Citrus Sinensis ID: 006771

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630--

MIELIEMENHSKRRVVCAENEELAMYMLQKRQEMAETPKGLSENIDMTLSKAYNNICDAKNPIKTLKDLSQVKGVGKWILKLMQEFFETDSGGSEPEDLTAKSKKSKAVKTKGTKRYMPQRNSVAYALLITLYRGTTNGNEFMRKQDLIDAAEASGLSHTPIMPEKGKGKPRQFGSSPRDWYSGWSCMKTLITKGLVVKSSCPAKYMLTPGGREAARECLSRSGFADSIENVVNGKDSDKNELSELDLVLAHPDSNGEVTECFVPLSRKEKSTDVPFESLERFTRMGYSKEQVLRAFGEVSETSQHKEISSLWPAVLCRLQEDEVYALHSELHSVREDYDAASRTCISTNDDPKTRVNLLSVPPLSFGERFEDAYEVVLILDDREQFAVQGSRSRRIIENVCSQFKIQMEVRRLPVGDGIWIARHRQTQSEYVLDFIVERKKVDDLRSSIRDNRYRDQKLRLVRCGLKKLIYLVEGDPNSSEAAESIKTACFTTEILEGFDVQRTSGLADTLRKYGYITQAITEYYKVELPEDQLKCAAVCPPFDEFLKRCQDLDKMTVSDVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASRNIFQLVWGK

ccccEEccccccccccccccHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHccccccccHHHHHHcccccHHHHHHHHHHHHHHcccccccccHHHHHHccccccccccccccccccHHHHHHHHHHHccccccccccHHHHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHHcccccccccccEEEcccccHHHHHHHHHHcccccccccccccccccccccHHHHHHcccccccccccccccccccccccccccccccHHHccccccHHHHHHHcccccccccccccccccHHHHccccHHHHHHHHcccccccccccHHccccccccccccccccccccccccccccccccEEEEEEEEccccccccccccHHHHHHHHHHccccEEEEEcccccEEEEEEccccccEEEccEEEEEccHHHHHHHHcccHHHHHHHHHHHHccccEEEEEccccccccHHHHHHHHccccEEcccccccccccHHHHHHHHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHcccccccHHHHHHHHHHccccccHHHHHHHHHHcccHHHHHHHHHHHcccHHHHHHHHHHHccccccHHHHHHHHHHHHcc

cEEEEEEcccccccccccccHHHHHHHHHHcHHHHHHHccccHHHHHHHHHHHHHHHHHcccccccccHHHcccccccccHHcccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHcccccccccHHHHHHHHHHHccccccccccccccccccccccccccccHHHHHHHHHHcccEEEcccccEEEccHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEccccccccccccHHHHHHHHHHccccEEEEEEccccEEEEEEccccccEEEEHHHEEHHHHHHHHHHHHcccHHHHHHHHHHcccccEEEEEEcccccccHHHHHHHHHHHHEEEccEEEEEcccHHHHHHHHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHcccccccHHHHHHHHHHHcccccHHHHHHHHHHcccHHHHHHHHHHccccHHHHHHHHHHHHcccccHHHHHHHHHHHccc

MIELIEMenhskrrvVCAENEELAMYMLQKRQEmaetpkglsenIDMTLSKAYNNicdaknpiktlkdlsqvKGVGKWILKLMQEFfetdsggsepedltakskkskavktkgtkrympqrNSVAYALLITLYrgttngnefMRKQDLIDAaeasglshtpimpekgkgkprqfgssprdwysgwSCMKTLITKGLvvksscpakymltpggreAAREClsrsgfadsienvvngkdsdknelSELDLVlahpdsngevtecfvplsrkekstdvpfeslerftrmgySKEQVLRAFGevsetsqhkeisslWPAVLCRLQEDEVYALHSELHSVredydaasrtcistnddpktrvnllsvpplsfgerfEDAYEVVLILDDREQFAVQGSRSRRIIENVCSQFKIQMevrrlpvgdgiwIARHRQTQSEYVLDFIVERKKVDDLRSSIRDNRYRDQKLRLVRCGLKKLIYLvegdpnsseaAESIKTACFTTEILEGFDVQRTSGLADTLRKYGYITQAITEYYKvelpedqlkcaavcppfDEFLKRCQDLDKMTVSDVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASRNIFQLVWGK

mieliemenhskrrvvcAENEELAMYMLQKRQEMAETPKGLSENIDMTLSKAYNNICDAknpiktlkdlsQVKGVGKWILKLMQEFFetdsggsepedltakskkskavktkgtkrympqrnsVAYALLITLYRGTTNGNEFMRKQDLIDAAEASGlshtpimpekgkgkprqfgssprdwysgWSCMKTLITKGLVVKSSCPAKYMLTPGGREAARECLSRSGFADSIENVVNGKDSDKNELSELDLVlahpdsngevtecfvplsrkekstdvpfeslerftrmgysKEQVLRAFGEVSETSQHKEISSLWPAVLCRLQEDEVYALHSELHSVREDYDAASRTcistnddpktrvnllsvpplsfgerFEDAYEVVLILDDREQfavqgsrsrriIENVcsqfkiqmevrrLPVGDGIWIArhrqtqseyvldfiverkkvddlrssirdnryrdqklrlvrCGLKKLIYLvegdpnsseAAESIKTACFTTEILEGFDVQRTSGLADTLRKYGYITQAITEYYKVELPEDQLKCAAVCPPFDEFLKRCQDLDKMTVSDVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSnnavsasasrnifqlvwgk

MIELIEMENHSKRRVVCAENEELAMYMLQKRQEMAETPKGLSENIDMTLSKAYNNICDAKNPIKTLKDLSQVKGVGKWILKLMQEFFETDSGGSEPEDLtakskkskavktkgtkRYMPQRNSVAYALLITLYRGTTNGNEFMRKQDLIDAAEASGLSHTPIMPEKGKGKPRQFGSSPRDWYSGWSCMKTLITKGLVVKSSCPAKYMLTPGGREAARECLSRSGFADSIENVVNGKDSDKNELSELDLVLAHPDSNGEVTECFVPLSRKEKSTDVPFESLERFTRMGYSKEQVLRAFGEVSETSQHKEISSLWPAVLCRLQEDEVYALHSELHSVREDYDAASRTCISTNDDPKTRVNLLSVPPLSFGERFEDAYEVVLILDDREQFAVQGSRSRRIIENVCSQFKIQMEVRRLPVGDGIWIARHRQTQSEYVLDFIVERKKVDDLRSSIRDNRYRDQKLRLVRCGLKKLIYLVEGDPNSSEAAESIKTACFTTEILEGFDVQRTSGLADTLRKYGYITQAITEYYKVELPEDQLKCAAVCPPFDEFLKRCQDLDKMTVSDVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQsnnavsasasrnIFQLVWGK

***************VC*****LAMY*******************DMTLSKAYNNICDAKNPIKTLKDLSQVKGVGKWILKLMQEFF**********************************NSVAYALLITLYRGTTNGNEFM************************************DWYSGWSCMKTLITKGLVVKSSCPAKYMLTPG*************************************V*********VTECFVP*****************FTRMGYSKEQVLRAFGE*******KEISSLWPAVLCRLQEDEVYALHSELHSVREDYDAASRTCISTN***KTRVNLLSVPPLSFGERFEDAYEVVLILDDREQFAVQGSRSRRIIENVCSQFKIQMEVRRLPVGDGIWIARHRQTQSEYVLDFIVERKKVDDLRSSIRDNRYRDQKLRLVRCGLKKLIYLVEG*********SIKTACFTTEILEGFDVQRTSGLADTLRKYGYITQAITEYYKVELPEDQLKCAAVCPPFDEFLKRCQDLDKMTVSDVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAV****SRNIFQLVW**

*IEL***************NEELAMYMLQKRQEMA***********MTLSKAYNNICDAKNPIKTLKDLSQVKGVGKWILKLMQ*************************************NSVAYALLITLYRGTT******R****IDAAE*****************************SGWSCMKTLITKGLVVKSSCPAKYMLTPGGREAARECLS*************************************VTECFVP*****************************************************************************************************FGERFEDAYEVVLILDDREQFAV***RSRRIIENVCSQFKIQMEVRRLPVGDGIWIARHRQTQSEYVLDFIVERKKVDDLRSSIRDNRYRDQKLRLVRCGLKKLIYLVEGDPNSSEAAESIKTACFTTEILEGFDVQRTSGLADTLRKYGYITQAITEYYKVELPEDQ****AVCPPFDEFLKRCQDLDKMTVSDVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSI***********************ASRNIFQLVWGK

MIELIEMENHSKRRVVCAENEELAMYMLQKRQEMAETPKGLSENIDMTLSKAYNNICDAKNPIKTLKDLSQVKGVGKWILKLMQEFFET**************************RYMPQRNSVAYALLITLYRGTTNGNEFMRKQDLIDAAEASGLSHTPIMPE*************RDWYSGWSCMKTLITKGLVVKSSCPAKYMLTPGGREAARECLSRSGFADSIENVVNGKDSDKNELSELDLVLAHPDSNGEVTECFVPLSRKEKSTDVPFESLERFTRMGYSKEQVLRAFGE*********ISSLWPAVLCRLQEDEVYALHSELHSVREDYDAASRTCISTNDDPKTRVNLLSVPPLSFGERFEDAYEVVLILDDREQFAVQGSRSRRIIENVCSQFKIQMEVRRLPVGDGIWIARHRQTQSEYVLDFIVERKKVDDLRSSIRDNRYRDQKLRLVRCGLKKLIYLVEG********ESIKTACFTTEILEGFDVQRTSGLADTLRKYGYITQAITEYYKVELPEDQLKCAAVCPPFDEFLKRCQDLDKMTVSDVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASRNIFQLVWGK

MIELIEMENHSKRRVVCAENEELAMYMLQKRQEMAETPKGLSENIDMTLSKAYNNICDAKNP*****************************************************RYMPQRNSVAYALLITLYRGTTNGNEFMRKQDLIDAAEASGLSHTP*****************RDWYSGWSCMKTLITKGLVVKSSCPAKYMLTPGGREAARECLSRS****************************************************************************************************************************************LSVPPLSFGERFEDAYEVVLILDDREQFAVQGSRSRRIIENVCSQFKIQMEVRRLPVGDGIWIARHRQTQSEYVLDFIVERKKVDDLRSSIRDNRYRDQKLRLVRCGLKKLIYLVEGDPNSSEAAESIKTACFTTEILEGFDVQRTSGLADTLRKYGYITQAITEYYKVELPEDQLKCAAVCPPFDEFLKRCQDLDKMTVSDVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASRNIFQLVWGK

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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	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		632	2.2.26 [Sep-21-2011]
Q5W9E7		659	Crossover junction endonu	yes	no	0.962	0.922	0.572	0.0
Q8GT06		660	Crossover junction endonu	yes	no	0.427	0.409	0.618	3e-96
P87231		608	Crossover junction endonu	yes	no	0.781	0.812	0.261	2e-33
Q6BJ48		651	Crossover junction endonu	yes	no	0.675	0.655	0.268	4e-32
Q6CPQ8		614	Crossover junction endonu	yes	no	0.792	0.815	0.239	1e-31
Q7SD49		645	Crossover junction endonu	N/A	no	0.724	0.710	0.254	1e-28
Q6FYA6		628	Crossover junction endonu	yes	no	0.838	0.843	0.252	1e-27
Q7SXA9		604	Crossover junction endonu	yes	no	0.381	0.399	0.322	3e-25
Q04149		632	Crossover junction endonu	yes	no	0.819	0.819	0.238	4e-25
Q91ZJ0		551	Crossover junction endonu	yes	no	0.386	0.442	0.313	3e-24

>sp\|Q5W9E7\|MUS81_ARATH Crossover junction endonuclease MUS81 OS=Arabidopsis thaliana GN=MUS81 PE=1 SV=1	Back alignment and function desciption

 Score =  742 bits (1915), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 383/669 (57%), Positives = 469/669 (70%), Gaps = 61/669 (9%)

Query: 12  KRRVVCAENEELAMYMLQKRQEMAETPKGLSENIDMTLSKAYNNICDAKNPIKTLKDLSQ 71
           +RRV+C EN  LA Y+LQK+QE AE PKGLSEN++ T  K Y ++CDAK+PI TLKDLSQ
Sbjct: 4   ERRVLCPENRGLAAYVLQKKQEYAEKPKGLSENLERTFVKGYRSVCDAKDPINTLKDLSQ 63

