Citrus Sinensis ID: 017612

---

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-------37
Protein Sequence
MLVNIIKSPPSRQPFPPPLPNSFTANLKNGRNLMENEEQNNESAKAQPPQNKKKTIITIPSYQEVINATNPPQNLFTPSQSFSQAFSFIKSSEFYNPPPPPPANPPTTSQNPTLSQGGEQNVGTASASASSSQSIQSRNAILVSQRQKGNPLLKYIRNVRWAFADVVCDYLVGQNSCALYLSLEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKRVVSSHPPIPETPSQKDVERSSVNEVTEVEKDTEDVNKRRKKETESTVKSALSAAFAKYADKIGKKKNRSSQVGETSVSNSGTENSNSGQPDS
Secondary Structure (PSIPRED)
ccEEEEcccccccccccccccccccccccccccccHHHHccccccccccccccccccccccHHHHHcccccccccccccccHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccEEEccccccccccHHHcccccccccccccEEEcccEEEEEccHHHHHHHHHHHHHHcccccHHHHcccccHHHHHHHHHHcccccccHHHHHHHHHHcccHHHHHHccHHHHccccccHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccHHHHHHcccccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccEEEEcccccccccccccccccccccccccccccccccccccccccccccccEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEcccccccHHHHHHcccccHHccccHHHHHccccEEEEEcHHHHHHHHHHHHHHHcccHHHHHHHccccHHHHHHHHHcccccccHHHHHHHHHHHccHHHHHHccHHHHHccccccHHHHHHHHHHHccccHHcccccccccccccHHcccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mlvniiksppsrqpfppplpnsftanLKNGRNLMENeeqnnesakaqppqnkkktiitipsyqevinatnppqnlftpsqsfSQAFSFIkssefynppppppanppttsqnptlsqggeqnvgtasasasssqSIQSRNAILVSQrqkgnpllKYIRNVRWAFADVVCDYLVGQNSCALYLSLEECGRYLETIKvyenkpadliqgqmDTDYLSRLTHALTSvrsvnktdvvtlGSTFGSLSHIMDASMedlarcpgigerkVKRLYDtfhepfkrvvsshppipetpsqkdverssvnevtevekdTEDVNKRRKKETESTVKSALSAAFAKYADKigkkknrssqvgetsvsnsgtensnsgqpds
Flexible Loop (DISEMBL)
MLVniiksppsrqpfppplpNSFTANLKNGRNLMENEEQNnesakaqppqnkkKTIITIPSYQEVINATNPPQNLFTPSQSFSQAFSFIKSSEFYNPPPPPPANPPTTSQNPTLSQGGEQNVGTASASASSSQSIQSRNAILVSQRQKGNPLLKYIRNVRWAFADVVCDYLVGQNSCALYLSLEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALtsvrsvnktdvVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEpfkrvvsshppipetpsqkdverssvnevtevekdtedvnkrrkketestvksaLSAAFAKYAdkigkkknrssqvgetsvsnsgtensnsgqpds
Low Complexity Region (SEG)
MLVNIIKsppsrqpfppplpnsFTANLKNGRNLMENEEQNNESAKAQPPQNKKKTIITIPSYQEVINATNPPQNLFTPSQSFSQAFSFIKSSEFYnppppppanppttsqnptLSQGGEQNVGTasasasssqsiqsRNAILVSQRQKGNPLLKYIRNVRWAFADVVCDYLVGQNSCALYLSLEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKRVVSSHPPIPETPSQKDVERSSvnevtevekdtedvnKRRKKETESTVKSALSAAFAKYADKIGKKKNRSSQVGETSVSNSGTENSNSGQPDS
Disordered region (IsUnstruct)
*******************************************************IITIPSYQEVI**********************************************************************************GNPLLKYIRNVRWAFADVVCDYLVGQNSCALYLSLEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFK*********************************************************************************************
Disordered Region (DISOPRED)
*******************************************************************************************************************************************AILVSQRQKGNPLLKYIRNVRWAFADVVCDYLVGQNSCALYLSLEECGRYLETIKVYENKPAD*********YLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFK*********************************************************************************************
Disordered Region (DISEMBL)
MLVNIIKSPPSRQPFPPPLPNSFTANLKNGRNLME*****************KKTIITIPSYQEVINATNPPQNLFTPSQSFSQAFSFIKSSEFYNPP**************************************SRNAILVSQRQKGNPLLKYIRNVRWAFADVVCDYLVGQNSCALYLSLEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKRVVSSHPPI*****************************************ALSAAFAKYADKI******************************
Disordered Region (DISPRO)
MLVNIIKSPPSRQPFPPPLPN*****************************NKKKTIITIPSYQEVIN**********************************************************************RNAILVSQRQKGNPLLKYIRNVRWAFADVVCDYLVGQNSCALYLSLEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKRV*******************************************************************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MLVNIIKSPPSRQPFPPPLPNSFTANxxxxxxxxxxxxxxxxxxxxxPPQNKKKTIITIPSYQEVINATNPPQNLFTPSQSFSQAFSFIKSSEFYNPPPPPPANPPTTSQNPTLSQGGEQNVGTASASASSSQSIQSRNAILVSQRQKGNPLLKYIRNVRWAFADVVCDYLVGQNSCALYLSLEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKRVVSSHPPIPETPSQKDVERSSVNEVTEVEKDTEDVNKRRKKETESTVKSALSAAFAKYADKIGKKKNRSSQVGETSVSNSGTENSNSGQPDS
Positional Conservation
no confident homologs detected

---

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	368	2.2.26 [Sep-21-2011]
Q9MA98	410	DNA excision repair prote	yes	no	0.880	0.790	0.482	4e-83
P07992	297	DNA excision repair prote	yes	no	0.377	0.468	0.404	3e-35
P07903	298	DNA excision repair prote	yes	no	0.437	0.540	0.380	7e-34
Q1LZ75	294	DNA excision repair prote	yes	no	0.274	0.343	0.563	2e-28
Q06182	252	Mating-type switching pro	yes	no	0.334	0.488	0.390	1e-15
Q55GG6	514	DNA excision repair prote	yes	no	0.361	0.258	0.292	3e-10

>sp|Q9MA98|ERCC1_ARATH DNA excision repair protein ERCC-1 OS=Arabidopsis thaliana GN=ERCC1 PE=2 SV=1

 Score =  308 bits (789), Expect = 4e-83,   Method: Compositional matrix adjust.
 Identities = 198/410 (48%), Positives = 249/410 (60%), Gaps = 86/410 (20%)

Query: 34  MENEEQNNESAKAQPPQNKKK----TIITIPSYQEVINAT---NPPQNLFTPSQSFSQAF 86
           M NE+ + E +++   Q  +K     +I +PSYQEV+ ++   + P +LF PSQSFSQAF
Sbjct: 1   MANEDDDGEKSRSLHQQIARKPKTQIVIGVPSYQEVLESSQTKSTPPSLFKPSQSFSQAF 60

Query: 87  SFIKSSEFYNPPPPPPANPPTTS-----QNPTLSQGGEQNVGTASAS------ASSSQSI 135
           +F+KSS+ Y+PPPP  A   ++      Q P  S    Q  G +S+S      +  S + 
Sbjct: 61  AFVKSSDVYSPPPPSSAAASSSQPSGASQVPHSSSQTHQTDGASSSSTPVATGSVPSNTT 120

Query: 136 QSRNAILVSQRQKGNPLLKYIRNVRWAFADVV---------C-------------DYLVG 173
           Q+RNAILVS RQKGNPLLK+IRNV+W F+D++         C             DYL  
Sbjct: 121 QNRNAILVSHRQKGNPLLKHIRNVKWVFSDIIPDYVLGQNSCALYLSLRYHLLHPDYLYF 180

Query: 174 Q-----------------------------------NSCALY--LSLEECGRYLETIKVY 196
           +                                   + C L    S+ EC RYLETIKVY
Sbjct: 181 RIRELQKNFKLSVVLCHVDVEDTVKPLLEVTKTALLHDCTLLCAWSMTECARYLETIKVY 240

Query: 197 ENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCP 256
           ENKPADLIQGQMDTDYLSRL H+LTS+R VNK+DVVTLGSTFGSL+HI+DASMEDLARCP
Sbjct: 241 ENKPADLIQGQMDTDYLSRLNHSLTSIRHVNKSDVVTLGSTFGSLAHIIDASMEDLARCP 300

Query: 257 GIGERKVKRLYDTFHEPFKRVVSSH-----PPIPETPSQKDVERSSVNEVTEVEKDTEDV 311
           GIGERKVKRLYDTFHEPFKR  SS+     PPIPE P +KDV  +S   V E E   ED 
Sbjct: 301 GIGERKVKRLYDTFHEPFKRATSSYPSVVEPPIPEAPVEKDV--NSEEPVEEDEDFVEDS 358

Query: 312 NKRRKK--ETESTVKSALSAAFAKYADKIGKKKNRSSQVGETSVSNSGTE 359
            KR+KK  E E TVK+ALSA FA+Y+D++ KKK +  +   T+ S++ T 
Sbjct: 359 RKRKKKEPEPEKTVKTALSAVFARYSDRLSKKKEKQKEKDTTTASDAETH 408

Seems to be involved in nucleotide excision repair (NER) of damaged DNA (dark repair mechanism). The UVH1/RAD1-ERCC1/RAD10 complex may act as an endonuclease making DNA incision 5' to the lesion site. In vitro, is implicated in double strand breaks (DSBs) repair and is required for homologous recombination in the presence of non-homologous overhangs. In vitro, is involved in chromosomal recombination between tandem repeats in both direct and inverted orientations. May mediate the induction of a DNA-damage sensitive cell-cycle checkpoint during the G2 phase.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 1EC: .EC: -EC: .EC: -

>sp|P07992|ERCC1_HUMAN DNA excision repair protein ERCC-1 OS=Homo sapiens GN=ERCC1 PE=1 SV=1

 Score =  149 bits (376), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 80/198 (40%), Positives = 108/198 (54%), Gaps = 59/198 (29%)

Query: 139 NAILVSQRQKGNPLLKYIRNVRWAFADVVCDYL--------------------------- 171
           N+I+VS RQ+GNP+LK++RNV W F DV+ DY+                           
Sbjct: 99  NSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQ 158

Query: 172 -VGQN-----------------------------SCALYLSL--EECGRYLETIKVYENK 199
            +G+N                              C L L+   EE GRYLET K YE K
Sbjct: 159 SLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQK 218

Query: 200 PADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIG 259
           PADL+  +++ D++SR+T  LT+V+SVNKTD  TL +TFGSL  ++ AS EDLA CPG+G
Sbjct: 219 PADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLG 278

Query: 260 ERKVKRLYDTFHEPFKRV 277
            +K +RL+D  HEPF +V
Sbjct: 279 PQKARRLFDVLHEPFLKV 296

Structure-specific DNA repair endonuclease responsible for the 5'-incision during DNA repair.

Homo sapiens (taxid: 9606)

>sp|P07903|ERCC1_MOUSE DNA excision repair protein ERCC-1 OS=Mus musculus GN=Ercc1 PE=2 SV=2

 Score =  144 bits (364), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 86/226 (38%), Positives = 118/226 (52%), Gaps = 65/226 (28%)

Query: 117 GGEQNVGTASASASS---SQSIQS---RNAILVSQRQKGNPLLKYIRNVRWAFADVVCDY 170
           G    V T S  A+    SQ++++    N+I+VS RQ+GNP+LK++RNV W F +V+ DY
Sbjct: 71  GAGATVPTGSEPAAGENPSQTLKTGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGEVIPDY 130

Query: 171 L----------------------------VGQN--------------------------- 175
           +                            +G+N                           
Sbjct: 131 VLGQSTCALFLSLRYHNLHPDYIHERLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCI 190

Query: 176 --SCALYL--SLEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDV 231
              C L L  S EE GRYLET K YE KPADL+  +++ ++LSR T  LT+V+SVNKTD 
Sbjct: 191 LADCTLVLAWSAEEAGRYLETYKAYEQKPADLLMEKLEQNFLSRATECLTTVKSVNKTDS 250

Query: 232 VTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKRV 277
            TL +TFGSL  +  AS EDLA CPG+G +K +RL++  HEPF +V
Sbjct: 251 QTLLATFGSLEQLFTASREDLALCPGLGPQKARRLFEVLHEPFLKV 296

Structure-specific DNA repair endonuclease responsible for the 5'-incision during DNA repair.

Mus musculus (taxid: 10090)

>sp|Q1LZ75|ERCC1_BOVIN DNA excision repair protein ERCC-1 OS=Bos taurus GN=ERCC1 PE=2 SV=1

 Score =  126 bits (317), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 58/103 (56%), Positives = 77/103 (74%), Gaps = 2/103 (1%)

Query: 177 CALYLSL--EECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTL 234
           C L L+   EE GRYLET K YE KPADL+  +++ D++SR+T  LT+V+SVNKTD  TL
Sbjct: 190 CTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTL 249

Query: 235 GSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKRV 277
            +TFGSL  ++ AS EDL+ CPG+G +K +RL+D FHEPF +V
Sbjct: 250 LTTFGSLEQLIAASREDLSLCPGLGPQKARRLFDVFHEPFLKV 292

Structure-specific DNA repair endonuclease responsible for the 5'-incision during DNA repair.

Bos taurus (taxid: 9913)

>sp|Q06182|SWI10_SCHPO Mating-type switching protein swi10 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=swi10 PE=3 SV=1

 Score = 84.7 bits (208), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 48/123 (39%), Positives = 70/123 (56%)

Query: 152 LLKYIRNVRWAFADVVCDYLVGQNSCALYLSLEECGRYLETIKVYENKPADLIQGQMDTD 211
           +L  + N + +  ++V   +V Q +  L  S EE  RYLET K YEN    LI  +  TD
Sbjct: 113 ILVDVENHQASIQELVKTSIVNQYTLILAWSSEEAARYLETYKAYENMSPALIMEKPSTD 172

Query: 212 YLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271
           YLS++   LTS+R +NK+D ++L S FGSL   + AS ++L +  G G  KV R  +   
Sbjct: 173 YLSQVQSFLTSIRGINKSDSLSLLSKFGSLERALVASRDELEQLEGWGPTKVNRFLEAVQ 232

Query: 272 EPF 274
           +PF
Sbjct: 233 QPF 235

Involved in termination of copy-synthesis during mating-type switching. Involved in nucleotide excision repair of DNA damaged with UV light, bulky adducts, or cross-linking agents. Along with RAD16 forms an endonuclease that specifically degrades single-stranded DNA.

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

>sp|Q55GG6|ERCC1_DICDI DNA excision repair protein ERCC-1 OS=Dictyostelium discoideum GN=ercc1 PE=3 SV=1

 Score = 66.6 bits (161), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 45/154 (29%), Positives = 70/154 (45%), Gaps = 21/154 (13%)

Query: 142 LVSQRQKGNPLL-----KYIRNVRWAFADVV----CDYLVGQ-NSCALYLSLE------- 184
           L+  R KG   L      +   +   FAD+     C+  + + N  A+ L          
Sbjct: 271 LIQDRIKGLSTLMTNSDSFTLRILLVFADLSDSDNCEQFINELNLIAIKLQFTLIVCWSQ 330

Query: 185 -ECGRYLETIKVYENKPADLIQGQMDTDYL---SRLTHALTSVRSVNKTDVVTLGSTFGS 240
            E  +YLE  K + N+  D I+ +     L   S+    LTS++SVNKTD  TL   F +
Sbjct: 331 IEAAKYLEAYKTFNNRAPDPIKARAQPIELGGKSKNEQVLTSIKSVNKTDATTLLKNFQT 390

Query: 241 LSHIMDASMEDLARCPGIGERKVKRLYDTFHEPF 274
           +  I       L++ PG G  KV++ Y+T ++PF
Sbjct: 391 MQQIFTCQKTTLSKLPGFGPVKVQKFYNTINQPF 424

Structure-specific DNA repair endonuclease responsible for the 5'-incision during DNA repair.

Dictyostelium discoideum (taxid: 44689)

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	368
255542562	392	excision repair cross-complementing 1 er	0.823	0.772	0.569	1e-102
224130994	382	predicted protein [Populus trichocarpa]	0.826	0.795	0.578	1e-100
356533598	398	PREDICTED: DNA excision repair protein E	0.769	0.711	0.530	8e-92
357441595	401	DNA excision repair protein ERCC-1 [Medi	0.842	0.773	0.510	1e-90
359487720	398	PREDICTED: DNA excision repair protein E	0.796	0.736	0.584	2e-88
449441216	391	PREDICTED: DNA excision repair protein E	0.779	0.734	0.556	5e-88
449520473	412	PREDICTED: DNA excision repair protein E	0.809	0.723	0.545	9e-88
15229933	410	DNA excision repair protein ERCC-1 [Arab	0.880	0.790	0.482	3e-81
297829042	407	hypothetical protein ARALYDRAFT_477808 [	0.823	0.744	0.5	3e-81
242033937	397	hypothetical protein SORBIDRAFT_01g01698	0.793	0.735	0.435	1e-61

>gi|255542562|ref|XP_002512344.1| excision repair cross-complementing 1 ercc1, putative [Ricinus communis] gi|223548305|gb|EEF49796.1| excision repair cross-complementing 1 ercc1, putative [Ricinus communis]

 Score =  376 bits (966), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 218/383 (56%), Positives = 248/383 (64%), Gaps = 80/383 (20%)

Query: 51  NKKKTIITIPSYQEVINATNPP--QNLFTPSQSFSQAFSFIKSSEFYNPPPPPPANPPTT 108
           N KK +I IPSYQEVI ++  P  ++LF PSQ+FSQAFSFIK SEFY PPP   A     
Sbjct: 18  NAKKVVIQIPSYQEVIESSQNPKTESLFKPSQTFSQAFSFIKDSEFYTPPPQSSA----V 73

Query: 109 SQNPTLSQGGEQNVGTASASASSSQSI----QSRNAILVSQRQKGNPLLKYIRNVRWAFA 164
           S N         ++ T  +  S SQS+      RN+ILVS RQKGNPLLK+IRNVRWAFA
Sbjct: 74  SNNA-------NSIQTTQSVPSPSQSVALTGNYRNSILVSHRQKGNPLLKHIRNVRWAFA 126

Query: 165 DVVC----------------------DYLVGQ---------------------------- 174
           DVVC                      DYL  +                            
Sbjct: 127 DVVCDYLLGQNCCSLYLSLRYHLLHPDYLYYRIRELQKNYKLRVVLCHVDVEDVVKPLLE 186

Query: 175 -------NSCALY--LSLEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRS 225
                  + C L    SLEECGRYLETIK+YENKPADLIQGQMDTDYLSRLTHALT++R 
Sbjct: 187 VTKTALLHDCTLLCAWSLEECGRYLETIKMYENKPADLIQGQMDTDYLSRLTHALTTIRH 246

Query: 226 VNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKRVVSSHPPIP 285
           VNKTDVVTLGSTFGSLS+IMDASMEDLARCPGIGERKVKRLYDTFHEPFKRVVSSHP +P
Sbjct: 247 VNKTDVVTLGSTFGSLSNIMDASMEDLARCPGIGERKVKRLYDTFHEPFKRVVSSHPAVP 306

Query: 286 ETPSQKDVERSSVNEVTEVEKDTEDVNKRRKKETESTVKSALSAAFAKYADKIGKKKNRS 345
           ET SQKD E + V+EVTEV K   D +K RKKE E TVKSALSAAF+KYA+   K+ ++S
Sbjct: 307 ET-SQKDSEPALVDEVTEVGKGEYDESKWRKKEPELTVKSALSAAFSKYANTFVKRTDKS 365

Query: 346 --SQVGETSVS-NSGTENSNSGQ 365
                GETS S  +GT+N N G+
Sbjct: 366 EGENAGETSCSVETGTDNRNPGE 388

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224130994|ref|XP_002328427.1| predicted protein [Populus trichocarpa] gi|222838142|gb|EEE76507.1| predicted protein [Populus trichocarpa]

 Score =  370 bits (951), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 224/387 (57%), Positives = 257/387 (66%), Gaps = 83/387 (21%)

Query: 34  MENEEQNNESAKAQPPQNKKKTIITIPSYQEVINATN--PPQ----NLFTPSQSFSQAFS 87
           ME EE+  E       QNKK  +I IPSYQEVI ++   P Q    +LF PSQ+FSQAFS
Sbjct: 1   MEREERGEEQNTNSSNQNKK-VLIQIPSYQEVIESSQVKPTQTQESSLFKPSQTFSQAFS 59

Query: 88  FIKSSEFYNPPPPPPANPPTTSQNPTLSQGGEQNVGTASASASSSQSIQSRNAILVSQRQ 147
           FIK+SEFY+PPPPPP+           S+ G       S ++SS Q+ QSRNAILVS RQ
Sbjct: 60  FIKNSEFYSPPPPPPSK----------SEHG------PSMASSSVQNNQSRNAILVSHRQ 103

Query: 148 KGNPLLKYIRNVRWAFADVVCDYLVG---------------------------QNSCALY 180
           KGNPLLK+IRNV+WAFADVVCDYL+G                           Q +C L 
Sbjct: 104 KGNPLLKHIRNVKWAFADVVCDYLLGQSSCALYLSLRYHLLHPDYLYYRIRELQKNCKLR 163

Query: 181 L--------------------------------SLEECGRYLETIKVYENKPADLIQGQM 208
           +                                SLEECGRYLETIK+YENKPADLIQGQM
Sbjct: 164 VVLCHVDVEDVVKPLLEVTKTALLHDCTLLCAWSLEECGRYLETIKMYENKPADLIQGQM 223

Query: 209 DTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYD 268
           DTDY SRL HALT+VR VNKTDVVTLGSTFGSLS+IMDASMEDLARCPGIGERKVKRLYD
Sbjct: 224 DTDYSSRLHHALTTVRRVNKTDVVTLGSTFGSLSNIMDASMEDLARCPGIGERKVKRLYD 283

Query: 269 TFHEPFKRVVSSHPPIPETPSQKDVERSSVNEVTEVEKDTEDVNKRRKKETESTVKSALS 328
           TFHEPFKRVVSSHP +P+TP QKD E SSV+EV E+E +  + NK RKKE E TVKSALS
Sbjct: 284 TFHEPFKRVVSSHPVVPQTPVQKDTEPSSVDEVAEMEMEEANANKHRKKEPELTVKSALS 343

Query: 329 AAFAKYA-DKIGKKKNRSSQVGETSVS 354
           +AFAK A +K+G KK +  +VGETS +
Sbjct: 344 SAFAKCATNKLGNKKFQREKVGETSTA 370

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356533598|ref|XP_003535349.1| PREDICTED: DNA excision repair protein ERCC-1-like [Glycine max]

 Score =  343 bits (880), Expect = 8e-92,   Method: Compositional matrix adjust.
 Identities = 201/379 (53%), Positives = 242/379 (63%), Gaps = 96/379 (25%)

Query: 55  TIITIPSYQEVI---NATNPPQNLFTPSQSFSQAFSFIKSSEFYNPPPPP----PANPPT 107
            +I IPSYQEV+    A + P +LF PSQ+FS+AF+F+KSS+FY+PPP       ++ P+
Sbjct: 19  VVIRIPSYQEVVESSQAKSTPSSLFVPSQTFSEAFAFVKSSDFYSPPPKSRETGQSDAPS 78

Query: 108 TSQNPTLSQGGEQNVGTASASASSSQ-SIQSRNAILVSQRQ-----KGNPLLKYIRNVRW 161
           ++  P+           A+A+ASS+  S Q+RN+ILVS RQ     KGNPLLK+IRNVRW
Sbjct: 79  STSTPS----------PATAAASSTIPSSQNRNSILVSHRQCIILQKGNPLLKHIRNVRW 128

Query: 162 AFADVVC----------------------DYLVGQ------------------------- 174
           AFADVVC                      DYL  +                         
Sbjct: 129 AFADVVCDYMLGQSSCALYLSLRYHLLHPDYLYYRIRELQKNFKLRVVLCHVDVEDVIKP 188

Query: 175 ----------NSCALY--LSLEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTS 222
                     + C L    SLEECGRYLETIKVYENKPAD+IQGQMDTDYLSRLTH+LT+
Sbjct: 189 LLEVTKTAMLHDCTLLCGWSLEECGRYLETIKVYENKPADIIQGQMDTDYLSRLTHSLTT 248

Query: 223 VRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKRVVSSHP 282
           VR VNKTDVVTLG+TFGSLS+IM ASMEDLARCPGIGERKVKRL+DTFHEPFKRV SS  
Sbjct: 249 VRHVNKTDVVTLGTTFGSLSNIMGASMEDLARCPGIGERKVKRLFDTFHEPFKRVESSRQ 308

Query: 283 PIPETPSQ-----------KDVERSSVNEVTEVEKDTEDVNKRRKKETESTVKSALSAAF 331
            IPET  Q              E SS+ E  + ++DTEDV+KRRKKE E TVKSALSAAF
Sbjct: 309 AIPETSVQNKPASPESSIRNKAESSSLIE--DKQEDTEDVSKRRKKEPEVTVKSALSAAF 366

Query: 332 AKYADKIGKKKNRSSQVGE 350
           AKY+ ++GK+K+ +SQV E
Sbjct: 367 AKYSGRVGKRKS-TSQVEE 384

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357441595|ref|XP_003591075.1| DNA excision repair protein ERCC-1 [Medicago truncatula] gi|355480123|gb|AES61326.1| DNA excision repair protein ERCC-1 [Medicago truncatula]

 Score =  339 bits (870), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 201/394 (51%), Positives = 242/394 (61%), Gaps = 84/394 (21%)

Query: 34  MENE--EQNNESAKAQPPQNKKKTIITIPSYQEVINAT---NPPQNLFTPSQSFSQAFSF 88
           MENE  +QNN   K      K  T+I IPSYQEVI ++   + P +LF PSQ+FSQAF+F
Sbjct: 1   MENEAEKQNNSINK------KSSTVIRIPSYQEVIESSQTKSTPPSLFVPSQTFSQAFAF 54

Query: 89  IKSSEFYNPPPPPPANPPTTSQNPTLSQGGEQNVGTASAS----ASSSQSIQSRNAILVS 144
           +KSSEFY+PPP  P     ++ + +            +AS     S+SQ  Q+RNAILVS
Sbjct: 55  VKSSEFYSPPPSLPKENAPSNASSSTPSTSSATNNAPAASPNLPNSNSQPTQNRNAILVS 114

Query: 145 QRQKGNPLLKYIRNVRWAFADVVC----------------------DYLVGQ-------- 174
            RQKGNPLLK+IRNVRW FADVVC                      DYL  +        
Sbjct: 115 NRQKGNPLLKHIRNVRWTFADVVCDFLLGQSSCALYLSLRYHLLHPDYLYHRIRELQKNF 174

Query: 175 ---------------------------NSCALY--LSLEECGRYLETIKVYENKPADLIQ 205
                                      + C L    SLEECGRYLETIKVYENKPAD+IQ
Sbjct: 175 KLRVVLCHVDVEDVVKPLLEVTKTALLHDCTLLCGWSLEECGRYLETIKVYENKPADIIQ 234

Query: 206 GQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKR 265
           GQMDTDYLSRLTHALT+VR VNKTDVVTLG+ FGSLS+IM ASMEDLARCPGIGERKVKR
Sbjct: 235 GQMDTDYLSRLTHALTTVRHVNKTDVVTLGTNFGSLSNIMGASMEDLARCPGIGERKVKR 294

Query: 266 LYDTFHEPFKRVVSSHPPIPET-----PSQKDVE----RSSVNEVTEVEKDTEDVNKRRK 316
           L+DTFHEPFKRV SS   IPET     P+ +D        S + + ++ KD +  +KR+K
Sbjct: 295 LFDTFHEPFKRVESSRQAIPETSVQNQPTSQDTSVINNTESSSSLEDIHKDADSASKRKK 354

Query: 317 KETESTVKSALSAAFAKYADKIGKKKNRSSQVGE 350
           KE E TV+SALS AFAK +++ G K+N SS++ E
Sbjct: 355 KEPEFTVRSALSVAFAKLSERAG-KRNISSKLKE 387

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359487720|ref|XP_002281063.2| PREDICTED: DNA excision repair protein ERCC-1-like [Vitis vinifera] gi|296088298|emb|CBI36743.3| unnamed protein product [Vitis vinifera]

 Score =  332 bits (851), Expect = 2e-88,   Method: Compositional matrix adjust.
 Identities = 208/356 (58%), Positives = 236/356 (66%), Gaps = 63/356 (17%)

Query: 50  QNKKKTIITIPSYQEVINATNPP--QNLFTPSQSFSQAFSFIKSSEFYNPPPPPPANPPT 107
           +NK   +I IPSYQEV+ ++      +LFTPS SFSQAFSF+KSS+ Y PPPP    PP 
Sbjct: 17  KNKSSIVIKIPSYQEVLESSQSKTTSSLFTPSPSFSQAFSFVKSSQSYTPPPPATPPPPP 76

Query: 108 TSQNPTLSQGGEQNVGTASASASSSQSIQSRNAILVSQRQKGNPLLKYIRNVRWAFADVV 167
              +  + Q   +   ++S+S S S+S QSRNAILVS RQKGNPLLK+IRNVRW FAD+V
Sbjct: 77  PPSSRQVEQL--EAPSSSSSSPSLSRSAQSRNAILVSHRQKGNPLLKHIRNVRWDFADIV 134

Query: 168 C----------------------DYLVGQ------------------------------- 174
           C                      DYL  +                               
Sbjct: 135 CDYLLGQNSCALYLSLRYHLLHPDYLYYRIRELQKNFKLRVVLCHVDVEDVIKPLLEVTR 194

Query: 175 ----NSCALY--LSLEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNK 228
               + C L    SLEECGRYLETIKVYENK AD+IQGQ DTDYLSRLTHALT+VR VNK
Sbjct: 195 TALLHDCTLLCAWSLEECGRYLETIKVYENKSADIIQGQTDTDYLSRLTHALTTVRHVNK 254

Query: 229 TDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKRVVSSHPPIPETP 288
           TDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKRVV S P +PE P
Sbjct: 255 TDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKRVVPSCPAVPENP 314

Query: 289 SQKDVERSSVNEVTEVEKDTEDVNKRRKKETESTVKSALSAAFAKYADKIGKKKNR 344
              + E SSVNEV EVE D ED +KRRKKE E TVKSALSAAFA+Y++KIGK+ NR
Sbjct: 315 VHNNAEPSSVNEVVEVENDVEDASKRRKKEPELTVKSALSAAFAQYSEKIGKRNNR 370

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449441216|ref|XP_004138378.1| PREDICTED: DNA excision repair protein ERCC-1-like [Cucumis sativus]

 Score =  330 bits (847), Expect = 5e-88,   Method: Compositional matrix adjust.
 Identities = 203/365 (55%), Positives = 229/365 (62%), Gaps = 78/365 (21%)

Query: 48  PPQNKKKTIITIPSYQEVINATNPPQNLFTPSQSFSQAFSFIKSSEFYNPPPPPPA---- 103
           PP  K KTII IPSYQEVI+++ P       SQSFSQAF+F+KSSEFY+PPP PP+    
Sbjct: 14  PPHKKSKTIIKIPSYQEVIDSSQPN------SQSFSQAFAFLKSSEFYSPPPKPPSPSSS 67

Query: 104 ------NPPTTSQNPTLSQGGEQNVGTASA--SASSSQSIQSRNAILVSQRQKGNPLLKY 155
                 N     +N  L         +A+   ++ S  S  SRNAILVS RQKGNPLLK+
Sbjct: 68  QSLPPSNITNPRKNDQLDTSSSSTSASAATPVNSLSVSSSVSRNAILVSNRQKGNPLLKH 127

Query: 156 IRNVRWAFADVV---------C-------------DYLVGQ------------------- 174
           IRNVRWAFADVV         C             DYL  +                   
Sbjct: 128 IRNVRWAFADVVPDYLLGQSSCALYLSLRYHLLHPDYLYYRIRELQKNFKLRVILCHVDV 187

Query: 175 ----------------NSCALY--LSLEECGRYLETIKVYENKPADLIQGQMDTDYLSRL 216
                           + C L    SLEECGRYLETIKVYENKPADLIQG MDTDYLSRL
Sbjct: 188 EDVVKPLLEVTKTALLHDCTLLCAWSLEECGRYLETIKVYENKPADLIQGHMDTDYLSRL 247

Query: 217 THALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKR 276
           TH LTSVR VNKTDVVTLG+TFGSLSHIMDASMEDLARCPGIGERKV+RLYDTFHEPFKR
Sbjct: 248 THVLTSVRHVNKTDVVTLGTTFGSLSHIMDASMEDLARCPGIGERKVRRLYDTFHEPFKR 307

Query: 277 VVSSHPPIPETPSQKDVERSSVNEVTEVE-KDTEDVNKRRKKETESTVKSALSAAFAKYA 335
           VVS+HP +PETP+Q   +  S NE  +V+ K  E+   + KKE +  VKSALSAAFAKYA
Sbjct: 308 VVSTHPAVPETPTQISTKPRSSNEEQDVDGKRIEEDGSQHKKEPKLNVKSALSAAFAKYA 367

Query: 336 DKIGK 340
           DKI K
Sbjct: 368 DKIAK 372

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449520473|ref|XP_004167258.1| PREDICTED: DNA excision repair protein ERCC-1-like [Cucumis sativus]

 Score =  330 bits (845), Expect = 9e-88,   Method: Compositional matrix adjust.
 Identities = 205/376 (54%), Positives = 232/376 (61%), Gaps = 78/376 (20%)

Query: 37  EEQNNESAKAQPPQNKKKTIITIPSYQEVINATNPPQNLFTPSQSFSQAFSFIKSSEFYN 96
           EE + E    Q P  K KTII IPSYQEVI+++ P       SQSFSQAF+F+KSSEFY+
Sbjct: 2   EEGSAEDNFQQTPHKKSKTIIKIPSYQEVIDSSQPN------SQSFSQAFAFLKSSEFYS 55

Query: 97  PPPPPPA----------NPPTTSQNPTLSQGGEQNVGTASA--SASSSQSIQSRNAILVS 144
           PPP PP+          N     +N  L         +A+   ++ S  S  SRNAILVS
Sbjct: 56  PPPKPPSPSSSQSLPPSNITNPRKNDQLDTSSSSTSASAATPVNSLSVSSSVSRNAILVS 115

Query: 145 QRQKGNPLLKYIRNVRWAFADVV---------C-------------DYLVGQ-------- 174
            RQKGNPLLK+IRN RWAFADVV         C             DYL  +        
Sbjct: 116 NRQKGNPLLKHIRNARWAFADVVPDYLLGQSSCALYLSLRYHLLHPDYLYYRIRELQKNF 175

Query: 175 ---------------------------NSCALY--LSLEECGRYLETIKVYENKPADLIQ 205
                                      + C L    SLEECGRYLETIKVYENKPADLIQ
Sbjct: 176 KLRVILCHVDVEDVVKPLLEVTKTALLHDCTLLCAWSLEECGRYLETIKVYENKPADLIQ 235

Query: 206 GQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKR 265
           G MDTDYLSRLTH LTSVR VNKTDVVTLG+TFGSLSHIMDASMEDLARCPGIGERKV+R
Sbjct: 236 GHMDTDYLSRLTHVLTSVRHVNKTDVVTLGTTFGSLSHIMDASMEDLARCPGIGERKVRR 295

Query: 266 LYDTFHEPFKRVVSSHPPIPETPSQKDVERSSVNEVTEVE-KDTEDVNKRRKKETESTVK 324
           LYDTFHEPFKRVVS+HP +PETP+Q   +  S NE  +V+ K  E+   + KKE +  VK
Sbjct: 296 LYDTFHEPFKRVVSTHPAVPETPTQISTKPRSSNEEQDVDGKRIEEDGSQHKKEPKLNVK 355

Query: 325 SALSAAFAKYADKIGK 340
           SALSAAFAKYADKI K
Sbjct: 356 SALSAAFAKYADKIAK 371

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15229933|ref|NP_187172.1| DNA excision repair protein ERCC-1 [Arabidopsis thaliana] gi|55976606|sp|Q9MA98.1|ERCC1_ARATH RecName: Full=DNA excision repair protein ERCC-1; Short=AtERCC1; Short=AtRAD10; AltName: Full=Ultraviolet hypersensitive 7 gi|6729031|gb|AAF27027.1|AC009177_17 putative nucleotide repair protein [Arabidopsis thaliana] gi|9800490|gb|AAF99316.1|AF276082_1 ERCC1 [Arabidopsis thaliana] gi|15215614|gb|AAK91352.1| AT3g05210/T12H1_18 [Arabidopsis thaliana] gi|21435979|gb|AAM51569.1| AT3g05210/T12H1_18 [Arabidopsis thaliana] gi|21618171|gb|AAM67221.1| putative nucleotide repair protein [Arabidopsis thaliana] gi|332640684|gb|AEE74205.1| DNA excision repair protein ERCC-1 [Arabidopsis thaliana]

 Score =  308 bits (789), Expect = 3e-81,   Method: Compositional matrix adjust.
 Identities = 198/410 (48%), Positives = 249/410 (60%), Gaps = 86/410 (20%)

Query: 34  MENEEQNNESAKAQPPQNKKK----TIITIPSYQEVINAT---NPPQNLFTPSQSFSQAF 86
           M NE+ + E +++   Q  +K     +I +PSYQEV+ ++   + P +LF PSQSFSQAF
Sbjct: 1   MANEDDDGEKSRSLHQQIARKPKTQIVIGVPSYQEVLESSQTKSTPPSLFKPSQSFSQAF 60

Query: 87  SFIKSSEFYNPPPPPPANPPTTS-----QNPTLSQGGEQNVGTASAS------ASSSQSI 135
           +F+KSS+ Y+PPPP  A   ++      Q P  S    Q  G +S+S      +  S + 
Sbjct: 61  AFVKSSDVYSPPPPSSAAASSSQPSGASQVPHSSSQTHQTDGASSSSTPVATGSVPSNTT 120

Query: 136 QSRNAILVSQRQKGNPLLKYIRNVRWAFADVV---------C-------------DYLVG 173
           Q+RNAILVS RQKGNPLLK+IRNV+W F+D++         C             DYL  
Sbjct: 121 QNRNAILVSHRQKGNPLLKHIRNVKWVFSDIIPDYVLGQNSCALYLSLRYHLLHPDYLYF 180

Query: 174 Q-----------------------------------NSCALY--LSLEECGRYLETIKVY 196
           +                                   + C L    S+ EC RYLETIKVY
Sbjct: 181 RIRELQKNFKLSVVLCHVDVEDTVKPLLEVTKTALLHDCTLLCAWSMTECARYLETIKVY 240

Query: 197 ENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCP 256
           ENKPADLIQGQMDTDYLSRL H+LTS+R VNK+DVVTLGSTFGSL+HI+DASMEDLARCP
Sbjct: 241 ENKPADLIQGQMDTDYLSRLNHSLTSIRHVNKSDVVTLGSTFGSLAHIIDASMEDLARCP 300

Query: 257 GIGERKVKRLYDTFHEPFKRVVSSH-----PPIPETPSQKDVERSSVNEVTEVEKDTEDV 311
           GIGERKVKRLYDTFHEPFKR  SS+     PPIPE P +KDV  +S   V E E   ED 
Sbjct: 301 GIGERKVKRLYDTFHEPFKRATSSYPSVVEPPIPEAPVEKDV--NSEEPVEEDEDFVEDS 358

Query: 312 NKRRKK--ETESTVKSALSAAFAKYADKIGKKKNRSSQVGETSVSNSGTE 359
            KR+KK  E E TVK+ALSA FA+Y+D++ KKK +  +   T+ S++ T 
Sbjct: 359 RKRKKKEPEPEKTVKTALSAVFARYSDRLSKKKEKQKEKDTTTASDAETH 408

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297829042|ref|XP_002882403.1| hypothetical protein ARALYDRAFT_477808 [Arabidopsis lyrata subsp. lyrata] gi|297328243|gb|EFH58662.1| hypothetical protein ARALYDRAFT_477808 [Arabidopsis lyrata subsp. lyrata]

 Score =  308 bits (789), Expect = 3e-81,   Method: Compositional matrix adjust.
 Identities = 193/386 (50%), Positives = 239/386 (61%), Gaps = 83/386 (21%)

Query: 34  MENEEQNNESAKAQPPQNKKK----TIITIPSYQEVINAT---NPPQNLFTPSQSFSQAF 86
           M NE+ + E +++   Q  KK     II +PSYQEVI ++   + P +LF PSQSFSQAF
Sbjct: 1   MANEDDDGEKSRSLHQQIAKKPKTQIIIGVPSYQEVIESSQTKSTPPSLFKPSQSFSQAF 60

Query: 87  SFIKSSEFYNPPPPPPANPPT-----TSQNPTLSQGGEQNVGTASASASSSQSI-----Q 136
           +F+KSS+ Y+PPP   A   +      SQ P  SQ  + +  ++S++  ++ S+     Q
Sbjct: 61  AFVKSSDVYSPPPSSSAASSSSQPPGASQVPNSSQPLQTDGASSSSTPVATGSLPSNTTQ 120

Query: 137 SRNAILVSQRQKGNPLLKYIRNVRWAFADVV---------C-------------DYLVGQ 174
           +RNAILVS RQKGNPLLK+IRNV+W F+D++         C             DYL  +
Sbjct: 121 TRNAILVSHRQKGNPLLKHIRNVKWVFSDIIPDYVLGQSSCALYLSLRYHLLHPDYLYFR 180

Query: 175 -----------------------------------NSCALY--LSLEECGRYLETIKVYE 197
                                              + C L    S+ EC RYLETIKVYE
Sbjct: 181 IRELQKNFKLSVVLCHVDVEDTVKPLLEVTKTALLHDCTLLCAWSMTECARYLETIKVYE 240

Query: 198 NKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPG 257
           NKPADLIQGQMDTDYLSRL H+LTS+R VNK+DVVTLGSTFGSL+HI+DASMEDLARCPG
Sbjct: 241 NKPADLIQGQMDTDYLSRLNHSLTSIRHVNKSDVVTLGSTFGSLAHIIDASMEDLARCPG 300

Query: 258 IGERKVKRLYDTFHEPFKRVVSSH-----PPIPETPSQKDVERSSVNEVTEVEKDTEDVN 312
           IGERKV+RLYDTFHEPFKR  SS+     P IPE P QK+V  SS   V E E   ED  
Sbjct: 301 IGERKVRRLYDTFHEPFKRATSSYPSVVEPTIPEAPVQKNV--SSKEPVVEDEDFVEDSR 358

Query: 313 KRRKKETESTVKSALSAAFAKYADKI 338
           KR+KKE E TVK+ALSA FA+Y+DK+
Sbjct: 359 KRKKKEPEKTVKTALSAVFARYSDKL 384

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242033937|ref|XP_002464363.1| hypothetical protein SORBIDRAFT_01g016980 [Sorghum bicolor] gi|241918217|gb|EER91361.1| hypothetical protein SORBIDRAFT_01g016980 [Sorghum bicolor]

 Score =  243 bits (619), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 173/397 (43%), Positives = 222/397 (55%), Gaps = 105/397 (26%)

Query: 48  PPQNK-KKTIITIPSYQEVIN-----------ATNPP------------QNLFTPSQSFS 83
           PP+ +  K +I IPSYQEV             + NPP             +  + S SFS
Sbjct: 10  PPEGQPGKNLIKIPSYQEVFGTGASSSSSKPASYNPPLASSGGTAAAAASSSSSSSGSFS 69

Query: 84  QAFSFIKSSEFYNPPPPPPANPPTTSQNPTLSQGGEQNVGTASASASSSQSIQSRNAILV 143
           QAFSF+KSSEFY             S  P               ++ S+ + QS+NAILV
Sbjct: 70  QAFSFLKSSEFY-------------SPPPPPPPQPTTTTPRPPQASPSAPTRQSKNAILV 116

Query: 144 SQRQKGNPLLKYIRNVRWAFADVV---------C-------------DYLVGQ------- 174
           S RQ+GNPLLK+IRN RW FADVV         C             DYL  +       
Sbjct: 117 SHRQRGNPLLKHIRNARWTFADVVPDYVLGQSSCALYLSIRYHLLHPDYLYYRIRELQKN 176

Query: 175 ----------------------------NSCALY--LSLEECGRYLETIKVYENKPADLI 204
                                       + C L    SLEECGRYLETIKVYENKPAD+I
Sbjct: 177 FRLRVILCHVDVEDVIKPLHEITRTALLHDCTLLCGWSLEECGRYLETIKVYENKPADII 236

Query: 205 QGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVK 264
           +  MD DYLSRL+H+LTS+R VNKTDVVTLGS+FGSLS IM+ASME+LARCPGIGERKVK
Sbjct: 237 REHMDNDYLSRLSHSLTSIRHVNKTDVVTLGSSFGSLSQIMNASMEELARCPGIGERKVK 296

Query: 265 RLYDTFHEPFKRVVSSHP--PIPETPSQKDVER--SSVNEVTEVEKDTEDVNKRRKKETE 320
           RLYDTFHEPFKR VS+ P   +P+TP ++  +   SS ++  +   +  D  K++K    
Sbjct: 297 RLYDTFHEPFKR-VSARPNLVVPDTPDREKAKGQPSSTDDSLQDAVEKPDAPKKKKG--- 352

Query: 321 STVKSALSAAFAKYADKI-GKKKNRSSQVGETSVSNS 356
           S V+SAL+AAFAKY++KI  +  + +++ GE++ S++
Sbjct: 353 SDVRSALTAAFAKYSEKIRSQGHDAANEAGESTSSST 389

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

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	368
TAIR|locus:2096329	410	ERCC1 [Arabidopsis thaliana (t	0.508	0.456	0.608	5.7e-86
UNIPROTKB|Q9QYP5	293	ERCC1 "ERCC1 protein" [Cricetu	0.274	0.344	0.572	1.5e-45
MGI|MGI:95412	298	Ercc1 "excision repair cross-c	0.274	0.338	0.563	4e-45
UNIPROTKB|P07992	297	ERCC1 "DNA excision repair pro	0.274	0.340	0.572	1.1e-42
UNIPROTKB|Q1LZ75	294	ERCC1 "DNA excision repair pro	0.274	0.343	0.572	1.8e-42
UNIPROTKB|Q6UIQ5	251	ERCC1 "Excision repair protein	0.266	0.390	0.58	2.8e-42
ZFIN|ZDB-GENE-040426-2606	342	ercc1 "excision repair cross-c	0.266	0.286	0.58	1.1e-40
RGD|1306992	298	Ercc1 "excision repair cross-c	0.274	0.338	0.563	2.2e-40
UNIPROTKB|B3KRR0	225	ERCC1 "cDNA FLJ34720 fis, clon	0.274	0.448	0.572	1.5e-39
UNIPROTKB|F1PPD0	323	ERCC1 "Uncharacterized protein	0.244	0.278	0.576	2.2e-38

TAIR|locus:2096329 ERCC1 [Arabidopsis thaliana (taxid:3702)]

 Score = 593 (213.8 bits), Expect = 5.7e-86, Sum P(2) = 5.7e-86
 Identities = 118/194 (60%), Positives = 141/194 (72%)

Query:   175 NSCALYL--SLEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVV 232
             + C L    S+ EC RYLETIKVYENKPADLIQGQMDTDYLSRL H+LTS+R VNK+DVV
Sbjct:   217 HDCTLLCAWSMTECARYLETIKVYENKPADLIQGQMDTDYLSRLNHSLTSIRHVNKSDVV 276

Query:   233 TLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKRVVSSHP-----PIPET 287
             TLGSTFGSL+HI+DASMEDLARCPGIGERKVKRLYDTFHEPFKR  SS+P     PIPE 
Sbjct:   277 TLGSTFGSLAHIIDASMEDLARCPGIGERKVKRLYDTFHEPFKRATSSYPSVVEPPIPEA 336

Query:   288 PSQKDVERSSXXXXXXXXXXXXXXXKRRKKETESTVKSALSAAFAKYADKIGKKKNRSSQ 347
             P +KDV                   K+++ E E TVK+ALSA FA+Y+D++ KKK +  +
Sbjct:   337 PVEKDVNSEEPVEEDEDFVEDSRKRKKKEPEPEKTVKTALSAVFARYSDRLSKKKEKQKE 396

Query:   348 VGETSVSNSGTENS 361
                T+ S++ T  +
Sbjct:   397 KDTTTASDAETHQN 410

GO:0003677 "DNA binding" evidence=IEA

GO:0003684 "damaged DNA binding" evidence=IEA

GO:0004519 "endonuclease activity" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006284 "base-excision repair" evidence=ISS

GO:0010332 "response to gamma radiation" evidence=IMP

GO:0000724 "double-strand break repair via homologous recombination" evidence=IMP

GO:0006294 "nucleotide-excision repair, preincision complex assembly" evidence=IMP

GO:0017108 "5'-flap endonuclease activity" evidence=IMP

GO:0000956 "nuclear-transcribed mRNA catabolic process" evidence=RCA

GO:0010213 "non-photoreactive DNA repair" evidence=IMP

GO:0010224 "response to UV-B" evidence=IMP

UNIPROTKB|Q9QYP5 ERCC1 "ERCC1 protein" [Cricetulus griseus (taxid:10029)]

 Score = 302 (111.4 bits), Expect = 1.5e-45, Sum P(3) = 1.5e-45
 Identities = 59/103 (57%), Positives = 75/103 (72%)

Query:   177 CALYL--SLEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTL 234
             C L L  S EE GRYLET K YE KPADL+  +++ ++LSR T  LT+V+SVNKTD  TL
Sbjct:   189 CTLVLAWSAEEAGRYLETYKAYEQKPADLLMEKLEQNFLSRATECLTTVKSVNKTDSQTL 248

Query:   235 GSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKRV 277
              +TFGSL  ++ AS EDLA CPG+G +K +RL+D  HEPF +V
Sbjct:   249 LATFGSLEQLLTASREDLALCPGLGPQKARRLFDVLHEPFLKV 291

GO:0000109 "nucleotide-excision repair complex" evidence=ISS

GO:0000784 "nuclear chromosome, telomeric region" evidence=ISS

GO:0003684 "damaged DNA binding" evidence=ISS

GO:0003697 "single-stranded DNA binding" evidence=ISS

GO:0006295 "nucleotide-excision repair, DNA incision, 3'-to lesion" evidence=ISS

GO:0006296 "nucleotide-excision repair, DNA incision, 5'-to lesion" evidence=ISS

GO:0006312 "mitotic recombination" evidence=ISS

GO:0006979 "response to oxidative stress" evidence=ISS

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

GO:0032205 "negative regulation of telomere maintenance" evidence=ISS

GO:0000014 "single-stranded DNA specific endodeoxyribonuclease activity" evidence=ISS

GO:0043566 "structure-specific DNA binding" evidence=ISS

MGI|MGI:95412 Ercc1 "excision repair cross-complementing rodent repair deficiency, complementation group 1" [Mus musculus (taxid:10090)]

 Score = 296 (109.3 bits), Expect = 4.0e-45, Sum P(3) = 4.0e-45
 Identities = 58/103 (56%), Positives = 74/103 (71%)

Query:   177 CALYL--SLEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTL 234
             C L L  S EE GRYLET K YE KPADL+  +++ ++LSR T  LT+V+SVNKTD  TL
Sbjct:   194 CTLVLAWSAEEAGRYLETYKAYEQKPADLLMEKLEQNFLSRATECLTTVKSVNKTDSQTL 253

Query:   235 GSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKRV 277
              +TFGSL  +  AS EDLA CPG+G +K +RL++  HEPF +V
Sbjct:   254 LATFGSLEQLFTASREDLALCPGLGPQKARRLFEVLHEPFLKV 296

GO:0000109 "nucleotide-excision repair complex" evidence=ISO

GO:0000720 "pyrimidine dimer repair by nucleotide-excision repair" evidence=IMP

GO:0000784 "nuclear chromosome, telomeric region" evidence=ISO

GO:0001094 "TFIID-class transcription factor binding" evidence=IDA

GO:0001302 "replicative cell aging" evidence=IMP

GO:0003677 "DNA binding" evidence=IEA

GO:0003684 "damaged DNA binding" evidence=ISO

GO:0003697 "single-stranded DNA binding" evidence=ISO

GO:0004518 "nuclease activity" evidence=IEA

GO:0004519 "endonuclease activity" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO

GO:0005669 "transcription factor TFIID complex" evidence=IDA

GO:0006281 "DNA repair" evidence=IMP

GO:0006289 "nucleotide-excision repair" evidence=ISO;IMP

GO:0006295 "nucleotide-excision repair, DNA incision, 3'-to lesion" evidence=ISO

GO:0006296 "nucleotide-excision repair, DNA incision, 5'-to lesion" evidence=ISO

GO:0006302 "double-strand break repair" evidence=IMP

GO:0006310 "DNA recombination" evidence=ISO;IMP

GO:0006312 "mitotic recombination" evidence=ISO

GO:0006949 "syncytium formation" evidence=IMP

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

GO:0006979 "response to oxidative stress" evidence=ISO

GO:0007281 "germ cell development" evidence=IMP

GO:0007283 "spermatogenesis" evidence=IMP

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

GO:0008283 "cell proliferation" evidence=IMP

GO:0008584 "male gonad development" evidence=IMP

GO:0009650 "UV protection" evidence=IMP

GO:0010165 "response to X-ray" evidence=IMP

GO:0010259 "multicellular organismal aging" evidence=IMP

GO:0016787 "hydrolase activity" evidence=IEA

GO:0017025 "TBP-class protein binding" evidence=IPI

GO:0019904 "protein domain specific binding" evidence=ISO

GO:0032205 "negative regulation of telomere maintenance" evidence=ISO

GO:0035166 "post-embryonic hemopoiesis" evidence=IMP

GO:0035264 "multicellular organism growth" evidence=IGI;IMP

GO:0043066 "negative regulation of apoptotic process" evidence=IMP

GO:0045190 "isotype switching" evidence=IMP

GO:0048468 "cell development" evidence=IMP

GO:0048477 "oogenesis" evidence=IMP

GO:0051276 "chromosome organization" evidence=IMP

UNIPROTKB|P07992 ERCC1 "DNA excision repair protein ERCC-1" [Homo sapiens (taxid:9606)]

