4678999999999999999


Q ss_pred             hhhhhHHhhh
Q 017048          273 KHVQRLVHIS  282 (378)
Q Consensus       273 ~~~qr~~~~s  282 (378)
                      +..++.-.|.
T Consensus        86 g~~ldE~~Y~   95 (109)
T 2cou_A           86 DARAGETMYL   95 (109)
T ss_dssp             TSCCCGGGTB
T ss_pred             CCcCChhccC
Confidence            9988876663

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

Probab=99.45  E-value=4.4e-14  Score=117.16  Aligned_cols=84  Identities=13%  Similarity=0.134  Sum_probs=73.9

Q ss_pred             cCccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEecccchhhh---hcCCCCccchhhHHhhhhH
Q 017048          196 MNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKY---MGHSNNLVTPVWVLKTAKE  272 (378)
Q Consensus       196 ~~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~s~~~~---l~~~~~IVt~~WI~dcik~  272 (378)
                      +...|+||+|++ .||++.++..|+++|+.+||++...  ++..|||||+...+.++|   ..++++||+++||+||++.
T Consensus        18 ~~p~F~g~~Ic~-sGf~~~er~~l~~~i~~~GG~~~~~--l~~~cTHLV~~~~~~~K~~~A~~~~i~IVs~eWl~dsi~~   94 (112)
T 3l46_A           18 GVPPFQDCILSF-LGFSDEEKTNMEEMTEMQGGKYLPL--GDERCTHLVVEENIVKDLPFEPSKKLYVVKQEWFWGSIQM   94 (112)
T ss_dssp             CCCTTTTCEECE-ESCCHHHHHHHHHHHHHTTCEECCT--TCTTCSEEEECTTTBSSCSSCCCSSCEEEEHHHHHHHHHH
T ss_pred             CCCccCCeEEEE-eCCCHHHHHHHHHHHHHcCCEECcc--cCCCceEEEecCCchhhHHHHHHCCeeEecHHHHHHHHHc
Confidence            357899999999 8999999999999999999999998  699999999998665555   4689999999999999999


Q ss_pred             hhhhhHHhhh
Q 017048          273 KHVQRLVHIS  282 (378)
Q Consensus       273 ~~~qr~~~~s  282 (378)
                      |..++.-.|.
T Consensus        95 g~~ldE~~Y~  104 (112)
T 3l46_A           95 DARAGETMYL  104 (112)
T ss_dssp             TSCCCGGGSB
T ss_pred             CCccChhhce
Confidence            9887765553

>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=99.43  E-value=1.1e-13  Score=117.87  Aligned_cols=85  Identities=18%  Similarity=0.343  Sum_probs=71.7

Q ss_pred             cccCccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEecc--cchhhhh---cCCCCccchhhHHh
Q 017048          194 RSMNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEE--DSVQKYM---GHSNNLVTPVWVLK  268 (378)
Q Consensus       194 ~~~~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~--~s~~~~l---~~~~~IVt~~WI~d  268 (378)
                      +.+..+|+||+||| .|+....+..|.++|+.+||++++.  ++..+||||+..  ..+++++   ...++||+++||+|
T Consensus        35 ~~~~~lF~g~~i~i-~G~~~~~~~~L~~~i~~~Gg~v~~~--l~~~vTHvI~~~~~~~~~~~~~~~~~~~~iV~~~Wv~d  111 (132)
T 1wf6_A           35 QAPEDLLDGCRIYL-CGFSGRKLDKLRRLINSGGGVRFNQ--LNEDVTHVIVGDYDDELKQFWNKSAHRPHVVGAKWLLE  111 (132)
T ss_dssp             CCCTTTTTTCEEEE-ESCCSHHHHHHHHHHHHTTCEEESS--CCSSCCEEEESSCCSHHHHHHHHSCCCCCEEEHHHHHH
T ss_pred             cccccccCCEEEEE-ECCChHHHHHHHHHHHHCCCEEeCc--CCCCCeEEEECCchHHHHHHHHhhCCCCeEechHHHHH
Confidence            44578999999999 6887788899999999999999998  589999999975  3344442   35789999999999


Q ss_pred             hhhHhhhhhHHhh
Q 017048          269 TAKEKHVQRLVHI  281 (378)
Q Consensus       269 cik~~~~qr~~~~  281 (378)
                      |++++.+.+.-.|
T Consensus       112 si~~~~ll~e~~Y  124 (132)
T 1wf6_A          112 CFSKGYMLSEEPY  124 (132)
T ss_dssp             HHHHSSCCCSGGG
T ss_pred             HHHcCCcCCHhhc
Confidence            9999998877666

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

Probab=99.42  E-value=6.3e-14  Score=111.18  Aligned_cols=83  Identities=16%  Similarity=0.315  Sum_probs=67.6

Q ss_pred             CccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeec--cCCceEEecccchhhh-hcCCCCccchhhHHhhhhHh
Q 017048          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVG--CGASYVVCEEDSVQKY-MGHSNNLVTPVWVLKTAKEK  273 (378)
Q Consensus       197 ~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~--~~vTHVV~~~~s~~~~-l~~~~~IVt~~WI~dcik~~  273 (378)
                      ..+|+|++||+ .|+..+.+..|+++|+.+||++.+.  ++  ..+||||+......++ ...+++||+++||+||++++
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 6655455788999999999999998  46  7999999987544343 23689999999999999999


Q ss_pred             hhhhHHhhh
Q 017048          274 HVQRLVHIS  282 (378)
Q Consensus       274 ~~qr~~~~s  282 (378)
                      .+++.-.|.
T Consensus        82 ~~l~e~~Y~   90 (92)
T 4id3_A           82 RLLPWQNYS   90 (92)
T ss_dssp             SCCCGGGGB
T ss_pred             CcCChhhcc
Confidence            888776653

>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=99.37  E-value=3e-13  Score=108.73  Aligned_cols=84  Identities=11%  Similarity=0.246  Sum_probs=67.1

Q ss_pred             cCccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEecccchhhh-hcCCCCccchhhHHhhhhHhh
Q 017048          196 MNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKY-MGHSNNLVTPVWVLKTAKEKH  274 (378)
Q Consensus       196 ~~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~s~~~~-l~~~~~IVt~~WI~dcik~~~  274 (378)
                      ...+|+|+.||+ .|+....++.|+++|+.+||++...+ ....+||+|+......++ ...+++||+|+||.||++++.
T Consensus         9 ~~~lF~g~~~~i-sg~~~~~~~~L~~~i~~~GG~~~~~~-~~~~~THlI~~~~~~~k~~~~~~~~iV~p~Wl~dci~~~~   86 (97)
T 2ebw_A            9 SSTIFSGVAIYV-NGYTDPSAEELRKLMMLHGGQYHVYY-SRSKTTHIIATNLPNAKIKELKGEKVIRPEWIVESIKAGR   86 (97)
T ss_dssp             CCCTTTTCEEEE-CSSCSSCHHHHHHHHHHTTCEECSSC-CSSSCCEEECSCCCTTHHHHTSSSCCBCTHHHHHHHHHTS
T ss_pred             CCCCCCCeEEEE-eCCCcccHHHHHHHHHHcCCEEeeec-CCCCCEEEEecCCChHHHHHhcCCCEeChHHHHHHHHcCC
Confidence            367999999999 67765668899999999999988763 237899999997543333 123889999999999999998


Q ss_pred             hhhHHhh
Q 017048          275 VQRLVHI  281 (378)
Q Consensus       275 ~qr~~~~  281 (378)
                      +++.-.|
T Consensus        87 ~l~~~~Y   93 (97)
T 2ebw_A           87 LLSYIPY   93 (97)
T ss_dssp             CCCSGGG
T ss_pred             ccCchHc
Confidence            8776555

>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=99.28  E-value=2.3e-12  Score=105.43  Aligned_cols=83  Identities=11%  Similarity=0.258  Sum_probs=66.5

Q ss_pred             CccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEeccc---chhhhh--cCCCCccchhhHHhhhh
Q 017048          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED---SVQKYM--GHSNNLVTPVWVLKTAK  271 (378)
Q Consensus       197 ~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~---s~~~~l--~~~~~IVt~~WI~dcik  271 (378)
                      .++|+|+.|||+..++..+++.|.++|.+.||++.+.  .++++||||++..   +++...  ..+..+|+|.||++|++
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            5799999999965564567889999999999998887  6899999999873   333323  24678999999999999


Q ss_pred             HhhhhhHHhh
Q 017048          272 EKHVQRLVHI  281 (378)
Q Consensus       272 ~~~~qr~~~~  281 (378)
                      ++++...-.|
T Consensus        83 ~~klvp~~~y   92 (104)
T 3pc6_A           83 KQKLLPHQLY   92 (104)
T ss_dssp             HTSCCCGGGG
T ss_pred             cCccCCcccc
Confidence            9887655443

>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=2.4e-12  Score=103.07  Aligned_cols=76  Identities=24%  Similarity=0.303  Sum_probs=70.5

Q ss_pred             CCCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCchhhHhhhhcCCCceEEEEeehhhhhhh
Q 017048           54 ANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVR  133 (378)
Q Consensus        54 ~~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci~  133 (378)
                      +.++|.|.+|||||..+..|.+++++|+.+||+++.+++.++||||++...+.|+++|.+    +||+||+.+|+.+++.
T Consensus         4 ~~~~l~G~~~v~TG~l~~~R~e~~~~i~~~Gg~v~~sVskkt~~LV~g~~~gsK~~kA~~----lgI~Ii~E~~f~~~l~   79 (92)
T 1l7b_A            4 GGEALKGLTFVITGELSRPREEVKALLRRLGAKVTDSVSRKTSYLVVGENPGSKLEKARA----LGVPTLTEEELYRLLE   79 (92)
T ss_dssp             CCCSSTTCEEECSTTTTSCHHHHHHHHHHTTCEEESCCSSSCCCBEECSSSSTTHHHHHC----SSSCCEEHHHHHHHHH
T ss_pred             CCCCcCCcEEEEecCCCCCHHHHHHHHHHcCCEEeCcccCCeeEEEeCCCCChHHHHHHH----cCCcEEeHHHHHHHHH
Confidence            456799999999998655999999999999999999999999999999999999999997    6999999999999986

>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=99.18  E-value=8.8e-12  Score=105.70  Aligned_cols=82  Identities=18%  Similarity=0.319  Sum_probs=69.5

Q ss_pred             CccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEecccchhhh---hcCCCCccchhhHHhhhhHh
Q 017048          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKY---MGHSNNLVTPVWVLKTAKEK  273 (378)
Q Consensus       197 ~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~s~~~~---l~~~~~IVt~~WI~dcik~~  273 (378)
                      ..+|+|++|+| .|+....++.|+++|+.+||++...  ++.++||||+......+|   ...+++||+++||+||++.+
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            56899999999 6776667899999999999999998  688999999987433333   45799999999999999999


Q ss_pred             hhhhHHhh
Q 017048          274 HVQRLVHI  281 (378)
Q Consensus       274 ~~qr~~~~  281 (378)
                      .+++.-.|
T Consensus        97 ~~l~e~~Y  104 (129)
T 2d8m_A           97 RRLPSQRY  104 (129)
T ss_dssp             SCCCGGGG
T ss_pred             CcCChHhc
Confidence            88776555

>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=1.3e-11  Score=101.72  Aligned_cols=79  Identities=23%  Similarity=0.331  Sum_probs=71.3

Q ss_pred             CCCCCccceEEEEcccCH-HHHHHHHHHHHHhcCccCCCCCCccceEEEeeecC-chhhHhhhhcCCCceEEEEeehhhh
Q 017048           53 PANAPFSGLVICVTGLSK-EARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGG-RKFEHALKHGSRNGLYIVTLGWFVD  130 (378)
Q Consensus        53 ~~~~~F~g~~I~vsG~~~-~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~-~Ky~~A~k~~~~~gi~IV~~~Wl~d  130 (378)
                      ....+|.|.+|||||..+ -.|.+++++|+.+||+++..++.+|+|||++...+ .|+.+|.+    +||+||+.+||.+
T Consensus        28 ~~~~~l~G~~~v~TG~l~~~~R~e~~~~i~~~Gg~v~~sVSkkTd~LV~G~~~g~sK~~kA~~----lgI~Ii~E~~f~~  103 (109)
T 2k6g_A           28 GAENCLEGLIFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGQSKSDKAAA----LGTKIIDEDGLLN  103 (109)
T ss_dssp             CCTTTTTTCEEEEESBCSSCCHHHHHHHHHHTTCEEESSCCTTCCEEEECBCCCHHHHHHHHH----HTCEEECHHHHHH
T ss_pred             CCCCCCCCCEEEEeeeCCCCCHHHHHHHHHHcCCEeeCcccCCceEEEECCCCChHHHHHHHH----cCCeEEeHHHHHH
Confidence            456689999999999874 58999999999999999999999999999998877 89999998    5999999999999


Q ss_pred             hhhcc
Q 017048          131 SVRRN  135 (378)
Q Consensus       131 ci~~g  135 (378)
                      .+..+
T Consensus       104 ll~~~  108 (109)
T 2k6g_A          104 LIRNL  108 (109)
T ss_dssp             HHHHT
T ss_pred             HHHhC
Confidence            98654

>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=99.14  E-value=2.7e-11  Score=95.81  Aligned_cols=73  Identities=14%  Similarity=0.293  Sum_probs=60.0

Q ss_pred             cCccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEecccchhhhhcCCCCccchhhHHhhhhHhhh
Q 017048          196 MNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHV  275 (378)
Q Consensus       196 ~~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~s~~~~l~~~~~IVt~~WI~dcik~~~~  275 (378)
                      ...+|+|++|||..+++..  +.|.++|.++||++++.. ..+++||||.+.+     ...+..+|+|+||+|||++|.+
T Consensus        13 LpdiFsg~~~~l~~~v~~~--~~l~RyiiAfgG~v~~~~-~~~~vTHvI~~~~-----~~~~~~~V~p~WI~dcI~k~~L   84 (88)
T 3pc7_A           13 LLDIFTGVRLYLPPSTPDF--SRLRRYFVAFDGDLVQEF-DMTSATHVLGSRD-----KNPAAQQVSPEWIWACIRKRRL   84 (88)
T ss_dssp             CCCCSTTCEECCCTTSTTH--HHHHHHHHHTTCEECCGG-GGGGCSEEESCCT-----TCTTSEEECHHHHHHHHHHTSC
T ss_pred             CChhhcCeEEEccCCcCch--hhheeeeeecCCEEeccc-CCCcCeEEecCCC-----cCCCCcEEchHHHHHHHhCCcc
Confidence            3789999999997777643  679999999999998863 3469999998764     2346678999999999999876


Q ss_pred             h
Q 017048          276 Q  276 (378)
Q Consensus       276 q  276 (378)
                      .
T Consensus        85 l   85 (88)
T 3pc7_A           85 V   85 (88)
T ss_dssp             C
T ss_pred             c
Confidence            4

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

Probab=99.13  E-value=1.7e-11  Score=99.63  Aligned_cols=82  Identities=24%  Similarity=0.314  Sum_probs=65.9

Q ss_pred             CCCCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCC-----------CCCccceEEEeeecCchhhHhhhhcCCCceE
Q 017048           53 PANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPD-----------LHPQCTHLVVQSFGGRKFEHALKHGSRNGLY  121 (378)
Q Consensus        53 ~~~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~-----------lt~~~THLI~~~~~~~Ky~~A~k~~~~~gi~  121 (378)
                      ....+|+|++|++++-.  .+..|+.+|..+||.+..+           .+...||+|+..+...+     +   ..+..
T Consensus         8 ~~~~LF~g~~F~i~~e~--p~~~le~~I~~~GG~v~~~~~~~~g~~~~~~~~~iTh~I~drp~~~~-----~---~~~r~   77 (100)
T 2ep8_A            8 KHKKLFEGLKFFLNREV--PREALAFIIRSFGGEVSWDKSLCIGATYDVTDSRITHQIVDRPGQQT-----S---VIGRC   77 (100)
T ss_dssp             CSCCTTSSCEEECCSSS--CHHHHHHHHHHTTCEEECCTTTSSCCCSCTTCTTCCEEECSCTTTSC-----C---BTTBE
T ss_pred             chHHHcCCcEEEEecCC--CHHHHHHHHHHcCCEEEeccccccCcccccCCCceEEEEecccchhh-----h---cCCCe
Confidence            35789999999997643  4667889999999998875           24689999997653322     1   13678


Q ss_pred             EEEeehhhhhhhcccccccceee
Q 017048          122 IVTLGWFVDSVRRNVRLSESLYT  144 (378)
Q Consensus       122 IV~~~Wl~dci~~g~~l~e~~Y~  144 (378)
                      +|.|+||+||+.++++||+.+|.
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            99999999999999999999884

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

Probab=99.11  E-value=3.5e-11  Score=97.70  Aligned_cols=82  Identities=11%  Similarity=0.203  Sum_probs=62.4