Query: 72  VKGVGKWILKLMQEFFETDSGGSEPEDLTAKSKKSKAVKTKGTKRYMPQRNSVAYALLIT 131
           +KG GKW++KLM+ +F+T    SE EDL       KA    G KRY+PQRNSV YALLIT
Sbjct: 64  IKGFGKWMVKLMKGYFDTAVESSEQEDLPDNRAGKKA---NGKKRYIPQRNSVGYALLIT 120

Query: 132 LYRGTTNGNEFMRKQDLIDAAEASGLSHTPIMPEKGKGKPRQFGSSPRDWYSGWSCMKTL 191
           L+R TTNG EFMRKQ+LIDAA+A+GLSH P+ PEKGKGK    G S R+WYSGWSCM TL
Sbjct: 121 LHRRTTNGKEFMRKQELIDAADANGLSHAPVGPEKGKGKA-GLGHSKREWYSGWSCMTTL 179

Query: 192 ITKGLVVKSSCPAKYMLTPGGREAARECLSRSGFADSIENVVNGKDSDKNELSELDLVLA 251
           I KGLVVKSS PAKYMLT  GRE A EC+ RSG  DS++ +          + E+D    
Sbjct: 180 IQKGLVVKSSNPAKYMLTVEGREVANECILRSGLPDSVDIL---------SVDEMDPTPQ 230

Query: 252 HPDSNGEVTECFVPL--------SRKEKSTDVPFESLERFTRMGYSKEQVLRAFGEVSET 303
              +  +   C   +         R    + +P + LE+FT  GYSKEQV+ AF EVS+ 
Sbjct: 231 AKKTPNQNPTCSFTMREELPYVDPRCRAQSAIPSDILEKFTPFGYSKEQVVAAFREVSDG 290

Query: 304 SQHKEISSLWPAVLCRLQEDEVYALHSELHSVREDYDA---------------------- 341
           S  K+ S+LW +V+C L++ EVY    +  + ++D                         
Sbjct: 291 SGDKDPSTLWLSVMCHLRQAEVYNSCPDSRNSKKDSSGPFKSQIRQVDLEGSRAKKFRSC 350

Query: 342 ---------------ASRTCIST--NDDPKTRVNLLSVPPLSFGERFEDAYEVVLILDDR 384
                          A + C S+  +D  K   N+  +PPL FGE FE+AY+V+LILDDR
Sbjct: 351 NDGSTLNPCSSGSSHAVKACSSSLASDGTKGITNIPRLPPLQFGETFEEAYDVILILDDR 410

Query: 385 EQFAVQGSRSRRIIENVCSQFKIQMEVRRLPVGDGIWIARHRQTQSEYVLDFIVERKKVD 444
           E+FA +GSRSR I+EN+CS+F I++EVRRLPVGD IWIARH+  ++EYVLDFI ERK VD
Sbjct: 411 EKFATKGSRSRNIVENICSEFNIKIEVRRLPVGDCIWIARHKYLETEYVLDFIAERKNVD 470

Query: 445 DLRSSIRDNRYRDQKLRLVRCGLKKLIYLVEGDPNSSEAAESIKTACFTTEILEGFDVQR 504
           D+RSSIRDNRYRDQKLRL R G KKLIY++EGDPN S+AAESIKTACFTTEILEGFDV R
Sbjct: 471 DMRSSIRDNRYRDQKLRLQRSGFKKLIYILEGDPNHSDAAESIKTACFTTEILEGFDVLR 530

Query: 505 TSGLADTLRKYGYITQAITEYYKVELPE-DQLKCAAVCPPFDEFLKRCQDLDKMTVSDVF 563
           T GL +TLRKYGY+T++I +YYK+ + + DQ K AA CP FD F+KRCQDLDKMT+SDVF
Sbjct: 531 THGLGETLRKYGYLTKSIYQYYKLRVNDNDQSKGAASCPSFDSFVKRCQDLDKMTISDVF 590

Query: 564 AVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASR 623
           A+QLMQVPQVTEEIAI VLD+YPTLLSLA AYS LE DV AQEEML  +SNN + ASAS+
Sbjct: 591 AIQLMQVPQVTEEIAIAVLDMYPTLLSLASAYSHLEADVSAQEEMLRNRSNNVICASASK 650

Query: 624 NIFQLVWGK 632
           NIF+LVWG+
Sbjct: 651 NIFKLVWGE 659

Interacts with EME1 to form a DNA structure-specific endonuclease with substrate preference for branched DNA structures with a 5'-end at the branch nick. Typical substrates include 3'-flap structures, D-loops, replication forks, nicked Holliday junctions and also intact Holliday junctions with a reduced efficiency. May be required in mitosis for the processing of stalled or collapsed replication fork intermediates. Plays a role in DNA repair and in genotoxic stress-induced homologous recombination (HR) in somatic cells. Mediates a subset of meiotic recombination events that are insensitive to crossover interference.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 1EC: .EC: 2EC: 2EC: .EC: -

>sp\|Q8GT06\|MUS81_ORYSJ Crossover junction endonuclease MUS81 OS=Oryza sativa subsp. japonica GN=MUS81 PE=1 SV=1	Back alignment and function description

>sp\|P87231\|MUS81_SCHPO Crossover junction endonuclease mus81 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=mus81 PE=1 SV=2	Back alignment and function description

>sp\|Q6BJ48\|MUS81_DEBHA Crossover junction endonuclease MUS81 OS=Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) GN=MUS81 PE=3 SV=2	Back alignment and function description

>sp\|Q6CPQ8\|MUS81_KLULA Crossover junction endonuclease MUS81 OS=Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) GN=MUS81 PE=3 SV=1	Back alignment and function description

>sp\|Q7SD49\|MUS81_NEUCR Crossover junction endonuclease mus-81 OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN=mus-81 PE=3 SV=1	Back alignment and function description

>sp\|Q6FYA6\|MUS81_CANGA Crossover junction endonuclease MUS81 OS=Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) GN=MUS81 PE=3 SV=1	Back alignment and function description

>sp\|Q7SXA9\|MUS81_DANRE Crossover junction endonuclease MUS81 OS=Danio rerio GN=mus81 PE=1 SV=1	Back alignment and function description

>sp\|Q04149\|MUS81_YEAST Crossover junction endonuclease MUS81 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=MUS81 PE=1 SV=1	Back alignment and function description

>sp\|Q91ZJ0\|MUS81_MOUSE Crossover junction endonuclease MUS81 OS=Mus musculus GN=Mus81 PE=1 SV=2	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		632
255544095		669	endonuclease, putative [Ricinus communis	0.974	0.920	0.669	0.0
296081297		672	unnamed protein product [Vitis vinifera]	0.973	0.915	0.650	0.0
356539474		643	PREDICTED: crossover junction endonuclea	0.966	0.950	0.663	0.0
307136394		680	endonuclease [Cucumis melo subsp. melo]	0.916	0.851	0.659	0.0
449518475		682	PREDICTED: LOW QUALITY PROTEIN: crossove	0.928	0.860	0.643	0.0
449449284		681	PREDICTED: LOW QUALITY PROTEIN: crossove	0.916	0.850	0.650	0.0
357457189		735	Crossover junction endonuclease MUS81 [M	0.871	0.749	0.638	0.0
297798882		659	ATMUS81 [Arabidopsis lyrata subsp. lyrat	0.960	0.921	0.577	0.0
79491861		659	crossover junction endonuclease MUS81 [A	0.962	0.922	0.572	0.0
119732361		660	endonuclease [Arabidopsis thaliana]	0.963	0.922	0.563	0.0

>gi\|255544095\|ref\|XP_002513110.1\| endonuclease, putative [Ricinus communis] gi\|223548121\|gb\|EEF49613.1\| endonuclease, putative [Ricinus communis]	Back alignment and taxonomy information

 Score =  893 bits (2308), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 449/671 (66%), Positives = 517/671 (77%), Gaps = 55/671 (8%)

Query: 10  HSKRRVVCAENEELAMYMLQKRQEMAETPKGLSENIDMTLSKAYNNICDAKNPIKTLKDL 69
            +++RV C ENEELA YMLQKRQ +A++PKG+SEN+DMTLSKAY+++C AK PIKTLKDL
Sbjct: 2   QNQKRVFCPENEELASYMLQKRQVLADSPKGISENLDMTLSKAYSSVCTAKTPIKTLKDL 61

Query: 70  SQVKGVGKWILKLMQEFFETDSGGSEPEDLTAKSKKSKAVKTKGTKRYMPQRNSVAYALL 129
           S +KGVGKWILKLMQ FF+     SEPEDLT K K+ K  K     +YMPQ+NSVAYALL
Sbjct: 62  SLIKGVGKWILKLMQGFFDGGPENSEPEDLTNKVKRGKEAK-----QYMPQKNSVAYALL 116

Query: 130 ITLYRGTTNGNEFMRKQDLIDAAEASGLSHTPIMPEKGKGKPRQFGSSPRDWYSGWSCMK 189
           ITLYRGT+NGNEFMRKQ+LIDAAEASGLS  PI PEKG+GKP QFGSSPRDWYSGW+CMK
Sbjct: 117 ITLYRGTSNGNEFMRKQELIDAAEASGLSRVPIAPEKGRGKPAQFGSSPRDWYSGWNCMK 176

Query: 190 TLITKGLVVKSSCPAKYMLTPGGREAARECLSRSGFADSIENVVNGKDS-DKNELSELDL 248
           TLITKGLVVKSSCPAKYMLT  GRE A ECL RS  +D  E   N ++  D +  S LDL
Sbjct: 177 TLITKGLVVKSSCPAKYMLTEEGRETACECLMRSRLSDPREGSANAEEPFDADMSSALDL 236

Query: 249 VLAHPDSNGEVTECFVPLSRKEKSTDVPFESLERFTRMGYSKEQVLRAFGEVSETSQHKE 308
             A  DS G VT   V +S ++K  DVP ESL+RF RMGYSK QVL AF EVSETS +KE
Sbjct: 237 DSARLDSAGAVTSSSVAVSGQKKPIDVPLESLQRFLRMGYSKVQVLHAFTEVSETSWNKE 296

Query: 309 ISSLWPAVLCRLQEDEVYALHSELHSVRED------------------------------ 338
           ISSLWPAVLCRL+ED+VY LHSEL S R+D                              
Sbjct: 297 ISSLWPAVLCRLREDQVYGLHSELQSFRKDCQFTTTAYTYTNGIVDFVDHQSVTDLTSDG 356

Query: 339 ------------YDA------ASRTCISTNDDPKTRVNLLSVPPLSFGERFEDAYEVVLI 380
                       +D+      +S  C+  N   +  +N LS+PPLS GERFED YEVVL+
Sbjct: 357 GETSNSCSVRSAHDSFSLRACSSSVCVHLNG-LEANLNTLSMPPLSLGERFEDVYEVVLV 415

Query: 381 LDDREQFAVQGSRSRRIIENVCSQFKIQMEVRRLPVGDGIWIARHRQTQSEYVLDFIVER 440
           LDDREQFAVQGS+  ++IEN+C + KI++ VRRLPVGDGIWIARH+   SEYVLDFIVER
Sbjct: 416 LDDREQFAVQGSKCSKLIENICKEHKIKIVVRRLPVGDGIWIARHKYLHSEYVLDFIVER 475

Query: 441 KKVDDLRSSIRDNRYRDQKLRLVRCGLKKLIYLVEGDPNSSEAAESIKTACFTTEILEGF 500
           KKV+DLRSSIRD+RY+DQKLRL+RCGL+KLIYLVEGDPN  EAAESIKTACFTTEILEGF
Sbjct: 476 KKVEDLRSSIRDHRYKDQKLRLLRCGLRKLIYLVEGDPNFCEAAESIKTACFTTEILEGF 535

Query: 501 DVQRTSGLADTLRKYGYITQAITEYYKVELPEDQLKCAAVCPPFDEFLKRCQDLDKMTVS 560
           DVQRTS L DTL+KYGY+T +IT+YY  +L  DQ KC  VCP FDEF+KRCQDL+KMT+S
Sbjct: 536 DVQRTSCLRDTLKKYGYLTHSITQYYSSQLLADQPKCNEVCPSFDEFIKRCQDLEKMTIS 595