 Score = 302 (111.4 bits), Expect = 1.1e-42, Sum P(2) = 1.1e-42
 Identities = 59/103 (57%), Positives = 76/103 (73%)

Query:   177 CALYL--SLEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTL 234
             C L L  S EE GRYLET K YE KPADL+  +++ D++SR+T  LT+V+SVNKTD  TL
Sbjct:   194 CTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTL 253

Query:   235 GSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKRV 277
              +TFGSL  ++ AS EDLA CPG+G +K +RL+D  HEPF +V
Sbjct:   254 LTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKV 296

GO:0000720 "pyrimidine dimer repair by nucleotide-excision repair" evidence=IEA

GO:0001302 "replicative cell aging" evidence=IEA

GO:0006302 "double-strand break repair" evidence=IEA

GO:0006949 "syncytium formation" evidence=IEA

GO:0007281 "germ cell development" evidence=IEA

GO:0007283 "spermatogenesis" evidence=IEA

GO:0007584 "response to nutrient" evidence=IEA

GO:0008283 "cell proliferation" evidence=IEA

GO:0008584 "male gonad development" evidence=IEA

GO:0009650 "UV protection" evidence=IEA

GO:0009744 "response to sucrose stimulus" evidence=IEA

GO:0010165 "response to X-ray" evidence=IEA

GO:0010259 "multicellular organismal aging" evidence=IEA

GO:0035166 "post-embryonic hemopoiesis" evidence=IEA

GO:0035264 "multicellular organism growth" evidence=IEA

GO:0043066 "negative regulation of apoptotic process" evidence=IEA

GO:0045190 "isotype switching" evidence=IEA

GO:0048477 "oogenesis" evidence=IEA

GO:0048568 "embryonic organ development" evidence=IEA

GO:0051276 "chromosome organization" evidence=IEA

GO:0000784 "nuclear chromosome, telomeric region" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0043566 "structure-specific DNA binding" evidence=IDA

GO:0032205 "negative regulation of telomere maintenance" evidence=IMP

GO:0006296 "nucleotide-excision repair, DNA incision, 5'-to lesion" evidence=IMP

GO:0006295 "nucleotide-excision repair, DNA incision, 3'-to lesion" evidence=IMP

GO:0006312 "mitotic recombination" evidence=IMP

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

GO:0000014 "single-stranded DNA specific endodeoxyribonuclease activity" evidence=IDA

GO:0000109 "nucleotide-excision repair complex" evidence=IDA

GO:0003697 "single-stranded DNA binding" evidence=IDA

GO:0006979 "response to oxidative stress" evidence=IMP

GO:0003684 "damaged DNA binding" evidence=IDA

GO:0019904 "protein domain specific binding" evidence=IPI

GO:0006289 "nucleotide-excision repair" evidence=IGI;IDA;TAS

GO:0006310 "DNA recombination" evidence=IGI

GO:0000718 "nucleotide-excision repair, DNA damage removal" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

GO:0006283 "transcription-coupled nucleotide-excision repair" evidence=TAS

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|Q1LZ75 ERCC1 "DNA excision repair protein ERCC-1" [Bos taurus (taxid:9913)]

 Score = 305 (112.4 bits), Expect = 1.8e-42, Sum P(2) = 1.8e-42
 Identities = 59/103 (57%), Positives = 77/103 (74%)

Query:   177 CALYL--SLEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTL 234
             C L L  S EE GRYLET K YE KPADL+  +++ D++SR+T  LT+V+SVNKTD  TL
Sbjct:   190 CTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTL 249

Query:   235 GSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKRV 277
              +TFGSL  ++ AS EDL+ CPG+G +K +RL+D FHEPF +V
Sbjct:   250 LTTFGSLEQLIAASREDLSLCPGLGPQKARRLFDVFHEPFLKV 292

GO:0006295 "nucleotide-excision repair, DNA incision, 3'-to lesion" evidence=ISS

GO:0003684 "damaged DNA binding" evidence=ISS

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

GO:0006979 "response to oxidative stress" evidence=ISS

GO:0006312 "mitotic recombination" evidence=ISS

GO:0006296 "nucleotide-excision repair, DNA incision, 5'-to lesion" evidence=ISS

GO:0003697 "single-stranded DNA binding" evidence=ISS

GO:0000109 "nucleotide-excision repair complex" evidence=ISS

GO:0000014 "single-stranded DNA specific endodeoxyribonuclease activity" evidence=ISS

GO:0000784 "nuclear chromosome, telomeric region" evidence=ISS

GO:0043566 "structure-specific DNA binding" evidence=ISS

GO:0032205 "negative regulation of telomere maintenance" evidence=ISS

GO:0051276 "chromosome organization" evidence=IEA

GO:0048477 "oogenesis" evidence=IEA

GO:0045190 "isotype switching" evidence=IEA

GO:0043066 "negative regulation of apoptotic process" evidence=IEA

GO:0035264 "multicellular organism growth" evidence=IEA

GO:0035166 "post-embryonic hemopoiesis" evidence=IEA

GO:0019904 "protein domain specific binding" evidence=IEA

GO:0010259 "multicellular organismal aging" evidence=IEA

GO:0010165 "response to X-ray" evidence=IEA

GO:0009650 "UV protection" evidence=IEA

GO:0008584 "male gonad development" evidence=IEA

GO:0008283 "cell proliferation" evidence=IEA

GO:0007283 "spermatogenesis" evidence=IEA

GO:0007281 "germ cell development" evidence=IEA

GO:0006949 "syncytium formation" evidence=IEA

GO:0006302 "double-strand break repair" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0001302 "replicative cell aging" evidence=IEA

GO:0000720 "pyrimidine dimer repair by nucleotide-excision repair" evidence=IEA

UNIPROTKB|Q6UIQ5 ERCC1 "Excision repair protein" [Pan troglodytes (taxid:9598)]

 Score = 298 (110.0 bits), Expect = 2.8e-42, Sum P(2) = 2.8e-42
 Identities = 58/100 (58%), Positives = 74/100 (74%)

Query:   177 CALYL--SLEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTL 234
             C L L  S EE GRYLET K YE KPADL+  +++ D++SR+T  LT+V+SVNKTD  TL
Sbjct:   151 CTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTL 210

Query:   235 GSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPF 274
              +TFGSL  ++ AS EDLA CPG+G +K +RL+D  HEPF
Sbjct:   211 LTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPF 250

GO:0000109 "nucleotide-excision repair complex" evidence=ISS

GO:0000784 "nuclear chromosome, telomeric region" evidence=ISS

GO:0003684 "damaged DNA binding" evidence=ISS

GO:0003697 "single-stranded DNA binding" evidence=ISS

GO:0006295 "nucleotide-excision repair, DNA incision, 3'-to lesion" evidence=ISS

GO:0006296 "nucleotide-excision repair, DNA incision, 5'-to lesion" evidence=ISS

GO:0006312 "mitotic recombination" evidence=ISS

GO:0006979 "response to oxidative stress" evidence=ISS

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

GO:0032205 "negative regulation of telomere maintenance" evidence=ISS

GO:0000014 "single-stranded DNA specific endodeoxyribonuclease activity" evidence=ISS

GO:0043566 "structure-specific DNA binding" evidence=ISS

ZFIN|ZDB-GENE-040426-2606 ercc1 "excision repair cross-complementing rodent repair deficiency, complementation group 1" [Danio rerio (taxid:7955)]

 Score = 293 (108.2 bits), Expect = 1.1e-40, Sum P(2) = 1.1e-40
 Identities = 58/100 (58%), Positives = 74/100 (74%)

Query:   177 CALYL--SLEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTL 234
             C L L  S EE GRYLET K YE KPADL++ Q++ +YLS++T  LT+V+SVNKTD +TL
Sbjct:   235 CTLILAWSPEEAGRYLETYKSYEKKPADLLKEQVEKNYLSQVTDCLTTVKSVNKTDAMTL 294

Query:   235 GSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPF 274
              STF SL  I+ AS E+L  CPG+G +K +RLYD  H+PF
Sbjct:   295 LSTFSSLEGIIKASKEELVLCPGLGPQKARRLYDVLHQPF 334

GO:0003677 "DNA binding" evidence=IEA

GO:0004519 "endonuclease activity" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003684 "damaged DNA binding" evidence=IEA

RGD|1306992 Ercc1 "excision repair cross-complementing rodent repair deficiency, complementation group 1" [Rattus norvegicus (taxid:10116)]

 Score = 297 (109.6 bits), Expect = 2.2e-40, Sum P(2) = 2.2e-40
 Identities = 58/103 (56%), Positives = 75/103 (72%)

Query:   177 CALYL--SLEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTL 234
             C L L  S EE GRYLET K YE KPADL+  +++ ++LSR T  LT+V+SVNKTD  TL
Sbjct:   194 CTLVLAWSAEEAGRYLETYKAYEQKPADLLMEKLEQNFLSRATECLTTVKSVNKTDSQTL 253

Query:   235 GSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKRV 277
              +TFGSL  ++ AS EDLA CPG+G +K +RL++  HEPF +V
Sbjct:   254 LTTFGSLEQLITASREDLALCPGLGPQKARRLFEVLHEPFLKV 296

GO:0000014 "single-stranded DNA specific endodeoxyribonuclease activity" evidence=IEA;ISO

GO:0000109 "nucleotide-excision repair complex" evidence=IEA;ISO

GO:0000720 "pyrimidine dimer repair by nucleotide-excision repair" evidence=IEA;ISO

GO:0000784 "nuclear chromosome, telomeric region" evidence=IEA;ISO

GO:0001094 "TFIID-class transcription factor binding" evidence=ISO

GO:0001302 "replicative cell aging" evidence=IEA;ISO

GO:0003674 "molecular_function" evidence=ND

GO:0003684 "damaged DNA binding" evidence=IEA;ISO

GO:0003697 "single-stranded DNA binding" evidence=IEA;ISO

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0005669 "transcription factor TFIID complex" evidence=ISO

GO:0005737 "cytoplasm" evidence=IEA;ISO

GO:0006281 "DNA repair" evidence=ISO

GO:0006289 "nucleotide-excision repair" evidence=ISO

GO:0006295 "nucleotide-excision repair, DNA incision, 3'-to lesion" evidence=IEA;ISO

GO:0006296 "nucleotide-excision repair, DNA incision, 5'-to lesion" evidence=IEA;ISO

GO:0006302 "double-strand break repair" evidence=IEA;ISO

GO:0006310 "DNA recombination" evidence=ISO

GO:0006312 "mitotic recombination" evidence=IEA;ISO

GO:0006949 "syncytium formation" evidence=IEA;ISO

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

GO:0006979 "response to oxidative stress" evidence=IEA;ISO

GO:0007281 "germ cell development" evidence=IEA;ISO

GO:0007283 "spermatogenesis" evidence=IEA;ISO

GO:0007584 "response to nutrient" evidence=IEP

GO:0008022 "protein C-terminus binding" evidence=IEA;ISO

GO:0008283 "cell proliferation" evidence=IEA;ISO

GO:0008584 "male gonad development" evidence=IEA;ISO

GO:0009628 "response to abiotic stimulus" evidence=IEP

GO:0009650 "UV protection" evidence=IEA;ISO

GO:0009744 "response to sucrose stimulus" evidence=IEP

GO:0010165 "response to X-ray" evidence=IEA;ISO

GO:0010259 "multicellular organismal aging" evidence=IEA;ISO

GO:0017025 "TBP-class protein binding" evidence=ISO

GO:0019904 "protein domain specific binding" evidence=IEA;ISO

GO:0032205 "negative regulation of telomere maintenance" evidence=IEA;ISO

GO:0035166 "post-embryonic hemopoiesis" evidence=IEA;ISO

GO:0035264 "multicellular organism growth" evidence=IEA;ISO

GO:0043066 "negative regulation of apoptotic process" evidence=IEA;ISO

GO:0045190 "isotype switching" evidence=IEA;ISO

GO:0048468 "cell development" evidence=ISO

GO:0048477 "oogenesis" evidence=IEA;ISO

GO:0048568 "embryonic organ development" evidence=IEP

GO:0051276 "chromosome organization" evidence=IEA;ISO

GO:0005730 "nucleolus" evidence=ISO

GO:0043566 "structure-specific DNA binding" evidence=ISO

UNIPROTKB|B3KRR0 ERCC1 "cDNA FLJ34720 fis, clone MESAN2005724, highly similar to DNA EXCISION REPAIR PROTEIN ERCC-1" [Homo sapiens (taxid:9606)]

 Score = 302 (111.4 bits), Expect = 1.5e-39, Sum P(2) = 1.5e-39
 Identities = 59/103 (57%), Positives = 76/103 (73%)

Query:   177 CALYL--SLEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTL 234
             C L L  S EE GRYLET K YE KPADL+  +++ D++SR+T  LT+V+SVNKTD  TL
Sbjct:   122 CTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTL 181

Query:   235 GSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKRV 277
              +TFGSL  ++ AS EDLA CPG+G +K +RL+D  HEPF +V
Sbjct:   182 LTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKV 224

GO:0003684 "damaged DNA binding" evidence=IEA

GO:0004519 "endonuclease activity" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|F1PPD0 ERCC1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 263 (97.6 bits), Expect = 2.2e-38, Sum P(2) = 2.2e-38
 Identities = 53/92 (57%), Positives = 68/92 (73%)

Query:   177 CALYL--SLEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTL 234
             C L L  S EE GRYLET K YE KPADL+  +++ D++SR+T  LT+V+SVNKTD  TL
Sbjct:   194 CTLVLAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTL 253

Query:   235 GSTFGSLSHIMDASMEDLARCPGIGERKVKRL 266
              +TFGSL  +M AS EDLA CPG+G +KV+ +
Sbjct:   254 LTTFGSLEQLMAASREDLALCPGLGPQKVRAM 285

GO:0006281 "DNA repair" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0004519 "endonuclease activity" evidence=IEA

GO:0003684 "damaged DNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	368
pfam03834	68	pfam03834, Rad10, Binding domain of DNA repair pro	3e-18
TIGR00597	112	TIGR00597, rad10, DNA repair protein rad10	2e-13
COG5241	224	COG5241, RAD10, Nucleotide excision repair endonuc	3e-08
PRK00558	598	PRK00558, uvrC, excinuclease ABC subunit C; Valida	8e-06
pfam12826	64	pfam12826, HHH_2, Helix-hairpin-helix motif	1e-05
TIGR00575	652	TIGR00575, dnlj, DNA ligase, NAD-dependent	9e-05
PRK07956	665	PRK07956, ligA, NAD-dependent DNA ligase LigA; Val	1e-04
COG0272	667	COG0272, Lig, NAD-dependent DNA ligase (contains B	2e-04
PRK13482	352	PRK13482, PRK13482, DNA integrity scanning protein	6e-04
PRK00024	224	PRK00024, PRK00024, hypothetical protein; Reviewed	7e-04
pfam00633	30	pfam00633, HHH, Helix-hairpin-helix motif	0.002
COG1948	254	COG1948, MUS81, ERCC4-type nuclease [DNA replicati	0.003

>gnl|CDD|190768 pfam03834, Rad10, Binding domain of DNA repair protein Ercc1 (rad10/Swi10)

 Score = 77.6 bits (192), Expect = 3e-18
 Identities = 27/45 (60%), Positives = 38/45 (84%)

Query: 139 NAILVSQRQKGNPLLKYIRNVRWAFADVVCDYLVGQNSCALYLSL 183
           ++ILVS RQKGNPLLK+++NV W ++D+V DY+VG+  C L+LSL
Sbjct: 1   SSILVSPRQKGNPLLKHLKNVPWEYSDIVPDYVVGKTRCVLFLSL 45

Ercc1 and XPF (xeroderma pigmentosum group F-complementing protein) are two structure-specific endonucleases of a class of seven containing an ERCC4 domain. Together they form an obligate complex that functions primarily in nucleotide excision repair (NER), a versatile pathway able to detect and remove a variety of DNA lesions induced by UV light and environmental carcinogens, and secondarily in DNA interstrand cross-link repair and telomere maintenance. This domain in fact binds simultaneously to both XPF and single-stranded DNA; this ternary complex explains the important role of Ercc1 in targeting its catalytic XPF partner to the NER pre-incision complex. Length = 68

>gnl|CDD|129685 TIGR00597, rad10, DNA repair protein rad10

 Score = 65.6 bits (160), Expect = 2e-13
 Identities = 29/45 (64%), Positives = 39/45 (86%)

Query: 139 NAILVSQRQKGNPLLKYIRNVRWAFADVVCDYLVGQNSCALYLSL 183
           N+ILV+ RQKGNPLLK++RNV W + DV+ DY++GQ +CAL+LSL
Sbjct: 1   NSILVNPRQKGNPLLKHVRNVPWEYGDVIPDYVLGQGTCALFLSL 45

All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs). This complex is used primarily for nucleotide excision repair but also for some aspects of recombination repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 112

>gnl|CDD|227566 COG5241, RAD10, Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, and repair]

 Score = 53.5 bits (128), Expect = 3e-08
 Identities = 34/140 (24%), Positives = 55/140 (39%), Gaps = 5/140 (3%)

Query: 135 IQSRNAILVSQRQKGNPLLKYIRNVRWAFADVVCDYLVGQNSCALYLSLEECGRYLETIK 194
           I  R + L S   K  PLL ++ +  W  +        G N+  L  S+EE  RY  T+ 
Sbjct: 89  IVLRISKLKSY--KERPLLNHVDSTNWRASIQELVSTTGINTIYLDYSVEERSRYFLTLT 146

Query: 195 VYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLAR 254
            ++     +I+     D  +     L  +  VNK+D     +  G L     AS ++   
Sbjct: 147 YHKLYSDYIIRRMQSLDRSNEF---LILIFIVNKSDSEDTLNDIGKLCRFNGASRDEFEL 203

Query: 255 CPGIGERKVKRLYDTFHEPF 274
             G G  K  +  +  + PF
Sbjct: 204 LLGFGFEKAAKYIEYLNLPF 223

Length = 224

>gnl|CDD|234792 PRK00558, uvrC, excinuclease ABC subunit C; Validated

 Score = 47.4 bits (114), Expect = 8e-06
 Identities = 15/35 (42%), Positives = 25/35 (71%)

Query: 238 FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272
           FGSL  I +AS+E+LA+ PGI ++  + +Y+  H+
Sbjct: 563 FGSLKAIKEASVEELAKVPGISKKLAEAIYEALHK 597

Length = 598

>gnl|CDD|205093 pfam12826, HHH_2, Helix-hairpin-helix motif

 Score = 42.1 bits (100), Expect = 1e-05
 Identities = 19/59 (32%), Positives = 28/59 (47%), Gaps = 1/59 (1%)

Query: 215 RLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEP 273
           RL  AL  +R V +     L   FGSL  + +AS+E+L     IG    + + + F  P
Sbjct: 1   RLLFAL-GIRHVGEKTAKLLAKHFGSLDALANASVEELLEIDDIGPIVAQSIVEFFANP 58

The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain. Length = 64

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

 Score = 44.2 bits (105), Expect = 9e-05
 Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 213 LSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272
           L+RL  AL  +R V +     L   FG+L  +  AS+E+L    G+G +  + + + FH+
Sbjct: 494 LARLLFAL-GIRHVGEVTAKNLAKHFGTLDKLKAASLEELLSVEGVGPKVAESIVNFFHD 552

Query: 273 P 273
           P
Sbjct: 553 P 553

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

>gnl|CDD|236137 PRK07956, ligA, NAD-dependent DNA ligase LigA; Validated

 Score = 43.6 bits (104), Expect = 1e-04
 Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 1/61 (1%)

Query: 213 LSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272
           L+R  +AL  +R V +     L   FGSL  +  AS E+LA   G+GE   + + + F  
Sbjct: 507 LARFLYAL-GIRHVGEKAAKALARHFGSLEALRAASEEELAAVEGVGEVVAQSIVEFFAV 565

Query: 273 P 273
            
Sbjct: 566 E 566

Length = 665

>gnl|CDD|223350 COG0272, Lig, NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]

 Score = 43.0 bits (102), Expect = 2e-04
 Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 212 YLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271
            L+R  +AL  +R V +T   +L   FG+L  ++ AS E+LA  PGIGE   + + + F 
Sbjct: 506 PLARFLYAL-GIRHVGETTAKSLARHFGTLEALLAASEEELASIPGIGEVVARSIIEFFA 564

Query: 272 EP 273
             
Sbjct: 565 NE 566

Length = 667

>gnl|CDD|237395 PRK13482, PRK13482, DNA integrity scanning protein DisA; Provisional

 Score = 40.9 bits (97), Expect = 6e-04
 Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 3/48 (6%)

Query: 220 LTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGE---RKVK 264
           L+ +  +    +  L   FGSL  ++ AS+EDL    GIGE   R ++
Sbjct: 289 LSKIPRLPSAVIENLVEHFGSLQGLLAASIEDLDEVEGIGEVRARAIR 336

Length = 352

>gnl|CDD|178801 PRK00024, PRK00024, hypothetical protein; Reviewed

 Score = 40.4 bits (96), Expect = 7e-04
 Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 4/37 (10%)

Query: 230 DVVTLG----STFGSLSHIMDASMEDLARCPGIGERK 262
            V+ L       FGSL  ++DAS+E+L    GIG  K
Sbjct: 42  SVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAK 78

Length = 224

>gnl|CDD|109681 pfam00633, HHH, Helix-hairpin-helix motif

 Score = 35.1 bits (82), Expect = 0.002
 Identities = 9/29 (31%), Positives = 16/29 (55%)

Query: 240 SLSHIMDASMEDLARCPGIGERKVKRLYD 268
           SL  ++ AS E+L   PG+G +  + +  
Sbjct: 1   SLEGLIPASREELLALPGVGPKTAEAILS 29

The helix-hairpin-helix DNA-binding motif is found to be duplicated in the central domain of RuvA. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain. Length = 30

>gnl|CDD|224859 COG1948, MUS81, ERCC4-type nuclease [DNA replication, recombination, and repair]

 Score = 38.5 bits (90), Expect = 0.003
 Identities = 17/66 (25%), Positives = 29/66 (43%)

Query: 211 DYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTF 270
                  + L S+  +       L   FGS+  ++ AS E+L +  GIGE+K + +Y   
Sbjct: 175 TLKELQLYILESIPGIGPKLAERLLKKFGSVEDVLTASEEELMKVKGIGEKKAREIYRFL 234

Query: 271 HEPFKR 276
              +K 
Sbjct: 235 RTEYKL 240

Length = 254

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	368
KOG2841	254	consensus Structure-specific endonuclease ERCC1-XP	100.0
COG5241	224	RAD10 Nucleotide excision repair endonuclease NEF1	99.9
TIGR00597	112	rad10 DNA repair protein rad10. All proteins in th	99.82
PF03834	69	Rad10: Binding domain of DNA repair protein Ercc1	99.77
COG1948	254	MUS81 ERCC4-type nuclease [DNA replication, recomb	99.53
PF12826	64	HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS	99.49
PRK13766	773	Hef nuclease; Provisional	99.27
PRK14670	574	uvrC excinuclease ABC subunit C; Provisional	99.12
PRK14667	567	uvrC excinuclease ABC subunit C; Provisional	99.06
PF14520	60	HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU	99.02
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	99.0
PRK14669	624	uvrC excinuclease ABC subunit C; Provisional	98.99
PRK14666	694	uvrC excinuclease ABC subunit C; Provisional	98.98
PRK00558	598	uvrC excinuclease ABC subunit C; Validated	98.97
PRK14672	691	uvrC excinuclease ABC subunit C; Provisional	98.89
COG0322	581	UvrC Nuclease subunit of the excinuclease complex	98.83
PRK14668	577	uvrC excinuclease ABC subunit C; Provisional	98.81
PRK13482	352	DNA integrity scanning protein DisA; Provisional	98.76
TIGR00575	652	dnlj DNA ligase, NAD-dependent. The member of this	98.76
PRK00116	192	ruvA Holliday junction DNA helicase RuvA; Reviewed	98.73
PRK12766	232	50S ribosomal protein L32e; Provisional	98.68
PRK07956	665	ligA NAD-dependent DNA ligase LigA; Validated	98.66
COG0272	667	Lig NAD-dependent DNA ligase (contains BRCT domain	98.65
PRK14351	689	ligA NAD-dependent DNA ligase LigA; Provisional	98.63
PRK14671	621	uvrC excinuclease ABC subunit C; Provisional	98.62
PRK14350	669	ligA NAD-dependent DNA ligase LigA; Provisional	98.37
PRK08097	562	ligB NAD-dependent DNA ligase LigB; Reviewed	98.23
PRK00254	720	ski2-like helicase; Provisional	98.02
TIGR00194	574	uvrC excinuclease ABC, C subunit. This family cons	97.92
PF00633	30	HHH: Helix-hairpin-helix motif; InterPro: IPR00044	97.91
TIGR00426	69	competence protein ComEA helix-hairpin-helix repea	97.84
COG1623	349	Predicted nucleic-acid-binding protein (contains t	97.8
TIGR01259	120	comE comEA protein. This model describes the ComEA	97.76
KOG0442	892	consensus Structure-specific endonuclease ERCC1-XP	97.72
PRK14605	194	ruvA Holliday junction DNA helicase RuvA; Provisio	97.56
PRK14602	203	ruvA Holliday junction DNA helicase RuvA; Provisio	97.55
PRK13901	196	ruvA Holliday junction DNA helicase RuvA; Provisio	97.43
PRK14606	188	ruvA Holliday junction DNA helicase RuvA; Provisio	97.42
PRK14604	195	ruvA Holliday junction DNA helicase RuvA; Provisio	97.36
PRK14601	183	ruvA Holliday junction DNA helicase RuvA; Provisio	97.35
PRK00024	224	hypothetical protein; Reviewed	97.34
TIGR00084	191	ruvA Holliday junction DNA helicase, RuvA subunit.	97.33
PRK14600	186	ruvA Holliday junction DNA helicase RuvA; Provisio	97.3
COG2003	224	RadC DNA repair proteins [DNA replication, recombi	97.29
PRK14603	197	ruvA Holliday junction DNA helicase RuvA; Provisio	97.27
TIGR00608	218	radc DNA repair protein radc. This family is based	97.2
COG0632	201	RuvA Holliday junction resolvasome, DNA-binding su	97.11
TIGR02236	310	recomb_radA DNA repair and recombination protein R	96.95
PRK04301	317	radA DNA repair and recombination protein RadA; Va	96.62
PRK02515	132	psbU photosystem II complex extrinsic protein prec	95.94
cd00141	307	NT_POLXc Nucleotidyltransferase (NT) domain of fam	95.47
COG1555	149	ComEA DNA uptake protein and related DNA-binding p	95.43
PRK02515	132	psbU photosystem II complex extrinsic protein prec	95.42
COG1796	326	POL4 DNA polymerase IV (family X) [DNA replication	95.23
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	95.22
PRK07956	665	ligA NAD-dependent DNA ligase LigA; Validated	95.17
TIGR00575	652	dnlj DNA ligase, NAD-dependent. The member of this	95.16
PF12836	65	HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE	95.11
TIGR01954	50	nusA_Cterm_rpt transcription termination factor Nu	95.04
PRK01172	674	ski2-like helicase; Provisional	94.99
smart00483	334	POLXc DNA polymerase X family. includes vertebrate	94.84
cd00080	75	HhH2_motif Helix-hairpin-helix class 2 (Pol1 famil	94.28
PRK08609	570	hypothetical protein; Provisional	94.06
TIGR01259	120	comE comEA protein. This model describes the ComEA	93.98
PF03118	66	RNA_pol_A_CTD: Bacterial RNA polymerase, alpha cha	93.8
PRK14351	689	ligA NAD-dependent DNA ligase LigA; Provisional	93.61
cd00008	240	53EXOc 5'-3' exonuclease; T5 type 5'-3' exonucleas	93.47
PRK02362	737	ski2-like helicase; Provisional	93.36
smart00278	26	HhH1 Helix-hairpin-helix DNA-binding motif class 1	93.33
COG1555	149	ComEA DNA uptake protein and related DNA-binding p	93.23
PRK09482	256	flap endonuclease-like protein; Provisional	93.18
PRK08609	570	hypothetical protein; Provisional	92.84
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	92.72
smart00475	259	53EXOc 5'-3' exonuclease.	92.67
PF12836	65	HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE	92.49
PRK14976	281	5'-3' exonuclease; Provisional	92.45
PTZ00035	337	Rad51 protein; Provisional	92.43
PRK08097	562	ligB NAD-dependent DNA ligase LigB; Reviewed	91.98
PF01367	101	5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold	91.79
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	91.53
PF00730	108	HhH-GPD: HhH-GPD superfamily base excision DNA rep	90.81
PRK07758	95	hypothetical protein; Provisional	89.94
TIGR03252	177	uncharacterized HhH-GPD family protein. This model	89.11
TIGR00593	887	pola DNA polymerase I. This family is based on the	88.73
PRK14350	669	ligA NAD-dependent DNA ligase LigA; Provisional	88.41
PRK03980	292	flap endonuclease-1; Provisional	88.15
PRK10736	374	hypothetical protein; Provisional	88.06
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	87.83
TIGR00426	69	competence protein ComEA helix-hairpin-helix repea	87.61
COG0258	310	Exo 5'-3' exonuclease (including N-terminal domain	87.59
PRK10702	211	endonuclease III; Provisional	87.01
PF14716	68	HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HU	86.51
PRK13913	218	3-methyladenine DNA glycosylase; Provisional	86.51
PF14520	60	HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU	86.31
COG0177	211	Nth Predicted EndoIII-related endonuclease [DNA re	86.18
PRK05755	880	DNA polymerase I; Provisional	84.81
PRK00116	192	ruvA Holliday junction DNA helicase RuvA; Reviewed	84.57
cd00128	316	XPG Xeroderma pigmentosum G N- and I-regions (XPGN	84.42
PRK14973	936	DNA topoisomerase I; Provisional	83.92
smart00279	36	HhH2 Helix-hairpin-helix class 2 (Pol1 family) mot	83.88
smart00611	312	SEC63 Domain of unknown function in Sec63p, Brr2p	83.68
TIGR03674	338	fen_arch flap structure-specific endonuclease. End	83.22
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	83.22
PF11731	93	Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd	83.07
PTZ00217	393	flap endonuclease-1; Provisional	82.7
cd00080	75	HhH2_motif Helix-hairpin-helix class 2 (Pol1 famil	82.39
PF02371	87	Transposase_20: Transposase IS116/IS110/IS902 fami	80.54
PRK10702	211	endonuclease III; Provisional	80.41
smart00478	149	ENDO3c endonuclease III. includes endonuclease III	80.04

>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]

Probab=100.00  E-value=4.9e-46  Score=348.93  Aligned_cols=187  Identities=42%  Similarity=0.681  Sum_probs=162.5

Q ss_pred             CCCCCCCccCCccHHHHhhhhhcccccCCCCCCCCCCCCCCCCCCcCCCCCcccCCCcccCCccccCCCCCeEEEcCCcc
Q 017612           69 TNPPQNLFTPSQSFSQAFSFIKSSEFYNPPPPPPANPPTTSQNPTLSQGGEQNVGTASASASSSQSIQSRNAILVSQRQK  148 (368)
Q Consensus        69 ~~~~~~~~~~s~~f~~~f~~~k~~~~y~~p~~~~~~~~~~~~~~t~~~~~~~~~~~p~~~~~~~~~~~~~~~IlVS~rQr  148 (368)
                      ...|+++++||+.+.+++.+++.-..+..-           ..+       ....+|.-+   ..+...+++|+||+|||
T Consensus         7 ~s~~~~~~s~s~~~~~~~~~v~~p~~~~~~-----------~~p-------~~s~~P~~~---g~~~~~~~~Ilvn~rQk   65 (254)
T KOG2841|consen    7 KSFPDSLGSPSLEIDAKKLFVQAPARIASN-----------PIP-------MNSQPPDGS---GPVTVPGGHILVNPRQK   65 (254)
T ss_pred             cccCccccCcchHHHHhhhhccCcHhHhcC-----------CCc-------ccCCCCCCC---CCCCCCCceEEeccccc
Confidence            446899999999999999999921000000           000       011112111   23456789999999999


Q ss_pred             CChhHHhhhccceEee-ecccceEeccceeeeeec---------------------------------------------
Q 017612          149 GNPLLKYIRNVRWAFA-DVVCDYLVGQNSCALYLS---------------------------------------------  182 (368)
Q Consensus       149 GNPLLk~IrnVpwefa-DIvpDY~Ig~ttcILFLS---------------------------------------------  182 (368)
                      |||||+|||||+|+|+ ||.|||++|+++||||||                                             
T Consensus        66 GNplLk~vrnv~w~f~ddi~PDf~lg~~~cvLyLSl~yH~l~pdYi~~Ri~~l~k~yk~~VLl~~vd~~e~~~~l~el~k  145 (254)
T KOG2841|consen   66 GNPLLKHVRNVKWEFGDDIIPDFVLGRGCCVLYLSLKYHKLHPDYIYRRIRKLGKNYKLRVLLVHVDMEEPYKPLLELTK  145 (254)
T ss_pred             cChHHHHHhcCCeEecCCCCcceEecCceEEEEeehHhhhcCcHHHHHHHHHhcccccceEEEEEecCcchHHHHHHHHH
Confidence            9999999999999999 799999999999999999                                             


Q ss_pred             --------------hhhHHHHHHHHHHhhcCCcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCC
Q 017612          183 --------------LEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDAS  248 (368)
Q Consensus       183 --------------~EEAArYIEt~K~~E~K~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS  248 (368)
                                    .||||+|||+|+.||+++++.|+++.++||.++++.+||+||||||+||..||.+||||++|++||
T Consensus       146 ~~~l~~~Tl~lA~s~EeaaryIE~~k~~ek~p~dli~~~~~~d~ls~~~~~Lt~i~~VnKtda~~LL~~FgsLq~~~~AS  225 (254)
T KOG2841|consen  146 TCDLNDVTLVLAWSMEEAARYIETYKEYEKKPIDLIMERKDRDLLSSLLGFLTTIPGVNKTDAQLLLQKFGSLQQISNAS  225 (254)
T ss_pred             HHHhhceeeeeeccHHHHHHHHHHHHHhhcCCchhhhhcccccHHHHHHHHHHhCCCCCcccHHHHHHhcccHHHHHhcC
Confidence                          999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhhcCCCCCHHHHHHHHHHhcccccc
Q 017612          249 MEDLARCPGIGERKVKRLYDTFHEPFKR  276 (368)
Q Consensus       249 ~EELa~VPGIG~kKA~rI~e~F~ePF~~  276 (368)
                      .+||++|+|+|+.||++|+++||+||..
T Consensus       226 ~~ele~~~G~G~~kak~l~~~l~~pf~~  253 (254)
T KOG2841|consen  226 EGELEQCPGLGPAKAKRLHKFLHQPFLS  253 (254)
T ss_pred             HhHHHhCcCcCHHHHHHHHHHHhccccC
Confidence            9999999999999999999999999974

>COG5241 RAD10 Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, and repair]

Probab=99.90  E-value=3.3e-25  Score=203.46  Aligned_cols=136  Identities=27%  Similarity=0.332  Sum_probs=129.8

Q ss_pred             CCCeEEEcCCccCChhHHhhhccceEeee-cccceEeccceeeeeec---------------------------------
Q 017612          137 SRNAILVSQRQKGNPLLKYIRNVRWAFAD-VVCDYLVGQNSCALYLS---------------------------------  182 (368)
Q Consensus       137 ~~~~IlVS~rQrGNPLLk~IrnVpwefaD-IvpDY~Ig~ttcILFLS---------------------------------  182 (368)
                      ....|.||++|+|||+|-|.+|++|+|.+ |+|||.++...|-||||                                 
T Consensus        32 ~s~~I~vsplQkgnp~l~~~~N~~w~y~~~i~Pd~~~~s~~~~lflslrfhs~~Peyi~~riSklKsYk~r~LL~hvd~~  111 (224)
T COG5241          32 QSLEIDVSPLQKGNPQLSRRINSNWVYNAFIKPDEWTDSKATDLFLSLRFHSTRPEYIVLRISKLKSYKERPLLNHVDST  111 (224)
T ss_pred             eeeEEecChhhcCCCcccccccCcceeccccCcchhhcchHHHHHHHHhhhcCCCceEEEeeeccccccccceeeeeccc
Confidence            35699999999999999999999999998 99999999999999999                                 


Q ss_pred             -----------------------hhhHHHHHHHHHHhhcCCcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcC
Q 017612          183 -----------------------LEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFG  239 (368)
Q Consensus       183 -----------------------~EEAArYIEt~K~~E~K~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FG  239 (368)
                                             .|||+|||++|+.++......||++...|+ +  .+.|+.|++|||.|+..+|..||
T Consensus       112 N~~asIqElv~Tt~inti~l~~svee~sry~~t~~~~~~~s~~iir~~~s~d~-s--~~fl~~i~~Vnksds~~~L~d~g  188 (224)
T COG5241         112 NWRASIQELVSTTGINTIYLDYSVEERSRYFLTLTYHKLYSDYIIRRMQSLDR-S--NEFLILIFIVNKSDSEDTLNDIG  188 (224)
T ss_pred             cHHHHHHHHHHhcccceeehhhhhhHHHHHHHHhHHHhhcCHHHHHhcCCCcc-c--ccceEEEEeeccccHHHHHHHHH
Confidence                                   899999999999999999999999888887 2  67899999999999999999999


Q ss_pred             CHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612          240 SLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFK  275 (368)
Q Consensus       240 SLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~  275 (368)
                      +|+....||.+|+..+.|+|..||.++.++++.||.
T Consensus       189 ~L~rf~gaSrdE~e~l~g~g~~ka~~~ieyln~pFm  224 (224)
T COG5241         189 KLCRFNGASRDEFELLLGFGFEKAAKYIEYLNLPFM  224 (224)
T ss_pred             HHHHHhccchhHHHHHHccCHHHHHHHHHHhcccCC
Confidence            999999999999999999999999999999999994

>TIGR00597 rad10 DNA repair protein rad10

Probab=99.82  E-value=8.4e-21  Score=161.85  Aligned_cols=44  Identities=64%  Similarity=1.158  Sum_probs=43.0

Q ss_pred             CeEEEcCCccCChhHHhhhccceEeeecccceEeccceeeeeec
Q 017612          139 NAILVSQRQKGNPLLKYIRNVRWAFADVVCDYLVGQNSCALYLS  182 (368)
Q Consensus       139 ~~IlVS~rQrGNPLLk~IrnVpwefaDIvpDY~Ig~ttcILFLS  182 (368)
                      ++|+||+||||||||+|||+|+|+|+||+|||++|+++||||||
T Consensus         1 ~~ilvs~~QkgNPlL~~i~nv~wey~di~~Dy~~g~~~~vLFLS   44 (112)
T TIGR00597         1 NSILVNPRQKGNPLLKHVRNVPWEYGDVIPDYVLGQGTCALFLS   44 (112)
T ss_pred             CcEEeCccccCChHHHHHhcCCeEecCcCCCEEEcCccEEEEEE
Confidence            47999999999999999999999999999999999999999999

All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs). This complex is used primarily for nucleotide excision repair but also for some aspects of recombination repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PF03834 Rad10: Binding domain of DNA repair protein Ercc1 (rad10/Swi10); InterPro: IPR004579 All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs)

Probab=99.77  E-value=1.9e-19  Score=142.21  Aligned_cols=44  Identities=64%  Similarity=1.146  Sum_probs=35.1

Q ss_pred             CeEEEcCCccCChhHHhhhccceEe-eecccceEeccceeeeeec
Q 017612          139 NAILVSQRQKGNPLLKYIRNVRWAF-ADVVCDYLVGQNSCALYLS  182 (368)
Q Consensus       139 ~~IlVS~rQrGNPLLk~IrnVpwef-aDIvpDY~Ig~ttcILFLS  182 (368)
                      ++|+||++|||||||++|++||||| +||+|||+||+++||||||
T Consensus         1 ~~I~vn~~QkGNplL~~i~nv~we~~~~i~~Dy~vg~~~~vLFLS   45 (69)
T PF03834_consen    1 NSILVNPRQKGNPLLKHIRNVPWEYDSDIVPDYVVGSTTCVLFLS   45 (69)
T ss_dssp             SSEEE-GGGTT-CHHHH--SS-EEE----SSSEEEETTEEEEEEE
T ss_pred             CcEEECchhcCChHHHHHhcCCeEecCCCCCCEEECCeEEEEEEe
Confidence            4799999999999999999999999 8999999999999999999

This complex is used primarily for nucleotide excision repair but also for some aspects of recombination repair. In yeast, Rad10 works as a heterodimer with Rad1, and is involved in nucleotide excision repair of DNA damaged with UV light, bulky adducts or cross-linking agents. The complex forms an endonuclease which specifically degrades single-stranded DNA. Ercc1 and XPF (xeroderma pigmentosum group F-complementing protein) are two structure-specific endonucleases of a class of seven containing an ERCC4 domain. Together they form an obligate complex that functions primarily in nucleotide excision repair (NER), a versatile pathway able to detect and remove a variety of DNA lesions induced by UV light and environmental carcinogens, and secondarily in DNA inter-strand cross-link repair and telomere maintenance. This domain in fact binds simultaneously to both XPF and single-stranded DNA; this ternary complex explains the important role of Ercc1 in targeting its catalytic XPF partner to the NER pre-incision complex [].; GO: 0003684 damaged DNA binding, 0004519 endonuclease activity, 0006281 DNA repair, 0005634 nucleus; PDB: 2JNW_A 2JPD_A 2A1I_A.

>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]

Probab=99.53  E-value=2.5e-14  Score=136.63  Aligned_cols=108  Identities=21%  Similarity=0.328  Sum_probs=96.8

Q ss_pred             ecccceEeccceeeeeec-hhhHHHHHHHHHHhhc---CCcchhcc-cccccHHHHHHHhhccCCCCCHHHHHHHHHhcC
Q 017612          165 DVVCDYLVGQNSCALYLS-LEECGRYLETIKVYEN---KPADLIQG-QMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFG  239 (368)
Q Consensus       165 DIvpDY~Ig~ttcILFLS-~EEAArYIEt~K~~E~---K~~d~Ire-k~e~dy~srL~saLTsIpgVnKTDA~~LLs~FG  239 (368)
                      .+..||.+    .|+|.+ .+|++.+|..|++.++   +.....+. +...++.+++.+.|.+|||||...|.+||.+||
T Consensus       128 s~~vdfg~----~vi~t~~~~~Ta~~i~~la~req~e~~r~v~~~~~~~~~t~~e~q~~il~s~pgig~~~a~~ll~~fg  203 (254)
T COG1948         128 SLAVDFGL----PVIWTRSPEETAELIHELARREQEERKRSVNPHGKKKAKTLKELQLYILESIPGIGPKLAERLLKKFG  203 (254)
T ss_pred             HHHhhcCc----eEEEeCCHHHHHHHHHHHHHHHHHhccccccccccccccchHHHHHHHHHcCCCccHHHHHHHHHHhc
Confidence            46788987    799996 9999999999999988   43333444 444789999999999999999999999999999


Q ss_pred             CHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcccccc
Q 017612          240 SLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKR  276 (368)
Q Consensus       240 SLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~~  276 (368)
                      |++++++||.+||..+.|||+++|.+|+++|..+|..
T Consensus       204 S~~~~~tas~~eL~~v~gig~k~A~~I~~~~~t~~~~  240 (254)
T COG1948         204 SVEDVLTASEEELMKVKGIGEKKAREIYRFLRTEYKL  240 (254)
T ss_pred             CHHHHhhcCHHHHHHhcCccHHHHHHHHHHHhchhhh
Confidence            9999999999999999999999999999999999984

>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B

Probab=99.49  E-value=3.3e-14  Score=109.08  Aligned_cols=60  Identities=35%  Similarity=0.658  Sum_probs=50.0

Q ss_pred             HHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612          215 RLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFK  275 (368)
Q Consensus       215 rL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~  275 (368)
                      |++.+| +|||||.+.|+.|+++|||+++|++|+.|||..|+|||++.|+.|+++|+.+-+
T Consensus         1 R~l~aL-GI~~VG~~~ak~L~~~f~sl~~l~~a~~e~L~~i~gIG~~~A~si~~ff~~~~n   60 (64)
T PF12826_consen    1 RFLFAL-GIPGVGEKTAKLLAKHFGSLEALMNASVEELSAIPGIGPKIAQSIYEFFQDPEN   60 (64)
T ss_dssp             HHHHHC-TSTT--HHHHHHHHHCCSCHHHHCC--HHHHCTSTT--HHHHHHHHHHHH-HHH
T ss_pred             CeeeeC-CCCCccHHHHHHHHHHcCCHHHHHHcCHHHHhccCCcCHHHHHHHHHHHCCHHh
Confidence            577888 899999999999999999999999999999999999999999999999998754

>PRK13766 Hef nuclease; Provisional

Probab=99.27  E-value=7e-11  Score=124.36  Aligned_cols=140  Identities=21%  Similarity=0.286  Sum_probs=112.8

Q ss_pred             CCCCeEEEcCCccCChhHHhh--hccceEeeec-ccceEeccceeeeeec------------------------------
Q 017612          136 QSRNAILVSQRQKGNPLLKYI--RNVRWAFADV-VCDYLVGQNSCALYLS------------------------------  182 (368)
Q Consensus       136 ~~~~~IlVS~rQrGNPLLk~I--rnVpwefaDI-vpDY~Ig~ttcILFLS------------------------------  182 (368)
                      ...-.|+|-.|-....|..+|  .+|+++...+ +-||+++...||=-=|                              
T Consensus       560 ~~~~~i~vD~RE~~~~~~~~l~~~g~~~~~~~L~~gDy~~~~~~~vERK~~~Dl~~s~~~~r~~~q~~~l~~~~~~~~ll  639 (773)
T PRK13766        560 PEGPKIIVDSRELRSNVARHLKRLGAEVELKTLEVGDYVVSDRVAVERKTAEDFVDSIIDRRLFEQVKDLKRAYERPVLI  639 (773)
T ss_pred             CCCcEEEEeCCCccchhhHHHHhCCCEEEEEecCCCCEEccCCeEEEeCcHHHHHHHhhcCcHHHHHHHHHhcCCCcEEE
Confidence            344578999886555566665  3588888776 7899999888881000                              


Q ss_pred             ------------------------------------hhhHHHHHHHHHHhhcCCc----chhcccccccHHHHHHHhhcc
Q 017612          183 ------------------------------------LEECGRYLETIKVYENKPA----DLIQGQMDTDYLSRLTHALTS  222 (368)
Q Consensus       183 ------------------------------------~EEAArYIEt~K~~E~K~~----d~Irek~e~dy~srL~saLTs  222 (368)
                                                          .+|+|.||+.|+.+++..+    ....++...+..++....|.+
T Consensus       640 iE~~~~~~~~~~~~~i~~~l~~l~~~~~~~ii~~~~~~eta~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~  719 (773)
T PRK13766        640 IEGDLYTIRNIHPNAIRGALASIAVDFGIPILFTRDEEETADLLKVIAKREQEEEKREVSVHGEKKAMTLKEQQEYIVES  719 (773)
T ss_pred             EEcCchhhcccCHHHHHHHHHHHHHHcCceEEEeCCHHHHHHHHHHHHhhccccCCCCcccccCCCCCCHHHHHHHHHhc
Confidence                                                8999999999999886332    233445555555666668999


Q ss_pred             CCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612          223 VRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFK  275 (368)
Q Consensus       223 IpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~  275 (368)
                      |||||...+.+|+++|||+++|++|+.++|..|+|||+++|++|+++|+.+|.
T Consensus       720 ipgig~~~a~~Ll~~fgs~~~i~~as~~~L~~i~Gig~~~a~~i~~~~~~~~~  772 (773)
T PRK13766        720 LPDVGPVLARNLLEHFGSVEAVMTASEEELMEVEGIGEKTAKRIREVVTSEYK  772 (773)
T ss_pred             CCCCCHHHHHHHHHHcCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHhhhhc
Confidence            99999999999999999999999999999999999999999999999999885

>PRK14670 uvrC excinuclease ABC subunit C; Provisional

Probab=99.12  E-value=6.1e-11  Score=124.06  Aligned_cols=88  Identities=11%  Similarity=0.159  Sum_probs=74.3

Q ss_pred             Eeccceeeeee-c--hhhHHHHHHHHHHhhcCCcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcC
Q 017612          171 LVGQNSCALYL-S--LEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDA  247 (368)
Q Consensus       171 ~Ig~ttcILFL-S--~EEAArYIEt~K~~E~K~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~A  247 (368)
                      .+..++.+|+| .  .+||+||-.+|++.-.       .+        +.+.|..|||||++..+.||+||||+++|.+|
T Consensus       479 ~l~~~s~~l~lLq~iRDEaHRFAit~hRk~R-------~k--------~~s~L~~I~GiG~kr~~~LL~~Fgs~~~I~~A  543 (574)
T PRK14670        479 KLPKGNPALRILQNVRDEAHRKANGFNKKLR-------EN--------IKLNYTKIKGIGEKKAKKILKSLGTYKDILLL  543 (574)
T ss_pred             ecCCCCHHHHHHHHHHHHHHHHHHHHHHHhh-------cc--------cccccccCCCCCHHHHHHHHHHhCCHHHHHhC
Confidence            34455555533 3  9999999999998641       11        34689999999999999999999999999999


Q ss_pred             CHHhhhcCCCCCHHHHHHHHHHhccc
Q 017612          248 SMEDLARCPGIGERKVKRLYDTFHEP  273 (368)
Q Consensus       248 S~EELa~VPGIG~kKA~rI~e~F~eP  273 (368)
                      |.|||+.|||||++.|+.|+++|+..
T Consensus       544 s~eeL~~v~gi~~~~A~~I~~~l~~~  569 (574)
T PRK14670        544 NEDEIAEKMKINIKMAKKIKKFAEKQ  569 (574)
T ss_pred             CHHHHHhCCCCCHHHHHHHHHHHHHh
Confidence            99999999999999999999999754

>PRK14667 uvrC excinuclease ABC subunit C; Provisional

Probab=99.06  E-value=1.9e-10  Score=120.28  Aligned_cols=88  Identities=14%  Similarity=0.167  Sum_probs=74.4

Q ss_pred             eEeccceeeeeec---hhhHHHHHHHHHHhhcCCcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHc
Q 017612          170 YLVGQNSCALYLS---LEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMD  246 (368)
Q Consensus       170 Y~Ig~ttcILFLS---~EEAArYIEt~K~~E~K~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~  246 (368)
                      +.+..++.+|+|=   .+||+||-.+|++.-.         .    ...+.+.|..|+|||++..+.||+||||+++|.+
T Consensus       476 ~~l~~~s~~l~lLq~irDEaHRFAi~~hR~~r---------~----k~~~~S~Ld~I~GiG~kr~~~Ll~~Fgs~~~ik~  542 (567)
T PRK14667        476 IPLKENPILYKVFGLIRDEAHRFALSYNRKLR---------E----KEGLKDILDKIKGIGEVKKEIIYRNFKTLYDFLK  542 (567)
T ss_pred             eeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHh---------h----cccccCccccCCCCCHHHHHHHHHHhCCHHHHHh
Confidence            4555555555443   9999999999998631         1    1224678999999999999999999999999999


Q ss_pred             CCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          247 ASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       247 AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      ||.|||+.| |||++.|+.|++.|+
T Consensus       543 As~eeL~~v-gi~~~~A~~I~~~l~  566 (567)
T PRK14667        543 ADDEELKKL-GIPPSVKQEVKKYLS  566 (567)
T ss_pred             CCHHHHHHc-CCCHHHHHHHHHHhc
Confidence            999999999 999999999999986

>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A

Probab=99.02  E-value=3.9e-10  Score=84.79  Aligned_cols=56  Identities=23%  Similarity=0.422  Sum_probs=52.5

Q ss_pred             HHHhhccCCCCCHHHHHHHHHh-cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          216 LTHALTSVRSVNKTDVVTLGST-FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       216 L~saLTsIpgVnKTDA~~LLs~-FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      +...|..|+|||++++.+|++. |+|+++|.+++.++|..|+|||+++|++|.+.++
T Consensus         3 ~~~~L~~I~Gig~~~a~~L~~~G~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~~   59 (60)
T PF14520_consen    3 VFDDLLSIPGIGPKRAEKLYEAGIKTLEDLANADPEELAEIPGIGEKTAEKIIEAAR   59 (60)
T ss_dssp             HHHHHHTSTTCHHHHHHHHHHTTCSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHHHH
T ss_pred             HHHhhccCCCCCHHHHHHHHhcCCCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHHHh
Confidence            3456779999999999999999 9999999999999999999999999999999875

...

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=99.00  E-value=7.9e-10  Score=119.70  Aligned_cols=97  Identities=20%  Similarity=0.256  Sum_probs=77.1

Q ss_pred             eeeeec-hhhHHHHHHHHHHhhcCCc----chhcc-----cccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHc
Q 017612          177 CALYLS-LEECGRYLETIKVYENKPA----DLIQG-----QMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMD  246 (368)
Q Consensus       177 cILFLS-~EEAArYIEt~K~~E~K~~----d~Ire-----k~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~  246 (368)
                      .|||.+ ++|+|.+|..||..++.+.    ..++.     .....+.......|.+|||||...|.+||.+|||+++|++
T Consensus       706 ~IiwS~s~~~TA~i~~~Lk~~e~epd~~~~v~i~~~~~~~~k~~~~~~~~q~~L~~lPgI~~~~a~~ll~~f~si~~l~~  785 (814)
T TIGR00596       706 RIIWSSSPYATAEIFEELKLGKEEPDPATAAALGSDENTTAEGLKFNDGPQDFLLKLPGVTKKNYRNLRKKVKSIRELAK  785 (814)
T ss_pred             eEEecCCHHHHHHHHHHHHhcCCCCCcccceecCcccccccccccccHHHHHHHHHCCCCCHHHHHHHHHHcCCHHHHHh
Confidence            577776 9999999999999987542    22331     1111233333445779999999999999999999999999


Q ss_pred             CCHHhhhcCCCCC-HHHHHHHHHHhccccc
Q 017612          247 ASMEDLARCPGIG-ERKVKRLYDTFHEPFK  275 (368)
Q Consensus       247 AS~EELa~VPGIG-~kKA~rI~e~F~ePF~  275 (368)
                      ||.+||..+  || +++|++||++||.++.
T Consensus       786 as~eeL~~~--iG~~~~A~~i~~fl~~~~~  813 (814)
T TIGR00596       786 LSQNELNEL--IGDEEAAKRLYDFLRTEKL  813 (814)
T ss_pred             CCHHHHHHH--hCCHHHHHHHHHHhccccC
Confidence            999999996  88 9999999999998753

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit

>PRK14669 uvrC excinuclease ABC subunit C; Provisional

Probab=98.99  E-value=7e-10  Score=117.20  Aligned_cols=91  Identities=22%  Similarity=0.249  Sum_probs=76.5

Q ss_pred             Eeccceeeeee-c--hhhHHHHHHHHHHhhcCCcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcC
Q 017612          171 LVGQNSCALYL-S--LEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDA  247 (368)
Q Consensus       171 ~Ig~ttcILFL-S--~EEAArYIEt~K~~E~K~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~A  247 (368)
                      .+..++.+|+| .  .+||+||-.+|++.-         +.    ...+.+.|.+|||||++.++.||+||||+++|.+|
T Consensus       515 ~l~~~s~~l~lLq~iRDEaHRFAIt~hRk~---------R~----k~~~~S~L~~IpGIG~kr~~~LL~~FgSi~~I~~A  581 (624)
T PRK14669        515 VLDRFSPVLHLVQSIRDEAHRFAITFHRKR---------RE----TRDRTSELLEIPGVGAKTVQRLLKHFGSLERVRAA  581 (624)
T ss_pred             ecCCCCHHHHHHHHHHHHHHHHHHHHhHHH---------hh----HHHHHHHHhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence            34445555533 2  999999999998863         11    33467899999999999999999999999999999


Q ss_pred             CHHhhhcCCCCCHHHHHHHHHHhcccccc
Q 017612          248 SMEDLARCPGIGERKVKRLYDTFHEPFKR  276 (368)
Q Consensus       248 S~EELa~VPGIG~kKA~rI~e~F~ePF~~  276 (368)
                      |.+||+.|  ||.++|++|+++|+.+|-.
T Consensus       582 s~eeL~~v--i~~k~A~~I~~~l~~~~~~  608 (624)
T PRK14669        582 TETQLAAV--VGRAAAEAIIAHFTTEEAA  608 (624)
T ss_pred             CHHHHHHH--hCHHHHHHHHHHhcCcCCC
Confidence            99999999  9999999999999987763

>PRK14666 uvrC excinuclease ABC subunit C; Provisional

Probab=98.98  E-value=7.5e-10  Score=118.02  Aligned_cols=79  Identities=25%  Similarity=0.309  Sum_probs=71.7

Q ss_pred             hhhHHHHHHHHHHhhcCCcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHH
Q 017612          183 LEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERK  262 (368)
Q Consensus       183 ~EEAArYIEt~K~~E~K~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kK  262 (368)
                      .+||+||-.+|++.-.         .    ...+.+.|..|+|||++.+++||++|||+++|..|+.+||+.|+|||+++
T Consensus       615 RDEaHRfAi~~hR~~r---------~----k~~~~s~L~~IPGIGpkr~k~LL~~FGSle~I~~AS~eELa~V~Gig~k~  681 (694)
T PRK14666        615 RDTVHDYAIGRHRRAR---------A----GAALTGELQRVEGIGPATARLLWERFGSLQAMAAAGEEGLAAVPGIGPAR  681 (694)
T ss_pred             HHHHHHHHHHHHHHHH---------H----hhhhHhHHhhCCCCCHHHHHHHHHHhCCHHHHHhcCHHHHHhcCCcCHHH
Confidence            9999999999998641         1    23457899999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcccc
Q 017612          263 VKRLYDTFHEPF  274 (368)
Q Consensus       263 A~rI~e~F~ePF  274 (368)
                      |++|++.|+.-|
T Consensus       682 Ae~I~~~L~~~~  693 (694)
T PRK14666        682 AAALHEHLKTLF  693 (694)
T ss_pred             HHHHHHHHHHhh
Confidence            999999998766

>PRK00558 uvrC excinuclease ABC subunit C; Validated

Probab=98.97  E-value=7.1e-10  Score=116.37  Aligned_cols=90  Identities=32%  Similarity=0.514  Sum_probs=75.5

Q ss_pred             eEeccceeeeeec---hhhHHHHHHHHHHhhcCCcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHc
Q 017612          170 YLVGQNSCALYLS---LEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMD  246 (368)
Q Consensus       170 Y~Ig~ttcILFLS---~EEAArYIEt~K~~E~K~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~  246 (368)
                      +.+..++.+|+|=   .+||+||-.+|++.-         +.    ...+...|+.|||||+..++.||++|||+++|..
T Consensus       505 ~~l~~~~~~l~llq~irDEaHRFAi~~hR~~---------R~----k~~~~s~L~~IpGIG~k~~k~Ll~~FgS~~~i~~  571 (598)
T PRK00558        505 IILPPDSPALYLLQRIRDEAHRFAITFHRKK---------RS----KARLTSALDDIPGIGPKRRKALLKHFGSLKAIKE  571 (598)
T ss_pred             EecCCCCHHHHHHHHHHHHhhhhhhhhhccc---------cc----cchhhhhHhhCCCcCHHHHHHHHHHcCCHHHHHh
Confidence            4455555555443   999999999998853         11    1225678999999999999999999999999999


Q ss_pred             CCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          247 ASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       247 AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      |+.+||..|+|||++.|+.|+++|+.
T Consensus       572 As~eeL~~v~Gig~~~A~~I~~~l~~  597 (598)
T PRK00558        572 ASVEELAKVPGISKKLAEAIYEALHK  597 (598)
T ss_pred             CCHHHHhhcCCcCHHHHHHHHHHhcc
Confidence            99999999999999999999999975

>PRK14672 uvrC excinuclease ABC subunit C; Provisional

Probab=98.89  E-value=2.3e-09  Score=114.21  Aligned_cols=90  Identities=18%  Similarity=0.194  Sum_probs=74.7

Q ss_pred             eEeccceeeeeec---hhhHHHHHHHHHHhhcCCcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHc
Q 017612          170 YLVGQNSCALYLS---LEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMD  246 (368)
Q Consensus       170 Y~Ig~ttcILFLS---~EEAArYIEt~K~~E~K~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~  246 (368)
                      +.+.....+|++=   .+||+||-.+|++.-.         .    ...+.+.|..|+|||++....||+||||+++|..
T Consensus       570 ~~L~~~s~~l~lLq~iRDEaHRFAIt~hR~~R---------~----k~~~~s~L~~IpGiG~kr~~~LL~~FgS~~~i~~  636 (691)
T PRK14672        570 LVLDRRNPALHMLQRIRDEAHRFAITRNRHLR---------T----KKELVLSFERLPHVGKVRAHRLLAHFGSFRSLQS  636 (691)
T ss_pred             eecCCCCHHHHHHHHHHHHHHHHHHHHHHHHh---------h----hhhcccccccCCCCCHHHHHHHHHHhcCHHHHHh
Confidence            4444555555332   9999999999988631         1    2335678999999999999999999999999999


Q ss_pred             CCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          247 ASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       247 AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      ||.+||+.|+|||.+.|+.|+.+...
T Consensus       637 As~eel~~v~gi~~~~A~~i~~~~~~  662 (691)
T PRK14672        637 ATPQDIATAIHIPLTQAHTILHAATR  662 (691)
T ss_pred             CCHHHHHhCCCCCHHHHHHHHHHhhc
Confidence            99999999999999999999998753

>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]

Probab=98.83  E-value=4.2e-09  Score=110.64  Aligned_cols=86  Identities=29%  Similarity=0.417  Sum_probs=72.6

Q ss_pred             Eeccceeeeeec---hhhHHHHHHHHHHhhcCCcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcC
Q 017612          171 LVGQNSCALYLS---LEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDA  247 (368)
Q Consensus       171 ~Ig~ttcILFLS---~EEAArYIEt~K~~E~K~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~A  247 (368)
                      .+.+.+.+||+=   .+||+||-.++++-.         +    ....+.+.|..|+|||++..+.||+||||+++|..|
T Consensus       493 ~l~~~~p~l~~lq~irDEaHrfAi~~hR~~---------R----~k~~~~s~Ld~I~GiG~~r~~~LL~~Fgs~~~i~~A  559 (581)
T COG0322         493 DLPPNSPALYLLQRIRDEAHRFAITYHRKK---------R----SKAMLQSSLDDIPGIGPKRRKALLKHFGSLKGIKSA  559 (581)
T ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHHHHHHH---------h----hhhhhcCccccCCCcCHHHHHHHHHHhhCHHHHHhc
Confidence            334444444443   999999999998853         1    245578899999999999999999999999999999


Q ss_pred             CHHhhhcCCCCCHHHHHHHHHHh
Q 017612          248 SMEDLARCPGIGERKVKRLYDTF  270 (368)
Q Consensus       248 S~EELa~VPGIG~kKA~rI~e~F  270 (368)
                      |.+||+.| ||+.+.|++|++.|
T Consensus       560 s~eel~~v-gi~~~~a~~i~~~~  581 (581)
T COG0322         560 SVEELAKV-GISKKLAEKIYEAL  581 (581)
T ss_pred             CHHHHHHc-CCCHHHHHHHHhhC
Confidence            99999999 99999999999865

>PRK14668 uvrC excinuclease ABC subunit C; Provisional

Probab=98.81  E-value=8e-09  Score=108.37  Aligned_cols=86  Identities=24%  Similarity=0.368  Sum_probs=72.1

Q ss_pred             eEeccceeeeee-c--hhhHHHHHHHHHHhhcCCcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHc
Q 017612          170 YLVGQNSCALYL-S--LEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMD  246 (368)
Q Consensus       170 Y~Ig~ttcILFL-S--~EEAArYIEt~K~~E~K~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~  246 (368)
                      +.+..++.+|+| .  .+||+||-.+|++.-.               ..+...|+.|+|||+..++.||++|||+++|..
T Consensus       489 ~~l~~~~~~l~lL~~irDEaHRFAi~~hR~~r---------------~~~~~~L~~IpGIG~kr~~~LL~~FGS~~~I~~  553 (577)
T PRK14668        489 YDWPDDAPQLHLLQRVRDEAHRFAVQYHQTLR---------------DDVSTVLDDVPGVGPETRKRLLRRFGSVEGVRE  553 (577)
T ss_pred             eecCCCCHHHHHHHHHHHHHHHHHhhHHHHHH---------------HHHHhHHhcCCCCCHHHHHHHHHHcCCHHHHHh
Confidence            334445544433 3  9999999999998631               125689999999999999999999999999999


Q ss_pred             CCHHhhhcCCCCCHHHHHHHHHHh
Q 017612          247 ASMEDLARCPGIGERKVKRLYDTF  270 (368)
Q Consensus       247 AS~EELa~VPGIG~kKA~rI~e~F  270 (368)
                      ||.+||..+||||.+.|+.|++++
T Consensus       554 As~eeL~~vpGi~~~~A~~I~~~~  577 (577)
T PRK14668        554 ASVEDLRDVPGVGEKTAETIRERL  577 (577)
T ss_pred             CCHHHHHhCCCCCHHHHHHHHHhC
Confidence            999999999999999999998764

>PRK13482 DNA integrity scanning protein DisA; Provisional

Probab=98.76  E-value=1e-08  Score=102.35  Aligned_cols=59  Identities=25%  Similarity=0.388  Sum_probs=54.8

Q ss_pred             HHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcccc
Q 017612          216 LTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPF  274 (368)
Q Consensus       216 L~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF  274 (368)
                      -.-+|++||+|++..|++|+++|||+++|++|+.+||..|+|||+++|+.|++.+.+-.
T Consensus       285 GyRiLs~IPrl~k~iAk~Ll~~FGSL~~Il~As~eeL~~VeGIGe~rA~~I~e~l~Rl~  343 (352)
T PRK13482        285 GYRLLSKIPRLPSAVIENLVEHFGSLQGLLAASIEDLDEVEGIGEVRARAIREGLSRLA  343 (352)
T ss_pred             HHHHHhcCCCCCHHHHHHHHHHcCCHHHHHcCCHHHHhhCCCcCHHHHHHHHHHHHHHH
Confidence            34589999999999999999999999999999999999999999999999999987543

>TIGR00575 dnlj DNA ligase, NAD-dependent

Probab=98.76  E-value=6.7e-09  Score=110.14  Aligned_cols=65  Identities=32%  Similarity=0.589  Sum_probs=60.7

Q ss_pred             cHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcccccc
Q 017612          211 DYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKR  276 (368)
Q Consensus       211 dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~~  276 (368)
                      ..+.+++.+| +|||||++.|+.|+++|||+++|.+|+.++|..|+|||+++|++|+++|+.++..
T Consensus       492 ~~l~r~L~aL-gIpgVG~~~ak~L~~~f~sl~~l~~As~eeL~~i~GIG~~~A~~I~~ff~~~~~~  556 (652)
T TIGR00575       492 KPLARLLFAL-GIRHVGEVTAKNLAKHFGTLDKLKAASLEELLSVEGVGPKVAESIVNFFHDPNNR  556 (652)
T ss_pred             CcHHHHHhhc-cCCCcCHHHHHHHHHHhCCHHHHHhCCHHHHhcCCCcCHHHHHHHHHHHhhhhHH
Confidence            3457889999 8999999999999999999999999999999999999999999999999998753

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.

>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed

Probab=98.73  E-value=2.2e-08  Score=91.38  Aligned_cols=83  Identities=20%  Similarity=0.293  Sum_probs=67.7

Q ss_pred             eeeeec---hhhHHHHHHHHHHhhcCCcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCC---HHHHHcCCHH
Q 017612          177 CALYLS---LEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGS---LSHIMDASME  250 (368)
Q Consensus       177 cILFLS---~EEAArYIEt~K~~E~K~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGS---Lk~I~~AS~E  250 (368)
                      +.||+-   .||+.++ ..|+..+               ...+...|..|+|||++.|..||++||.   .+.|.+++.+
T Consensus        45 ~~l~~~~~~rd~~~~l-~gF~~~~---------------ek~~f~~L~~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~~  108 (192)
T PRK00116         45 VKLYTHLVVREDAILL-YGFLTKE---------------ERELFRLLISVSGVGPKLALAILSGLSPEELVQAIANGDVK  108 (192)
T ss_pred             EEEEEEEEEechhHHH-cCcCCHH---------------HHHHHHHHhcCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHH
Confidence            445554   8888887 5554322               1123456778999999999999999999   9999999999


Q ss_pred             hhhcCCCCCHHHHHHHHHHhccccc
Q 017612          251 DLARCPGIGERKVKRLYDTFHEPFK  275 (368)
Q Consensus       251 ELa~VPGIG~kKA~rI~e~F~ePF~  275 (368)
                      +|..|||||+++|++|+..|+..+.
T Consensus       109 ~L~~v~Gig~k~A~~I~~~l~~~~~  133 (192)
T PRK00116        109 ALTKVPGIGKKTAERIVLELKDKLA  133 (192)
T ss_pred             HHHhCCCCCHHHHHHHHHHHHHHhh
Confidence            9999999999999999999987764

>PRK12766 50S ribosomal protein L32e; Provisional

Probab=98.68  E-value=2.8e-08  Score=94.50  Aligned_cols=53  Identities=23%  Similarity=0.361  Sum_probs=51.6

Q ss_pred             hhccCCCCCHHHHHHHHHh-cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          219 ALTSVRSVNKTDVVTLGST-FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs~-FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      .|..|+|||+.++..|+++ |+|+++|..|+.++|..|+|||.++|++|++.|+
T Consensus         4 ~L~~IpGIG~krakkLl~~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l~   57 (232)
T PRK12766          4 ELEDISGVGPSKAEALREAGFESVEDVRAADQSELAEVDGIGNALAARIKADVG   57 (232)
T ss_pred             ccccCCCcCHHHHHHHHHcCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHhc
Confidence            5789999999999999999 9999999999999999999999999999999997

>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated

Probab=98.66  E-value=1.8e-08  Score=107.15  Aligned_cols=63  Identities=32%  Similarity=0.442  Sum_probs=59.4

Q ss_pred             HHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612          212 YLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFK  275 (368)
Q Consensus       212 y~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~  275 (368)
                      .+.+++.+| +|||||++.|+.|+++|+|+++|.+|+.+||..|+|||+++|+.|+++|+.+..
T Consensus       506 ~l~R~l~al-gi~~IG~~~ak~L~~~f~sl~~l~~As~eeL~~i~GIG~~~A~sI~~ff~~~~~  568 (665)
T PRK07956        506 SLARFLYAL-GIRHVGEKAAKALARHFGSLEALRAASEEELAAVEGVGEVVAQSIVEFFAVEEN  568 (665)
T ss_pred             CHHHhhHhh-hccCcCHHHHHHHHHHcCCHHHHHhCCHHHHhccCCcCHHHHHHHHHHHhhhhH
Confidence            457899999 899999999999999999999999999999999999999999999999998763

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

Probab=98.65  E-value=2.2e-08  Score=106.42  Aligned_cols=85  Identities=32%  Similarity=0.493  Sum_probs=70.0

Q ss_pred             HHHHHHhhcCCcch----hcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHH
Q 017612          190 LETIKVYENKPADL----IQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKR  265 (368)
Q Consensus       190 IEt~K~~E~K~~d~----Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~r  265 (368)
                      |..+..+..+....    |...+ +..+++++.+| +||+||.+.|+.|..+|||+++|+.|+.++|..|+|||++.|++
T Consensus       481 l~~l~~~~~ks~~nLl~aIe~sK-~~~l~r~l~aL-GIr~VG~~~Ak~La~~f~sl~~l~~a~~e~l~~i~giG~~vA~s  558 (667)
T COG0272         481 LLSLEGFGEKSAENLLNAIEKSK-KQPLARFLYAL-GIRHVGETTAKSLARHFGTLEALLAASEEELASIPGIGEVVARS  558 (667)
T ss_pred             HhhccchhhhHHHHHHHHHHHhc-cCCHHHHHHHc-CCchhhHHHHHHHHHHhhhHHHHHhcCHHHHhhccchhHHHHHH
Confidence            33444444455433    33322 34579999999 99999999999999999999999999999999999999999999


Q ss_pred             HHHHhcccccc
Q 017612          266 LYDTFHEPFKR  276 (368)
Q Consensus       266 I~e~F~ePF~~  276 (368)
                      |.++|+.+.+.
T Consensus       559 i~~ff~~~~~~  569 (667)
T COG0272         559 IIEFFANEENR  569 (667)
T ss_pred             HHHHHcCHHHH
Confidence            99999988764

>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=98.63  E-value=3e-08  Score=105.97  Aligned_cols=64  Identities=25%  Similarity=0.353  Sum_probs=60.2

Q ss_pred             ccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcccc
Q 017612          210 TDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPF  274 (368)
Q Consensus       210 ~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF  274 (368)
                      ...+.+++.+| +|||||++.|+.|+.+|||+++|.+|+.++|..|+|||++.|+.|+++|+.+.
T Consensus       521 ~~~l~r~l~AL-gIpgIG~~~ak~L~~~F~si~~L~~As~eeL~~i~GIG~k~A~sI~~ff~~~~  584 (689)
T PRK14351        521 EPPLADFLVAL-GIPEVGPTTARNLAREFGTFEAIMDADEEALRAVDDVGPTVAEEIREFFDSER  584 (689)
T ss_pred             cCCHHHHHHHc-CCCCcCHHHHHHHHHHhCCHHHHHhCCHHHHhccCCcCHHHHHHHHHHHhhhH
Confidence            34578999999 89999999999999999999999999999999999999999999999998875

>PRK14671 uvrC excinuclease ABC subunit C; Provisional

Probab=98.62  E-value=8.1e-08  Score=101.60  Aligned_cols=87  Identities=25%  Similarity=0.375  Sum_probs=72.2

Q ss_pred             eEeccceeeeeec---hhhHHHHHHHHHHhhcCCcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHc
Q 017612          170 YLVGQNSCALYLS---LEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMD  246 (368)
Q Consensus       170 Y~Ig~ttcILFLS---~EEAArYIEt~K~~E~K~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~  246 (368)
                      +.+..+..+|+|-   .||++||-.+|++..         +.    ...+.+.|.+|+|||++.+..||++|||+++|.+
T Consensus       531 ~~L~~~~~~l~ll~~iRDEaHrfAi~yhr~~---------r~----k~~~~s~L~~I~GIG~k~a~~Ll~~Fgs~~~i~~  597 (621)
T PRK14671        531 FNLPKTSPALKLLQQLRDEAHRFAITYHRKL---------RS----KRTLQTELTDIAGIGEKTAEKLLEHFGSVEKVAK  597 (621)
T ss_pred             eecCCCCcceEEEEEEehHHHHHHHHhChhh---------HH----HHHhhhhhhcCCCcCHHHHHHHHHHcCCHHHHHh
Confidence            4454555555443   999999999987753         11    2335678899999999999999999999999999


Q ss_pred             CCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          247 ASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       247 AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      |+.++|..|  ||++.|++|+++|+
T Consensus       598 As~eeL~~v--ig~k~A~~I~~~~~  620 (621)
T PRK14671        598 ASLEELAAV--AGPKTAETIYRYYH  620 (621)
T ss_pred             CCHHHHHHH--hCHHHHHHHHHHhC
Confidence            999999999  99999999999986

>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=98.37  E-value=3.1e-07  Score=98.08  Aligned_cols=64  Identities=17%  Similarity=0.398  Sum_probs=59.2

Q ss_pred             ccHHHHHHHhhccCCCCCHHHHHHHH-HhcCCHHHHHc------CCHHhhhcCCCCCHHHHHHHHHHhcccc
Q 017612          210 TDYLSRLTHALTSVRSVNKTDVVTLG-STFGSLSHIMD------ASMEDLARCPGIGERKVKRLYDTFHEPF  274 (368)
Q Consensus       210 ~dy~srL~saLTsIpgVnKTDA~~LL-s~FGSLk~I~~------AS~EELa~VPGIG~kKA~rI~e~F~ePF  274 (368)
                      ...+.+++.+| +||+||.+.|+.|+ .+|++++++++      ++.++|..|+|||++.|.+|+++|+.+.
T Consensus       495 ~~~l~r~l~AL-GI~~vG~~~ak~La~~~f~~~~~l~~~~~~~~~~~e~l~~i~giG~~~a~si~~ff~~~~  565 (669)
T PRK14350        495 KRPFSKLLLSM-GIKDLGENTILLLINNNLNSFDKISTLCQDREFALSKLLKIKGIGEKIALNIIEAFNDKI  565 (669)
T ss_pred             CCCHHHHHHHc-CCCchhHHHHHHHHHHhhCCHHHHHhhhhccCCCHHHHhhCCCccHHHHHHHHHHHcCHH
Confidence            34578999999 79999999999999 99999999987      6899999999999999999999998875

>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed

Probab=98.23  E-value=6.9e-07  Score=93.92  Aligned_cols=62  Identities=21%  Similarity=0.268  Sum_probs=56.3

Q ss_pred             ccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612          210 TDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFK  275 (368)
Q Consensus       210 ~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~  275 (368)
                      ...+++++.+| +||+||++.|+.   +|+++++|++|+.|+|..|+|||+++|+.|+++|+.+..
T Consensus       484 ~~~l~r~l~aL-GI~~vG~~~ak~---~~~~i~~l~~a~~e~l~~i~gIG~~~a~si~~~f~~~~~  545 (562)
T PRK08097        484 QQPFSRWLKAL-GIPLPQAALNAL---DDRSWQQLLSRSEQQWQQLPGIGEGRARQLIAFLQHPEV  545 (562)
T ss_pred             CCCHHHHHHHc-CCccHHHHHHHH---hcCCHHHHHcCCHHHHhcCCCchHHHHHHHHHHHcCHHH
Confidence            34578999999 899999987775   999999999999999999999999999999999987653

>PRK00254 ski2-like helicase; Provisional

Probab=98.02  E-value=7.3e-06  Score=87.06  Aligned_cols=55  Identities=20%  Similarity=0.389  Sum_probs=52.2

Q ss_pred             hhccCCCCCHHHHHHHHHh-cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccc
Q 017612          219 ALTSVRSVNKTDVVTLGST-FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEP  273 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs~-FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~eP  273 (368)
                      .|..|||||+..+++|+++ |+|+++|+.|+.+||..|+|||+++|+.|++.++..
T Consensus       646 ~L~~ipgig~~~~~~l~~~g~~s~~~i~~a~~~el~~~~gi~~~~a~~i~~~~~~~  701 (720)
T PRK00254        646 ELMRLPMIGRKRARALYNAGFRSIEDIVNAKPSELLKVEGIGAKIVEGIFKHLGVE  701 (720)
T ss_pred             hhhcCCCCCHHHHHHHHHccCCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHhccc
Confidence            5668999999999999999 999999999999999999999999999999999844

>TIGR00194 uvrC excinuclease ABC, C subunit

Probab=97.92  E-value=8.9e-06  Score=85.74  Aligned_cols=68  Identities=29%  Similarity=0.349  Sum_probs=54.1

Q ss_pred             Eeccceeeeee-c--hhhHHHHHHHHHHhhcCCcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcC
Q 017612          171 LVGQNSCALYL-S--LEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDA  247 (368)
Q Consensus       171 ~Ig~ttcILFL-S--~EEAArYIEt~K~~E~K~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~A  247 (368)
                      .+..++.+|+| .  .+||+||-.+|++.-         +.    ...+.+.|..|||||++..+.||+||||+++|..|
T Consensus       504 ~l~~~s~~l~lLq~irDEaHRFAi~~hR~~---------r~----k~~~~S~Ld~I~GIG~kr~~~LL~~Fgs~~~i~~A  570 (574)
T TIGR00194       504 NIDLNSPALQLLQHIRDEAHRFAISFHRKK---------RL----KASLQSPLLKIPGVGEKRVQKLLKYFGSLKGIKKA  570 (574)
T ss_pred             ecCCCCHHHHHHHHHHHHHHHHHHHHHHHH---------HH----HHHHHHHHhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence            34444444433 2  999999999999863         11    34467899999999999999999999999999999


Q ss_pred             CHHh
Q 017612          248 SMED  251 (368)
Q Consensus       248 S~EE  251 (368)
                      |.||
T Consensus       571 s~ee  574 (574)
T TIGR00194       571 SVEE  574 (574)
T ss_pred             CccC
Confidence            9875

This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.

>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]

Probab=97.91  E-value=1.5e-05  Score=53.98  Aligned_cols=30  Identities=33%  Similarity=0.626  Sum_probs=26.7

Q ss_pred             CHHHHHcCCHHhhhcCCCCCHHHHHHHHHH
Q 017612          240 SLSHIMDASMEDLARCPGIGERKVKRLYDT  269 (368)
Q Consensus       240 SLk~I~~AS~EELa~VPGIG~kKA~rI~e~  269 (368)
                      ++..++.++.|||..+||||+++|..|+.+
T Consensus         1 ~~~g~~pas~eeL~~lpGIG~~tA~~I~~~   30 (30)
T PF00633_consen    1 SLDGLIPASIEELMKLPGIGPKTANAILSF   30 (30)
T ss_dssp             SHHHHHTSSHHHHHTSTT-SHHHHHHHHHH
T ss_pred             CCCCcCCCCHHHHHhCCCcCHHHHHHHHhC
Confidence            578899999999999999999999999864

The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....

>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region

Probab=97.84  E-value=2.7e-05  Score=59.89  Aligned_cols=48  Identities=25%  Similarity=0.458  Sum_probs=42.9

Q ss_pred             hhcc-CCCCCHHHHHHHHHh---cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          219 ALTS-VRSVNKTDVVTLGST---FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       219 aLTs-IpgVnKTDA~~LLs~---FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      .|.. ++|||...|++|+.+   ||.++     +.+||..|+|||++++++|+.++.
T Consensus        17 ~L~~~ipgig~~~a~~Il~~R~~~g~~~-----s~~dL~~v~gi~~~~~~~i~~~~~   68 (69)
T TIGR00426        17 ELQRAMNGVGLKKAEAIVSYREEYGPFK-----TVEDLKQVPGIGNSLVEKNLAVIT   68 (69)
T ss_pred             HHHhHCCCCCHHHHHHHHHHHHHcCCcC-----CHHHHHcCCCCCHHHHHHHHhhcc
Confidence            5556 999999999999999   88776     889999999999999999998763

Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.

>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]

Probab=97.80  E-value=2.1e-05  Score=77.78  Aligned_cols=55  Identities=29%  Similarity=0.445  Sum_probs=52.3

Q ss_pred             HHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          217 THALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       217 ~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      .-.|..||.+-+..+.+|...||++.+|..||.|||..|.|||+.+|+.|++.+.
T Consensus       292 YR~l~kIpRlp~~iv~nlV~~F~~l~~il~As~edL~~VeGIGe~rAr~i~~Gl~  346 (349)
T COG1623         292 YRLLNKIPRLPFAIVENLVRAFGTLDGILEASAEDLDAVEGIGEARARAIKEGLS  346 (349)
T ss_pred             hHHHhcCcCccHHHHHHHHHHHhhHHHHHHhcHhHHhhhcchhHHHHHHHHHhHh
Confidence            4478899999999999999999999999999999999999999999999999875

>TIGR01259 comE comEA protein

Probab=97.76  E-value=2.6e-05  Score=66.88  Aligned_cols=53  Identities=19%  Similarity=0.270  Sum_probs=45.3

Q ss_pred             HHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          217 THALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       217 ~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      ...|..|||||...|.+|+.+|..  +..-+|.+||..|+|||++++++|+++|.
T Consensus        67 ~~eL~~lpGIG~~~A~~Ii~~R~~--~g~f~s~eeL~~V~GIg~k~~~~i~~~l~  119 (120)
T TIGR01259        67 LEELQALPGIGPAKAKAIIEYREE--NGAFKSVDDLTKVSGIGEKSLEKLKDYAT  119 (120)
T ss_pred             HHHHhcCCCCCHHHHHHHHHHHHh--cCCcCCHHHHHcCCCCCHHHHHHHHhceE
Confidence            456778999999999999999954  22347899999999999999999998863

This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.

>KOG0442 consensus Structure-specific endonuclease ERCC1-XPF, catalytic component XPF/ERCC4 [Replication, recombination and repair]

Probab=97.72  E-value=0.0001  Score=80.71  Aligned_cols=94  Identities=26%  Similarity=0.328  Sum_probs=78.7

Q ss_pred             hhhHHHHHHHHHHhhcCCc--chhcc-c------ccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhh
Q 017612          183 LEECGRYLETIKVYENKPA--DLIQG-Q------MDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLA  253 (368)
Q Consensus       183 ~EEAArYIEt~K~~E~K~~--d~Ire-k------~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa  253 (368)
                      +..+|.+++.+|.-+..+.  ..|.- .      ....|.+.....|-.+|||...+..+|+.+|+|++++.+.|.++|+
T Consensus       777 p~~Ta~if~eLKl~~~epD~~~Ai~lg~~~~~~~~~~~~n~~~~~fll~lPgVs~~n~~~l~~k~ks~~~La~sS~~el~  856 (892)
T KOG0442|consen  777 PLATAEIFEELKLSEPEPDPARAISLGTDEEGNSESESYNSSALDFLLSLPGVSYINYRNLRHKFKSLKELANSSQEELS  856 (892)
T ss_pred             hhHHHHHHHHHhhcCCCCCcchheeecccccccccccccCchHHHHHhcCCCccHHHHHHHHHHhhHHHHHHhCcHHHHH
Confidence            8999999999999988773  22221 1      1234667778888899999999999999999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHhccccccc
Q 017612          254 RCPGIGERKVKRLYDTFHEPFKRV  277 (368)
Q Consensus       254 ~VPGIG~kKA~rI~e~F~ePF~~~  277 (368)
                      ..-|. ...|+.||++||..|...
T Consensus       857 el~~~-~~~a~~LYdFi~~~~~~~  879 (892)
T KOG0442|consen  857 ELLGV-HENAKLLYDFIHTEFADQ  879 (892)
T ss_pred             HHhcc-hHHHHHHHHHHHHhhhhh
Confidence            99554 999999999999888643

>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=97.56  E-value=0.00014  Score=67.16  Aligned_cols=60  Identities=20%  Similarity=0.323  Sum_probs=49.1

Q ss_pred             HHHhhccCCCCCHHHHHHHHHhcCCHH---HHHcCCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612          216 LTHALTSVRSVNKTDVVTLGSTFGSLS---HIMDASMEDLARCPGIGERKVKRLYDTFHEPFK  275 (368)
Q Consensus       216 L~saLTsIpgVnKTDA~~LLs~FGSLk---~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~  275 (368)
                      +-..|.+|+|||++.|..+|++|+-=+   .|.+-+.+.|.+|||||+|+|++|.--|...+.
T Consensus        71 lF~~Li~V~GIGpK~Al~ILs~~~~~~l~~aI~~~D~~~L~~vpGIGkKtAerIilELk~Ki~  133 (194)
T PRK14605         71 LFETLIDVSGIGPKLGLAMLSAMNAEALASAIISGNAELLSTIPGIGKKTASRIVLELKDKIA  133 (194)
T ss_pred             HHHHHhCCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHHHH
Confidence            345667999999999999999997433   455778899999999999999997766666653

>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=97.55  E-value=0.00016  Score=67.32  Aligned_cols=60  Identities=18%  Similarity=0.325  Sum_probs=50.9

Q ss_pred             HHHhhccCCCCCHHHHHHHHHhcCCH---HHHHcCCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612          216 LTHALTSVRSVNKTDVVTLGSTFGSL---SHIMDASMEDLARCPGIGERKVKRLYDTFHEPFK  275 (368)
Q Consensus       216 L~saLTsIpgVnKTDA~~LLs~FGSL---k~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~  275 (368)
                      +-..|.+|.|||++.|..+|.+|+.-   ..|.+-+...|.++||||+|+|++|.--|+..+.
T Consensus        72 lF~~Li~V~GIGpK~Al~iLs~~~~~~l~~aI~~~D~~~L~~ipGIGkKtAerIilELkdK~~  134 (203)
T PRK14602         72 TFIVLISISKVGAKTALAILSQFRPDDLRRLVAEEDVAALTRVSGIGKKTAQHIFLELKYKLK  134 (203)
T ss_pred             HHHHHhCCCCcCHHHHHHHHhhCCHHHHHHHHHhCCHHHHhcCCCcCHHHHHHHHHHHHHhhc
Confidence            34566799999999999999997554   4566668999999999999999999988888774

>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=97.43  E-value=0.00022  Score=66.53  Aligned_cols=59  Identities=14%  Similarity=0.292  Sum_probs=49.2

Q ss_pred             HHHhhccCCCCCHHHHHHHHHhcCCHHHHHc----CCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612          216 LTHALTSVRSVNKTDVVTLGSTFGSLSHIMD----ASMEDLARCPGIGERKVKRLYDTFHEPFK  275 (368)
Q Consensus       216 L~saLTsIpgVnKTDA~~LLs~FGSLk~I~~----AS~EELa~VPGIG~kKA~rI~e~F~ePF~  275 (368)
                      +-..|.+|.|||++.|..+|+.| ++++|+.    -+...|.++||||+|.|+||.--|...+.
T Consensus        70 lF~~LisVsGIGPK~ALaILs~~-~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIIlELkdKl~  132 (196)
T PRK13901         70 VFEELIGVDGIGPRAALRVLSGI-KYNEFRDAIDREDIELISKVKGIGNKMAGKIFLKLRGKLV  132 (196)
T ss_pred             HHHHHhCcCCcCHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHhhc
Confidence            34456689999999999999987 5555554    47889999999999999999988877764

>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=97.42  E-value=0.00024  Score=65.56  Aligned_cols=59  Identities=20%  Similarity=0.380  Sum_probs=49.6

Q ss_pred             HHHhhccCCCCCHHHHHHHHHhcCCHHHHHc----CCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612          216 LTHALTSVRSVNKTDVVTLGSTFGSLSHIMD----ASMEDLARCPGIGERKVKRLYDTFHEPFK  275 (368)
Q Consensus       216 L~saLTsIpgVnKTDA~~LLs~FGSLk~I~~----AS~EELa~VPGIG~kKA~rI~e~F~ePF~  275 (368)
                      +-..|.+|.|||++.|..+|.+| +.++++.    -+...|.++||||+|.|++|.--|...+.
T Consensus        71 lF~~Li~V~GIGpK~AL~iLs~~-~~~el~~aI~~~D~~~L~~vpGIGkKtAerIilELkdK~~  133 (188)
T PRK14606         71 LFLSLTKVSRLGPKTALKIISNE-DAETLVTMIASQDVEGLSKLPGISKKTAERIVMELKDEFE  133 (188)
T ss_pred             HHHHHhccCCccHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHhhc
Confidence            44566799999999999999987 5665554    47889999999999999999988887764

>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=97.36  E-value=0.0003  Score=65.20  Aligned_cols=58  Identities=24%  Similarity=0.324  Sum_probs=49.2

Q ss_pred             HHhhccCCCCCHHHHHHHHHhcCCHHHHHcC----CHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612          217 THALTSVRSVNKTDVVTLGSTFGSLSHIMDA----SMEDLARCPGIGERKVKRLYDTFHEPFK  275 (368)
Q Consensus       217 ~saLTsIpgVnKTDA~~LLs~FGSLk~I~~A----S~EELa~VPGIG~kKA~rI~e~F~ePF~  275 (368)
                      -..|.+|.|||++.|..+|+.| +.++|+.|    +...|.++||||+|.|+||.--|+..+.
T Consensus        72 F~~Li~V~GIGpK~Al~iLs~~-~~~el~~aI~~~D~~~L~kvpGIGkKtAerIilELk~K~~  133 (195)
T PRK14604         72 FELLIGVSGVGPKAALNLLSSG-TPDELQLAIAGGDVARLARVPGIGKKTAERIVLELKGKID  133 (195)
T ss_pred             HHHHhCcCCcCHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHHhc
Confidence            4456689999999999999985 66666544    7888999999999999999988888774

>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=97.35  E-value=0.00031  Score=64.70  Aligned_cols=58  Identities=19%  Similarity=0.379  Sum_probs=48.9

Q ss_pred             HHHhhccCCCCCHHHHHHHHHhcCCHHHHHcC----CHHhhhcCCCCCHHHHHHHHHHhcccc
Q 017612          216 LTHALTSVRSVNKTDVVTLGSTFGSLSHIMDA----SMEDLARCPGIGERKVKRLYDTFHEPF  274 (368)
Q Consensus       216 L~saLTsIpgVnKTDA~~LLs~FGSLk~I~~A----S~EELa~VPGIG~kKA~rI~e~F~ePF  274 (368)
                      +-..|.++.|||++.|..+|..| +.+++..|    +...|.++||||+|.|+||.--|...+
T Consensus        71 lF~~Li~VsGIGpK~Al~ILs~~-~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIilELkdK~  132 (183)
T PRK14601         71 MFEMLLKVNGIGANTAMAVCSSL-DVNSFYKALSLGDESVLKKVPGIGPKSAKRIIAELSDAK  132 (183)
T ss_pred             HHHHHhccCCccHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHHh
Confidence            34566789999999999999996 66666554    778899999999999999998887776

>PRK00024 hypothetical protein; Reviewed

Probab=97.34  E-value=0.00033  Score=65.90  Aligned_cols=50  Identities=30%  Similarity=0.424  Sum_probs=42.9

Q ss_pred             cCCCCC-HHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          222 SVRSVN-KTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       222 sIpgVn-KTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      ++++-. +.-|..||++||++.+|++|+.+||..|+|||+.||..|..++.
T Consensus        37 g~~~~~~~~LA~~LL~~fgsL~~l~~as~~eL~~i~GIG~akA~~L~a~~E   87 (224)
T PRK00024         37 GTKGKSVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQLKAALE   87 (224)
T ss_pred             CCCCCCHHHHHHHHHHHcCCHHHHHhCCHHHHhhccCccHHHHHHHHHHHH
Confidence            345544 34788999999999999999999999999999999999977765

>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit

Probab=97.33  E-value=0.00041  Score=63.92  Aligned_cols=58  Identities=19%  Similarity=0.332  Sum_probs=46.8

Q ss_pred             HHhhccCCCCCHHHHHHHHHhcCCHHHHHc----CCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612          217 THALTSVRSVNKTDVVTLGSTFGSLSHIMD----ASMEDLARCPGIGERKVKRLYDTFHEPFK  275 (368)
Q Consensus       217 ~saLTsIpgVnKTDA~~LLs~FGSLk~I~~----AS~EELa~VPGIG~kKA~rI~e~F~ePF~  275 (368)
                      -..|.+|+|||++.|..||..|+ ++++..    -+...|..+||||+|+|++|.--|...+.
T Consensus        71 F~~L~~V~GIGpK~Al~iL~~~~-~~el~~aI~~~d~~~L~~ipGiGkKtAerIileLk~k~~  132 (191)
T TIGR00084        71 FKELIKVNGVGPKLALAILSNMS-PEEFVYAIETEEVKALVKIPGVGKKTAERLLLELKGKLK  132 (191)
T ss_pred             HHHHhCCCCCCHHHHHHHHhcCC-HHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHhhhc
Confidence            34556999999999999999874 555554    45678999999999999999977766653

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=97.30  E-value=0.00032  Score=64.65  Aligned_cols=58  Identities=21%  Similarity=0.349  Sum_probs=48.3

Q ss_pred             HHHhhccCCCCCHHHHHHHHHhcCCHHHHHcC----CHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612          216 LTHALTSVRSVNKTDVVTLGSTFGSLSHIMDA----SMEDLARCPGIGERKVKRLYDTFHEPFK  275 (368)
Q Consensus       216 L~saLTsIpgVnKTDA~~LLs~FGSLk~I~~A----S~EELa~VPGIG~kKA~rI~e~F~ePF~  275 (368)
                      +-..|.++.|||++.|..+|++| ++++++.|    +..-| ++||||+|.|+||.--|+..+.
T Consensus        71 lF~~LisV~GIGpK~Al~iLs~~-~~~~l~~aI~~~D~~~L-~vpGIGkKtAerIilELk~K~~  132 (186)
T PRK14600         71 CLRMLVKVSGVNYKTAMSILSKL-TPEQLFSAIVNEDKAAL-KVNGIGEKLINRIITELQYKVS  132 (186)
T ss_pred             HHHHHhCcCCcCHHHHHHHHccC-CHHHHHHHHHcCCHhhe-ECCCCcHHHHHHHHHHHHHHhh
Confidence            34466699999999999999996 66666544    77889 9999999999999988887774

>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]

Probab=97.29  E-value=0.00048  Score=65.75  Aligned_cols=52  Identities=27%  Similarity=0.372  Sum_probs=45.2

Q ss_pred             hccCCCCC-HHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          220 LTSVRSVN-KTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       220 LTsIpgVn-KTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      -|+++|-. ..-|+.||.+|||+.+++.|+.++|+.++|||..||-.|..++.
T Consensus        35 rtG~~~~~~~~la~~lL~~fg~L~~l~~a~~~el~~v~GiG~aka~~l~a~~E   87 (224)
T COG2003          35 RTGTKGESVLDLAKELLQEFGSLAELLKASVEELSSVKGIGLAKAIQIKAAIE   87 (224)
T ss_pred             hcCCCCCCHHHHHHHHHHHcccHHHHHhCCHHHHhhCCCccHHHHHHHHHHHH
Confidence            35677666 45688999999999999999999999999999999999877764

>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=97.27  E-value=0.00044  Score=64.17  Aligned_cols=59  Identities=17%  Similarity=0.224  Sum_probs=49.0

Q ss_pred             HHHhhccCCCCCHHHHHHHHHhcCCHHHHH----cCCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612          216 LTHALTSVRSVNKTDVVTLGSTFGSLSHIM----DASMEDLARCPGIGERKVKRLYDTFHEPFK  275 (368)
Q Consensus       216 L~saLTsIpgVnKTDA~~LLs~FGSLk~I~----~AS~EELa~VPGIG~kKA~rI~e~F~ePF~  275 (368)
                      +-..|.++.|||++.|..+|+.| +.++++    +-+..-|.++||||+|+|++|.--|...+.
T Consensus        70 lF~~L~~V~GIGpK~AL~iLs~~-~~~~l~~aI~~~D~~~L~kvpGIGkKtAerIilELkdK~~  132 (197)
T PRK14603         70 LFELLLGVSGVGPKLALALLSAL-PPALLARALLEGDARLLTSASGVGKKLAERIALELKGKVP  132 (197)
T ss_pred             HHHHHhCcCCcCHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHHhh
Confidence            34466689999999999999986 555544    558889999999999999999988887764

>TIGR00608 radc DNA repair protein radc

Probab=97.20  E-value=0.00049  Score=64.78  Aligned_cols=50  Identities=30%  Similarity=0.412  Sum_probs=43.1

Q ss_pred             cCCCC-C-HHHHHHHHHhc---CCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          222 SVRSV-N-KTDVVTLGSTF---GSLSHIMDASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       222 sIpgV-n-KTDA~~LLs~F---GSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      ++++- + ..-|+.||++|   |++.+++.|+.+||..|+|||+.||..|..++.
T Consensus        27 g~~~~~~~~~lA~~ll~~f~~~g~l~~l~~a~~~eL~~i~GiG~aka~~l~a~~E   81 (218)
T TIGR00608        27 GTPKGLDVLSLSKRLLDVFGRQDSLGHLLSAPPEELSSVPGIGEAKAIQLKAAVE   81 (218)
T ss_pred             CCCCCCCHHHHHHHHHHHhcccCCHHHHHhCCHHHHHhCcCCcHHHHHHHHHHHH
Confidence            45555 3 35788999999   999999999999999999999999999977764

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]

Probab=97.11  E-value=0.001  Score=62.41  Aligned_cols=59  Identities=19%  Similarity=0.353  Sum_probs=49.4

Q ss_pred             HhhccCCCCCHHHHHHHHHhcCCHHHHHcC----CHHhhhcCCCCCHHHHHHHHHHhccccccc
Q 017612          218 HALTSVRSVNKTDVVTLGSTFGSLSHIMDA----SMEDLARCPGIGERKVKRLYDTFHEPFKRV  277 (368)
Q Consensus       218 saLTsIpgVnKTDA~~LLs~FGSLk~I~~A----S~EELa~VPGIG~kKA~rI~e~F~ePF~~~  277 (368)
                      ..|.++.|||++.|..||+.+ ++.+|+.|    +..-|.++||||+|.|++|.--+...|...
T Consensus        73 ~~LisVnGIGpK~ALaiLs~~-~~~~l~~aI~~~d~~~L~k~PGIGkKtAerivleLk~K~~~~  135 (201)
T COG0632          73 RLLISVNGIGPKLALAILSNL-DPEELAQAIANEDVKALSKIPGIGKKTAERIVLELKGKLAAF  135 (201)
T ss_pred             HHHHccCCccHHHHHHHHcCC-CHHHHHHHHHhcChHhhhcCCCCCHHHHHHHHHHHhhhhhhh
Confidence            455589999999999999984 56665544    778899999999999999999998888754

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=96.95  E-value=0.0015  Score=62.37  Aligned_cols=52  Identities=19%  Similarity=0.315  Sum_probs=49.2

Q ss_pred             hccCCCCCHHHHHHHHHh-cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          220 LTSVRSVNKTDVVTLGST-FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       220 LTsIpgVnKTDA~~LLs~-FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      |..|+|||+..+.+|.+. |.|+++|..++.++|..+.|+++..|+.|++...
T Consensus         1 l~~i~gig~~~~~~L~~~Gi~ti~dl~~~~~~~L~~~~g~~~~~a~~l~~~~~   53 (310)
T TIGR02236         1 LEDLPGVGPATAEKLREAGYDTFEAIAVASPKELSEIAGISEGTAAKIIQAAR   53 (310)
T ss_pred             CcccCCCCHHHHHHHHHcCCCCHHHHHcCCHHHHHhccCCCHHHHHHHHHHHH
Confidence            457899999999999999 9999999999999999999999999999998876

This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=96.62  E-value=0.0032  Score=60.79  Aligned_cols=54  Identities=22%  Similarity=0.386  Sum_probs=50.7

Q ss_pred             hhccCCCCCHHHHHHHHHh-cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          219 ALTSVRSVNKTDVVTLGST-FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs~-FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      .|..+||||+..+..|.+. |.|+++|..++.++|..+.|+++++|+.|++..+.
T Consensus         7 ~l~~l~gIg~~~a~~L~~~Gi~t~~dl~~~~~~~L~~~~g~~~~~a~~l~~~a~~   61 (317)
T PRK04301          7 DLEDLPGVGPATAEKLREAGYDTVEAIAVASPKELSEAAGIGESTAAKIIEAARE   61 (317)
T ss_pred             cHhhcCCCCHHHHHHHHHcCCCCHHHHHcCCHHHHHHhcCCCHHHHHHHHHHHHH
Confidence            4678999999999999998 99999999999999999999999999999988765

>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional

Probab=95.94  E-value=0.014  Score=52.08  Aligned_cols=50  Identities=20%  Similarity=0.281  Sum_probs=36.4

Q ss_pred             HHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          217 THALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       217 ~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      ...|..+||||++.|++++.+ |-++     +.|||.+|+|||+++.+.|.+....
T Consensus        60 ~~el~~lpGigP~~A~~IV~n-Gpf~-----sveDL~~V~GIgekqk~~l~k~~~~  109 (132)
T PRK02515         60 VRAFRQFPGMYPTLAGKIVKN-APYD-----SVEDVLNLPGLSERQKELLEANLDN  109 (132)
T ss_pred             HHHHHHCCCCCHHHHHHHHHC-CCCC-----CHHHHHcCCCCCHHHHHHHHHhhcc
Confidence            345667899999999999963 2222     3478888999999887777766543

>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases

Probab=95.47  E-value=0.045  Score=53.59  Aligned_cols=49  Identities=20%  Similarity=0.421  Sum_probs=37.3

Q ss_pred             hhccCCCCCHHHHHHHHH--hcCCHHHHHcCC------HHhhhcCCCCCHHHHHHHH
Q 017612          219 ALTSVRSVNKTDVVTLGS--TFGSLSHIMDAS------MEDLARCPGIGERKVKRLY  267 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs--~FGSLk~I~~AS------~EELa~VPGIG~kKA~rI~  267 (368)
                      .++.|||||+..|..+-+  .=|++..+-..-      .-+|.+|+|||+++|++|+
T Consensus        46 ~~~~ipgiG~~ia~kI~E~~~tG~~~~le~l~~~~~~~l~~l~~i~GiGpk~a~~l~  102 (307)
T cd00141          46 EAKKLPGIGKKIAEKIEEILETGKLRKLEELREDVPPGLLLLLRVPGVGPKTARKLY  102 (307)
T ss_pred             HhcCCCCccHHHHHHHHHHHHcCCHHHHHHHhccchHHHHHHHcCCCCCHHHHHHHH
Confidence            447999999998876644  126666555332      3489999999999999999

X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this

>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]

Probab=95.43  E-value=0.03  Score=50.11  Aligned_cols=48  Identities=23%  Similarity=0.435  Sum_probs=38.1

Q ss_pred             HhhccCCCCCHHHHHHHHHh---cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHh
Q 017612          218 HALTSVRSVNKTDVVTLGST---FGSLSHIMDASMEDLARCPGIGERKVKRLYDTF  270 (368)
Q Consensus       218 saLTsIpgVnKTDA~~LLs~---FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F  270 (368)
                      +-|..+||||+..|..|+.+   +|-+     .+.+||.+|+|||+++.+++...+
T Consensus        97 eeL~~lpgIG~~kA~aIi~yRe~~G~f-----~sv~dL~~v~GiG~~~~ekl~~~i  147 (149)
T COG1555          97 EELQALPGIGPKKAQAIIDYREENGPF-----KSVDDLAKVKGIGPKTLEKLKDYI  147 (149)
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHcCCC-----CcHHHHHhccCCCHHHHHHHHhhc
Confidence            34478999999999999874   2211     456899999999999999998875

>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional

Probab=95.42  E-value=0.015  Score=51.81  Aligned_cols=47  Identities=21%  Similarity=0.448  Sum_probs=40.8

Q ss_pred             CCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcccccc
Q 017612          226 VNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKR  276 (368)
Q Consensus       226 VnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~~  276 (368)
                      +|..|++ |. .+|.-=+|=+|+.+||..+||||+++|++|.+  |.||..
T Consensus        39 ~N~~d~k-l~-~~~~kIdiN~A~~~el~~lpGigP~~A~~IV~--nGpf~s   85 (132)
T PRK02515         39 QNVADAK-LG-EFGEKIDLNNSSVRAFRQFPGMYPTLAGKIVK--NAPYDS   85 (132)
T ss_pred             cChhhHH-HH-hcCCcccCCccCHHHHHHCCCCCHHHHHHHHH--CCCCCC
Confidence            5888855 34 78999999999999999999999999999995  778874

>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]

Probab=95.23  E-value=0.024  Score=56.92  Aligned_cols=58  Identities=21%  Similarity=0.442  Sum_probs=46.4

Q ss_pred             HHHHHh--hccCCCCCHHHHHHHHH--hcCCHHHHHc------CCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          214 SRLTHA--LTSVRSVNKTDVVTLGS--TFGSLSHIMD------ASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       214 srL~sa--LTsIpgVnKTDA~~LLs--~FGSLk~I~~------AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      +.+.+.  +|.|||||+..|..|..  ..|+++-+..      ...++|..+||+|++|..++|+.|.
T Consensus        47 ~ei~e~~~~t~l~gIGk~ia~~I~e~l~tG~~~~le~lk~~~P~gl~~Ll~v~GlGpkKi~~Ly~elg  114 (326)
T COG1796          47 EEIEERGRLTELPGIGKGIAEKISEYLDTGEVKKLEALKKEVPEGLEPLLKVPGLGPKKIVSLYKELG  114 (326)
T ss_pred             HHHHhhcccCCCCCccHHHHHHHHHHHHcCccHHHHHHHHhCCcchHHHhhCCCCCcHHHHHHHHHHC
Confidence            446666  99999999999988865  4566554443      3567999999999999999999995

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=95.22  E-value=0.036  Score=60.17  Aligned_cols=56  Identities=23%  Similarity=0.456  Sum_probs=45.0

Q ss_pred             HHHhhcc--CCCCCHHHHHHHHHhcCC--HHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          216 LTHALTS--VRSVNKTDVVTLGSTFGS--LSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       216 L~saLTs--IpgVnKTDA~~LLs~FGS--Lk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      +...|.+  |+|||++.|++|.++||.  ++.| .-..+.|..|+|||+++++.|++.+..
T Consensus        80 i~~yL~s~~~~GIG~~~A~~iv~~fg~~~~~~i-~~~~~~L~~v~gi~~~~~~~i~~~~~~  139 (720)
T TIGR01448        80 IVAYLSSRSIKGVGKKLAQRIVKTFGEAAFDVL-DDDPEKLLEVPGISKANLEKFVSQWSQ  139 (720)
T ss_pred             HHHHHhcCCCCCcCHHHHHHHHHHhCHhHHHHH-HhCHHHHhcCCCCCHHHHHHHHHHHHH
Confidence            4445543  999999999999999994  4444 445889999999999999999887754

This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.

>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated

Probab=95.17  E-value=0.046  Score=59.14  Aligned_cols=51  Identities=18%  Similarity=0.288  Sum_probs=47.4

Q ss_pred             cCCCCCHHHHHHHHHhc--CCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          222 SVRSVNKTDVVTLGSTF--GSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       222 sIpgVnKTDA~~LLs~F--GSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      .|+|+|++.+..|.++-  .++.+|..+..++|..++|||+++|++|++.+..
T Consensus       449 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~ll~~Ie~  501 (665)
T PRK07956        449 DIDGLGEKIIEQLFEKGLIHDPADLFKLTAEDLLGLEGFGEKSAQNLLDAIEK  501 (665)
T ss_pred             CCCCcCHHHHHHHHHcCCCCCHHHHHhcCHHHHhcCcCcchHHHHHHHHHHHH
Confidence            69999999999999874  5999999999999999999999999999999974

>TIGR00575 dnlj DNA ligase, NAD-dependent

Probab=95.16  E-value=0.042  Score=59.25  Aligned_cols=51  Identities=18%  Similarity=0.309  Sum_probs=46.9

Q ss_pred             cCCCCCHHHHHHHHHhc--CCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          222 SVRSVNKTDVVTLGSTF--GSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       222 sIpgVnKTDA~~LLs~F--GSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      .|+|+|++.+..|.+.-  .++.+|..+..++|..++|||+++|++|++.+..
T Consensus       436 ~I~GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L~~L~GfG~Ksa~nIl~~Ie~  488 (652)
T TIGR00575       436 DIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLELEGFGEKSAQNLLNAIEK  488 (652)
T ss_pred             CCCCcCHHHHHHHHHcCCcCCHHHHHhcCHHHHhhccCccHHHHHHHHHHHHH
Confidence            59999999999999864  5999999999999999999999999999999974

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.

>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A

Probab=95.11  E-value=0.024  Score=43.57  Aligned_cols=51  Identities=20%  Similarity=0.277  Sum_probs=33.6

Q ss_pred             HhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHh
Q 017612          218 HALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTF  270 (368)
Q Consensus       218 saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F  270 (368)
                      +-|..+||||...|.+|+++=. ... .=.|.+||..|+|||+.+.++|..++
T Consensus        14 ~eL~~lpgi~~~~A~~Iv~~R~-~~G-~f~s~~dL~~v~gi~~~~~~~l~~~l   64 (65)
T PF12836_consen   14 EELQALPGIGPKQAKAIVEYRE-KNG-PFKSLEDLKEVPGIGPKTYEKLKPYL   64 (65)
T ss_dssp             HHHHTSTT--HHHHHHHHHHHH-HH--S-SSGGGGGGSTT--HHHHHHHCCCE
T ss_pred             HHHHHcCCCCHHHHHHHHHHHH-hCc-CCCCHHHHhhCCCCCHHHHHHHHhhc
Confidence            4566899999999999997511 000 11356899999999999999987654

>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication

Probab=95.04  E-value=0.075  Score=37.83  Aligned_cols=46  Identities=15%  Similarity=0.256  Sum_probs=38.9

Q ss_pred             CHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          227 NKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       227 nKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      ....+..|.. -|.|+++|..++.++|..++||++.+|..|....++
T Consensus         2 ~~~~~~~L~~~G~~s~e~la~~~~~eL~~i~g~~~e~a~~ii~~a~~   48 (50)
T TIGR01954         2 DEEIAQLLVEEGFTTVEDLAYVPIDELLSIEGFDEETAKELINRARN   48 (50)
T ss_pred             CHHHHHHHHHcCCCCHHHHHccCHHHHhcCCCCCHHHHHHHHHHHHH
Confidence            3455666665 699999999999999999999999999999877653

NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model represents an acidic 50-residue region found in two copies toward the C-terminus of most Proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic.

>PRK01172 ski2-like helicase; Provisional

Probab=94.99  E-value=0.032  Score=59.09  Aligned_cols=53  Identities=15%  Similarity=0.218  Sum_probs=48.9

Q ss_pred             hhccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          219 ALTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      .|-.|||||+..|++|.+ -|.|+.+|+.++.++|..|.|+|++.|+.|.+.++
T Consensus       613 ~L~~ip~~~~~~a~~l~~~g~~~~~di~~~~~~~~~~i~~~~~~~~~~i~~~~~  666 (674)
T PRK01172        613 DLVLIPKVGRVRARRLYDAGFKTVDDIARSSPERIKKIYGFSDTLANAIVNRAM  666 (674)
T ss_pred             hhcCCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHHHhccCHHHHHHHHHHHH
Confidence            455899999999999998 69999999999999999999999999999998754

>smart00483 POLXc DNA polymerase X family

Probab=94.84  E-value=0.052  Score=53.82  Aligned_cols=52  Identities=12%  Similarity=0.258  Sum_probs=39.8

Q ss_pred             hhccCCCCCHHHHHHHHH--hcCCHHHH---HcCC----HHhhhcCCCCCHHHHHHHHHHhc
Q 017612          219 ALTSVRSVNKTDVVTLGS--TFGSLSHI---MDAS----MEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs--~FGSLk~I---~~AS----~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      -|+.|||||+.-|..+-+  .=|++..+   ....    .-+|.+|+|||+++|++|++ +.
T Consensus        49 ~l~~lpgIG~~ia~kI~Eil~tG~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l~~-lG  109 (334)
T smart00483       49 DLKGLPGIGDKIKKKIEEIIETGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKWYR-KG  109 (334)
T ss_pred             HHhcCCCccHHHHHHHHHHHHhCcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHHHH-hC
Confidence            467999999998877653  33887633   3332    45899999999999999998 64

includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases

>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif

Probab=94.28  E-value=0.042  Score=43.58  Aligned_cols=30  Identities=17%  Similarity=0.368  Sum_probs=27.1

Q ss_pred             hccCCCCCHHHHHHHHHhcCCHHHHHcCCH
Q 017612          220 LTSVRSVNKTDVVTLGSTFGSLSHIMDASM  249 (368)
Q Consensus       220 LTsIpgVnKTDA~~LLs~FGSLk~I~~AS~  249 (368)
                      +.+|||||++.|..|+..||++++|+.+-.
T Consensus        24 i~gv~giG~k~A~~ll~~~~~~~~~~~~~~   53 (75)
T cd00080          24 IPGVPGIGPKTALKLLKEYGSLENLLENLD   53 (75)
T ss_pred             CCCCCcccHHHHHHHHHHhCCHHHHHHHHH
Confidence            568999999999999999999999997643

HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.

>PRK08609 hypothetical protein; Provisional

Probab=94.06  E-value=0.083  Score=55.98  Aligned_cols=52  Identities=21%  Similarity=0.468  Sum_probs=30.3

Q ss_pred             hhccCCCCCHHHHHHHHH--hcCCHHHHHcC------CHHhhhcCCCCCHHHHHHHHHHh
Q 017612          219 ALTSVRSVNKTDVVTLGS--TFGSLSHIMDA------SMEDLARCPGIGERKVKRLYDTF  270 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs--~FGSLk~I~~A------S~EELa~VPGIG~kKA~rI~e~F  270 (368)
                      .|+.|||||+.-|..+-+  .=|++..+-..      ..-+|.+|||||+++|++||+-+
T Consensus        49 ~l~~ipgIG~~ia~kI~Eil~tG~~~~le~l~~~~p~~~~~l~~i~GiGpk~a~~l~~~l  108 (570)
T PRK08609         49 DFTKLKGIGKGTAEVIQEYRETGESSVLQELKKEVPEGLLPLLKLPGLGGKKIAKLYKEL  108 (570)
T ss_pred             hhccCCCcCHHHHHHHHHHHHhCChHHHHHHHhhCcHHHHHHhcCCCCCHHHHHHHHHHh
Confidence            466777777776654433  12444333321      24467777777777777777654

>TIGR01259 comE comEA protein

Probab=93.98  E-value=0.056  Score=46.52  Aligned_cols=31  Identities=39%  Similarity=0.543  Sum_probs=27.8

Q ss_pred             HHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          242 SHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       242 k~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      =+|=.|+.++|..+||||+++|++|.+++..
T Consensus        60 iniNtA~~~eL~~lpGIG~~~A~~Ii~~R~~   90 (120)
T TIGR01259        60 VNINAASLEELQALPGIGPAKAKAIIEYREE   90 (120)
T ss_pred             EeCCcCCHHHHhcCCCCCHHHHHHHHHHHHh
Confidence            3566899999999999999999999999954

This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.

>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals

Probab=93.80  E-value=0.1  Score=40.84  Aligned_cols=43  Identities=12%  Similarity=0.254  Sum_probs=34.3

Q ss_pred             HHHHHHHH--hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          229 TDVVTLGS--TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       229 TDA~~LLs--~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      ..+.+.|.  .+.|+.+|+..+.++|..++|||++-+..|.+.++
T Consensus        21 ~Ra~n~L~~~~I~tv~dL~~~s~~~L~~i~n~G~ksl~EI~~~L~   65 (66)
T PF03118_consen   21 VRAYNCLKRAGIHTVGDLVKYSEEDLLKIKNFGKKSLEEIKEKLK   65 (66)
T ss_dssp             HHHHHHHHCTT--BHHHHHCS-HHHHHTSTTSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCcCHHHHHhCCHHHHHhCCCCCHhHHHHHHHHHc
Confidence            44555555  46699999999999999999999999999999875

The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact. The alpha subunit consists of a N-terminal domain (NTD) and a C-terminal domain (CTD), connected by a short linker. The NTD is essential for RNAP assembly, while the CTD is necessary for transcription regulation, interacting with transcription factors and promoter upstream elements. In Escherichia coli, the catabolite activator protein (CAP or CRP) was shown to exert its effect through its interactions with the CTD, where CAP binding to CTD promotes RNAP binding to promoter DNA, thereby stimulating transcription initiation at class I CAP-dependent promoters. At class II CAP-dependent promoters, the interaction of CAP with CTD is one of multiple interactions involved in activation []. The CTD has a compact structure of four helices and two long arms enclosing its hydrophobic core, making its folding topology distinct from most other binding proteins. The upstream promoter element-binding site is formed from helices 1 and 4 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3N97_B 1XS9_D 3K4G_A 3N4M_B 1COO_A 1LB2_E 3IYD_A 1Z3E_B 3GFK_B 3IHQ_B ....

>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=93.61  E-value=0.15  Score=55.63  Aligned_cols=60  Identities=22%  Similarity=0.321  Sum_probs=50.4

Q ss_pred             HHHHHHhhc----cCCCCCHHHHHHHHHhc--CCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          213 LSRLTHALT----SVRSVNKTDVVTLGSTF--GSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       213 ~srL~saLT----sIpgVnKTDA~~LLs~F--GSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      ..++.++.+    .|+|+|++.+..|.+.-  .++.+|..+..++|..++|||+++|++|++.+..
T Consensus       453 ~~~l~hf~sr~al~I~GLG~k~i~~L~~~g~V~~~~Dl~~L~~~~L~~l~g~g~Ksa~~Ll~~Ie~  518 (689)
T PRK14351        453 ERSIEHYASRDALDIEGLGEERVQQLVDAGLVESLADLYDLTVADLAELEGWGETSAENLLAELEA  518 (689)
T ss_pred             HHHHHHHhcccccCCCCcCHHHHHHHHHcCCCCCHHHHHHcCHHHHhcCcCcchhHHHHHHHHHHH
Confidence            344444442    69999999999999874  5999999999999999999999999999999863

>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes

Probab=93.47  E-value=0.099  Score=49.41  Aligned_cols=30  Identities=20%  Similarity=0.384  Sum_probs=27.1

Q ss_pred             hhccCCCCCHHHHHHHHHhcCCHHHHHcCC
Q 017612          219 ALTSVRSVNKTDVVTLGSTFGSLSHIMDAS  248 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs~FGSLk~I~~AS  248 (368)
                      -+.+|||||++.|..||++|||+++|+.+-
T Consensus       184 nipGv~GiG~ktA~~Ll~~~gsle~i~~~~  213 (240)
T cd00008         184 NIPGVPGIGEKTAAKLLKEYGSLEGILENL  213 (240)
T ss_pred             CCCCCCccCHHHHHHHHHHhCCHHHHHHhH
Confidence            567899999999999999999999999653

They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.

>PRK02362 ski2-like helicase; Provisional

Probab=93.36  E-value=0.13  Score=55.54  Aligned_cols=51  Identities=16%  Similarity=0.212  Sum_probs=47.2

Q ss_pred             hhccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          219 ALTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      .|..|||||+..|++|.+ -|.|+.+|+.++.++|..+  ||++.|++|++.++
T Consensus       653 ~L~~ip~i~~~~a~~l~~~gi~s~~dl~~~~~~~l~~~--~g~~~~~~i~~~~~  704 (737)
T PRK02362        653 DLVGLRGVGRVRARRLYNAGIESRADLRAADKSVVLAI--LGEKIAENILEQAG  704 (737)
T ss_pred             HHhCCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHHH--HCHHHHHHHHHHhC
Confidence            455899999999999987 4889999999999999999  99999999999987

>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1

Probab=93.33  E-value=0.07  Score=34.48  Aligned_cols=21  Identities=29%  Similarity=0.782  Sum_probs=18.0

Q ss_pred             HhhhcCCCCCHHHHHHHHHHh
Q 017612          250 EDLARCPGIGERKVKRLYDTF  270 (368)
Q Consensus       250 EELa~VPGIG~kKA~rI~e~F  270 (368)
                      ++|..|+|||+++|++|.+..
T Consensus         1 ~~L~~i~GiG~k~A~~il~~~   21 (26)
T smart00278        1 EELLKVPGIGPKTAEKILEAX   21 (26)
T ss_pred             ChhhhCCCCCHHHHHHHHHhc
Confidence            368899999999999998754

>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]

Probab=93.23  E-value=0.056  Score=48.36  Aligned_cols=37  Identities=41%  Similarity=0.593  Sum_probs=29.7

Q ss_pred             CCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc--ccc
Q 017612          239 GSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE--PFK  275 (368)
Q Consensus       239 GSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e--PF~  275 (368)
                      ...=+|=.||.+||..+||||+++|++|.++-.+  +|.
T Consensus        86 ~~~vNiNtAs~eeL~~lpgIG~~kA~aIi~yRe~~G~f~  124 (149)
T COG1555          86 EKKVNINTASAEELQALPGIGPKKAQAIIDYREENGPFK  124 (149)
T ss_pred             cccccccccCHHHHHHCCCCCHHHHHHHHHHHHHcCCCC
Confidence            3344566899999999999999999999887643  565

>PRK09482 flap endonuclease-like protein; Provisional

Probab=93.18  E-value=0.11  Score=50.36  Aligned_cols=29  Identities=21%  Similarity=0.362  Sum_probs=26.4

Q ss_pred             hhccCCCCCHHHHHHHHHhcCCHHHHHcC
Q 017612          219 ALTSVRSVNKTDVVTLGSTFGSLSHIMDA  247 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs~FGSLk~I~~A  247 (368)
                      -+.+|||||++.|..||+.|||+++|+..
T Consensus       183 nIpGVpGIG~KtA~~LL~~~gsle~i~~~  211 (256)
T PRK09482        183 KIPGVAGIGPKSAAELLNQFRSLENIYES  211 (256)
T ss_pred             CCCCCCCcChHHHHHHHHHhCCHHHHHHh
Confidence            45689999999999999999999999954

>PRK08609 hypothetical protein; Provisional

Probab=92.84  E-value=0.12  Score=54.79  Aligned_cols=53  Identities=9%  Similarity=0.231  Sum_probs=45.5

Q ss_pred             hhccCCCCCHHHHHHHHH--hcCCHHHHHcCCHH-hhhcCCCCCHHHHHHHHHHhc
Q 017612          219 ALTSVRSVNKTDVVTLGS--TFGSLSHIMDASME-DLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs--~FGSLk~I~~AS~E-ELa~VPGIG~kKA~rI~e~F~  271 (368)
                      .|+.|+|||++.|.+|-.  .+.|+++|..|-.+ .|..++|||++.++.|.+.+.
T Consensus        89 ~l~~i~GiGpk~a~~l~~~lGi~tl~~L~~a~~~~~~~~~~gfg~k~~~~il~~i~  144 (570)
T PRK08609         89 PLLKLPGLGGKKIAKLYKELGVVDKESLKEACENGKVQALAGFGKKTEEKILEAVK  144 (570)
T ss_pred             HHhcCCCCCHHHHHHHHHHhCCCCHHHHHHHHHhCChhhccCcchhHHHHHHHHHH
Confidence            455899999999999997  56799999988754 599999999999999977764

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=92.72  E-value=0.21  Score=49.30  Aligned_cols=50  Identities=18%  Similarity=0.355  Sum_probs=46.0

Q ss_pred             CCCCHHHHHHHHHh-cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccc
Q 017612          224 RSVNKTDVVTLGST-FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEP  273 (368)
Q Consensus       224 pgVnKTDA~~LLs~-FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~eP  273 (368)
                      .|||..++.+|-+. |.|+++|..++..||..+.||+..+|++|.+....-
T Consensus         7 ~g~~~~~~~~L~~~g~~t~~~~~~~~~~~L~~~~gls~~~~~~i~~~~~~~   57 (313)
T TIGR02238         7 HGINAADIKKLKSAGICTVNGVIMTTRRALCKIKGLSEAKVDKIKEAASKI   57 (313)
T ss_pred             CCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHhh
Confidence            47999999999985 999999999999999999999999999999877653

This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.

>smart00475 53EXOc 5'-3' exonuclease

Probab=92.67  E-value=0.13  Score=49.59  Aligned_cols=29  Identities=24%  Similarity=0.472  Sum_probs=26.4

Q ss_pred             hhccCCCCCHHHHHHHHHhcCCHHHHHcC
Q 017612          219 ALTSVRSVNKTDVVTLGSTFGSLSHIMDA  247 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs~FGSLk~I~~A  247 (368)
                      -+.+|||||++.|..||.+|||+++|+.+
T Consensus       187 nipGV~GIG~KtA~~Ll~~ygsle~i~~~  215 (259)
T smart00475      187 NIPGVPGIGEKTAAKLLKEFGSLENILEN  215 (259)
T ss_pred             CCCCCCCCCHHHHHHHHHHhCCHHHHHHH
Confidence            46789999999999999999999999854

>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A

Probab=92.49  E-value=0.12  Score=39.66  Aligned_cols=31  Identities=39%  Similarity=0.620  Sum_probs=22.2

Q ss_pred             HcCCHHhhhcCCCCCHHHHHHHHHHhc--cccc
Q 017612          245 MDASMEDLARCPGIGERKVKRLYDTFH--EPFK  275 (368)
Q Consensus       245 ~~AS~EELa~VPGIG~kKA~rI~e~F~--ePF~  275 (368)
                      =.|+.+||..+||||++.|++|.++=.  .+|.
T Consensus         9 N~as~~eL~~lpgi~~~~A~~Iv~~R~~~G~f~   41 (65)
T PF12836_consen    9 NTASAEELQALPGIGPKQAKAIVEYREKNGPFK   41 (65)
T ss_dssp             TTS-HHHHHTSTT--HHHHHHHHHHHHHH-S-S
T ss_pred             ccCCHHHHHHcCCCCHHHHHHHHHHHHhCcCCC
Confidence            368999999999999999999987753  3565

>PRK14976 5'-3' exonuclease; Provisional

Probab=92.45  E-value=0.15  Score=49.69  Aligned_cols=28  Identities=14%  Similarity=0.474  Sum_probs=25.7

Q ss_pred             hhccCCCCCHHHHHHHHHhcCCHHHHHc
Q 017612          219 ALTSVRSVNKTDVVTLGSTFGSLSHIMD  246 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs~FGSLk~I~~  246 (368)
                      -+.+|||||++.|..||+.|||+++|+.
T Consensus       192 nipGVpGIG~KtA~~LL~~~gsle~i~~  219 (281)
T PRK14976        192 NIKGVKGIGPKTAIKLLNKYGNIENIYE  219 (281)
T ss_pred             CCCCCCcccHHHHHHHHHHcCCHHHHHH
Confidence            4568999999999999999999999984

>PTZ00035 Rad51 protein; Provisional

Probab=92.43  E-value=0.22  Score=49.58  Aligned_cols=49  Identities=22%  Similarity=0.392  Sum_probs=45.4

Q ss_pred             CCCCHHHHHHHHHh-cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          224 RSVNKTDVVTLGST-FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       224 pgVnKTDA~~LLs~-FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      +|||..++.+|-+. |.|+++|+.++..||..+.||+..+|++|.+....
T Consensus        29 ~g~~~~~~~kL~~~g~~t~~~~~~~~~~~L~~~~gis~~~~~~i~~~~~~   78 (337)
T PTZ00035         29 AGINAADIKKLKEAGICTVESVAYATKKDLCNIKGISEAKVEKIKEAASK   78 (337)
T ss_pred             CCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhhCCCHHHHHHHHHHHHH
Confidence            78999999999985 99999999999999999999999999999876654

>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed

Probab=91.98  E-value=0.29  Score=52.43  Aligned_cols=59  Identities=25%  Similarity=0.413  Sum_probs=50.6

Q ss_pred             HHHHHhhc----cCCCCCHHHHHHHHHh--cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          214 SRLTHALT----SVRSVNKTDVVTLGST--FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       214 srL~saLT----sIpgVnKTDA~~LLs~--FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      .++.++.+    .|.|+|.+.+..|.+.  ..++.+|...+.++|..++|||+++|++|++.+..
T Consensus       417 ~~i~hf~Sr~amdI~GlGe~~i~~L~~~G~i~~~~Diy~L~~~~l~~l~gfgeks~~nll~aIe~  481 (562)
T PRK08097        417 ARLVWLSGKQGLGLDGIGEGTWRALHQTGLFEHLFSWLALTPEQLANTPGIGKARAEQLWHQFNL  481 (562)
T ss_pred             HHhHhhhcccccCCCCcCHHHHHHHHHcCCcCCHHHHhcCCHHHHhcCcCccHHHHHHHHHHHHH
Confidence            34555432    4999999999999974  58999999999999999999999999999999863

>PF01367 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases

Probab=91.79  E-value=0.0099  Score=50.30  Aligned_cols=28  Identities=21%  Similarity=0.414  Sum_probs=23.3

Q ss_pred             hhccCCCCCHHHHHHHHHhcCCHHHHHc
Q 017612          219 ALTSVRSVNKTDVVTLGSTFGSLSHIMD  246 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs~FGSLk~I~~  246 (368)
                      -+-+|+|||.+.|..||++||||++|+.
T Consensus        19 NIPGV~GIG~KtA~~LL~~ygsle~i~~   46 (101)
T PF01367_consen   19 NIPGVPGIGPKTAAKLLQEYGSLENILA   46 (101)
T ss_dssp             TB---TTSTCHCCCCCHHHHTSCHCCCC
T ss_pred             CCCCCCCCCHHHHHHHHHHcCCHHHHHH
Confidence            3568999999999999999999999996

The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include: Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins []. 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [, ]. Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases []. Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair []. ; GO: 0003677 DNA binding, 0003824 catalytic activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B.

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=91.53  E-value=0.32  Score=48.90  Aligned_cols=48  Identities=21%  Similarity=0.344  Sum_probs=44.2

Q ss_pred             CCCCHHHHHHHHHh-cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          224 RSVNKTDVVTLGST-FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       224 pgVnKTDA~~LLs~-FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      .|||..++.+|.+. |.|+++|+.++..||..+.||++.+|.+|.+...
T Consensus        37 ~g~~~~~~~kL~~~g~~tv~~~~~~~~~~L~~~~g~s~~~~~ki~~~a~   85 (344)
T PLN03187         37 QGINAGDVKKLQDAGIYTCNGLMMHTKKNLTGIKGLSEAKVDKICEAAE   85 (344)
T ss_pred             CCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHH
Confidence            58999999999985 9999999999999999999999999999876544

>PF00730 HhH-GPD: HhH-GPD superfamily base excision DNA repair protein This entry corresponds to Endonuclease III This entry corresponds to Alkylbase DNA glycosidase; InterPro: IPR003265 Endonuclease III (4

Probab=90.81  E-value=0.22  Score=40.39  Aligned_cols=43  Identities=23%  Similarity=0.275  Sum_probs=37.2

Q ss_pred             HHHHHHHhcC--CHHHHHcCCHHhhhcC---CCCCHHHHHHHHHHhcc
Q 017612          230 DVVTLGSTFG--SLSHIMDASMEDLARC---PGIGERKVKRLYDTFHE  272 (368)
Q Consensus       230 DA~~LLs~FG--SLk~I~~AS~EELa~V---PGIG~kKA~rI~e~F~e  272 (368)
                      --.+|.++||  +.+.|..++.+||..+   -|++..||+.|.++.+.
T Consensus        17 ~~~~l~~~~g~pt~~~l~~~~~~el~~~i~~~G~~~~ka~~i~~~a~~   64 (108)
T PF00730_consen   17 IYRRLFERYGFPTPEALAEASEEELRELIRPLGFSRRKAKYIIELARA   64 (108)
T ss_dssp             HHHHHHHHHSCSSHHHHHCSHHHHHHHHHTTSTSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCCHHHHHhCCHHHHHHHhhccCCCHHHHHHHHHHHHH
Confidence            3467888887  9999999999999877   89999999999988754

2.99.18 from EC) is a DNA repair enzyme which removes a number of damaged pyrimidines from DNA via its glycosylase activity and also cleaves the phosphodiester backbone at apurinic / apyrimidinic sites via a beta-elimination mechanism [, ]. The structurally related DNA glycosylase MutY recognises and excises the mutational intermediate 8-oxoguanine-adenine mispair []. The 3-D structures of Escherichia coli endonuclease III [] and catalytic domain of MutY [] have been determined. The structures contain two all-alpha domains: a sequence-continuous, six-helix domain (residues 22-132) and a Greek-key, four-helix domain formed by one N-terminal and three C-terminal helices (residues 1-21 and 133-211) together with the [Fe4S4] cluster. The cluster is bound entirely within the C-terminal loop by four cysteine residues with a ligation pattern Cys-(Xaa)6-Cys-(Xaa)2-Cys-(Xaa)5-Cys which is distinct from all other known Fe4S4 proteins. This structural motif is referred to as a [Fe4S4] cluster loop (FCL) []. Two DNA-binding motifs have been proposed, one at either end of the interdomain groove: the helix-hairpin-helix (HhH) and FCL motifs (see IPR003651 from INTERPRO). The primary role of the iron-sulphur cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone by forming the loop of the FCL motif [, ]. The HhH-GPD domain gets its name from its hallmark helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This domain is found in a diverse range of structurally related DNA repair proteins that include: endonuclease III, 4.2.99.18 from EC and DNA glycosylase MutY, an A/G-specific adenine glycosylase. Both of these enzymes have a C-terminal iron-sulphur cluster loop (FCL). The methyl-CPG binding protein (MBD4) also contain a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II 3.2.2.21 from EC, 8-oxoguanine DNA glycosylases and other members of the AlkA family.; GO: 0006284 base-excision repair; PDB: 3F0Z_A 3I0X_A 3F10_A 3I0W_A 3S6I_D 3N5N_Y 1PU7_A 1PU8_B 1PU6_B 1NGN_A ....

>PRK07758 hypothetical protein; Provisional

Probab=89.94  E-value=0.62  Score=39.70  Aligned_cols=49  Identities=12%  Similarity=0.241  Sum_probs=40.6

Q ss_pred             CCCCHHHHHHHH-HhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          224 RSVNKTDVVTLG-STFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       224 pgVnKTDA~~LL-s~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      ++++..-...|. ..+.+|.+|+.-+.+||.++.|||++-.+.|.+.|.+
T Consensus        40 ~~LSvRA~N~Lk~AGI~TL~dLv~~te~ELl~iknlGkKSL~EIkekL~E   89 (95)
T PRK07758         40 SLLSAPARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRKALEE   89 (95)
T ss_pred             ccccHHHHHHHHHcCCCcHHHHHcCCHHHHHHccCCCHHHHHHHHHHHHH
Confidence            455555555553 3689999999999999999999999999999999865

>TIGR03252 uncharacterized HhH-GPD family protein

Probab=89.11  E-value=0.71  Score=42.98  Aligned_cols=49  Identities=14%  Similarity=0.262  Sum_probs=36.6

Q ss_pred             HHHHHHhcC-CHHHHHcC----C---HHhhhcCCCCCHHHHHHHHHHhcccccccCC
Q 017612          231 VVTLGSTFG-SLSHIMDA----S---MEDLARCPGIGERKVKRLYDTFHEPFKRVVS  279 (368)
Q Consensus       231 A~~LLs~FG-SLk~I~~A----S---~EELa~VPGIG~kKA~rI~e~F~ePF~~~~~  279 (368)
                      ++.|+++|+ .+..|...    +   .++|..+||||++.|.-+..+|...|.-.+.
T Consensus        88 a~~iie~y~G~v~~L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL~~l~~~~~~~~~  144 (177)
T TIGR03252        88 AQYVVDTYDGDATAVWTEGDPDGKELLRRLKALPGFGKQKAKIFLALLGKQLGVTPE  144 (177)
T ss_pred             HHHHHHHhCCChhhhhcccCCCcHHHHHHHHcCCCCCHHHHHHHHHHHHHHhCCCCc
Confidence            344455555 56777651    2   3789999999999999999999999975444

This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).

>TIGR00593 pola DNA polymerase I

Probab=88.73  E-value=0.54  Score=52.68  Aligned_cols=29  Identities=24%  Similarity=0.480  Sum_probs=26.1

Q ss_pred             hhccCCCCCHHHHHHHHHhcCCHHHHHcC
Q 017612          219 ALTSVRSVNKTDVVTLGSTFGSLSHIMDA  247 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs~FGSLk~I~~A  247 (368)
                      -+.+|||||++.|..||.+|||+++|+..
T Consensus       186 nIpGVpGIG~KtA~kLL~~ygsle~i~~~  214 (887)
T TIGR00593       186 NIPGVKGIGEKTAAKLLQEFGSLENIYEN  214 (887)
T ss_pred             CCCCCCCcCHHHHHHHHHHcCCHHHHHHH
Confidence            45679999999999999999999999853

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=88.41  E-value=0.68  Score=50.55  Aligned_cols=51  Identities=10%  Similarity=0.218  Sum_probs=46.2

Q ss_pred             cCCCCCHHHHHHHHHh--cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          222 SVRSVNKTDVVTLGST--FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       222 sIpgVnKTDA~~LLs~--FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      .|.|+|......|+++  ..++.+|+..+.++|..++|||++.|++|++.+..
T Consensus       440 dI~GlG~~~i~~L~~~G~i~~~~Dly~L~~~~l~~l~g~geksa~nl~~~Ie~  492 (669)
T PRK14350        440 NIVGLSDKTIEFLFEKKFISSEIDLYTFNFDRLINLKGFKDKRINNLKRSIEA  492 (669)
T ss_pred             cccCcCHHHHHHHHHcCCcCCHHHHhhCCHHHHhhccCccHHHHHHHHHHHHH
Confidence            5999999999999964  47888999999999999999999999999999863

>PRK03980 flap endonuclease-1; Provisional

Probab=88.15  E-value=0.52  Score=46.34  Aligned_cols=27  Identities=11%  Similarity=0.357  Sum_probs=25.2

Q ss_pred             hccCCCCCHHHHHHHHHhcCCHHHHHc
Q 017612          220 LTSVRSVNKTDVVTLGSTFGSLSHIMD  246 (368)
Q Consensus       220 LTsIpgVnKTDA~~LLs~FGSLk~I~~  246 (368)
                      ..+|+|||.+.|..|++.||||++|+.
T Consensus       191 ~~GI~GIG~ktA~kLi~~~~sle~i~~  217 (292)
T PRK03980        191 NPGIKGIGPKTALKLIKKHGDLEKVLE  217 (292)
T ss_pred             CCCCCCccHHHHHHHHHHCCCHHHHHH
Confidence            348999999999999999999999997

>PRK10736 hypothetical protein; Provisional

Probab=88.06  E-value=0.71  Score=47.26  Aligned_cols=47  Identities=19%  Similarity=0.220  Sum_probs=40.7

Q ss_pred             HhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHH
Q 017612          218 HALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYD  268 (368)
Q Consensus       218 saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e  268 (368)
                      -.|..++|||.....+|+.+||+.+   .++.++|..+ |++++.+..+.+
T Consensus         8 l~L~~~~giG~~~~~~L~~~~~~~~---~~~~~~l~~~-g~~~~~~~~~~~   54 (374)
T PRK10736          8 LRLMSVSSLYGDKMVRIAHRLLAQS---QIDAVVLQAT-GLTLRQAQQFLQ   54 (374)
T ss_pred             HHHHhCCCCCHHHHHHHHHHhcChh---hCCHHHHHHc-CCCHHHHHHHhc
Confidence            3778899999999999999999999   4788999887 999988877643

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=87.83  E-value=0.92  Score=45.56  Aligned_cols=48  Identities=21%  Similarity=0.360  Sum_probs=43.6

Q ss_pred             CCCCHHHHHHHHHh-cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          224 RSVNKTDVVTLGST-FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       224 pgVnKTDA~~LLs~-FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      .||+..|+.+|-++ |.|+++|+.++..+|..+-||...+|+++.+...
T Consensus        34 ~gi~~~~i~kL~~~g~~T~~~~~~~~~~~L~~i~~is~~~~~~~~~~~~   82 (342)
T PLN03186         34 SGIAALDIKKLKDAGIHTVESLAYAPKKDLLQIKGISEAKVEKILEAAS   82 (342)
T ss_pred             CCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHH
Confidence            58999999999885 9999999999999999999999999987776553

>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region

Probab=87.61  E-value=0.46  Score=36.48  Aligned_cols=29  Identities=28%  Similarity=0.424  Sum_probs=25.6

Q ss_pred             HHHcCCHHhhhc-CCCCCHHHHHHHHHHhc
Q 017612          243 HIMDASMEDLAR-CPGIGERKVKRLYDTFH  271 (368)
Q Consensus       243 ~I~~AS~EELa~-VPGIG~kKA~rI~e~F~  271 (368)
                      +|=.|+.++|.. +||||++.|++|.+...
T Consensus         9 nvNta~~~~L~~~ipgig~~~a~~Il~~R~   38 (69)
T TIGR00426         9 NINTATAEELQRAMNGVGLKKAEAIVSYRE   38 (69)
T ss_pred             ECcCCCHHHHHhHCCCCCHHHHHHHHHHHH
Confidence            455689999999 99999999999999974

Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.

>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]

Probab=87.59  E-value=0.61  Score=45.41  Aligned_cols=50  Identities=16%  Similarity=0.303  Sum_probs=35.6

Q ss_pred             hhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612          219 ALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFK  275 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~  275 (368)
                      -+.+|+|||++.|..||..|||++.|...-.       .++.+-...+.+....-|.
T Consensus       199 nipGV~GIG~ktA~~Ll~~~gs~e~i~~~~~-------~~~~~~~~~l~~~~~~afl  248 (310)
T COG0258         199 NIPGVKGIGPKTALKLLQEYGSLEGLYENLD-------IIKKKTREKLLEDKEKAFL  248 (310)
T ss_pred             CCCCCCCcCHHHHHHHHHHhCCHHHHHHhhh-------hhcchhhHHHHHHHHHHhc
Confidence            3557999999999999999999999985432       3444555555555544444

>PRK10702 endonuclease III; Provisional

Probab=87.01  E-value=0.63  Score=43.69  Aligned_cols=37  Identities=16%  Similarity=0.242  Sum_probs=26.3

Q ss_pred             HHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHh
Q 017612          231 VVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTF  270 (368)
Q Consensus       231 A~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F  270 (368)
                      |+.+++.||.   -.-.+.++|..+||||++.|.-|.-+.
T Consensus        93 a~~i~~~~~~---~~p~~~~~Ll~lpGVG~ktA~~ill~a  129 (211)
T PRK10702         93 CRILLEQHNG---EVPEDRAALEALPGVGRKTANVVLNTA  129 (211)
T ss_pred             HHHHHHHcCC---CCCchHHHHhcCCcccHHHHHHHHHHH
Confidence            3344455543   234578999999999999999987543

>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A

Probab=86.51  E-value=0.7  Score=35.74  Aligned_cols=20  Identities=35%  Similarity=0.722  Sum_probs=18.4

Q ss_pred             hhhcCCCCCHHHHHHHHHHh
Q 017612          251 DLARCPGIGERKVKRLYDTF  270 (368)
Q Consensus       251 ELa~VPGIG~kKA~rI~e~F  270 (368)
                      +|..+||||++.|.+|.+++
T Consensus        48 ~~~~l~gIG~~ia~kI~E~l   67 (68)
T PF14716_consen   48 DLKKLPGIGKSIAKKIDEIL   67 (68)
T ss_dssp             HHCTSTTTTHHHHHHHHHHH
T ss_pred             HHhhCCCCCHHHHHHHHHHH
Confidence            49999999999999999886

...

>PRK13913 3-methyladenine DNA glycosylase; Provisional

Probab=86.51  E-value=0.95  Score=43.09  Aligned_cols=46  Identities=17%  Similarity=0.203  Sum_probs=33.9

Q ss_pred             HHHHHHHhcCCHHHHH-cCCHHhhhcCCCCCHHHHHHHHH-Hhccccc
Q 017612          230 DVVTLGSTFGSLSHIM-DASMEDLARCPGIGERKVKRLYD-TFHEPFK  275 (368)
Q Consensus       230 DA~~LLs~FGSLk~I~-~AS~EELa~VPGIG~kKA~rI~e-~F~ePF~  275 (368)
                      -|..+++.||++..+. ....++|..+||||++.|..|.- +|++|..
T Consensus       100 la~~i~~~~g~~~~~~~~~~re~Ll~l~GIG~kTAd~iLlya~~rp~f  147 (218)
T PRK13913        100 LSENILKDFGSFENFKQEVTREWLLDQKGIGKESADAILCYVCAKEVM  147 (218)
T ss_pred             HHHHHHHHcCCchhccCchHHHHHHcCCCccHHHHHHHHHHHcCCCcc
Confidence            3445667788876654 34678999999999999999876 5555543

>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A

Probab=86.31  E-value=0.53  Score=35.33  Aligned_cols=22  Identities=36%  Similarity=0.898  Sum_probs=19.9

Q ss_pred             HhhhcCCCCCHHHHHHHHHH-hc
Q 017612          250 EDLARCPGIGERKVKRLYDT-FH  271 (368)
Q Consensus       250 EELa~VPGIG~kKA~rI~e~-F~  271 (368)
                      ++|..|+|||++.|++|++. |.
T Consensus         5 ~~L~~I~Gig~~~a~~L~~~G~~   27 (60)
T PF14520_consen    5 DDLLSIPGIGPKRAEKLYEAGIK   27 (60)
T ss_dssp             HHHHTSTTCHHHHHHHHHHTTCS
T ss_pred             HhhccCCCCCHHHHHHHHhcCCC
Confidence            68999999999999999998 54

...

>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]

Probab=86.18  E-value=0.88  Score=43.39  Aligned_cols=45  Identities=22%  Similarity=0.327  Sum_probs=33.6

Q ss_pred             HHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHH-hcccccc
Q 017612          229 TDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDT-FHEPFKR  276 (368)
Q Consensus       229 TDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~-F~ePF~~  276 (368)
                      .-++.|+++||+   -+-.+.+||..+||+|.|.|.-+... |..|-..
T Consensus        91 ~~~~~l~e~~~g---~vP~~~~eL~~LPGVGrKTAnvVL~~a~g~p~i~  136 (211)
T COG0177          91 ELARILLEKFGG---EVPDTREELLSLPGVGRKTANVVLSFAFGIPAIA  136 (211)
T ss_pred             HHHHHHHHHcCC---CCCchHHHHHhCCCcchHHHHHHHHhhcCCCccc
Confidence            344556777777   34556789999999999999998876 6666443

>PRK05755 DNA polymerase I; Provisional

Probab=84.81  E-value=0.76  Score=51.00  Aligned_cols=29  Identities=17%  Similarity=0.374  Sum_probs=26.3

Q ss_pred             hhccCCCCCHHHHHHHHHhcCCHHHHHcC
Q 017612          219 ALTSVRSVNKTDVVTLGSTFGSLSHIMDA  247 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs~FGSLk~I~~A  247 (368)
                      -+-+|||||++.|..||++|||+++|+.+
T Consensus       188 nipGv~GiG~ktA~~Ll~~~gsle~i~~~  216 (880)
T PRK05755        188 NIPGVPGIGEKTAAKLLQEYGSLEGLYEN  216 (880)
T ss_pred             CCCCCCCccHHHHHHHHHHcCCHHHHHHh
Confidence            46789999999999999999999999944

>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed

Probab=84.57  E-value=1.2  Score=41.09  Aligned_cols=42  Identities=14%  Similarity=0.185  Sum_probs=30.8

Q ss_pred             HHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          228 KTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       228 KTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      +.++.+| =.|.+.++--.  ...|..|+|||+++|.+|.+.|..
T Consensus        54 rd~~~~l-~gF~~~~ek~~--f~~L~~i~GIGpk~A~~il~~fg~   95 (192)
T PRK00116         54 REDAILL-YGFLTKEEREL--FRLLISVSGVGPKLALAILSGLSP   95 (192)
T ss_pred             echhHHH-cCcCCHHHHHH--HHHHhcCCCCCHHHHHHHHHhCCH
Confidence            3455555 44555554333  678999999999999999999974

>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases

Probab=84.42  E-value=0.93  Score=44.07  Aligned_cols=52  Identities=15%  Similarity=0.321  Sum_probs=34.2

Q ss_pred             hccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccc
Q 017612          220 LTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEP  273 (368)
Q Consensus       220 LTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~eP  273 (368)
                      +.+|+|||.+.|..|++.||+++.++..=...+..+|  ..-.-..++++|..|
T Consensus       225 ~~gv~giG~k~A~~li~~~~~~~~~~~~l~~~~~~~~--~~~~~~~~~~~f~~p  276 (316)
T cd00128         225 TEGIPGIGPVTALKLIKKYGDIEKDIERLKKKLYRSP--EDFPLKEAREFFLNP  276 (316)
T ss_pred             CCCCCCccHHHHHHHHHHcCChHHHHHHHHHhCccCC--CcCChHHHHHHHcCC
Confidence            4589999999999999999998777644333333433  112234556666533

XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.

>PRK14973 DNA topoisomerase I; Provisional

Probab=83.92  E-value=1.5  Score=49.55  Aligned_cols=52  Identities=25%  Similarity=0.264  Sum_probs=47.1

Q ss_pred             hccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          220 LTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       220 LTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      |..|+|||.+.+..|-. -.-+++.+.+|+.++|+.+.|||.++++.|+..+.
T Consensus       879 l~~vkg~ge~t~~~l~~ag~~~~e~l~~~d~~~la~~~~i~~k~~~~~~~~~~  931 (936)
T PRK14973        879 LLSVPGLGETTLEKLYLAGVYDGDLLVSADPKKLAKVTGIDEKKLRNLQAYAK  931 (936)
T ss_pred             hhhccCCCHHHHHHHHHcCCCCHHHhccCCHHHHhhhcCCCHHHHHHHHHHHh
Confidence            77999999999977755 68899999999999999999999999999998774

>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs

Probab=83.88  E-value=0.69  Score=32.53  Aligned_cols=28  Identities=14%  Similarity=0.360  Sum_probs=15.0

Q ss_pred             HHHHHcCCHHhhhcCCCCCHHHHHHHHH
Q 017612          241 LSHIMDASMEDLARCPGIGERKVKRLYD  268 (368)
Q Consensus       241 Lk~I~~AS~EELa~VPGIG~kKA~rI~e  268 (368)
                      +..|+.-..+.+..|||||+++|.+|.+
T Consensus         7 ~~~L~GD~~dni~Gv~giG~ktA~~ll~   34 (36)
T smart00279        7 YAILVGDYSDNIPGVKGIGPKTALKLLR   34 (36)
T ss_pred             HHHHhCcCCCCCCCCCcccHHHHHHHHH
Confidence            3444443333455666666666666554

>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins

Probab=83.68  E-value=1.8  Score=41.21  Aligned_cols=54  Identities=15%  Similarity=0.228  Sum_probs=48.8

Q ss_pred             hhccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          219 ALTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      .|-++|+||+..++.|-. ...++.+|+..+.+++..+-|+++..++.|+++++.
T Consensus       152 ~L~Qlp~i~~~~~~~l~~~~i~s~~~l~~~~~~~~~~ll~~~~~~~~~i~~~~~~  206 (312)
T smart00611      152 PLLQLPHLPEEILKRLEKKKVLSLEDLLELEDEERGELLGLLDAEGERVYKVLSR  206 (312)
T ss_pred             ccccCCCCCHHHHHHHHhCCCCCHHHHHhcCHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            566899999999999987 468999999999999999999999999999998864

>TIGR03674 fen_arch flap structure-specific endonuclease

Probab=83.22  E-value=1  Score=44.86  Aligned_cols=27  Identities=19%  Similarity=0.395  Sum_probs=25.6

Q ss_pred             ccCCCCCHHHHHHHHHhcCCHHHHHcC
Q 017612          221 TSVRSVNKTDVVTLGSTFGSLSHIMDA  247 (368)
Q Consensus       221 TsIpgVnKTDA~~LLs~FGSLk~I~~A  247 (368)
                      .+|+|||.+.|..|++.|||+++|+..
T Consensus       239 ~Gv~GIG~ktA~kli~~~gsie~il~~  265 (338)
T TIGR03674       239 EGVKGIGPKTALKLIKEHGDLEKVLKA  265 (338)
T ss_pred             CCCCCccHHHHHHHHHHcCCHHHHHHh
Confidence            699999999999999999999999875

Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=83.22  E-value=1.9  Score=42.55  Aligned_cols=47  Identities=17%  Similarity=0.291  Sum_probs=43.2

Q ss_pred             CCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          225 SVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       225 gVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      ||+..++..|-+ .|.|+++|+.++..||.++-||...+++.+...+.
T Consensus         8 ~~~~~~~~~l~~~g~~t~~~~~~~~~~~L~~i~~ls~~~~~~~~~~~~   55 (316)
T TIGR02239         8 GITAADIKKLQEAGLHTVESVAYAPKKQLLEIKGISEAKADKILAEAA   55 (316)
T ss_pred             CCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            699999999987 79999999999999999999999999999887554

This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).

>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []

Probab=83.07  E-value=2.4  Score=35.96  Aligned_cols=38  Identities=18%  Similarity=0.171  Sum_probs=33.2

Q ss_pred             HHHHhhccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhh
Q 017612          215 RLTHALTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDL  252 (368)
Q Consensus       215 rL~saLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EEL  252 (368)
                      .....|+.||+||+..|+-|.. =+.++++|...+.++|
T Consensus         9 ~~~~~L~~iP~IG~a~a~DL~~LGi~s~~~L~g~dP~~L   47 (93)
T PF11731_consen    9 AGLSDLTDIPNIGKATAEDLRLLGIRSPADLKGRDPEEL   47 (93)
T ss_pred             HHHHHHhcCCCccHHHHHHHHHcCCCCHHHHhCCCHHHH
Confidence            3567889999999999999987 6889999999998765

Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.

>PTZ00217 flap endonuclease-1; Provisional

Probab=82.70  E-value=1.2  Score=45.70  Aligned_cols=28  Identities=11%  Similarity=0.315  Sum_probs=25.5

Q ss_pred             hccCCCCCHHHHHHHHHhcCCHHHHHcC
Q 017612          220 LTSVRSVNKTDVVTLGSTFGSLSHIMDA  247 (368)
Q Consensus       220 LTsIpgVnKTDA~~LLs~FGSLk~I~~A  247 (368)
                      +.+|+|||.+.|..|++.||++++|+..
T Consensus       237 ~pgi~GIG~ktA~~Li~~~gsle~il~~  264 (393)
T PTZ00217        237 CDTIKGIGPKTAYKLIKKYKSIEEILEH  264 (393)
T ss_pred             CCCCCCccHHHHHHHHHHcCCHHHHHHH
Confidence            4589999999999999999999999853

>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif

Probab=82.39  E-value=0.93  Score=35.98  Aligned_cols=36  Identities=19%  Similarity=0.481  Sum_probs=28.5

Q ss_pred             hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          237 TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       237 ~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      .|-.+..++.-+.+-+..|||||+++|.+|..-+..
T Consensus         9 q~~d~~~L~GD~~D~i~gv~giG~k~A~~ll~~~~~   44 (75)
T cd00080           9 QFIDLAILVGDKSDNIPGVPGIGPKTALKLLKEYGS   44 (75)
T ss_pred             HHHHHHHHcCCccccCCCCCcccHHHHHHHHHHhCC
Confidence            455566667766778899999999999999988753

HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.

>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA

Probab=80.54  E-value=1.3  Score=35.66  Aligned_cols=38  Identities=29%  Similarity=0.434  Sum_probs=19.2

Q ss_pred             hhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCC
Q 017612          219 ALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGI  258 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGI  258 (368)
                      .|.+|||||...|..|+..+|.++..-++  .+|...-|+
T Consensus         3 ~l~sipGig~~~a~~llaeigd~~rF~~~--~~l~~~~Gl   40 (87)
T PF02371_consen    3 LLTSIPGIGPITAATLLAEIGDISRFKSA--KQLASYAGL   40 (87)
T ss_pred             hhcCCCCccHHHHHHHHHHHcCchhcccc--hhhhhcccc
Confidence            34555666666666666555555443322  344444443

This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated

>PRK10702 endonuclease III; Provisional

Probab=80.41  E-value=3.6  Score=38.68  Aligned_cols=61  Identities=18%  Similarity=0.206  Sum_probs=43.5

Q ss_pred             cHHHHHHHhh----ccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcC-C--CCCHHHHHHHHHHhcc
Q 017612          211 DYLSRLTHAL----TSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARC-P--GIGERKVKRLYDTFHE  272 (368)
Q Consensus       211 dy~srL~saL----TsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~V-P--GIG~kKA~rI~e~F~e  272 (368)
                      ++.+.++.++    |+++.|++. ...|...|.+++.|.+|+.+||..+ .  |+-..||++|++..+.
T Consensus        28 ~p~e~lvs~iLsq~t~~~~v~~~-~~~L~~~~pt~e~l~~a~~~~l~~~i~~~G~y~~kA~~l~~~a~~   95 (211)
T PRK10702         28 SPFELLIAVLLSAQATDVSVNKA-TAKLYPVANTPAAMLELGVEGVKTYIKTIGLYNSKAENVIKTCRI   95 (211)
T ss_pred             ChHHHHHHHHHHhhcCHHHHHHH-HHHHHHHcCCHHHHHCCCHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            4445554433    455555544 4577789999999999999999874 3  5557899998877764

>smart00478 ENDO3c endonuclease III

Probab=80.04  E-value=2.3  Score=36.48  Aligned_cols=45  Identities=16%  Similarity=0.215  Sum_probs=26.6

Q ss_pred             CCCHHHHHHHHHhcCCHHHHHc----CCHHhhhcCCCCCHHHHHHHHHH
Q 017612          225 SVNKTDVVTLGSTFGSLSHIMD----ASMEDLARCPGIGERKVKRLYDT  269 (368)
Q Consensus       225 gVnKTDA~~LLs~FGSLk~I~~----AS~EELa~VPGIG~kKA~rI~e~  269 (368)
                      |.....|+.|.+--..+.+-.+    ...++|..++|||++.|..+.-+
T Consensus        43 g~~~~ka~~i~~~a~~~~~~~~~~~~~~~~~L~~l~GIG~~tA~~~l~~   91 (149)
T smart00478       43 GFYRRKAKYLIELARILVEEYGGEVPDDREELLKLPGVGRKTANAVLSF   91 (149)
T ss_pred             CChHHHHHHHHHHHHHHHHHHCCCccHHHHHHHcCCCCcHHHHHHHHHH
Confidence            5556666666654433333222    24567777888888887776544

includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	368
2a1j_B	91	Crystal Structure Of The Complex Between The C-Term		4e-20
1z00_A	89	Solution Structure Of The C-Terminal Domain Of Ercc		2e-19
2jpd_A	135	Solution Structure Of The Ercc1 Central Domain Leng		3e-13
2jnw_A	133	Solution Structure Of A Ercc1-Xpa Heterodimer Lengt		3e-13
2a1i_A	146	Crystal Structure Of The Central Domain Of Human Er		3e-13

>pdb|2A1J|B Chain B, Crystal Structure Of The Complex Between The C-Terminal Domains Of Human Xpf And Ercc1 Length = 91

Iteration: 1
 Score = 95.5 bits (236), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 43/78 (55%), Positives = 60/78 (76%)
Query: 200 PADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIG 259
           PADL+  +++ D++SR+T  LT+V+SVNKTD  TL +TFGSL  ++ AS EDLA CPG+G
Sbjct: 14  PADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLG 73
Query: 260 ERKVKRLYDTFHEPFKRV 277
            +K +RL+D  HEPF +V
Sbjct: 74  PQKARRLFDVLHEPFLKV 91

>pdb|1Z00|A Chain A, Solution Structure Of The C-Terminal Domain Of Ercc1 Complexed With The C-Terminal Domain Of Xpf Length = 89

Iteration: 1
 Score = 93.6 bits (231), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 42/77 (54%), Positives = 59/77 (76%)
Query: 201 ADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGE 260
           ADL+  +++ D++SR+T  LT+V+SVNKTD  TL +TFGSL  ++ AS EDLA CPG+G 
Sbjct: 2   ADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGP 61
Query: 261 RKVKRLYDTFHEPFKRV 277
           +K +RL+D  HEPF +V
Sbjct: 62  QKARRLFDVLHEPFLKV 78

>pdb|2JPD|A Chain A, Solution Structure Of The Ercc1 Central Domain Length = 135

Iteration: 1
 Score = 73.2 bits (178), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 33/72 (45%), Positives = 48/72 (66%), Gaps = 11/72 (15%)
Query: 139 NAILVSQRQKGNPLLKYIRNVRWAFADVVCDYLVGQNSCALYLSLEECGRYLETIKVYEN 198
           N+I+VS RQ+GNP+LK++RNV W F DV+ DY++GQ++CAL+LSL            Y N
Sbjct: 5   NSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLR-----------YHN 53
Query: 199 KPADLIQGQMDT 210
              D I G++ +
Sbjct: 54  LHPDYIHGRLQS 65

>pdb|2JNW|A Chain A, Solution Structure Of A Ercc1-Xpa Heterodimer Length = 133

Iteration: 1
 Score = 72.8 bits (177), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 33/72 (45%), Positives = 48/72 (66%), Gaps = 11/72 (15%)
Query: 139 NAILVSQRQKGNPLLKYIRNVRWAFADVVCDYLVGQNSCALYLSLEECGRYLETIKVYEN 198
           N+I+VS RQ+GNP+LK++RNV W F DV+ DY++GQ++CAL+LSL            Y N
Sbjct: 18  NSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLR-----------YHN 66
Query: 199 KPADLIQGQMDT 210
              D I G++ +
Sbjct: 67  LHPDYIHGRLQS 78

>pdb|2A1I|A Chain A, Crystal Structure Of The Central Domain Of Human Ercc1 Length = 146

Iteration: 1
 Score = 72.8 bits (177), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 33/72 (45%), Positives = 48/72 (66%), Gaps = 11/72 (15%)
Query: 139 NAILVSQRQKGNPLLKYIRNVRWAFADVVCDYLVGQNSCALYLSLEECGRYLETIKVYEN 198
           N+I+VS RQ+GNP+LK++RNV W F DV+ DY++GQ++CAL+LSL            Y N
Sbjct: 18  NSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLR-----------YHN 66
Query: 199 KPADLIQGQMDT 210
              D I G++ +
Sbjct: 67  LHPDYIHGRLQS 78

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	368
2a1j_B	91	DNA excision repair protein ERCC-1; XPF, xeroderma	4e-39
1z00_A	89	DNA excision repair protein ERCC-1; helix-hairpin-	7e-35
2a1i_A	146	DNA excision repair protein ERCC-1; XPF, central d	3e-21
2a1i_A	146	DNA excision repair protein ERCC-1; XPF, central d	1e-07
1x2i_A	75	HEF helicase/nuclease; alpha helix, helix-hairpin-	3e-10
2bgw_A	219	XPF endonuclease; hydrolase, structure specific en	3e-10
1kft_A	78	UVRC, excinuclease ABC subunit C; helix-hairpin-he	3e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-07
3c1y_A	377	DNA integrity scanning protein DISA; DNA damage, D	3e-07
3sgi_A	615	DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tub	1e-06
2owo_A	671	DNA ligase; protein-DNA complex, ligase-DNA comple	1e-05
1dgs_A	667	DNA ligase; AMP complex, NAD+-dependent; HET: DNA	1e-05
3c65_A	226	Uvrabc system protein C; UVRC, endonuclease, nucle	1e-05

>2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 Length = 91

 Score =  133 bits (337), Expect = 4e-39
 Identities = 43/84 (51%), Positives = 61/84 (72%)

Query: 194 KVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLA 253
             +   PADL+  +++ D++SR+T  LT+V+SVNKTD  TL +TFGSL  ++ AS EDLA
Sbjct: 8   HHHSQDPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLA 67

Query: 254 RCPGIGERKVKRLYDTFHEPFKRV 277
            CPG+G +K +RL+D  HEPF +V
Sbjct: 68  LCPGLGPQKARRLFDVLHEPFLKV 91

>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 Length = 89

 Score =  122 bits (308), Expect = 7e-35
 Identities = 42/77 (54%), Positives = 59/77 (76%)

Query: 201 ADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGE 260
           ADL+  +++ D++SR+T  LT+V+SVNKTD  TL +TFGSL  ++ AS EDLA CPG+G 
Sbjct: 2   ADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGP 61

Query: 261 RKVKRLYDTFHEPFKRV 277
           +K +RL+D  HEPF +V
Sbjct: 62  QKARRLFDVLHEPFLKV 78

>2a1i_A DNA excision repair protein ERCC-1; XPF, central domain, DNA repair, endonuclease, DNA binding protein; HET: DNA; 1.90A {Homo sapiens} SCOP: c.52.1.20 PDB: 2jnw_A* 2jpd_A* Length = 146

 Score = 88.0 bits (218), Expect = 3e-21
 Identities = 31/62 (50%), Positives = 46/62 (74%)

Query: 122 VGTASASASSSQSIQSRNAILVSQRQKGNPLLKYIRNVRWAFADVVCDYLVGQNSCALYL 181
           +G++      SQ     N+I+VS RQ+GNP+LK++RNV W F DV+ DY++GQ++CAL+L
Sbjct: 1   MGSSHHHHHHSQDPAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFL 60

Query: 182 SL 183
           SL
Sbjct: 61  SL 62

>2a1i_A DNA excision repair protein ERCC-1; XPF, central domain, DNA repair, endonuclease, DNA binding protein; HET: DNA; 1.90A {Homo sapiens} SCOP: c.52.1.20 PDB: 2jnw_A* 2jpd_A* Length = 146

 Score = 49.9 bits (119), Expect = 1e-07
 Identities = 20/36 (55%), Positives = 23/36 (63%), Gaps = 2/36 (5%)

Query: 175 NSCALYL--SLEECGRYLETIKVYENKPADLIQGQM 208
             C L L  S EE GRYLET K YE KPADL+  ++
Sbjct: 111 ADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKL 146

>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} SCOP: a.60.2.5 Length = 75

 Score = 55.0 bits (133), Expect = 3e-10
 Identities = 16/62 (25%), Positives = 27/62 (43%)

Query: 215 RLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPF 274
           R    +  +  V+ T    L   FGS+  +  AS+ +L +  GIGE+  K +      P+
Sbjct: 11  RQRLIVEGLPHVSATLARRLLKHFGSVERVFTASVAELMKVEGIGEKIAKEIRRVITAPY 70

Query: 275 KR 276
             
Sbjct: 71  IE 72

>2bgw_A XPF endonuclease; hydrolase, structure specific endonuclease, nucleotide excision repair; 2.8A {Aeropyrum pernix} SCOP: a.60.2.5 c.52.1.20 PDB: 2bhn_A Length = 219

 Score = 58.7 bits (141), Expect = 3e-10
 Identities = 17/113 (15%), Positives = 38/113 (33%)

Query: 163 FADVVCDYLVGQNSCALYLSLEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTS 222
            A  +   +   N+     +                +   + +    +D      + L S
Sbjct: 107 AALQLDYGIRLMNTMDPKGTALVIESLARLSTREGGQRIVIHKKPRLSDVREWQLYILQS 166

Query: 223 VRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFK 275
              + +     +   FGSL     AS  ++++  GIGE++ + +      P+K
Sbjct: 167 FPGIGRRTAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIKKILMTPYK 219

>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} SCOP: a.60.2.3 Length = 78

 Score = 49.1 bits (118), Expect = 3e-08
 Identities = 9/34 (26%), Positives = 21/34 (61%)

Query: 238 FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271
            G L  + +AS+E++A+ PGI +   ++++ +  
Sbjct: 44  MGGLQGLRNASVEEIAKVPGISQGLAEKIFWSLK 77

>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 = 52.9 bits (126), Expect = 1e-07
 Identities = 42/251 (16%), Positives = 78/251 (31%), Gaps = 79/251 (31%)

Query: 114 LSQGGEQNVGTASASASSSQSIQSRNAILVSQRQKGNPLLKYI-RNVRW------AFADV 166
           +          +S       SIQ+    L+  +   N LL  +  NV        AF ++
Sbjct: 209 IDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLL--VLLNV-QNAKAWNAF-NL 264

Query: 167 VC------------DYLVGQNSCALYLSLEECG---RYLETI--KVYENKPADL------ 203
            C            D+L    +  + L           ++++  K  + +P DL      
Sbjct: 265 SCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLT 324

Query: 204 -------IQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCP 256
                  I  +   D L+   +     + VN             L+ I+++S+  L   P
Sbjct: 325 TNPRRLSIIAESIRDGLATWDN----WKHVNCDK----------LTTIIESSLNVLE--P 368

Query: 257 GIGERKVKRLYDTFHEPFKRVVSSHPPIPET--------PSQKDVERSSVNEVTEVEKDT 308
                  ++++D        V      IP            + DV       V ++ K +
Sbjct: 369 AE----YRKMFDRL-----SVFPPSAHIPTILLSLIWFDVIKSDVMV----VVNKLHKYS 415

Query: 309 EDVNKRRKKET 319
             V K+ K+ T
Sbjct: 416 -LVEKQPKEST 425

>3c1y_A DNA integrity scanning protein DISA; DNA damage, DNA repair, DNA-binding, DNA binding protein; HET: DNA 2BA; 2.10A {Thermotoga maritima} PDB: 3c1z_A* 3c21_A* 3c23_A* Length = 377

 Score = 50.6 bits (121), Expect = 3e-07
 Identities = 16/63 (25%), Positives = 30/63 (47%)

Query: 208 MDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLY 267
            D    +R    L +V  +  +    +   F +L  I  AS+EDL +  GIGE++ + + 
Sbjct: 305 DDVLVSARGYRLLKTVARIPLSIGYNVVRMFKTLDQISKASVEDLKKVEGIGEKRARAIS 364

Query: 268 DTF 270
           ++ 
Sbjct: 365 ESI 367

>3sgi_A DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tuberculosis} Length = 615

 Score = 49.1 bits (118), Expect = 1e-06
 Identities = 21/61 (34%), Positives = 28/61 (45%), Gaps = 1/61 (1%)

Query: 213 LSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272
           L R+  AL S+R V  T    L + FGSL  I  AS + LA   G+G      + + F  
Sbjct: 525 LWRVLVAL-SIRHVGPTAARALATEFGSLDAIAAASTDQLAAVEGVGPTIAAAVTEWFAV 583

Query: 273 P 273
            
Sbjct: 584 D 584

>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli} Length = 671

 Score = 46.4 bits (111), Expect = 1e-05
 Identities = 17/61 (27%), Positives = 31/61 (50%), Gaps = 1/61 (1%)

Query: 213 LSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272
            +R  +AL  +R V +     L + FG+L  +  AS+E+L + P +G      +++ F E
Sbjct: 508 FARFLYAL-GIREVGEATAAGLAAYFGTLEALEAASIEELQKVPDVGIVVASHVHNFFAE 566

Query: 273 P 273
            
Sbjct: 567 E 567

>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* Length = 667

 Score = 46.0 bits (110), Expect = 1e-05
 Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 1/66 (1%)

Query: 213 LSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272
           L RL +AL  +  V +     L   FG++  +++AS+E+L     +GE   + + +T  +
Sbjct: 503 LERLLYAL-GLPGVGEVLARNLARRFGTMDRLLEASLEELIEVEEVGELTARAILETLKD 561

Query: 273 PFKRVV 278
           P  R +
Sbjct: 562 PAFRDL 567

>3c65_A Uvrabc system protein C; UVRC, endonuclease, nucleotide excision repair, DNA repair, RNAse H, cytoplasm, DNA damage, DNA excision; 1.90A {Bacillus stearothermophilus} Length = 226

 Score = 44.8 bits (107), Expect = 1e-05
 Identities = 11/35 (31%), Positives = 21/35 (60%), Gaps = 1/35 (2%)

Query: 238 FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272
           FGS+  + +A++E+L R   I     +++Y+  HE
Sbjct: 193 FGSVKKMKEATVEELQR-ANIPRAVAEKIYEKLHE 226

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	368
2a1i_A	146	DNA excision repair protein ERCC-1; XPF, central d	99.92
2bgw_A	219	XPF endonuclease; hydrolase, structure specific en	99.86
2a1j_B	91	DNA excision repair protein ERCC-1; XPF, xeroderma	99.56
1z00_A	89	DNA excision repair protein ERCC-1; helix-hairpin-	99.55
1x2i_A	75	HEF helicase/nuclease; alpha helix, helix-hairpin-	99.45
2a1j_A	63	DNA repair endonuclease XPF; XPF, xeroderma pigmen	99.39
1z00_B	84	DNA repair endonuclease XPF; helix-hairpin-helix,	99.2
1kft_A	78	UVRC, excinuclease ABC subunit C; helix-hairpin-he	99.16
3c65_A	226	Uvrabc system protein C; UVRC, endonuclease, nucle	99.15
2nrt_A	220	Uvrabc system protein C; UVRC, endonuclease, RNAse	99.12
2owo_A	671	DNA ligase; protein-DNA complex, ligase-DNA comple	98.87
3c1y_A	377	DNA integrity scanning protein DISA; DNA damage, D	98.86
4glx_A	586	DNA ligase; inhibitor, ligase-ligase inhibitor-DNA	98.81
1dgs_A	667	DNA ligase; AMP complex, NAD+-dependent; HET: DNA	98.8
3sgi_A	615	DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tub	98.76
1ixr_A	191	Holliday junction DNA helicase RUVA; heterooligome	98.75
1cuk_A	203	RUVA protein; DNA repair, SOS response, DNA-bindin	98.7
4gfj_A	685	Topoisomerase V; helix-hairpin-helix, DNA repair e	98.61
1vq8_Y	241	50S ribosomal protein L32E; ribosome 50S, protein-	98.22
2ztd_A	212	Holliday junction ATP-dependent DNA helicase RUVA;	98.21
2duy_A	75	Competence protein comea-related protein; helix-ha	98.17
2ziu_A	311	MUS81 protein; helix-hairpin-helix, alternative sp	97.86
2edu_A	98	Kinesin-like protein KIF22; kinesin-like DNA bindi	97.69
1wcn_A	70	Transcription elongation protein NUSA; RNA-binding	97.28
2w9m_A	578	Polymerase X; SAXS, DNA repair, DNA polymerase, DN	97.04
1b22_A	114	DNA repair protein RAD51; DNA binding, riken struc	97.01
3arc_U	97	Photosystem II 12 kDa extrinsic protein; PSII, mem	96.8
1u9l_A	70	Transcription elongation protein NUSA; escherichia	96.79
2zix_A	307	Crossover junction endonuclease MUS81; helix-hairp	96.65
1s5l_U	134	Photosystem II 12 kDa extrinsic protein; photosynt	96.63
3b0x_A	575	DNA polymerase beta family (X family); structural	96.31
2fmp_A	335	DNA polymerase beta; nucleotidyl transferase, tran	95.92
2ihm_A	360	POL MU, DNA polymerase MU; helix-turn-helix, trans	95.43
1jms_A	381	Terminal deoxynucleotidyltransferase; polymerase;	95.28
3arc_U	97	Photosystem II 12 kDa extrinsic protein; PSII, mem	95.25
2bcq_A	335	DNA polymerase lambda; misalignment, extrahelical,	95.18
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	94.75
1dgs_A	667	DNA ligase; AMP complex, NAD+-dependent; HET: DNA	94.55
1s5l_U	134	Photosystem II 12 kDa extrinsic protein; photosynt	94.41
2duy_A	75	Competence protein comea-related protein; helix-ha	94.32
2edu_A	98	Kinesin-like protein KIF22; kinesin-like DNA bindi	93.41
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	93.26
2owo_A	671	DNA ligase; protein-DNA complex, ligase-DNA comple	93.16
4e9f_A	161	Methyl-CPG-binding domain protein 4; HHH DNA glyco	93.11
1exn_A	290	5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Ent	92.83
4glx_A	586	DNA ligase; inhibitor, ligase-ligase inhibitor-DNA	92.66
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	92.01
2i5h_A	205	Hypothetical protein AF1531; PFAM:DUF655, PSI-2, s	90.09
2w9m_A	578	Polymerase X; SAXS, DNA repair, DNA polymerase, DN	89.96
1z3e_B	73	DNA-directed RNA polymerase alpha chain; bacterial	89.74
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	89.57
2csb_A	519	Topoisomerase V, TOP61; topoisomerase IB, helix-tu	89.55
3q8k_A	341	Flap endonuclease 1; helix-3 turn-helix, hydrophob	89.34
2i5h_A	205	Hypothetical protein AF1531; PFAM:DUF655, PSI-2, s	88.84
1rxw_A	336	Flap structure-specific endonuclease; helical clam	88.7
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	88.64
2a1j_A	63	DNA repair endonuclease XPF; XPF, xeroderma pigmen	88.61
3k4g_A	86	DNA-directed RNA polymerase subunit alpha; bacteri	88.42
2ziu_B	341	Crossover junction endonuclease EME1; helix-hairpi	87.85
2csb_A	519	Topoisomerase V, TOP61; topoisomerase IB, helix-tu	87.49
3gfk_B	79	DNA-directed RNA polymerase subunit alpha; protein	87.11
3b0x_A	575	DNA polymerase beta family (X family); structural	86.98
1b43_A	340	Protein (FEN-1); nuclease, DNA repair, DNA replica	86.67
1pu6_A	218	3-methyladenine DNA glycosylase; helix-hairpin-hel	86.44
3im1_A	328	Protein SNU246, PRE-mRNA-splicing helicase BRR2; A	86.23
2izo_A	346	FEN1, flap structure-specific endonuclease; hydrol	85.89
1ul1_X	379	Flap endonuclease-1; protein complex, DNA-binding	85.66
1coo_A	98	RNA polymerase alpha subunit; transcription regula	85.21
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	85.2
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	84.54
1kg2_A	225	A/G-specific adenine glycosylase; DNA repair, hydr	83.81
2h56_A	233	DNA-3-methyladenine glycosidase; 10174367, EC 3.2.	83.68
2z43_A	324	DNA repair and recombination protein RADA; archaea	83.59
1z00_B	84	DNA repair endonuclease XPF; helix-hairpin-helix,	83.41
4b21_A	232	Probable DNA-3-methyladenine glycosylase 2; hydrol	83.19
3ory_A	363	Flap endonuclease 1; hydrolase; 2.00A {Desulfuroco	83.19
1z00_A	89	DNA excision repair protein ERCC-1; helix-hairpin-	82.86

>2a1i_A DNA excision repair protein ERCC-1; XPF, central domain, DNA repair, endonuclease, DNA binding protein; HET: DNA; 1.90A {Homo sapiens} SCOP: c.52.1.20 PDB: 2jnw_A* 2jpd_A*

Probab=99.92  E-value=6.6e-26  Score=199.24  Aligned_cols=74  Identities=58%  Similarity=1.042  Sum_probs=67.7

Q ss_pred             cCCCCCeEEEcCCccCChhHHhhhccceEeeecccceEeccceeeeeec-------------------------------
Q 017612          134 SIQSRNAILVSQRQKGNPLLKYIRNVRWAFADVVCDYLVGQNSCALYLS-------------------------------  182 (368)
Q Consensus       134 ~~~~~~~IlVS~rQrGNPLLk~IrnVpwefaDIvpDY~Ig~ttcILFLS-------------------------------  182 (368)
                      ..++++.|+||++|||||||++||||||+|+||+|||+||+++||||||                               
T Consensus        13 ~~~~~~~IlVs~rQkGNPlL~~irnv~we~~dI~~Dyvvg~~tcvLFLSLkYH~L~PeYI~~Ri~~L~~~y~lrVLL~~V   92 (146)
T 2a1i_A           13 DPAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQV   92 (146)
T ss_dssp             -----CCEEECGGGTTCGGGGGCCSSCEEECCCSSSEEEETTEEEEEEEHHHHHHSTTHHHHHHHHHTTSSSEEEEEEEC
T ss_pred             CCCCCceEEECchhcCChHHHHHhcCCeEecCcCCCEEecCeeEEEEEecHHhccCHHHHHHHHHHhccccceEEEEEEE
Confidence            3466889999999999999999999999999999999999999999999                               


Q ss_pred             ----------------------------hhhHHHHHHHHHHhhcCCcchhccc
Q 017612          183 ----------------------------LEECGRYLETIKVYENKPADLIQGQ  207 (368)
Q Consensus       183 ----------------------------~EEAArYIEt~K~~E~K~~d~Irek  207 (368)
                                                  .||||+|||+||.||+++++.|+++
T Consensus        93 Dv~d~~~~L~eL~~~c~~~~~TLiLawS~eEaa~Yle~~k~~e~k~~d~i~~~  145 (146)
T 2a1i_A           93 DVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEK  145 (146)
T ss_dssp             CSSSCHHHHHHHHHHHHHHTCEEEEESSHHHHHHHHHHHHTCCSSCCCHHHHH
T ss_pred             eCCChHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHHHHHHhccCChhHhhcC
Confidence                                        9999999999999999999999875

>2bgw_A XPF endonuclease; hydrolase, structure specific endonuclease, nucleotide excision repair; 2.8A {Aeropyrum pernix} SCOP: a.60.2.5 c.52.1.20 PDB: 2bhn_A

Probab=99.86  E-value=3e-21  Score=173.57  Aligned_cols=140  Identities=19%  Similarity=0.333  Sum_probs=121.6

Q ss_pred             CCCCeEEEcCCccCChhHHhhhc--cceEeeec-ccceEeccceeee------ee-c-----------------------
Q 017612          136 QSRNAILVSQRQKGNPLLKYIRN--VRWAFADV-VCDYLVGQNSCAL------YL-S-----------------------  182 (368)
Q Consensus       136 ~~~~~IlVS~rQrGNPLLk~Irn--VpwefaDI-vpDY~Ig~ttcIL------FL-S-----------------------  182 (368)
                      ...-.|+|..||+||+|+++|++  |+|++.++ +.||+++...||-      |+ |                       
T Consensus         6 ~~~~~iivD~RE~~s~~~~~l~~~gv~~~~~~L~vgDy~~~~~~~VERKs~~Dl~~Si~~~Rl~~Q~~~l~~~~~~~~ll   85 (219)
T 2bgw_A            6 GGRPRVYVDVREERSPVPSILESLGVQVIPKQLPMGDYLVSDSIIVERKTSSDFAKSLFDGRLFEQASRLAEHYETVFII   85 (219)
T ss_dssp             CSSCEEEEETTTTTSSHHHHHHHTTCEEEEECCSSSSEEEETTEEEEEEEHHHHHHHHHHSHHHHHHHHHHHHCSEEEEE
T ss_pred             CCCeEEEEECCCcccHhHHHHHhCCCEEEEEEcCcCCEEeeCCeEEEeCCHHHHHHHhhcCcHHHHHHHHHHhcCCcEEE
Confidence            34568999999999999999977  99999987 8999999977763      33 1                       


Q ss_pred             -------------------------------------hhhHHHHHHHHHHhhcCCcc---hh-cccccccHHHHHHHhhc
Q 017612          183 -------------------------------------LEECGRYLETIKVYENKPAD---LI-QGQMDTDYLSRLTHALT  221 (368)
Q Consensus       183 -------------------------------------~EEAArYIEt~K~~E~K~~d---~I-rek~e~dy~srL~saLT  221 (368)
                                                           .+|||+||+.|+.+++....   .+ +++...++.+.+...|+
T Consensus        86 iE~d~~~~~~~~~~~~i~~~l~~~~~~~~~~vi~t~s~~eta~~l~~l~~~~~~~~~~ai~~~~~~~~~~~~~~~~~~L~  165 (219)
T 2bgw_A           86 VEGPPVPRRYRGRERSLYAAMAALQLDYGIRLMNTMDPKGTALVIESLARLSTREGGQRIVIHKKPRLSDVREWQLYILQ  165 (219)
T ss_dssp             EESCSSCGGGTTTHHHHHHHHHHHHHHSCCEEEEESSHHHHHHHHHHHHHHHSCBCCTTCCCCCCCCCCHHHHHHHHHHH
T ss_pred             EEecCccccccCCHHHHHHHHHHHHHHCCceEEEcCCHHHHHHHHHHHHHhcccccccccccccccccccHHHHHHHHHh
Confidence                                                 89999999999999865432   22 33455677778888999


Q ss_pred             cCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612          222 SVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFK  275 (368)
Q Consensus       222 sIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~  275 (368)
                      +|||||+++|+.|+++|||+++|++|+.++|..|+|||+++|++|+++|+.+|.
T Consensus       166 ~i~gVg~~~a~~Ll~~fgs~~~l~~a~~e~L~~v~GiG~~~a~~i~~~~~~~~~  219 (219)
T 2bgw_A          166 SFPGIGRRTAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIKKILMTPYK  219 (219)
T ss_dssp             TSTTCCHHHHHHHHHHHSSHHHHTTCCHHHHHHSTTCCHHHHHHHHHHHHSCCC
T ss_pred             cCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHhcccC
Confidence            999999999999999999999999999999999999999999999999999884

>2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5

Probab=99.56  E-value=4.7e-15  Score=117.97  Aligned_cols=81  Identities=52%  Similarity=0.889  Sum_probs=75.4

Q ss_pred             hhcCCcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612          196 YENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFK  275 (368)
Q Consensus       196 ~E~K~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~  275 (368)
                      ..+.+++.|+++...++..++...|++|||||++.|+.|+++||++++|+.|+.++|..|+|||+++|++|+++|+.+|.
T Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~L~~IpgIG~~~A~~Ll~~fgs~~~l~~as~~eL~~i~GIG~~~a~~I~~~l~~~~~   89 (91)
T 2a1j_B           10 HSQDPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFL   89 (91)
T ss_dssp             ---CCSHHHHHHHHHHHHHHHHHHHTTSTTCCHHHHHHHHHHHSSHHHHHSCCHHHHHTSSSCCSHHHHHHHHHHHSCSC
T ss_pred             cccCCHHHHhhhccCCHHHHHHHHHHcCCCCCHHHHHHHHHHCCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHhhhhc
Confidence            35678899999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             c
Q 017612          276 R  276 (368)
Q Consensus       276 ~  276 (368)
                      .
T Consensus        90 ~   90 (91)
T 2a1j_B           90 K   90 (91)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5

Probab=99.55  E-value=8.2e-15  Score=115.74  Aligned_cols=78  Identities=54%  Similarity=0.901  Sum_probs=73.9

Q ss_pred             cchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcccccccC
Q 017612          201 ADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKRVV  278 (368)
Q Consensus       201 ~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~~~~  278 (368)
                      ++.|+++...+|..++...|++|||||++.|+.|+++||++++|+.|+.++|..|+|||+++|++|+.+|+.+|....
T Consensus         2 ~~~i~~~~~~~~~~~~~~~L~~IpgIG~~~A~~Ll~~fgsl~~l~~a~~~eL~~i~GIG~~~a~~I~~~l~~~~~~~~   79 (89)
T 1z00_A            2 ADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP   79 (89)
T ss_dssp             CTTCHHHHHHHHHHHHHHHHTTSSSCCHHHHHHHHHHTCBHHHHHHCCHHHHHTSTTCCHHHHHHHHHHHHSCSSSCS
T ss_pred             chHhhhcccccHHHHHHHHHHcCCCCCHHHHHHHHHHCCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHHhccch
Confidence            467888888999999999999999999999999999999999999999999999999999999999999999998544

>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} SCOP: a.60.2.5

Probab=99.45  E-value=2.3e-13  Score=102.45  Aligned_cols=70  Identities=23%  Similarity=0.359  Sum_probs=63.7

Q ss_pred             cccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcccccc
Q 017612          207 QMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKR  276 (368)
Q Consensus       207 k~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~~  276 (368)
                      +...+....+...|++|||||...|..|+++||++.+|+.|+.++|..|+|||+++|..|+.+|+.+|..
T Consensus         3 ~~~~~~~~~~~~~L~~i~giG~~~a~~Ll~~fgs~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~~~~~~~   72 (75)
T 1x2i_A            3 KKALTLAERQRLIVEGLPHVSATLARRLLKHFGSVERVFTASVAELMKVEGIGEKIAKEIRRVITAPYIE   72 (75)
T ss_dssp             --CCCHHHHHHHHHTTSTTCCHHHHHHHHHHHCSHHHHHHCCHHHHTTSTTCCHHHHHHHHHHHHSCCCC
T ss_pred             CCcccHHHHHHHHHcCCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHHhCcccc
Confidence            3445667778889999999999999999999999999999999999999999999999999999999875

>2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 PDB: 2kn7_A*

Probab=99.39  E-value=1.9e-13  Score=103.66  Aligned_cols=57  Identities=23%  Similarity=0.399  Sum_probs=54.5

Q ss_pred             HhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHH-HHHHHHHhcccccc
Q 017612          218 HALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERK-VKRLYDTFHEPFKR  276 (368)
Q Consensus       218 saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kK-A~rI~e~F~ePF~~  276 (368)
                      +.|+.|||||+++++.||+||||+++|.+||.|||+.|  ||.++ |++|+++||.+|..
T Consensus         4 s~L~~IpGIG~kr~~~LL~~Fgs~~~i~~As~eeL~~v--ig~~~~A~~I~~~l~~~~~~   61 (63)
T 2a1j_A            4 DFLLKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSI--LGNAANAKQLYDFIHTSFAE   61 (63)
T ss_dssp             HHHHTSTTCCHHHHHHHHHHCSSHHHHHTCCHHHHHHH--HSCHHHHHHHHHHHHCCCCC
T ss_pred             hHHHcCCCCCHHHHHHHHHHcCCHHHHHHCCHHHHHHH--cCchHHHHHHHHHHhccccc
Confidence            57889999999999999999999999999999999999  99999 99999999998874

>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 PDB: 2aq0_A*

Probab=99.20  E-value=8e-12  Score=100.31  Aligned_cols=64  Identities=22%  Similarity=0.368  Sum_probs=59.0

Q ss_pred             cHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHH-HHHHHHHhcccccc
Q 017612          211 DYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERK-VKRLYDTFHEPFKR  276 (368)
Q Consensus       211 dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kK-A~rI~e~F~ePF~~  276 (368)
                      .|.....+.|..|||||++.++.||.+|||+++|.+||.+||..|  ||... |+.|+++||.+|..
T Consensus        11 ~~N~~~~s~L~~IpGIG~kr~~~LL~~FgSl~~i~~AS~eEL~~v--ig~~~~A~~I~~~l~~~~~~   75 (84)
T 1z00_B           11 KYNPGPQDFLLKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSI--LGNAANAKQLYDFIHTSFAE   75 (84)
T ss_dssp             TSCHHHHHHHHTCSSCCHHHHHHHHHHSSCHHHHHHSCHHHHHHH--HSCHHHHHHHHHHHTSBHHH
T ss_pred             cccccHHHHHHhCCCCCHHHHHHHHHHcCCHHHHHHCCHHHHHHH--hCchHHHHHHHHHHHhhhhh
Confidence            355667889999999999999999999999999999999999999  99999 99999999988763

>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} SCOP: a.60.2.3

Probab=99.16  E-value=1.6e-11  Score=94.84  Aligned_cols=58  Identities=22%  Similarity=0.390  Sum_probs=53.3

Q ss_pred             HHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          214 SRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       214 srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      ..+...|..|||||++.|+.|+++||++++|+.|+.++|..|+|||+++|.+|+++|+
T Consensus        20 ~~~~~~L~~I~gIG~~~A~~Ll~~fgsl~~l~~a~~eeL~~i~GIG~~~a~~I~~~~~   77 (78)
T 1kft_A           20 HMNTSSLETIEGVGPKRRQMLLKYMGGLQGLRNASVEEIAKVPGISQGLAEKIFWSLK   77 (78)
T ss_dssp             ---CCGGGGCTTCSSSHHHHHHHHHSCHHHHHHCCHHHHTTSSSTTSHHHHHHHHHHT
T ss_pred             HHHHHHHhcCCCCCHHHHHHHHHHcCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHh
Confidence            4456789999999999999999999999999999999999999999999999999986

>3c65_A Uvrabc system protein C; UVRC, endonuclease, nucleotide excision repair, DNA repair, RNAse H, cytoplasm, DNA damage, DNA excision; 1.90A {Bacillus stearothermophilus}

Probab=99.15  E-value=1.7e-12  Score=120.65  Aligned_cols=88  Identities=20%  Similarity=0.364  Sum_probs=17.6

Q ss_pred             eEeccceeeeeec---hhhHHHHHHHHHHhhcCCcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHc
Q 017612          170 YLVGQNSCALYLS---LEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMD  246 (368)
Q Consensus       170 Y~Ig~ttcILFLS---~EEAArYIEt~K~~E~K~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~  246 (368)
                      +.+..++.+|+|=   .+||+||-.+|++..         +.    ...+.+.|++|||||++.++.||++|||+++|++
T Consensus       135 ~~l~~~s~~l~llq~irDEaHRFAIt~hr~~---------r~----k~~~~s~L~~IpGIG~k~ak~Ll~~FGSl~~i~~  201 (226)
T 3c65_A          135 VPLDRQSQEFYLLQRIQDEVHRFAVMFHRKT---------RQ----KTMFHSVLDDIPGVGEKRKKALLNYFGSVKKMKE  201 (226)
T ss_dssp             CCCCTTSHHHHHHHHHHHHHHHHTTC------------------------------------------------------
T ss_pred             EecCCCCHHHhhhhhccchhhhhhhhccccc---------cc----cccccccccccCCCCHHHHHHHHHHhCCHHHHHh
Confidence            5556666666664   999999999998732         11    2235778999999999999999999999999999


Q ss_pred             CCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          247 ASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       247 AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      |+.|||..| |||+++|+.|+++|+
T Consensus       202 As~eeL~~V-GIG~~~A~~I~~~f~  225 (226)
T 3c65_A          202 ATVEELQRA-NIPRAVAEKIYEKLH  225 (226)
T ss_dssp             -------------------------
T ss_pred             CCHHHHHHc-CCCHHHHHHHHHHhh
Confidence            999999999 999999999999996

>2nrt_A Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB: 2nrv_A 2nrw_A 2nrx_A 2nrz_A

Probab=99.12  E-value=3e-11  Score=112.10  Aligned_cols=87  Identities=25%  Similarity=0.329  Sum_probs=74.5

Q ss_pred             eEeccceeeeeec---hhhHHHHHHHHHHhhcCCcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHc
Q 017612          170 YLVGQNSCALYLS---LEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMD  246 (368)
Q Consensus       170 Y~Ig~ttcILFLS---~EEAArYIEt~K~~E~K~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~  246 (368)
                      +.+..++.+|+|=   .+||+||-.+|++..         +    ....+.+.|++|||||++.++.||++|||+++|++
T Consensus       130 ~~l~~~s~~l~llq~iRDEaHRFAIt~hr~~---------R----~k~~~~s~LdgIpGIG~k~ak~Ll~~FgSl~~i~~  196 (220)
T 2nrt_A          130 IHLPHDHPVLRLLVQIRDETHRFAVSYHRKR---------R----EKESLRSVLDNVPGIGPIRKKKLIEHFGSLENIRS  196 (220)
T ss_dssp             ECCCTTCHHHHHHHHHHHHHHHHHHGGGHHH---------H----HHHHHHHHHTTSTTCCHHHHHHHHHHHCSHHHHHT
T ss_pred             eecCCCCHHHHhhhhhcchhhhccccccccc---------c----ccccccccccCCCCcCHHHHHHHHHHcCCHHHHHh
Confidence            6666677776664   999999999998742         1    13346789999999999999999999999999999


Q ss_pred             CCHHhhhcCCCCCH-HHHHHHHHHhc
Q 017612          247 ASMEDLARCPGIGE-RKVKRLYDTFH  271 (368)
Q Consensus       247 AS~EELa~VPGIG~-kKA~rI~e~F~  271 (368)
                      |+.|||..|  ||+ ++|+.|+++|+
T Consensus       197 As~EeL~~V--IG~~~~A~~I~~~f~  220 (220)
T 2nrt_A          197 ASLEEIARV--IGSTEIARRVLDILG  220 (220)
T ss_dssp             SCHHHHHHH--HTCHHHHHHHHHHC-
T ss_pred             CCHHHHHHH--hChHHHHHHHHHHhC
Confidence            999999999  999 99999999984

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

Probab=98.87  E-value=7.1e-10  Score=116.42  Aligned_cols=63  Identities=27%  Similarity=0.452  Sum_probs=59.5

Q ss_pred             HHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612          212 YLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFK  275 (368)
Q Consensus       212 y~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~  275 (368)
                      .+.+++.+| +|||||++.|+.|+.||||+++|+.|+.+||..|+|||+++|++|+++|+.+.+
T Consensus       507 ~l~R~L~al-gi~~VG~~~Ak~La~~Fgsl~~l~~As~eeL~~i~GIG~~~A~sI~~ff~~~~~  569 (671)
T 2owo_A          507 TFARFLYAL-GIREVGEATAAGLAAYFGTLEALEAASIEELQKVPDVGIVVASHVHNFFAEESN  569 (671)
T ss_dssp             CHHHHHHHT-TCTTCCHHHHHHHHHHHCSHHHHHTCCHHHHTTSTTCCHHHHHHHHHHHTCHHH
T ss_pred             Chhheehhh-cccCccHHHHHHHHHHcCCHHHHHhCCHHHHhhcCCCCHHHHHHHHHHHHhHHH
Confidence            457888898 899999999999999999999999999999999999999999999999998764

>3c1y_A DNA integrity scanning protein DISA; DNA damage, DNA repair, DNA-binding, DNA binding protein; HET: DNA 2BA; 2.10A {Thermotoga maritima} PDB: 3c1z_A* 3c21_A* 3c23_A*

Probab=98.86  E-value=1.6e-09  Score=107.38  Aligned_cols=57  Identities=25%  Similarity=0.387  Sum_probs=53.6

Q ss_pred             HHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccc
Q 017612          217 THALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEP  273 (368)
Q Consensus       217 ~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~eP  273 (368)
                      ...|.+||+||+..|++|+++|||+++|++||.+||..|+|||+++|++|++.|.+-
T Consensus       314 yRiLs~IPrl~~~iae~Lv~~FGsLq~Il~AS~eEL~~VeGIGe~rAr~IregL~r~  370 (377)
T 3c1y_A          314 YRLLKTVARIPLSIGYNVVRMFKTLDQISKASVEDLKKVEGIGEKRARAISESISSL  370 (377)
T ss_dssp             HHHHHHTSCCCHHHHHHHHHHHCSHHHHTTCCHHHHTTSTTCCHHHHHHHHHHHHHH
T ss_pred             HHHHhhCCCCCHHHHHHHHHHhCCHHHHHhCCHHHHHhccCccHHHHHHHHHHHHHH
Confidence            347888999999999999999999999999999999999999999999999999753

>4glx_A DNA ligase; inhibitor, ligase-ligase inhibitor-DNA complex; HET: DNA 0XS; 1.90A {Escherichia coli}

Probab=98.81  E-value=1.6e-09  Score=112.28  Aligned_cols=64  Identities=27%  Similarity=0.445  Sum_probs=60.4

Q ss_pred             cHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612          211 DYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFK  275 (368)
Q Consensus       211 dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~  275 (368)
                      ..+.+++.+| +||+||.+.|+.|+.+|||+++|++|+.+||..|+|||++.|+.|+++|+.+.+
T Consensus       506 ~~l~r~l~aL-GI~~vG~~~a~~La~~f~sl~~l~~a~~e~l~~i~giG~~~A~si~~ff~~~~n  569 (586)
T 4glx_A          506 TTFARFLYAL-GIREVGEATAAGLAAYFGTLEALEAASIEELQKVPDVGIVVASHVHNFFAEESN  569 (586)
T ss_dssp             CCHHHHHHHT-TCTTCCHHHHHHHHHHHCSHHHHHHCCHHHHTTSTTCCHHHHHHHHHHHHSHHH
T ss_pred             CCHHHHHHHc-CCCchhHHHHHHHHHHcCCHHHHHccCHHHHhcCCCccHHHHHHHHHHHcCHHH
Confidence            4568999999 899999999999999999999999999999999999999999999999988754

>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=98.80  E-value=2.4e-09  Score=112.37  Aligned_cols=85  Identities=25%  Similarity=0.380  Sum_probs=68.3

Q ss_pred             HHHHHHhhcCCcchhccc---ccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHH
Q 017612          190 LETIKVYENKPADLIQGQ---MDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRL  266 (368)
Q Consensus       190 IEt~K~~E~K~~d~Irek---~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI  266 (368)
                      |..+..+..|....|...   .....+.+++.+| +|||||++.|+.|+.+|||+++|+.|+.++|..|+|||+++|++|
T Consensus       477 L~~l~g~G~Ksa~nLl~aIe~sk~~~l~R~L~al-GI~~VG~~~Ak~La~~Fgsl~~l~~As~eeL~~I~GIG~~~A~sI  555 (667)
T 1dgs_A          477 LLGLERMGEKSAQNLLRQIEESKHRGLERLLYAL-GLPGVGEVLARNLARRFGTMDRLLEASLEELIEVEEVGELTARAI  555 (667)
T ss_dssp             HHTTSSCCSTTHHHHHHHHHHGGGCCHHHHHHHT-TCSSCCHHHHHHHHHTTSBHHHHTTCCHHHHHTSTTCCHHHHHHH
T ss_pred             HhcccccchhhHHHHHHHHHHHhcCcHHHhhHhh-ccCCccHHHHHHHHHHcCCHHHHHhCCHHHHHhccCcCHHHHHHH
Confidence            333444555555444331   1123357888888 899999999999999999999999999999999999999999999


Q ss_pred             HHHhccccc
Q 017612          267 YDTFHEPFK  275 (368)
Q Consensus       267 ~e~F~ePF~  275 (368)
                      +++|+.+++
T Consensus       556 ~~ff~~~~~  564 (667)
T 1dgs_A          556 LETLKDPAF  564 (667)
T ss_dssp             HHHHHCHHH
T ss_pred             HHHHhhHHH
Confidence            999998874

>3sgi_A DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tuberculosis}

Probab=98.76  E-value=8.7e-10  Score=114.85  Aligned_cols=78  Identities=28%  Similarity=0.359  Sum_probs=0.0

Q ss_pred             cCCcchhccc---ccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcccc
Q 017612          198 NKPADLIQGQ---MDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPF  274 (368)
Q Consensus       198 ~K~~d~Irek---~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF  274 (368)
                      .|.+..|...   .....+.+++.+| +|||||.+.|+.|+++|||+++|+.|+.+||..|+|||++.|++|+++|+.+.
T Consensus       507 ~ksa~nLl~aIe~sk~~~l~r~L~aL-GIp~VG~~~ak~La~~Fgsle~L~~As~eeL~~I~GIG~~~A~sI~~ff~~~~  585 (615)
T 3sgi_A          507 SANGKRLLVNLDKAKAAPLWRVLVAL-SIRHVGPTAARALATEFGSLDAIAAASTDQLAAVEGVGPTIAAAVTEWFAVDW  585 (615)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             chHHHHHHHHHHHhcCCCHHHHHHHc-CCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHcCHH
Confidence            4555544432   2234578999999 89999999999999999999999999999999999999999999999999887


Q ss_pred             cc
Q 017612          275 KR  276 (368)
Q Consensus       275 ~~  276 (368)
                      +.
T Consensus       586 n~  587 (615)
T 3sgi_A          586 HR  587 (615)
T ss_dssp             --
T ss_pred             HH
Confidence            64

>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex, octameric RUVA, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.30A {Thermus thermophilus} SCOP: a.60.2.1 b.40.4.2

Probab=98.75  E-value=1.2e-08  Score=92.36  Aligned_cols=56  Identities=20%  Similarity=0.267  Sum_probs=53.6

Q ss_pred             hhccCCCCCHHHHHHHHHhcCC---HHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcccc
Q 017612          219 ALTSVRSVNKTDVVTLGSTFGS---LSHIMDASMEDLARCPGIGERKVKRLYDTFHEPF  274 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs~FGS---Lk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF  274 (368)
                      .|.+|+|||++.|..||++||+   ++.|.+++.++|.+|||||+++|++|+..|+..+
T Consensus        73 ~L~~v~GIGpk~A~~iL~~f~~~~l~~aI~~~d~~~L~~vpGIG~K~A~rI~~~lk~k~  131 (191)
T 1ixr_A           73 LLLSVSGVGPKVALALLSALPPRLLARALLEGDARLLTSASGVGRRLAERIALELKGKV  131 (191)
T ss_dssp             HHHSSSCCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHTTSTTCCHHHHHHHHHHHTTTS
T ss_pred             HHhcCCCcCHHHHHHHHHhCChHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHhh
Confidence            6778999999999999999999   9999999999999999999999999999998766

>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination; 1.90A {Escherichia coli} SCOP: a.5.1.1 a.60.2.1 b.40.4.2 PDB: 1hjp_A 1bdx_A* 1c7y_A 1d8l_A

Probab=98.70  E-value=1.3e-08  Score=92.84  Aligned_cols=57  Identities=21%  Similarity=0.391  Sum_probs=54.0

Q ss_pred             hhccCCCCCHHHHHHHHHhcCC---HHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612          219 ALTSVRSVNKTDVVTLGSTFGS---LSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFK  275 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs~FGS---Lk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~  275 (368)
                      .|.+|+|||++.|..||++||+   ++.|.+++.++|.+|||||+++|++|+..|+..+.
T Consensus        74 ~L~~V~GIGpk~A~~iL~~f~~~~l~~aI~~~d~~~L~~vpGIG~K~A~rI~~elk~kl~  133 (203)
T 1cuk_A           74 ELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKTAERLIVEMKDRFK  133 (203)
T ss_dssp             HHHHSSSCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHHTSTTCCHHHHHHHHHHHHHHGG
T ss_pred             HHhcCCCcCHHHHHHHHhhCChHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHhhh
Confidence            6778999999999999999999   99999999999999999999999999999987764

>4gfj_A Topoisomerase V; helix-hairpin-helix, DNA repair enzyme, DNA B isomerase; 2.91A {Methanopyrus kandleri AV19}

Probab=98.61  E-value=1.4e-08  Score=102.95  Aligned_cols=96  Identities=16%  Similarity=0.229  Sum_probs=68.9

Q ss_pred             eEeeecccceEeccceeeeeechhhHHHHHHHHHHh----hc----CC------cchhcccccccHHHHHHHhhccCCCC
Q 017612          161 WAFADVVCDYLVGQNSCALYLSLEECGRYLETIKVY----EN----KP------ADLIQGQMDTDYLSRLTHALTSVRSV  226 (368)
Q Consensus       161 wefaDIvpDY~Ig~ttcILFLS~EEAArYIEt~K~~----E~----K~------~d~Irek~e~dy~srL~saLTsIpgV  226 (368)
                      ...+.+..||.+|          +|+|..++++..+    ++    ..      ..-|.++....... ....|++|+||
T Consensus       408 iqLASLAvkfG~g----------~eTAe~L~~~agr~l~leqi~rdrEvgkL~SVpGikek~sktL~e-qeamLtAIaGI  476 (685)
T 4gfj_A          408 IQLAELTKKEGVG----------RKTAERLLRAFGNPERVKQLAREFEIEKLASVEGVGERVLRSLVP-GYASLISIRGI  476 (685)
T ss_dssp             HHHHHHHTSTTCC----------HHHHHHHHHHHSSHHHHHHHHHTTCHHHHHTSTTCCHHHHHHHST-THHHHHTSTTC
T ss_pred             hhhhhhhhhcCCc----------hHHHHHHHHHhcchhhhhhhhhhhhhhcccccccchhhhhccccc-ceeeeeccCCC
Confidence            3345678899886          5666666655544    22    11      12222222222111 26789999999


Q ss_pred             CHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHH
Q 017612          227 NKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYD  268 (368)
Q Consensus       227 nKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e  268 (368)
                      |+..|++||++|||++.|++|+.+||.. .|||+++|++|.-
T Consensus       477 Gp~tAeRLLEkFGSVe~Vm~AteDELRe-dGIGekqarrI~g  517 (685)
T 4gfj_A          477 DRERAERLLKKYGGYSKVREAGVEELRE-DGLTDAQIRELKG  517 (685)
T ss_dssp             CHHHHHHHHHHHTSHHHHHHSCHHHHHH-TTCCHHHHHHHHT
T ss_pred             CHHHHHHHHHHhcCHHHHHhCCHHHHHH-ccccHHHHHHHhh
Confidence            9999999999999999999999999955 9999999999953

>1vq8_Y 50S ribosomal protein L32E; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: c.9.2.1 PDB: 1vq4_Y* 1vq5_Y* 1vq6_Y* 1vq7_Y* 1s72_Y* 1vq9_Y* 1vqk_Y* 1vql_Y* 1vqm_Y* 1vqn_Y* 1vqo_Y* 1vqp_Y* 1yhq_Y* 1yi2_Y* 1yij_Y* 1yit_Y* 1yj9_Y* 1yjn_Y* 1yjw_Y* 2otj_Y* ...

Probab=98.22  E-value=1.5e-07  Score=87.98  Aligned_cols=55  Identities=24%  Similarity=0.349  Sum_probs=0.0

Q ss_pred             HhhccCCCCCHHHHHHHHHh-cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          218 HALTSVRSVNKTDVVTLGST-FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       218 saLTsIpgVnKTDA~~LLs~-FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      ..|..|+|||++.|..|+.+ |+|+++|..|+.++|..++|||+++|++|++.++.
T Consensus        15 ~~L~~IpGIGpk~a~~Ll~~gf~sve~L~~a~~~eL~~v~GIG~ktAe~I~~~l~~   70 (241)
T 1vq8_Y           15 TELTDISGVGPSKAESLREAGFESVEDVRGADQSALADVSGIGNALAARIKADVGG   70 (241)
T ss_dssp             --------------------------------------------------------
T ss_pred             hHHhcCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHhccCCCHHHHHHHHHHHHH
Confidence            36778999999999999999 99999999999999999999999999999999864

>2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA BIND oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A

Probab=98.21  E-value=2e-06  Score=79.27  Aligned_cols=59  Identities=22%  Similarity=0.310  Sum_probs=53.8

Q ss_pred             HHhhccCCCCCHHHHHHHHHhcCC---HHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612          217 THALTSVRSVNKTDVVTLGSTFGS---LSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFK  275 (368)
Q Consensus       217 ~saLTsIpgVnKTDA~~LLs~FGS---Lk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~  275 (368)
                      ...|.+|+|||++.|.+||++||.   ...|+..+.+.|.+|||||+|+|++|..-+...+.
T Consensus        87 f~~L~sv~GIGpk~A~~Ils~~~~~~l~~aI~~~d~~~L~~vpGIG~KtA~rIi~elk~kl~  148 (212)
T 2ztd_A           87 FLTLLSVSGVGPRLAMAALAVHDAPALRQVLADGNVAALTRVPGIGKRGAERMVLELRDKVG  148 (212)
T ss_dssp             HHHHHTSTTCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHHTSTTCCHHHHHHHHHHHTTTCC
T ss_pred             HHHhcCcCCcCHHHHHHHHHhCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHhhc
Confidence            344667999999999999999999   77899999999999999999999999999988774

>2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus} SCOP: a.60.2.7

Probab=98.17  E-value=1.3e-06  Score=66.88  Aligned_cols=49  Identities=20%  Similarity=0.240  Sum_probs=44.0

Q ss_pred             HHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          217 THALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       217 ~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      ...|..|+|||+..|.+|+++|      .-++.+||..|+|||++++++|+.+|+
T Consensus        26 ~~~L~~ipGIG~~~A~~Il~~r------~~~s~~eL~~v~Gig~k~~~~i~~~l~   74 (75)
T 2duy_A           26 LEELMALPGIGPVLARRIVEGR------PYARVEDLLKVKGIGPATLERLRPYLR   74 (75)
T ss_dssp             HHHHTTSTTCCHHHHHHHHHTC------CCSSGGGGGGSTTCCHHHHHHHGGGEE
T ss_pred             HHHHHhCCCCCHHHHHHHHHHc------ccCCHHHHHhCCCCCHHHHHHHHHhcc
Confidence            4467889999999999999998      358999999999999999999998874

>2ziu_A MUS81 protein; helix-hairpin-helix, alternative splicing, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; 2.70A {Danio rerio} PDB: 2ziv_A 2ziw_A

Probab=97.86  E-value=1.5e-05  Score=75.13  Aligned_cols=102  Identities=13%  Similarity=0.184  Sum_probs=75.9

Q ss_pred             cceEeccceeeeee-chhhHHHHHHHHHHhhc-----CCc----c-h------h----------------------cccc
Q 017612          168 CDYLVGQNSCALYL-SLEECGRYLETIKVYEN-----KPA----D-L------I----------------------QGQM  208 (368)
Q Consensus       168 pDY~Ig~ttcILFL-S~EEAArYIEt~K~~E~-----K~~----d-~------I----------------------rek~  208 (368)
                      .+|.+    .|+|+ +.+|+|+||..|+....     ++.    + .      +                      .+..
T Consensus       152 v~~g~----~Vi~t~s~~eTa~~l~~lt~~i~~~y~~~~l~~~p~~~~~~~~~~~~~~~~~~~~~~~~f~~f~~~~~k~~  227 (311)
T 2ziu_A          152 VVDGF----FVKRVQDAKESAAYLTIMTRYLQKLYQNCTLFCRSRELEGDGEAESEKMVANLSCSLMAFTEFNYGAIKNK  227 (311)
T ss_dssp             HTTCC----EEEECSSHHHHHHHHHHHHHHHHHTTTTCCBCCC----------------CCSCSCCEEHHHHHHHHHHHT
T ss_pred             hhcCe----EEEEeCCHHHHHHHHHHHHHHHHHHhccccccccCcchhccccccccccccCcccccccHHHHHHhccccc
Confidence            45555    78888 49999999999997543     110    0 0      0                      0112


Q ss_pred             cccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHH-----h----hhcCC-C-----CCHHHHHHHHHHhccc
Q 017612          209 DTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASME-----D----LARCP-G-----IGERKVKRLYDTFHEP  273 (368)
Q Consensus       209 e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~E-----E----La~VP-G-----IG~kKA~rI~e~F~eP  273 (368)
                      ..++.+.....|.+||||+...|..|+++|+|+..|++|-.+     |    |+.+. |     ||+..+++|+++|+..
T Consensus       228 ~~t~~e~~~~mL~~IpGVs~~~A~~I~~~ypTp~~L~~Ay~~~~~~~e~~~lL~~i~~g~~~r~IG~~lS~kI~~~f~~~  307 (311)
T 2ziu_A          228 CQTVREVFARQLMQISGVSGDKAAAVLEHYSTVSSLLQAYDKCSSETEKEKLLSSVKYGKLKRNLGPALSRTIYQLYCTR  307 (311)
T ss_dssp             CCBHHHHHHHHHTTBTTCCHHHHHHHHHHCSSHHHHHHHHHHCSSHHHHTTTTTTCEETTTTEECHHHHHHHHHHHHHCS
T ss_pred             CCcHHHHHHHHHHhccCCCHHHHHHHHHHCCCHHHHHHHHHhcCCHHHHHHHHHhcccCCCCCCcCHHHHHHHHHHhccC
Confidence            234455667889999999999999999999999999998643     2    77774 3     9999999999999753

>2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix turn helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.60.2.7

Probab=97.69  E-value=3.4e-05  Score=62.02  Aligned_cols=48  Identities=19%  Similarity=0.356  Sum_probs=42.6

Q ss_pred             HHhhccCCCCCHHHHHHHHHhc---CCHHHHHcCCHHhhhcCCCCCHHHHHHHHHH
Q 017612          217 THALTSVRSVNKTDVVTLGSTF---GSLSHIMDASMEDLARCPGIGERKVKRLYDT  269 (368)
Q Consensus       217 ~saLTsIpgVnKTDA~~LLs~F---GSLk~I~~AS~EELa~VPGIG~kKA~rI~e~  269 (368)
                      ...|..|+|||+..|..|+++|   |.+     ++.+||..|+|||++++++|++.
T Consensus        39 ~~~L~~ipGIG~~~A~~Il~~r~~~g~f-----~s~edL~~v~Gig~k~~~~l~~~   89 (98)
T 2edu_A           39 ARDLRSLQRIGPKKAQLIVGWRELHGPF-----SQVEDLERVEGITGKQMESFLKA   89 (98)
T ss_dssp             HHHHHHSTTCCHHHHHHHHHHHHHHCCC-----SSGGGGGGSTTCCHHHHHHHHHH
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHhcCCc-----CCHHHHHhCCCCCHHHHHHHHHC
Confidence            3457789999999999999998   565     78899999999999999999875

>1wcn_A Transcription elongation protein NUSA; RNA-binding protein, escherichia coli NUSA, transcription regulation, regulation of RNA binding; NMR {Escherichia coli} PDB: 2jzb_B

Probab=97.28  E-value=0.00035  Score=54.03  Aligned_cols=57  Identities=18%  Similarity=0.288  Sum_probs=51.5

Q ss_pred             hhccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc-ccc
Q 017612          219 ALTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE-PFK  275 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e-PF~  275 (368)
                      -|..++|||..++..|.. -|.|+++|..++.++|..+.||++.+|.+|...-+. +|.
T Consensus         8 ~l~~L~Gi~~~~~~kL~e~Gi~TvedlA~~~~~eL~~i~gise~kA~~ii~aAr~~~w~   66 (70)
T 1wcn_A            8 DLLNLEGVDRDLAFKLAARGVCTLEDLAEQGIDDLADIEGLTDEKAGALIMAARNICWF   66 (70)
T ss_dssp             HHHSSTTCCHHHHHHHHTTTCCSHHHHHTSCHHHHHTSSSCCHHHHHHHHHHHHHHHTT
T ss_pred             HHHHcCCCCHHHHHHHHHcCCCcHHHHHcCCHHHHHHccCCCHHHHHHHHHHHHHccCc
Confidence            456788999999999998 599999999999999999999999999999988876 544

>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans}

Probab=97.04  E-value=0.00052  Score=70.27  Aligned_cols=54  Identities=20%  Similarity=0.324  Sum_probs=46.9

Q ss_pred             HHhhccCCCCCHHHHHHHHHh-cCCHHHHHcC-CHHhhhcCCCCCHHHHHHHHHHh
Q 017612          217 THALTSVRSVNKTDVVTLGST-FGSLSHIMDA-SMEDLARCPGIGERKVKRLYDTF  270 (368)
Q Consensus       217 ~saLTsIpgVnKTDA~~LLs~-FGSLk~I~~A-S~EELa~VPGIG~kKA~rI~e~F  270 (368)
                      ...|.+|+|||++.|..|++. |.|+++|..| ....|..+||||+|.|++|...+
T Consensus        96 ~~~L~~v~GVGpk~A~~i~~~G~~s~edL~~a~~~~~L~~~~GiG~Ktaq~I~~~l  151 (578)
T 2w9m_A           96 LLDLLGVRGLGPKKIRSLWLAGIDSLERLREAAESGELAGLKGFGAKSAATILENV  151 (578)
T ss_dssp             HHHHTTSTTCCHHHHHHHHHTTCCSHHHHHHHHHHTTTTTSTTCCHHHHHHHHHHH
T ss_pred             HHHHhCCCCcCHHHHHHHHHcCCCCHHHHHHHHhhCccccCCCCCHHHHHHHHHHH
Confidence            345679999999999999997 8999999987 45689999999999999995555

>1b22_A DNA repair protein RAD51; DNA binding, riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: a.60.4.1

Probab=97.01  E-value=0.0002  Score=60.33  Aligned_cols=53  Identities=23%  Similarity=0.362  Sum_probs=47.5

Q ss_pred             hhccCCCCCHHHHHHHHHh-cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          219 ALTSVRSVNKTDVVTLGST-FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs~-FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      .|..+ |||..++.+|... |.|++.|..|+.++|..++|||+.||.+|.+..++
T Consensus        27 ~L~~~-GIg~~~i~kL~eAG~~Tve~va~a~~~eL~~i~GIse~ka~kIi~aA~k   80 (114)
T 1b22_A           27 RLEQC-GINANDVKKLEEAGFHTVEAVAYAPKKELINIKGISEAKADKILAEAAK   80 (114)
T ss_dssp             HHHHT-TCSHHHHHHHHTTCCSSGGGBTSSBHHHHHTTTTCSTTHHHHHHHHHHH
T ss_pred             HHHhc-CCCHHHHHHHHHcCcCcHHHHHhCCHHHHHHccCCCHHHHHHHHHHHHH
Confidence            34344 9999999999985 99999999999999999999999999999988754

>3arc_U Photosystem II 12 kDa extrinsic protein; PSII, membrane-protein complex, transmembrane alpha-helix, E transport, photosynthesis; HET: OEX CLA PHO BCR PL9 SQD LMG UNL LMT HTG DGD LHG HEM; 1.90A {Thermosynechococcus vulcanus} PDB: 3bz1_U* 2axt_U* 3bz2_U* 3kzi_U* 3prq_U* 3prr_U* 3a0b_U* 3a0h_U*

Probab=96.80  E-value=0.0013  Score=54.05  Aligned_cols=50  Identities=22%  Similarity=0.309  Sum_probs=41.7

Q ss_pred             HHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          217 THALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       217 ~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      ...|..|||||++.|.+|+.+ |-+     .+.+||.+|+|||+++.++|..++..
T Consensus        25 ~~eL~~lpGIG~~~A~~IV~~-GpF-----~s~edL~~V~Gig~~~~e~l~~~l~~   74 (97)
T 3arc_U           25 IAAFIQYRGLYPTLAKLIVKN-APY-----ESVEDVLNIPGLTERQKQILRENLEH   74 (97)
T ss_dssp             GGGGGGSTTCTTHHHHHHHHH-CCC-----SSGGGGGGCTTCCHHHHHHHHHTGGG
T ss_pred             HHHHhHCCCCCHHHHHHHHHc-CCC-----CCHHHHHhccCCCHHHHHHHHHHhce
Confidence            357889999999999999994 332     35579999999999999999998754

>1u9l_A Transcription elongation protein NUSA; escherichia coli NUSA, phage lambda protein N, regulation of RNA binding, transcription antitermination, X-RAY crystallography; 1.90A {Escherichia coli} SCOP: a.60.4.2 PDB: 1wcl_A

Probab=96.79  E-value=0.0018  Score=50.26  Aligned_cols=50  Identities=18%  Similarity=0.279  Sum_probs=45.5

Q ss_pred             cCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          222 SVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       222 sIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      .+.||+..++..|.. =|.|++.|..++.++|..|+||.+.+|..|++.-+
T Consensus        10 ~~lgI~e~~a~~L~~~Gf~tve~vA~~~~~eL~~I~G~dE~~a~~l~~~A~   60 (70)
T 1u9l_A           10 KYLDIDEDFATVLVEEGFSTLEELAYVPMKELLEIEGLDEPTVEALRERAK   60 (70)
T ss_dssp             HHHTCCHHHHHHHHHTTCCCHHHHHHSCHHHHTTSTTCCHHHHHHHHHHHH
T ss_pred             HhCCCCHHHHHHHHHcCcCcHHHHHcCCHHHHhhccCCCHHHHHHHHHHHH
Confidence            344999999999998 59999999999999999999999999999987654

>2zix_A Crossover junction endonuclease MUS81; helix-hairpin-helix, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium, metal-binding, nucleus; 3.50A {Homo sapiens}

Probab=96.65  E-value=0.00047  Score=65.14  Aligned_cols=97  Identities=13%  Similarity=0.177  Sum_probs=71.7

Q ss_pred             eeeeec-hhhHHHHHHHHHHhhcCC-----c---------c-------------hhc---------cc-ccccHHHHHHH
Q 017612          177 CALYLS-LEECGRYLETIKVYENKP-----A---------D-------------LIQ---------GQ-MDTDYLSRLTH  218 (368)
Q Consensus       177 cILFLS-~EEAArYIEt~K~~E~K~-----~---------d-------------~Ir---------ek-~e~dy~srL~s  218 (368)
                      .|+|++ .+|+|+||..|+.....-     .         .             .+.         .+ ...+..+....
T Consensus       154 ~i~~t~~~~~Ta~~l~~lt~~l~e~y~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~f~~f~~~~~Ks~~~tv~~v~~~  233 (307)
T 2zix_A          154 FVKRTADIKESAAYLALLTRGLQRLYQGHTLRSRPWGTPGNPESGAMTSPNPLCSLLTFSDFNAGAIKNKAQSVREVFAR  233 (307)
T ss_dssp             CCCBCCSHHHHTHHHHHHHTTTTTSSCSSCCCCCC----------------CCCCSCCSSTTTTGGGTTTSCCTTTHHHH
T ss_pred             EEEEeCCHHHHHHHHHHHHHHHHHHHhcCcccccchhhhhhhhhhhccccCcccccccHHHHHHhhccccCCcHHHHHHH
Confidence            677774 999999999999875531     0         0             000         00 11223344577


Q ss_pred             hhccCCCCCHHHHHHHHHhcCCHHHHHcCCHH-----h----hhcCC-C-----CCHHHHHHHHHHhccc
Q 017612          219 ALTSVRSVNKTDVVTLGSTFGSLSHIMDASME-----D----LARCP-G-----IGERKVKRLYDTFHEP  273 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~E-----E----La~VP-G-----IG~kKA~rI~e~F~eP  273 (368)
                      .|..||||+...|..|+++|.|+..++.|-.+     |    |+.+. |     ||+..+++|+++|+..
T Consensus       234 ~L~~I~GVs~~~A~~I~~~ypTp~~L~~Ay~~~~~~~e~~~lL~~l~~g~~~r~IG~~lSrkI~~~f~~~  303 (307)
T 2zix_A          234 QLMQVRGVSGEKAAALVDRYSTPASLLAAYDACATPKEQETLLSTIKCGRLQRNLGPALSRTLSQLYCSY  303 (307)
T ss_dssp             TTTCSTTCCSTTTTTSSSSSCSHHHHHHHHHCCSSGGGTTTTTSCCCCTTTTCCCCHHHHHHHHHHHTCS
T ss_pred             HHHhccCCCHHHHHHHHHHcCCHHHHHHHHHhcCCHHHHHHHHHhcccCCCCCccCHHHHHHHHHHHccC
Confidence            88899999999999999999999999988653     2    76663 2     9999999999999753

>1s5l_U Photosystem II 12 kDa extrinsic protein; photosynthesis, oxygen-evolving, tetra- manganese, membrane; HET: CL1 PHO HEM PL9 LMT BCR; 3.50A {Thermosynechococcus elongatus}

Probab=96.63  E-value=0.0022  Score=55.95  Aligned_cols=47  Identities=23%  Similarity=0.350  Sum_probs=39.0

Q ss_pred             HHhhccCCCCCHHHHHHHHHh--cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          217 THALTSVRSVNKTDVVTLGST--FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       217 ~saLTsIpgVnKTDA~~LLs~--FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      ...|..+||||++.|..+++|  |.|        .|||.+|+|||+++.+.|.+...
T Consensus        62 ~~eL~~LpGiGp~~A~~II~~GpF~s--------vedL~~V~GIg~k~~e~l~~~~~  110 (134)
T 1s5l_U           62 IAAFIQYRGLYPTLAKLIVKNAPYES--------VEDVLNIPGLTERQKQILRENLE  110 (134)
T ss_dssp             GGGGGGSTTCTHHHHHHHHHTCCCSS--------GGGGGGCTTCCHHHHHHHHHHHT
T ss_pred             HHHHHHCCCCCHHHHHHHHHcCCCCC--------HHHHHhCCCCCHHHHHHHHHhhc
Confidence            456778999999999999976  554        47999999999998888876654

>3b0x_A DNA polymerase beta family (X family); structural genomics, riken structural genomics/proteomics in RSGI, polxc, PHP, DRP lyase; HET: DNA DGT; 1.36A {Thermus thermophilus} PDB: 3au2_A* 3au6_A* 3auo_A* 3b0y_A*

Probab=96.31  E-value=0.0036  Score=63.86  Aligned_cols=54  Identities=22%  Similarity=0.311  Sum_probs=46.1

Q ss_pred             HHhhccCCCCCHHHHHHHHHh--cCCHHHHHcCC-HHhhhcCCCCCHHHHHHHHHHh
Q 017612          217 THALTSVRSVNKTDVVTLGST--FGSLSHIMDAS-MEDLARCPGIGERKVKRLYDTF  270 (368)
Q Consensus       217 ~saLTsIpgVnKTDA~~LLs~--FGSLk~I~~AS-~EELa~VPGIG~kKA~rI~e~F  270 (368)
                      ...|.+|+|||++.|..|+..  +.|+++|..|- .++|..+||||+|.|++|..-+
T Consensus        92 ~~~l~~v~GvGpk~A~~~~~~lg~~~~~~l~~a~~~~~l~~~~GiG~k~a~~i~~~l  148 (575)
T 3b0x_A           92 VLEVMEVPGVGPKTARLLYEGLGIDSLEKLKAALDRGDLTRLKGFGPKRAERIREGL  148 (575)
T ss_dssp             HHHHHTSTTTCHHHHHHHHHTSCCCSHHHHHHHHHHTGGGGSTTCCHHHHHHHHHHH
T ss_pred             HHHHhcCCCcCHHHHHHHHHhcCCCCHHHHHHHHHcCCcccCCCCCccHHHHHHHHH
Confidence            345669999999999999996  79999999874 4679999999999999995544

>2fmp_A DNA polymerase beta; nucleotidyl transferase, transferase/DNA complex; HET: DNA DOC DCT; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1bpx_A* 1bpz_A* 1mq2_A* 1mq3_A* 1bpy_A* 1tva_A* 1zjm_A* 1zjn_A* 1zqa_A* 1zqb_A* 1zqc_A* 1zqd_A* 1zqe_A* 1zqf_A* 1zqg_A* 1zqh_A* 1zqi_A* 1zqj_A* 1zqk_A* 1zql_A* ...

Probab=95.92  E-value=0.011  Score=57.04  Aligned_cols=50  Identities=20%  Similarity=0.327  Sum_probs=39.2

Q ss_pred             hccCCCCCHHHHHHHHHh--cCCHHHHHc-------CCHHhhhcCCCCCHHHHHHHHHH
Q 017612          220 LTSVRSVNKTDVVTLGST--FGSLSHIMD-------ASMEDLARCPGIGERKVKRLYDT  269 (368)
Q Consensus       220 LTsIpgVnKTDA~~LLs~--FGSLk~I~~-------AS~EELa~VPGIG~kKA~rI~e~  269 (368)
                      |+.|||||+..|..+.+-  =|.++.+-.       .+..+|.+|+|||+++|++|++-
T Consensus        59 l~~LpGIG~~~A~kI~E~l~tG~~~~le~l~~~~~~~~l~~l~~V~GiGpk~a~~l~~~  117 (335)
T 2fmp_A           59 AKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDE  117 (335)
T ss_dssp             HHTSTTCCHHHHHHHHHHHHHSSCHHHHHHHHCHHHHHHHHHTTSTTCCHHHHHHHHHT
T ss_pred             HhcCCCCcHHHHHHHHHHHHhCCcHHHHHHHcccchhHHHHHhCCCCCCHHHHHHHHHc
Confidence            789999999999877653  355544332       35678999999999999999874

>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus}

Probab=95.43  E-value=0.011  Score=57.62  Aligned_cols=50  Identities=14%  Similarity=0.318  Sum_probs=39.4

Q ss_pred             hccCCCCCHHHHHHHHHh--cCCHHHHHcC-------CHHhhhcCCCCCHHHHHHHHHH
Q 017612          220 LTSVRSVNKTDVVTLGST--FGSLSHIMDA-------SMEDLARCPGIGERKVKRLYDT  269 (368)
Q Consensus       220 LTsIpgVnKTDA~~LLs~--FGSLk~I~~A-------S~EELa~VPGIG~kKA~rI~e~  269 (368)
                      |+.|||||+..|..+.+-  -|.++.+-..       ...+|.+|+|||+++|++|++-
T Consensus        63 l~~lpGIG~~~A~kI~E~l~tG~~~~le~L~~d~~~~~l~~l~~I~GvG~kta~~l~~~  121 (360)
T 2ihm_A           63 LHGLPYFGEHSTRVIQELLEHGTCEEVKQVRCSERYQTMKLFTQVFGVGVKTANRWYQE  121 (360)
T ss_dssp             GTTCTTCCHHHHHHHHHHHHHSCCHHHHHHHHSHHHHHHHHHHTSTTCCHHHHHHHHHT
T ss_pred             HhcCCCCCHHHHHHHHHHHHcCChHHHHHHhcccchHHHHHHhCCCCCCHHHHHHHHHc
Confidence            889999999999887652  4666555432       3468999999999999999875

>1jms_A Terminal deoxynucleotidyltransferase; polymerase; 2.36A {Mus musculus} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1kdh_A* 1kej_A*

Probab=95.28  E-value=0.01  Score=58.53  Aligned_cols=50  Identities=10%  Similarity=0.159  Sum_probs=39.2

Q ss_pred             hccCCCCCHHHHHHHHHh--cCCHHHHHcC-------CHHhhhcCCCCCHHHHHHHHHH
Q 017612          220 LTSVRSVNKTDVVTLGST--FGSLSHIMDA-------SMEDLARCPGIGERKVKRLYDT  269 (368)
Q Consensus       220 LTsIpgVnKTDA~~LLs~--FGSLk~I~~A-------S~EELa~VPGIG~kKA~rI~e~  269 (368)
                      |..|||||+..|..+.+-  -|.++.+-..       ...+|.+|+|||+++|++||+.
T Consensus        82 l~~lpGIG~~ia~kI~E~l~tG~~~~le~l~~d~~~~~l~~l~~I~GvGpk~a~~ly~~  140 (381)
T 1jms_A           82 TEGIPCLGDKVKSIIEGIIEDGESSEAKAVLNDERYKSFKLFTSVFGVGLKTAEKWFRM  140 (381)
T ss_dssp             GTTCSSCCHHHHHHHHHHHHHSSCHHHHHHHHCHHHHHHHHHHTSTTCCHHHHHHHHHT
T ss_pred             HhcCCCCcHHHHHHHHHHHHcCCcHHHHHHhcCcchhHHHHHHccCCCCHHHHHHHHHc
Confidence            889999999999887652  4666554432       3458999999999999999875

>3arc_U Photosystem II 12 kDa extrinsic protein; PSII, membrane-protein complex, transmembrane alpha-helix, E transport, photosynthesis; HET: OEX CLA PHO BCR PL9 SQD LMG UNL LMT HTG DGD LHG HEM; 1.90A {Thermosynechococcus vulcanus} PDB: 3bz1_U* 2axt_U* 3bz2_U* 3kzi_U* 3prq_U* 3prr_U* 3a0b_U* 3a0h_U*

Probab=95.25  E-value=0.008  Score=49.35  Aligned_cols=38  Identities=11%  Similarity=0.331  Sum_probs=32.0

Q ss_pred             hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcccccc
Q 017612          237 TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKR  276 (368)
Q Consensus       237 ~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~~  276 (368)
                      .++..=+|=.||.++|+.+||||+++|++|.+  +.||..
T Consensus        13 ~~~~~vdiNtAs~~eL~~lpGIG~~~A~~IV~--~GpF~s   50 (97)
T 3arc_U           13 AYGEKIDLNNTNIAAFIQYRGLYPTLAKLIVK--NAPYES   50 (97)
T ss_dssp             GGGTSEETTTSCGGGGGGSTTCTTHHHHHHHH--HCCCSS
T ss_pred             ccCCceeCCcCCHHHHhHCCCCCHHHHHHHHH--cCCCCC
Confidence            34444467789999999999999999999999  788874

>2bcq_A DNA polymerase lambda; misalignment, extrahelical, mutagenesis, mutation, deletion, streisinger, slippage, transferase, lyase/DNA complex; HET: DNA; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1xsl_A* 2bcr_A* 2bcs_A* 2bcu_A* 2bcv_A* 2gws_A* 3c5g_A* 3c5f_A* 2pfn_A* 1xsp_A* 1xsn_A* 2pfo_A* 2pfp_A* 2pfq_A* 3hw8_A* 3hwt_A* 1rzt_A* 3hx0_A* 3mdc_A* 3mda_A* ...

Probab=95.18  E-value=0.017  Score=55.83  Aligned_cols=50  Identities=18%  Similarity=0.236  Sum_probs=37.7

Q ss_pred             hccCCCCCHHHHHHHHHh--cCCHHHHHcCC-----HHhhhcCCCCCHHHHHHHHHH
Q 017612          220 LTSVRSVNKTDVVTLGST--FGSLSHIMDAS-----MEDLARCPGIGERKVKRLYDT  269 (368)
Q Consensus       220 LTsIpgVnKTDA~~LLs~--FGSLk~I~~AS-----~EELa~VPGIG~kKA~rI~e~  269 (368)
                      |..|||||+..|..+.+-  -|.++.+-...     .+.|.+|+|||+++|++|++.
T Consensus        59 l~~lpGIG~~~A~kI~E~l~tG~~~~le~l~~~~p~l~ll~~v~GiG~k~a~~l~~~  115 (335)
T 2bcq_A           59 ACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQ  115 (335)
T ss_dssp             HHTSTTCCHHHHHHHHHHHHSSSCGGGGGCCTTHHHHHHHHTSTTCCHHHHHHHHHT
T ss_pred             HhcCCCccHHHHHHHHHHHHcCCchHHHHHhhhhHHHHHHhcCCCcCHHHHHHHHHc
Confidence            789999999999887653  46666554432     233469999999999999864

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=94.75  E-value=0.04  Score=56.44  Aligned_cols=53  Identities=25%  Similarity=0.402  Sum_probs=50.1

Q ss_pred             hhccCCCCCHHHHHHHHHh-cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          219 ALTSVRSVNKTDVVTLGST-FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs~-FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      .|..|||||...|+.|.+. |.|+.+|++++.++|..++|+|++.++.+..++.
T Consensus       647 ~L~qlp~v~~~rar~L~~~G~~s~~dl~~~~~~~l~~~~~~~~~i~~~~~~~~~  700 (720)
T 2zj8_A          647 PLMQLPLVGRRRARALYNSGFRSIEDISQARPEELLKIEGIGVKTVEAIFKFLG  700 (720)
T ss_dssp             GGTTSTTCCHHHHHHHHTTTCCSHHHHHTCCHHHHHTSTTCCHHHHHHHHHHHC
T ss_pred             hhhhCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHHhHhHHHHHHHHHHHhcc
Confidence            5679999999999999987 9999999999999999999999999999999886

>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2 PDB: 1v9p_A*

Probab=94.55  E-value=0.017  Score=60.95  Aligned_cols=61  Identities=15%  Similarity=0.214  Sum_probs=53.9

Q ss_pred             HHHHHHHhhc----cCCCCCHHHHHHHHHhcC--CHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          212 YLSRLTHALT----SVRSVNKTDVVTLGSTFG--SLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       212 y~srL~saLT----sIpgVnKTDA~~LLs~FG--SLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      ...++.++++    .|+|+|.+.+..|.++++  ++.+|+.+..++|..++|||+++|++|++.+..
T Consensus       431 ~~~~l~hf~sr~aldI~GLG~k~i~~L~~~g~I~~~~DL~~L~~e~L~~l~g~G~Ksa~nLl~aIe~  497 (667)
T 1dgs_A          431 RFEAIRHYASRKAMDIEGLGEKLIERLLEKGLVRDVADLYHLRKEDLLGLERMGEKSAQNLLRQIEE  497 (667)
T ss_dssp             HHHHHHHHHSTTSSCCTTCCHHHHHHHHHTTSCSSGGGGGGGCCHHHHTTSSCCSTTHHHHHHHHHH
T ss_pred             HHHHHHHHhcccccCcCcCCHHHHHHHHHcCCCCCHHHHHhcCHHHHhcccccchhhHHHHHHHHHH
Confidence            4566666663    699999999999999976  999999999999999999999999999999864

>1s5l_U Photosystem II 12 kDa extrinsic protein; photosynthesis, oxygen-evolving, tetra- manganese, membrane; HET: CL1 PHO HEM PL9 LMT BCR; 3.50A {Thermosynechococcus elongatus}

Probab=94.41  E-value=0.022  Score=49.67  Aligned_cols=38  Identities=11%  Similarity=0.331  Sum_probs=31.4

Q ss_pred             hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcccccc
Q 017612          237 TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKR  276 (368)
Q Consensus       237 ~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~~  276 (368)
                      .++.-=+|=+|+.+||..+||||+++|++|.+  |.||..
T Consensus        50 ~~~~kIniNtA~~~eL~~LpGiGp~~A~~II~--~GpF~s   87 (134)
T 1s5l_U           50 AYGEKIDLNNTNIAAFIQYRGLYPTLAKLIVK--NAPYES   87 (134)
T ss_dssp             TSTTSEETTTSCGGGGGGSTTCTHHHHHHHHH--TCCCSS
T ss_pred             ccCCeeeCcccCHHHHHHCCCCCHHHHHHHHH--cCCCCC
Confidence            34454567789999999999999999999994  778874

>2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus} SCOP: a.60.2.7

Probab=94.32  E-value=0.015  Score=43.99  Aligned_cols=28  Identities=32%  Similarity=0.546  Sum_probs=25.0

Q ss_pred             HHHcCCHHhhhcCCCCCHHHHHHHHHHh
Q 017612          243 HIMDASMEDLARCPGIGERKVKRLYDTF  270 (368)
Q Consensus       243 ~I~~AS~EELa~VPGIG~kKA~rI~e~F  270 (368)
                      +|-.|+.++|..+||||++.|++|.+.+
T Consensus        20 diN~a~~~~L~~ipGIG~~~A~~Il~~r   47 (75)
T 2duy_A           20 SLNEASLEELMALPGIGPVLARRIVEGR   47 (75)
T ss_dssp             ETTTCCHHHHTTSTTCCHHHHHHHHHTC
T ss_pred             ChhhCCHHHHHhCCCCCHHHHHHHHHHc
Confidence            3556889999999999999999999987

>2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix turn helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.60.2.7

Probab=93.41  E-value=0.14  Score=40.77  Aligned_cols=47  Identities=19%  Similarity=0.250  Sum_probs=35.8

Q ss_pred             CCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc--ccc
Q 017612          226 VNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH--EPF  274 (368)
Q Consensus       226 VnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~--ePF  274 (368)
                      |......+....+  .-+|-.|+.++|..|||||++.|++|.+.+.  .+|
T Consensus        18 ~~pe~~~~~~~~~--~i~iN~a~~~~L~~ipGIG~~~A~~Il~~r~~~g~f   66 (98)
T 2edu_A           18 ISPELLAHGRQKI--LDLLNEGSARDLRSLQRIGPKKAQLIVGWRELHGPF   66 (98)
T ss_dssp             SCHHHHHHHHHHH--HHHHHHSCHHHHHHSTTCCHHHHHHHHHHHHHHCCC
T ss_pred             cCHHHHHHHHhcc--CeehhhCCHHHHHHCCCCCHHHHHHHHHHHHhcCCc
Confidence            4455444444332  4568889999999999999999999999985  466

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=93.26  E-value=0.14  Score=47.28  Aligned_cols=54  Identities=19%  Similarity=0.278  Sum_probs=48.6

Q ss_pred             hhccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          219 ALTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      -|..++||+..++..|.+ -|.|+++|..++.++|..+.||.+.+|.+|.+....
T Consensus         4 ~~~~l~gi~~~~~~kL~~~gi~t~~~~~~~~~~~L~~~~gis~~~a~~~i~~a~~   58 (322)
T 2i1q_A            4 NLTDLPGVGPSTAEKLVEAGYIDFMKIATATVGELTDIEGISEKAAAKMIMGARD   58 (322)
T ss_dssp             -CTTSTTCCHHHHHHHHHHTCCSHHHHHTCCHHHHHTSTTCCHHHHHHHHHHHHH
T ss_pred             cHhhcCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhhCcCHHHHHHHHHHHHH
Confidence            466788999999999987 699999999999999999999999999999887654

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

Probab=93.16  E-value=0.1  Score=55.21  Aligned_cols=60  Identities=10%  Similarity=0.177  Sum_probs=50.8

Q ss_pred             HHHHHHhh----ccCCCCCHHHHHHHHHhc--CCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          213 LSRLTHAL----TSVRSVNKTDVVTLGSTF--GSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       213 ~srL~saL----TsIpgVnKTDA~~LLs~F--GSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      ..++.++.    -.|+|+|.+.+..|.++-  .++.+|..+..++|..++|||++.|++|++.+..
T Consensus       437 ~~~l~hf~sr~aldI~GLG~k~i~~L~~~g~I~~~aDL~~L~~~~L~~l~gfG~Ksa~nLl~aIe~  502 (671)
T 2owo_A          437 KESLKHFVSRRAMDVDGMGDKIIDQLVEKEYVHTPADLFKLTAGKLTGLERMGPKSAQNVVNALEK  502 (671)
T ss_dssp             HHHHHHHHSTTTTCCTTCCHHHHHHHHHTTCCSSGGGGGTCCHHHHHTSTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhhhhcCCCCCCHHHHHHHHHcCCCCCHHHHHhhCHHHhhcccccchhHHHHHHHHHHH
Confidence            44555544    279999999999999974  5999999999999999999999999999998864

>4e9f_A Methyl-CPG-binding domain protein 4; HHH DNA glycosylase family, hydrolase-DNA complex; HET: DNA 3DR; 1.79A {Homo sapiens} PDB: 4e9e_A* 4e9g_A* 4e9h_A* 4ea5_A* 4dk9_A* 1ngn_A 4ea4_A* 4ew4_A* 4evv_A* 4ew0_A* 3iho_A

Probab=93.11  E-value=0.068  Score=46.95  Aligned_cols=48  Identities=8%  Similarity=0.001  Sum_probs=39.2

Q ss_pred             CCCCC--HHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccc
Q 017612          223 VRSVN--KTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEP  273 (368)
Q Consensus       223 IpgVn--KTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~eP  273 (368)
                      |+++|  ...|++|.+.+   +.++-.+.++|..+||||+..|..|.-+....
T Consensus        78 i~~lG~y~~KAk~i~~~a---~~~vp~~~~~L~~LpGVG~yTAdav~~F~~~e  127 (161)
T 4e9f_A           78 LKPLGLYDLRAKTIVKFS---DEYLTKQWKYPIELHGIGKYGNDSYRIFCVNE  127 (161)
T ss_dssp             HGGGSCHHHHHHHHHHHH---HHHHHSCCSSGGGSTTCCHHHHHHHHHHTSSC
T ss_pred             hhhcCCHHHHHHHHHHHh---CCcCCCChhhhhcCCCchHHHHHHHHHHHCCC
Confidence            34555  78899998876   47788899999999999999999998876443

>1exn_A 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Enterobacteria phage T5} SCOP: a.60.7.1 c.120.1.2 PDB: 1ut5_A 1ut8_A 1xo1_A

Probab=92.83  E-value=0.1  Score=49.91  Aligned_cols=29  Identities=17%  Similarity=0.340  Sum_probs=25.8

Q ss_pred             hhccCCCCCHHHHHHHHHhcCCHHHHHcC
Q 017612          219 ALTSVRSVNKTDVVTLGSTFGSLSHIMDA  247 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs~FGSLk~I~~A  247 (368)
                      -+.+|||||++.|..||+.|||+++|+..
T Consensus       204 niPGVpGIG~KTA~kLL~~~gsle~i~~~  232 (290)
T 1exn_A          204 NIRGVEGIGAKRGYNIIREFGNVLDIIDQ  232 (290)
T ss_dssp             TBCCCTTCCHHHHHHHHHHHCSHHHHHHH
T ss_pred             CCCCCCcCCHhHHHHHHHHcCCHHHHHHH
Confidence            35679999999999999999999999843

>4glx_A DNA ligase; inhibitor, ligase-ligase inhibitor-DNA complex; HET: DNA 0XS; 1.90A {Escherichia coli}

Probab=92.66  E-value=0.14  Score=53.36  Aligned_cols=61  Identities=10%  Similarity=0.198  Sum_probs=52.6

Q ss_pred             HHHHHHHhhc----cCCCCCHHHHHHHHHh--cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          212 YLSRLTHALT----SVRSVNKTDVVTLGST--FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       212 y~srL~saLT----sIpgVnKTDA~~LLs~--FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      ...++.++.+    .|.|+|...+..|++.  ..++.+|+..+.++|..++|||++.|++|++.+..
T Consensus       436 ~~~~l~hf~sr~amdI~GlG~~~i~~L~~~g~i~~~~Dly~L~~~~L~~l~g~geKsa~nL~~aIe~  502 (586)
T 4glx_A          436 RKESLKHFVSRRAMDVDGMGDKIIDQLVEKEYVHTPADLFKLTAGKLTGLERMGPKSAQNVVNALEK  502 (586)
T ss_dssp             HHHHHHHHHSTTTTCCTTCCHHHHHHHHHTTCCSSGGGGGTCCHHHHHTSTTCCHHHHHHHHHHHHH
T ss_pred             HHhHHHhhhccccccCCCcCHHHHHHHHhcCCCCCHHHHhCCCHHHHhcccCccHHHHHHHHHHHHH
Confidence            3456665542    5999999999999986  48999999999999999999999999999999963

>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerizat motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11

Probab=92.01  E-value=0.13  Score=48.95  Aligned_cols=55  Identities=18%  Similarity=0.272  Sum_probs=49.9

Q ss_pred             hhccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccc
Q 017612          219 ALTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEP  273 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~eP  273 (368)
                      .|..++|||..++..|.+ -|.|++.|..++..+|..+.||++.+|.+|.+.....
T Consensus        36 ~l~~l~Gi~~~~~~kL~~ag~~t~~~~~~~~~~~L~~~~~~s~~~~~~~l~~~~~~   91 (349)
T 1pzn_A           36 SIEDLPGVGPATAEKLREAGYDTLEAIAVASPIELKEVAGISEGTALKIIQAARKA   91 (349)
T ss_dssp             CSSCCTTCCHHHHHHHHTTTCCSHHHHHTCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             cHHHcCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHhhcCCCHHHHHHHHHHHhhh
Confidence            477889999999999988 6999999999999999999999999999998877543

>2i5h_A Hypothetical protein AF1531; PFAM:DUF655, PSI-2, structural genomics, protein structure initiative; 1.74A {Archaeoglobus fulgidus} SCOP: e.71.1.1

Probab=90.09  E-value=0.14  Score=47.29  Aligned_cols=35  Identities=29%  Similarity=0.368  Sum_probs=21.5

Q ss_pred             hhccCCCCCHHHHHHHHHh-----cCCHHHHHcCCHHhhhc-CCCCCHH
Q 017612          219 ALTSVRSVNKTDVVTLGST-----FGSLSHIMDASMEDLAR-CPGIGER  261 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs~-----FGSLk~I~~AS~EELa~-VPGIG~k  261 (368)
                      .|..+||||++.|.++++.     |.|        .+||.. |+|||..
T Consensus       133 eL~~LpGIG~k~A~~IIeyRe~G~F~s--------~eDL~~RV~GIg~~  173 (205)
T 2i5h_A          133 QLELLPGVGKKMMWAIIEERKKRPFES--------FEDIAQRVKGIQRP  173 (205)
T ss_dssp             GGGGSTTCCHHHHHHHHHHHHHSCCCS--------HHHHHHHSTTCCCH
T ss_pred             HHhcCCCcCHHHHHHHHHHHhcCCCCC--------HHHHHHhcCCCCcc
Confidence            4566777777777777764     333        345644 7774443

>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans}

Probab=89.96  E-value=0.18  Score=51.72  Aligned_cols=50  Identities=20%  Similarity=0.342  Sum_probs=37.2

Q ss_pred             hccCCCCCHHHHHHHHHh--------cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHH
Q 017612          220 LTSVRSVNKTDVVTLGST--------FGSLSHIMDASMEDLARCPGIGERKVKRLYDT  269 (368)
Q Consensus       220 LTsIpgVnKTDA~~LLs~--------FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~  269 (368)
                      |..+||||+..+..+-..        ||-+..-..+...+|..|+|||+++|++|++.
T Consensus        59 ~~~lp~iG~~~~~~i~~~v~~g~~~~~~~~~~~~~~~~~~L~~v~GVGpk~A~~i~~~  116 (578)
T 2w9m_A           59 FTGIPKVGKGIAAELSDFARSGTFAPLEAAAGQLPPGLLDLLGVRGLGPKKIRSLWLA  116 (578)
T ss_dssp             CCSSTTCCHHHHHHHHHHHHHSSCHHHHHHHHHSCHHHHHHTTSTTCCHHHHHHHHHT
T ss_pred             hhhcCCCChhHHHHHHHHHcCChHHHHHHHhhhhHHHHHHHhCCCCcCHHHHHHHHHc
Confidence            789999999877765433        23333333445578999999999999999985

>1z3e_B DNA-directed RNA polymerase alpha chain; bacterial transcription regulation, disulfide stress; 1.50A {Bacillus subtilis} SCOP: a.60.3.1 PDB: 3ihq_B

Probab=89.74  E-value=0.29  Score=38.18  Aligned_cols=43  Identities=9%  Similarity=0.265  Sum_probs=36.5

Q ss_pred             HHHHHHH--hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          230 DVVTLGS--TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       230 DA~~LLs--~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      .+.+-|+  ...|+.+++.-+.+||.+++|||++-.+.|.+.+.+
T Consensus        19 Ra~NcLkragI~Tv~dL~~~s~~dLlki~n~G~kSl~EI~~~L~~   63 (73)
T 1z3e_B           19 RSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEE   63 (73)
T ss_dssp             HHHHHHHHTTCCBHHHHHTSCHHHHHTSTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCcHHHHHcCCHHHHHHcCCCCHHHHHHHHHHHHH
Confidence            3444444  367999999999999999999999999999999975

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=89.57  E-value=0.24  Score=50.47  Aligned_cols=51  Identities=10%  Similarity=0.223  Sum_probs=42.2

Q ss_pred             hhccCCCCCHHHHHHHHHh-cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          219 ALTSVRSVNKTDVVTLGST-FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs~-FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      .|..|||||+..|+.|-+. |.|+++|+ ++.++|..+  ||++.+++|++.+++
T Consensus       658 ~L~qlp~i~~~rar~L~~~g~~s~~~l~-~~~~~l~~~--l~~~~~~~i~~~~~~  709 (715)
T 2va8_A          658 ELVQISGVGRKRARLLYNNGIKELGDVV-MNPDKVKNL--LGQKLGEKVVQEAAR  709 (715)
T ss_dssp             HHHTSTTCCHHHHHHHHHTTCCSHHHHH-HCHHHHHHH--HCHHHHHHHHHHHHH
T ss_pred             chhhCCCCCHHHHHHHHHcCCCCHHHHh-CCHHHHHHH--hChhHHHHHHHHHHH
Confidence            4559999999999999884 78999999 999999999  557777777765544

>2csb_A Topoisomerase V, TOP61; topoisomerase IB, helix-turn-helix, helix-H helix, HHH motif, three helix bundle, methanopyrus kandleri isomerase; 2.30A {Methanopyrus kandleri} SCOP: a.60.2.4 a.60.2.4 a.60.2.4 a.60.2.4 a.267.1.1 PDB: 2csd_A

Probab=89.55  E-value=0.52  Score=46.30  Aligned_cols=53  Identities=26%  Similarity=0.394  Sum_probs=44.9

Q ss_pred             HHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcC----CHHhhhcCCCCCHHHHHHH
Q 017612          214 SRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDA----SMEDLARCPGIGERKVKRL  266 (368)
Q Consensus       214 srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~A----S~EELa~VPGIG~kKA~rI  266 (368)
                      +..+.-||.-.|||++.|.+||..||..+.+...    ..+.|+.|.|+|+...+.+
T Consensus       407 eiqlaeltkkegvgrktaerllrafgnpervkqlarefeieklasvegvgervlrsl  463 (519)
T 2csb_A          407 EIQLAELTKKEGVGRKTAERLLRAFGNPERVKQLAREFEIEKLASVEGVGERVLRSL  463 (519)
T ss_dssp             HHHHHHHHTSTTCCHHHHHHHHHHHSSHHHHHHHHHTTCHHHHHTSTTCSHHHHHHH
T ss_pred             HHHHHHHhhhcccchhHHHHHHHHhCCHHHHHHHHHHHhHHHHhhccchHHHHHHHh
Confidence            3345678899999999999999999999888754    5789999999999877665

>3q8k_A Flap endonuclease 1; helix-3 turn-helix, hydrophobic wedge, 3' flap binding site, hydrolase-DNA complex, DNA repair, replication; HET: DNA; 2.20A {Homo sapiens} PDB: 3q8l_A* 3q8m_A*

Probab=89.34  E-value=0.22  Score=48.15  Aligned_cols=28  Identities=21%  Similarity=0.286  Sum_probs=25.6

Q ss_pred             hccCCCCCHHHHHHHHHhcCCHHHHHcC
Q 017612          220 LTSVRSVNKTDVVTLGSTFGSLSHIMDA  247 (368)
Q Consensus       220 LTsIpgVnKTDA~~LLs~FGSLk~I~~A  247 (368)
                      +.+|||||.+.|..|+++|||+++|+..
T Consensus       234 ~~gipGiG~KtA~kll~~~gsle~i~~~  261 (341)
T 3q8k_A          234 CESIRGIGPKRAVDLIQKHKSIEEIVRR  261 (341)
T ss_dssp             SCCCTTCCHHHHHHHHHHHCSHHHHHHH
T ss_pred             CCCCCCccHHHHHHHHHHcCCHHHHHHH
Confidence            5589999999999999999999999854

>2i5h_A Hypothetical protein AF1531; PFAM:DUF655, PSI-2, structural genomics, protein structure initiative; 1.74A {Archaeoglobus fulgidus} SCOP: e.71.1.1

Probab=88.84  E-value=0.26  Score=45.61  Aligned_cols=31  Identities=23%  Similarity=0.520  Sum_probs=26.9

Q ss_pred             cCCHHhhhcCCCCCHHHHHHHHHHhc-ccccc
Q 017612          246 DASMEDLARCPGIGERKVKRLYDTFH-EPFKR  276 (368)
Q Consensus       246 ~AS~EELa~VPGIG~kKA~rI~e~F~-ePF~~  276 (368)
                      .|+.++|..+||||+++|++|.++=. .+|..
T Consensus       128 TA~~~eL~~LpGIG~k~A~~IIeyRe~G~F~s  159 (205)
T 2i5h_A          128 TTRMHQLELLPGVGKKMMWAIIEERKKRPFES  159 (205)
T ss_dssp             CSSSBGGGGSTTCCHHHHHHHHHHHHHSCCCS
T ss_pred             cCCHHHHhcCCCcCHHHHHHHHHHHhcCCCCC
Confidence            99999999999999999999988754 46753

>1rxw_A Flap structure-specific endonuclease; helical clamp, helix-3 turn-helix, hydrophobic wedge, 3' FLA site, hydrolase-DNA complex; 2.00A {Archaeoglobus fulgidus} SCOP: a.60.7.1 c.120.1.2 PDB: 1rxv_A

Probab=88.70  E-value=0.26  Score=46.97  Aligned_cols=28  Identities=18%  Similarity=0.296  Sum_probs=26.0

Q ss_pred             hccCCCCCHHHHHHHHHhcCCHHHHHcC
Q 017612          220 LTSVRSVNKTDVVTLGSTFGSLSHIMDA  247 (368)
Q Consensus       220 LTsIpgVnKTDA~~LLs~FGSLk~I~~A  247 (368)
                      +.+|||||.+.|..|+++|||+++|+..
T Consensus       237 ipGv~GiG~KtA~kLl~~~gsle~i~~~  264 (336)
T 1rxw_A          237 NEGVKGVGVKKALNYIKTYGDIFRALKA  264 (336)
T ss_dssp             BCCCTTCCHHHHHHHHHHHSSHHHHHHH
T ss_pred             CCCCCCcCHHHHHHHHHHcCCHHHHHHh
Confidence            5589999999999999999999999976

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=88.64  E-value=0.52  Score=46.27  Aligned_cols=49  Identities=22%  Similarity=0.304  Sum_probs=44.2

Q ss_pred             CCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          224 RSVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       224 pgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      -||+..++.+|.+ .|.|+++|..++..||..+.||++.+|.+|.+...+
T Consensus        89 ~gi~~~~~~~L~~ag~~tv~~~~~~~~~~L~~~~gis~~~~~~i~~~a~~  138 (400)
T 3lda_A           89 NGITMADVKKLRESGLHTAEAVAYAPRKDLLEIKGISEAKADKLLNEAAR  138 (400)
T ss_dssp             TTCCHHHHHHHHHTTCCBHHHHHHSCHHHHHTSTTCCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            3699999999988 599999999999999999999999999999776543

>2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 PDB: 2kn7_A*

Probab=88.61  E-value=0.23  Score=37.12  Aligned_cols=24  Identities=17%  Similarity=0.432  Sum_probs=21.3

Q ss_pred             HHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          249 MEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       249 ~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      .+.|..|||||++.+++|.+.|..
T Consensus         3 ~s~L~~IpGIG~kr~~~LL~~Fgs   26 (63)
T 2a1j_A            3 QDFLLKMPGVNAKNCRSLMHHVKN   26 (63)
T ss_dssp             CHHHHTSTTCCHHHHHHHHHHCSS
T ss_pred             HhHHHcCCCCCHHHHHHHHHHcCC
Confidence            467999999999999999999954

>3k4g_A DNA-directed RNA polymerase subunit alpha; bacterial transcription regulation, DNA-directed RNA polymer nucleotidyltransferase; HET: MLY; 2.05A {Escherichia coli k-12} SCOP: a.60.3.1 PDB: 3n4m_B* 1lb2_B* 3n97_B* 1xs9_D

Probab=88.42  E-value=0.41  Score=38.69  Aligned_cols=37  Identities=11%  Similarity=0.335  Sum_probs=34.3

Q ss_pred             hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccc
Q 017612          237 TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEP  273 (368)
Q Consensus       237 ~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~eP  273 (368)
                      ...|+.+++..+.+||.+++|||++-.+.|.+.+.+-
T Consensus        31 gI~Tv~dL~~~se~dLlki~n~G~KSl~EI~~~L~~~   67 (86)
T 3k4g_A           31 AIHYIGDLVQRTEVELLXTPNLGXXSLTEIXDVLASR   67 (86)
T ss_dssp             TCCBHHHHHHSCHHHHHTSTTCCHHHHHHHHHHHHTT
T ss_pred             CCCcHHHHHhCCHHHHhhccccCcccHHHHHHHHHHc
Confidence            4679999999999999999999999999999999764

>2ziu_B Crossover junction endonuclease EME1; helix-hairpin-helix, alternative splicing, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; 2.70A {Homo sapiens} PDB: 2ziw_B 2zix_B 2ziv_B

Probab=87.85  E-value=1.8  Score=41.80  Aligned_cols=95  Identities=14%  Similarity=0.110  Sum_probs=66.8

Q ss_pred             eeeeec-hhhHHHHHHHHHHhhc-CCc-------------c-----hhcc-cccccHHHHHHHhhccCCCCCHHHHHHHH
Q 017612          177 CALYLS-LEECGRYLETIKVYEN-KPA-------------D-----LIQG-QMDTDYLSRLTHALTSVRSVNKTDVVTLG  235 (368)
Q Consensus       177 cILFLS-~EEAArYIEt~K~~E~-K~~-------------d-----~Ire-k~e~dy~srL~saLTsIpgVnKTDA~~LL  235 (368)
                      -|..+. .+|+++||..|-..=. .+-             .     .++. +...+..+.....|..|+||....|..|+
T Consensus       193 ~v~~t~~~~Et~~~l~~~T~~Ia~~pyk~~r~~~~~~~~~~~~~~~~vk~~~~~~~~~d~w~~~L~qi~gVS~ekA~aI~  272 (341)
T 2ziu_B          193 QAQIVQSWKELADFTCAFTKAVAEAPFKKLRDETTFSFCLESDWAGGVKVDLAGRGLALVWRRQIQQLNRVSLEMASAVV  272 (341)
T ss_dssp             BCCEESSHHHHHHHHHHHHHHHHCCC---CCSCCHHHHHTSCCTTCCBCCCTTCTTHHHHHHHHHTTSTTCCHHHHHHHH
T ss_pred             EEEEeCCHHHHHHHHHHHHHHHHhCcchhhhccCCcceeecCccccccccCCCCCcHHHHHHHHHHHccCCCHHHHHHHH
Confidence            344443 9999999988876411 110             0     0111 12355667778889999999999999999


Q ss_pred             HhcCCHHHHHcC-----CHH----hhhcC------------CCCCHHHHHHHHHHhc
Q 017612          236 STFGSLSHIMDA-----SME----DLARC------------PGIGERKVKRLYDTFH  271 (368)
Q Consensus       236 s~FGSLk~I~~A-----S~E----ELa~V------------PGIG~kKA~rI~e~F~  271 (368)
                      ++|-|+..|+.|     +.+    -|+.+            .-||+...++|+++|.
T Consensus       273 ~~YPTp~~L~~Ay~~~~~~~e~~~lL~~~~~~~~~g~~~~~r~iG~~lS~rI~~~f~  329 (341)
T 2ziu_B          273 NAYPSPQLLVQAYQQCFSDKERQNLLADIQVRRGEGVTSTSRRIGPELSRRIYLQMT  329 (341)
T ss_dssp             HHSCSHHHHHHHHHTCSCHHHHTTTTTTCBTTTTC----CCCBCCHHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHhcCChHHHHHHHHhhhcccccCCcccCCccCHHHHHHHHHHHh
Confidence            999999999876     222    23333            2399999999999996

>2csb_A Topoisomerase V, TOP61; topoisomerase IB, helix-turn-helix, helix-H helix, HHH motif, three helix bundle, methanopyrus kandleri isomerase; 2.30A {Methanopyrus kandleri} SCOP: a.60.2.4 a.60.2.4 a.60.2.4 a.60.2.4 a.267.1.1 PDB: 2csd_A

Probab=87.49  E-value=0.9  Score=44.63  Aligned_cols=52  Identities=23%  Similarity=0.443  Sum_probs=45.1

Q ss_pred             CCCCCHHHHHHHHHhcCCHHHHHcCCHH-------------------------hhhcCCCCCHHHHHHHHHHhcccc
Q 017612          223 VRSVNKTDVVTLGSTFGSLSHIMDASME-------------------------DLARCPGIGERKVKRLYDTFHEPF  274 (368)
Q Consensus       223 IpgVnKTDA~~LLs~FGSLk~I~~AS~E-------------------------ELa~VPGIG~kKA~rI~e~F~ePF  274 (368)
                      -.|+.+..|..|+.||.|+..|+..+.+                         ||.+-.|+|.+.|+++..+|..|-
T Consensus       359 ehglspdaadeliehfesiagilatdleeiermyeegrlseeayraaveiqlaeltkkegvgrktaerllrafgnpe  435 (519)
T 2csb_A          359 EHGLSPDAADELIEHFESIAGILATDLEEIERMYEEGRLSEEAYRAAVEIQLAELTKKEGVGRKTAERLLRAFGNPE  435 (519)
T ss_dssp             HHCCCHHHHHHHHHHHSSHHHHHTSCHHHHHHHHHHTSSCHHHHHHHHHHHHHHHHTSTTCCHHHHHHHHHHHSSHH
T ss_pred             hcCCCcchHHHHHHHHHHHHHHHhccHHHHHHHHHcccccHHHHHHHHHHHHHHHhhhcccchhHHHHHHHHhCCHH
Confidence            3588899999999999999999987654                         566789999999999999998764

>3gfk_B DNA-directed RNA polymerase subunit alpha; protein-protein complex, cytoplasm, redox-active center, stress response, transcription; 2.30A {Bacillus subtilis} SCOP: a.60.3.1

Probab=87.11  E-value=0.38  Score=38.29  Aligned_cols=43  Identities=9%  Similarity=0.265  Sum_probs=36.6

Q ss_pred             HHHHHHH--hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          230 DVVTLGS--TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       230 DA~~LLs--~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      .+.+-|+  ...|+.+++..+.+||..+.|||++-.+.|.+.+.+
T Consensus        26 Ra~NcLk~agI~Tv~dL~~~se~dLlki~n~G~kSl~EI~~~L~e   70 (79)
T 3gfk_B           26 RSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEE   70 (79)
T ss_dssp             HHHHHHHHTTCCBHHHHTTCCHHHHTTSTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCHHHHHhCCHHHHHHcCCCCHhHHHHHHHHHHH
Confidence            3444444  467999999999999999999999999999999875

>3b0x_A DNA polymerase beta family (X family); structural genomics, riken structural genomics/proteomics in RSGI, polxc, PHP, DRP lyase; HET: DNA DGT; 1.36A {Thermus thermophilus} PDB: 3au2_A* 3au6_A* 3auo_A* 3b0y_A*

Probab=86.98  E-value=0.34  Score=49.44  Aligned_cols=51  Identities=16%  Similarity=0.323  Sum_probs=36.5

Q ss_pred             hccCCCCCHHHHHHHHHh--cCCHHHH------HcCCHHhhhcCCCCCHHHHHHHHHHh
Q 017612          220 LTSVRSVNKTDVVTLGST--FGSLSHI------MDASMEDLARCPGIGERKVKRLYDTF  270 (368)
Q Consensus       220 LTsIpgVnKTDA~~LLs~--FGSLk~I------~~AS~EELa~VPGIG~kKA~rI~e~F  270 (368)
                      |..|||||+.-+..+-..  =|.+..+      -.....+|..|+|||+++|.+|++.+
T Consensus        55 ~~~lp~iG~~~~~~i~~~v~~g~~~l~~~~~~~~~~~~~~l~~v~GvGpk~A~~~~~~l  113 (575)
T 3b0x_A           55 LMELPGVGPDLAEKILEFLRTGKVRKHEELSRKVPRGVLEVMEVPGVGPKTARLLYEGL  113 (575)
T ss_dssp             HHTSTTCCHHHHHHHHHHHHHSSCHHHHHHHHHSCHHHHHHHTSTTTCHHHHHHHHHTS
T ss_pred             HHhCCCCCHHHHHHHHHHHHcCcHHHHhhhhhhhHHHHHHHhcCCCcCHHHHHHHHHhc
Confidence            889999998877655332  1333222      22345689999999999999999874

>1b43_A Protein (FEN-1); nuclease, DNA repair, DNA replication, transferase; 2.00A {Pyrococcus furiosus} SCOP: a.60.7.1 c.120.1.2 PDB: 1mc8_A

Probab=86.67  E-value=0.37  Score=45.94  Aligned_cols=28  Identities=0%  Similarity=-0.022  Sum_probs=25.8

Q ss_pred             hc-cCCCCCHHHHHHHHHhcCCHHHHHcC
Q 017612          220 LT-SVRSVNKTDVVTLGSTFGSLSHIMDA  247 (368)
Q Consensus       220 LT-sIpgVnKTDA~~LLs~FGSLk~I~~A  247 (368)
                      +. +|||||.+.|..|++.|||+++|+..
T Consensus       238 ~p~gv~GiG~ktA~kli~~~gsle~il~~  266 (340)
T 1b43_A          238 NPGGIKGIGLKKALEIVRHSKDPLAKFQK  266 (340)
T ss_dssp             STTCSTTCCHHHHHHHHHTCSSGGGGTGG
T ss_pred             CCCCCCCccHHHHHHHHHHcCCHHHHHcC
Confidence            45 89999999999999999999999876

>1pu6_A 3-methyladenine DNA glycosylase; helix-hairpin-helix, base excision repair, hydrolase; HET: KCX; 1.64A {Helicobacter pylori} SCOP: a.96.1.5 PDB: 1pu7_A* 1pu8_A*

Probab=86.44  E-value=1  Score=40.69  Aligned_cols=42  Identities=17%  Similarity=0.138  Sum_probs=31.8

Q ss_pred             HHHHHHHHhcCCHHHH-HcCCHHhhhcCCCCCHHHHHHHHHHh
Q 017612          229 TDVVTLGSTFGSLSHI-MDASMEDLARCPGIGERKVKRLYDTF  270 (368)
Q Consensus       229 TDA~~LLs~FGSLk~I-~~AS~EELa~VPGIG~kKA~rI~e~F  270 (368)
                      .-|+.+++.|+.+..+ .....++|..+||||++.|..|.-+-
T Consensus        99 ~~a~~i~~~~~~l~~~~~~~~~~~L~~lpGIG~kTA~~il~~a  141 (218)
T 1pu6_A           99 DLSGNILKDFQSFENFKQEVTREWLLDQKGIGKESADAILCYA  141 (218)
T ss_dssp             HHHHHHHHHHSSHHHHHHHCCHHHHHTSTTCCHHHHHHHHHHT
T ss_pred             HHHHHHHHhcCChhhccchHHHHHHHcCCCcCHHHHHHHHHHH
Confidence            3444556778887754 24568899999999999999998754

>3im1_A Protein SNU246, PRE-mRNA-splicing helicase BRR2; ATPase, RNA helicase, rnpase, RNA unwindase, molecular model mRNA splicing; 1.65A {Saccharomyces cerevisiae} PDB: 3im2_A* 3hib_A

Probab=86.23  E-value=0.87  Score=42.97  Aligned_cols=54  Identities=9%  Similarity=0.107  Sum_probs=48.0

Q ss_pred             hhccCCCCCHHHHHHHHHh-cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          219 ALTSVRSVNKTDVVTLGST-FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs~-FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      .|..+||||+..+++|-++ +.|+.+|+.++.+++..+-|+++..++.|+++++.
T Consensus       158 pL~Qlp~i~~~~~~~l~~~~i~s~~~l~~~~~~e~~~ll~~~~~~~~~v~~~~~~  212 (328)
T 3im1_A          158 PLRQIPHFNNKILEKCKEINVETVYDIMALEDEERDEILTLTDSQLAQVAAFVNN  212 (328)
T ss_dssp             GGGGSTTCCHHHHHHHHHTTCCSHHHHHHSCHHHHHHHCCCCHHHHHHHHHHHHH
T ss_pred             ceeCCCCCCHHHHHHHHhCCCCCHHHHhcCCHHHHHhHhCCCHHHHHHHHHHHHh
Confidence            4678999999999988653 66999999999999999889999999999999874

>2izo_A FEN1, flap structure-specific endonuclease; hydrolase, DNA repair, DNA-binding, endonuclease, metal-BIND excision repair, DNA replication, PCNA; HET: DNA; 2.9A {Sulfolobus solfataricus}

Probab=85.89  E-value=0.31  Score=46.77  Aligned_cols=29  Identities=10%  Similarity=0.329  Sum_probs=20.8

Q ss_pred             hc-cCCCCCHHHHHHHHHhcCCHHHHHcCC
Q 017612          220 LT-SVRSVNKTDVVTLGSTFGSLSHIMDAS  248 (368)
Q Consensus       220 LT-sIpgVnKTDA~~LLs~FGSLk~I~~AS  248 (368)
                      +. +|||||.+.|..|+++|||+++|+..-
T Consensus       235 ~p~Gv~GIG~KtA~kLi~~~gsle~i~~~~  264 (346)
T 2izo_A          235 NPDGIRGIGPERALKIIKKYGKIEKAMEYG  264 (346)
T ss_dssp             STTCSTTCCHHHHHHHHHHSSCC-------
T ss_pred             CCCCCCCcCHHHHHHHHHHcCCHHHHHHHH
Confidence            55 899999999999999999999998663

>1ul1_X Flap endonuclease-1; protein complex, DNA-binding protein, flap DNA, flap endonuclease, sliding clamp, DNA clamp; 2.90A {Homo sapiens} SCOP: a.60.7.1 c.120.1.2

Probab=85.66  E-value=0.53  Score=45.86  Aligned_cols=29  Identities=21%  Similarity=0.251  Sum_probs=25.9

Q ss_pred             hhccCCCCCHHHHHHHHHhcCCHHHHHcC
Q 017612          219 ALTSVRSVNKTDVVTLGSTFGSLSHIMDA  247 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs~FGSLk~I~~A  247 (368)
                      ...+|||||.+.|..|+..|||+++|+..
T Consensus       233 ~~d~IpGIG~KtA~kLl~~~gsle~i~~~  261 (379)
T 1ul1_X          233 YCESIRGIGPKRAVDLIQKHKSIEEIVRR  261 (379)
T ss_dssp             SSCCCTTCCHHHHHHHHHHSSSHHHHHTT
T ss_pred             cCCCCCCcCHHHHHHHHHHcCCHHHHHHH
Confidence            34469999999999999999999999866

>1coo_A RNA polymerase alpha subunit; transcription regulation, nucleotidyl transferase; NMR {Escherichia coli} SCOP: a.60.3.1 PDB: 2jzb_A

Probab=85.21  E-value=0.74  Score=37.98  Aligned_cols=37  Identities=11%  Similarity=0.375  Sum_probs=34.3

Q ss_pred             hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccc
Q 017612          237 TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEP  273 (368)
Q Consensus       237 ~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~eP  273 (368)
                      ...|+.+++.-+.+||.+++|||++-...|.+.|.+-
T Consensus        43 gI~Tv~dL~~~se~dLlki~n~G~KSl~EI~~~L~~~   79 (98)
T 1coo_A           43 AIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASR   79 (98)
T ss_dssp             TCCBHHHHHTSCHHHHTTSTTCCHHHHHHHHHHHHHT
T ss_pred             CCCcHHHHHhCCHHHHHhcCCCCHHHHHHHHHHHHHc
Confidence            4679999999999999999999999999999999754

>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} SCOP: a.60.2.6 a.60.2.6 a.294.1.1 b.40.4.5 c.55.3.13 PDB: 3bzk_A 2oce_A

Probab=85.20  E-value=0.61  Score=50.17  Aligned_cols=51  Identities=12%  Similarity=0.183  Sum_probs=40.5

Q ss_pred             HhhccCCCCCHHHHHHHHHhcCCHHHHHc--CCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          218 HALTSVRSVNKTDVVTLGSTFGSLSHIMD--ASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       218 saLTsIpgVnKTDA~~LLs~FGSLk~I~~--AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      ..|..|+|||+..|.+|+.+-    +--.  .+.+||..|+|||+++.+++..++.-
T Consensus       508 ~~L~~v~GiG~~~A~~Iv~yR----~~~G~f~sr~~L~~V~giG~k~~ekl~~FL~i  560 (785)
T 3bzc_A          508 ALLARISGLNSTLAQNIVAHR----DANGAFRTRDELKKVSRLGEKTFEQAAGFLRV  560 (785)
T ss_dssp             HHHHTSTTCCHHHHHHHHHHH----HHHCCCSSGGGGGGSTTCCHHHHHHHGGGEEC
T ss_pred             HHHhhcCCCCHHHHHHHHHHH----HhcCCCCCHHHHHhcCCCCHHHHHHhhheEEE
Confidence            467889999999999999851    1111  25689999999999999999888853

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A

Probab=84.54  E-value=0.43  Score=48.70  Aligned_cols=57  Identities=16%  Similarity=0.203  Sum_probs=46.9

Q ss_pred             hhccCCCCCHHHHHHHHHh-cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcccccccC
Q 017612          219 ALTSVRSVNKTDVVTLGST-FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKRVV  278 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs~-FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~~~~  278 (368)
                      .|..|||||+..|+.|.+. |.|+.+|++++ ++|..+  ||++.+++|++.++-|+....
T Consensus       633 ~L~qlp~v~~~~ar~l~~~g~~s~~~l~~~~-~~l~~l--l~~~~~~~i~~~~~~p~~~~~  690 (702)
T 2p6r_A          633 ELVRIRHIGRVRARKLYNAGIRNAEDIVRHR-EKVASL--IGRGIAERVVEGISVKSLNPE  690 (702)
T ss_dssp             HHHTSTTCCHHHHHHHHTTTCCSHHHHHHTH-HHHHHH--HCHHHHHHHHHHHHHHC----
T ss_pred             hhhcCCCCCHHHHHHHHHcCCCCHHHHHhhh-HHHHHH--hChhHHHHHHHhcCCCccCcc
Confidence            4568999999999999975 99999999999 999987  568889999998887766543

>1kg2_A A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A {Escherichia coli} SCOP: a.96.1.2 PDB: 1kg3_A 1muy_A 1kg6_A 1kg5_A 1mun_A 1mud_A 1kg4_A 1weg_A 1wei_A* 1wef_A* 1kg7_A 1kqj_A

Probab=83.81  E-value=0.97  Score=40.79  Aligned_cols=39  Identities=15%  Similarity=0.383  Sum_probs=27.1

Q ss_pred             HHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHH-hcc
Q 017612          231 VVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDT-FHE  272 (368)
Q Consensus       231 A~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~-F~e  272 (368)
                      |+.|++.|+.   -+....++|..+||||++.|..|.-+ |+.
T Consensus        93 a~~i~~~~~g---~~p~~~~~L~~lpGIG~~TA~~il~~a~~~  132 (225)
T 1kg2_A           93 AQQVATLHGG---KFPETFEEVAALPGVGRSTAGAILSLSLGK  132 (225)
T ss_dssp             HHHHHHHSTT---SCCCSHHHHHTSTTCCHHHHHHHHHHHHCC
T ss_pred             HHHHHHHhCC---CchHHHHHHhcCCCCcHHHHHHHHHHhCCC
Confidence            3344445543   12346899999999999999998765 443

>2h56_A DNA-3-methyladenine glycosidase; 10174367, EC 3.2.2.-, struc genomics, PSI-2, protein structure initiative, joint center structural genomics; 2.55A {Bacillus halodurans}

Probab=83.68  E-value=1.4  Score=40.24  Aligned_cols=48  Identities=19%  Similarity=0.241  Sum_probs=34.6

Q ss_pred             CCCHHHHHHH-------HHhcCCHHHHHcCC----HHhhhcCCCCCHHHHHHHHHH-hcc
Q 017612          225 SVNKTDVVTL-------GSTFGSLSHIMDAS----MEDLARCPGIGERKVKRLYDT-FHE  272 (368)
Q Consensus       225 gVnKTDA~~L-------Ls~FGSLk~I~~AS----~EELa~VPGIG~kKA~rI~e~-F~e  272 (368)
                      |++...|+.|       ++.+.+++.+...+    .++|..+||||++.|..|.-+ |+.
T Consensus       102 G~~~~KA~~I~~~A~~i~~~~~~~~~l~~~p~~~~~~~L~~lpGIG~kTA~~ill~alg~  161 (233)
T 2h56_A          102 GVSKRKIEYIRHVCEHVESGRLDFTELEGAEATTVIEKLTAIKGIGQWTAEMFMMFSLGR  161 (233)
T ss_dssp             TCCHHHHHHHHHHHHHHHTTSSCHHHHTTSCHHHHHHHHHTSTTCCHHHHHHHHHHTTCC
T ss_pred             CCCHHHHHHHHHHHHHHHhCCCCHHHHhcCCHHHHHHHHHhCCCcCHHHHHHHHHHhCCC
Confidence            6776555444       34446788786555    568999999999999999875 443

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=83.59  E-value=0.22  Score=46.45  Aligned_cols=54  Identities=19%  Similarity=0.295  Sum_probs=0.0

Q ss_pred             hhccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          219 ALTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      -|..++||+..++.+|-+ .|.|+++|..++..+|..+.||.+.+|.+|.+....
T Consensus        13 ~~~~l~g~~~~~~~~l~~~g~~t~~~~~~~~~~~l~~~~g~s~~~~~~~~~~~~~   67 (324)
T 2z43_A           13 TINDLPGISQTVINKLIEAGYSSLETLAVASPQDLSVAAGIPLSTAQKIIKEARD   67 (324)
T ss_dssp             -------------------------------------------------------
T ss_pred             cHHHcCCCCHHHHHHHHHcCCCcHHHHHcCCHHHHHHhhCCCHHHHHHHHHHHHh
Confidence            456677999999999976 699999999999999999999999999999877654

>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 PDB: 2aq0_A*

Probab=83.41  E-value=0.74  Score=36.54  Aligned_cols=24  Identities=17%  Similarity=0.432  Sum_probs=21.3

Q ss_pred             HHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          249 MEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       249 ~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      .+.|..|||||++.+++|.+.|..
T Consensus        17 ~s~L~~IpGIG~kr~~~LL~~FgS   40 (84)
T 1z00_B           17 QDFLLKMPGVNAKNCRSLMHHVKN   40 (84)
T ss_dssp             HHHHHTCSSCCHHHHHHHHHHSSC
T ss_pred             HHHHHhCCCCCHHHHHHHHHHcCC
Confidence            457999999999999999999954

>4b21_A Probable DNA-3-methyladenine glycosylase 2; hydrolase-DNA complex, helix-hairpin-helix; HET: BGC 3DR; 1.45A {Schizosaccharomyces pombe} PDB: 4b22_A* 4b23_A* 4b24_A*

Probab=83.19  E-value=1.8  Score=39.69  Aligned_cols=60  Identities=15%  Similarity=0.285  Sum_probs=44.1

Q ss_pred             ccHHHHHHHhhccCCCCCHHH----HHHHHHhcC------CHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          210 TDYLSRLTHALTSVRSVNKTD----VVTLGSTFG------SLSHIMDASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       210 ~dy~srL~saLTsIpgVnKTD----A~~LLs~FG------SLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      .++.+.++.++- -..++-..    ..+|...||      +.+.|..++.++|..| |+|..||+.|+++..
T Consensus        58 ~dpfe~Lv~~Il-~Qq~s~~~a~~~~~rL~~~~G~~~~fPtpe~la~~~~e~Lr~~-Gl~~~Ka~~l~~~A~  127 (232)
T 4b21_A           58 HAPYEGIIRAIT-SQKLSDAATNSIINKFCTQCSDNDEFPTPKQIMETDVETLHEC-GFSKLKSQEIHIVAE  127 (232)
T ss_dssp             SCHHHHHHHHHH-TTTCCHHHHHHHHHHHHHHHCSSSSCCCHHHHHTSCHHHHHTT-TCCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHH-hCcCcHHHHHHHHHHHHHHhCCCCCCCCHHHHHcCCHHHHHHc-CCcHHHHHHHHHHHH
Confidence            366666666552 23444433    456677755      8999999999999876 999999999988764

>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus amylolyticus}

Probab=83.19  E-value=0.28  Score=47.94  Aligned_cols=48  Identities=13%  Similarity=0.294  Sum_probs=33.7

Q ss_pred             hc-cCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccc
Q 017612          220 LT-SVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEP  273 (368)
Q Consensus       220 LT-sIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~eP  273 (368)
                      +. +|||||.+.|..|+++|||+++|+..-..  ..++ +   -.+.++++|-.|
T Consensus       252 ~p~GVpGIG~KtA~kLl~~~gsle~il~~~~~--~~~~-~---~~~~~~~~f~~p  300 (363)
T 3ory_A          252 NPDGFEGIGPKKALQLVKAYGGIEKIPKPILK--SPIE-V---DVIAIKKYFLQP  300 (363)
T ss_dssp             BTTCSTTCCHHHHHHHHHHHTSSTTSCGGGCC--CSSC-C---CHHHHHHHHHSC
T ss_pred             CCCCCCCcCHHHHHHHHHHcCCHHHHHHhccc--ccCC-C---CHHHHHHHhcCC
Confidence            35 99999999999999999999999864211  1222 2   235666776433

>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5

Probab=82.86  E-value=0.71  Score=35.72  Aligned_cols=28  Identities=18%  Similarity=0.265  Sum_probs=23.1

Q ss_pred             HcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          245 MDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       245 ~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      ..+....|..|||||++.|++|.+.|..
T Consensus        14 ~~~~~~~L~~IpgIG~~~A~~Ll~~fgs   41 (89)
T 1z00_A           14 VSRVTECLTTVKSVNKTDSQTLLTTFGS   41 (89)
T ss_dssp             HHHHHHHHTTSSSCCHHHHHHHHHHTCB
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHCCC
Confidence            3444577999999999999999999853

---

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	368
d2a1ia1	129	c.52.1.20 (A:99-227) DNA excision repair protein E	3e-21
d2a1ia1	129	c.52.1.20 (A:99-227) DNA excision repair protein E	1e-08
d2a1jb1	78	a.60.2.5 (B:219-296) DNA excision repair protein E	1e-18
d2bgwa1	70	a.60.2.5 (A:160-229) DNA repair endonuclease XPF {	7e-11
d2a1ja1	62	a.60.2.5 (A:837-898) DNA repair endonuclease XPF {	5e-10
d1x2ia1	68	a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF201	5e-09
d1kfta_	56	a.60.2.3 (A:) Excinuclease UvrC C-terminal domain	5e-07
d2i1qa1	60	a.60.4.1 (A:5-64) DNA repair protein Rad51, N-term	4e-06
d1pzna1	61	a.60.4.1 (A:35-95) DNA repair protein Rad51, N-ter	6e-06
d1wuda1	77	a.60.8.1 (A:530-606) HRDC domain from RecQ helicas	0.003

>d2a1ia1 c.52.1.20 (A:99-227) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]} Length = 129

class: Alpha and beta proteins (a/b)
fold: Restriction endonuclease-like
superfamily: Restriction endonuclease-like
family: XPF/Rad1/Mus81 nuclease
domain: DNA excision repair protein ERCC-1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 85.9 bits (213), Expect = 3e-21
 Identities = 28/45 (62%), Positives = 40/45 (88%)

Query: 139 NAILVSQRQKGNPLLKYIRNVRWAFADVVCDYLVGQNSCALYLSL 183
           N+I+VS RQ+GNP+LK++RNV W F DV+ DY++GQ++CAL+LSL
Sbjct: 1   NSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSL 45

>d2a1ia1 c.52.1.20 (A:99-227) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]} Length = 129

class: Alpha and beta proteins (a/b)
fold: Restriction endonuclease-like
superfamily: Restriction endonuclease-like
family: XPF/Rad1/Mus81 nuclease
domain: DNA excision repair protein ERCC-1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.4 bits (121), Expect = 1e-08
 Identities = 20/36 (55%), Positives = 23/36 (63%), Gaps = 2/36 (5%)

Query: 175 NSCALYL--SLEECGRYLETIKVYENKPADLIQGQM 208
             C L L  S EE GRYLET K YE KPADL+  ++
Sbjct: 94  ADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKL 129

>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]} Length = 78

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA excision repair protein ERCC-1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 77.3 bits (190), Expect = 1e-18
 Identities = 43/78 (55%), Positives = 60/78 (76%)

Query: 200 PADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIG 259
           PADL+  +++ D++SR+T  LT+V+SVNKTD  TL +TFGSL  ++ AS EDLA CPG+G
Sbjct: 1   PADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLG 60

Query: 260 ERKVKRLYDTFHEPFKRV 277
            +K +RL+D  HEPF +V
Sbjct: 61  PQKARRLFDVLHEPFLKV 78

>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]} Length = 70

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA repair endonuclease XPF
species: Aeropyrum pernix [TaxId: 56636]

 Score = 55.6 bits (134), Expect = 7e-11
 Identities = 14/57 (24%), Positives = 26/57 (45%)

Query: 219 ALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFK 275
            L S   + +     +   FGSL     AS  ++++  GIGE++ + +      P+K
Sbjct: 14  ILQSFPGIGRRTAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIKKILMTPYK 70

>d2a1ja1 a.60.2.5 (A:837-898) DNA repair endonuclease XPF {Human (Homo sapiens) [TaxId: 9606]} Length = 62

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA repair endonuclease XPF
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.5 bits (126), Expect = 5e-10
 Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 1/59 (1%)

Query: 220 LTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKRVV 278
           L  +  VN  +  +L     +++ +   S ++L    G      K+LYD  H  F  VV
Sbjct: 5   LLKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSILG-NAANAKQLYDFIHTSFAEVV 62

>d1x2ia1 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 68

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

 Score = 49.8 bits (119), Expect = 5e-09
 Identities = 16/61 (26%), Positives = 27/61 (44%)

Query: 215 RLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPF 274
           R    +  +  V+ T    L   FGS+  +  AS+ +L +  GIGE+  K +      P+
Sbjct: 7   RQRLIVEGLPHVSATLARRLLKHFGSVERVFTASVAELMKVEGIGEKIAKEIRRVITAPY 66

Query: 275 K 275
            
Sbjct: 67  I 67

>d1kfta_ a.60.2.3 (A:) Excinuclease UvrC C-terminal domain {Escherichia coli [TaxId: 562]} Length = 56

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Excinuclease UvrC C-terminal domain
domain: Excinuclease UvrC C-terminal domain
species: Escherichia coli [TaxId: 562]

 Score = 43.9 bits (104), Expect = 5e-07
 Identities = 13/55 (23%), Positives = 28/55 (50%)

Query: 217 THALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271
           T +L ++  V       L    G L  + +AS+E++A+ PGI +   ++++ +  
Sbjct: 1   TSSLETIEGVGPKRRQMLLKYMGGLQGLRNASVEEIAKVPGISQGLAEKIFWSLK 55

>d2i1qa1 a.60.4.1 (A:5-64) DNA repair protein Rad51, N-terminal domain {Archaeon Methanococcus voltae [TaxId: 2188]} Length = 60

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

 Score = 41.6 bits (98), Expect = 4e-06
 Identities = 10/54 (18%), Positives = 21/54 (38%), Gaps = 1/54 (1%)

Query: 220 LTSVRSVNKTDVVTL-GSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272
           LT +  V  +    L  + +     I  A++ +L    GI E+   ++     +
Sbjct: 1   LTDLPGVGPSTAEKLVEAGYIDFMKIATATVGELTDIEGISEKAAAKMIMGARD 54

>d1pzna1 a.60.4.1 (A:35-95) DNA repair protein Rad51, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 61

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

 Score = 41.2 bits (97), Expect = 6e-06
 Identities = 8/35 (22%), Positives = 14/35 (40%)

Query: 238 FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272
           + +L  I  AS  +L    GI E    ++     +
Sbjct: 22  YDTLEAIAVASPIELKEVAGISEGTALKIIQAARK 56

>d1wuda1 a.60.8.1 (A:530-606) HRDC domain from RecQ helicase {Escherichia coli [TaxId: 562]} Length = 77

class: All alpha proteins
fold: SAM domain-like
superfamily: HRDC-like
family: HRDC domain from helicases
domain: HRDC domain from RecQ helicase
species: Escherichia coli [TaxId: 562]

 Score = 34.0 bits (78), Expect = 0.003
 Identities = 11/46 (23%), Positives = 24/46 (52%), Gaps = 4/46 (8%)

Query: 236 STFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKRVVSSH 281
           +T   ++  M  +  ++    G+G RK++R    F +PF  ++ +H
Sbjct: 32  ATLIEMAEQMPITASEMLSVNGVGMRKLER----FGKPFMALIRAH 73

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	368
d2a1ia1	129	DNA excision repair protein ERCC-1 {Human (Homo sa	99.92
d2a1jb1	78	DNA excision repair protein ERCC-1 {Human (Homo sa	99.81
d2bgwa1	70	DNA repair endonuclease XPF {Aeropyrum pernix [Tax	99.64
d1x2ia1	68	ATP-dependent RNA helicase PF2015 {Pyrococcus furi	99.63
d1kfta_	56	Excinuclease UvrC C-terminal domain {Escherichia c	99.54
d2a1ja1	62	DNA repair endonuclease XPF {Human (Homo sapiens)	99.53
d1dgsa1	181	NAD+-dependent DNA ligase, domain 3 {Thermus filif	99.2
d2i1qa1	60	DNA repair protein Rad51, N-terminal domain {Archa	99.18
d1pzna1	61	DNA repair protein Rad51, N-terminal domain {Archa	99.02
d1szpa1	64	DNA repair protein Rad51, N-terminal domain {Baker	98.22
d1cuka2	78	DNA helicase RuvA subunit, middle domain {Escheric	98.14
d1ixra1	73	DNA helicase RuvA subunit, middle domain {Thermus	98.11
d1bvsa2	71	DNA helicase RuvA subunit, middle domain {Mycobact	98.06
d1b22a_	70	DNA repair protein Rad51, N-terminal domain {Human	97.72
d2axtu1	98	Photosystem II 12 kDa extrinsic protein PsbU {Ther	96.79
d2csba3	55	Topoisomerase V {Methanopyrus kandleri [TaxId: 232	96.42
d2duya1	65	Uncharacterized protein TTHA1967 {Thermus thermoph	96.39
d2axtu1	98	Photosystem II 12 kDa extrinsic protein PsbU {Ther	95.43
d2edua1	91	KIF22, C-terminal domain {Human (Homo sapiens) [Ta	95.4
d1ul1x1	140	Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo	95.03
d3bzka1	90	Transcriptional accessory factor Tex {Pseudomonas	94.97
d1rxwa1	105	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Arc	94.93
d2csba4	55	Topoisomerase V {Methanopyrus kandleri [TaxId: 232	94.92
d1xo1a1	105	T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]	94.74
d2p6ra2	198	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	94.57
d2duya1	65	Uncharacterized protein TTHA1967 {Thermus thermoph	93.85
d1a77a1	108	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Met	93.61
d3bzka1	90	Transcriptional accessory factor Tex {Pseudomonas	93.27
d1doqa_	69	C-terminal domain of RNA polymerase alpha subunit	92.74
d2edua1	91	KIF22, C-terminal domain {Human (Homo sapiens) [Ta	92.51
d1u9la_	68	Transcription elongation protein NusA {Escherichia	91.55
d1dgsa1	181	NAD+-dependent DNA ligase, domain 3 {Thermus filif	91.17
d2abka_	211	Endonuclease III {Escherichia coli [TaxId: 562]}	91.05
d1keaa_	217	Thymine-DNA glycosylase {Archaeon Methanobacterium	90.32
d1lb2b_	72	C-terminal domain of RNA polymerase alpha subunit	90.22
d2i1qa1	60	DNA repair protein Rad51, N-terminal domain {Archa	89.88
d1kfta_	56	Excinuclease UvrC C-terminal domain {Escherichia c	89.55
d1cmwa1	116	5' to 3' exonuclease domain of DNA polymerase Taq	89.11
d1z3eb1	67	C-terminal domain of RNA polymerase alpha subunit	88.83
d2bcqa1	76	DNA polymerase lambda {Human (Homo sapiens) [TaxId	88.45
d2bgwa1	70	DNA repair endonuclease XPF {Aeropyrum pernix [Tax	87.93
d1orna_	214	Endonuclease III {Escherichia coli [TaxId: 562]}	87.49
d2a1ja1	62	DNA repair endonuclease XPF {Human (Homo sapiens)	86.73
d1pzna1	61	DNA repair protein Rad51, N-terminal domain {Archa	86.34
d1kg2a_	224	Catalytic domain of MutY {Escherichia coli [TaxId:	86.17
d1b43a1	120	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyr	86.12
d2fmpa1	82	DNA polymerase beta, N-terminal (8 kD)-domain {Hum	86.02
d1ngna_	144	Mismatch-specific thymine glycosylase domain of th	85.57
d1jmsa3	60	Terminal deoxynucleotidyl transferase {Mouse (Mus	85.52
d1pu6a_	217	3-Methyladenine DNA glycosylase III (MagIII) {Heli	84.99
d1rrqa1	221	Catalytic domain of MutY {Bacillus stearothermophi	83.98
d1keaa_	217	Thymine-DNA glycosylase {Archaeon Methanobacterium	83.9
d2fmpa2	57	DNA polymerase beta {Human (Homo sapiens) [TaxId:	83.72
d1jmsa3	60	Terminal deoxynucleotidyl transferase {Mouse (Mus	83.15
d1xo1a1	105	T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]	83.05
d1fx0b1	108	F1 ATP synthase beta subunit, domain 3 {Spinach (S	82.6
d1x2ia1	68	ATP-dependent RNA helicase PF2015 {Pyrococcus furi	82.34
d1jmsa1	95	Terminal deoxynucleotidyl transferase {Mouse (Mus	82.3
d2bcqa2	57	DNA polymerase lambda {Human (Homo sapiens) [TaxId	81.21

>d2a1ia1 c.52.1.20 (A:99-227) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Restriction endonuclease-like
superfamily: Restriction endonuclease-like
family: XPF/Rad1/Mus81 nuclease
domain: DNA excision repair protein ERCC-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.92  E-value=3.3e-26  Score=195.57  Aligned_cols=69  Identities=62%  Similarity=1.129  Sum_probs=67.2

Q ss_pred             CeEEEcCCccCChhHHhhhccceEeeecccceEeccceeeeeec------------------------------------
Q 017612          139 NAILVSQRQKGNPLLKYIRNVRWAFADVVCDYLVGQNSCALYLS------------------------------------  182 (368)
Q Consensus       139 ~~IlVS~rQrGNPLLk~IrnVpwefaDIvpDY~Ig~ttcILFLS------------------------------------  182 (368)
                      ++|+||+||||||||++||+|||+|+||+|||++|+++||||||                                    
T Consensus         1 ~~ilVs~rQkgNplL~~i~~v~we~~di~~Dyvvg~~~~vLFLSLkYH~L~peYI~~Ri~~L~~~y~lrVLL~~VDv~d~   80 (129)
T d2a1ia1           1 NSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDP   80 (129)
T ss_dssp             CCEEECGGGTTCGGGGGCCSSCEEECCCSSSEEEETTEEEEEEEHHHHHHSTTHHHHHHHHHTTSSSEEEEEEECCSSSC
T ss_pred             CcEEEcchhcCCcHHHHHhcCCeeecCcCCCeEecCccEEEEEehhhhccChHHHHHHHHHhccCcceEEEEEEEeCCCh
Confidence            57999999999999999999999999999999999999999999                                    


Q ss_pred             -----------------------hhhHHHHHHHHHHhhcCCcchhccc
Q 017612          183 -----------------------LEECGRYLETIKVYENKPADLIQGQ  207 (368)
Q Consensus       183 -----------------------~EEAArYIEt~K~~E~K~~d~Irek  207 (368)
                                             +||||+|||+||.||+++++.|+++
T Consensus        81 ~~~L~eL~~~c~~~~~TLilaws~eEaa~YlE~~k~~e~~~~d~i~~~  128 (129)
T d2a1ia1          81 QQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEK  128 (129)
T ss_dssp             HHHHHHHHHHHHHHTCEEEEESSHHHHHHHHHHHHTCCSSCCCHHHHH
T ss_pred             HHHHHHHHHHHHHcCCEEEEEcCHHHHHHHHHHHHHhcCCCHHHHHhc
Confidence                                   9999999999999999999999876

>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA excision repair protein ERCC-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=1.2e-20  Score=146.46  Aligned_cols=77  Identities=55%  Similarity=0.938  Sum_probs=74.5

Q ss_pred             CcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcccccc
Q 017612          200 PADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKR  276 (368)
Q Consensus       200 ~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~~  276 (368)
                      |++.|+++...++.++++++|++|||||+++|++|+++|||+++|++|+.+||..|+|||+++|++|+++|++||.+
T Consensus         1 p~daike~~~~~~~~~~~~~L~~I~gIg~~~a~~L~~~F~s~~~i~~A~~eeL~~i~GiG~~~A~~i~~~f~~pf~~   77 (78)
T d2a1jb1           1 PADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLK   77 (78)
T ss_dssp             CSHHHHHHHHHHHHHHHHHHHTTSTTCCHHHHHHHHHHHSSHHHHHSCCHHHHHTSSSCCSHHHHHHHHHHHSCSCC
T ss_pred             CchHHHHHHcCCcHHHHHHHhcCCCCcCHHHHHHHHHHhCCcHHHHhhhHHHHHHhhhhhHHHHHHHHHHHcCcccc
Confidence            57889998889999999999999999999999999999999999999999999999999999999999999999986

>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA repair endonuclease XPF
species: Aeropyrum pernix [TaxId: 56636]

Probab=99.64  E-value=1.5e-16  Score=120.57  Aligned_cols=65  Identities=23%  Similarity=0.424  Sum_probs=61.0

Q ss_pred             cHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612          211 DYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFK  275 (368)
Q Consensus       211 dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~  275 (368)
                      +.......+|++|||||+++|++|++||||+++|++||.+||..|+|||+++|+.|+++|+.||+
T Consensus         6 ~~~~~~~~~L~~IpgIG~~~a~~L~~~F~s~~~l~~As~eeL~~v~GIG~~~A~~I~~~~~~~~k   70 (70)
T d2bgwa1           6 DVREWQLYILQSFPGIGRRTAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIKKILMTPYK   70 (70)
T ss_dssp             HHHHHHHHHHHTSTTCCHHHHHHHHHHHSSHHHHTTCCHHHHHHSTTCCHHHHHHHHHHHHSCCC
T ss_pred             CHHHHHHHHHcCCCCcCHHHHHHHHHHhCCHHHHHHcCHHHHHcCCCCCHHHHHHHHHHHhCccC
Confidence            44566678899999999999999999999999999999999999999999999999999999995

>d1x2ia1 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=99.63  E-value=3e-16  Score=118.81  Aligned_cols=65  Identities=25%  Similarity=0.395  Sum_probs=61.2

Q ss_pred             HHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcccccc
Q 017612          212 YLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKR  276 (368)
Q Consensus       212 y~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~~  276 (368)
                      ..++...+|++|||||+..|++|+++|||+++|++|+.+||..|+|||+++|+.|+++|+.+|..
T Consensus         4 ~~~~~~~~L~~I~gIG~~~a~~L~~~f~s~~~i~~As~eeL~~i~GIG~~~A~~I~~~~~~~~~~   68 (68)
T d1x2ia1           4 LAERQRLIVEGLPHVSATLARRLLKHFGSVERVFTASVAELMKVEGIGEKIAKEIRRVITAPYIE   68 (68)
T ss_dssp             HHHHHHHHHTTSTTCCHHHHHHHHHHHCSHHHHHHCCHHHHTTSTTCCHHHHHHHHHHHHSCCCC
T ss_pred             HHHHHHHHHcCCCCcCHHHHHHHHHHcCCHHHHHHhHHHHHHhCCCcCHHHHHHHHHHHhchhcC
Confidence            35667789999999999999999999999999999999999999999999999999999999963

>d1kfta_ a.60.2.3 (A:) Excinuclease UvrC C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Excinuclease UvrC C-terminal domain
domain: Excinuclease UvrC C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=99.54  E-value=1.4e-15  Score=111.79  Aligned_cols=54  Identities=22%  Similarity=0.433  Sum_probs=52.6

Q ss_pred             HhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          218 HALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       218 saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      +.|+.|||||++.++.|+++|||+++|++|+.+||..|+|||+++|+.|+++||
T Consensus         2 S~L~~I~gVG~~~a~~L~~~F~s~~~i~~As~eeL~~v~GIg~~~A~~I~~~l~   55 (56)
T d1kfta_           2 SSLETIEGVGPKRRQMLLKYMGGLQGLRNASVEEIAKVPGISQGLAEKIFWSLK   55 (56)
T ss_dssp             CGGGGCTTCSSSHHHHHHHHHSCHHHHHHCCHHHHTTSSSTTSHHHHHHHHHHT
T ss_pred             CCcccCCCccHHHHHHHHHHhCCHHHHHHhhHHHHHhcCCCCHHHHHHHHHHHc
Confidence            578999999999999999999999999999999999999999999999999997

>d2a1ja1 a.60.2.5 (A:837-898) DNA repair endonuclease XPF {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA repair endonuclease XPF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=3.3e-15  Score=111.08  Aligned_cols=58  Identities=22%  Similarity=0.367  Sum_probs=55.7

Q ss_pred             HhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcccccc
Q 017612          218 HALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKR  276 (368)
Q Consensus       218 saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~~  276 (368)
                      +.|.+|||||++++++|+++|||+++|++||.+||..|+| |++.|++|+++||.+|..
T Consensus         3 d~L~~iPGIg~~~~~~Ll~~f~Si~~l~~As~~eL~~v~G-~~~~A~~i~~f~~~~~~~   60 (62)
T d2a1ja1           3 DFLLKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSILG-NAANAKQLYDFIHTSFAE   60 (62)
T ss_dssp             HHHHTSTTCCHHHHHHHHHHCSSHHHHHTCCHHHHHHHHS-CHHHHHHHHHHHHCCCCC
T ss_pred             hHHhcCCCCCHHHHHHHHHHhccHHHHHhCCHHHHHHCcC-cHHHHHHHHHHHhhhhcc
Confidence            4688999999999999999999999999999999999999 999999999999999975

>d1dgsa1 a.60.2.2 (A:401-581) NAD+-dependent DNA ligase, domain 3 {Thermus filiformis [TaxId: 276]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: NAD+-dependent DNA ligase, domain 3
domain: NAD+-dependent DNA ligase, domain 3
species: Thermus filiformis [TaxId: 276]

Probab=99.20  E-value=4.9e-12  Score=111.03  Aligned_cols=81  Identities=25%  Similarity=0.405  Sum_probs=67.5

Q ss_pred             HHHhhcCCcch----hcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHH
Q 017612          193 IKVYENKPADL----IQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYD  268 (368)
Q Consensus       193 ~K~~E~K~~d~----Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e  268 (368)
                      +..+..+....    |.... .....+++.+| +||+||++.|+.|+++|||+++|++|+.+||..|+|||++.|+.|++
T Consensus        80 l~~~g~ksa~nl~~~Ie~sk-~~~l~r~l~aL-GI~~vG~~~Ak~La~~f~sl~~l~~as~eeL~~I~GIG~~~A~si~~  157 (181)
T d1dgsa1          80 LERMGEKSAQNLLRQIEESK-HRGLERLLYAL-GLPGVGEVLARNLARRFGTMDRLLEASLEELIEVEEVGELTARAILE  157 (181)
T ss_dssp             TSSCCSTTHHHHHHHHHHGG-GCCHHHHHHHT-TCSSCCHHHHHHHHHTTSBHHHHTTCCHHHHHTSTTCCHHHHHHHHH
T ss_pred             ccccchHHHHHHHHHHHhhc-chhHHHHHHHH-HhhhhhHHHHHHHHHHhhhhhhhhhhHHHHHhhcCCcCHHHHHHHHH
Confidence            34455555543    33333 33468999999 89999999999999999999999999999999999999999999999


Q ss_pred             Hhccccc
Q 017612          269 TFHEPFK  275 (368)
Q Consensus       269 ~F~ePF~  275 (368)
                      +|+.+.+
T Consensus       158 ff~~~~n  164 (181)
T d1dgsa1         158 TLKDPAF  164 (181)
T ss_dssp             HHHCHHH
T ss_pred             HHCCHHH
Confidence            9987753

>d2i1qa1 a.60.4.1 (A:5-64) DNA repair protein Rad51, N-terminal domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=99.18  E-value=1.6e-11  Score=90.81  Aligned_cols=53  Identities=19%  Similarity=0.296  Sum_probs=50.3

Q ss_pred             hccCCCCCHHHHHHHHHh-cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          220 LTSVRSVNKTDVVTLGST-FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       220 LTsIpgVnKTDA~~LLs~-FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      |+.|||||++.+++|+++ |+|+++|..|+.+||..|+|||+++|++|++.+++
T Consensus         1 L~~IpGIG~~~a~~L~~~G~~tv~~l~~a~~eeL~~i~Gi~~~~A~~i~~~ar~   54 (60)
T d2i1qa1           1 LTDLPGVGPSTAEKLVEAGYIDFMKIATATVGELTDIEGISEKAAAKMIMGARD   54 (60)
T ss_dssp             CTTSTTCCHHHHHHHHHHTCCSHHHHHTCCHHHHHTSTTCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHccCCCHHHHHhCCHHHHHHCCCCCHHHHHHHHHHHHH
Confidence            678999999999999998 99999999999999999999999999999888754

>d1pzna1 a.60.4.1 (A:35-95) DNA repair protein Rad51, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=99.02  E-value=7e-11  Score=87.31  Aligned_cols=54  Identities=19%  Similarity=0.275  Sum_probs=50.6

Q ss_pred             hhccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          219 ALTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      .|..|+|||+..|.+|++ +|+|+++|++|+.+||..|+|||+++|++|++.+++
T Consensus         2 ~L~~i~GIG~~~a~~L~~~g~~sv~~l~~a~~~eL~~i~Gi~~~~A~~i~~~ar~   56 (61)
T d1pzna1           2 SIEDLPGVGPATAEKLREAGYDTLEAIAVASPIELKEVAGISEGTALKIIQAARK   56 (61)
T ss_dssp             CSSCCTTCCHHHHHHHHTTTCCSHHHHHTCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_pred             ccccCCCCCHHHHHHHHHhcCCCHHHHHhCCHHHHHHCCCCCHHHHHHHHHHHHH
Confidence            478999999999999998 589999999999999999999999999999998764

>d1szpa1 a.60.4.1 (A:81-144) DNA repair protein Rad51, N-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.22  E-value=6e-07  Score=66.99  Aligned_cols=54  Identities=24%  Similarity=0.338  Sum_probs=49.0

Q ss_pred             HhhccCCCCCHHHHHHHHHh-cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          218 HALTSVRSVNKTDVVTLGST-FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       218 saLTsIpgVnKTDA~~LLs~-FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      +.| .++|||+.++..|-+. |.|+++|..++.+||..|+|||+++|++|.+..+.
T Consensus         4 ~~L-~~~Gig~~~~~kL~~aG~~Tve~ia~~t~~~L~~i~Gi~e~~a~KIi~~A~k   58 (64)
T d1szpa1           4 EKL-QVNGITMADVKKLRESGLHTAEAVAYAPRKDLLEIKGISEAKADKLLNEAAR   58 (64)
T ss_dssp             GGG-CCTTCCHHHHHHHHTTSCCSHHHHHHSCSHHHHTSTTCCHHHHHHHHHHHHH
T ss_pred             HHH-hHCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHcCCCCHHHHHHHHHHHHH
Confidence            345 4789999999999998 99999999999999999999999999999987653

>d1cuka2 a.60.2.1 (A:65-142) DNA helicase RuvA subunit, middle domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Escherichia coli [TaxId: 562]

Probab=98.14  E-value=2.2e-06  Score=66.44  Aligned_cols=61  Identities=20%  Similarity=0.361  Sum_probs=51.8

Q ss_pred             HHhhccCCCCCHHHHHHHHHhcCC---HHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccccccc
Q 017612          217 THALTSVRSVNKTDVVTLGSTFGS---LSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKRV  277 (368)
Q Consensus       217 ~saLTsIpgVnKTDA~~LLs~FGS---Lk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~~~  277 (368)
                      -..|.+|.|||++.|..+|+.|+-   ...|.+-+.+.|..+||||+++|++|.--|...+...
T Consensus         8 F~~Li~V~GIGpK~Al~iLs~~~~~~l~~aI~~~D~~~L~~vpGIG~KtA~rIi~eLk~K~~~~   71 (78)
T d1cuka2           8 FKELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKTAERLIVEMKDRFKGL   71 (78)
T ss_dssp             HHHHHHSSSCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHHTSTTCCHHHHHHHHHHHHHHGGGC
T ss_pred             HHHHHccCCccHHHHHHHHHhCCHHHHHHHHHccCHHHhhcCCCCCHHHHHHHHHHHHHHHHhh
Confidence            345668999999999999999975   5556677899999999999999999999888877654

>d1ixra1 a.60.2.1 (A:63-135) DNA helicase RuvA subunit, middle domain {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=98.11  E-value=3.2e-06  Score=64.83  Aligned_cols=58  Identities=19%  Similarity=0.248  Sum_probs=49.1

Q ss_pred             HHhhccCCCCCHHHHHHHHHhcCC---HHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcccc
Q 017612          217 THALTSVRSVNKTDVVTLGSTFGS---LSHIMDASMEDLARCPGIGERKVKRLYDTFHEPF  274 (368)
Q Consensus       217 ~saLTsIpgVnKTDA~~LLs~FGS---Lk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF  274 (368)
                      -..|-+|.|||++.|..+|+.|.-   ++.|.+.+.+.|..+||||++.|++|.--|....
T Consensus         9 F~~Li~V~GIGpk~Al~iLs~~~~~~l~~aI~~~D~~~L~~vpGIG~KtA~rIi~eLk~K~   69 (73)
T d1ixra1           9 FELLLSVSGVGPKVALALLSALPPRLLARALLEGDARLLTSASGVGRRLAERIALELKGKV   69 (73)
T ss_dssp             HHHHHSSSCCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHTTSTTCCHHHHHHHHHHHTTTS
T ss_pred             HHHHhccCCcCHHHHHHHHHHccHHHHHHHHHhcCHHHhhcCCCCCHHHHHHHHHHHHhcc
Confidence            345558999999999999999886   5566677999999999999999999998876543

>d1bvsa2 a.60.2.1 (A:64-134) DNA helicase RuvA subunit, middle domain {Mycobacterium leprae [TaxId: 1769]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Mycobacterium leprae [TaxId: 1769]

Probab=98.06  E-value=2.6e-06  Score=64.97  Aligned_cols=56  Identities=25%  Similarity=0.344  Sum_probs=46.2

Q ss_pred             HHhhccCCCCCHHHHHHHHHhcCCHHHHH----cCCHHhhhcCCCCCHHHHHHHHHHhccc
Q 017612          217 THALTSVRSVNKTDVVTLGSTFGSLSHIM----DASMEDLARCPGIGERKVKRLYDTFHEP  273 (368)
Q Consensus       217 ~saLTsIpgVnKTDA~~LLs~FGSLk~I~----~AS~EELa~VPGIG~kKA~rI~e~F~eP  273 (368)
                      -..|.+|.|||++.|..+|+.| ++++|+    +-+.+.|..+||||++.|++|.--|...
T Consensus         8 F~~Li~V~GIGpK~Al~iLs~~-~~~~l~~aI~~~D~~~L~~vpGIG~KtA~rIi~eLk~K   67 (71)
T d1bvsa2           8 FLALLSVSGVGPRLAMATLAVH-DAAALRQALADSDVASLTRVPGIGRRGAERIVLELADK   67 (71)
T ss_dssp             HHHHHTSSSCCHHHHHHHHHHS-CHHHHHHHTTTTCHHHHHTSTTCCHHHHHHHHHHSSGG
T ss_pred             HHHHhccCCcCHHHHHHHHHhC-CHHHHHHHHHcCCHHHhhcCCCCCHHHHHHHHHHHHHh
Confidence            3456689999999999999998 455544    5578899999999999999998776543

>d1b22a_ a.60.4.1 (A:) DNA repair protein Rad51, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.72  E-value=3.7e-06  Score=63.66  Aligned_cols=54  Identities=22%  Similarity=0.311  Sum_probs=48.6

Q ss_pred             HHhhccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          217 THALTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       217 ~saLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      ++.| .++|||+.++..|-+ -|.|++.|+.|+.++|..|+|||+++|++|.+..+
T Consensus        10 i~~L-~~~Gig~~~i~kL~~aG~~Tv~~i~~at~~~L~~i~G~~e~~A~KIi~~a~   64 (70)
T d1b22a_          10 ISRL-EQCGINANDVKKLEEAGFHTVEAVAYAPKKELINIKGISEAKADKILAEAA   64 (70)
T ss_dssp             HHHH-HHTTCSHHHHHHHHTTCCSSGGGBTSSBHHHHHTTTTCSTTHHHHHHHHHH
T ss_pred             HHHH-hhCCCCHHHHHHHHHcCcchHHHHHhCCHHHHHHcCCCCHHHHHHHHHHHH
Confidence            4455 458999999999998 49999999999999999999999999999998775

>d2axtu1 a.60.12.2 (U:37-134) Photosystem II 12 kDa extrinsic protein PsbU {Thermosynechococcus elongatus [TaxId: 146786]}

class: All alpha proteins
fold: SAM domain-like
superfamily: PsbU/PolX domain-like
family: PsbU-like
domain: Photosystem II 12 kDa extrinsic protein PsbU
species: Thermosynechococcus elongatus [TaxId: 146786]

Probab=96.79  E-value=0.00056  Score=54.70  Aligned_cols=52  Identities=23%  Similarity=0.333  Sum_probs=43.5

Q ss_pred             HHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612          217 THALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFK  275 (368)
Q Consensus       217 ~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~  275 (368)
                      ...|..|||||++.|.+++++ |-+     .+.+||..|+|||+++.++|++++. .|.
T Consensus        26 ~~eL~~lpGIg~~~A~~Iv~~-gpf-----~s~edL~~V~GIg~~~~e~lk~yl~-~f~   77 (98)
T d2axtu1          26 IAAFIQYRGLYPTLAKLIVKN-APY-----ESVEDVLNIPGLTERQKQILRENLE-HFT   77 (98)
T ss_dssp             GGGGTTSTTCTHHHHHHHHHS-CCC-----SSGGGGGGCTTCCTTHHHHHHHHGG-GEE
T ss_pred             HHHHHHhhhhcHHHHHHHHHc-CCc-----CCHHHHhhCCCCCHHHHHHHHHHHh-cce
Confidence            456789999999999999974 543     3568999999999999999999886 443

>d2csba3 a.60.2.4 (A:410-464) Topoisomerase V {Methanopyrus kandleri [TaxId: 2320]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Topoisomerase V repeat domain
domain: Topoisomerase V
species: Methanopyrus kandleri [TaxId: 2320]

Probab=96.42  E-value=0.0028  Score=45.07  Aligned_cols=48  Identities=29%  Similarity=0.476  Sum_probs=41.3

Q ss_pred             hhccCCCCCHHHHHHHHHhcCCHHHHHcC----CHHhhhcCCCCCHHHHHHH
Q 017612          219 ALTSVRSVNKTDVVTLGSTFGSLSHIMDA----SMEDLARCPGIGERKVKRL  266 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs~FGSLk~I~~A----S~EELa~VPGIG~kKA~rI  266 (368)
                      .||.-.|||++.|.+||..||..+.+...    ..|.|+.|.|+|+...+.+
T Consensus         3 eltkkegvgrktaerllrafgnpervkqlarefeieklasvegvgervlrsl   54 (55)
T d2csba3           3 ELTKKEGVGRKTAERLLRAFGNPERVKQLAREFEIEKLASVEGVGERVLRSL   54 (55)
T ss_dssp             HHHTSTTCCHHHHHHHHHHHSSHHHHHHHHHTTCHHHHHTSTTCSHHHHHHH
T ss_pred             hhhhhccccHhHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcchHHHHHHhc
Confidence            46778899999999999999999988754    5789999999999876654

>d2duya1 a.60.2.7 (A:11-75) Uncharacterized protein TTHA1967 {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: ComEA-like
domain: Uncharacterized protein TTHA1967
species: Thermus thermophilus [TaxId: 274]

Probab=96.39  E-value=0.0017  Score=47.57  Aligned_cols=49  Identities=20%  Similarity=0.274  Sum_probs=40.5

Q ss_pred             HHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          217 THALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       217 ~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      ...|..+||||...|.++++. +-     =.|.+||..|+|||+++.++|..+++
T Consensus        16 ~~eL~~lpgig~~~A~~Iv~~-R~-----f~s~edL~~v~gi~~~~~~~i~~~lr   64 (65)
T d2duya1          16 LEELMALPGIGPVLARRIVEG-RP-----YARVEDLLKVKGIGPATLERLRPYLR   64 (65)
T ss_dssp             HHHHTTSTTCCHHHHHHHHHT-CC-----CSSGGGGGGSTTCCHHHHHHHGGGEE
T ss_pred             HHHHHHCCCCCHHHHHHHHHc-CC-----CCCHHHHHhCCCCCHHHHHHHHHHcC
Confidence            345678999999999999974 43     24679999999999999999987764

>d2axtu1 a.60.12.2 (U:37-134) Photosystem II 12 kDa extrinsic protein PsbU {Thermosynechococcus elongatus [TaxId: 146786]}

class: All alpha proteins
fold: SAM domain-like
superfamily: PsbU/PolX domain-like
family: PsbU-like
domain: Photosystem II 12 kDa extrinsic protein PsbU
species: Thermosynechococcus elongatus [TaxId: 146786]

Probab=95.43  E-value=0.00094  Score=53.35  Aligned_cols=42  Identities=14%  Similarity=0.396  Sum_probs=34.6

Q ss_pred             HHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcccccc
Q 017612          233 TLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKR  276 (368)
Q Consensus       233 ~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~~  276 (368)
                      +|...+|.-=+|=.|+.++|..+||||+.+|++|.+  +.||..
T Consensus        10 ~~~~~~g~kidlN~As~~eL~~lpGIg~~~A~~Iv~--~gpf~s   51 (98)
T d2axtu1          10 KLGTAYGEKIDLNNTNIAAFIQYRGLYPTLAKLIVK--NAPYES   51 (98)
T ss_dssp             HTTSSBTTBEESSSSCGGGGTTSTTCTHHHHHHHHH--SCCCSS
T ss_pred             HHhhhcCCceecccccHHHHHHhhhhcHHHHHHHHH--cCCcCC
Confidence            455566665677789999999999999999999996  678874

>d2edua1 a.60.2.7 (A:8-98) KIF22, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: ComEA-like
domain: KIF22, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.40  E-value=0.012  Score=45.74  Aligned_cols=48  Identities=21%  Similarity=0.385  Sum_probs=37.9

Q ss_pred             HHhhccCCCCCHHHHHHHHHh---cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHH
Q 017612          217 THALTSVRSVNKTDVVTLGST---FGSLSHIMDASMEDLARCPGIGERKVKRLYDT  269 (368)
Q Consensus       217 ~saLTsIpgVnKTDA~~LLs~---FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~  269 (368)
                      ..-|..+||||...|.+|+.+   .|.+.     +.+||..|+|||++++++|++.
T Consensus        32 ~~eL~~lpgig~~~A~~II~yR~~~G~f~-----sledL~~V~Gi~~k~~eki~k~   82 (91)
T d2edua1          32 ARDLRSLQRIGPKKAQLIVGWRELHGPFS-----QVEDLERVEGITGKQMESFLKA   82 (91)
T ss_dssp             HHHHHHSTTCCHHHHHHHHHHHHHHCCCS-----SGGGGGGSTTCCHHHHHHHHHH
T ss_pred             HHHHhhCCCCCHHHHHHHHHHHHHcCCCC-----CHHHHhcCCCCCHHHHHHHHHc
Confidence            346678999999999999964   23322     4579999999999999999875

>d1ul1x1 a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.03  E-value=0.0076  Score=48.69  Aligned_cols=29  Identities=21%  Similarity=0.252  Sum_probs=26.9

Q ss_pred             hccCCCCCHHHHHHHHHhcCCHHHHHcCC
Q 017612          220 LTSVRSVNKTDVVTLGSTFGSLSHIMDAS  248 (368)
Q Consensus       220 LTsIpgVnKTDA~~LLs~FGSLk~I~~AS  248 (368)
                      +.+|||||.+.|..||..||++++|+..-
T Consensus        18 ~pgv~gIG~ktA~kli~~~~~le~i~~~~   46 (140)
T d1ul1x1          18 CESIRGIGPKRAVDLIQKHKSIEEIVRRL   46 (140)
T ss_dssp             SCCCTTCCHHHHHHHHHHSSSHHHHHTTC
T ss_pred             CCCCCCccHHHHHHHHHHhCCHHHHHHHH
Confidence            56999999999999999999999999774

>d3bzka1 a.60.2.6 (A:474-563) Transcriptional accessory factor Tex {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Tex HhH-containing domain-like
domain: Transcriptional accessory factor Tex
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=94.97  E-value=0.0039  Score=48.27  Aligned_cols=50  Identities=14%  Similarity=0.285  Sum_probs=38.1

Q ss_pred             HHhhccCCCCCHHHHHHHHHh---cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          217 THALTSVRSVNKTDVVTLGST---FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       217 ~saLTsIpgVnKTDA~~LLs~---FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      .+.|..+||||+..|.+|+..   .|.+     -+.+||..|+|||+++.++|..+|+
T Consensus        34 ~~~L~~lpGig~~~A~~Iv~~R~~~G~f-----~s~edL~~v~gi~~k~~e~i~~~l~   86 (90)
T d3bzka1          34 AALLARISGLNSTLAQNIVAHRDANGAF-----RTRDELKKVSRLGEKTFEQAAGFLR   86 (90)
T ss_dssp             HHHHTTSTTCCHHHHHHHHHHHHHHCSC-----SSSGGGGGSTTCCHHHHHHHHTTEE
T ss_pred             HHHHhHCCCCCHHHHHHHHHHHHHcCCC-----CCHHHHhhCCCCCHHHHHHhcCCEe
Confidence            456778899999999988874   1222     3568899999999999998877664

>d1rxwa1 a.60.7.1 (A:220-324) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=94.93  E-value=0.0078  Score=47.17  Aligned_cols=44  Identities=18%  Similarity=0.253  Sum_probs=31.7

Q ss_pred             hccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612          220 LTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH  271 (368)
Q Consensus       220 LTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~  271 (368)
                      ..+|||||.+.|..|+++|||+++|+..    +...    ....+.+++.|.
T Consensus        18 ~pGV~GIG~ktA~kli~~~gsle~i~~~----~~~~----~~~~~~~r~l~~   61 (105)
T d1rxwa1          18 NEGVKGVGVKKALNYIKTYGDIFRALKA----LKVN----IDHVEEIRNFFL   61 (105)
T ss_dssp             BCCCTTCCHHHHHHHHHHHSSHHHHHHH----HTC--------CHHHHHHHH
T ss_pred             CCCCCCcCHHHHHHHHHHhCCHHHHHHH----HHhh----HHHHHHHHHHhc
Confidence            4689999999999999999999999853    2221    223556666664

>d2csba4 a.60.2.4 (A:465-519) Topoisomerase V {Methanopyrus kandleri [TaxId: 2320]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Topoisomerase V repeat domain
domain: Topoisomerase V
species: Methanopyrus kandleri [TaxId: 2320]

Probab=94.92  E-value=0.026  Score=39.96  Aligned_cols=46  Identities=24%  Similarity=0.538  Sum_probs=39.5

Q ss_pred             hccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHH
Q 017612          220 LTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRL  266 (368)
Q Consensus       220 LTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI  266 (368)
                      |-+|+||.+..|.+||++||....+..|..|||.. .|+.....+.|
T Consensus         6 lisirgidreraerllkkyggyskvreagveelre-dgltdaqirel   51 (55)
T d2csba4           6 LISIRGIDRERAERLLKKYGGYSKVREAGVEELRE-DGLTDAQIREL   51 (55)
T ss_dssp             HHTSTTCCHHHHHHHHHHHTSHHHHHTSCHHHHHH-TTCCHHHHHHH
T ss_pred             eeeeecccHHHHHHHHHHhcChhHHHHhhHHHHHH-ccccHHHHHHh
Confidence            44899999999999999999999999999999976 57776655544

>d1xo1a1 a.60.7.1 (A:186-290) T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: T5 5'-exonuclease
species: Bacteriophage T5 [TaxId: 10726]

Probab=94.74  E-value=0.0095  Score=47.04  Aligned_cols=30  Identities=17%  Similarity=0.334  Sum_probs=27.0

Q ss_pred             HhhccCCCCCHHHHHHHHHhcCCHHHHHcC
Q 017612          218 HALTSVRSVNKTDVVTLGSTFGSLSHIMDA  247 (368)
Q Consensus       218 saLTsIpgVnKTDA~~LLs~FGSLk~I~~A  247 (368)
                      .-+.+|||||.+.|..|+..|||+++|+..
T Consensus        19 DnipGV~GiG~KtA~kli~~~gsle~i~~~   48 (105)
T d1xo1a1          19 DNIRGVEGIGAKRGYNIIREFGNVLDIIDQ   48 (105)
T ss_dssp             GTBCCCTTCCHHHHHHHHHHHCSHHHHHHH
T ss_pred             cCCcCcCCcCHHHHHHHHHHcchhHHHHHh
Confidence            357799999999999999999999999853

>d2p6ra2 a.289.1.2 (A:489-686) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: Sec63 N-terminal domain-like
superfamily: Sec63 N-terminal domain-like
family: Achaeal helicase C-terminal domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=94.57  E-value=0.0047  Score=54.03  Aligned_cols=48  Identities=19%  Similarity=0.239  Sum_probs=40.8

Q ss_pred             hccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcC-CCCCHHHHHHHH
Q 017612          220 LTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLARC-PGIGERKVKRLY  267 (368)
Q Consensus       220 LTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~V-PGIG~kKA~rI~  267 (368)
                      |..|||||+..|+.|.+ -|.|+++|..|+.+.+..+ +|||++.+++|.
T Consensus       146 L~~i~gvgr~rAr~L~~~Gi~t~~dl~~a~~~~~~~~~~g~g~ki~~~i~  195 (198)
T d2p6ra2         146 LVRIRHIGRVRARKLYNAGIRNAEDIVRHREKVASLIGRGIAERVVEGIS  195 (198)
T ss_dssp             HHTSTTCCHHHHHHHHTTTCCSHHHHHHTHHHHHHHHCHHHHHHHHHHHH
T ss_pred             HhcCCCCCHHHHHHHHHcCCCCHHHHHHccHhhHHHHhcchHHHHHHHhc
Confidence            45899999999999987 4899999999987766666 788888888774

>d2duya1 a.60.2.7 (A:11-75) Uncharacterized protein TTHA1967 {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: ComEA-like
domain: Uncharacterized protein TTHA1967
species: Thermus thermophilus [TaxId: 274]

Probab=93.85  E-value=0.017  Score=42.03  Aligned_cols=30  Identities=33%  Similarity=0.688  Sum_probs=25.6

Q ss_pred             HHcCCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612          244 IMDASMEDLARCPGIGERKVKRLYDTFHEPFK  275 (368)
Q Consensus       244 I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~  275 (368)
                      |=.|+.+||..+||||++.|++|.++  ++|.
T Consensus        11 iNtA~~~eL~~lpgig~~~A~~Iv~~--R~f~   40 (65)
T d2duya1          11 LNEASLEELMALPGIGPVLARRIVEG--RPYA   40 (65)
T ss_dssp             TTTCCHHHHTTSTTCCHHHHHHHHHT--CCCS
T ss_pred             cccCCHHHHHHCCCCCHHHHHHHHHc--CCCC
Confidence            44789999999999999999999986  3454

>d1a77a1 a.60.7.1 (A:209-316) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=93.61  E-value=0.016  Score=45.30  Aligned_cols=28  Identities=7%  Similarity=-0.057  Sum_probs=25.7

Q ss_pred             hhccCCCCCHHHHHHHHHhcCCHHHHHc
Q 017612          219 ALTSVRSVNKTDVVTLGSTFGSLSHIMD  246 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs~FGSLk~I~~  246 (368)
                      .+.+|||||.+.|..|++.|||++.|+.
T Consensus        18 n~pGV~GIGpktA~klIk~~g~ie~l~~   45 (108)
T d1a77a1          18 NPGGVKGIGFKRAYELVRSGVAKDVLKK   45 (108)
T ss_dssp             STTCSTTCCHHHHHHHHHTTCHHHHHHH
T ss_pred             CCCCCCCcCHHHHHHHHHHcCCHHHHHH
Confidence            4568999999999999999999999985

>d3bzka1 a.60.2.6 (A:474-563) Transcriptional accessory factor Tex {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Tex HhH-containing domain-like
domain: Transcriptional accessory factor Tex
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=93.27  E-value=0.026  Score=43.42  Aligned_cols=33  Identities=21%  Similarity=0.285  Sum_probs=27.6

Q ss_pred             HHcCCHHhhhcCCCCCHHHHHHHHHHhc--ccccc
Q 017612          244 IMDASMEDLARCPGIGERKVKRLYDTFH--EPFKR  276 (368)
Q Consensus       244 I~~AS~EELa~VPGIG~kKA~rI~e~F~--ePF~~  276 (368)
                      |=.|+.++|..+||||+++|++|.++-.  .+|..
T Consensus        29 iN~As~~~L~~lpGig~~~A~~Iv~~R~~~G~f~s   63 (90)
T d3bzka1          29 VNTASAALLARISGLNSTLAQNIVAHRDANGAFRT   63 (90)
T ss_dssp             TTTCCHHHHTTSTTCCHHHHHHHHHHHHHHCSCSS
T ss_pred             hhhCCHHHHhHCCCCCHHHHHHHHHHHHHcCCCCC
Confidence            4578999999999999999999988764  36753

>d1doqa_ a.60.3.1 (A:) C-terminal domain of RNA polymerase alpha subunit {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: SAM domain-like
superfamily: C-terminal domain of RNA polymerase alpha subunit
family: C-terminal domain of RNA polymerase alpha subunit
domain: C-terminal domain of RNA polymerase alpha subunit
species: Thermus thermophilus [TaxId: 274]

Probab=92.74  E-value=0.048  Score=40.38  Aligned_cols=43  Identities=23%  Similarity=0.474  Sum_probs=36.7

Q ss_pred             HHHHHHH--hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          230 DVVTLGS--TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       230 DA~~LLs--~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      .+.+-|.  ...++.+++..+.+||..++|||++....|.+.|.+
T Consensus        18 R~~N~L~~~gI~tv~dL~~~s~~dLl~i~n~G~ksl~EI~~~L~~   62 (69)
T d1doqa_          18 RVLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIKEALEK   62 (69)
T ss_dssp             HHHHHHHHTTCCSHHHHHHSCHHHHTTSTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCccHHHHHHCCHHHHHhCCCCCHHHHHHHHHHHHH
Confidence            3444444  467999999999999999999999999999999864

>d2edua1 a.60.2.7 (A:8-98) KIF22, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: ComEA-like
domain: KIF22, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.51  E-value=0.046  Score=42.24  Aligned_cols=35  Identities=23%  Similarity=0.342  Sum_probs=29.6

Q ss_pred             HHHHcCCHHhhhcCCCCCHHHHHHHHHHhc--ccccc
Q 017612          242 SHIMDASMEDLARCPGIGERKVKRLYDTFH--EPFKR  276 (368)
Q Consensus       242 k~I~~AS~EELa~VPGIG~kKA~rI~e~F~--ePF~~  276 (368)
                      .+|=.||.++|..+||||++.|++|.++-.  .+|..
T Consensus        25 ~~iNtAs~~eL~~lpgig~~~A~~II~yR~~~G~f~s   61 (91)
T d2edua1          25 DLLNEGSARDLRSLQRIGPKKAQLIVGWRELHGPFSQ   61 (91)
T ss_dssp             HHHHHSCHHHHHHSTTCCHHHHHHHHHHHHHHCCCSS
T ss_pred             cccccCCHHHHhhCCCCCHHHHHHHHHHHHHcCCCCC
Confidence            356789999999999999999999988764  47764

>d1u9la_ a.60.4.2 (A:) Transcription elongation protein NusA {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: NusA extra C-terminal domains
domain: Transcription elongation protein NusA
species: Escherichia coli [TaxId: 562]

Probab=91.55  E-value=0.34  Score=36.03  Aligned_cols=54  Identities=20%  Similarity=0.336  Sum_probs=47.2

Q ss_pred             HHHHHHhhccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHh
Q 017612          213 LSRLTHALTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTF  270 (368)
Q Consensus       213 ~srL~saLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F  270 (368)
                      ...+...|    +|...-|..|.. -|.|+++|..++.+||..|.||-+..|..|++--
T Consensus         5 ~~~F~~~L----dVDe~lA~lLv~EGF~siEeIAyv~~~eL~~IegfDee~a~eL~~RA   59 (68)
T d1u9la_           5 IDTFTKYL----DIDEDFATVLVEEGFSTLEELAYVPMKELLEIEGLDEPTVEALRERA   59 (68)
T ss_dssp             HHHHHHHH----TCCHHHHHHHHHTTCCCHHHHHHSCHHHHTTSTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHc----CCcHHHHHHHHHhccCcHHHHhcCCHHHHHHhcccCHHHHHHHHHHH
Confidence            34456777    699999999998 5999999999999999999999999999997643

>d1dgsa1 a.60.2.2 (A:401-581) NAD+-dependent DNA ligase, domain 3 {Thermus filiformis [TaxId: 276]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: NAD+-dependent DNA ligase, domain 3
domain: NAD+-dependent DNA ligase, domain 3
species: Thermus filiformis [TaxId: 276]

Probab=91.17  E-value=0.06  Score=45.79  Aligned_cols=51  Identities=16%  Similarity=0.270  Sum_probs=44.3

Q ss_pred             cCCCCCHHHHHHHHHh--cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          222 SVRSVNKTDVVTLGST--FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       222 sIpgVnKTDA~~LLs~--FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      .|.|+|.+.+..|.+.  ..++.+|...+.++|..++|+|++.|.+|.+.++.
T Consensus        45 dI~GlG~~~i~~L~~~g~i~~~~Dly~L~~~~l~~l~~~g~ksa~nl~~~Ie~   97 (181)
T d1dgsa1          45 DIEGLGEKLIERLLEKGLVRDVADLYHLRKEDLLGLERMGEKSAQNLLRQIEE   97 (181)
T ss_dssp             CCTTCCHHHHHHHHHTTSCSSGGGGGGGCCHHHHTTSSCCSTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhcCCcchhhhhhhhhhHHHhcccccchHHHHHHHHHHHh
Confidence            6889999999999875  47888999999999999999999999999888864

>d2abka_ a.96.1.1 (A:) Endonuclease III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Endonuclease III
domain: Endonuclease III
species: Escherichia coli [TaxId: 562]

Probab=91.05  E-value=0.083  Score=45.55  Aligned_cols=49  Identities=14%  Similarity=0.268  Sum_probs=34.5

Q ss_pred             hhccCCCCC--HHHHH-------HHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHh
Q 017612          219 ALTSVRSVN--KTDVV-------TLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTF  270 (368)
Q Consensus       219 aLTsIpgVn--KTDA~-------~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F  270 (368)
                      ++..|+|+|  ...|+       .|.++||.   .+-.+.++|..+||||++.|..|..+-
T Consensus        72 l~~~i~~~G~y~~Ka~~l~~~a~~i~~~~~g---~~p~~~~~L~~LpGVG~~TA~~Il~~a  129 (211)
T d2abka_          72 VKTYIKTIGLYNSKAENIIKTCRILLEQHNG---EVPEDRAALEALPGVGRKTANVVLNTA  129 (211)
T ss_dssp             HHHHHTTSTTHHHHHHHHHHHHHHHHHHTTT---SCCSCHHHHHHSTTCCHHHHHHHHHHH
T ss_pred             hHHHHHHhhhhhhHHHHHHHHHHHHHHHhcC---chhHHHHHHHHHHhhchHHHHHHHHHH
Confidence            344455666  33443       45566665   345678999999999999999998763

>d1keaa_ a.96.1.2 (A:) Thymine-DNA glycosylase {Archaeon Methanobacterium thermoformicicum [TaxId: 145262]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Mismatch glycosylase
domain: Thymine-DNA glycosylase
species: Archaeon Methanobacterium thermoformicicum [TaxId: 145262]

Probab=90.32  E-value=0.11  Score=45.00  Aligned_cols=46  Identities=9%  Similarity=0.248  Sum_probs=34.5

Q ss_pred             cCCCCC--HHHHHH-------HHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHh
Q 017612          222 SVRSVN--KTDVVT-------LGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTF  270 (368)
Q Consensus       222 sIpgVn--KTDA~~-------LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F  270 (368)
                      -|+++|  ...|.+       |+++||+   .+-.+.++|..+||||++.|..|..+.
T Consensus        79 ~i~~~G~~~~KA~~l~~~a~~i~~~~~g---~~p~~~~~L~~LpGVG~kTA~~il~~~  133 (217)
T d1keaa_          79 DIKEIGLSNQRAEQLKELARVVINDYGG---RVPRNRKAILDLPGVGKYTCAAVMCLA  133 (217)
T ss_dssp             HTGGGSCHHHHHHHHHHHHHHHHHHHTT---SCCSCHHHHHTSTTCCHHHHHHHHHHT
T ss_pred             HHHHHHhhhHHHHHHHHHHHHHHhhccC---CcchhhHHHHHHHhhhhhhhHHHHHHh
Confidence            355666  455544       4556655   456789999999999999999998874

>d1lb2b_ a.60.3.1 (B:) C-terminal domain of RNA polymerase alpha subunit {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: SAM domain-like
superfamily: C-terminal domain of RNA polymerase alpha subunit
family: C-terminal domain of RNA polymerase alpha subunit
domain: C-terminal domain of RNA polymerase alpha subunit
species: Escherichia coli [TaxId: 562]

Probab=90.22  E-value=0.11  Score=38.84  Aligned_cols=36  Identities=11%  Similarity=0.394  Sum_probs=33.7

Q ss_pred             hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          237 TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       237 ~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      ...++.+++..+.+||..++|+|.+-...|.+.|.+
T Consensus        25 gI~tvgdL~~~s~~dLl~~~n~G~KSl~EI~~~L~~   60 (72)
T d1lb2b_          25 AIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS   60 (72)
T ss_dssp             TCCBHHHHHTCCHHHHHHSTTCCHHHHHHHHHHHHH
T ss_pred             CCcCHHHHHhCCHHHHHhCCCCcHhHHHHHHHHHHH
Confidence            467999999999999999999999999999999865

>d2i1qa1 a.60.4.1 (A:5-64) DNA repair protein Rad51, N-terminal domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=89.88  E-value=0.073  Score=37.88  Aligned_cols=20  Identities=25%  Similarity=0.654  Sum_probs=17.9

Q ss_pred             hhcCCCCCHHHHHHHHHH-hc
Q 017612          252 LARCPGIGERKVKRLYDT-FH  271 (368)
Q Consensus       252 La~VPGIG~kKA~rI~e~-F~  271 (368)
                      |..|||||++.|++|++. |.
T Consensus         1 L~~IpGIG~~~a~~L~~~G~~   21 (60)
T d2i1qa1           1 LTDLPGVGPSTAEKLVEAGYI   21 (60)
T ss_dssp             CTTSTTCCHHHHHHHHHHTCC
T ss_pred             CCCCCCCCHHHHHHHHHccCC
Confidence            678999999999999998 64

>d1kfta_ a.60.2.3 (A:) Excinuclease UvrC C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Excinuclease UvrC C-terminal domain
domain: Excinuclease UvrC C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=89.55  E-value=0.061  Score=37.89  Aligned_cols=24  Identities=17%  Similarity=0.263  Sum_probs=21.2

Q ss_pred             hhhcCCCCCHHHHHHHHHHhcccc
Q 017612          251 DLARCPGIGERKVKRLYDTFHEPF  274 (368)
Q Consensus       251 ELa~VPGIG~kKA~rI~e~F~ePF  274 (368)
                      .|..|||||++.|++|.+.|...-
T Consensus         3 ~L~~I~gVG~~~a~~L~~~F~s~~   26 (56)
T d1kfta_           3 SLETIEGVGPKRRQMLLKYMGGLQ   26 (56)
T ss_dssp             GGGGCTTCSSSHHHHHHHHHSCHH
T ss_pred             CcccCCCccHHHHHHHHHHhCCHH
Confidence            589999999999999999997543

>d1cmwa1 a.60.7.1 (A:174-289) 5' to 3' exonuclease domain of DNA polymerase Taq {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: 5' to 3' exonuclease domain of DNA polymerase Taq
species: Thermus aquaticus [TaxId: 271]

Probab=89.11  E-value=0.0065  Score=47.62  Aligned_cols=30  Identities=20%  Similarity=0.367  Sum_probs=26.9

Q ss_pred             hhccCCCCCHHHHHHHHHhcCCHHHHHcCC
Q 017612          219 ALTSVRSVNKTDVVTLGSTFGSLSHIMDAS  248 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs~FGSLk~I~~AS  248 (368)
                      -+.+|+|||.+.|..|+.+|||+++|+...
T Consensus        19 nipGv~GiG~KtA~kll~~~gsle~i~~~~   48 (116)
T d1cmwa1          19 NLPGVKGIGEKTARKLLEEWGSLEALLKNL   48 (116)
T ss_dssp             CCCCCCCSTTCTTTTTGGGGGTTCSSSSSC
T ss_pred             CcccccccCchhHHHHHHhcchHHHHHHHH
Confidence            467899999999999999999999999653

>d1z3eb1 a.60.3.1 (B:245-311) C-terminal domain of RNA polymerase alpha subunit {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: SAM domain-like
superfamily: C-terminal domain of RNA polymerase alpha subunit
family: C-terminal domain of RNA polymerase alpha subunit
domain: C-terminal domain of RNA polymerase alpha subunit
species: Bacillus subtilis [TaxId: 1423]

Probab=88.83  E-value=0.18  Score=37.06  Aligned_cols=36  Identities=11%  Similarity=0.387  Sum_probs=33.5

Q ss_pred             hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          237 TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       237 ~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      ...++.+++..+.+||..++|+|.+-...|.+.+..
T Consensus        26 ~I~tv~dL~~~s~~dLl~~~nfG~kSl~EIk~~L~~   61 (67)
T d1z3eb1          26 GINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEE   61 (67)
T ss_dssp             TCCBHHHHHTSCHHHHHTSTTCCHHHHHHHHHHHHH
T ss_pred             CCcCHHHHHHCCHHHHHhCCCCchhhHHHHHHHHHH
Confidence            578999999999999999999999999999999864

>d2bcqa1 a.60.6.1 (A:252-327) DNA polymerase lambda {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: DNA polymerase beta, N-terminal domain-like
family: DNA polymerase beta, N-terminal domain-like
domain: DNA polymerase lambda
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.45  E-value=0.15  Score=37.43  Aligned_cols=24  Identities=21%  Similarity=0.588  Sum_probs=21.6

Q ss_pred             HHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          249 MEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       249 ~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      .++|..+||||++.+.+|.+++..
T Consensus        45 ~~~l~~lpGiG~~i~~kI~Eil~t   68 (76)
T d2bcqa1          45 YQEACSIPGIGKRMAEKIIEILES   68 (76)
T ss_dssp             HHHHHTSTTCCHHHHHHHHHHHHS
T ss_pred             HHHHhcCCCccHHHHHHHHHHHHh
Confidence            467999999999999999999975

>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA repair endonuclease XPF
species: Aeropyrum pernix [TaxId: 56636]

Probab=87.93  E-value=0.14  Score=36.93  Aligned_cols=22  Identities=36%  Similarity=0.699  Sum_probs=19.8

Q ss_pred             hhhcCCCCCHHHHHHHHHHhcc
Q 017612          251 DLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       251 ELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      -|..|||||++.|++|.+.|..
T Consensus        14 ~L~~IpgIG~~~a~~L~~~F~s   35 (70)
T d2bgwa1          14 ILQSFPGIGRRTAERILERFGS   35 (70)
T ss_dssp             HHHTSTTCCHHHHHHHHHHHSS
T ss_pred             HHcCCCCcCHHHHHHHHHHhCC
Confidence            3779999999999999999964

>d1orna_ a.96.1.1 (A:) Endonuclease III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Endonuclease III
domain: Endonuclease III
species: Escherichia coli [TaxId: 562]

Probab=87.49  E-value=0.23  Score=42.54  Aligned_cols=43  Identities=9%  Similarity=0.305  Sum_probs=30.7

Q ss_pred             CCCHHHHHHH-------HHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHh
Q 017612          225 SVNKTDVVTL-------GSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTF  270 (368)
Q Consensus       225 gVnKTDA~~L-------Ls~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F  270 (368)
                      |.....|+.|       .++||.   .+-.+.++|..+||||++.|..|..+.
T Consensus        81 g~y~~ka~~l~~~a~~i~~~~~g---~vp~~~~~L~~LpGVG~kTA~~il~~a  130 (214)
T d1orna_          81 GLYRNKARNIQKLCAMLIDKYNG---EVPRDRDELMKLPGVGRKTANVVVSVA  130 (214)
T ss_dssp             SSHHHHHHHHHHHHHHHHHHSTT---SCCSCHHHHTTSTTCCHHHHHHHHHHH
T ss_pred             hhhhHHHHHHHHHhhhHHHHhCC---CCCCCHHHHHhCcCcccchHHHHHHHH
Confidence            3335555554       445554   345578999999999999999998764

>d2a1ja1 a.60.2.5 (A:837-898) DNA repair endonuclease XPF {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA repair endonuclease XPF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.73  E-value=0.18  Score=35.75  Aligned_cols=23  Identities=17%  Similarity=0.465  Sum_probs=20.2

Q ss_pred             HhhhcCCCCCHHHHHHHHHHhcc
Q 017612          250 EDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       250 EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      +=|..|||||++.+++|.+.|..
T Consensus         3 d~L~~iPGIg~~~~~~Ll~~f~S   25 (62)
T d2a1ja1           3 DFLLKMPGVNAKNCRSLMHHVKN   25 (62)
T ss_dssp             HHHHTSTTCCHHHHHHHHHHCSS
T ss_pred             hHHhcCCCCCHHHHHHHHHHhcc
Confidence            45899999999999999999854

>d1pzna1 a.60.4.1 (A:35-95) DNA repair protein Rad51, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=86.34  E-value=0.12  Score=36.74  Aligned_cols=22  Identities=18%  Similarity=0.596  Sum_probs=18.7

Q ss_pred             hhhcCCCCCHHHHHHHHHH-hcc
Q 017612          251 DLARCPGIGERKVKRLYDT-FHE  272 (368)
Q Consensus       251 ELa~VPGIG~kKA~rI~e~-F~e  272 (368)
                      .|..|||||++.|++|++. |..
T Consensus         2 ~L~~i~GIG~~~a~~L~~~g~~s   24 (61)
T d1pzna1           2 SIEDLPGVGPATAEKLREAGYDT   24 (61)
T ss_dssp             CSSCCTTCCHHHHHHHHTTTCCS
T ss_pred             ccccCCCCCHHHHHHHHHhcCCC
Confidence            4889999999999999986 443

>d1kg2a_ a.96.1.2 (A:) Catalytic domain of MutY {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Mismatch glycosylase
domain: Catalytic domain of MutY
species: Escherichia coli [TaxId: 562]

Probab=86.17  E-value=0.29  Score=42.13  Aligned_cols=30  Identities=20%  Similarity=0.498  Sum_probs=24.7

Q ss_pred             HcCCHHhhhcCCCCCHHHHHHHHHH-hcccc
Q 017612          245 MDASMEDLARCPGIGERKVKRLYDT-FHEPF  274 (368)
Q Consensus       245 ~~AS~EELa~VPGIG~kKA~rI~e~-F~ePF  274 (368)
                      +-.+.++|..+||||++.|..|..+ |+.|+
T Consensus       104 vp~~~~~L~~LpGVG~kTA~~il~~a~~~~~  134 (224)
T d1kg2a_         104 FPETFEEVAALPGVGRSTAGAILSLSLGKHF  134 (224)
T ss_dssp             CCCSHHHHHTSTTCCHHHHHHHHHHHHCCSC
T ss_pred             cchHHHHHHHHHhhhhhhhHHHHHHhhhccc
Confidence            5668899999999999999999865 54444

>d1b43a1 a.60.7.1 (A:220-339) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=86.12  E-value=0.25  Score=39.33  Aligned_cols=27  Identities=0%  Similarity=-0.039  Sum_probs=23.7

Q ss_pred             hhccCCCCCHHHHHHHHHhcCCHHHHH
Q 017612          219 ALTSVRSVNKTDVVTLGSTFGSLSHIM  245 (368)
Q Consensus       219 aLTsIpgVnKTDA~~LLs~FGSLk~I~  245 (368)
                      ...+|+|||++.|..|+++||+++.+.
T Consensus        18 ~~~gI~GIGpktAlklikk~~~~~~~~   44 (120)
T d1b43a1          18 NPGGIKGIGLKKALEIVRHSKDPLAKF   44 (120)
T ss_dssp             STTCSTTCCHHHHHHHHHTCSSGGGGT
T ss_pred             CcccCCCcCHHHHHHHHHHhCCHHHHH
Confidence            346899999999999999999997765

>d2fmpa1 a.60.6.1 (A:10-91) DNA polymerase beta, N-terminal (8 kD)-domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: DNA polymerase beta, N-terminal domain-like
family: DNA polymerase beta, N-terminal domain-like
domain: DNA polymerase beta, N-terminal (8 kD)-domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.02  E-value=0.2  Score=37.38  Aligned_cols=25  Identities=16%  Similarity=0.414  Sum_probs=22.3

Q ss_pred             CHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          248 SMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       248 S~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      +.++|..+||||+..|++|.+++..
T Consensus        46 ~~~~l~~i~GIGk~ia~kI~E~~~T   70 (82)
T d2fmpa1          46 SGAEAKKLPGVGTKIAEKIDEFLAT   70 (82)
T ss_dssp             CHHHHHTSTTCCHHHHHHHHHHHHH
T ss_pred             CHHHHhcCCCccHHHHHHHHHHHHh
Confidence            4678999999999999999999864

>d1ngna_ a.96.1.2 (A:) Mismatch-specific thymine glycosylase domain of the methyl-GpG binding protein mbd4 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Mismatch glycosylase
domain: Mismatch-specific thymine glycosylase domain of the methyl-GpG binding protein mbd4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=85.57  E-value=0.61  Score=37.82  Aligned_cols=45  Identities=9%  Similarity=-0.057  Sum_probs=34.4

Q ss_pred             CCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          225 SVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       225 gVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      |.-++.|+.|.+-.   +.++.-+.++|..+||||+..|..+.-+...
T Consensus        71 G~~~~KAk~I~~~a---~~~ip~~~~~l~~LpGVG~~tad~~~if~~~  115 (144)
T d1ngna_          71 GLYDLRAKTIIKFS---DEYLTKQWRYPIELHGIGKYGNDSYRIFCVN  115 (144)
T ss_dssp             SCHHHHHHHHHHHH---HHHHHSCCSSGGGSTTCCHHHHHHHHHHTSS
T ss_pred             hhHHHHHHHHHHHH---hhHhhhhhhhHHhcCCccHHHHHHHHHHHcC
Confidence            44477888887654   5667778899999999999999988665543

>d1jmsa3 a.60.12.1 (A:243-302) Terminal deoxynucleotidyl transferase {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: SAM domain-like
superfamily: PsbU/PolX domain-like
family: DNA polymerase beta-like, second domain
domain: Terminal deoxynucleotidyl transferase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=85.52  E-value=0.49  Score=34.05  Aligned_cols=33  Identities=24%  Similarity=0.147  Sum_probs=27.7

Q ss_pred             HHHHHhhccCCCCCHHHHHHHHHh-cCCHHHHHc
Q 017612          214 SRLTHALTSVRSVNKTDVVTLGST-FGSLSHIMD  246 (368)
Q Consensus       214 srL~saLTsIpgVnKTDA~~LLs~-FGSLk~I~~  246 (368)
                      -+....|++|-|||++.|+.|.+. |.||++|..
T Consensus         4 ~~~l~~f~~I~GvGp~~A~~l~~~Gi~ti~dL~~   37 (60)
T d1jmsa3           4 YKSFKLFTSVFGVGLKTAEKWFRMGFRTLSKIQS   37 (60)
T ss_dssp             HHHHHHHHTSTTCCHHHHHHHHHTTCCSHHHHHH
T ss_pred             hHHHHHHhccccccHHHHHHHHHhCCCCHHHHHh
Confidence            345678899999999999999886 779998874

>d1pu6a_ a.96.1.5 (A:) 3-Methyladenine DNA glycosylase III (MagIII) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: 3-Methyladenine DNA glycosylase III (MagIII)
domain: 3-Methyladenine DNA glycosylase III (MagIII)
species: Helicobacter pylori [TaxId: 210]

Probab=84.99  E-value=0.62  Score=40.14  Aligned_cols=39  Identities=18%  Similarity=0.199  Sum_probs=30.4

Q ss_pred             HHHHHHhcCCHHHHH-cCCHHhhhcCCCCCHHHHHHHHHH
Q 017612          231 VVTLGSTFGSLSHIM-DASMEDLARCPGIGERKVKRLYDT  269 (368)
Q Consensus       231 A~~LLs~FGSLk~I~-~AS~EELa~VPGIG~kKA~rI~e~  269 (368)
                      |+.|.+.|+.+.++- ....++|..+||||++.|..|.-+
T Consensus       100 a~~i~~~~~~~~~~~~~~~~~~L~~lpGIG~kTA~~vl~~  139 (217)
T d1pu6a_         100 SGNILKDFQSFENFKQEVTREWLLDQKGIGKESADAILCY  139 (217)
T ss_dssp             HHHHHHHHSSHHHHHHHCCHHHHHTSTTCCHHHHHHHHHH
T ss_pred             HHHHHHhhhhcccCCcHHHHHHHHHHhhhhhHHHHHHHHH
Confidence            344566788876654 456899999999999999999755

>d1rrqa1 a.96.1.2 (A:9-229) Catalytic domain of MutY {Bacillus stearothermophilus [TaxId: 1422]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Mismatch glycosylase
domain: Catalytic domain of MutY
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=83.98  E-value=0.4  Score=41.13  Aligned_cols=29  Identities=17%  Similarity=0.415  Sum_probs=24.0

Q ss_pred             HcCCHHhhhcCCCCCHHHHHHHHHH-hccc
Q 017612          245 MDASMEDLARCPGIGERKVKRLYDT-FHEP  273 (368)
Q Consensus       245 ~~AS~EELa~VPGIG~kKA~rI~e~-F~eP  273 (368)
                      +-.+.++|..+||||++.|..|..+ |+.|
T Consensus       102 vp~~~~~Ll~LpGIG~kTA~~il~~a~~~p  131 (221)
T d1rrqa1         102 VPDDPDEFSRLKGVGPYTVGAVLSLAYGVP  131 (221)
T ss_dssp             CCCSHHHHHTSTTCCHHHHHHHHHHHTCCC
T ss_pred             CchHHHHHHHHHHhhhHHHHHHHHHHhcCc
Confidence            4568899999999999999999866 4433

>d1keaa_ a.96.1.2 (A:) Thymine-DNA glycosylase {Archaeon Methanobacterium thermoformicicum [TaxId: 145262]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Mismatch glycosylase
domain: Thymine-DNA glycosylase
species: Archaeon Methanobacterium thermoformicicum [TaxId: 145262]

Probab=83.90  E-value=0.42  Score=41.12  Aligned_cols=41  Identities=12%  Similarity=0.254  Sum_probs=34.4

Q ss_pred             HHHHHHhcCCHHHHHcCCHHhhh-cCCCCC--HHHHHHHHHHhc
Q 017612          231 VVTLGSTFGSLSHIMDASMEDLA-RCPGIG--ERKVKRLYDTFH  271 (368)
Q Consensus       231 A~~LLs~FGSLk~I~~AS~EELa-~VPGIG--~kKA~rI~e~F~  271 (368)
                      ..+|.++|.++++|.+|+.+||. .+.|+|  ..||++|+++..
T Consensus        55 ~~~l~~~~pt~~~la~a~~~~l~~~i~~~G~~~~KA~~l~~~a~   98 (217)
T d1keaa_          55 YDKFFVKYKCFEDILKTPKSEIAKDIKEIGLSNQRAEQLKELAR   98 (217)
T ss_dssp             HHHHHHHCCSHHHHHHSCHHHHHHHTGGGSCHHHHHHHHHHHHH
T ss_pred             HHHHHHhcccHHHHHHhhHHHHHHHHHHHHhhhHHHHHHHHHHH
Confidence            36788999999999999999977 578888  679999977554

>d2fmpa2 a.60.12.1 (A:92-148) DNA polymerase beta {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: PsbU/PolX domain-like
family: DNA polymerase beta-like, second domain
domain: DNA polymerase beta
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.72  E-value=0.22  Score=35.69  Aligned_cols=22  Identities=32%  Similarity=0.575  Sum_probs=18.4

Q ss_pred             CHHhhhcCCCCCHHHHHHHHHH
Q 017612          248 SMEDLARCPGIGERKVKRLYDT  269 (368)
Q Consensus       248 S~EELa~VPGIG~kKA~rI~e~  269 (368)
                      +.+.|..|.|||+++|++|++.
T Consensus         5 ~l~~l~~I~GvGp~~A~~l~~~   26 (57)
T d2fmpa2           5 SINFLTRVSGIGPSAARKFVDE   26 (57)
T ss_dssp             HHHHHTTSTTCCHHHHHHHHHT
T ss_pred             HHHHHhccccccHHHHHHHHHh
Confidence            3578899999999999999753

>d1jmsa3 a.60.12.1 (A:243-302) Terminal deoxynucleotidyl transferase {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: SAM domain-like
superfamily: PsbU/PolX domain-like
family: DNA polymerase beta-like, second domain
domain: Terminal deoxynucleotidyl transferase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=83.15  E-value=0.35  Score=34.84  Aligned_cols=21  Identities=10%  Similarity=0.338  Sum_probs=18.5

Q ss_pred             HHhhhcCCCCCHHHHHHHHHH
Q 017612          249 MEDLARCPGIGERKVKRLYDT  269 (368)
Q Consensus       249 ~EELa~VPGIG~kKA~rI~e~  269 (368)
                      ..+|..|.|||+++|+++++.
T Consensus         7 l~~f~~I~GvGp~~A~~l~~~   27 (60)
T d1jmsa3           7 FKLFTSVFGVGLKTAEKWFRM   27 (60)
T ss_dssp             HHHHHTSTTCCHHHHHHHHHT
T ss_pred             HHHHhccccccHHHHHHHHHh
Confidence            468999999999999999764

>d1xo1a1 a.60.7.1 (A:186-290) T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: T5 5'-exonuclease
species: Bacteriophage T5 [TaxId: 10726]

Probab=83.05  E-value=0.24  Score=38.61  Aligned_cols=36  Identities=25%  Similarity=0.388  Sum_probs=30.4

Q ss_pred             hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          237 TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       237 ~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      +|=.++.|+.-+.+-+-.|||||+++|.+|..-|..
T Consensus         6 q~~d~~aL~GD~sDnipGV~GiG~KtA~kli~~~gs   41 (105)
T d1xo1a1           6 QFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGN   41 (105)
T ss_dssp             HHHHHHHHHCBGGGTBCCCTTCCHHHHHHHHHHHCS
T ss_pred             HHHHHHHHhCCcccCCcCcCCcCHHHHHHHHHHcch
Confidence            455567788888899999999999999999988853

>d1fx0b1 a.69.1.1 (B:378-485) F1 ATP synthase beta subunit, domain 3 {Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]}

class: All alpha proteins
fold: Left-handed superhelix
superfamily: C-terminal domain of alpha and beta subunits of F1 ATP synthase
family: C-terminal domain of alpha and beta subunits of F1 ATP synthase
domain: F1 ATP synthase beta subunit, domain 3
species: Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]

Probab=82.60  E-value=0.16  Score=40.92  Aligned_cols=50  Identities=12%  Similarity=0.236  Sum_probs=44.6

Q ss_pred             HHHHHHHHhcCCHHHHHcC-CHHhhhcCCCCCHHHHHHHHHHhcccccccC
Q 017612          229 TDVVTLGSTFGSLSHIMDA-SMEDLARCPGIGERKVKRLYDTFHEPFKRVV  278 (368)
Q Consensus       229 TDA~~LLs~FGSLk~I~~A-S~EELa~VPGIG~kKA~rI~e~F~ePF~~~~  278 (368)
                      ..++.+|.+|..|++|+.. -.+||+.-+.+--.+|++|.++|.+||.-..
T Consensus        12 ~~v~~iLqrYkeLqdIIailG~dELSeeDk~~v~RArklq~FLtQpFfvae   62 (108)
T d1fx0b1          12 QRVKETLQRYKELQDIIAILGLDELSEEDRLTVARARKIERFLSQPFFVAE   62 (108)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCSTTSCTTTHHHHHHHHHHHHHTCCCCSSCT
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhcChhhhHHHHHHHHHHHHhccccccce
Confidence            5789999999999999965 6899999999999999999999999997543

>d1x2ia1 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=82.34  E-value=0.39  Score=34.53  Aligned_cols=22  Identities=18%  Similarity=0.311  Sum_probs=20.0

Q ss_pred             hhhcCCCCCHHHHHHHHHHhcc
Q 017612          251 DLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       251 ELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      -|..|||||++.|++|.+.|..
T Consensus        11 ~L~~I~gIG~~~a~~L~~~f~s   32 (68)
T d1x2ia1          11 IVEGLPHVSATLARRLLKHFGS   32 (68)
T ss_dssp             HHTTSTTCCHHHHHHHHHHHCS
T ss_pred             HHcCCCCcCHHHHHHHHHHcCC
Confidence            3779999999999999999975

>d1jmsa1 a.60.6.1 (A:148-242) Terminal deoxynucleotidyl transferase {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: SAM domain-like
superfamily: DNA polymerase beta, N-terminal domain-like
family: DNA polymerase beta, N-terminal domain-like
domain: Terminal deoxynucleotidyl transferase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=82.30  E-value=0.29  Score=37.50  Aligned_cols=25  Identities=20%  Similarity=0.367  Sum_probs=22.3

Q ss_pred             CHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612          248 SMEDLARCPGIGERKVKRLYDTFHE  272 (368)
Q Consensus       248 S~EELa~VPGIG~kKA~rI~e~F~e  272 (368)
                      +.+||..+||||+..+.+|.+++..
T Consensus        60 ~~~~l~~i~GIGk~i~~kI~Eil~t   84 (95)
T d1jmsa1          60 SMKDTEGIPCLGDKVKSIIEGIIED   84 (95)
T ss_dssp             SGGGGTTCSSCCHHHHHHHHHHHHH
T ss_pred             CHHHHHhccchhHHHHHHHHHHHHH
Confidence            4578999999999999999999864

>d2bcqa2 a.60.12.1 (A:329-385) DNA polymerase lambda {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: PsbU/PolX domain-like
family: DNA polymerase beta-like, second domain
domain: DNA polymerase lambda
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.21  E-value=0.74  Score=32.86  Aligned_cols=32  Identities=13%  Similarity=0.157  Sum_probs=27.8

Q ss_pred             HHHHhhccCCCCCHHHHHHHHHh-cCCHHHHHc
Q 017612          215 RLTHALTSVRSVNKTDVVTLGST-FGSLSHIMD  246 (368)
Q Consensus       215 rL~saLTsIpgVnKTDA~~LLs~-FGSLk~I~~  246 (368)
                      .++..|++|-|||++.|+.|.+. +.||++|..
T Consensus         5 ~~l~~ft~I~GvGp~~A~~l~~~Gi~ti~dLr~   37 (57)
T d2bcqa2           5 PVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRS   37 (57)
T ss_dssp             HHHHHHHTSTTCCHHHHHHHHHTTCCSHHHHHH
T ss_pred             HHHHHHhccccccHHHHHHHHHhCCCCHHHHHh
Confidence            46788999999999999999886 779999875