Q ss_pred             cCccccccceeecchhhHHHHHHHHHHHhhccceeeeee---------eeccCCceEEecccchhhhhcCCCCccchhhH
Q 017048          196 MNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQW---------FVGCGASYVVCEEDSVQKYMGHSNNLVTPVWV  266 (378)
Q Consensus       196 ~~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~---------~~~~~vTHVV~~~~s~~~~l~~~~~IVt~~WI  266 (378)
                      ...+|+|++||++...+   ++.|+.+|+++||+++...         ..+..+||+|++.....+ ...+..+|+|+||
T Consensus         9 ~~~LF~g~~F~i~~e~p---~~~le~~I~~~GG~v~~~~~~~~g~~~~~~~~~iTh~I~drp~~~~-~~~~r~~VqPqWV   84 (100)
T 2ep8_A            9 HKKLFEGLKFFLNREVP---REALAFIIRSFGGEVSWDKSLCIGATYDVTDSRITHQIVDRPGQQT-SVIGRCYVQPQWV   84 (100)
T ss_dssp             SCCTTSSCEEECCSSSC---HHHHHHHHHHTTCEEECCTTTSSCCCSCTTCTTCCEEECSCTTTSC-CBTTBEEECTHHH
T ss_pred             hHHHcCCcEEEEecCCC---HHHHHHHHHHcCCEEEeccccccCcccccCCCceEEEEecccchhh-hcCCCeEEcchHH
Confidence            36899999999965554   5678889999999998641         025789999999865433 1234589999999


Q ss_pred             HhhhhHhhhhhHHhh
Q 017048          267 LKTAKEKHVQRLVHI  281 (378)
Q Consensus       267 ~dcik~~~~qr~~~~  281 (378)
                      +||++++.+++.-+|
T Consensus        85 ~Dcin~~~lLp~~~Y   99 (100)
T 2ep8_A           85 FDSVNARLLLPVAEY   99 (100)
T ss_dssp             HHHHHHTSCCCTTTC
T ss_pred             HHHHhcCCcCChhhc
Confidence            999999988765444

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

Probab=99.10  E-value=2.7e-11  Score=99.55  Aligned_cols=85  Identities=16%  Similarity=0.156  Sum_probs=67.0

Q ss_pred             CccccccceeecchhhH---HHHHHHHHHHhhccceeeeeeeeccCCceEEecccc---hhhhhcCCCCccchhhHHhhh
Q 017048          197 NSTLSGCSMYVDSDVSE---ELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDS---VQKYMGHSNNLVTPVWVLKTA  270 (378)
Q Consensus       197 ~~lF~G~~fyl~~gfs~---~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~s---~~~~l~~~~~IVt~~WI~dci  270 (378)
                      ..+|+|+++|++..-.+   ...+.+..+++++||++++.  ++..+||||+.++.   .++....+++||++.||+||+
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            46899999999533211   23467999999999999999  58999999998643   333345679999999999999


Q ss_pred             hHhhhhhHHhhhH
Q 017048          271 KEKHVQRLVHISA  283 (378)
Q Consensus       271 k~~~~qr~~~~s~  283 (378)
                      +++...+.-.|..
T Consensus        83 ~~~~~vdE~~Y~i   95 (107)
T 3pa6_A           83 TAGAHIDESLFPA   95 (107)
T ss_dssp             HHTSCCCGGGSBC
T ss_pred             HhCccCChhcccC
Confidence            9999888766654

>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=99.10  E-value=5.6e-11  Score=112.56  Aligned_cols=92  Identities=13%  Similarity=0.148  Sum_probs=70.8

Q ss_pred             CCCCccceEEEEcccC----------HHHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCc-hhhHhhhhcCCCceEE
Q 017048           54 ANAPFSGLVICVTGLS----------KEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGR-KFEHALKHGSRNGLYI  122 (378)
Q Consensus        54 ~~~~F~g~~I~vsG~~----------~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~-Ky~~A~k~~~~~gi~I  122 (378)
                      +..+|+||+|++.++.          ......++.++..+||+++..++..+||+|+...... ....+++.....+++|
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            5679999999997652          1133446899999999999999999999999764331 1222333222357899


Q ss_pred             EEeehhhhhhhcccccccceeee
Q 017048          123 VTLGWFVDSVRRNVRLSESLYTV  145 (378)
Q Consensus       123 V~~~Wl~dci~~g~~l~e~~Y~~  145 (378)
                      |+++||.||++.|+++||++|.+
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

>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=8.7e-11  Score=97.20  Aligned_cols=78  Identities=23%  Similarity=0.346  Sum_probs=70.7

Q ss_pred             CCCCCccceEEEEcccCH-HHHHHHHHHHHHhcCccCCCCCCccceEEEeeecC-chhhHhhhhcCCCceEEEEeehhhh
Q 017048           53 PANAPFSGLVICVTGLSK-EARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGG-RKFEHALKHGSRNGLYIVTLGWFVD  130 (378)
Q Consensus        53 ~~~~~F~g~~I~vsG~~~-~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~-~Ky~~A~k~~~~~gi~IV~~~Wl~d  130 (378)
                      ....+|.|.+|||||... -.|.+++++|+.+||+++..++.+++|||++...+ .|+.+|.+    +||+||+.+||.+
T Consensus        18 ~~~~~l~G~~~v~TG~l~~~~R~e~~~~i~~~Ggkv~~sVSkkTd~LV~G~~~g~sKl~KA~~----lgI~IisE~~f~~   93 (112)
T 2ebu_A           18 GAENCLEGLIFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGQSKSDKAAA----LGTKIIDEDGLLN   93 (112)
T ss_dssp             CCSSSSTTCEEEECSCCSSSCHHHHHHHHHHTTCEECSSCCSSCCEEEECSSCCSHHHHHHHH----HTCEEEEHHHHHH
T ss_pred             CCCCCcCCCEEEEeeeCCCCCHHHHHHHHHHcCCEEeccccCCeeEEEecCCCChHHHHHHHH----cCCeEEeHHHHHH
Confidence            445689999999999874 58999999999999999999999999999998877 89999998    5999999999999


Q ss_pred             hhhc
Q 017048          131 SVRR  134 (378)
Q Consensus       131 ci~~  134 (378)
                      .+..
T Consensus        94 ll~~   97 (112)
T 2ebu_A           94 LIRT   97 (112)
T ss_dssp             HHHH
T ss_pred             HHhh
Confidence            9864

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

Probab=99.06  E-value=1.2e-10  Score=97.33  Aligned_cols=82  Identities=13%  Similarity=0.289  Sum_probs=67.2

Q ss_pred             ccCccccccceeec-chhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEecccc---hhhhhc-------CCCCccch
Q 017048          195 SMNSTLSGCSMYVD-SDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDS---VQKYMG-------HSNNLVTP  263 (378)
Q Consensus       195 ~~~~lF~G~~fyl~-~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~s---~~~~l~-------~~~~IVt~  263 (378)
                      .+..+|.|+++||. .++...+++.+.++++++||+|++.  +++.+||||+++.+   +.+++.       .+.+||+.
T Consensus        16 ~p~~~F~g~~iy~v~~~~g~~R~~~l~~l~r~~G~~V~~~--ls~~VTHVVve~~~~~e~~~~l~~~~l~~~~~~~lv~i   93 (120)
T 2coe_A           16 PQDIKFQDLVVFILEKKMGTTRRALLMELARRKGFRVENE--LSDSVTHIVAENNSGSDVLEWLQAQKVQVSSQPELLDV   93 (120)
T ss_dssp             SSCCSCTTCEEEEECTTTCHHHHHHHHHHHHHHTCEECSS--CCTTCCEEEESSCCHHHHHHHHHHCCCCCSSCCEEEEH
T ss_pred             CcccccCCeEEEEeecccchHHHHHHHHHHHHcCCEEeec--cCCCcCEEEecCCCHHHHHHHHhccccccccccEEeec
Confidence            34789999999993 4677778899999999999999999  59999999997533   333322       36899999


Q ss_pred             hhHHhhhhHhhhhhH
Q 017048          264 VWVLKTAKEKHVQRL  278 (378)
Q Consensus       264 ~WI~dcik~~~~qr~  278 (378)
                      .|+.+|+++|.+++.
T Consensus        94 ~Wl~esmk~g~lv~e  108 (120)
T 2coe_A           94 SWLIECIGAGKPVEM  108 (120)
T ss_dssp             HHHHHHHHTTSCCCC
T ss_pred             HHHHHHHHcCCccCc
Confidence            999999999987653

>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=99.04  E-value=8.2e-11  Score=96.53  Aligned_cols=91  Identities=22%  Similarity=0.303  Sum_probs=69.0

Q ss_pred             CCCCccceEEEEc--ccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCchhhHhhhhc----CCCceEEEEeeh
Q 017048           54 ANAPFSGLVICVT--GLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHG----SRNGLYIVTLGW  127 (378)
Q Consensus        54 ~~~~F~g~~I~vs--G~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~Ky~~A~k~~----~~~gi~IV~~~W  127 (378)
                      +..+|+|++|++-  +.....++-....+..+||++...++..+||+|+.+..  .+...+++.    ...+++||+++|
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 AEEWLSSLRAHVVRTGIGRARAELFEKQIVQHGGQLCPAQGPGVTHIVVDEGM--DYERALRLLRLPQLPPGAQLVKSAW   85 (106)
T ss_dssp             GGGCGGGSCCCBCTTTCCSSSTTHHHHHHHHTTCCCCSTTCTTCCEEEECSSS--CHHHHHHHTTCSSCCSSCEEEEHHH
T ss_pred             CcCEeCCeEEEEEecCCchHHHHHHHHHHHHcCCEEeeccCCCccEEEEcCCC--CHHHHHHHHhhcccCCCcEEecCch
Confidence            5779999999984  33233444556688899999999999999999996432  233333321    225679999999


Q ss_pred             hhhhhhcccccccceeeee
Q 017048          128 FVDSVRRNVRLSESLYTVK  146 (378)
Q Consensus       128 l~dci~~g~~l~e~~Y~~~  146 (378)
                      +.||++.|+++||+.|.+.
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            9999999999999999753

>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=99.04  E-value=3.7e-11  Score=98.64  Aligned_cols=84  Identities=15%  Similarity=0.218  Sum_probs=64.7

Q ss_pred             cCccccccceeecc-hhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEecc-c---chhhh-----hcCCCCccchhh
Q 017048          196 MNSTLSGCSMYVDS-DVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEE-D---SVQKY-----MGHSNNLVTPVW  265 (378)
Q Consensus       196 ~~~lF~G~~fyl~~-gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~-~---s~~~~-----l~~~~~IVt~~W  265 (378)
                      ++.+|+||+|||.+ +.....++.....++.+||++++.  +++++||||+++ .   ...++     +...++||+++|
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            47899999999942 443345666777999999999999  588999999984 2   22222     234668999999


Q ss_pred             HHhhhhHhhhhhHHhh
Q 017048          266 VLKTAKEKHVQRLVHI  281 (378)
Q Consensus       266 I~dcik~~~~qr~~~~  281 (378)
                      +.||++++.+++.-+|
T Consensus        86 v~dci~~~~llde~~y  101 (106)
T 2jw5_A           86 LSLCLQERRLVDVAGF  101 (106)
T ss_dssp             HHHHHHTCSCCCGGGT
T ss_pred             HHHHHhcCcccCcccc
Confidence            9999999998876555

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

Probab=99.02  E-value=1e-10  Score=110.28  Aligned_cols=95  Identities=12%  Similarity=0.121  Sum_probs=52.0

Q ss_pred             CCCCCccceEEEEcccC-HHHHHHHHHHHHHhcCccCCCCCCccceEEEeeecC--chhhHhhhh--cCC-------Cce
Q 017048           53 PANAPFSGLVICVTGLS-KEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGG--RKFEHALKH--GSR-------NGL  120 (378)
Q Consensus        53 ~~~~~F~g~~I~vsG~~-~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~--~Ky~~A~k~--~~~-------~gi  120 (378)
                      .+..+|+||+|+++|+. ...+..++.+|..+||+++.+++..+||+|+.....  .+...+++.  ..+       .++
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            46779999999999975 445566788999999999999987777777743221  222112211  001       244


Q ss_pred             -EEEEeehhhhhhhcccccccceeeeec
Q 017048          121 -YIVTLGWFVDSVRRNVRLSESLYTVKS  147 (378)
Q Consensus       121 -~IV~~~Wl~dci~~g~~l~e~~Y~~~~  147 (378)
                       +||+++||.||++.|+++||+.|.+.+
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             999999999999999999999997654

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

Probab=98.96  E-value=1.7e-10  Score=95.63  Aligned_cols=78  Identities=17%  Similarity=0.277  Sum_probs=68.1

Q ss_pred             CCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeee---cCchhhHhhhhcCCCceEEEEeehhhhh
Q 017048           55 NAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSF---GGRKFEHALKHGSRNGLYIVTLGWFVDS  131 (378)
Q Consensus        55 ~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~---~~~Ky~~A~k~~~~~gi~IV~~~Wl~dc  131 (378)
                      ..+|.|++|++||.....|.+++++|+.+||+++..++.+|+|||++..   .+.|+.+|.+    .||+||+.+||.++
T Consensus         8 ~~~l~G~~~ViTG~l~~~R~e~k~~ie~~Ggkv~~sVskkT~~lV~g~~~e~~gsKl~kA~~----lgI~IvsE~~l~~~   83 (113)
T 2cok_A            8 DKPLSNMKILTLGKLSRNKDEVKAMIEKLGGKLTGTANKASLCISTKKEVEKMNKKMEEVKE----ANIRVVSEDFLQDV   83 (113)
T ss_dssp             CCSSSSCEEEECSCCSSCHHHHHHHHHHTTCEEESCSTTCSEEECCHHHHHHCCHHHHHHHH----TTCCEECTHHHHHH
T ss_pred             CCCcCCCEEEEEecCCCCHHHHHHHHHHCCCEEcCccccCccEEEECCCCCCCChHHHHHHH----CCCcEEeHHHHHHH
Confidence            5679999999999765589999999999999999999999999999843   6789999987    69999999997776


Q ss_pred             hhccc
Q 017048          132 VRRNV  136 (378)
Q Consensus       132 i~~g~  136 (378)
                      ...+.
T Consensus        84 ~~~~~   88 (113)
T 2cok_A           84 SASTK   88 (113)
T ss_dssp             HSCCS
T ss_pred             Hhhch
Confidence            65443

>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=98.94  E-value=2.9e-10  Score=89.91  Aligned_cols=76  Identities=13%  Similarity=0.201  Sum_probs=61.7

Q ss_pred             CCCCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCCCC-CccceEEEeeecCchhhHhhhhcCCCceEEEEeehhhhh
Q 017048           53 PANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLH-PQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDS  131 (378)
Q Consensus        53 ~~~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt-~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~dc  131 (378)
                      .-+.+|.|++|++.+-.+.. ..|+++|.++||.+....+ .++||+|+...         +   ..+..+|+|+||+||
T Consensus        12 ~LpdiFsg~~~~l~~~v~~~-~~l~RyiiAfgG~v~~~~~~~~vTHvI~~~~---------~---~~~~~~V~p~WI~dc   78 (88)
T 3pc7_A           12 VLLDIFTGVRLYLPPSTPDF-SRLRRYFVAFDGDLVQEFDMTSATHVLGSRD---------K---NPAAQQVSPEWIWAC   78 (88)
T ss_dssp             CCCCCSTTCEECCCTTSTTH-HHHHHHHHHTTCEECCGGGGGGCSEEESCCT---------T---CTTSEEECHHHHHHH
T ss_pred             cCChhhcCeEEEccCCcCch-hhheeeeeecCCEEecccCCCcCeEEecCCC---------c---CCCCcEEchHHHHHH
Confidence            35789999999996543322 6789999999999988777 48999997552         1   257889999999999


Q ss_pred             hhcccccccc
Q 017048          132 VRRNVRLSES  141 (378)
Q Consensus       132 i~~g~~l~e~  141 (378)
                      ++++++|+++
T Consensus        79 I~k~~Ll~~~   88 (88)
T 3pc7_A           79 IRKRRLVAPS   88 (88)
T ss_dssp             HHHTSCCSCC
T ss_pred             HhCCcccCCC
Confidence            9999999753

>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=98.92  E-value=2.8e-10  Score=103.41  Aligned_cols=82  Identities=17%  Similarity=0.274  Sum_probs=68.0