Query: 561 DVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSAS 620
           DVFA+QLMQVPQVTEEIAI VLDLYPTL+SLA AYS+L+GDVCAQEEML K SNNA+SA+
Sbjct: 596 DVFAIQLMQVPQVTEEIAIAVLDLYPTLISLACAYSLLDGDVCAQEEMLRKHSNNAISAT 655

Query: 621 ASRNIFQLVWG 631
           ASRNIF+LVWG
Sbjct: 656 ASRNIFRLVWG 666

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|296081297\|emb\|CBI17741.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356539474\|ref\|XP_003538223.1\| PREDICTED: crossover junction endonuclease MUS81-like [Glycine max]	Back alignment and taxonomy information

>gi\|307136394\|gb\|ADN34204.1\| endonuclease [Cucumis melo subsp. melo]	Back alignment and taxonomy information

>gi\|449518475\|ref\|XP_004166267.1\| PREDICTED: LOW QUALITY PROTEIN: crossover junction endonuclease MUS81-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449449284\|ref\|XP_004142395.1\| PREDICTED: LOW QUALITY PROTEIN: crossover junction endonuclease MUS81-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|357457189\|ref\|XP_003598875.1\| Crossover junction endonuclease MUS81 [Medicago truncatula] gi\|355487923\|gb\|AES69126.1\| Crossover junction endonuclease MUS81 [Medicago truncatula]	Back alignment and taxonomy information

>gi\|297798882\|ref\|XP_002867325.1\| ATMUS81 [Arabidopsis lyrata subsp. lyrata] gi\|297313161\|gb\|EFH43584.1\| ATMUS81 [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|79491861\|ref\|NP_194816.2\| crossover junction endonuclease MUS81 [Arabidopsis thaliana] gi\|75252152\|sp\|Q5W9E7.1\|MUS81_ARATH RecName: Full=Crossover junction endonuclease MUS81; AltName: Full=Protein MMS AND UV SENSITIVE 81; Short=AtMUS81 gi\|54606637\|dbj\|BAD66696.1\| endonuclease [Arabidopsis thaliana] gi\|332660422\|gb\|AEE85822.1\| crossover junction endonuclease MUS81 [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|119732361\|gb\|ABL98212.1\| endonuclease [Arabidopsis thaliana]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		632
TAIR\|locus:2126729		659	MUS81 "AT4G30870" [Arabidopsis	0.460	0.441	0.680	1.1e-187
TAIR\|locus:2167057		1272	AT5G39770 "AT5G39770" [Arabido	0.322	0.160	0.602	2.5e-121
POMBASE\|SPCC4G3.05c		608	mus81 "Holliday junction resol	0.234	0.243	0.348	1.7e-30
SGD\|S000002794		632	MUS81 "Subunit of the structur	0.235	0.235	0.337	8.1e-25
ASPGD\|ASPL0000038580		677	AN3118 [Emericella nidulans (t	0.246	0.230	0.372	7.7e-24
ZFIN\|ZDB-GENE-040426-2923		612	mus81 "MUS81 endonuclease homo	0.231	0.238	0.371	1.8e-23
DICTYBASE\|DDB_G0284175		921	DDB_G0284175 "putative crossov	0.267	0.183	0.340	2.8e-22
UNIPROTKB\|G4MSU8		594	MGG_04585 "Crossover junction	0.238	0.254	0.329	2.9e-22
UNIPROTKB\|E1B8J2		552	MUS81 "Uncharacterized protein	0.25	0.286	0.354	3.2e-22
UNIPROTKB\|H0YDE3		389	MUS81 "Crossover junction endo	0.237	0.385	0.354	3.7e-22

TAIR\|locus:2126729 MUS81 "AT4G30870" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1026 (366.2 bits), Expect = 1.1e-187, Sum P(2) = 1.1e-187
 Identities = 200/294 (68%), Positives = 237/294 (80%)

Query:   342 ASRTCIST--NDDPKTRVNLLSVPPLSFGERFEDAYEVVLILDDREQFAVQGSRSRRIIE 399
             A + C S+  +D  K   N+  +PPL FGE FE+AY+V+LILDDRE+FA +GSRSR I+E
Sbjct:   366 AVKACSSSLASDGTKGITNIPRLPPLQFGETFEEAYDVILILDDREKFATKGSRSRNIVE 425

Query:   400 NVCSQFKIQMEVRRLPVGDGIWIARHRQTQSEYVLDFIVERKKVDDLRSSIRDNRYRDQK 459
             N+CS+F I++EVRRLPVGD IWIARH+  ++EYVLDFI ERK VDD+RSSIRDNRYRDQK
Sbjct:   426 NICSEFNIKIEVRRLPVGDCIWIARHKYLETEYVLDFIAERKNVDDMRSSIRDNRYRDQK 485

Query:   460 LRLVRCGLKKLIYLVEGDPNSSEAAESIKTACFTTEILEGFDVQRTSGLADTLRKYGYIT 519
             LRL R G KKLIY++EGDPN S+AAESIKTACFTTEILEGFDV RT GL +TLRKYGY+T
Sbjct:   486 LRLQRSGFKKLIYILEGDPNHSDAAESIKTACFTTEILEGFDVLRTHGLGETLRKYGYLT 545

Query:   520 QAITEYYKVELPE-DQLKCAAVCPPFDEFLKRCQDLDKMTVSDVFAVQLMQVPQVTEEIA 578
             ++I +YYK+ + + DQ K AA CP FD F+KRCQDLDKMT+SDVFA+QLMQVPQVTEEIA
Sbjct:   546 KSIYQYYKLRVNDNDQSKGAASCPSFDSFVKRCQDLDKMTISDVFAIQLMQVPQVTEEIA 605

Query:   579 ITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQXXXXXXXXXXXXIFQLVWGK 632
             I VLD+YPTLLSLA AYS LE DV AQEEML  +            IF+LVWG+
Sbjct:   606 IAVLDMYPTLLSLASAYSHLEADVSAQEEMLRNRSNNVICASASKNIFKLVWGE 659

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003677 "DNA binding" evidence=IEA

GO:0004518 "nuclease activity" evidence=IEA

GO:0004519 "endonuclease activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0006281 "DNA repair" evidence=ISS;IMP

GO:0006312 "mitotic recombination" evidence=RCA;IMP

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

GO:0000794 "condensed nuclear chromosome" evidence=IDA

GO:0051026 "chiasma assembly" evidence=IGI

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

GO:0000278 "mitotic cell cycle" evidence=RCA

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

GO:0006355 "regulation of transcription, DNA-dependent" evidence=RCA

GO:0006396 "RNA processing" evidence=RCA

GO:0007062 "sister chromatid cohesion" evidence=RCA

GO:0007129 "synapsis" evidence=RCA

GO:0007131 "reciprocal meiotic recombination" evidence=RCA

GO:0007140 "male meiosis" evidence=RCA

GO:0008284 "positive regulation of cell proliferation" evidence=RCA

GO:0009410 "response to xenobiotic stimulus" evidence=RCA

GO:0009560 "embryo sac egg cell differentiation" evidence=RCA

GO:0016444 "somatic cell DNA recombination" evidence=RCA

GO:0042138 "meiotic DNA double-strand break formation" evidence=RCA

GO:0043687 "post-translational protein modification" evidence=RCA

GO:0045132 "meiotic chromosome segregation" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA

GO:0048522 "positive regulation of cellular process" evidence=RCA

GO:0051276 "chromosome organization" evidence=RCA

TAIR\|locus:2167057 AT5G39770 "AT5G39770" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

POMBASE\|SPCC4G3.05c mus81 "Holliday junction resolvase subunit Mus81" [Schizosaccharomyces pombe (taxid:4896)]	Back alignment and assigned GO terms

SGD\|S000002794 MUS81 "Subunit of the structure-specific Mms4p-Mus81p endonuclease that clea" [Saccharomyces cerevisiae (taxid:4932)]	Back alignment and assigned GO terms

ASPGD\|ASPL0000038580 AN3118 [Emericella nidulans (taxid:162425)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-040426-2923 mus81 "MUS81 endonuclease homolog (yeast)" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

DICTYBASE\|DDB_G0284175 DDB_G0284175 "putative crossover junction endonuclease" [Dictyostelium discoideum (taxid:44689)]	Back alignment and assigned GO terms

UNIPROTKB\|G4MSU8 MGG_04585 "Crossover junction endonuclease MUS81" [Magnaporthe oryzae 70-15 (taxid:242507)]	Back alignment and assigned GO terms

UNIPROTKB\|E1B8J2 MUS81 "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|H0YDE3 MUS81 "Crossover junction endonuclease MUS81" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q5W9E7	MUS81_ARATH	3, ., 1, ., 2, 2, ., -	0.5724	0.9620	0.9226	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.1.22	0.691

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	Alignment Graph	Length	Definition	E-value
Query		632
smart00891		98	smart00891, ERCC4, ERCC4 domain	1e-24
pfam02732		102	pfam02732, ERCC4, ERCC4 domain	9e-20
COG1948		254	COG1948, MUS81, ERCC4-type nuclease [DNA replicati	2e-15
PRK13766		773	PRK13766, PRK13766, Hef nuclease; Provisional	2e-04

>gnl\|CDD\|214888 smart00891, ERCC4, ERCC4 domain	Back alignment and domain information

 Score = 97.8 bits (244), Expect = 1e-24
 Identities = 31/101 (30%), Positives = 51/101 (50%), Gaps = 5/101 (4%)

Query: 378 VLILDDREQFAVQGSRSRRIIENVCSQFKIQMEVRRLPVGDGIWIARHRQT--QSEYVLD 435
            +I+D RE    + +    I  ++  +  +++E  RL  GD + +AR +Q+       L+
Sbjct: 1   EIIVDSREL---RSALEAPIPRSLRWKRGVKVEYDRLEAGDFVLVARDKQSLLPHVNSLN 57

Query: 436 FIVERKKVDDLRSSIRDNRYRDQKLRLVRCGLKKLIYLVEG 476
            +VERK + DL +SI D R  +Q  RL +        LVEG
Sbjct: 58  ELVERKSLTDLVASIPDGRLFEQVRRLQQIAYPSPQLLVEG 98

This entry represents a structural motif found in several DNA repair nucleases, such as Rad1/Mus81/XPF endonucleases, and in ATP-dependent helicases. The XPF/Rad1/Mus81-dependent nuclease family specifically cleaves branched structures generated during DNA repair, replication, and recombination, and is essential for maintaining genome stability. The nuclease domain architecture exhibits remarkable similarity to those of restriction endonucleases. Length = 98

>gnl\|CDD\|217207 pfam02732, ERCC4, ERCC4 domain	Back alignment and domain information

>gnl\|CDD\|224859 COG1948, MUS81, ERCC4-type nuclease [DNA replication, recombination, and repair]	Back alignment and domain information

>gnl\|CDD\|237496 PRK13766, PRK13766, Hef nuclease; Provisional	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		632
KOG2379		501	consensus Endonuclease MUS81 [Replication, recombi	100.0
COG1948		254	MUS81 ERCC4-type nuclease [DNA replication, recomb	100.0
PRK13766		773	Hef nuclease; Provisional	99.95
TIGR00596		814	rad1 DNA repair protein (rad1). This family is bas	99.94
PF02732		143	ERCC4: ERCC4 domain; InterPro: IPR006166 This entr	99.91
KOG0442		892	consensus Structure-specific endonuclease ERCC1-XP	99.78
PF14716		68	HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HU	98.16
KOG2534		353	consensus DNA polymerase IV (family X) [Replicatio	97.18
KOG2841		254	consensus Structure-specific endonuclease ERCC1-XP	97.0
smart00483		334	POLXc DNA polymerase X family. includes vertebrate	96.61
PF12826		64	HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS	95.79
cd00141		307	NT_POLXc Nucleotidyltransferase (NT) domain of fam	95.44
PRK08609		570	hypothetical protein; Provisional	93.93
TIGR00084		191	ruvA Holliday junction DNA helicase, RuvA subunit.	92.55
PRK13901		196	ruvA Holliday junction DNA helicase RuvA; Provisio	92.41
PRK14602		203	ruvA Holliday junction DNA helicase RuvA; Provisio	92.21
PRK14605		194	ruvA Holliday junction DNA helicase RuvA; Provisio	92.08
PRK14601		183	ruvA Holliday junction DNA helicase RuvA; Provisio	91.98
PRK14603		197	ruvA Holliday junction DNA helicase RuvA; Provisio	91.78
PRK14604		195	ruvA Holliday junction DNA helicase RuvA; Provisio	91.78
PRK14600		186	ruvA Holliday junction DNA helicase RuvA; Provisio	91.55
PRK14606		188	ruvA Holliday junction DNA helicase RuvA; Provisio	91.49
COG1948		254	MUS81 ERCC4-type nuclease [DNA replication, recomb	91.4
TIGR03433		100	padR_acidobact transcriptional regulator, Acidobac	91.12
PF14520		60	HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU	91.06
TIGR02337		118	HpaR homoprotocatechuate degradation operon regula	90.99
PF13463		68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	89.35
PF14947		77	HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_	89.22
PF01638		90	HxlR: HxlR-like helix-turn-helix; InterPro: IPR002	89.16
PF00633		30	HHH: Helix-hairpin-helix motif; InterPro: IPR00044	89.07
PRK14671		621	uvrC excinuclease ABC subunit C; Provisional	88.14
PF00633		30	HHH: Helix-hairpin-helix motif; InterPro: IPR00044	87.69
PRK14669		624	uvrC excinuclease ABC subunit C; Provisional	87.56
PF09114		96	MotA_activ: Transcription factor MotA, activation	87.38
cd00080		75	HhH2_motif Helix-hairpin-helix class 2 (Pol1 famil	86.54
PRK00116		192	ruvA Holliday junction DNA helicase RuvA; Reviewed	85.03
PF13601		80	HTH_34: Winged helix DNA-binding domain; PDB: 1UB9	84.59
PF12826		64	HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS	84.34
PRK14667		567	uvrC excinuclease ABC subunit C; Provisional	82.64
TIGR02719		138	repress_PhaQ poly-beta-hydroxybutyrate-responsive	82.53
PF11313		85	DUF3116: Protein of unknown function (DUF3116); In	82.26
PF03551		75	PadR: Transcriptional regulator PadR-like family;	82.26
PF14277		163	DUF4364: Domain of unknown function (DUF4364)	81.99
PRK03902		142	manganese transport transcriptional regulator; Pro	81.89
PRK00558		598	uvrC excinuclease ABC subunit C; Validated	81.66
PF07848		70	PaaX: PaaX-like protein; InterPro: IPR012906 This	81.2
COG1695		138	Predicted transcriptional regulators [Transcriptio	80.8
PF14338		92	Mrr_N: Mrr N-terminal domain	80.63
COG1555		149	ComEA DNA uptake protein and related DNA-binding p	80.56
COG1733		120	Predicted transcriptional regulators [Transcriptio	80.5
PRK13777		185	transcriptional regulator Hpr; Provisional	80.4
PRK09482		256	flap endonuclease-like protein; Provisional	80.4

>KOG2379 consensus Endonuclease MUS81 [Replication, recombination and repair]	Back alignment and domain information

Probab=100.00  E-value=9.9e-72  Score=598.64  Aligned_cols=471  Identities=36%  Similarity=0.472  Sum_probs=348.9

Q ss_pred             ccccccccccCCCCHHHHHHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHhccCCCCCChhhhhccccchH-HHHHHHHH
Q 006771            7 MENHSKRRVVCAENEELAMYMLQKRQEMAETPKGLSENIDMTLSKAYNNICDAKNPIKTLKDLSQVKGVGK-WILKLMQE   85 (632)
Q Consensus         7 ~~~~~~~~~~~~~N~~l~~~~~ew~~e~~e~~~g~~~~~~~ty~kA~~sl~~~p~~~~~~k~l~~lkG~G~-~i~~~L~~   85 (632)
                      |+|+. +.+....++ +  .+.+|.....++++|...+..++|.||+++||+||.|+-+.+++++++|||+ ||++.++.
T Consensus         1 m~~~~-~~~~~s~~g-~--~~~~~~~~~~~~~~~~~~~~~~s~~ka~r~l~~~~~~l~tl~dl~~ikG~G~~~~~k~~~~   76 (501)
T KOG2379|consen    1 MENPS-LQLTSSLRG-R--TFRRKVNRLDHKPKGESRKSEYSLKKALRNLCKAKDPLMTLPDLSSIKGFGKKWIVKLMEA   76 (501)
T ss_pred             CCccc-cccccCCCC-c--hhhhhhhhhhhcccccchhhcccHHHHHHHhhcccCcccchhhcccccCccchhHHHHHhH
Confidence            66663 444445555 2  5666666667777888889999999999999999999999999999999999 88888776


Q ss_pred             H---hhcCCCC-CCCchhhhhcccccccccCCCcccccCCCchHHHHHHHHHhcCCCCCCCCCHHHHHHHHHhcCCCCCC
Q 006771           86 F---FETDSGG-SEPEDLTAKSKKSKAVKTKGTKRYMPQRNSVAYALLITLYRGTTNGNEFMRKQDLIDAAEASGLSHTP  161 (632)
Q Consensus        86 ~---~~~~~~~-~p~~~~~~~~~~~~~kk~r~~k~YvP~~rSGaYAiLlaL~~~~~~~~~~mtK~eLi~~Aq~~~~ss~~  161 (632)
                      |   |.++... .-|.  +..|+     +.....+|+|+++|-.|+.+..+++....+..            ..++.   
T Consensus        77 ~~~~~~~~~e~~~~~~--n~~gk-----~~~~~ee~~~~R~s~~~~~~~~~~r~~~~~~~------------r~~l~---  134 (501)
T KOG2379|consen   77 YSVLCVENNEQLSLPT--NRSGK-----KALDDEEYRPQRYSVEDAGVTDGHRLPTKDKA------------RSGLE---  134 (501)
T ss_pred             HHHHhhcccccccccc--ccccc-----cccccchhhhhhhhhcccccccccccCccchh------------hcccC---
Confidence            5   4444332 1111  22333     67778999999999999999888776554332            11111   


Q ss_pred             CCCCCCCCCCCCCCCCCCcccccchhhHHHHhcCcEeeecCCCceecChhHHHHHHHHHhhcCCCCCcc-cccCCCCCCC
Q 006771          162 IMPEKGKGKPRQFGSSPRDWYSGWSCMKTLITKGLVVKSSCPAKYMLTPGGREAARECLSRSGFADSIE-NVVNGKDSDK  240 (632)
Q Consensus       162 ~~p~~~~~~~~~~~~~~~~fYtaWsSmktLi~k~LV~~~grP~rY~LTdeG~elA~~l~~~~~~~~~~~-~~~~~~~~~~  240 (632)
                        |+            ... ++-|..+..++..|++.+++.|..+..|+.+....-.       ..+.+ ..+..-. + 
T Consensus       135 --~~------------~~~-~~~~~~~n~~~~~G~~~~~~~~~~~~~~~~~~n~~~~-------~~~~~r~q~~~~~-~-  190 (501)
T KOG2379|consen  135 --PQ------------ERT-GTHQIMANLLIREGLSKDEIAPLPRNYTDALLNSVPV-------ESPRSRMQSLVPK-G-  190 (501)
T ss_pred             --cc------------ccc-cchHHHHHHhhcCccccccccccchhccchhhccCCc-------CCcHHHhhccCcc-c-
Confidence              11            011 3449999999999999999999999999999883322       11111 1111000 0 


Q ss_pred             cccchhhhhccCCCCCCCcccccccCccCCCCCCCCchhhhhhhhcCcchhHHhhhcccccccccccccccchhhhhhhc
Q 006771          241 NELSELDLVLAHPDSNGEVTECFVPLSRKEKSTDVPFESLERFTRMGYSKEQVLRAFGEVSETSQHKEISSLWPAVLCRL  320 (632)
Q Consensus       241 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~s~~~~~~~~~  320 (632)
                          .....       ......       .  ++ |                                 ..+++...|..
T Consensus       191 ----s~~~~-------~~~~~q-------~--~d-~---------------------------------~e~r~~~~~~~  216 (501)
T KOG2379|consen  191 ----SHLLS-------EVSNQQ-------T--LD-P---------------------------------LEKRLLKTCRY  216 (501)
T ss_pred             ----hhhhe-------eccccc-------c--cC-h---------------------------------hhcCccccccc
Confidence                00000       000000       0  00 0                                 00000000000


Q ss_pred             chhhhhhhccccccccccccccccccccCCCCCCcccccccCCCCCcCCCCCCceeEEEEEeCcccccccCCchHHHHHH
Q 006771          321 QEDEVYALHSELHSVREDYDAASRTCISTNDDPKTRVNLLSVPPLSFGERFEDAYEVVLILDDREQFAVQGSRSRRIIEN  400 (632)
Q Consensus       321 ~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~pp~~~~~~~~~~y~V~LvVD~RE~~s~~~~~~r~~i~~  400 (632)
                                                   ++     .....+-        .|+.++. |+|+||+++ ..  .+.++.+
T Consensus       217 -----------------------------~~-----~~~~~~c--------~d~~e~~-~~d~~~iks-~~--~~l~~~~  250 (501)
T KOG2379|consen  217 -----------------------------SN-----QPTELVC--------SDNREVF-IIDTREIKS-LL--RRLFFGE  250 (501)
T ss_pred             -----------------------------cc-----cceeEEe--------cCCceee-eccCccccc-cc--hhhhhhh
Confidence                                         00     0000000        2456888 999999984 22  3567777


Q ss_pred             HHhhCCCcEEEEeccCCCEEEEeeccCCCcceeeceeEEEechhHHHhhhccchHHHHHHHHHHcCCCceEEEEeCC--C
Q 006771          401 VCSQFKIQMEVRRLPVGDGIWIARHRQTQSEYVLDFIVERKKVDDLRSSIRDNRYRDQKLRLVRCGLKKLIYLVEGD--P  478 (632)
Q Consensus       401 ~l~~~gV~~evr~L~vGD~iWvar~k~~~~E~VLd~IVERKrldDL~~SI~DGRf~eQK~RLk~sG~~~~iYLVEg~--~  478 (632)
                      .+...||+++||+|+||||||||+|+..|.|+||||||||||+|||++||+||||+|||+||++||++++||||||+  .
T Consensus       251 ~~~~~~v~~evR~L~vGD~lWVa~~k~~g~E~VLd~IVERKr~DDl~SSIrDgRf~EQK~RLq~sGik~~iYlvE~~~~~  330 (501)
T KOG2379|consen  251 YFELEGVKHEVRSLEVGDFLWVARHKYDGTELVLDFIVERKRLDDLVSSIRDGRFKEQKNRLQRSGIKRIIYLVEEDGNP  330 (501)
T ss_pred             hhhhccceeeEEEecccceEEEecccCCCceEeeeeheeecchHHHHHHHhccchHHHHHHHHhcCcceEEEEEeccCCc
Confidence            78889999999999999999999999999999999999999999999999999999999999999999999999998  5


Q ss_pred             CCchhHHHHHHHHHHhhhhcCceEEEcCCHHHHHHHHHHHHHHHHHhhhhcCCc--------cccc-----cCcCCCChh
Q 006771          479 NSSEAAESIKTACFTTEILEGFDVQRTSGLADTLRKYGYITQAITEYYKVELPE--------DQLK-----CAAVCPPFD  545 (632)
Q Consensus       479 ~~~~~~e~i~tAl~~tqv~~gf~V~rT~~~~eT~~~L~~lt~~i~~~y~~~~~~--------~~~~-----~~~~~~~f~  545 (632)
                      +.+.+.++|++|+++|+|.+||+|+||.|+.||+++|+++|+.+.+.|.....+        ++..     +...|++|+
T Consensus       331 n~~~~~eslktA~~~t~v~~GF~V~RT~~l~et~s~l~y~tr~~~~~~~~~~~~~~d~~~~~~q~~~~~~~p~~~~~~f~  410 (501)
T KOG2379|consen  331 NQSKPAESLKTAVTNTLVLEGFDVIRTRDLGETVSKLAYLTRGLLQIYASLLLDKEDYRERDDQLKGAMTVPSETELSFS  410 (501)
T ss_pred             ccccHHHHHHHHHHHHhhhcceEEEEecChhHHHHHHHHHhHHHHHHHHHhhccccccccchhhhhcccCCCCcccccHH
Confidence            566789999999999999999999999999999999999999999998775432        1111     123457899