Q ss_pred             CCCCccce-EEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCchhhHhhhhcCCCceEEEEeehhhhhh
Q 017048           54 ANAPFSGL-VICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSV  132 (378)
Q Consensus        54 ~~~~F~g~-~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci  132 (378)
                      ..++|+|+ ++|++++....++.|+.+|+.+||++..++. .++++|+. ...     +.    ..++++|+|+||+||+
T Consensus       116 ~~~LF~g~~~~~v~~~~~~~~~~L~~lI~~~GG~v~~~~~-~~~iiI~~-~~~-----~~----~~~~~~V~p~Wi~DsI  184 (199)
T 3u3z_A          116 RGTLFADQPVMFVSPASSPPVAKLCELVHLCGGRVSQVPR-QASIVIGP-YSG-----KK----KATVKYLSEKWVLDSI  184 (199)
T ss_dssp             CCCTTTTSCCEEECTTCSSCHHHHHHHHHHTTCCBCSSGG-GCSEEESC-CCS-----CC----CTTCEEECHHHHHHHH
T ss_pred             cchhhCCCeEEEECCCCCCCHHHHHHHHHHcCCEEeccCC-CCEEEEeC-Cch-----hc----cCCCcEEChhHHHHHH
Confidence            46899999 6888998777788999999999999999984 56666653 211     22    2689999999999999


Q ss_pred             hcccccccceeeee
Q 017048          133 RRNVRLSESLYTVK  146 (378)
Q Consensus       133 ~~g~~l~e~~Y~~~  146 (378)
                      .+++.+|+++|.+.
T Consensus       185 ~~~~llp~~~Y~~~  198 (199)
T 3u3z_A          185 TQHKVCAPENYLLS  198 (199)
T ss_dssp             HHTSCCCGGGGBCC
T ss_pred             HcCCcCChHhccCC
Confidence            99999999999764

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

Probab=98.87  E-value=6e-09  Score=87.07  Aligned_cols=90  Identities=17%  Similarity=0.264  Sum_probs=70.6

Q ss_pred             CCCCCccceEEEEccc--CHHHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCchhhHhhhhc------CCCceEEEE
Q 017048           53 PANAPFSGLVICVTGL--SKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHG------SRNGLYIVT  124 (378)
Q Consensus        53 ~~~~~F~g~~I~vsG~--~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~Ky~~A~k~~------~~~gi~IV~  124 (378)
                      ++...|.|++|++-.+  ...-++-+.+++..+||++.+.+++.+||+|+.+.   ....+.+|.      ...+.+||+
T Consensus        16 ~p~~~F~g~~iy~v~~~~g~~R~~~l~~l~r~~G~~V~~~ls~~VTHVVve~~---~~~e~~~~l~~~~l~~~~~~~lv~   92 (120)
T 2coe_A           16 PQDIKFQDLVVFILEKKMGTTRRALLMELARRKGFRVENELSDSVTHIVAENN---SGSDVLEWLQAQKVQVSSQPELLD   92 (120)
T ss_dssp             SSCCSCTTCEEEEECTTTCHHHHHHHHHHHHHHTCEECSSCCTTCCEEEESSC---CHHHHHHHHHHCCCCCSSCCEEEE
T ss_pred             CcccccCCeEEEEeecccchHHHHHHHHHHHHcCCEEeeccCCCcCEEEecCC---CHHHHHHHHhccccccccccEEee
Confidence            5678999999999654  45677788999999999999999999999999533   222222221      123689999


Q ss_pred             eehhhhhhhcccccccceeee
Q 017048          125 LGWFVDSVRRNVRLSESLYTV  145 (378)
Q Consensus       125 ~~Wl~dci~~g~~l~e~~Y~~  145 (378)
                      .+||.||+++|+++||+.|..
T Consensus        93 i~Wl~esmk~g~lv~ee~~~~  113 (120)
T 2coe_A           93 VSWLIECIGAGKPVEMTGKHQ  113 (120)
T ss_dssp             HHHHHHHHHTTSCCCCSSSSB
T ss_pred             cHHHHHHHHcCCccCcccceE
Confidence            999999999999999866654

>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=98.86  E-value=1.1e-09  Score=99.51  Aligned_cols=90  Identities=22%  Similarity=0.275  Sum_probs=69.2

Q ss_pred             CCCCccceEEEEcc-cCHHHHHHHHHHHHHhcCccCCCCCCc----cce-EEEeeecC----chhhH-hhhhcCCCceEE
Q 017048           54 ANAPFSGLVICVTG-LSKEARKQVMEATERLGGQYSPDLHPQ----CTH-LVVQSFGG----RKFEH-ALKHGSRNGLYI  122 (378)
Q Consensus        54 ~~~~F~g~~I~vsG-~~~~~r~~L~~lI~~~GG~~~~~lt~~----~TH-LI~~~~~~----~Ky~~-A~k~~~~~gi~I  122 (378)
                      ..++|.|+.||++| +....+..|+.+|+.+||++...+...    .+| +|+..++.    .++.. |.    ..+++|
T Consensus       112 ~~~lF~g~~~~~~~~~~~~~~~~l~~li~~~GG~v~~~~~~~~~~~~~~~ivi~~~~~~~~~~~~~~~a~----~~~~~i  187 (214)
T 1t15_A          112 DRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTLGTGVHPIVVVQPDAWTEDNGFHAIGQ----MCEAPV  187 (214)
T ss_dssp             TSCTTTTCEEEECSCCSSSCHHHHHHHHHHTTCEECCSGGGCCCSTTCCEEEEECGGGCSSCGGGGSSTT----TCSSCE
T ss_pred             CCcccCCCEEEEEecCCCCCHHHHHHHHHHCCCEEecCccccccCCCCccEEEECCCcccchhhHHHHHH----hcCCcE
Confidence            56799999999987 555678899999999999999987642    224 55544322    13332 22    368999


Q ss_pred             EEeehhhhhhhcccccccceeeeec
Q 017048          123 VTLGWFVDSVRRNVRLSESLYTVKS  147 (378)
Q Consensus       123 V~~~Wl~dci~~g~~l~e~~Y~~~~  147 (378)
                      |+++||.||+.+++.+|++.|.+..
T Consensus       188 V~~~Wi~dsi~~~~~l~~~~Y~l~~  212 (214)
T 1t15_A          188 VTREWVLDSVALYQCQELDTYLIPQ  212 (214)
T ss_dssp             EEHHHHHHHHHHTSCCCSGGGBCCC
T ss_pred             EeccHHHHhHhhcCcCCCcceeecc
Confidence            9999999999999999999998753

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

Probab=98.84  E-value=2.1e-09  Score=99.06  Aligned_cols=135  Identities=10%  Similarity=0.029  Sum_probs=93.6

Q ss_pred             CccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEeccc-chhhh---hcCCCCccchhhHHhhhhH
Q 017048          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED-SVQKY---MGHSNNLVTPVWVLKTAKE  272 (378)
Q Consensus       197 ~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~-s~~~~---l~~~~~IVt~~WI~dcik~  272 (378)
                      ...+.|+.|.+ +||++.+++.+.++|+.+||++++.   ..++||+|+... ...+|   ++.++.||+++||.+|+++
T Consensus        11 ~~~~~~~~i~~-SG~~~~~~~~l~~~i~~lGg~v~~~---~~~~THLI~~~~~rT~K~l~A~~~g~~IVs~~Wl~~c~~~   86 (219)
T 3sqd_A           11 LTPELTPFVLF-TGFEPVQVQQYIKKLYILGGEVAES---AQKCTHLIASKVTRTVKFLTAISVVKHIVTPEWLEECFRC   86 (219)
T ss_dssp             CCGGGCCEEEE-CSCCHHHHHHHHHHHHHTTCEECSS---GGGCSEEECSSCCCCHHHHHHTTTCSEEECHHHHHHHHHH
T ss_pred             cCCCCCeEEEE-eCCChHHHHHHHHHHHHCCCEEeCC---CCCceEEEECCCCCCHHHHHHHHcCCCEecHHHHHHHHHc
Confidence            35578999999 7999888889999999999999988   389999999862 22334   5688999999999999999


Q ss_pred             hhhhhHHhhhH-h--HHHHHhH----HHHhh--hccchhhhhcCCCCCCCchhhhhhccHHHHHHHHHhhhhhhccchhh
Q 017048          273 KHVQRLVHISA-D--LARQVGM----MLENI--QNGIAREEINGGNVPEDAQSCKNKISQEKRQQTVNLAKNGVRSRRSR  343 (378)
Q Consensus       273 ~~~qr~~~~s~-d--l~~~~~~----~le~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~  343 (378)
                      +.+.+.-.|.. |  .....+.    .+...  .....+..+.-        ++....+.++-++||+++.+.|-.+.+.
T Consensus        87 ~~~l~e~~y~l~d~~~e~~~~~~l~~~l~ra~~~~LF~G~~f~i--------t~~~~~~~~~l~~lI~~~GG~v~~~~p~  158 (219)
T 3sqd_A           87 QKFIDEQNYILRDAEAEVLFSFSLEESLKRAHVSPLFKAKYFYI--------TPGICPSLSTMKAIVECAGGKVLSKQPS  158 (219)
T ss_dssp             TSCCCSGGGBCCCHHHHHHTTCCHHHHHHHHHHSCTTTTEEEEE--------CTTCSSCHHHHHHHHHHTTCEEESSCCC
T ss_pred             CCCCChHhccCCCchhhhhcCCChHHHhhhhccccccCCcEEEE--------eCCCCCCHHHHHHHHHHCCCEEECCCCc
Confidence            98876666532 1  1111111    11111  12222222111        2223346789999999999999888764

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

Probab=98.82  E-value=1.5e-09  Score=99.84  Aligned_cols=91  Identities=15%  Similarity=0.175  Sum_probs=63.0

Q ss_pred             CCCccceEEEEcc-cCHHHHHHHHHHHHHhcCccCCCCCCc-----cceEEEeee----cCchhhHhhhhcCCCceEEEE
Q 017048           55 NAPFSGLVICVTG-LSKEARKQVMEATERLGGQYSPDLHPQ-----CTHLVVQSF----GGRKFEHALKHGSRNGLYIVT  124 (378)
Q Consensus        55 ~~~F~g~~I~vsG-~~~~~r~~L~~lI~~~GG~~~~~lt~~-----~THLI~~~~----~~~Ky~~A~k~~~~~gi~IV~  124 (378)
                      .++|.|+.|+++| +....+..|..+|+.+||++...+...     ++|+|+..+    ...++..+.+   ..+++||+
T Consensus       115 ~~lF~g~~~~~~~~~~~~~~~~l~~li~~~GG~v~~~~~~~~~~~~~~~~vvv~~~~~~~~~~~~~l~~---~~~i~iVs  191 (229)
T 1l0b_A          115 EKLFEGLQIYCCEPFTNMPKDELERMLQLCGASVVKELPLLTRDTGAHPIVLVQPSAWTEDNDCPDIGQ---LCKGRLVM  191 (229)
T ss_dssp             --CCTTCEEEECSCCSSSCHHHHHHHHHHTTCEEECSSSCGGGCCSSCCEEEEC----------------------CEEE
T ss_pred             hhhhcCceEEEEecCCCCCHHHHHHHHHHCCCEEeCCcccccccCCCceEEEEcCCccchhhhHHHHHH---HcCCeEee
Confidence            4799999999977 555678899999999999999998752     578655443    2344443322   36899999


Q ss_pred             eehhhhhhhcccccccceeeeecc
Q 017048          125 LGWFVDSVRRNVRLSESLYTVKSI  148 (378)
Q Consensus       125 ~~Wl~dci~~g~~l~e~~Y~~~~~  148 (378)
                      ++||+||+.+++.++++.|.+...
T Consensus       192 ~~WlldsI~~~~~~~~~~Y~l~~~  215 (229)
T 1l0b_A          192 WDWVLDSISVYRCRDLDAYLVQNI  215 (229)
T ss_dssp             THHHHHHHHTTSCCCGGGGBCC--
T ss_pred             hhHHHHHHhcCCcCCccceEcccc
Confidence            999999999999999999988753

>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=98.72  E-value=8.3e-09  Score=93.87  Aligned_cols=133  Identities=14%  Similarity=0.058  Sum_probs=88.7

Q ss_pred             ccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEeccc---chhhh---hcCCCCccchhhHHhhhhHhhh
Q 017048          202 GCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED---SVQKY---MGHSNNLVTPVWVLKTAKEKHV  275 (378)
Q Consensus       202 G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~---s~~~~---l~~~~~IVt~~WI~dcik~~~~  275 (378)
                      |+.|++ +|+++++++.|.++++.+||++++.  .+.++||||+..+   ...+|   +..++.||+++||.+|++++.+
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            566777 8999889999999999999999998  5889999999762   23344   4578999999999999999998


Q ss_pred             hhHHhhhHhHHHHHhHHHHhhhccchhhhhc-CCCCCCCchhhhhhccHHHHHHHHHhhhhhhccchhh
Q 017048          276 QRLVHISADLARQVGMMLENIQNGIAREEIN-GGNVPEDAQSCKNKISQEKRQQTVNLAKNGVRSRRSR  343 (378)
Q Consensus       276 qr~~~~s~dl~~~~~~~le~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~  343 (378)
                      .+.-+|...-....+.+-.  +.  ....++ |..+--..  +-.+.+.++-+++|+++++.|..+.+.
T Consensus        79 ~~e~~y~~~~~~~~~r~~~--~~--~~~~lF~g~~~~l~~--~~~~~~~~~l~~lI~~~GG~v~~~~p~  141 (210)
T 2nte_A           79 EQEEKYEIPEGPRRSRLNR--EQ--LLPKLFDGCYFYLWG--TFKHHPKDNLIKLVTAGGGQILSRKPK  141 (210)
T ss_dssp             CCGGGTBCTTHHHHHHHHH--HT--TCCCTTTTCEEEECS--CCSSSCHHHHHHHHHHTTCEEESSCCC
T ss_pred             CChhhccCCCCChhhhhcc--cc--ccccccCceEEEEec--cCCCCCHHHHHHHHHHCCCEEEecCCC
Confidence            7766664321111111111  00  001122 22211100  112245778899999999988876654

>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=98.65  E-value=1.7e-08  Score=85.19  Aligned_cols=79  Identities=16%  Similarity=0.270  Sum_probs=64.5

Q ss_pred             Cccccccceeec-chhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEecccc---hhhhh-------c---CCCCccc
Q 017048          197 NSTLSGCSMYVD-SDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDS---VQKYM-------G---HSNNLVT  262 (378)
Q Consensus       197 ~~lF~G~~fyl~-~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~s---~~~~l-------~---~~~~IVt  262 (378)
                      ...|.|+++||- .+....+++.|.++++..|+++.+.  +.+.|||||++..+   +.+|+       .   .++++|+
T Consensus         8 ~~~F~~v~iyive~kmG~sRr~fL~~la~~kGf~v~~~--~S~~VTHVV~E~~s~~~~~~~L~~~~~~l~~~~~~~~lLd   85 (133)
T 2dun_A            8 STRFPGVAIYLVEPRMGRSRRAFLTGLARSKGFRVLDA--CSSEATHVVMEETSAEEAVSWQERRMAAAPPGCTPPALLD   85 (133)
T ss_dssp             SCSEEEEEEEECHHHHCSHHHHHHHHHHHHHTEEECSS--CCTTCCEEEESSCCHHHHHHHHHHHHHHSCTTCCCCEEEE
T ss_pred             ccccCccEEEEecCCcCHHHHHHHHHHHHhcCCEeccc--cCCCceEEEecCCCHHHHHHHHHHhhcccCcCCCCcEEec
Confidence            578999999992 2444568999999999999999999  69999999998743   34444       1   4578999


Q ss_pred             hhhHHhhhhHhhhhh
Q 017048          263 PVWVLKTAKEKHVQR  277 (378)
Q Consensus       263 ~~WI~dcik~~~~qr  277 (378)
                      ..|+.+|+++|.+..
T Consensus        86 isWltecm~~g~pV~  100 (133)
T 2dun_A           86 ISWLTESLGAGQPVP  100 (133)
T ss_dssp             HHHHHHHHHHTSCCC
T ss_pred             cHHHHHHHhcCCcCC
Confidence            999999999997644

>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=98.60  E-value=2.8e-08  Score=92.52  Aligned_cols=82  Identities=9%  Similarity=0.079  Sum_probs=66.0

Q ss_pred             cccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEeccc-chhhh---hcCCCCccchhhHHhhhhHhh
Q 017048          199 TLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED-SVQKY---MGHSNNLVTPVWVLKTAKEKH  274 (378)
Q Consensus       199 lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~-s~~~~---l~~~~~IVt~~WI~dcik~~~  274 (378)
                      .-.+.+|.+ +|+++++++.+.++|+.+||+++++...+.+|||||+... ...+|   ++.++.||+++||.+|+++|.
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            346778888 7888888889999999999999863114789999999973 34455   568999999999999999999


Q ss_pred             hhhHHhh
Q 017048          275 VQRLVHI  281 (378)
Q Consensus       275 ~qr~~~~  281 (378)
                      +.+.-+|
T Consensus        85 ~l~E~~y   91 (235)
T 3al2_A           85 FVQEEDY   91 (235)
T ss_dssp             CCCSGGG
T ss_pred             CCChhce
Confidence            8776555

>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=98.59  E-value=1.3e-08  Score=100.75  Aligned_cols=83  Identities=16%  Similarity=0.208  Sum_probs=65.7

Q ss_pred             CccccccceeecchhhH----HHHHHHHHHHhhccceeeeeeeeccCCceEEecccchhhh---hcC-CCCccchhhHHh
Q 017048          197 NSTLSGCSMYVDSDVSE----ELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKY---MGH-SNNLVTPVWVLK  268 (378)
Q Consensus       197 ~~lF~G~~fyl~~gfs~----~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~s~~~~---l~~-~~~IVt~~WI~d  268 (378)
                      ..+|+||+|+| +|+-+    ..+..+.++++.+||++++.  ++.++||||+......++   ... +++||++.||++
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            57899999999 55532    23567999999999999999  689999999987433333   344 789999999999


Q ss_pred             hhhHhhhhhHHhhh
Q 017048          269 TAKEKHVQRLVHIS  282 (378)
Q Consensus       269 cik~~~~qr~~~~s  282 (378)
                      |++.+...+.-.|.
T Consensus       357 c~~~~~~vdE~~Y~  370 (372)
T 3ef0_A          357 SLSQWKRLPESDYL  370 (372)
T ss_dssp             HHHTTSCCCGGGGB
T ss_pred             HHHhCCcCChhhce
Confidence            99988777665553

>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=98.59  E-value=2.2e-08  Score=94.51  Aligned_cols=82  Identities=10%  Similarity=0.223  Sum_probs=63.3

Q ss_pred             CccccccceeecchhhHH-----------------------------HHHHHHHHHhhccceeeeeeeecc------CCc
Q 017048          197 NSTLSGCSMYVDSDVSEE-----------------------------LRNKVFEAATNEGATLVNQWFVGC------GAS  241 (378)
Q Consensus       197 ~~lF~G~~fyl~~gfs~~-----------------------------~~~~L~~lI~~~GG~vv~~~~~~~------~vT  241 (378)
                      ..+|.|+.|++ ++...+                             .+..|+++|+.+||++++++  ..      .+|
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            68999999999 444322                             34689999999999999884  32      258


Q ss_pred             eEEecc-cchhhh---hcCCCCccchhhHHhhhhHhhhhhHHhh
Q 017048          242 YVVCEE-DSVQKY---MGHSNNLVTPVWVLKTAKEKHVQRLVHI  281 (378)
Q Consensus       242 HVV~~~-~s~~~~---l~~~~~IVt~~WI~dcik~~~~qr~~~~  281 (378)
                      |+|++. ....+|   ++.++.||++.||.||++++.+.++-+|
T Consensus        90 ~LIa~~~~rt~K~l~ala~g~~iVs~~Wl~dc~~~~~~l~~~~Y  133 (259)
T 1kzy_C           90 LLIADQHCRTRKYFLCLASGIPCVSHVWVHDSCHANQLQNYRNY  133 (259)
T ss_dssp             EEEESSCCCSHHHHHHHHHTCCEEETHHHHHHHHHTSCCCGGGS
T ss_pred             EEEcCCCCCcHHHHHHHhcCCCCccHHHHHHHHHcCCcCCHHHc
Confidence            999987 223344   4689999999999999999988776655

>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=98.58  E-value=5.7e-08  Score=81.94  Aligned_cols=90  Identities=13%  Similarity=0.208  Sum_probs=71.9

Q ss_pred             CCCCCccceEEEEccc--CHHHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCchhhHhhhhc---------CCCceE
Q 017048           53 PANAPFSGLVICVTGL--SKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHG---------SRNGLY  121 (378)
Q Consensus        53 ~~~~~F~g~~I~vsG~--~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~Ky~~A~k~~---------~~~gi~  121 (378)
                      .....|.|++|++-..  ...-++-|.+++..+|+.+.+.+++.+||+|+.+.+   +..+++|.         ...+..
T Consensus         6 ~~~~~F~~v~iyive~kmG~sRr~fL~~la~~kGf~v~~~~S~~VTHVV~E~~s---~~~~~~~L~~~~~~l~~~~~~~~   82 (133)
T 2dun_A            6 SGSTRFPGVAIYLVEPRMGRSRRAFLTGLARSKGFRVLDACSSEATHVVMEETS---AEEAVSWQERRMAAAPPGCTPPA   82 (133)
T ss_dssp             CSSCSEEEEEEEECHHHHCSHHHHHHHHHHHHHTEEECSSCCTTCCEEEESSCC---HHHHHHHHHHHHHHSCTTCCCCE
T ss_pred             CCccccCccEEEEecCCcCHHHHHHHHHHHHhcCCEeccccCCCceEEEecCCC---HHHHHHHHHHhhcccCcCCCCcE
Confidence            3568899999999765  346788999999999999999999999999994332   33344332         235789


Q ss_pred             EEEeehhhhhhhcccccccceeee
Q 017048          122 IVTLGWFVDSVRRNVRLSESLYTV  145 (378)
Q Consensus       122 IV~~~Wl~dci~~g~~l~e~~Y~~  145 (378)
                      +|+..||.+|++.|+.+|++.|..
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            999999999999999999855543

>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=98.57  E-value=2.4e-08  Score=91.00  Aligned_cols=90  Identities=17%  Similarity=0.243  Sum_probs=71.3

Q ss_pred             CCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCc--cceEEEee-ecCchhhHhhhhcCCCceEEEEeehhhhh
Q 017048           55 NAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQ--CTHLVVQS-FGGRKFEHALKHGSRNGLYIVTLGWFVDS  131 (378)
Q Consensus        55 ~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~--~THLI~~~-~~~~Ky~~A~k~~~~~gi~IV~~~Wl~dc  131 (378)
                      .++|+|+.|++++.....+..|..+|+.+||++...+.+.  .+|+|... .+..++..+.+    .+++||+++||++|
T Consensus       113 ~~lF~g~~~~~~~~~~~~~~~l~~li~~~GG~v~~~~~~~~~~~~ivI~~~~d~~~~~~~~~----~~i~vvs~eWi~~s  188 (209)
T 2etx_A          113 RRLLEGYEIYVTPGVQPPPPQMGEIISCCGGTYLPSMPRSYKPQRVVITCPQDFPHCSIPLR----VGLPLLSPEFLLTG  188 (209)
T ss_dssp             SCTTTTCEEEECTTCSSCHHHHHHHHHHTTCEECSSCCCSCCTTEEEECCGGGGGGCHHHHH----HTCCEECTHHHHHH
T ss_pred             CCCcCCcEEEEeCCCCCCHHHHHHHHHHCCCEEECCCCCCCCCceEEEECcccHHHHHHHHH----CCCeEEcHHHHHHH
Confidence            3899999999998866667899999999999999887643  25666643 34455666665    58999999999999


Q ss_pred             hhcccccccceeeeeccC
Q 017048          132 VRRNVRLSESLYTVKSID  149 (378)
Q Consensus       132 i~~g~~l~e~~Y~~~~~~  149 (378)
                      +..++ ++++.|.+..+.
T Consensus       189 I~~q~-ld~e~y~l~~~~  205 (209)
T 2etx_A          189 VLKQE-AKPEAFVLSPLE  205 (209)
T ss_dssp             HHHTC-CCGGGGBCCTTC
T ss_pred             HHhcc-cChHHheecCCC
Confidence            99866 599999887643

>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=98.56  E-value=1.9e-08  Score=94.01  Aligned_cols=83  Identities=14%  Similarity=0.213  Sum_probs=63.3

Q ss_pred             ccccccceeecch--hhHHHHHHHHHHHhhccceeeeee----e-ecc-------------------CCceEEeccc-ch
Q 017048          198 STLSGCSMYVDSD--VSEELRNKVFEAATNEGATLVNQW----F-VGC-------------------GASYVVCEED-SV  250 (378)
Q Consensus       198 ~lF~G~~fyl~~g--fs~~~~~~L~~lI~~~GG~vv~~~----~-~~~-------------------~vTHVV~~~~-s~  250 (378)
                      .+|+|+.|+|...  +++..+..|+++|+.+||++++..    | ...                   ..||+|++.. ..
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            3799999999544  456678889999999999999861    1 111                   2499999863 23


Q ss_pred             hhh---hcCCCCccchhhHHhhhhHhhhhhHHh
Q 017048          251 QKY---MGHSNNLVTPVWVLKTAKEKHVQRLVH  280 (378)
Q Consensus       251 ~~~---l~~~~~IVt~~WI~dcik~~~~qr~~~  280 (378)
                      .+|   ++.++.||++.||.||++++.+++.-.
T Consensus        81 ~K~~~ala~gipiV~~~Wi~dc~~~~~~~~~~~  113 (241)
T 2vxb_A           81 VKYLEALAFNIPCVHPQFIKQCLKMNRVVDFSP  113 (241)
T ss_dssp             HHHHHHHHHTCCEECTHHHHHHHHHTSCCCSGG
T ss_pred             HHHHHHHHcCCCEecHHHHHHHHHcCCcCChhh
Confidence            344   568999999999999999998766543

>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=98.45  E-value=3.5e-08  Score=99.39  Aligned_cols=82  Identities=16%  Similarity=0.215  Sum_probs=65.0

Q ss_pred             CccccccceeecchhhHH----HHHHHHHHHhhccceeeeeeeeccCCceEEecccchhhh---hcC-CCCccchhhHHh
Q 017048          197 NSTLSGCSMYVDSDVSEE----LRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKY---MGH-SNNLVTPVWVLK  268 (378)
Q Consensus       197 ~~lF~G~~fyl~~gfs~~----~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~s~~~~---l~~-~~~IVt~~WI~d  268 (378)
                      ..+|.||+|+| +|+-+.    .+..+.++++.+||++...  ++..+||||+......++   ... +++||++.||++
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            56899999999 565321    3567999999999999999  699999999987433333   333 689999999999


Q ss_pred             hhhHhhhhhHHhh
Q 017048          269 TAKEKHVQRLVHI  281 (378)
Q Consensus       269 cik~~~~qr~~~~  281 (378)
                      |++.+...+.-.|
T Consensus       427 cl~~~krldE~~Y  439 (442)
T 3ef1_A          427 SLSQWKRLPESDY  439 (442)
T ss_dssp             HHHHTSCCCGGGT
T ss_pred             HHHcCCcCChhcc
Confidence            9999877665544

>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=98.36  E-value=8.8e-08  Score=88.27  Aligned_cols=124  Identities=8%  Similarity=0.044  Sum_probs=82.7

Q ss_pred             cccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEeccc-chhhh---hcCCCCccchhhHHhhhhHhhhh
Q 017048          201 SGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED-SVQKY---MGHSNNLVTPVWVLKTAKEKHVQ  276 (378)
Q Consensus       201 ~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~-s~~~~---l~~~~~IVt~~WI~dcik~~~~q  276 (378)
                      .+..|.| +|+++.+   ..++|+.+||.+++.   .+++||+|++.. ...+|   ++.++.||+++||.+|++++.+.
T Consensus         7 ~~~~v~f-SG~~~~~---~~~~i~~lGg~v~~~---~~~~THlV~~~~~RT~K~l~Aia~g~~IVs~~Wl~~~~~~~~~l   79 (220)
T 3l41_A            7 KRVYITF-TGYDKKP---SIDNLKKLDMSITSN---PSKCTHLIAPRILRTSKFLCSIPYGPCVVTMDWINSCLKTHEIV   79 (220)
T ss_dssp             CCEEEEE-CSCSSCC---CCGGGGGGTEEECSC---TTTCSEEECSSCCCBHHHHHHGGGCCEEECHHHHHHHHHHTSCC
T ss_pred             ceEEEEE-eccCCCC---CcchHhhcceeeccC---chhhhhhhhhhHhhhcceeecCCCCCeEEEhHHHHhhhhhhhcc
Confidence            4567777 6887643   388999999999998   357999999862 23444   57899999999999999999887


Q ss_pred             hHHhhhH---hHHHHHhHHHHh--------hhccchhhhhcCCCCCCCchhhhh--hccHHHHHHHHHhhhhhhcc
Q 017048          277 RLVHISA---DLARQVGMMLEN--------IQNGIAREEINGGNVPEDAQSCKN--KISQEKRQQTVNLAKNGVRS  339 (378)
Q Consensus       277 r~~~~s~---dl~~~~~~~le~--------~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~a~~~~~~  339 (378)
                      +.-+|..   +.....+.-|+.        -.....+..+.-        ++..  ..+.++-++||++|.+.|-.
T Consensus        80 ~e~~y~l~d~~~e~~~~~~l~~~~~rar~~~~~LF~G~~f~i--------t~~~~~~p~~~~l~~iI~~~GG~v~~  147 (220)
T 3l41_A           80 DEEPYLLNDPEKELELGCTLESALKRARAQGPSLLEDYVVYL--------TSKTVAPENVPAVISIVKSNGGVCST  147 (220)
T ss_dssp             CSGGGBCCCHHHHHHHTSCHHHHHHHHHHHCSCTTTTSEEEE--------ETTSSCGGGHHHHHHHHHHTTCEEEE
T ss_pred             ccCccccCCcHHHhhccccHHHHHHHHHhcCchhhhheeEEE--------eccccCCCCCceEEEEEecCCcEech
Confidence            7766632   122222221211        112222211111        2222  35678999999999999988

>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=98.27  E-value=8.9e-07  Score=70.53  Aligned_cols=73  Identities=19%  Similarity=0.255  Sum_probs=61.3

Q ss_pred             CccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEeccc---chhhhhcCCCCccchhhHHhhhhH
Q 017048          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED---SVQKYMGHSNNLVTPVWVLKTAKE  272 (378)
Q Consensus       197 ~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~---s~~~~l~~~~~IVt~~WI~dcik~  272 (378)
                      ...|.|.+|+|...++. .|+.++.+|+.+||++.++  +..+++|||+.+.   .+++....+++||+.+|+++++..
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            45799999999555655 7899999999999999999  7999999999873   334445679999999999999864

>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=98.14  E-value=3e-07  Score=97.00  Aligned_cols=77  Identities=26%  Similarity=0.332  Sum_probs=0.0

Q ss_pred             CCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCchhhHhhhhcCCCceEEEEeehhhhhhhc
Q 017048           55 NAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVRR  134 (378)
Q Consensus        55 ~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci~~  134 (378)
                      ..+|.|.+|++||.....|.+++++|+.+||+++.+++++|++||++...|.|+.+|.+    .||+|++.+|+.+.+..
T Consensus       585 ~~~l~G~~~v~TG~l~~~R~e~~~~i~~~Ggkv~~sVSkkTd~lV~G~~~gsKl~KA~~----lgI~Ii~E~~f~~~l~~  660 (667)
T 1dgs_A          585 SDLLSGLTFVLTGELSRPREEVKALLGRLGAKVTDSVSRKTSYLVVGENPGSKLEKARA----LGVAVLTEEEFWRFLKE  660 (667)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccccCCCEEEEeCCCCCCHHHHHHHHHHcCCEEcCcccCCeeEEEECCCCChHHHHHHH----CCCeEEeHHHHHHHHhc
Confidence            45799999999998655999999999999999999999999999999999999999997    69999999999999865


Q ss_pred             c
Q 017048          135 N  135 (378)
Q Consensus       135 g  135 (378)
                      +
T Consensus       661 ~  661 (667)
T 1dgs_A          661 K  661 (667)
T ss_dssp             -
T ss_pred             C
Confidence            4

>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=98.12  E-value=1.7e-06  Score=80.22  Aligned_cols=170  Identities=13%  Similarity=0.174  Sum_probs=110.8

Q ss_pred             cceEEEEcccC-H----HHHHHHHHHHHHhcCccCCCCC--CccceEEEeee-cCchhhHhhhhcCCCceEEEEeehhhh
Q 017048           59 SGLVICVTGLS-K----EARKQVMEATERLGGQYSPDLH--PQCTHLVVQSF-GGRKFEHALKHGSRNGLYIVTLGWFVD  130 (378)
Q Consensus        59 ~g~~I~vsG~~-~----~~r~~L~~lI~~~GG~~~~~lt--~~~THLI~~~~-~~~Ky~~A~k~~~~~gi~IV~~~Wl~d  130 (378)
                      -.+.+++||+. .    .++    +....+|=.+.++.+  ..|+||||... .+.||..|+.++  .--.||+|+||.+
T Consensus        21 ~~i~ai~TGc~~~~~~~~D~----~~Lr~LGI~Iv~d~~~~~~~n~LiAPkilRT~KFL~sLa~~--P~~~il~p~FI~~   94 (256)
T 3t7k_A           21 YDLKAVCTGCFHDGFNEVDI----EILNQLGIKIFDNIKETDKLNCIFAPKILRTEKFLKSLSFE--PLKFALKPEFIID   94 (256)
T ss_dssp             CCEEEEESSSCSSCCCHHHH----HHHHHTTEEECSSCCGGGCCCEEECSSCCCBHHHHHHTTST--TCCEEECTHHHHH
T ss_pred             eeEEEEecCCcccccCHHHH----HHHHHcCeEEEecCcccCCCCEEEcCchhhHHHHHHHhccC--ccceEeCHHHHHH
Confidence            56888999987 2    333    455677988999986  48999999775 899999999742  1236999999999


Q ss_pred             hhhc---cc------ccccceeeeeccCccCcccccccccccccCCCccccccchhhhhhhhccCCCccccccccCcccc
Q 017048          131 SVRR---NV------RLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLS  201 (378)
Q Consensus       131 ci~~---g~------~l~e~~Y~~~~~~~~~~~~d~~~~l~~~s~~e~s~lp~~i~E~~~s~~~e~~~~~~~~~~~~lF~  201 (378)
                      |++.   ++      .++.++|.+.+...                           |.-        ++  ....+.+|+
T Consensus        95 ~Lk~ih~~~~~~~~~~l~~~dY~L~d~~~---------------------------E~l--------~r--~~~~gkLf~  137 (256)
T 3t7k_A           95 LLKQIHSKKDKLSQININLFDYEINGINE---------------------------SII--------SK--TKLPTKVFE  137 (256)
T ss_dssp             HHHHHC-------CCCCCSSTTBCTTCCH---------------------------HHH--------HH--TTSSSCHHH
T ss_pred             HHHHhhcCCcccccccCChhhccCCCcch---------------------------hHH--------hh--hcccccccc
Confidence            9988   76      66677777644211                           100        00  112478999


Q ss_pred             ccceee---cchhhHHHHHHHHHHHhhccceeeeee----eec--------------cCCceEEecc-c-chhhh---h-
Q 017048          202 GCSMYV---DSDVSEELRNKVFEAATNEGATLVNQW----FVG--------------CGASYVVCEE-D-SVQKY---M-  254 (378)
Q Consensus       202 G~~fyl---~~gfs~~~~~~L~~lI~~~GG~vv~~~----~~~--------------~~vTHVV~~~-~-s~~~~---l-  254 (378)
                      |+.||.   ..++..- .+.++.+++++||.=+...    +..              ....||++.. + ..++|   + 
T Consensus       138 ~~~I~ciNls~dI~GG-~e~issIleahG~~~~~~l~~~~~~~~dl~~n~~~~~~~~~~~~~ILia~K~~q~k~Fkk~~~  216 (256)
T 3t7k_A          138 RANIRCINLVNDIPGG-VDTIGSVLKAHGIEKINVLRSKKCTFEDIIPNDVSKQENGGIFKYVLIVTKASQVKKFTKLIN  216 (256)
T ss_dssp             HTTCCEEEEETTCTTC-HHHHHHHHHHTTCCEEEEECTTTCCGGGCCCCC--------CCSEEEECSCHHHHHHHHHHHH
T ss_pred             CCcceeeeeccCCCCC-HHHHHHHHHHcCCceeeecccccccHHHhhhccccccccCCCCCEEEEEccHHHHHHHHHHhh
Confidence            995554   6555432 4568999999999644321    111              1234655543 2 23344   2 


Q ss_pred             --c--CCCCccchhhHHhhhhH
Q 017048          255 --G--HSNNLVTPVWVLKTAKE  272 (378)
Q Consensus       255 --~--~~~~IVt~~WI~dcik~  272 (378)
                        .  ...-+|.=.|..+||-.
T Consensus       217 ~~~~n~~~lvveWdWCVksIF~  238 (256)
T 3t7k_A          217 DRDKNETILIVEWNWCVESIFH  238 (256)
T ss_dssp             HHSTTSCEEEECHHHHHHHHHT
T ss_pred             cccccceEEEEEcHHHHHHHhh
Confidence              1  34568899999999865

>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli}

Probab=98.05  E-value=5.7e-07  Score=94.90  Aligned_cols=75  Identities=16%  Similarity=0.300  Sum_probs=0.0

Q ss_pred             CCCccceEEEEcccCH-HHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCchhhHhhhhcCCCceEEEEeehhhhhhh
Q 017048           55 NAPFSGLVICVTGLSK-EARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVR  133 (378)
Q Consensus        55 ~~~F~g~~I~vsG~~~-~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci~  133 (378)
                      ..+|.|.+|++||... -.|.+++++|+.+||+++.+++++|++||++...|.|+++|.+    .||+|++.+|+.+.+.
T Consensus       595 ~~~l~G~~~v~TG~l~~~~R~e~~~~i~~~Ggkv~~sVSkkTd~lV~G~~~gsKl~KA~~----lgI~Ii~E~~f~~~l~  670 (671)
T 2owo_A          595 DSPFAGKTVVLTGSLSQMSRDDAKARLVELGAKVAGSVSKKTDLVIAGEAAGSKLAKAQE----LGIEVIDEAEMLRLLG  670 (671)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CCcccCcEEEEcCCCCCCCHHHHHHHHHHcCCEEeCcccCceeEEEECCCCChHHHHHHH----CCCcEEcHHHHHHHhc
Confidence            4579999999999875 4899999999999999999999999999999999999999997    6999999999988763

>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=97.90  E-value=6e-06  Score=67.76  Aligned_cols=75  Identities=15%  Similarity=0.190  Sum_probs=60.5

Q ss_pred             CccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEecccc----hhhhhcCCCCccchhhHHhhhhH
Q 017048          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDS----VQKYMGHSNNLVTPVWVLKTAKE  272 (378)
Q Consensus       197 ~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~s----~~~~l~~~~~IVt~~WI~dcik~  272 (378)
                      ...|.|.+|+|...++.-.|+.++++|+.+||++.++  +..+++|||+.+..    +++....++.||+.+|+++.+..
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            3569999999955554435788999999999999999  79999999998732    23334568999999999999865


Q ss_pred             h
Q 017048          273 K  273 (378)
Q Consensus       273 ~  273 (378)
                      +
T Consensus       108 ~  108 (109)
T 2k6g_A          108 L  108 (109)
T ss_dssp             T
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=97.82  E-value=1.1e-05  Score=66.60  Aligned_cols=74  Identities=9%  Similarity=0.156  Sum_probs=59.4

Q ss_pred             CccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEeccc------chhhhhcCCCCccchhhHHhhh
Q 017048          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED------SVQKYMGHSNNLVTPVWVLKTA  270 (378)
Q Consensus       197 ~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~------s~~~~l~~~~~IVt~~WI~dci  270 (378)
                      ...|.|++|.|...++. .|+.++++|+.+||++.++  +..+++|||+..+      .+++....+++||+.+||.++.
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            45699999999666765 6888999999999999999  7899999999831      2344455789999999977766


Q ss_pred             hHh
Q 017048          271 KEK  273 (378)
Q Consensus       271 k~~  273 (378)
                      ..+
T Consensus        85 ~~~   87 (113)
T 2cok_A           85 AST   87 (113)
T ss_dssp             SCC
T ss_pred             hhc
Confidence            543

>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=97.78  E-value=4.9e-05  Score=72.96  Aligned_cols=171  Identities=14%  Similarity=0.020  Sum_probs=98.3

Q ss_pred             ccceEEEEcccCHHHHHHHHHHHHHhcCccCCCC-CCccceEEEeeecCch----hhHhhhhcCCCceEEEEeehhhhhh
Q 017048           58 FSGLVICVTGLSKEARKQVMEATERLGGQYSPDL-HPQCTHLVVQSFGGRK----FEHALKHGSRNGLYIVTLGWFVDSV  132 (378)
Q Consensus        58 F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~l-t~~~THLI~~~~~~~K----y~~A~k~~~~~gi~IV~~~Wl~dci  132 (378)
                      +.-+++|++  +.+.+.+|.+.++.+||.+. +. +..|||||.....+.|    ...|+-    .|.+||+++||.+..
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            455666773  33467779999999999999 55 6789999997555555    667764    699999999999876


Q ss_pred             hccc--------ccccceeeeeccCccCcccccccccccccCCCccccccchhhhhhhhccCCCccccccccCccccccc
Q 017048          133 RRNV--------RLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYEAKQFNATGKHERDSNRSMNSTLSGCS  204 (378)
Q Consensus       133 ~~g~--------~l~e~~Y~~~~~~~~~~~~d~~~~l~~~s~~e~s~lp~~i~E~~~s~~~e~~~~~~~~~~~~lF~G~~  204 (378)
                      ...+        +-+..+|.+.-.                .+.|++-.                   +.+.--.-|+|++
T Consensus       186 ~~e~~~~~~~~~wPdp~dflP~i~----------------~g~Ep~~~-------------------~~~~~~~~~~~~~  230 (325)
T 3huf_A          186 TVKESVIEDASLMPDALECFKNII----------------KNNDQFPS-------------------SPEDCINSLEGFS  230 (325)
T ss_dssp             TCTTCCCCTTSSHHHHHHHHHHHH----------------TTCTTCCS-------------------CHHHHTTTTTTCE
T ss_pred             HhhhhhhhcccCCCChHHcCCCCC----------------CCCCCCCC-------------------CHHHhhcccCceE
Confidence            4321        111222322200                00011100                   0011134689998


Q ss_pred             eeecchhhHHHHHHHHHHHhhccceeeeeee-------eccCCceEEeccc---chhhhhcCCCCccchhhHHhhhhHhh
Q 017048          205 MYVDSDVSEELRNKVFEAATNEGATLVNQWF-------VGCGASYVVCEED---SVQKYMGHSNNLVTPVWVLKTAKEKH  274 (378)
Q Consensus       205 fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~-------~~~~vTHVV~~~~---s~~~~l~~~~~IVt~~WI~dcik~~~  274 (378)
                      +++..|..     .+.-+++..|=.+..-+.       +.+..++||...+   +-+--...++...+.+=+++-+-+.+
T Consensus       231 ~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  305 (325)
T 3huf_A          231 CAMLNTSS-----ESHHLLELLGLRISTFMSLGDIDKELISKTDFVVLNNAVYDSEKISFPEGIFCLTIEQLWKIIIERN  305 (325)
T ss_dssp             EEEETCCH-----HHHHHHHHTTCEEEEEC------CCSSSSCSEEEEC-------------CCCEEEHHHHHHHHHSSS
T ss_pred             EEEEcCch-----hhhHHHHHhcceeeeeeecccchHhhhccccEEEEcccccccccccCCcceEEEEHHHHHHHHhhcc
Confidence            88844443     256677888877765321       2356677777652   21111345666777777776666544


Q ss_pred             h
Q 017048          275 V  275 (378)
Q Consensus       275 ~  275 (378)
                      -
T Consensus       306 ~  306 (325)
T 3huf_A          306 S  306 (325)
T ss_dssp             S
T ss_pred             h
Confidence            3

>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=97.77  E-value=1.4e-05  Score=65.93  Aligned_cols=74  Identities=15%  Similarity=0.197  Sum_probs=60.1

Q ss_pred             CccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEecccc----hhhhhcCCCCccchhhHHhhhhH
Q 017048          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDS----VQKYMGHSNNLVTPVWVLKTAKE  272 (378)
Q Consensus       197 ~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~s----~~~~l~~~~~IVt~~WI~dcik~  272 (378)
                      ...|.|.+|+|...++.-.|+.++++|+.+||++.++  +..+++|||+....    +++....++.|++.+|+++.+..
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            3569999999955554435788999999999999999  79999999998732    33444568999999999999864

>2l42_A DNA-binding protein RAP1; BRCT domain, protein binding; NMR {Saccharomyces cerevisiae}

Probab=97.56  E-value=5e-05  Score=60.40  Aligned_cols=81  Identities=12%  Similarity=0.190  Sum_probs=59.7

Q ss_pred             cCccccccceeecchh----hHHHHHHHHHHHhhccceeeeeeeeccCCceEEecccchhhhhcCCCCccchhhHHhhhh
Q 017048          196 MNSTLSGCSMYVDSDV----SEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAK  271 (378)
Q Consensus       196 ~~~lF~G~~fyl~~gf----s~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~s~~~~l~~~~~IVt~~WI~dcik  271 (378)
                      ....|+|..|||..+-    +....+.|+++|+.+||+|+..+|..+.-.+.|+++     |-......|+|.+|.+|+.
T Consensus         8 ~~~vF~g~~Fyin~d~~a~ds~~d~d~L~~lI~~nGG~Vl~~lP~~s~~~~yVVSp-----yN~t~LpTVtpTYI~aC~~   82 (106)
T 2l42_A            8 SGPPLSNMKFYLNRDADAHDSLNDIDQLARLIRANGGEVLDSKPRESKENVFIVSP-----YNHTNLPTVTPTYIKACCQ   82 (106)
T ss_dssp             SSCSSCCCCBEECCSSSCSSCSSTHHHHHHHHHTTTSCCCEECCCCCSSCCCCBCT-----TCCCSSSBCCTTHHHHHHH
T ss_pred             cCccccCcEEEEcCCCccchhhhHHHHHHHHHHhcCcEEhhhCcccccCCeEEEeC-----CCCCCCccccHHHHHHHHh
Confidence            4678999999995431    123467899999999999999965333223444443     2234677999999999999


Q ss_pred             HhhhhhHHhh
Q 017048          272 EKHVQRLVHI  281 (378)
Q Consensus       272 ~~~~qr~~~~  281 (378)
                      .+.+.+.-+|
T Consensus        83 ~nTLLnv~~Y   92 (106)
T 2l42_A           83 SNSLLNMENY   92 (106)
T ss_dssp             STTSCGGGGC
T ss_pred             cCceeccccc
Confidence            9999887666

>2l42_A DNA-binding protein RAP1; BRCT domain, protein binding; NMR {Saccharomyces cerevisiae}

Probab=97.10  E-value=7e-05  Score=59.56  Aligned_cols=82  Identities=16%  Similarity=0.193  Sum_probs=64.1

Q ss_pred             CCCCccceEEEEcccC-----HHHHHHHHHHHHHhcCccCCCCCCcc--ceEEEeeecCchhhHhhhhcCCCceEEEEee
Q 017048           54 ANAPFSGLVICVTGLS-----KEARKQVMEATERLGGQYSPDLHPQC--THLVVQSFGGRKFEHALKHGSRNGLYIVTLG  126 (378)
Q Consensus        54 ~~~~F~g~~I~vsG~~-----~~~r~~L~~lI~~~GG~~~~~lt~~~--THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~  126 (378)
                      ...+|+|+.|.+.--+     -.+.++|+.+|..+||.+...+.++.  .+.|++....            .+++.|+|.
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            4567999999996432     24678899999999999999887433  3444433221            368899999


Q ss_pred             hhhhhhhcccccccceeeeec
Q 017048          127 WFVDSVRRNVRLSESLYTVKS  147 (378)
Q Consensus       127 Wl~dci~~g~~l~e~~Y~~~~  147 (378)
                      +|.+|+..+.+|+-..|.++.
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            999999999999999999865

>4gns_A Chitin biosynthesis protein CHS5; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=95.95  E-value=0.0035  Score=54.97  Aligned_cols=91  Identities=15%  Similarity=0.237  Sum_probs=66.0

Q ss_pred             CCCCCccceEEEEcccCH---HHHHHHHHHHHHhcCccCCC-CCCccceEEEeeecCchh----hHhhhhcCCCceEEEE
Q 017048           53 PANAPFSGLVICVTGLSK---EARKQVMEATERLGGQYSPD-LHPQCTHLVVQSFGGRKF----EHALKHGSRNGLYIVT  124 (378)
Q Consensus        53 ~~~~~F~g~~I~vsG~~~---~~r~~L~~lI~~~GG~~~~~-lt~~~THLI~~~~~~~Ky----~~A~k~~~~~gi~IV~  124 (378)
                      .+..-+.|+++|+.-+.+   -.--++.+.+...|+.-.+. +.-++||.||++.+.+.-    ..|..    ++|+||.
T Consensus       157 hkmtdmsgitvclgpldplkeisdlqisqclshigarplqrhvaidtthfvcndldneesneelirakh----nnipivr  232 (290)
T 4gns_A          157 HKMTDMSGITVCLGPLDPLKEISDLQISQCLSHIGARPLQRHVAIDTTHFVCNDLDNEESNEELIRAKH----NNIPIVR  232 (290)
T ss_dssp             CCTTCCTTCCEEECCCCGGGTCCHHHHHHHHHHTTCCCCBSSCCTTCCEEECSCCTTCTTCHHHHHHHH----TTCCEEC
T ss_pred             cccccccCceEEecCCChhhhhhhccHHHHHHHhCCchhhheeeeecceeeecCCCcccchHHHHhhhc----cCCCccC
Confidence            356678999999987764   23446788888889875444 446899999988754332    23332    7999999


Q ss_pred             eehhhhhhhcccccccceeeeec
Q 017048          125 LGWFVDSVRRNVRLSESLYTVKS  147 (378)
Q Consensus       125 ~~Wl~dci~~g~~l~e~~Y~~~~  147 (378)
                      |+|+-.|--..+.+.-.-|.+..
T Consensus       233 pewvracevekrivgvrgfylda  255 (290)
T 4gns_A          233 PEWVRACEVEKRIVGVRGFYLDA  255 (290)
T ss_dssp             THHHHHHHHTTSCCCSGGGBTTS
T ss_pred             HHHHHHHhhhheeeeeeeEEEcc
Confidence            99999998877777766665544

>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=95.42  E-value=0.0026  Score=67.18  Aligned_cols=74  Identities=24%  Similarity=0.287  Sum_probs=0.0

Q ss_pred             CccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEeccc---chhhhhcCCCCccchhhHHhhhhHh
Q 017048          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED---SVQKYMGHSNNLVTPVWVLKTAKEK  273 (378)
Q Consensus       197 ~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~---s~~~~l~~~~~IVt~~WI~dcik~~  273 (378)
                      ...|.|.+|.|...++. .|+.++.+|+.+||++.++  +..+++|||+...   .+++....++.|++.+|+++.+..+
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            45699999999656666 7899999999999999999  7999999999873   3344455789999999999999764

>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli}

Probab=94.56  E-value=0.0062  Score=64.30  Aligned_cols=73  Identities=15%  Similarity=0.197  Sum_probs=0.0

Q ss_pred             CccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEeccc---chhhhhcCCCCccchhhHHhhhh
Q 017048          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED---SVQKYMGHSNNLVTPVWVLKTAK  271 (378)
Q Consensus       197 ~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~---s~~~~l~~~~~IVt~~WI~dcik  271 (378)
                      ...|.|.+|.|...++.-.|+.++++|+.+||++.++  +..+++|||++..   .+++....++.|++.+|+++.+.
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            4569999999955565446888999999999999999  7999999999873   33444557899999999998763

>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=92.28  E-value=0.11  Score=49.75  Aligned_cols=87  Identities=7%  Similarity=0.005  Sum_probs=56.3

Q ss_pred             ccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEeccc---c----hhhhhcCCCCccchhhHHhhhhH
Q 017048          200 LSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED---S----VQKYMGHSNNLVTPVWVLKTAKE  272 (378)
Q Consensus       200 F~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~---s----~~~~l~~~~~IVt~~WI~dcik~  272 (378)
                      +....+++ ++  .+.+..|++.++..||.++ .| ..+.|||||+.+.   +    .-..+-.++.||++.|+.+..+.
T Consensus       113 W~P~Vl~~-Ss--ke~~~~L~~~L~~LGik~v-~~-~~detTHlVm~krnT~KvTvK~L~ALI~gkPIV~~~Fl~al~~~  187 (325)
T 3huf_A          113 WRSMCIQF-DN--PEMLSQWASNLNLLGIPTG-LR-DSDATTHFVMNRQAGSSITVGTMYAFLKKTVIIDDSYLQYLSTV  187 (325)
T ss_dssp             ECCCCEEE-SC--HHHHHHHHHHHHTTTCCEE-SS-CCTTCCEEECCCCCSSCCCHHHHHHHHTTCEEECHHHHHHHTTC
T ss_pred             EeeeEEEe-cC--HHHHHHHHHHHHHcCCEEE-Ec-cCCCEEEEEEeccccccchHHHHHHHHCCCcEecHHHHHHHHHh
Confidence            34455555 32  2345669999999999999 75 5777999999752   2    22225579999999999987642


Q ss_pred             h-h-hhhHHhhhHhHHHHHhHH
Q 017048          273 K-H-VQRLVHISADLARQVGMM  292 (378)
Q Consensus       273 ~-~-~qr~~~~s~dl~~~~~~~  292 (378)
                      . . ++. -.-.+|-..++|-.
T Consensus       188 e~~~~~~-~~~wPdp~dflP~i  208 (325)
T 3huf_A          188 KESVIED-ASLMPDALECFKNI  208 (325)
T ss_dssp             TTCCCCT-TSSHHHHHHHHHHH
T ss_pred             hhhhhhc-ccCCCChHHcCCCC
Confidence            1 1 111 12344556666654

>3qbz_A DDK kinase regulatory subunit DBF4; FHA domain,RAD53, replication checkpoint, cell cycle; 2.69A {Saccharomyces cerevisiae}

Probab=91.56  E-value=0.11  Score=44.68  Aligned_cols=66  Identities=12%  Similarity=0.047  Sum_probs=47.2

Q ss_pred             CCCcc-ceEEEEcccCHH-----HH-------HHHHHHHHHhcCccCCCCCCccceEEEeeecCc--------hhhHhhh
Q 017048           55 NAPFS-GLVICVTGLSKE-----AR-------KQVMEATERLGGQYSPDLHPQCTHLVVQSFGGR--------KFEHALK  113 (378)
Q Consensus        55 ~~~F~-g~~I~vsG~~~~-----~r-------~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~--------Ky~~A~k  113 (378)
                      .++|. +.+|+|-+.+++     .+       ..+++.+..+|+.+.+.++.++||+|+..+-..        -+..|.+
T Consensus        56 Rkifk~~~vfYFDt~~~~~~~~~~k~kl~K~~~llkr~f~~LGA~I~~FFd~~VTiVIT~R~i~~~~~~~~~Dil~~A~~  135 (160)
T 3qbz_A           56 KKIMKRDSRIYFDITDDVEMNTYNKSKMDKRRDLLKRGFLTLGAQITQFFDTTVTIVITRRSVENIYLLKDTDILSRAKK  135 (160)
T ss_dssp             HHHHHHHCEEEECCCCSSCCCHHHHHHHHHHHHHHHHHHHTTTCEEESSCCTTCCEEEESSCSSCGGGSCTTSHHHHHHH
T ss_pred             HHhCccCcEEEecCCChhhhhHHHHHHHHHHHHHHHHHHHHcCCEeeeeccCCeEEEEecCcCcccccCCchhHHHHHHH
Confidence            45788 899999876532     12       445678889999999999999999999776222        2445554


Q ss_pred             hcCCCceEEEE
Q 017048          114 HGSRNGLYIVT  124 (378)
Q Consensus       114 ~~~~~gi~IV~  124 (378)
                          .+++|=+
T Consensus       136 ----~~mKVW~  142 (160)
T 3qbz_A          136 ----NYMKVWS  142 (160)
T ss_dssp             ----TTCEEEE
T ss_pred             ----cCceecc
Confidence                5777733

>3oq4_A DBF4, protein DNA52; DDK, BRCT, RAD53, replication checkpoint, FHA domain, regula subunit of DDK, CDC7, phosphorylation, nuclear; 2.40A {Saccharomyces cerevisiae}

Probab=88.47  E-value=0.47  Score=39.69  Aligned_cols=54  Identities=15%  Similarity=0.070  Sum_probs=40.2

Q ss_pred             HHHHHHHHHHHhcCccCCCCCCccceEEEeeecC--------chhhHhhhhcCCCceEEEEeehhh
Q 017048           72 ARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGG--------RKFEHALKHGSRNGLYIVTLGWFV  129 (378)
Q Consensus        72 ~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~--------~Ky~~A~k~~~~~gi~IV~~~Wl~  129 (378)
                      .++.|++.+..+||++.+.++..+||+|+..+-.        +-+..|.+    .|++|=+.+=+.
T Consensus        31 ~~~llk~~f~~LGa~I~~FFd~~VTiiITrR~~~~~~~~p~~DIL~rAr~----~~mKIWs~EKl~   92 (134)
T 3oq4_A           31 RRDLLKRGFLTLGAQITQFFDTTVTIVITRRSVENIYLLKDTDILSRAKK----NYMKVWSYEKAA   92 (134)
T ss_dssp             HHHHHHHHHHHTTCEEESSCCTTCCEEEESSCGGGGGGSCTTSHHHHHHH----TTCEEEEHHHHH
T ss_pred             HHHHHHHHHHHcCCEEeeecCCceEEEEeCCcCcccccCCcchHHHHHHH----cCCeeeeHHHHH
Confidence            5678899999999999999999999999976522        22345555    588885544443

>3qbz_A DDK kinase regulatory subunit DBF4; FHA domain,RAD53, replication checkpoint, cell cycle; 2.69A {Saccharomyces cerevisiae}

Probab=86.95  E-value=0.3  Score=42.00  Aligned_cols=49  Identities=12%  Similarity=0.177  Sum_probs=36.1

Q ss_pred             Ccccc-ccceeecchhhH-----------HHHHHHHHHHhhccceeeeeeeeccCCceEEecc
Q 017048          197 NSTLS-GCSMYVDSDVSE-----------ELRNKVFEAATNEGATLVNQWFVGCGASYVVCEE  247 (378)
Q Consensus       197 ~~lF~-G~~fyl~~gfs~-----------~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~  247 (378)
                      -.+|. ++.||||+.-.+           ...+.|++.+...||+++.-  .+.+|||||+..
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            45787 899999643110           12244667788999999987  699999999986

>3oq0_A DBF4, protein DNA52; DDK, BRCT, RAD53, replication checkpoint, FHA domain, regula subunit of DDK, CDC7, phosphorylation, nuclear; 2.70A {Saccharomyces cerevisiae}

Probab=86.60  E-value=0.69  Score=39.43  Aligned_cols=74  Identities=14%  Similarity=0.065  Sum_probs=47.9

Q ss_pred             CCCCCc-cceEEEEccc--C----------HHHHHHHHHHHHHhcCccCCCCCCccceEEEeeecC--------chhhHh
Q 017048           53 PANAPF-SGLVICVTGL--S----------KEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGG--------RKFEHA  111 (378)
Q Consensus        53 ~~~~~F-~g~~I~vsG~--~----------~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~--------~Ky~~A  111 (378)
                      .=.+|+ ++-+|+|-.-  .          +..++.|++.+..+||++.+.++..+||+|+..+-.        +-+..|
T Consensus        16 ~WrkIM~r~s~iYFdt~~~~~~~~~~~~~l~k~~~llkk~f~~LGa~I~~FFd~~VTiIITrR~~~~~~~yp~~DIL~rA   95 (151)
T 3oq0_A           16 PRGSHMKRDSRIYFDITDDVEMNTYNKSKMDKRRDLLKRGFLTLGAQITQFFDTTVTIVITRRSVENIYLLKDTDILSRA   95 (151)
T ss_dssp             -----CCCCCEEEECCCCSSCCCHHHHHHHHHHHHHHHHHHHHHTCEEESSCCTTCCEEEESSCGGGGGGSCTTSHHHHH
T ss_pred             cHHHHhccCCEEEEeCCCcchhhHHHHHHHHHHHHHHHHHHHHcCCEEeeecCCceEEEEeCCcCcccccCCcchHHHHH
Confidence            345677 7778888532  2          124466788999999999999999999999976522        223455


Q ss_pred             hhhcCCCceEEEEeehhhh
Q 017048          112 LKHGSRNGLYIVTLGWFVD  130 (378)
Q Consensus       112 ~k~~~~~gi~IV~~~Wl~d  130 (378)
                      .+    .+++|=+.+=+..
T Consensus        96 r~----~~mKIWs~EKl~R  110 (151)
T 3oq0_A           96 KK----NYMKVWSYEKAAR  110 (151)
T ss_dssp             HH----TTCEEEEHHHHHH
T ss_pred             HH----cCCeeecHHHHHH
Confidence            55    6888855544443

>3oq0_A DBF4, protein DNA52; DDK, BRCT, RAD53, replication checkpoint, FHA domain, regula subunit of DDK, CDC7, phosphorylation, nuclear; 2.70A {Saccharomyces cerevisiae}

Probab=85.22  E-value=1.2  Score=37.98  Aligned_cols=48  Identities=15%  Similarity=0.224  Sum_probs=34.9

Q ss_pred             ccc-cccceeecch-h---h-------HHHHHHHHHHHhhccceeeeeeeeccCCceEEecc
Q 017048          198 STL-SGCSMYVDSD-V---S-------EELRNKVFEAATNEGATLVNQWFVGCGASYVVCEE  247 (378)
Q Consensus       198 ~lF-~G~~fyl~~g-f---s-------~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~  247 (378)
                      .+. ....||||.. .   +       +..++.|++.+...||+|+.-  ++.+|||||+..
T Consensus        19 kIM~r~s~iYFdt~~~~~~~~~~~~~l~k~~~llkk~f~~LGa~I~~F--Fd~~VTiIITrR   78 (151)
T 3oq0_A           19 SHMKRDSRIYFDITDDVEMNTYNKSKMDKRRDLLKRGFLTLGAQITQF--FDTTVTIVITRR   78 (151)
T ss_dssp             --CCCCCEEEECCCCSSCCCHHHHHHHHHHHHHHHHHHHHHTCEEESS--CCTTCCEEEESS
T ss_pred             HHhccCCEEEEeCCCcchhhHHHHHHHHHHHHHHHHHHHHcCCEEeee--cCCceEEEEeCC
Confidence            344 6678899743 1   1       123466778899999999986  699999999986

>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=80.37  E-value=1  Score=41.73  Aligned_cols=52  Identities=10%  Similarity=0.174  Sum_probs=39.3

Q ss_pred             HHHhhccceeeeeeeeccCCceEEecc-cchhhh---hcCCCC--ccchhhHHhhhhH
Q 017048          221 EAATNEGATLVNQWFVGCGASYVVCEE-DSVQKY---MGHSNN--LVTPVWVLKTAKE  272 (378)
Q Consensus       221 ~lI~~~GG~vv~~~~~~~~vTHVV~~~-~s~~~~---l~~~~~--IVt~~WI~dcik~  272 (378)
                      +.++..|=++++..-....++|++.+. -...+|   ++.++.  |++|.||.+|++.
T Consensus        41 ~~Lr~LGI~Iv~d~~~~~~~n~LiAPkilRT~KFL~sLa~~P~~~il~p~FI~~~Lk~   98 (256)
T 3t7k_A           41 EILNQLGIKIFDNIKETDKLNCIFAPKILRTEKFLKSLSFEPLKFALKPEFIIDLLKQ   98 (256)
T ss_dssp             HHHHHTTEEECSSCCGGGCCCEEECSSCCCBHHHHHHTTSTTCCEEECTHHHHHHHHH
T ss_pred             HHHHHcCeEEEecCcccCCCCEEEcCchhhHHHHHHHhccCccceEeCHHHHHHHHHH
Confidence            456788999998720125899999998 344555   566665  9999999999988

---

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	378
d1t15a1	109	c.15.1.3 (A:1649-1757) Breast cancer associated pr	2e-16
d1wf6a_	132	c.15.1.5 (A:) DNA topoisomerase II binding protein	7e-14
d1cdza_	96	c.15.1.1 (A:) DNA-repair protein XRCC1 {Human (Hom	2e-13
d1t15a2	102	c.15.1.3 (A:1758-1859) Breast cancer associated pr	5e-11
d1l7ba_	92	c.15.1.2 (A:) NAD+-dependent DNA ligase, domain 4	1e-07
d1in1a_	88	c.15.1.2 (A:) DNA ligase III alpha {Human (Homo sa	1e-04
d1kzyc1	153	c.15.1.4 (C:1714-1866) 53BP1 {Human (Homo sapiens)	0.004

>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 = 72.0 bits (176), Expect = 2e-16
 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 = 66.0 bits (160), Expect = 7e-14
 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 = 63.6 bits (154), Expect = 2e-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 = 57.1 bits (137), Expect = 5e-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 = 47.0 bits (112), Expect = 1e-07
 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 = 38.4 bits (89), Expect = 1e-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

>d1kzyc1 c.15.1.4 (C:1714-1866) 53BP1 {Human (Homo sapiens) [TaxId: 9606]} Length = 153

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: 53BP1
domain: 53BP1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.4 bits (81), Expect = 0.004
 Identities = 15/96 (15%), Positives = 28/96 (29%), Gaps = 14/96 (14%)

Query: 68  LSKEARKQVMEATERLGGQYSPDLHP------QCTHLVVQSFG-GRKFEHALKHGSRNGL 120
           +    ++          G    D +           L+       RK+   L  G    +
Sbjct: 55  IPPFNKQYTESQLRAGAGYILEDFNEAQCNTAYQCLLIADQHCRTRKYFLCLASG----I 110

Query: 121 YIVTLGWFVDSVRRNVRLSESLYTV---KSIDEHGM 153
             V+  W  DS   N   +   Y +    S++E  +
Sbjct: 111 PCVSHVWVHDSCHANQLQNYRNYLLPAGYSLEEQRI 146