Q ss_pred             hhhhhhcccccccchHHHHHHHhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhccccHHHHHHHhhhhc----CCcccHHH
Q 006771          546 EFLKRCQDLDKMTVSDVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQS----NNAVSASA  621 (632)
Q Consensus       546 ~f~~~~~K~~~~Tv~e~f~~mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~~~~~~e~mL~~~~----~~~IG~~l  621 (632)
                      +|++.++|++.+||+|+|++|||+|+|||.++|.||+++||||.+|+.||+.++. .+++..||..+.    .+.||++|
T Consensus       411 ~F~~~~~K~~~~TV~evf~~qLMqvkg~S~erAiAI~d~YpTl~sLl~AY~~s~~-~k~~~l~ln~~~~~~~~rn~~~~L  489 (501)
T KOG2379|consen  411 AFQERLSKGKALTVGEVFARQLMQVKGMSLERAIAIADRYPTLRSLLSAYEVSAD-DKLRLLLLNPIKCGPGSRNIGPAL  489 (501)
T ss_pred             HHHHHhhhcccccHHHHHHHHHHhccCccHHHHHHHHHhccCHHHHHHHHhccCc-HHHHhccccccccccccccccHHH
Confidence            9999999999999999999999999999999999999999999999999997654 566666666653    35699999


Q ss_pred             Hhhhhhh
Q 006771          622 SRNIFQL  628 (632)
Q Consensus       622 Sr~Iy~~  628 (632)
                      |.+||.+
T Consensus       490 s~~l~~~  496 (501)
T KOG2379|consen  490 SAKLYEF  496 (501)
T ss_pred             HHHHHHh
Confidence            9999973

>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]	Back alignment and domain information

>PRK13766 Hef nuclease; Provisional	Back alignment and domain information

>TIGR00596 rad1 DNA repair protein (rad1)	Back alignment and domain information

>PF02732 ERCC4: ERCC4 domain; InterPro: IPR006166 This entry represents a structural motif found in several DNA repair nucleases, such as Rad1/Mus81/XPF endonucleases (3	Back alignment and domain information

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

>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	Back alignment and domain information

>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]	Back alignment and domain information

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

>smart00483 POLXc DNA polymerase X family	Back alignment and domain information

>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B	Back alignment and domain information

>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases	Back alignment and domain information

>PRK08609 hypothetical protein; Provisional	Back alignment and domain information

>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit	Back alignment and domain information

>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional	Back alignment and domain information

>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional	Back alignment and domain information

>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional	Back alignment and domain information

>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional	Back alignment and domain information

>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional	Back alignment and domain information

>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional	Back alignment and domain information

>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional	Back alignment and domain information

>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional	Back alignment and domain information

>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]	Back alignment and domain information

>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family	Back alignment and domain information

>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	Back alignment and domain information

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR	Back alignment and domain information

>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A	Back alignment and domain information

>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A	Back alignment and domain information

>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure	Back alignment and domain information

>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 [, , ]	Back alignment and domain information

>PRK14671 uvrC excinuclease ABC subunit C; Provisional	Back alignment and domain information

>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 [, , ]	Back alignment and domain information

>PRK14669 uvrC excinuclease ABC subunit C; Provisional	Back alignment and domain information

>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase	Back alignment and domain information

>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif	Back alignment and domain information

>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed	Back alignment and domain information

>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A	Back alignment and domain information

>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B	Back alignment and domain information

>PRK14667 uvrC excinuclease ABC subunit C; Provisional	Back alignment and domain information

>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor	Back alignment and domain information

>PF11313 DUF3116: Protein of unknown function (DUF3116); InterPro: IPR021464 This family of proteins with unknown function appears to be restricted to Bacillales	Back alignment and domain information

>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles	Back alignment and domain information

>PF14277 DUF4364: Domain of unknown function (DUF4364)	Back alignment and domain information

>PRK03902 manganese transport transcriptional regulator; Provisional	Back alignment and domain information

>PRK00558 uvrC excinuclease ABC subunit C; Validated	Back alignment and domain information

>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT)	Back alignment and domain information

>COG1695 Predicted transcriptional regulators [Transcription]	Back alignment and domain information

>PF14338 Mrr_N: Mrr N-terminal domain	Back alignment and domain information

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

>COG1733 Predicted transcriptional regulators [Transcription]	Back alignment and domain information

>PRK13777 transcriptional regulator Hpr; Provisional	Back alignment and domain information

>PRK09482 flap endonuclease-like protein; Provisional	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		632
2ziu_A		311	Crystal Structure Of The Mus81-Eme1 Complex Length		1e-25
2zix_A		307	Crystal Structure Of The Mus81-Eme1 Complex Length		1e-24
2ziw_A		311	Crystal Structure Of The Mus81-Eme1 Complex Length		5e-24

>pdb|2ZIU|A Chain A, Crystal Structure Of The Mus81-Eme1 Complex Length = 311

Back alignment and structure

Iteration: 1

Score = 115 bits (287), Expect = 1e-25, Method: Compositional matrix adjust. Identities = 91/271 (33%), Positives = 138/271 (50%), Gaps = 52/271 (19%) Query: 374 AYEVVLILDDREQFAVQGSRSRRIIENVCSQFKIQMEVRRLPVGDGIWIARHRQT----- 428 +Y++VL +D E R + +++ + + + +VR+L VGD +W+AR R T Sbjct: 17 SYDIVLCVDLCETTGGSSVRKQELVKEL-QRNSVTFDVRKLNVGDFLWVARERVTPVPGQ 75 Query: 429 -----QSEYVLDFIVERKKVDDLRSSIRDNRYRDQKLRLVRCGLKKLIYLVEGDPNSSEA 483 E VLD+I+ERK++DDL SI D R+R+QK RL RCGL+K IYLVE + S+ A Sbjct: 76 LRPPVGKELVLDYIIERKRMDDLCGSIIDGRFREQKFRLKRCGLRKPIYLVE-ECGSAAA 134 Query: 484 AESI-----KTACFTTEILEGFDVQRTSGLADTLRKYGYITQAITEYYK--------VEL 530 SI + A T++++GF V+R ++ +T+ + + Y+ EL Sbjct: 135 HLSIPESTLQQAIVNTQVVDGFFVKRVQDAKESAAYLTIMTRYLQKLYQNCTLFCRSREL 194 Query: 531 PED----------QLKCAAVCPPFDEF-----LKRCQDLDKMTVSDVFAVQLMQVPQVTE 575 D L C+ + F EF +CQ TV +VFA QLMQ+ V+ Sbjct: 195 EGDGEAESEKMVANLSCSLM--AFTEFNYGAIKNKCQ-----TVREVFARQLMQISGVSG 247 Query: 576 EIAITVLDLYPTLLSLAHAYSILEGDVCAQE 606 + A VL+ Y T+ SL AY D C+ E Sbjct: 248 DKAAAVLEHYSTVSSLLQAY-----DKCSSE 273

PyMOL of 2ziu

>pdb|2ZIX|A Chain A, Crystal Structure Of The Mus81-Eme1 Complex Length = 307

Back alignment and structure

>pdb|2ZIW|A Chain A, Crystal Structure Of The Mus81-Eme1 Complex Length = 311

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		632
2ziu_A		311	MUS81 protein; helix-hairpin-helix, alternative sp	8e-42
2zix_A		307	Crossover junction endonuclease MUS81; helix-hairp	9e-41
1j23_A		143	HEF nuclease, ATP-dependent RNA helicase, putative	1e-20
2bgw_A		219	XPF endonuclease; hydrolase, structure specific en	1e-18
2ziu_B		341	Crossover junction endonuclease EME1; helix-hairpi	2e-18
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-14
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-06

>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 Length = 311	Back alignment and structure

 Score =  152 bits (385), Expect = 8e-42
 Identities = 84/293 (28%), Positives = 138/293 (47%), Gaps = 34/293 (11%)

Query: 373 DAYEVVLILDDREQFAVQGSRSRRIIENVCSQFKIQMEVRRLPVGDGIWIARHRQTQS-- 430
            +Y++VL +D  E       R + +++    +  +  +VR+L VGD +W+AR R T    
Sbjct: 16  GSYDIVLCVDLCETTGGSSVRKQELVKE-LQRNSVTFDVRKLNVGDFLWVARERVTPVPG 74

Query: 431 --------EYVLDFIVERKKVDDLRSSIRDNRYRDQKLRLVRCGLKKLIYLVEG----DP 478
                   E VLD+I+ERK++DDL  SI D R+R+QK RL RCGL+K IYLVE       
Sbjct: 75  QLRPPVGKELVLDYIIERKRMDDLCGSIIDGRFREQKFRLKRCGLRKPIYLVEECGSAAA 134

Query: 479 NSSEAAESIKTACFTTEILEGFDVQRTSGLADTLRKYGYITQAITEYYK----------- 527
           + S    +++ A   T++++GF V+R     ++      +T+ + + Y+           
Sbjct: 135 HLSIPESTLQQAIVNTQVVDGFFVKRVQDAKESAAYLTIMTRYLQKLYQNCTLFCRSREL 194

Query: 528 -----VELPEDQLKCAAVCPPFDEFLKRCQDLDKMTVSDVFAVQLMQVPQVTEEIAITVL 582
                 E  +     +     F EF          TV +VFA QLMQ+  V+ + A  VL
Sbjct: 195 EGDGEAESEKMVANLSCSLMAFTEFNYGAIKNKCQTVREVFARQLMQISGVSGDKAAAVL 254

Query: 583 DLYPTLLSLAHAYSILEGDVCAQ---EEMLWKQSNNAVSASASRNIFQLVWGK 632
           + Y T+ SL  AY     +   +     + + +    +  + SR I+QL   +
Sbjct: 255 EHYSTVSSLLQAYDKCSSETEKEKLLSSVKYGKLKRNLGPALSRTIYQLYCTR 307

PyMOL of 2ziu

>2zix_A Crossover junction endonuclease MUS81; helix-hairpin-helix, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium, metal-binding, nucleus; 3.50A {Homo sapiens} Length = 307	Back alignment and structure

>1j23_A HEF nuclease, ATP-dependent RNA helicase, putative; structure-specific endonuclease, hydrolase; 1.78A {Pyrococcus furiosus} SCOP: c.52.1.20 PDB: 1j22_A 1j24_A 1j25_A Length = 143	Back alignment and structure

>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	Back alignment and structure

>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 Length = 341	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		632
2ziu_A		311	MUS81 protein; helix-hairpin-helix, alternative sp	100.0
2zix_A		307	Crossover junction endonuclease MUS81; helix-hairp	100.0
2bgw_A		219	XPF endonuclease; hydrolase, structure specific en	100.0
1j23_A		143	HEF nuclease, ATP-dependent RNA helicase, putative	99.98
2ziu_B		341	Crossover junction endonuclease EME1; helix-hairpi	99.95
2kp7_A		87	Crossover junction endonuclease MUS81; helix-hairp	99.8
4gfj_A		685	Topoisomerase V; helix-hairpin-helix, DNA repair e	99.49
3c1y_A		377	DNA integrity scanning protein DISA; DNA damage, D	98.48
2fmp_A		335	DNA polymerase beta; nucleotidyl transferase, tran	96.9
2a1j_A		63	DNA repair endonuclease XPF; XPF, xeroderma pigmen	96.83
1z00_B		84	DNA repair endonuclease XPF; helix-hairpin-helix,	96.79
2ihm_A		360	POL MU, DNA polymerase MU; helix-turn-helix, trans	96.6
1jms_A		381	Terminal deoxynucleotidyltransferase; polymerase;	96.55
2bcq_A		335	DNA polymerase lambda; misalignment, extrahelical,	96.51
1x2i_A		75	HEF helicase/nuclease; alpha helix, helix-hairpin-	96.08
1z00_A		89	DNA excision repair protein ERCC-1; helix-hairpin-	95.14
2a1j_B		91	DNA excision repair protein ERCC-1; XPF, xeroderma	94.99
1tbx_A		99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	94.08
2nrt_A		220	Uvrabc system protein C; UVRC, endonuclease, RNAse	93.78
1kft_A		78	UVRC, excinuclease ABC subunit C; helix-hairpin-he	93.21
1ixr_A		191	Holliday junction DNA helicase RUVA; heterooligome	92.5
2esh_A		118	Conserved hypothetical protein TM0937; APC5794, st	91.43
3f8b_A		116	Transcriptional regulator, PADR-like family; winge	90.51
3c65_A		226	Uvrabc system protein C; UVRC, endonuclease, nucle	90.33
3b0x_A		575	DNA polymerase beta family (X family); structural	90.3
3oop_A		143	LIN2960 protein; protein structure initiative, PSI	90.2
3nrv_A		148	Putative transcriptional regulator (MARR/EMRR FAM;	90.15
3k0l_A		162	Repressor protein; helix-turn-helix, structural ge	89.96
3fm5_A		150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	89.86
1cuk_A		203	RUVA protein; DNA repair, SOS response, DNA-bindin	89.83
3g3z_A		145	NMB1585, transcriptional regulator, MARR family; t	89.76
3bja_A		139	Transcriptional regulator, MARR family, putative;	89.41
3ech_A		142	MEXR, multidrug resistance operon repressor; winge	89.15
3deu_A		166	Transcriptional regulator SLYA; MARR, WING-helix,	89.11
2qvo_A		95	Uncharacterized protein AF_1382; PSI, structural g	88.74
2dql_A		115	PEX protein; circadian clock associated protein, c	88.63
3boq_A		160	Transcriptional regulator, MARR family; MARR famil	88.61
1xma_A		145	Predicted transcriptional regulator; southea colla	88.58
3jw4_A		148	Transcriptional regulator, MARR/EMRR family; DNA-b	88.52
2wte_A		244	CSA3; antiviral protein, viral resistance, winged	88.41
3u1d_A		151	Uncharacterized protein; GNTR-superfamily, structu	87.99
3df8_A		111	Possible HXLR family transcriptional factor; APC89	87.88
3l7w_A		108	Putative uncharacterized protein SMU.1704; PADR, t	87.69
4esf_A		117	PADR-like transcriptional regulator; PADR family,	87.57
3s2w_A		159	Transcriptional regulator, MARR family; structural	87.36
2pg4_A		95	Uncharacterized protein; structural genomics, join	87.06
3hhh_A		116	Transcriptional regulator, PADR family; PF03551, s	86.28
4esb_A		115	Transcriptional regulator, PADR family; DNA bindin	86.19
2bv6_A		142	MGRA, HTH-type transcriptional regulator MGRA; mul	85.72
3f3x_A		144	Transcriptional regulator, MARR family, putative;	85.15
2frh_A		127	SARA, staphylococcal accessory regulator A; winged	84.98
1r7j_A		95	Conserved hypothetical protein SSO10A; winged heli	84.89
2co5_A		99	Viral protein F93; viral protein-winged helix comp	84.78
2nyx_A		168	Probable transcriptional regulatory protein, RV14;	84.6
1xmk_A		79	Double-stranded RNA-specific adenosine deaminase;	84.53
3kp7_A		151	Transcriptional regulator TCAR; multiple drug resi	84.39
3b73_A		111	PHIH1 repressor-like protein; winged-helix-turn-he	84.34
2fbk_A		181	Transcriptional regulator, MARR family; winged-hel	84.24
2w9m_A		578	Polymerase X; SAXS, DNA repair, DNA polymerase, DN	83.74
2duy_A		75	Competence protein comea-related protein; helix-ha	82.94
1jgs_A		138	Multiple antibiotic resistance protein MARR; trans	82.9
2duy_A		75	Competence protein comea-related protein; helix-ha	82.86
2fsw_A		107	PG_0823 protein; alpha-beta structure, helix-turn-	82.69
3eco_A		139	MEPR; mutlidrug efflux pump regulator winged helix	82.63
2e1n_A		138	PEX, period extender; circadian clock, DNA binding	82.52
2x4h_A		139	Hypothetical protein SSO2273; transcription; 2.30A	82.17
3hrs_A		214	Metalloregulator SCAR; DTXR/MNTR family member, tr	81.9
2hr3_A		147	Probable transcriptional regulator; MCSG, structur	81.87
3hsr_A		140	HTH-type transcriptional regulator SARZ; helix-tur	81.86
3cdh_A		155	Transcriptional regulator, MARR family; helix-turn	81.85
2fa5_A		162	Transcriptional regulator MARR/EMRR family; multip	81.83
1z7u_A		112	Hypothetical protein EF0647; winged-helix-turn-hel	81.73
4hbl_A		149	Transcriptional regulator, MARR family; HTH, trans	81.41
2rdp_A		150	Putative transcriptional regulator MARR; PFAM PF01	81.31
2fbh_A		146	Transcriptional regulator PA3341; MARR, transcript	80.56
3elk_A		117	Putative transcriptional regulator TA0346; structu	80.52
3e6m_A		161	MARR family transcriptional regulator; APC88769, s	80.5
2nnn_A		140	Probable transcriptional regulator; structural gen	80.36
4fx0_A		148	Probable transcriptional repressor protein; helix-	80.15

>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	Back alignment and structure

Probab=100.00  E-value=1.7e-56  Score=469.79  Aligned_cols=263  Identities=32%  Similarity=0.486  Sum_probs=225.0

Q ss_pred             ccccCCCCCcCCCCCCceeEEEEEeCcccccccCCchHHHHHHHHhhCCCcEEEEeccCCCEEEEeeccCC---------
Q 006771          358 NLLSVPPLSFGERFEDAYEVVLILDDREQFAVQGSRSRRIIENVCSQFKIQMEVRRLPVGDGIWIARHRQT---------  428 (632)
Q Consensus       358 ~~~~~pp~~~~~~~~~~y~V~LvVD~RE~~s~~~~~~r~~i~~~l~~~gV~~evr~L~vGD~iWvar~k~~---------  428 (632)
                      +++.++|        ++|+|+||||+||+++. ..++++.+.+.|.+.||++++++|++|||+|+++++..         
T Consensus         9 ~~~~~~~--------~~~~~~ivvD~RE~~~~-~~~~~~~~~~~l~~~gv~~~~~~L~vGDyiw~~~~~~~~~~~~~~~~   79 (311)
T 2ziu_A            9 MGWHLSP--------GSYDIVLCVDLCETTGG-SSVRKQELVKELQRNSVTFDVRKLNVGDFLWVARERVTPVPGQLRPP   79 (311)
T ss_dssp             -CCCBCT--------TSEEEEEEECGGGSCC------CCHHHHHHHTTTCCEECCCCSSCSEEEEEEECCCCCTTCSSCC
T ss_pred             CceeecC--------CCcEEEEEEECccccCC-ccchHHHHHHHHHHCCCCeEEEecCccCEEEEEecCCCccccccccc
Confidence            4455666        46899999999998732 11134567778999999999999999999999987763         


Q ss_pred             -CcceeeceeEEEechhHHHhhhccchHHHHHHHHHHcCCCceEEEEeCCCCC----chhHHHHHHHHHHhhhhcCceEE
Q 006771          429 -QSEYVLDFIVERKKVDDLRSSIRDNRYRDQKLRLVRCGLKKLIYLVEGDPNS----SEAAESIKTACFTTEILEGFDVQ  503 (632)
Q Consensus       429 -~~E~VLd~IVERKrldDL~~SI~DGRf~eQK~RLk~sG~~~~iYLVEg~~~~----~~~~e~i~tAl~~tqv~~gf~V~  503 (632)
                       ++|+|||||||||+++||++||+||||++|++||++||+++++|||||+.+.    ....++|++||+++++.+||.|+
T Consensus        80 ~~~e~vl~~~VERK~~~Dl~~Si~dgR~~~Q~~rl~~~g~~~~~ylIE~~~~~~~~~~~~~~~i~~aL~~l~v~~g~~Vi  159 (311)
T 2ziu_A           80 VGKELVLDYIIERKRMDDLCGSIIDGRFREQKFRLKRCGLRKPIYLVEECGSAAAHLSIPESTLQQAIVNTQVVDGFFVK  159 (311)
T ss_dssp             CCCEEEEEEEEEEEEHHHHHHHHHHTCHHHHHHHHHTTSCSEEEEEEESCSSSHHHHSSCHHHHHHHHHHHHHTTCCEEE
T ss_pred             cCceeeeeeEeEeccHHHHHHHHhcchHHHHHHHHHhCCCCCeEEEEecCCccccccCCCHHHHHHHHHHHhhhcCeEEE
Confidence             8899999999999999999999999999999999999999999999998652    23578999999999999999999


Q ss_pred             EcCCHHHHHHHHHHHHHHHHHhhhhcCC---ccc-------------cccCcCCCChhhhhhhhcccccccchHHHHHHH
Q 006771          504 RTSGLADTLRKYGYITQAITEYYKVELP---EDQ-------------LKCAAVCPPFDEFLKRCQDLDKMTVSDVFAVQL  567 (632)
Q Consensus       504 rT~~~~eT~~~L~~lt~~i~~~y~~~~~---~~~-------------~~~~~~~~~f~~f~~~~~K~~~~Tv~e~f~~mL  567 (632)
                      +|.++.||++||..||+.+.+.|+....   ++.             ......|++|++|+..+.|++++|++++|++||
T Consensus       160 ~t~s~~eTa~~l~~lt~~i~~~y~~~~l~~~p~~~~~~~~~~~~~~~~~~~~~~~~f~~f~~~~~k~~~~t~~e~~~~mL  239 (311)
T 2ziu_A          160 RVQDAKESAAYLTIMTRYLQKLYQNCTLFCRSRELEGDGEAESEKMVANLSCSLMAFTEFNYGAIKNKCQTVREVFARQL  239 (311)
T ss_dssp             ECSSHHHHHHHHHHHHHHHHHTTTTCCBCCC----------------CCSCSCCEEHHHHHHHHHHHTCCBHHHHHHHHH
T ss_pred             EeCCHHHHHHHHHHHHHHHHHHhccccccccCcchhccccccccccccCcccccccHHHHHHhcccccCCcHHHHHHHHH
Confidence            9999999999999999999998875421   110             112346789999999999999999999999999


Q ss_pred             hcCCCCCHHHHHHHHHhcCCHHHHHHHHhhccccHHHHHHHhhhhc----CCcccHHHHhhhhhhhcc
Q 006771          568 MQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQS----NNAVSASASRNIFQLVWG  631 (632)
Q Consensus       568 m~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~~~~~~e~mL~~~~----~~~IG~~lSr~Iy~~vwg  631 (632)
                      |||||||+++|.+|+++||||.+|++||++|.+ ..+++.||+++.    .++||+++|++||+ ||+
T Consensus       240 ~~IpGVs~~~A~~I~~~ypTp~~L~~Ay~~~~~-~~e~~~lL~~i~~g~~~r~IG~~lS~kI~~-~f~  305 (311)
T 2ziu_A          240 MQISGVSGDKAAAVLEHYSTVSSLLQAYDKCSS-ETEKEKLLSSVKYGKLKRNLGPALSRTIYQ-LYC  305 (311)
T ss_dssp             TTBTTCCHHHHHHHHHHCSSHHHHHHHHHHCSS-HHHHTTTTTTCEETTTTEECHHHHHHHHHH-HHH
T ss_pred             HhccCCCHHHHHHHHHHCCCHHHHHHHHHhcCC-HHHHHHHHHhcccCCCCCCcCHHHHHHHHH-Hhc
Confidence            999999999999999999999999999999976 567788898763    45699999999998 554

PyMOL of 2ziu

>2zix_A Crossover junction endonuclease MUS81; helix-hairpin-helix, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium, metal-binding, nucleus; 3.50A {Homo sapiens}	Back alignment and structure

>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	Back alignment and structure

>1j23_A HEF nuclease, ATP-dependent RNA helicase, putative; structure-specific endonuclease, hydrolase; 1.78A {Pyrococcus furiosus} SCOP: c.52.1.20 PDB: 1j22_A 1j24_A 1j25_A	Back alignment and structure

>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	Back alignment and structure

>2kp7_A Crossover junction endonuclease MUS81; helix-hairpin-helix, tumour suppressor, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; NMR {Mus musculus}	Back alignment and structure

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

>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*	Back alignment and structure

>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* ...	Back alignment and structure

>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*	Back alignment and structure

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

>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus}	Back alignment and structure

>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*	Back alignment and structure

>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* ...	Back alignment and structure

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

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

>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	Back alignment and structure