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	378
d1cdza_	96	DNA-repair protein XRCC1 {Human (Homo sapiens) [Ta	99.73
d1wf6a_	132	DNA topoisomerase II binding protein 1, TopBP1 {Hu	99.73
d1t15a1	109	Breast cancer associated protein, BRCA1 {Human (Ho	99.7
d1t15a2	102	Breast cancer associated protein, BRCA1 {Human (Ho	99.61
d1wf6a_	132	DNA topoisomerase II binding protein 1, TopBP1 {Hu	99.49
d1cdza_	96	DNA-repair protein XRCC1 {Human (Homo sapiens) [Ta	99.46
d1in1a_	88	DNA ligase III alpha {Human (Homo sapiens) [TaxId:	99.38
d1l7ba_	92	NAD+-dependent DNA ligase, domain 4 {Thermus therm	99.29
d1in1a_	88	DNA ligase III alpha {Human (Homo sapiens) [TaxId:	99.22
d1t15a2	102	Breast cancer associated protein, BRCA1 {Human (Ho	99.18
d1kzyc1	153	53BP1 {Human (Homo sapiens) [TaxId: 9606]}	99.17
d1t15a1	109	Breast cancer associated protein, BRCA1 {Human (Ho	99.01
d1l7ba_	92	NAD+-dependent DNA ligase, domain 4 {Thermus therm	98.22
d1l0ba2	97	Breast cancer associated protein, BRCA1 {Rat (Ratt	98.0
d1l0ba2	97	Breast cancer associated protein, BRCA1 {Rat (Ratt	97.88
d1kzyc1	153	53BP1 {Human (Homo sapiens) [TaxId: 9606]}	97.82
d1kzyc2	106	53BP1 {Human (Homo sapiens) [TaxId: 9606]}	97.05
d1kzyc2	106	53BP1 {Human (Homo sapiens) [TaxId: 9606]}	96.4

>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=99.73  E-value=1.1e-18  Score=138.10  Aligned_cols=90  Identities=18%  Similarity=0.304  Sum_probs=82.5

Q ss_pred             CCCccceEEEEcc-cCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCchhhHhhhhcCCCceEEEEeehhhhhhh
Q 017048           55 NAPFSGLVICVTG-LSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVR  133 (378)
Q Consensus        55 ~~~F~g~~I~vsG-~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci~  133 (378)
                      +.+|+|++||++| ++..++..|+++|..+||++...++.++||+|+....+.++..+..+  ..+++||+|+||.||++
T Consensus         3 pd~F~g~~f~v~g~~~~~~~~~l~~~i~~~GG~v~~~~~~~~THvI~~~~~~~~~~~~~~~--~~~i~iV~~~Wl~dc~~   80 (96)
T d1cdza_           3 PDFFQGKHFFLYGEFPGDERRKLIRYVTAFNGELEDYMSDRVQFVITAQEWDPSFEEALMD--NPSLAFVRPRWIYSCNE   80 (96)
T ss_dssp             CCTTTTCEEEECSCCCTHHHHHHHHHHHHTTCEECSSCSTTCSEEECSSCCCHHHHHHHTT--CTTCEEECTHHHHHHHT
T ss_pred             ccccCCcEEEEeCCCCHHHHHHHHHHHHHhCCEEeccCCCCceEEEEccCCcceeeehhhh--CCCCeEEEEhHHHHHHH
Confidence            4689999999998 78889999999999999999999999999999988888888888764  36899999999999999


Q ss_pred             cccccccceeeee
Q 017048          134 RNVRLSESLYTVK  146 (378)
Q Consensus       134 ~g~~l~e~~Y~~~  146 (378)
                      +++++|+++|.+.
T Consensus        81 ~~~~lp~~~Y~i~   93 (96)
T d1cdza_          81 KQKLLPHQLYGVV   93 (96)
T ss_dssp             TTSCCCGGGGBCC
T ss_pred             cCCcCCchhcEec
Confidence            9999999999874

>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=99.73  E-value=1.4e-18  Score=146.36  Aligned_cols=94  Identities=18%  Similarity=0.254  Sum_probs=83.3

Q ss_pred             CCCCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCchhhHhhhhcCCCceEEEEeehhhhhh
Q 017048           53 PANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSV  132 (378)
Q Consensus        53 ~~~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci  132 (378)
                      .+..+|.||+|+++||+..++..|.++|..+||++...++.+|||||+....+.++..+...  .++++||+++||+||+
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            35568999999999999999999999999999999999999999999988887777654332  3689999999999999


Q ss_pred             hcccccccceeeeecc
Q 017048          133 RRNVRLSESLYTVKSI  148 (378)
Q Consensus       133 ~~g~~l~e~~Y~~~~~  148 (378)
                      ++++++|++.|.+..+
T Consensus       114 ~~~~~l~~~~Y~~~~P  129 (132)
T d1wf6a_         114 SKGYMLSEEPYIHSGP  129 (132)
T ss_dssp             HHSSCCCSGGGBCCCS
T ss_pred             HcCCcCCHHhCcCCCC
Confidence            9999999999998653

>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=99.70  E-value=1e-17  Score=136.34  Aligned_cols=86  Identities=19%  Similarity=0.274  Sum_probs=78.3

Q ss_pred             eEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeee------cCchhhHhhhhcCCCceEEEEeehhhhhhhc
Q 017048           61 LVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSF------GGRKFEHALKHGSRNGLYIVTLGWFVDSVRR  134 (378)
Q Consensus        61 ~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~------~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci~~  134 (378)
                      ++|++||+++.++..|.+++..+||+|+..++++|||||+...      .+.||..|+.    +|++||+++||.||++.
T Consensus         2 ~~i~~SGl~~~e~~~l~~~i~~~Gg~~~~~~~~~~THlI~~~~~~~~~~rt~K~l~a~~----~g~~IV~~~Wl~~c~~~   77 (109)
T d1t15a1           2 MSMVVSGLTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIA----GGKWVVSYFWVTQSIKE   77 (109)
T ss_dssp             CEEEEESCCHHHHHHHHHHHHHHTCEECSSCCTTCCEEEECBCTTSEECCBHHHHHHHH----TTCEEEETHHHHHHHHT
T ss_pred             EEEEECCCCHHHHHHHHHHHHHcCCEEEeEecCCccEEEEecCcchhhHhhHHHHHHHH----CCCccccHHHHHHHHHh
Confidence            5899999999999999999999999999999999999999754      3568888887    59999999999999999


Q ss_pred             ccccccceeeeeccCc
Q 017048          135 NVRLSESLYTVKSIDE  150 (378)
Q Consensus       135 g~~l~e~~Y~~~~~~~  150 (378)
                      ++++||.+|++.....
T Consensus        78 ~~~l~e~~y~v~~~~~   93 (109)
T d1t15a1          78 RKMLNEHDFEVRGDVV   93 (109)
T ss_dssp             TSCCCGGGGBCCEETT
T ss_pred             CCcCCchheEEecccC
Confidence            9999999999876543

>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=99.61  E-value=8.5e-17  Score=127.86  Aligned_cols=88  Identities=20%  Similarity=0.217  Sum_probs=73.4

Q ss_pred             CCccceEEEEcc-cCHHHHHHHHHHHHHhcCccCCCCC-----CccceEEEeeecCc-----hhhHhhhhcCCCceEEEE
Q 017048           56 APFSGLVICVTG-LSKEARKQVMEATERLGGQYSPDLH-----PQCTHLVVQSFGGR-----KFEHALKHGSRNGLYIVT  124 (378)
Q Consensus        56 ~~F~g~~I~vsG-~~~~~r~~L~~lI~~~GG~~~~~lt-----~~~THLI~~~~~~~-----Ky~~A~k~~~~~gi~IV~  124 (378)
                      ++|+|+.||++| +++.++++|+++|+.+||+++..+.     ..+||+++......     ++..|.    .++++||+
T Consensus         2 kiF~g~~i~~~g~~~~~~~~~L~~li~~~GG~v~~~~~~~~~~~~~t~~~i~~~~~~~~~~~~~~~~~----~~~i~iV~   77 (102)
T d1t15a2           2 KIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTLGTGVHPIVVVQPDAWTEDNGFHAIGQ----MCEAPVVT   77 (102)
T ss_dssp             CTTTTCEEEECSCCSSSCHHHHHHHHHHTTCEECCSGGGCCCSTTCCEEEEECGGGCSSCGGGGSSTT----TCSSCEEE
T ss_pred             CCCCCcEEEEeCCCCCcCHHHHHHHHHHhCCEEeeccccccccccccchheecccccchhhHHHHHHH----hCCCcEEe
Confidence            689999999999 6778889999999999999987653     36789988765433     333333    36999999


Q ss_pred             eehhhhhhhcccccccceeeeec
Q 017048          125 LGWFVDSVRRNVRLSESLYTVKS  147 (378)
Q Consensus       125 ~~Wl~dci~~g~~l~e~~Y~~~~  147 (378)
                      ++||+||+.+++++|+++|.+..
T Consensus        78 ~~Wl~dsi~~~~~lp~~~Yll~~  100 (102)
T d1t15a2          78 REWVLDSVALYQCQELDTYLIPQ  100 (102)
T ss_dssp             HHHHHHHHHHTSCCCSGGGBCCC
T ss_pred             eHHHHHHHHhCCcCCchhccCCC
Confidence            99999999999999999998764

>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=99.49  E-value=1e-14  Score=122.20  Aligned_cols=87  Identities=16%  Similarity=0.270  Sum_probs=73.1

Q ss_pred             ccccCccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEecccchh--hh---hcCCCCccchhhHH
Q 017048          193 NRSMNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQ--KY---MGHSNNLVTPVWVL  267 (378)
Q Consensus       193 ~~~~~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~s~~--~~---l~~~~~IVt~~WI~  267 (378)
                      .+.+..+|+||+||| .||++.+++.|.++|..+||++.+.  +++.+||||+......  ++   ...+++||++.||+
T Consensus        34 ~~~~~~~f~G~~i~i-sGf~~~~~~~l~~~i~~~GG~~~~~--~~~~vTHvIv~~~~~~~~~~~~~~~~~i~iV~~~Wl~  110 (132)
T d1wf6a_          34 FQAPEDLLDGCRIYL-CGFSGRKLDKLRRLINSGGGVRFNQ--LNEDVTHVIVGDYDDELKQFWNKSAHRPHVVGAKWLL  110 (132)
T ss_dssp             CCCCTTTTTTCEEEE-ESCCSHHHHHHHHHHHHTTCEEESS--CCSSCCEEEESSCCSHHHHHHHHSCCCCCEEEHHHHH
T ss_pred             hcCchhhhCCeEEEE-eeCCCHHHHHHHHHHHHcCCEEecc--cCCCceEEEecCCCccHHHHHHHhcCCCCcCCHHHHH
Confidence            345678999999999 7999889999999999999999988  6899999999874322  22   34678999999999


Q ss_pred             hhhhHhhhhhHHhhh
Q 017048          268 KTAKEKHVQRLVHIS  282 (378)
Q Consensus       268 dcik~~~~qr~~~~s  282 (378)
                      +|++++.+++.-.|-
T Consensus       111 ~c~~~~~~l~~~~Y~  125 (132)
T d1wf6a_         111 ECFSKGYMLSEEPYI  125 (132)
T ss_dssp             HHHHHSSCCCSGGGB
T ss_pred             HHHHcCCcCCHHhCc
Confidence            999999988776664

>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=99.46  E-value=1.8e-14  Score=113.38  Aligned_cols=83  Identities=12%  Similarity=0.247  Sum_probs=68.7

Q ss_pred             CccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEecccchhhh---h--cCCCCccchhhHHhhhh
Q 017048          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKY---M--GHSNNLVTPVWVLKTAK  271 (378)
Q Consensus       197 ~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~s~~~~---l--~~~~~IVt~~WI~dcik  271 (378)
                      +.+|+|+.||+...++..+++.|+++|..+||++.+.  +++++||||+......++   .  ..++.||+++||.||++
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            4699999999965688888999999999999999988  689999999987432222   2  34678999999999999


Q ss_pred             HhhhhhHHhh
Q 017048          272 EKHVQRLVHI  281 (378)
Q Consensus       272 ~~~~qr~~~~  281 (378)
                      ++.+.+.-+|
T Consensus        81 ~~~~lp~~~Y   90 (96)
T d1cdza_          81 KQKLLPHQLY   90 (96)
T ss_dssp             TTSCCCGGGG
T ss_pred             cCCcCCchhc
Confidence            9987766554

>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=99.38  E-value=8.4e-14  Score=108.73  Aligned_cols=75  Identities=11%  Similarity=0.146  Sum_probs=63.9

Q ss_pred             CCCCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCCCCC-ccceEEEeeecCchhhHhhhhcCCCceEEEEeehhhhh
Q 017048           53 PANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHP-QCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDS  131 (378)
Q Consensus        53 ~~~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~-~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~dc  131 (378)
                      .-+.+|+|++|+++|..+ ++..|+++|..+||.+..+++. .+||+|+......            +++||+|+||+||
T Consensus        12 ~l~diF~G~~~~i~~~~p-~~~~L~r~i~a~GG~~~~~~~~~~vTHvI~~~~~~~------------~~~iV~p~Wi~dc   78 (88)
T d1in1a_          12 VLLDIFTGVRLYLPPSTP-DFSRLRRYFVAFDGDLVQEFDMTSATHVLGSRDKNP------------AAQQVSPEWIWAC   78 (88)
T ss_dssp             CCCSSSTTCBCCCCTTST-THHHHHHHHHHHTCBCCCTTCCTTCCCEESCCTTCT------------TSCEECHHHHHHH
T ss_pred             chhhHhCCeEEEECCCCC-CHHHHHHHHHHhCCEEeeeccCCCceEEEEcCCCCC------------CcEEEehHHHHHH
Confidence            468899999999988664 6778999999999999998884 6999999755333            4569999999999


Q ss_pred             hhccccccc
Q 017048          132 VRRNVRLSE  140 (378)
Q Consensus       132 i~~g~~l~e  140 (378)
                      ++++++||.
T Consensus        79 i~~~~lLPp   87 (88)
T d1in1a_          79 IRKRRLVAP   87 (88)
T ss_dssp             HHHTSCCCC
T ss_pred             HHcCCcCCC
Confidence            999999874

>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=99.29  E-value=4e-13  Score=105.65  Aligned_cols=79  Identities=23%  Similarity=0.290  Sum_probs=73.2

Q ss_pred             CCCCccceEEEEcccCHHHHHHHHHHHHHhcCccCCCCCCccceEEEeeecCchhhHhhhhcCCCceEEEEeehhhhhhh
Q 017048           54 ANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSRNGLYIVTLGWFVDSVR  133 (378)
Q Consensus        54 ~~~~F~g~~I~vsG~~~~~r~~L~~lI~~~GG~~~~~lt~~~THLI~~~~~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci~  133 (378)
                      ...+|.|.+|||||.....|.+++.+|+.+||.++..++.+|+|||+++..+.|+.+|.+    +||+||+.+|+.+.++
T Consensus         4 ~~~~l~G~~iv~TG~~~~~R~e~~~~i~~~Gg~v~~sVs~~t~~LV~g~~~g~K~~kA~~----~gI~IisE~~f~~~l~   79 (92)
T d1l7ba_           4 GGEALKGLTFVITGELSRPREEVKALLRRLGAKVTDSVSRKTSYLVVGENPGSKLEKARA----LGVPTLTEEELYRLLE   79 (92)
T ss_dssp             CCCSSTTCEEECSTTTTSCHHHHHHHHHHTTCEEESCCSSSCCCBEECSSSSTTHHHHHC----SSSCCEEHHHHHHHHH
T ss_pred             CCCCcCCCEEEEeCCccCCHHHHHHHHHHhCCEEcCccccceeEEEECCCCCcHHHHHHH----cCCcEecHHHHHHHHH
Confidence            567999999999998777899999999999999999999999999999888999999998    5899999999999998


Q ss_pred             ccc
Q 017048          134 RNV  136 (378)
Q Consensus       134 ~g~  136 (378)
                      ...
T Consensus        80 ~~~   82 (92)
T d1l7ba_          80 ART   82 (92)
T ss_dssp             HHH
T ss_pred             hCC
Confidence            644

>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=99.22  E-value=1.9e-12  Score=100.94  Aligned_cols=73  Identities=14%  Similarity=0.263  Sum_probs=58.2

Q ss_pred             cCccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEecccchhhhhcCCCCccchhhHHhhhhHhhh
Q 017048          196 MNSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDSVQKYMGHSNNLVTPVWVLKTAKEKHV  275 (378)
Q Consensus       196 ~~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~s~~~~l~~~~~IVt~~WI~dcik~~~~  275 (378)
                      ...+|+|++|||+ +..+ .++.|+++|.++||+++... ..+.+||||+....     ..+..+|+|+||+||++++.+
T Consensus        13 l~diF~G~~~~i~-~~~p-~~~~L~r~i~a~GG~~~~~~-~~~~vTHvI~~~~~-----~~~~~iV~p~Wi~dci~~~~l   84 (88)
T d1in1a_          13 LLDIFTGVRLYLP-PSTP-DFSRLRRYFVAFDGDLVQEF-DMTSATHVLGSRDK-----NPAAQQVSPEWIWACIRKRRL   84 (88)
T ss_dssp             CCSSSTTCBCCCC-TTST-THHHHHHHHHHHTCBCCCTT-CCTTCCCEESCCTT-----CTTSCEECHHHHHHHHHHTSC
T ss_pred             hhhHhCCeEEEEC-CCCC-CHHHHHHHHHHhCCEEeeec-cCCCceEEEEcCCC-----CCCcEEEehHHHHHHHHcCCc
Confidence            3789999999994 4333 46779999999999998763 34679999998643     234579999999999999876


Q ss_pred             h
Q 017048          276 Q  276 (378)
Q Consensus       276 q  276 (378)
                      .
T Consensus        85 L   85 (88)
T d1in1a_          85 V   85 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.18  E-value=4.4e-12  Score=99.96  Aligned_cols=84  Identities=17%  Similarity=0.155  Sum_probs=65.1

Q ss_pred             ccccccceeecchhhHHHHHHHHHHHhhccceeeeeee---eccCCceEEeccc-----chhhh---hcCCCCccchhhH
Q 017048          198 STLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWF---VGCGASYVVCEED-----SVQKY---MGHSNNLVTPVWV  266 (378)
Q Consensus       198 ~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~---~~~~vTHVV~~~~-----s~~~~---l~~~~~IVt~~WI  266 (378)
                      .+|+|+.||+...|+...++.|.++|+.+||++++...   ....+||+++...     ....+   ...++.||+++||
T Consensus         2 kiF~g~~i~~~g~~~~~~~~~L~~li~~~GG~v~~~~~~~~~~~~~t~~~i~~~~~~~~~~~~~~~~~~~~i~iV~~~Wl   81 (102)
T d1t15a2           2 KIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTLGTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWV   81 (102)
T ss_dssp             CTTTTCEEEECSCCSSSCHHHHHHHHHHTTCEECCSGGGCCCSTTCCEEEEECGGGCSSCGGGGSSTTTCSSCEEEHHHH
T ss_pred             CCCCCcEEEEeCCCCCcCHHHHHHHHHHhCCEEeeccccccccccccchheecccccchhhHHHHHHHhCCCcEEeeHHH
Confidence            48999999995448877788999999999999987642   2346788887541     11222   3568999999999


Q ss_pred             HhhhhHhhhhhHHhh
Q 017048          267 LKTAKEKHVQRLVHI  281 (378)
Q Consensus       267 ~dcik~~~~qr~~~~  281 (378)
                      +||+..+.+++.-.|
T Consensus        82 ~dsi~~~~~lp~~~Y   96 (102)
T d1t15a2          82 LDSVALYQCQELDTY   96 (102)
T ss_dssp             HHHHHHTSCCCSGGG
T ss_pred             HHHHHhCCcCCchhc
Confidence            999999988877666

>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=99.17  E-value=5.9e-12  Score=107.89  Aligned_cols=91  Identities=18%  Similarity=0.192  Sum_probs=75.2

Q ss_pred             CCCCCccceEEEEcccCHH-----------------------------HHHHHHHHHHHhcCccCCCCC------Cccce
Q 017048           53 PANAPFSGLVICVTGLSKE-----------------------------ARKQVMEATERLGGQYSPDLH------PQCTH   97 (378)
Q Consensus        53 ~~~~~F~g~~I~vsG~~~~-----------------------------~r~~L~~lI~~~GG~~~~~lt------~~~TH   97 (378)
                      ....+|.|+.|++|+.+..                             .+......|..+||.+...++      ..++|
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            5678999999999965311                             234567789999999888765      24678


Q ss_pred             EEEeee-cCchhhHhhhhcCCCceEEEEeehhhhhhhcccccccceeeeec
Q 017048           98 LVVQSF-GGRKFEHALKHGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKS  147 (378)
Q Consensus        98 LI~~~~-~~~Ky~~A~k~~~~~gi~IV~~~Wl~dci~~g~~l~e~~Y~~~~  147 (378)
                      ||+... .+.||..|+.    +|+|||+++||.||+++|+++||.+|.+..
T Consensus        91 LIa~~~~RT~Kyl~Ala----~g~piv~~~Wi~~c~~~~~~ld~~~YlLpa  137 (153)
T d1kzyc1          91 LIADQHCRTRKYFLCLA----SGIPCVSHVWVHDSCHANQLQNYRNYLLPA  137 (153)
T ss_dssp             EEESSCCCSHHHHHHHH----HTCCEEETHHHHHHHHHTSCCCGGGSBCCC
T ss_pred             EecCCCCchHHHHHHHc----cCCcEEcHHHHHHHHHcCCcCChHHccCCC
Confidence            999876 6999999998    599999999999999999999999999854

>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=99.01  E-value=9.1e-11  Score=94.46  Aligned_cols=75  Identities=27%  Similarity=0.327  Sum_probs=63.2

Q ss_pred             ceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEecccc------hhhh---hcCCCCccchhhHHhhhhHhh
Q 017048          204 SMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEEDS------VQKY---MGHSNNLVTPVWVLKTAKEKH  274 (378)
Q Consensus       204 ~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~s------~~~~---l~~~~~IVt~~WI~dcik~~~  274 (378)
                      +|++ +|+++++++.|.++++.+||++.+.  ++.++||||+....      ..+|   +..+++||++.||.+|++++.
T Consensus         3 ~i~~-SGl~~~e~~~l~~~i~~~Gg~~~~~--~~~~~THlI~~~~~~~~~~rt~K~l~a~~~g~~IV~~~Wl~~c~~~~~   79 (109)
T d1t15a1           3 SMVV-SGLTPEEFMLVYKFARKHHITLTNL--ITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERK   79 (109)
T ss_dssp             EEEE-ESCCHHHHHHHHHHHHHHTCEECSS--CCTTCCEEEECBCTTSEECCBHHHHHHHHTTCEEEETHHHHHHHHTTS
T ss_pred             EEEE-CCCCHHHHHHHHHHHHHcCCEEEeE--ecCCccEEEEecCcchhhHhhHHHHHHHHCCCccccHHHHHHHHHhCC
Confidence            5666 7999999999999999999999999  69999999997521      1234   457999999999999999998


Q ss_pred             hhhHHhh
Q 017048          275 VQRLVHI  281 (378)
Q Consensus       275 ~qr~~~~  281 (378)
                      +.+.-.|
T Consensus        80 ~l~e~~y   86 (109)
T d1t15a1          80 MLNEHDF   86 (109)
T ss_dssp             CCCGGGG
T ss_pred             cCCchhe
Confidence            8877555

>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=98.22  E-value=3.6e-07  Score=70.91  Aligned_cols=77  Identities=18%  Similarity=0.244  Sum_probs=63.0

Q ss_pred             CccccccceeecchhhHHHHHHHHHHHhhccceeeeeeeeccCCceEEeccc---chhhhhcCCCCccchhhHHhhhhHh
Q 017048          197 NSTLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFVGCGASYVVCEED---SVQKYMGHSNNLVTPVWVLKTAKEK  273 (378)
Q Consensus       197 ~~lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~~~~vTHVV~~~~---s~~~~l~~~~~IVt~~WI~dcik~~  273 (378)
                      +..|+|.+|+|...++ ..|+.++.+|+.+||++.+.  +..+++|+|+.+.   .+++....++.||+.+|+.+.++.+
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 GEALKGLTFVITGELS-RPREEVKALLRRLGAKVTDS--VSRKTSYLVVGENPGSKLEKARALGVPTLTEEELYRLLEAR   81 (92)
T ss_dssp             CCSSTTCEEECSTTTT-SCHHHHHHHHHHTTCEEESC--CSSSCCCBEECSSSSTTHHHHHCSSSCCEEHHHHHHHHHHH
T ss_pred             CCCcCCCEEEEeCCcc-CCHHHHHHHHHHhCCEEcCc--cccceeEEEECCCCCcHHHHHHHcCCcEecHHHHHHHHHhC
Confidence            5678999999954454 46888999999999999999  7999999999763   3444466899999999999999875


Q ss_pred             hhh
Q 017048          274 HVQ  276 (378)
Q Consensus       274 ~~q  276 (378)
                      .-+
T Consensus        82 ~~~   84 (92)
T d1l7ba_          82 TGK   84 (92)
T ss_dssp             HCS
T ss_pred             CCC
Confidence            433

>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=98.00  E-value=1.2e-06  Score=67.44  Aligned_cols=83  Identities=17%  Similarity=0.197  Sum_probs=55.4

Q ss_pred             cccccceeecchhhHHHHHHHHHHHhhccceeeeeee---eccCCc-eEEeccc---chhhh--h--cCCCCccchhhHH
Q 017048          199 TLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWF---VGCGAS-YVVCEED---SVQKY--M--GHSNNLVTPVWVL  267 (378)
Q Consensus       199 lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~---~~~~vT-HVV~~~~---s~~~~--l--~~~~~IVt~~WI~  267 (378)
                      +|+|+-||+-.-|++-.++.|+.+++.+||+|+.+..   .+.+.+ -||+.++   +...|  +  ..+..+|+.+|++
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            6899999996667666678899999999999998742   122223 3455542   23333  2  3567889999999


Q ss_pred             hhhhHhhhhhHHhh
Q 017048          268 KTAKEKHVQRLVHI  281 (378)
Q Consensus       268 dcik~~~~qr~~~~  281 (378)
                      |||.....|++-.|
T Consensus        81 DSIA~Y~~Q~l~~Y   94 (97)
T d1l0ba2          81 DSISVYRCRDLDAY   94 (97)
T ss_dssp             HHHHTTSCCCGGGG
T ss_pred             hhhhheeeeehHhh
Confidence            99999988887655

>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=97.88  E-value=3.9e-06  Score=64.50  Aligned_cols=86  Identities=17%  Similarity=0.246  Sum_probs=57.4

Q ss_pred             CccceEEEEcc-cCHHHHHHHHHHHHHhcCccCCCCC----Cccce-EEEeeec----CchhhHhhhhcCCCceEEEEee
Q 017048           57 PFSGLVICVTG-LSKEARKQVMEATERLGGQYSPDLH----PQCTH-LVVQSFG----GRKFEHALKHGSRNGLYIVTLG  126 (378)
Q Consensus        57 ~F~g~~I~vsG-~~~~~r~~L~~lI~~~GG~~~~~lt----~~~TH-LI~~~~~----~~Ky~~A~k~~~~~gi~IV~~~  126 (378)
                      +|+|..||+.| |++-.+++|+.+++..||.++..+.    ...+| +|+-.++    ..-|. ++  +.+.+.++|+-+
T Consensus         1 lf~~~~icc~gpFt~mt~d~Le~mv~lCGAsVvk~~~~l~~~~~~~~viVvqpda~t~~~~~~-~i--~~~~~~~vVtre   77 (97)
T d1l0ba2           1 LFEGLQIYCCEPFTNMPKDELERMLQLCGASVVKELPLLTRDTGAHPIVLVQPSAWTEDNDCP-DI--GQLCKGRLVMWD   77 (97)
T ss_dssp             CCTTCEEEECSCCSSSCHHHHHHHHHHTTCEEECSSSCGGGCCSSCCEEEEC----------------------CEEETH
T ss_pred             CCCCceEEEEccccCCCHHHHHHHHHHcCceeecChhhcCCCCCCeeEEEEcCCccccccccH-HH--HHhccccEEehh
Confidence            69999999988 5667788899999999999988765    23334 5554442    23333 22  124688999999


Q ss_pred             hhhhhhhcccccccceeee
Q 017048          127 WFVDSVRRNVRLSESLYTV  145 (378)
Q Consensus       127 Wl~dci~~g~~l~e~~Y~~  145 (378)
                      |+.||+..=+..+-..|.+
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            9999999888888777764

>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=97.82  E-value=3.3e-06  Score=71.33  Aligned_cols=64  Identities=11%  Similarity=0.205  Sum_probs=48.2

Q ss_pred             HHHHHHhhccceeeeeee----eccCCceEEecc-cchhhh---hcCCCCccchhhHHhhhhHhhhhhHHhh
Q 017048          218 KVFEAATNEGATLVNQWF----VGCGASYVVCEE-DSVQKY---MGHSNNLVTPVWVLKTAKEKHVQRLVHI  281 (378)
Q Consensus       218 ~L~~lI~~~GG~vv~~~~----~~~~vTHVV~~~-~s~~~~---l~~~~~IVt~~WI~dcik~~~~qr~~~~  281 (378)
                      .+...|+.+||.+.+.+.    ....++|+|++. ....+|   ++.++.||++.||.||++.|++++.-.|
T Consensus        62 ~~~~~i~~~gg~v~~~~~~~~~~~~~~~~LIa~~~~RT~Kyl~Ala~g~piv~~~Wi~~c~~~~~~ld~~~Y  133 (153)
T d1kzyc1          62 YTESQLRAGAGYILEDFNEAQCNTAYQCLLIADQHCRTRKYFLCLASGIPCVSHVWVHDSCHANQLQNYRNY  133 (153)
T ss_dssp             HHHHHHHTTTCEECSSCCTTTTTTTCEEEEEESSCCCSHHHHHHHHHTCCEEETHHHHHHHHHTSCCCGGGS
T ss_pred             hhhhhhhhcCCeEeeccccccccccceEEEecCCCCchHHHHHHHccCCcEEcHHHHHHHHHcCCcCChHHc
Confidence            456688999999988631    112346889887 335556   6789999999999999999988776554

>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=97.05  E-value=0.00024  Score=55.45  Aligned_cols=78  Identities=19%  Similarity=0.121  Sum_probs=55.4

Q ss_pred             cccccceeecchhhHHHHHHHHHHHhhccceeeeeeee--------ccCCceEEecc---cchhhh-hcCCCCccchhhH
Q 017048          199 TLSGCSMYVDSDVSEELRNKVFEAATNEGATLVNQWFV--------GCGASYVVCEE---DSVQKY-MGHSNNLVTPVWV  266 (378)
Q Consensus       199 lF~G~~fyl~~gfs~~~~~~L~~lI~~~GG~vv~~~~~--------~~~vTHVV~~~---~s~~~~-l~~~~~IVt~~WI  266 (378)
                      .|.|+.+++-+.-+...++....++..+||+++...+.        ...++.+|+++   +++.+. ...++.+|+.+|+
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            58999888843333334678999999999999876421        22446666665   334444 3469999999999


Q ss_pred             HhhhhHhhhh
Q 017048          267 LKTAKEKHVQ  276 (378)
Q Consensus       267 ~dcik~~~~q  276 (378)
                      ..|+-.|...
T Consensus        82 IQsLI~G~~~   91 (106)
T d1kzyc2          82 IQCLIVGERI   91 (106)
T ss_dssp             HHHHHHTSCC
T ss_pred             HHHHHccCcC
Confidence            9999988654

>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=96.40  E-value=0.00085  Score=52.21  Aligned_cols=81  Identities=14%  Similarity=0.133  Sum_probs=48.2

Q ss_pred             CCccceEEEEcccCHHHHHHH-HHHHHHhcCccCCC---------CC-CccceEEEeeecCc-hhhHhhhhcCCCceEEE
Q 017048           56 APFSGLVICVTGLSKEARKQV-MEATERLGGQYSPD---------LH-PQCTHLVVQSFGGR-KFEHALKHGSRNGLYIV  123 (378)
Q Consensus        56 ~~F~g~~I~vsG~~~~~r~~L-~~lI~~~GG~~~~~---------lt-~~~THLI~~~~~~~-Ky~~A~k~~~~~gi~IV  123 (378)
                      +||+|+.+.+.+-.+....++ ..++...||.....         .. ..++.+|+...-+. -...|..    +|++||
T Consensus         1 npF~~l~vl~vs~~~~~F~e~Ws~IL~~~Ga~vV~~~~~~~~~sd~~~~~~DVvvTD~scp~~vl~~a~~----~~ipvV   76 (106)
T d1kzyc2           1 NPFQNLKVLLVSDQQQNFLELWSEILMTGGAASVKQHHSSAHNKDIALGVFDVVVTDPSCPASVLKCAEA----LQLPVV   76 (106)
T ss_dssp             CTTTTCEEEEEESCTTTTHHHHHHHHHHTTCSEEEEEESSSSCCCSCGGGCSEEEECTTCCHHHHHHHHH----HTCCEE
T ss_pred             CCCcceEEEEEecccccHHHHHHHHHHhCCceEeeccccchhhccCccccccEEEeCCCCCHHHHHHHHH----cCCcEe
Confidence            489998776644333333344 45555555544221         11 35666666333221 1122332    599999


Q ss_pred             Eeehhhhhhhccccccc
Q 017048          124 TLGWFVDSVRRNVRLSE  140 (378)
Q Consensus       124 ~~~Wl~dci~~g~~l~e  140 (378)
                      +.+|+.+|+-.|++++.
T Consensus        77 S~EWVIQsLI~G~~~~~   93 (106)
T d1kzyc2          77 SQEWVIQCLIVGERIGF   93 (106)
T ss_dssp             CHHHHHHHHHHTSCCCT
T ss_pred             eHHHHHHHHHccCcCCC
Confidence            99999999999998863