>1tbx_A ORF F-93, hypothetical 11.0 kDa protein; sulfolobus spindle virus, winged helix, fusellovirus; 2.70A {Sulfolobus virus 1} SCOP: a.4.5.48	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>2esh_A Conserved hypothetical protein TM0937; APC5794, structural genomics, PSI, protein structure initiative; 2.30A {Thermotoga maritima} SCOP: a.4.5.61	Back alignment and structure

>3f8b_A Transcriptional regulator, PADR-like family; winged helix turn helix, transcription regulator; 2.00A {Lactococcus lactis subsp} SCOP: a.4.5.0 PDB: 3f8c_A* 3f8f_A*	Back alignment and structure

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

>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*	Back alignment and structure

>3oop_A LIN2960 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; 1.78A {Listeria innocua}	Back alignment and structure

>3nrv_A Putative transcriptional regulator (MARR/EMRR FAM; PSI-2, protein structure initiati structural genomics; HET: MSE; 2.00A {Acinetobacter SP}	Back alignment and structure

>3k0l_A Repressor protein; helix-turn-helix, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.35A {Acinetobacter SP}	Back alignment and structure

>3fm5_A Transcriptional regulator; MCSG, PF04017, PSI, MARR, structu genomics, protein structure initiative, midwest center for structural genomics; HET: GOL; 2.00A {Rhodococcus jostii}	Back alignment and structure

>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	Back alignment and structure

>3g3z_A NMB1585, transcriptional regulator, MARR family; transcription factor, structur genomics, oxford protein production facility; 2.10A {Neisseria meningitidis serogroup B}	Back alignment and structure

>3bja_A Transcriptional regulator, MARR family, putative; NP_978771.1, putative MARR-like transcription regulator, MAR structural genomics; 2.38A {Bacillus cereus}	Back alignment and structure

>3ech_A MEXR, multidrug resistance operon repressor; winged helix, helix-turn-helix, protein-peptide complex; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28 PDB: 1lnw_A 3mex_A	Back alignment and structure

>3deu_A Transcriptional regulator SLYA; MARR, WING-helix, transcription regulator, activator, DNA-binding, repressor; HET: SAL; 2.30A {Salmonella typhimurium} SCOP: a.4.5.28	Back alignment and structure

>2qvo_A Uncharacterized protein AF_1382; PSI, structural genomics, southeast collaboratory for structural genomics; 1.85A {Archaeoglobus fulgidus dsm 4304} PDB: 3o3k_A 3ov8_A	Back alignment and structure

>2dql_A PEX protein; circadian clock associated protein, circadian clock protein; 1.70A {Anabaena SP}	Back alignment and structure

>3boq_A Transcriptional regulator, MARR family; MARR famil structural genomics, PSI-2, protein structure initiative; 2.39A {Silicibacter pomeroyi dss-3}	Back alignment and structure

>1xma_A Predicted transcriptional regulator; southea collaboratory for structural genomics, secsg, protein struc initiative, PSI; 2.30A {Clostridium thermocellum} SCOP: a.4.5.61	Back alignment and structure

>3jw4_A Transcriptional regulator, MARR/EMRR family; DNA-binding protein, structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.10A {Clostridium acetobutylicum} SCOP: a.4.5.0	Back alignment and structure

>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix prnai nucleotide-binding domain; HET: MSE; 1.80A {Sulfolobus solfataricus}	Back alignment and structure

>3u1d_A Uncharacterized protein; GNTR-superfamily, structural genomics, PSI-biology, midwest for structural genomics, MCSG; 1.80A {Halomicrobium mukohataei}	Back alignment and structure

>3df8_A Possible HXLR family transcriptional factor; APC89000, structural genomics, midwest center for structural genomics, MCSG; 1.65A {Thermoplasma volcanium} SCOP: a.4.5.0	Back alignment and structure

>3l7w_A Putative uncharacterized protein SMU.1704; PADR, transcriptional factor, transcription; HET: MSE; 2.20A {Streptococcus mutans} SCOP: a.4.5.0	Back alignment and structure

>4esf_A PADR-like transcriptional regulator; PADR family, DNA binding protein, HTH fold; 2.20A {Bacillus cereus}	Back alignment and structure

>3s2w_A Transcriptional regulator, MARR family; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics; 2.45A {Methanosarcina mazei}	Back alignment and structure

>2pg4_A Uncharacterized protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2, DNA binding protein; HET: MSE CIT; 2.21A {Aeropyrum pernix} SCOP: a.4.5.48	Back alignment and structure

>3hhh_A Transcriptional regulator, PADR family; PF03551, structural PSI-2, protein structure initiative, midwest center for STR genomics, MCSG; 2.70A {Enterococcus faecalis} SCOP: a.4.5.0	Back alignment and structure

>4esb_A Transcriptional regulator, PADR family; DNA binding protein, HTH fold; 2.50A {Bacillus cereus}	Back alignment and structure

>2bv6_A MGRA, HTH-type transcriptional regulator MGRA; multidrug resistance regulator, virulence determinant, transcriptional factors; 2.8A {Staphylococcus aureus} SCOP: a.4.5.28	Back alignment and structure

>3f3x_A Transcriptional regulator, MARR family, putative; DNA binding protein, DNA-binding, transcription regulation; 1.90A {Sulfolobus solfataricus}	Back alignment and structure

>2frh_A SARA, staphylococcal accessory regulator A; winged-helix protein, divalent metal binding, transcription; 2.50A {Staphylococcus aureus} SCOP: a.4.5.28 PDB: 2fnp_A 1fzp_D	Back alignment and structure

>1r7j_A Conserved hypothetical protein SSO10A; winged helix-turn-helix, two-stranded antiparallel coiled CO structural genomics, PSI; 1.47A {Sulfolobus solfataricus} SCOP: a.4.5.49 PDB: 1xsx_A	Back alignment and structure

>2co5_A Viral protein F93; viral protein-winged helix complex, winged helix, DNA-bindin WHTH, disulfide bond, STIV; 2.2A {Sulfolobus turreted icosahedral virus} SCOP: a.4.5.48	Back alignment and structure

>2nyx_A Probable transcriptional regulatory protein, RV14; alpha/beta, structural genomics, PSI-2; 2.30A {Mycobacterium tuberculosis}	Back alignment and structure

>1xmk_A Double-stranded RNA-specific adenosine deaminase; winged helix-turn-helix, RNA editing, interferon, ADAR1, hydrolase; 0.97A {Homo sapiens} SCOP: a.4.5.19	Back alignment and structure

>3kp7_A Transcriptional regulator TCAR; multiple drug resistance, biofilm, transcription regulation, binding, transcription regulator; 2.30A {Staphylococcus epidermidis RP62A} PDB: 3kp3_A* 3kp4_A* 3kp5_A* 3kp2_A* 3kp6_A	Back alignment and structure

>3b73_A PHIH1 repressor-like protein; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 2.12A {Haloarcula marismortui atcc 43049}	Back alignment and structure

>2fbk_A Transcriptional regulator, MARR family; winged-helix-turn-helix; 2.30A {Deinococcus radiodurans} SCOP: a.4.5.28	Back alignment and structure

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

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

>1jgs_A Multiple antibiotic resistance protein MARR; transcription regulation, DNA-binding, repressor, transcription; HET: SAL; 2.30A {Escherichia coli} SCOP: a.4.5.28	Back alignment and structure

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

>2fsw_A PG_0823 protein; alpha-beta structure, helix-turn-helix, winged-helix-turn-HE structural genomics, PSI, protein structure initiative; HET: MSE; 2.16A {Porphyromonas gingivalis} SCOP: a.4.5.69	Back alignment and structure

>3eco_A MEPR; mutlidrug efflux pump regulator winged helix-turn-helix motif, DNA-binding, transcription, transcription regulation; 2.40A {Staphylococcus aureus} SCOP: a.4.5.0	Back alignment and structure

>2e1n_A PEX, period extender; circadian clock, DNA binding protein, circadian clock protei; 1.80A {Synechococcus elongatus pcc 7942}	Back alignment and structure

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}	Back alignment and structure

>3hrs_A Metalloregulator SCAR; DTXR/MNTR family member, transcription; 2.70A {Streptococcus gordonii} PDB: 3hrt_A 3hru_A	Back alignment and structure

>2hr3_A Probable transcriptional regulator; MCSG, structural genomics, PSI-2, protein structure initiati midwest center for structural genomics; 2.40A {Pseudomonas aeruginosa} SCOP: a.4.5.28	Back alignment and structure

>3hsr_A HTH-type transcriptional regulator SARZ; helix-turn-helix, cysteine disulfide, MARR-family transcript regulator, DNA-binding; 1.90A {Staphylococcus aureus subsp} PDB: 3hse_A 3hrm_A 4gxo_A	Back alignment and structure

>3cdh_A Transcriptional regulator, MARR family; helix-turn-hleix, structura genomics, PSI-2, protein structure initiative; 2.69A {Silicibacter pomeroyi dss-3}	Back alignment and structure

>2fa5_A Transcriptional regulator MARR/EMRR family; multiple antibiotics resistance repressor, XCC structural genomics, X-RAY diffraction; 1.80A {Xanthomonas campestris}	Back alignment and structure

>1z7u_A Hypothetical protein EF0647; winged-helix-turn-helix, MARR, structural genomics, PSI, Pro structure initiative; 2.20A {Enterococcus faecalis} SCOP: a.4.5.69	Back alignment and structure

>4hbl_A Transcriptional regulator, MARR family; HTH, transcription factor, DNA binding; 2.50A {Staphylococcus epidermidis}	Back alignment and structure

>2rdp_A Putative transcriptional regulator MARR; PFAM PF01047, winged-helix binding motif, structural genomics, PSI-2; 2.30A {Geobacillus stearothermophilus}	Back alignment and structure

>2fbh_A Transcriptional regulator PA3341; MARR, transcription regulator, APC5857, structural genomics, protein structure initiative; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28	Back alignment and structure

>3elk_A Putative transcriptional regulator TA0346; structural genomics, PSI-2, prote structure initiative; 1.70A {Thermoplasma acidophilum}	Back alignment and structure

>3e6m_A MARR family transcriptional regulator; APC88769, silicibacter pomeroyi DSS, structural genomics, PSI-2, protein structure initiative; 2.20A {Silicibacter pomeroyi}	Back alignment and structure

>2nnn_A Probable transcriptional regulator; structural genomics, PSI-2, protein structure initiative, M center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa}	Back alignment and structure

>4fx0_A Probable transcriptional repressor protein; helix-turn-helix, DNA binding, transcription regulator; 2.70A {Mycobacterium tuberculosis} PDB: 4fx4_A*	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Alignment Graph	Length	Definition	E-value
Query		632
d2bgwa2		133	c.52.1.20 (A:16-148) XPF endonuclease {Aeropyrum p	2e-20
d1j23a_		131	c.52.1.20 (A:) Putative ATP-dependent RNA helicase	2e-18
d2fmpa1		82	a.60.6.1 (A:10-91) DNA polymerase beta, N-terminal	4e-04
d2bcqa1		76	a.60.6.1 (A:252-327) DNA polymerase lambda {Human	0.001

>d2bgwa2 c.52.1.20 (A:16-148) XPF endonuclease {Aeropyrum pernix [TaxId: 56636]} Length = 133	Back information, alignment and structure


class: Alpha and beta proteins (a/b)
fold: Restriction endonuclease-like
superfamily: Restriction endonuclease-like
family: XPF/Rad1/Mus81 nuclease
domain: XPF endonuclease
species: Aeropyrum pernix [TaxId: 56636]

 Score = 85.4 bits (211), Expect = 2e-20
 Identities = 31/148 (20%), Positives = 54/148 (36%), Gaps = 23/148 (15%)

Query: 379 LILDDREQFAVQGSRSRRIIENVCSQFKIQMEVRRLPVGDGIWIARHRQTQSEYVLDFIV 438
           + +D RE+        R  + ++     +Q+  ++LP+GD +                IV
Sbjct: 6   VYVDVREE--------RSPVPSILESLGVQVIPKQLPMGDYLV-----------SDSIIV 46

Query: 439 ERKKVDDLRSSIRDNRYRDQKLRLVRCGLKKLIYLVEGDP---NSSEAAESIKTACFTTE 495
           ERK   D   S+ D R  +Q  RL     + +  +VEG P          S+  A    +
Sbjct: 47  ERKTSSDFAKSLFDGRLFEQASRLAEHY-ETVFIIVEGPPVPRRYRGRERSLYAAMAALQ 105

Query: 496 ILEGFDVQRTSGLADTLRKYGYITQAIT 523
           +  G  +  T     T      + +  T
Sbjct: 106 LDYGIRLMNTMDPKGTALVIESLARLST 133

PyMOL of d2bgwa2

>d1j23a_ c.52.1.20 (A:) Putative ATP-dependent RNA helicase Hef, nuclease domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 131	Back information, alignment and structure

>d2fmpa1 a.60.6.1 (A:10-91) DNA polymerase beta, N-terminal (8 kD)-domain {Human (Homo sapiens) [TaxId: 9606]} Length = 82	Back information, alignment and structure

>d2bcqa1 a.60.6.1 (A:252-327) DNA polymerase lambda {Human (Homo sapiens) [TaxId: 9606]} Length = 76	Back information, alignment and structure

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		632
d2bgwa2		133	XPF endonuclease {Aeropyrum pernix [TaxId: 56636]}	99.97
d1j23a_		131	Putative ATP-dependent RNA helicase Hef, nuclease	99.97
d1jmsa1		95	Terminal deoxynucleotidyl transferase {Mouse (Mus	98.49
d2bcqa1		76	DNA polymerase lambda {Human (Homo sapiens) [TaxId	98.15
d2fmpa1		82	DNA polymerase beta, N-terminal (8 kD)-domain {Hum	97.85
d1x2ia1		68	ATP-dependent RNA helicase PF2015 {Pyrococcus furi	97.6
d2bgwa1		70	DNA repair endonuclease XPF {Aeropyrum pernix [Tax	97.59
d1kfta_		56	Excinuclease UvrC C-terminal domain {Escherichia c	97.27
d2a1ja1		62	DNA repair endonuclease XPF {Human (Homo sapiens)	97.26
d2a1jb1		78	DNA excision repair protein ERCC-1 {Human (Homo sa	96.5
d1bvsa2		71	DNA helicase RuvA subunit, middle domain {Mycobact	95.88
d1cuka2		78	DNA helicase RuvA subunit, middle domain {Escheric	95.31
d1ixra1		73	DNA helicase RuvA subunit, middle domain {Thermus	94.95
d2i1qa1		60	DNA repair protein Rad51, N-terminal domain {Archa	93.63
d2bgwa1		70	DNA repair endonuclease XPF {Aeropyrum pernix [Tax	91.93
d1pzna1		61	DNA repair protein Rad51, N-terminal domain {Archa	90.95
d2e1fa1		94	Werner syndrome ATP-dependent helicase, WRN {Human	89.13
d1dgsa1		181	NAD+-dependent DNA ligase, domain 3 {Thermus filif	88.99
d2fbka1		172	Transcriptional regulator DR1159 {Deinococcus radi	88.05
d2a1jb1		78	DNA excision repair protein ERCC-1 {Human (Homo sa	87.44
d1rxwa1		105	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Arc	87.3
d1x2ia1		68	ATP-dependent RNA helicase PF2015 {Pyrococcus furi	85.0
d1ub9a_		100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	84.49
d2fswa1		102	Hypothetical protein PG0823 {Porphyromonas gingiva	84.39
d2axtu1		98	Photosystem II 12 kDa extrinsic protein PsbU {Ther	84.19
d3ctaa1		85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	84.16
d2esha1		114	Hypothetical protein TM0937 {Thermotoga maritima [	83.93
d2hr3a1		145	Probable transcriptional regulator PA3067 {Pseudom	83.64
d1ul1x1		140	Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo	83.6
d1r7ja_		90	Sso10a (SSO10449) {Archaeon Sulfolobus solfataricu	83.34
d3deua1		140	Transcriptional regulator SlyA {Salmonella typhimu	83.0
d2a61a1		139	Transcriptional regulator TM0710 {Thermotoga marit	82.5
d2frha1		115	Pleiotropic regulator of virulence genes, SarA {St	82.23
d1wuda1		77	HRDC domain from RecQ helicase {Escherichia coli [	82.03
d1jgsa_		138	Multiple antibiotic resistance repressor, MarR {Es	81.89
d1yyva1		114	Putative transcriptional regulator YtfH {Salmonell	81.05
d2f2ea1		142	Hypothetical protein PA1607 {Pseudomonas aeruginos	80.93
d1xo1a1		105	T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]	80.68
d2etha1		140	Putative transcriptional regulator TM0816 {Thermot	80.2

>d2bgwa2 c.52.1.20 (A:16-148) XPF endonuclease {Aeropyrum pernix [TaxId: 56636]}	Back information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: Restriction endonuclease-like
superfamily: Restriction endonuclease-like
family: XPF/Rad1/Mus81 nuclease
domain: XPF endonuclease
species: Aeropyrum pernix [TaxId: 56636]

Probab=99.97  E-value=1e-31  Score=247.18  Aligned_cols=127  Identities=23%  Similarity=0.292  Sum_probs=114.3

Q ss_pred             eEEEEEeCcccccccCCchHHHHHHHHhhCCCcEEEEeccCCCEEEEeeccCCCcceeeceeEEEechhHHHhhhccchH
Q 006771          376 EVVLILDDREQFAVQGSRSRRIIENVCSQFKIQMEVRRLPVGDGIWIARHRQTQSEYVLDFIVERKKVDDLRSSIRDNRY  455 (632)
Q Consensus       376 ~V~LvVD~RE~~s~~~~~~r~~i~~~l~~~gV~~evr~L~vGD~iWvar~k~~~~E~VLd~IVERKrldDL~~SI~DGRf  455 (632)
                      .+.||||+||.++        .+...|.+.||++++++|++|||+|..           ++|||||+++||++||+||||
T Consensus         3 ~p~IiiD~RE~~s--------~~~~~l~~~gi~~~~~~L~~GDy~i~~-----------~~iIERKt~~Dl~~Si~dgR~   63 (133)
T d2bgwa2           3 RPRVYVDVREERS--------PVPSILESLGVQVIPKQLPMGDYLVSD-----------SIIVERKTSSDFAKSLFDGRL   63 (133)
T ss_dssp             SCEEEEETTTTTS--------SHHHHHHHTTCEEEEECCSSSSEEEET-----------TEEEEEEEHHHHHHHHHHSHH
T ss_pred             CCEEEEECCCCcc--------hhhHHHHHCCCEEEEEEcCCcCEEEec-----------CEEEEEechhHhhhhccCChH
Confidence            4578899999762        366678899999999999999999986           799999999999999999999


Q ss_pred             HHHHHHHHHcCCCceEEEEeCCCCCc---hhHHHHHHHHHHhhhhcCceEEEcCCHHHHHHHHHHHHHHH
Q 006771          456 RDQKLRLVRCGLKKLIYLVEGDPNSS---EAAESIKTACFTTEILEGFDVQRTSGLADTLRKYGYITQAI  522 (632)
Q Consensus       456 ~eQK~RLk~sG~~~~iYLVEg~~~~~---~~~e~i~tAl~~tqv~~gf~V~rT~~~~eT~~~L~~lt~~i  522 (632)
                      ++|+.||+++ +++++|||||+....   ..++++.+|++++++.+||.|++|.|++||+.||..|++..
T Consensus        64 ~eQ~~rL~~~-~~~~~~LIEg~~~~~~~~~~~~~l~~al~~l~~~~g~~vi~t~~~~eTa~~l~~lak~~  132 (133)
T d2bgwa2          64 FEQASRLAEH-YETVFIIVEGPPVPRRYRGRERSLYAAMAALQLDYGIRLMNTMDPKGTALVIESLARLS  132 (133)
T ss_dssp             HHHHHHHHHH-CSEEEEEEESCSSCGGGTTTHHHHHHHHHHHHHHSCCEEEEESSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhc-CCCeEEEEEcCcchhhccCCHHHHHHHHHHHHHHcCceEEEeCCHHHHHHHHHHHhccc
Confidence            9999999999 589999999986532   35789999999999999999999999999999999999863

PyMOL of d2bgwa2

>d1j23a_ c.52.1.20 (A:) Putative ATP-dependent RNA helicase Hef, nuclease domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}	Back information, alignment and structure

>d1jmsa1 a.60.6.1 (A:148-242) Terminal deoxynucleotidyl transferase {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2bcqa1 a.60.6.1 (A:252-327) DNA polymerase lambda {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2fmpa1 a.60.6.1 (A:10-91) DNA polymerase beta, N-terminal (8 kD)-domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x2ia1 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}	Back information, alignment and structure

>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]}	Back information, alignment and structure

>d1kfta_ a.60.2.3 (A:) Excinuclease UvrC C-terminal domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d2a1ja1 a.60.2.5 (A:837-898) DNA repair endonuclease XPF {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1bvsa2 a.60.2.1 (A:64-134) DNA helicase RuvA subunit, middle domain {Mycobacterium leprae [TaxId: 1769]}	Back information, alignment and structure

>d1cuka2 a.60.2.1 (A:65-142) DNA helicase RuvA subunit, middle domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1ixra1 a.60.2.1 (A:63-135) DNA helicase RuvA subunit, middle domain {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d2i1qa1 a.60.4.1 (A:5-64) DNA repair protein Rad51, N-terminal domain {Archaeon Methanococcus voltae [TaxId: 2188]}	Back information, alignment and structure

>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]}	Back information, alignment and structure

>d1pzna1 a.60.4.1 (A:35-95) DNA repair protein Rad51, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}	Back information, alignment and structure

>d2e1fa1 a.60.8.1 (A:1142-1235) Werner syndrome ATP-dependent helicase, WRN {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1dgsa1 a.60.2.2 (A:401-581) NAD+-dependent DNA ligase, domain 3 {Thermus filiformis [TaxId: 276]}	Back information, alignment and structure

>d2fbka1 a.4.5.28 (A:8-179) Transcriptional regulator DR1159 {Deinococcus radiodurans [TaxId: 1299]}	Back information, alignment and structure

>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1rxwa1 a.60.7.1 (A:220-324) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d1x2ia1 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}	Back information, alignment and structure

>d1ub9a_ a.4.5.28 (A:) Hypothetical protein PH1061 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}	Back information, alignment and structure

>d2fswa1 a.4.5.69 (A:3-104) Hypothetical protein PG0823 {Porphyromonas gingivalis [TaxId: 837]}	Back information, alignment and structure

>d2axtu1 a.60.12.2 (U:37-134) Photosystem II 12 kDa extrinsic protein PsbU {Thermosynechococcus elongatus [TaxId: 146786]}	Back information, alignment and structure

>d3ctaa1 a.4.5.28 (A:5-89) Ta1064 (RFK), N-terminal domain {Thermoplasma acidophilum [TaxId: 2303]}	Back information, alignment and structure

>d2esha1 a.4.5.61 (A:4-117) Hypothetical protein TM0937 {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d2hr3a1 a.4.5.28 (A:2-146) Probable transcriptional regulator PA3067 {Pseudomonas aeruginosa [TaxId: 287]}	Back information, alignment and structure

>d1ul1x1 a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1r7ja_ a.4.5.49 (A:) Sso10a (SSO10449) {Archaeon Sulfolobus solfataricus [TaxId: 2287]}	Back information, alignment and structure

>d3deua1 a.4.5.28 (A:2-141) Transcriptional regulator SlyA {Salmonella typhimurium [TaxId: 90371]}	Back information, alignment and structure

>d2a61a1 a.4.5.28 (A:5-143) Transcriptional regulator TM0710 {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d2frha1 a.4.5.28 (A:102-216) Pleiotropic regulator of virulence genes, SarA {Staphylococcus aureus [TaxId: 1280]}	Back information, alignment and structure

>d1wuda1 a.60.8.1 (A:530-606) HRDC domain from RecQ helicase {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1jgsa_ a.4.5.28 (A:) Multiple antibiotic resistance repressor, MarR {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1yyva1 a.4.5.69 (A:9-122) Putative transcriptional regulator YtfH {Salmonella typhimurium [TaxId: 90371]}	Back information, alignment and structure

>d2f2ea1 a.4.5.69 (A:5-146) Hypothetical protein PA1607 {Pseudomonas aeruginosa [TaxId: 287]}	Back information, alignment and structure

>d1xo1a1 a.60.7.1 (A:186-290) T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]}	Back information, alignment and structure

>d2etha1 a.4.5.28 (A:1-140) Putative transcriptional regulator TM0816 {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure