Citrus Sinensis ID: 010353

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--

MLTEYGTKHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCPASEPLLMPISEEEGPARKKGSKSAKKIGEPETIEQQVVEAALPMEAMRFSVVTNVESDVGEKEKNSNNVTPGEKRKHDVLELDECGVADEQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQATSSAEKKVKTKNSVPLSLSSIYEEVIKSEAGRNMTLDHVRASLVQLDFEKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDEMFHAALNLSLRVSYELDREKELLNLPADKRTGPLQDRYNRIRKVRILLESSQMKLDDAILLFHDF

cccHHHHHHHHHHHHHHHcHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHHHHccEEEEEcccccccccccccccEEEEEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccHHHHHHHHHHccHHHHHcccccccccccccccccccccccccccccccccccccccccccccEEEEEHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHcccccccccccccEEEEcHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHccccccHHHHHHHccccccHHHHHHHHHHHcccEEEEEEEcccccccEEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccc

cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHHHHHccEEEEEEccccccccccccEEEEEEcHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHcccccHHHHHHHHHHHccccccccHHHHHHHHHHHHHcccEEEcccccccccccHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccEEEEEcHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHccccccccccccccHHHHHHHccccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHccccccHHHHHHHccccHHHHHHHHHHHHHcccEEEEEEccccccccEEEEEEEcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc

MLTEYGTKHAVHVITNHFGDLVAKVCECllrkgpltrqnvKRYTELSDEQVKNALLVLIQQNCVQaftteqpdgfadgpkantQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAkssekegnlvdlDSLRETLVKLVTAHyvercpasepllmpiseeegparkkgsksakkigepetIEQQVVEAALPMEAMRFSVVTNvesdvgekeknsnnvtpgekrkhdvleldecgvadeqsVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQATSSAekkvktknsvplsLSSIYEEVIKSEAGRNMTLDHVRASLVQLDFEKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKsgrlletdkisdttfvekkdapKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDEMFHAALNLSLRVSYELDREKEllnlpadkrtgplqdryNRIRKVRILLESSQMKLDDAILLFHDF

mlteygtkHAVHVITNHFGDLVAKVCECLLRkgpltrqnvkRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFdrakssekegnlvdldsLRETLVKLVTAHYVercpasepllmpiseeegparkkgsksakkigepetIEQQVVEAALPMEAMRFSVVtnvesdvgekeknsnnvtpgekrkhdVLELDEcgvadeqsvvYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQATssaekkvktknsvplslsSIYEEVIKSEAGRNMTLDHVRASLVQLDFEKIIEiaqneevesvvskrygrdaYRIFRllsksgrlletdkisdttfvekkdapkiLYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDEMFHAALNLSLRVSYELDREKEllnlpadkrtgplqdrynrIRKVRIllessqmklddailLFHDF

****YGTKHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMF***********LVDLDSLRETLVKLVTAHYVERCP******************************************************************************VLELDECGVADEQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAM**********************SIYEEVIKSEAGRNMTLDHVRASLVQLDFEKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDEMFHAALNLSLRVSYELDREKELLNLP*******LQDRYNRIRKVRILLESSQMKLDDAILLF***

***EYGTKHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQ******GPKANTQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFD**************DSLRETLVKLVTAHYVE*******************************************************************************************DEQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQATS*************LSLSSIYEEVI************VRASLVQLDFEKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLV***ARQSQFLLWKVNRQILWKHVLDEMFHAALNLSLRVSYELDREKELL*****************IRKVRILLESSQMKLDDAILLFHDF

MLTEYGTKHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCPASEPLLMPISEE***************GEPETIEQQVVEAALPMEAMRFSVVTNVE******************RKHDVLELDECGVADEQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQA**************PLSLSSIYEEVIKSEAGRNMTLDHVRASLVQLDFEKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDEMFHAALNLSLRVSYELDREKELLNLPADKRTGPLQDRYNRIRKVRILLESSQMKLDDAILLFHDF

*LTEYGTKHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCPASEPLLMP****E*********SAKKIGEPETIEQQVVEAALPMEAMRFSVVTNV*********************************DEQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQATSSAEKKVKTKNSVPLSLSSIYEEVIKSEAGRNMTLDHVRASLVQLDFEKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDEMFHAALNLSLRVSYELDREKELLNLPADKRTGPLQDRYNRIRKVRILLESSQMKLDDAILLFHDF

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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		512	2.2.26 [Sep-21-2011]
Q7ZUX1		539	DNA-directed RNA polymera	yes	no	0.841	0.799	0.240	4e-25
Q2TBL4		533	DNA-directed RNA polymera	yes	no	0.843	0.810	0.224	2e-22
Q9D483		533	DNA-directed RNA polymera	yes	no	0.822	0.789	0.209	2e-20
Q9BUI4		534	DNA-directed RNA polymera	yes	no	0.843	0.808	0.218	5e-20
Q5XIL3		533	DNA-directed RNA polymera	yes	no	0.843	0.810	0.205	2e-17
Q55FJ5		666	DNA-directed RNA polymera	yes	no	0.357	0.274	0.263	9e-12
A3LQX9		599	DNA-directed RNA polymera	yes	no	0.261	0.223	0.243	2e-05
Q9C106		591	DNA-directed RNA polymera	yes	no	0.572	0.495	0.190	0.0001
A2QUS7		627	DNA-directed RNA polymera	yes	no	0.220	0.180	0.239	0.0005
Q5A246		595	DNA-directed RNA polymera	N/A	no	0.271	0.233	0.222	0.0009

>sp\|Q7ZUX1\|RPC3_DANRE DNA-directed RNA polymerase III subunit RPC3 OS=Danio rerio GN=polr3c PE=2 SV=1	Back alignment and function desciption

 Score =  116 bits (290), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 116/482 (24%), Positives = 212/482 (43%), Gaps = 51/482 (10%)

Query: 13  VITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQP 72
           ++  HFGD+V  V   L+R G LT + +   T+L+ + VK +L VL+Q        T  P
Sbjct: 12  LLQEHFGDVVENVGTHLIRNGVLTLRALAHETKLALDLVKKSLCVLVQ----HGMCTFGP 67

Query: 73  DGFADGPKANTQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTL---- 128
                GP    +Y +  ++ILH +R+ +++      +      +V+ +L+ G++T+    
Sbjct: 68  G--RRGPAGPVEYHINCEHILHMLRYPRYIYTAKSLYGDTGELIVEEILQRGQMTMSSTV 125

Query: 129 KQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCPASEPLLMPISEEEGPARKKGS 188
           K + DR   +  EG  +D + +     +LV  H+++RCP      M  +E  G      +
Sbjct: 126 KTVADRLTHNMPEGQSMDYNEVVSAFSRLVETHFLQRCPP-----MASAESSGTG---SA 177

Query: 189 KSAKKIGEPETIEQQVVEAALPMEAMRFSVVTNVESDVGEKEKNSNNVTPGEKRKHDVLE 248
           ++   + +P   E       LP  ++         S+ GE ++ +      +K K D   
Sbjct: 178 ETPPAVTQPSNPESHPDCYKLPYISLSGHGKRRRSSEDGEADQRA-----AKKAKTDS-- 230

Query: 249 LDECGVADEQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAML---QATSSAE 305
             ECG   ++ + ++ NFE F    R +  I  V   LD  +  ++  ML   + T+SA 
Sbjct: 231 -SECG---DEGIHWQVNFERFHLHFRDQAIISAVSCKLDQTSGEIVRTMLRMSEVTTSAN 286

Query: 306 ---KKVKTKNSVPLSLSSIYEEVIKSEAGRNMTL------------DHVRASLVQLDFEK 350
               +  + N +  +L S Y  + +    + +TL                  +  ++  +
Sbjct: 287 AAFTQALSANEIFRALPSNY-NIARPILDQYLTLLVDDPMEFVGKAGDSGGGMFVVNLHR 345

Query: 351 IIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLW 410
            +       +ESVV +R+G  + RIFRLL +  R LE  ++ D   +  K+A ++LY L 
Sbjct: 346 ALANLARATLESVVQERFGSRSARIFRLLLRK-RHLEQKQVEDFAMIPAKEAKEMLYTLL 404

Query: 411 KDGYLLMEKLVVTG--ARQSQFLLWKVNRQILWKHVLDEMFHAALNLSLRVSYELDREKE 468
            +  + ++++  T   A    F L+ VN+    + +L   +    NL  R  YE    K 
Sbjct: 405 SENLVQLQEIPKTPDHAPSRTFYLYAVNQLPTARLLLQHCYKTVGNLIERRLYETKENKR 464

Query: 469 LL 470
           LL
Sbjct: 465 LL 466

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific core component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs.
Danio rerio (taxid: 7955)

>sp\|Q2TBL4\|RPC3_BOVIN DNA-directed RNA polymerase III subunit RPC3 OS=Bos taurus GN=POLR3C PE=2 SV=1	Back alignment and function description

>sp\|Q9D483\|RPC3_MOUSE DNA-directed RNA polymerase III subunit RPC3 OS=Mus musculus GN=Polr3c PE=2 SV=1	Back alignment and function description

>sp\|Q9BUI4\|RPC3_HUMAN DNA-directed RNA polymerase III subunit RPC3 OS=Homo sapiens GN=POLR3C PE=1 SV=1	Back alignment and function description

>sp\|Q5XIL3\|RPC3_RAT DNA-directed RNA polymerase III subunit RPC3 OS=Rattus norvegicus GN=Polr3c PE=2 SV=1	Back alignment and function description

>sp\|Q55FJ5\|RPC3_DICDI DNA-directed RNA polymerase III subunit rpc3 OS=Dictyostelium discoideum GN=polr3c PE=3 SV=1	Back alignment and function description

>sp\|A3LQX9\|RPC3_PICST DNA-directed RNA polymerase III subunit RPC3 OS=Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545) GN=RPC82 PE=3 SV=1	Back alignment and function description

>sp\|Q9C106\|RPC3_SCHPO DNA-directed RNA polymerase III subunit rpc3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpc82 PE=1 SV=1	Back alignment and function description

>sp\|A2QUS7\|RPC3_ASPNC DNA-directed RNA polymerase III subunit rpc3 OS=Aspergillus niger (strain CBS 513.88 / FGSC A1513) GN=rpc82 PE=3 SV=1	Back alignment and function description

>sp\|Q5A246\|RPC3_CANAL DNA-directed RNA polymerase III subunit RPC3 OS=Candida albicans (strain SC5314 / ATCC MYA-2876) GN=RPC82 PE=3 SV=1	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		512
302143859		524	unnamed protein product [Vitis vinifera]	0.992	0.969	0.638	0.0
359490507		511	PREDICTED: DNA-directed RNA polymerase I	0.966	0.968	0.621	0.0
224134849		519	predicted protein [Populus trichocarpa]	0.976	0.963	0.560	1e-162
255539431		485	DNA-directed RNA polymerase III 62 kDa p	0.861	0.909	0.597	1e-157
449446151		518	PREDICTED: DNA-directed RNA polymerase I	0.972	0.961	0.538	1e-155
449522480		518	PREDICTED: DNA-directed RNA polymerase I	0.972	0.961	0.536	1e-154
356534135		510	PREDICTED: DNA-directed RNA polymerase I	0.962	0.966	0.536	1e-150
356574495		518	PREDICTED: DNA-directed RNA polymerase I	0.974	0.963	0.536	1e-150
297737009		517	unnamed protein product [Vitis vinifera]	0.974	0.965	0.541	1e-150
297809071		521	RNA polymerase III subunit RPC82 family	0.968	0.952	0.485	1e-136

>gi\|302143859\|emb\|CBI22720.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

 Score =  679 bits (1752), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 337/528 (63%), Positives = 419/528 (79%), Gaps = 20/528 (3%)

Query: 1   MLTEYGTKHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQ 60
           M T+YG + AVH+I++HFG+LVAKVC+CLLRKG LT  +V R+TEL  +QVK+ +LVLIQ
Sbjct: 1   MATQYGVQLAVHLISSHFGNLVAKVCDCLLRKGTLTLASVIRFTELPPQQVKSCILVLIQ 60

Query: 61  QNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGL 120
            NCVQAF  +Q  GF + P+  TQY+ LF NILHR+RFAKFL I+S+E D++C E+++GL
Sbjct: 61  HNCVQAFAIQQEVGFGEAPRVVTQYMALFHNILHRMRFAKFLAIVSEELDKECEEILEGL 120

Query: 121 LEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCPASEPLLMPISEEE 180
           L+HGRLTL+Q+ DRAKS++ EG  V  D+LRE+ +KLV AH+VERCPASEP L P SEEE
Sbjct: 121 LQHGRLTLEQILDRAKSNQSEGEPVVQDALRESFLKLVRAHFVERCPASEPFLAPPSEEE 180

Query: 181 GPARKKGSKSAKKIGEPETIEQQVVEAALPMEAMRFSVVTNVESDVGEKEKNSNNVTPGE 240
            PARK+G+KSAK + EP+TIEQ+ + AA PM+A RFSV+ N  +DV     +S NVT GE
Sbjct: 181 TPARKRGAKSAKLVEEPQTIEQRAIAAAAPMDAKRFSVIINTGTDV----DDSPNVTAGE 236

Query: 241 KRKHDVLELD-ECGVADEQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQ 299
           KRK D LELD E G + E+ V++RANFE F+R LRHK CI +V+  LDDGAA VLSAML+
Sbjct: 237 KRKQDALELDKETGASCEKDVLWRANFEEFVRCLRHKACIANVKTRLDDGAAIVLSAMLE 296

Query: 300 ATSSAEKKVKTKNSVPLSLSSIYEEVIKSEAGRNMTLDHVRASLVQL------------- 346
           AT S EKKVKT+NSVPLS+ +I+E V+KSEAGR+MTL+ VR SL+QL             
Sbjct: 297 ATRSEEKKVKTENSVPLSMDTIFEGVMKSEAGRSMTLERVRGSLIQLGCAPCVRGAAESY 356

Query: 347 --DFEKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPK 404
             D + IIE+AQN+EVES+  KRYGRDAYRIFRLLSKS RLLETDKISDTTFVEKKD  K
Sbjct: 357 SVDLKNIIELAQNDEVESITLKRYGRDAYRIFRLLSKSCRLLETDKISDTTFVEKKDTAK 416

Query: 405 ILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDEMFHAALNLSLRVSYELD 464
           ILY+LWKD YL MEKL + G+RQSQFLLWKV +  LW HVL+EM+H+ALNLSLRV+YEL+
Sbjct: 417 ILYQLWKDEYLQMEKLNLHGSRQSQFLLWKVTKDTLWGHVLNEMYHSALNLSLRVAYELE 476

Query: 465 REKELLNLPADKRTGPLQDRYNRIRKVRILLESSQMKLDDAILLFHDF 512
           +E+E++ LP +KR G L +R+ R+RKVRILLESS MKLDDAI+LF+DF
Sbjct: 477 QEQEIIQLPREKRVGALGNRFERLRKVRILLESSLMKLDDAIMLFNDF 524

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|359490507\|ref\|XP_002267664.2\| PREDICTED: DNA-directed RNA polymerase III subunit RPC3 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|224134849\|ref\|XP_002321920.1\| predicted protein [Populus trichocarpa] gi\|222868916\|gb\|EEF06047.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|255539431\|ref\|XP_002510780.1\| DNA-directed RNA polymerase III 62 kDa polypeptide, putative [Ricinus communis] gi\|223549895\|gb\|EEF51382.1\| DNA-directed RNA polymerase III 62 kDa polypeptide, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|449446151\|ref\|XP_004140835.1\| PREDICTED: DNA-directed RNA polymerase III subunit RPC3-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449522480\|ref\|XP_004168254.1\| PREDICTED: DNA-directed RNA polymerase III subunit RPC3-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|356534135\|ref\|XP_003535613.1\| PREDICTED: DNA-directed RNA polymerase III subunit RPC3-like [Glycine max]	Back alignment and taxonomy information

>gi\|356574495\|ref\|XP_003555382.1\| PREDICTED: DNA-directed RNA polymerase III subunit RPC3-like [Glycine max]	Back alignment and taxonomy information

>gi\|297737009\|emb\|CBI26210.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|297809071\|ref\|XP_002872419.1\| RNA polymerase III subunit RPC82 family protein [Arabidopsis lyrata subsp. lyrata] gi\|297318256\|gb\|EFH48678.1\| RNA polymerase III subunit RPC82 family protein [Arabidopsis lyrata subsp. lyrata]	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		512
TAIR\|locus:2101268		523	AT3G49000 [Arabidopsis thalian	0.980	0.959	0.430	2.6e-109
DICTYBASE\|DDB_G0268080		666	rpc3 "RNA polymerase III subun	0.361	0.277	0.280	1.9e-20
UNIPROTKB\|F1SDD7		508	POLR3C "Uncharacterized protei	0.912	0.919	0.228	4.1e-20
UNIPROTKB\|Q2TBL4		533	POLR3C "DNA-directed RNA polym	0.853	0.819	0.227	1.8e-19
ZFIN\|ZDB-GENE-040426-992		539	polr3c "polymerase (RNA) III (	0.855	0.812	0.225	2.2e-19
UNIPROTKB\|F1MUY3		533	POLR3C "DNA-directed RNA polym	0.853	0.819	0.223	3e-19
MGI\|MGI:1921664		533	Polr3c "polymerase (RNA) III (	0.851	0.818	0.217	2.4e-18
UNIPROTKB\|E9PHH9		411	POLR3C "DNA-directed RNA polym	0.326	0.406	0.254	5.4e-18
UNIPROTKB\|Q9BUI4		534	POLR3C "DNA-directed RNA polym	0.326	0.312	0.254	5.7e-17
UNIPROTKB\|E2R8J4		511	POLR3C "Uncharacterized protei	0.306	0.307	0.258	3.7e-16

TAIR\|locus:2101268 AT3G49000 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1080 (385.2 bits), Expect = 2.6e-109, P = 2.6e-109
 Identities = 228/530 (43%), Positives = 353/530 (66%)

Query:     2 LTEYGTKHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTE--LSDEQVKNALLVLI 59
             ++E+G  +A+H+IT  FG +V+KVCECLLRKGPL+ +++ R  E  ++  +VK+ L +LI
Sbjct:     3 MSEFGIVYAIHIITVQFGSVVSKVCECLLRKGPLSSRDISRLAESDINHNKVKDILYLLI 62

Query:    60 QQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQG 119
             Q NCVQAF+ E PDG     KA  QY+VLF+NILHRVR+ KF  I+++E D +C  ++ G
Sbjct:    63 QHNCVQAFSIEPPDGSES--KAIVQYIVLFNNILHRVRYNKFSRIVNEELDSKCGAVLDG 120

Query:   120 LLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCPASEPLLMPISEE 179
             LL +GRLTL Q  +R + S   GN +  +++R++L KLV A +VER P+ EP+L   ++E
Sbjct:   121 LLSNGRLTLGQFIERDRDS---GNTIGSEAIRDSLQKLVAARFVERIPSPEPVLG--NKE 175

Query:   180 EGPARKKGSKSAKKIGEPETIEQQVVEAALPMEAMRFSVVTNVESDVGEKEKNSNNVTPG 239
             + PA+++G+K+AK + EPET+E+QVVEAA P++A+RF ++   +S+    + NSN +T G
Sbjct:   176 KEPAKRRGAKAAKILKEPETLEEQVVEAATPVDAIRFPLIFEEDSNSSLADDNSN-ITEG 234

Query:   240 EKRKHDVLELDEC-GVA---DEQSVVYRANFEG---FIRRLRHKGCIDHVRAHLDDGAAN 292
             ++++ DV   D   GV    + +  ++R   +     ++  R +GC   +RA L+ G + 
Sbjct:   235 KRKQRDVDTSDSSSGVIWRPNFEEFIHRLRHKACVEIVKERRDEGCAIVLRAMLEVGRSQ 294

Query:   293 VL------SAMLQATSSAEKKVKT---KNSVPLSLSSIYEEVIKSEAGRNMTLDHVRASL 343
                     SA +   S  E+ +KT   +  +   + +  +++  + +     ++ V  S 
Sbjct:   295 EKKVKTDNSAPMSVGSIYEEVIKTEAGRTMLQERVEACLDQLSATSSYLPAFVNEVNDSY 354

Query:   344 VQLDFEKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAP 403
             + +D++ II +AQ +E+E+VV +RYG++A+R+FR LS+ GR +ETDKI+D    EKKD P
Sbjct:   355 I-VDYKSIISVAQKDEIEAVVMRRYGKEAFRMFRYLSQEGRFVETDKIADAALTEKKDTP 413

Query:   404 KILYKLWKDGYLLMEKLVVTG-ARQSQFLLWKVNRQILWKHVLDEMFHAALNLSLRVSYE 462
             + L K+WKDGYL M+KL VT     + FLLWKVN+ I+   +LDEM+HA+LNLSLR+++E
Sbjct:   414 QFLLKMWKDGYLHMQKLAVTAPGMYTPFLLWKVNKLIVTTQMLDEMYHASLNLSLRLAHE 473

Query:   463 LDREKELLNLPADKRTGPLQDRYNRIRKVRILLESSQMKLDDAILLFHDF 512
             L+ EKELL LP DK  GPL++R  +++  R+LL S+  KLDDAI+LFHDF
Sbjct:   474 LEAEKELLLLPLDKLEGPLKERLKKVKAKRLLLSSTMFKLDDAIMLFHDF 523

GO:0003677 "DNA binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0006351 "transcription, DNA-dependent" evidence=IEA

DICTYBASE\|DDB_G0268080 rpc3 "RNA polymerase III subunit" [Dictyostelium discoideum (taxid:44689)]	Back alignment and assigned GO terms

UNIPROTKB\|F1SDD7 POLR3C "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|Q2TBL4 POLR3C "DNA-directed RNA polymerase III subunit RPC3" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-040426-992 polr3c "polymerase (RNA) III (DNA directed) polypeptide C" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|F1MUY3 POLR3C "DNA-directed RNA polymerase III subunit RPC3" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

MGI\|MGI:1921664 Polr3c "polymerase (RNA) III (DNA directed) polypeptide C" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

UNIPROTKB\|E9PHH9 POLR3C "DNA-directed RNA polymerase III subunit RPC3" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|Q9BUI4 POLR3C "DNA-directed RNA polymerase III subunit RPC3" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|E2R8J4 POLR3C "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	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

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00009152001	SubName- Full=Chromosome undetermined scaffold_222, whole genome shotgun sequence; (510 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00038611001	RecName- Full=Pyruvate kinase; EC=2.7.1.40; (573 aa)	•	0.899
	GSVIVG00036953001	SubName- Full=Chromosome chr1 scaffold_84, whole genome shotgun sequence; (417 aa)	•	0.899
	GSVIVG00034786001	SubName- Full=Chromosome chr5 scaffold_72, whole genome shotgun sequence; (471 aa)	•	0.899
	GSVIVG00034055001	RecName- Full=Nucleoside diphosphate kinase; EC=2.7.4.6; (159 aa)	•	0.899
	26N20_30	RecName- Full=Pyruvate kinase; EC=2.7.1.40; (493 aa)	•	0.899
	GSVIVG00028076001	SubName- Full=Chromosome chr7 scaffold_42, whole genome shotgun sequence; (533 aa)	•	0.899
	GSVIVG00025495001	RecName- Full=Pyruvate kinase; EC=2.7.1.40; (475 aa)	•	0.899
	GSVIVG00024850001	RecName- Full=Pyruvate kinase; EC=2.7.1.40; (491 aa)	•	0.899
	GSVIVG00023818001	RecName- Full=Pyruvate kinase; EC=2.7.1.40; (569 aa)	•	0.899
	GSVIVG00021710001	RecName- Full=Pyruvate kinase; EC=2.7.1.40; (264 aa)	•	0.899

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		512
pfam08221		62	pfam08221, HTH_9, RNA polymerase III subunit RPC82	5e-14
pfam05645		215	pfam05645, RNA_pol_Rpc82, RNA polymerase III subun	3e-12

>gnl\|CDD\|191971 pfam08221, HTH_9, RNA polymerase III subunit RPC82 helix-turn-helix domain	Back alignment and domain information

 Score = 66.5 bits (163), Expect = 5e-14
 Identities = 30/59 (50%), Positives = 41/59 (69%)

Query: 10 AVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFT 68
             ++  HFG++VAKV   LLRKG LT + + + T+LS +QVK +L+VLIQ NCVQ F 
Sbjct: 3  CTELLEEHFGEVVAKVVSTLLRKGRLTLREIVKLTKLSLDQVKKSLVVLIQHNCVQYFE 61

This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In Saccharomyces cerevisiae, the enzyme is composed of 15 subunits, ranging from 160 to about 10 kDa. This region is a probably DNA-binding helix-turn-helix. Length = 62

>gnl\|CDD\|191331 pfam05645, RNA_pol_Rpc82, RNA polymerase III subunit RPC82	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		512
KOG2587		551	consensus RNA polymerase III (C) subunit [Transcri	100.0
PF05645		258	RNA_pol_Rpc82: RNA polymerase III subunit RPC82; I	99.81
PF08221		62	HTH_9: RNA polymerase III subunit RPC82 helix-turn	99.8
PF02002		105	TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024	99.49
TIGR00373		158	conserved hypothetical protein TIGR00373. This fam	98.99
PRK06266		178	transcription initiation factor E subunit alpha; V	98.89
COG1675		176	TFA1 Transcription initiation factor IIE, alpha su	98.7
smart00531		147	TFIIE Transcription initiation factor IIE.	98.44
PF02002		105	TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024	98.1
PF08221		62	HTH_9: RNA polymerase III subunit RPC82 helix-turn	97.43
TIGR00373		158	conserved hypothetical protein TIGR00373. This fam	97.33
PRK06266		178	transcription initiation factor E subunit alpha; V	96.69
PHA02943		165	hypothetical protein; Provisional	95.94
smart00550		68	Zalpha Z-DNA-binding domain in adenosine deaminase	95.88
PF01978		68	TrmB: Sugar-specific transcriptional regulator Trm	95.68
KOG2593		436	consensus Transcription initiation factor IIE, alp	95.33
PF13412		48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	95.13
PF04337		148	DUF480: Protein of unknown function, DUF480; Inter	95.12
smart00531		147	TFIIE Transcription initiation factor IIE.	95.03
PF13601		80	HTH_34: Winged helix DNA-binding domain; PDB: 1UB9	94.91
KOG2587		551	consensus RNA polymerase III (C) subunit [Transcri	94.61
smart00550		68	Zalpha Z-DNA-binding domain in adenosine deaminase	94.58
PF04703		62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	94.55
PHA02943		165	hypothetical protein; Provisional	94.17
TIGR02702		203	SufR_cyano iron-sulfur cluster biosynthesis transc	93.48
PF01978		68	TrmB: Sugar-specific transcriptional regulator Trm	93.43
PF13412		48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	93.21
PF09339		52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	93.14
PRK10141		117	DNA-binding transcriptional repressor ArsR; Provis	93.14
COG3355		126	Predicted transcriptional regulator [Transcription	93.06
PF09339		52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	92.75
PRK11239		215	hypothetical protein; Provisional	92.22
COG3355		126	Predicted transcriptional regulator [Transcription	92.07
COG1510		177	Predicted transcriptional regulators [Transcriptio	92.01
smart00418		66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	91.83
KOG2593		436	consensus Transcription initiation factor IIE, alp	91.81
PF03962		188	Mnd1: Mnd1 family; InterPro: IPR005647 This family	91.18
smart00347		101	HTH_MARR helix_turn_helix multiple antibiotic resi	90.94
COG3132		215	Uncharacterized protein conserved in bacteria [Fun	90.82
cd00090		78	HTH_ARSR Arsenical Resistance Operon Repressor and	90.77
smart00420		53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	90.38
PF09012		69	FeoC: FeoC like transcriptional regulator; InterPr	90.34
COG1675		176	TFA1 Transcription initiation factor IIE, alpha su	90.34
PF10771		65	DUF2582: Protein of unknown function (DUF2582); In	90.33
PF03965		115	Penicillinase_R: Penicillinase repressor; InterPro	90.26
COG2345		218	Predicted transcriptional regulator [Transcription	90.07
COG2345		218	Predicted transcriptional regulator [Transcription	89.87
TIGR02698		130	CopY_TcrY copper transport repressor, CopY/TcrY fa	89.8
PF01022		47	HTH_5: Bacterial regulatory protein, arsR family;	89.46
COG5647		773	Cullin, a subunit of E3 ubiquitin ligase [Posttran	88.92
smart00344		108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	88.65
PF04703		62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	88.55
COG1378		247	Predicted transcriptional regulators [Transcriptio	88.53
PF12840		61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	88.39
smart00346		91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	88.24
PF12840		61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	88.24
PF08220		57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	87.96
PRK00135		188	scpB segregation and condensation protein B; Revie	86.48
PF10557		68	Cullin_Nedd8: Cullin protein neddylation domain; I	86.21
smart00344		108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	86.21
PF12802		62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	85.95
PF14947		77	HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_	85.43
PF06163		127	DUF977: Bacterial protein of unknown function (DUF	85.36
TIGR02702		203	SufR_cyano iron-sulfur cluster biosynthesis transc	85.29
PF02082		83	Rrf2: Transcriptional regulator; InterPro: IPR0009	84.62
PHA02701		183	ORF020 dsRNA-binding PKR inhibitor; Provisional	84.55
PRK11169		164	leucine-responsive transcriptional regulator; Prov	84.27
PF01638		90	HxlR: HxlR-like helix-turn-helix; InterPro: IPR002	83.77
PF01047		59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	83.42
COG3682		123	Predicted transcriptional regulator [Transcription	83.1
PF13463		68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	82.62
COG3388		101	Predicted transcriptional regulator [Transcription	82.51
PF10771		65	DUF2582: Protein of unknown function (DUF2582); In	82.41
PF01022		47	HTH_5: Bacterial regulatory protein, arsR family;	82.1
PRK11179		153	DNA-binding transcriptional regulator AsnC; Provis	81.83
PF12802		62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	81.64
smart00346		91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	81.28
PF01047		59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	80.56

>KOG2587 consensus RNA polymerase III (C) subunit [Transcription]	Back alignment and domain information

Probab=100.00  E-value=8.9e-79  Score=611.27  Aligned_cols=485  Identities=26%  Similarity=0.415  Sum_probs=368.8

Q ss_pred             ccHHHHHHHHHHHHhhhchhHHHHHHHHHhcCCCc-HHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCC
Q 010353            2 LTEYGTKHAVHVITNHFGDLVAKVCECLLRKGPLT-RQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPK   80 (512)
Q Consensus         2 ~s~~~~~Lc~~iv~~~FG~~v~~V~~~Ll~~G~lt-l~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~   80 (512)
                      ||+|+++||..||++|||++|++|+.+|+++|++| +.-+...++++..+||++|++|||||||.|+.....      .+
T Consensus         1 msq~eielc~~lie~~FGeivakV~~~Llr~G~lss~~~~~~~t~i~~~kVk~aL~sLiQh~~V~y~~~~~~------~g   74 (551)
T KOG2587|consen    1 MSQYEIELCSILIEEHFGEIVAKVGEHLLRTGRLSSLRVIAKDTGISLDKVKKALVSLIQHNCVSYQVHTRN------SG   74 (551)
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcchhHHHHhhcCCChHHHHHHHHHHHHhcceEEEEecCC------CC
Confidence            79999999999999999999999999999999999 777788899999999999999999999998776532      24


Q ss_pred             CccEEEechhhHHHHhchhhHHHHHHHHhhhhHHHHHHHHHHcccCCHHHHHHHHhhcccCCCccC-----HHHHHHHHH
Q 010353           81 ANTQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVD-----LDSLRETLV  155 (512)
Q Consensus        81 ~~~~Y~~~~~~il~rlR~pr~l~~i~~~~G~~a~~Iv~~lL~~G~l~~~~li~~~~~~~~~~~~~~-----~~~l~~~f~  155 (512)
                      .+|+|++.+++|+++||||+|+..++++||+.|+.|+++|+.+|++|++++++++..+.......+     ...|.+.|.
T Consensus        75 ~vt~Y~~~~~ei~hilry~r~~~i~~~~~~q~~~sIv~~Lls~GrLTv~e~i~rv~~~~~~~~~ss~~~ql~~lv~q~F~  154 (551)
T KOG2587|consen   75 KVTTYEAQCSEILHILRYPRYIYITKTLYSQTAESIVEELLSNGRLTVSEVIKRVADRLTTTMESSKTMQLCALVSQTFV  154 (551)
T ss_pred             ceEEEEehhhHHHHHHhcccceeeHHHHhhhHHHHHHHHHHhcCceeHHHHHHHHHhcccccchhhHHHHHHHHHHHHHH
Confidence            579999999999999999999999999999999999999999999999999999987644322111     134667777


Q ss_pred             HHHhc---ccccccCCCCCCCCCCCccCCcccccCCCCCcccCCchhhHHHHHHhhCchhhhhhhhhccccccccccccC
Q 010353          156 KLVTA---HYVERCPASEPLLMPISEEEGPARKKGSKSAKKIGEPETIEQQVVEAALPMEAMRFSVVTNVESDVGEKEKN  232 (512)
Q Consensus       156 ~Lv~~---~fi~rv~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~a~~~~~~r~~~~~~~~~~~~~~~~~  232 (512)
                      .++..   ||..++|.+.+.             .+.+.++++.++-+........++..++..++.+....+.+.    +
T Consensus       155 ~~~~~~ekH~~~r~~e~~~~-------------~~~~a~~~~~e~~~~~~~~~q~lt~~pkis~~~~~~~~s~s~----~  217 (551)
T KOG2587|consen  155 ELADPLEKHFVNRCPESVPT-------------VENSAAGPPPEAPTLVINEKQILTLVPKISLPGKGKRRSSSD----E  217 (551)
T ss_pred             HhhCchhhHhhccCCCcccc-------------cccccCCCCcccccchhhhccccccccccccCCCCCcccccc----c
Confidence            77777   777776542111             112222222222122222222223333344332221111111    1


Q ss_pred             CCCCCCCCcccCCcccccccCCCCCCccEEEecHHHHHHHHHHHHHHHHHHhhcChhHHHHHHHHHhccccc-cc-ccc-
Q 010353          233 SNNVTPGEKRKHDVLELDECGVADEQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQATSSA-EK-KVK-  309 (512)
Q Consensus       233 ~~~~~~~~Krk~~~~~~d~~~~~~~~~v~wrvN~~rf~~~lR~~~iv~~v~~r~g~~a~~v~~~~L~~~~~~-~~-~~~-  309 (512)
                      .+...++.++|.-  ..|.+...++.+++||+|++||+.++||++|+++|..|.|++++.|+++||...... +. .+. 
T Consensus       218 ~d~~~~~~~~k~l--~~D~~~~~~d~ga~wr~N~~rf~~~lRd~~~v~~v~~r~~e~ts~v~~a~Lt~~tie~~r~~~~~  295 (551)
T KOG2587|consen  218 DDRGEKKAKRKKL--TTDNKTPDPDDGAYWRINLDRFHQHLRDQAIVSAVANRMDEGTSEVLRAMLTRMTIELTRHSPAP  295 (551)
T ss_pred             ccccCcccccccc--ccccCCCCCCCceeEehhhHHhhHHhhhHHHHHHHHhcccchhHHHHHHHHHhhhhhhccCCchh
Confidence            1223333333321  112223345678999999999999999999999999999999999999999443211 11 110 


Q ss_pred             ---------ccCCCcc------ChHHHHHHhhh-----hhcCCCCcHHHHHHHHhhc---------------------CH
Q 010353          310 ---------TKNSVPL------SLSSIYEEVIK-----SEAGRNMTLDHVRASLVQL---------------------DF  348 (512)
Q Consensus       310 ---------~~~s~pi------s~~~i~~~l~~-----~~~~~~~~~~~i~~~L~~l---------------------~~  348 (512)
                               ...|.++      +...+-..+..     ++++.+...+.++.+|..|                     ||
T Consensus       296 l~~e~si~~~~~s~n~~s~~~~~~esl~~~~~l~Er~~~ee~~nl~~~~~~~ac~~l~d~slk~l~klges~~G~yiV~y  375 (551)
T KOG2587|consen  296 LDTELSINEIFRSLNVGSNGSISMESLDQYLTLLERGDTEEEENLDADTEDPACASLADDSLKFLGKLGESGGGMYIVNY  375 (551)
T ss_pred             hhchhhhhhhccCcccccchHHHHHhhhhHHHHHhhccchhhccccccchhhHHHHhhcchHHHHHHhccCCCCEEEEEH
Confidence                     0111111      11111111111     1233344444444444432                     99


Q ss_pred             HHHHHHHHHHHHHHHHHHHhCchHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCC--CC
Q 010353          349 EKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTG--AR  426 (512)
Q Consensus       349 ~~~~~~lr~~~le~~v~~~~G~~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~--~~  426 (512)
                      ++++..++..++|++|.++||..|.|+||+|..+|++ |||||++.|||+.||+|..||+|+++|||++||||||+  +|
T Consensus       376 ~k~i~vl~~~~~E~vI~~rfG~rAiRl~R~l~~k~~v-eekqv~~~Alm~~Kd~r~~L~~m~~~g~v~lQeVprTaD~~p  454 (551)
T KOG2587|consen  376 HKAIAVLATATYESVIQERFGSRAIRLFRLLLQKKHV-EEKQVEDFALMPAKDARDMLYKMLEEGYVELQEVPRTADRAP  454 (551)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhcccc-hHHHHHHhhccccccHHHHHHHHHHcCceeeeecCCCCCCCC
Confidence            9999999999999999999999999999999999876 99999999999999999999999999999999999998  99


Q ss_pred             CceEEEEEEehHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcccccccCC-----------hhHHHHHHHHHHHHHHH
Q 010353          427 QSQFLLWKVNRQILWKHVLDEMFHAALNLSLRVSYELDREKELLNLPADKRT-----------GPLQDRYNRIRKVRILL  495 (512)
Q Consensus       427 ~~t~~lw~v~~~~~~~~~l~~~~k~~~nl~~R~~~e~~~~k~ll~k~~~~~~-----------~~e~~~l~~~~~~~~~L  495 (512)
                      +||||||+||+.++++++++++||++.||+.|++||+.+++.||+|.++-+.           +.+..+++++...+-.+
T Consensus       455 srtF~L~~v~~~~a~~~lld~ly~~iaNL~~R~~~eraEn~~LL~Ka~rve~~Ik~~e~~~~k~~qlael~~~~~~ql~l  534 (551)
T KOG2587|consen  455 SRTFYLYTVNILRAYRMLLDELYKSIANLIERLRHERAENKRLLEKAQRVEAIIKGREATGAKEAQLAELEEMYTAQLNL  534 (551)
T ss_pred             cceEEEEEeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcccHhhhhhHHhhhhHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999765541           67888889999999999


Q ss_pred             HHHHhhhhhhhhccccC
Q 010353          496 ESSQMKLDDAILLFHDF  512 (512)
Q Consensus       496 ~~~~~rlD~~l~ll~d~  512 (512)
                      +....|+|+++++|++|
T Consensus       535 f~r~s~l~~~~~vf~~~  551 (551)
T KOG2587|consen  535 FKRASQLDETILVFESY  551 (551)
T ss_pred             HHHHHHHHHHHHHHhcC
Confidence            99999999999999987

>PF05645 RNA_pol_Rpc82: RNA polymerase III subunit RPC82; InterPro: IPR008806 DNA-directed RNA polymerases 2	Back alignment and domain information

>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2	Back alignment and domain information

>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors	Back alignment and domain information

>TIGR00373 conserved hypothetical protein TIGR00373	Back alignment and domain information

>PRK06266 transcription initiation factor E subunit alpha; Validated	Back alignment and domain information

>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]	Back alignment and domain information

>smart00531 TFIIE Transcription initiation factor IIE	Back alignment and domain information

>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors	Back alignment and domain information

>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2	Back alignment and domain information

>TIGR00373 conserved hypothetical protein TIGR00373	Back alignment and domain information

>PRK06266 transcription initiation factor E subunit alpha; Validated	Back alignment and domain information

>PHA02943 hypothetical protein; Provisional	Back alignment and domain information

>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases	Back alignment and domain information

>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis	Back alignment and domain information

>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]	Back alignment and domain information

>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A	Back alignment and domain information

>PF04337 DUF480: Protein of unknown function, DUF480; InterPro: IPR007432 This family consists of several proteins of uncharacterised function	Back alignment and domain information

>smart00531 TFIIE Transcription initiation factor IIE	Back alignment and domain information

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

>KOG2587 consensus RNA polymerase III (C) subunit [Transcription]	Back alignment and domain information

>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases	Back alignment and domain information

>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A	Back alignment and domain information

>PHA02943 hypothetical protein; Provisional	Back alignment and domain information

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR	Back alignment and domain information

>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis	Back alignment and domain information

>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A	Back alignment and domain information

>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities	Back alignment and domain information

>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional	Back alignment and domain information

>COG3355 Predicted transcriptional regulator [Transcription]	Back alignment and domain information

>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities	Back alignment and domain information

>PRK11239 hypothetical protein; Provisional	Back alignment and domain information

>COG3355 Predicted transcriptional regulator [Transcription]	Back alignment and domain information

>COG1510 Predicted transcriptional regulators [Transcription]	Back alignment and domain information

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor	Back alignment and domain information

>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]	Back alignment and domain information

>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast)	Back alignment and domain information

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein	Back alignment and domain information

>COG3132 Uncharacterized protein conserved in bacteria [Function unknown]	Back alignment and domain information

>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	Back alignment and domain information

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor	Back alignment and domain information

>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif	Back alignment and domain information

>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]	Back alignment and domain information

>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea	Back alignment and domain information

>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea	Back alignment and domain information

>COG2345 Predicted transcriptional regulator [Transcription]	Back alignment and domain information

>COG2345 Predicted transcriptional regulator [Transcription]	Back alignment and domain information

>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family	Back alignment and domain information

>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities	Back alignment and domain information

>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>smart00344 HTH_ASNC helix_turn_helix ASNC type	Back alignment and domain information

>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A	Back alignment and domain information

>COG1378 Predicted transcriptional regulators [Transcription]	Back alignment and domain information

>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B	Back alignment and domain information

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation	Back alignment and domain information

>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B	Back alignment and domain information

>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism	Back alignment and domain information

>PRK00135 scpB segregation and condensation protein B; Reviewed	Back alignment and domain information

>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain	Back alignment and domain information

>smart00344 HTH_ASNC helix_turn_helix ASNC type	Back alignment and domain information

>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B	Back alignment and domain information

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

>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function	Back alignment and domain information

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR	Back alignment and domain information

>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp	Back alignment and domain information

>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional	Back alignment and domain information

>PRK11169 leucine-responsive transcriptional regulator; Provisional	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

>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance	Back alignment and domain information

>COG3682 Predicted transcriptional regulator [Transcription]	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

>COG3388 Predicted transcriptional regulator [Transcription]	Back alignment and domain information

>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea	Back alignment and domain information

>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities	Back alignment and domain information

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional	Back alignment and domain information

>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B	Back alignment and domain information

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation	Back alignment and domain information

>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance	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		512
2xub_A		534	Human Rpc62 Subunit Structure Length = 534		3e-21

>pdb|2XUB|A Chain A, Human Rpc62 Subunit Structure Length = 534

Back alignment and structure

Iteration: 1

Score = 99.8 bits (247), Expect = 3e-21, Method: Compositional matrix adjust. Identities = 109/498 (21%), Positives = 215/498 (43%), Gaps = 66/498 (13%) Query: 2 LTEYGTKHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQ 61 +T+ K ++ HFG++V K+ L+R G + + T S +QVK AL VL+Q Sbjct: 1 MTQAEIKLCSLLLQEHFGEIVEKIGVHLIRTGSQPLRVIAHDTGTSLDQVKKALCVLVQH 60 Query: 62 NCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLL 121 N V + + +Y +L +R+ +++ + +V+ LL Sbjct: 61 NLV---------SYQVHKRGVVEYEAQCSRVLRMLRYPRYIYTTKTLYSDTGELIVEELL 111 Query: 122 EHGRLTL----KQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCPASEPLLMPIS 177 +G+LT+ K++ DR + ++G +D + T V+L H+V+RCP+ +P + Sbjct: 112 LNGKLTMSAVVKKVADRLTETMEDGKTMDYAEVSNTFVRLADTHFVQRCPS-----VPTT 166 Query: 178 EEEGPARKKGSKSAKKIGEPETIEQQVVEAALPMEAMRFSVVTNVESDVGEKEKNSNNVT 237 E P + + I E + +P + S++ G++ ++S+ Sbjct: 167 ENSDPGPPPPAPTL-VINEKDMY-------LVP----KLSLIGK-----GKRRRSSDEDA 209 Query: 238 PGE-KRKHDVLELDECGVADEQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSA 296 GE K K D + + ++AN + F + R + + V +D ++ ++ Sbjct: 210 AGEPKAKRPKYTTDNKEPIPDDGIYWQANLDRFHQHFRDQAIVSAVANRMDQTSSEIVRT 269 Query: 297 MLQATSSAEKKVKTKNSVPLSLSSIYEEVIKS-EAGRNMT---------------LDHVR 340 ML+ + ++ T +S P + E+ +S G N++ L+ V Sbjct: 270 MLRMS-----EITTSSSAPFTQPLSSNEIFRSLPVGYNISKQVLDQYLTLLADDPLEFVG 324 Query: 341 AS------LVQLDFEKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDT 394 S + ++ K + +ESVV +R+G RIFRL+ + + +E ++ D Sbjct: 325 KSGDSGGGMYVINLHKALASLATATLESVVQERFGSRCARIFRLVLQK-KHIEQKQVEDF 383 Query: 395 TFVEKKDAPKILYKLWKDGYLLMEKLVVTG--ARQSQFLLWKVNRQILWKHVLDEMFHAA 452 + K+A +LYK+ + ++ ++++ T A F L+ VN + +L + + Sbjct: 384 AMIPAKEAKDMLYKMLSENFMSLQEIPKTPDHAPSRTFYLYTVNILSAARMLLHRCYKSI 443 Query: 453 LNLSLRVSYELDREKELL 470 NL R +E K LL Sbjct: 444 ANLIERRQFETKENKRLL 461

PyMOL of 2xub

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		512
2xub_A		534	DNA-directed RNA polymerase III subunit RPC3; tran	2e-87
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-10
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-07
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-05
1q1h_A		110	TFE, transcription factor E, TFE; TFIIE, transcrip	2e-05

>2xub_A DNA-directed RNA polymerase III subunit RPC3; transcription, winged helix; 2.80A {Homo sapiens} PDB: 2xv4_S Length = 534	Back alignment and structure

 Score =  277 bits (710), Expect = 2e-87
 Identities = 105/560 (18%), Positives = 210/560 (37%), Gaps = 85/560 (15%)

Query: 3   TEYGTKHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQN 62
           T+   K    ++  HFG++V K+   L+R G    + +   T  S +QVK AL VL+Q N
Sbjct: 2   TQAEIKLCSLLLQEHFGEIVEKIGVHLIRTGSQPLRVIAHDTGTSLDQVKKALCVLVQHN 61

Query: 63  CVQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLE 122
            V               +   +Y      +L  +R+ +++      +      +V+ LL 
Sbjct: 62  LVSYQVH---------KRGVVEYEAQCSRVLRMLRYPRYIYTTKTLYSDTGELIVEELLL 112

Query: 123 HGRLT----LKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCPASEPLLMPISE 178
           +G+LT    +K++ DR   + ++G  +D   +  T V+L   H+V+RCP+          
Sbjct: 113 NGKLTMSAVVKKVADRLTETMEDGKTMDYAEVSNTFVRLADTHFVQRCPSVPTTENSDPG 172

Query: 179 EEGPARKKGSKSAKKIGEPETIEQQVVEAALPMEAMRFSVVTNVESDVGEKEKNSNNVTP 238
              PA             P+                      ++      +  +  +   
Sbjct: 173 PPPPAPTLVINEKDMYLVPK---------------------LSLIGKGKRRRSSDEDAAG 211

Query: 239 GEKRKHDVLELDECGVADEQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAML 298
             K K      D      +  + ++AN + F +  R +  +  V   +D  ++ ++  ML
Sbjct: 212 EPKAKRPKYTTDNKEPIPDDGIYWQANLDRFHQHFRDQAIVSAVANRMDQTSSEIVRTML 271

Query: 299 QATSSAEKKVKTKNSVPLSLSSIYEEVIKSEAGRNMTLDHVRASLVQL------------ 346
           + +           + PLS + I+  +     G N++   +   L  L            
Sbjct: 272 RMSEITTSSSAPF-TQPLSSNEIFRSL---PVGYNISKQVLDQYLTLLADDPLEFVGKSG 327

Query: 347 ---------DFEKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFV 397
                    +  K +       +ESVV +R+G    RIFRL+ +    +E  ++ D   +
Sbjct: 328 DSGGGMYVINLHKALASLATATLESVVQERFGSRCARIFRLVLQKK-HIEQKQVEDFAMI 386

Query: 398 EKKDAPKILYKLWKDGYLLMEKLVVTGAR--QSQFLLWKVNRQILWKHVLDEMFHAALNL 455
             K+A  +LYK+  + ++ ++++  T        F L+ VN     + +L   + +  NL
Sbjct: 387 PAKEAKDMLYKMLSENFMSLQEIPKTPDHAPSRTFYLYTVNILSAARMLLHRCYKSIANL 446

Query: 456 SLRVSYELDREKELLNL-----------------------PADKRTGPLQDRYNRIRKVR 492
             R  +E    K LL                           +  T P + +   +++  
Sbjct: 447 IERRQFETKENKRLLEKSQRVEAIIASMQATGAEEAQLQEIEEMITAPERQQLETLKRNV 506

Query: 493 ILLESSQMKLDDAILLFHDF 512
             L++S++++D+ I L   +
Sbjct: 507 NKLDASEIQVDETIFLLESY 526

PyMOL of 2xub

>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

>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

>1q1h_A TFE, transcription factor E, TFE; TFIIE, transcription initiation, preinitiation complex, RNA polymerase II, transcription bubble; 2.90A {Sulfolobus solfataricus} SCOP: a.4.5.41 Length = 110	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		512
2xub_A		534	DNA-directed RNA polymerase III subunit RPC3; tran	100.0
2xub_A		534	DNA-directed RNA polymerase III subunit RPC3; tran	99.14
1q1h_A		110	TFE, transcription factor E, TFE; TFIIE, transcrip	98.23
1q1h_A		110	TFE, transcription factor E, TFE; TFIIE, transcrip	96.55
2qlz_A		232	Transcription factor PF0095; 2.50A {Pyrococcus fur	96.25
2nr3_A		183	Hypothetical protein; APC84902, conserved domain,	95.41
1xmk_A		79	Double-stranded RNA-specific adenosine deaminase;	95.38
2oqg_A		114	Possible transcriptional regulator, ARSR family P;	95.3
1r1u_A		106	CZRA, repressor protein; zinc, DNA binding, transc	95.29
3pqk_A		102	Biofilm growth-associated repressor; helix-turn-he	94.76
3bz6_A		183	UPF0502 protein pspto_2686; APC84902, conserved do	94.7
2htj_A		81	P fimbrial regulatory protein KS71A; winged helix-	94.58
3r0a_A		123	Putative transcriptional regulator; structural gen	94.36
3jth_A		98	Transcription activator HLYU; transcription factor	94.26
1qbj_A		81	Protein (double-stranded RNA specific adenosine D	93.95
3cuo_A		99	Uncharacterized HTH-type transcriptional regulato;	93.93
3r0a_A		123	Putative transcriptional regulator; structural gen	93.6
1u2w_A		122	CADC repressor, cadmium efflux system accessory pr	93.57
2kko_A		108	Possible transcriptional regulatory protein (possi	93.48
1ku9_A		152	Hypothetical protein MJ223; putative transcription	93.42
2d1h_A		109	ST1889, 109AA long hypothetical transcriptional re	93.36
1oyi_A		82	Double-stranded RNA-binding protein; (alpha+beta)	93.31
3bdd_A		142	Regulatory protein MARR; putative multiple antibio	92.72
2lkp_A		119	Transcriptional regulator, ARSR family; symmetric	92.66
1r1t_A		122	Transcriptional repressor SMTB; zinc, transcriptio	92.66
1qgp_A		77	Protein (double stranded RNA adenosine deaminase);	92.64
1ub9_A		100	Hypothetical protein PH1061; helix-turn-helix moti	92.6
2jsc_A		118	Transcriptional regulator RV1994C/MT2050; cadmium,	92.36
1ldj_A		760	Cullin homolog 1, CUL-1; cullin, ROC1, HRT1, zinc	92.33
1qgp_A		77	Protein (double stranded RNA adenosine deaminase);	92.32
2zkz_A		99	Transcriptional repressor PAGR; protein-DNA, HTH m	92.15
1sfx_A		109	Conserved hypothetical protein AF2008; structural	92.15
3eyi_A		72	Z-DNA-binding protein 1; alternative splicing, DNA	91.93
1sfx_A		109	Conserved hypothetical protein AF2008; structural	91.75
1xmk_A		79	Double-stranded RNA-specific adenosine deaminase;	91.69
3f6o_A		118	Probable transcriptional regulator, ARSR family pr	91.26
2lnb_A		80	Z-DNA-binding protein 1; structural genomics, nort	90.59
1sfu_A		75	34L protein; protein/Z-DNA complex, DNA binding pr	90.45
3boq_A		160	Transcriptional regulator, MARR family; MARR famil	90.34
2fu4_A		83	Ferric uptake regulation protein; DNA binding doma	90.15
2hr3_A		147	Probable transcriptional regulator; MCSG, structur	90.06
1oyi_A		82	Double-stranded RNA-binding protein; (alpha+beta)	89.98
1ku9_A		152	Hypothetical protein MJ223; putative transcription	89.91
3f6v_A		151	Possible transcriptional regulator, ARSR family pr	89.89
2l02_A		82	Uncharacterized protein; structural genomics, nort	89.85
1z7u_A		112	Hypothetical protein EF0647; winged-helix-turn-hel	89.77
2pex_A		153	Transcriptional regulator OHRR; transcription regu	89.28
2htj_A		81	P fimbrial regulatory protein KS71A; winged helix-	89.15
2hzt_A		107	Putative HTH-type transcriptional regulator YTCD;	89.04
2vxz_A		165	Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Py	88.56
1xn7_A		78	Hypothetical protein YHGG; alpha+beta, GFT structu	88.48
2l02_A		82	Uncharacterized protein; structural genomics, nort	88.39
2nnn_A		140	Probable transcriptional regulator; structural gen	88.37
3bro_A		141	Transcriptional regulator; helix_TURN_helix, multi	88.35
1lj9_A		144	Transcriptional regulator SLYA; HTH DNA binding pr	88.31
2p4w_A		202	Transcriptional regulatory protein ARSR family; ar	88.25
2vxz_A		165	Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Py	88.19
3bja_A		139	Transcriptional regulator, MARR family, putative;	88.18
2eth_A		154	Transcriptional regulator, putative, MAR family; M	87.93
3bpv_A		138	Transcriptional regulator; MARR, DNA binding, tran	87.9
1y0u_A		96	Arsenical resistance operon repressor, putative; s	87.88
2fbh_A		146	Transcriptional regulator PA3341; MARR, transcript	87.81
1qbj_A		81	Protein (double-stranded RNA specific adenosine D	87.8
1jgs_A		138	Multiple antibiotic resistance protein MARR; trans	87.73
3lmm_A		583	Uncharacterized protein; multi-domained alpha-beta	87.67
3cjn_A		162	Transcriptional regulator, MARR family; silicibact	87.45
3tgn_A		146	ADC operon repressor ADCR; helix-turn-helix, trans	87.43
2xvc_A		59	ESCRT-III, SSO0910; cell cycle, cell division, cyt	87.31
2rdp_A		150	Putative transcriptional regulator MARR; PFAM PF01	87.09
2a61_A		145	Transcriptional regulator TM0710; APC4350, MCSG, m	87.07
2fbi_A		142	Probable transcriptional regulator; MARR, APC5816,	87.0
2d1h_A		109	ST1889, 109AA long hypothetical transcriptional re	86.99
2hye_C		759	Cullin-4A, CUL-4A; beta propeller, ring finger, zi	86.91
2l01_A		77	Uncharacterized protein; structural genomics, nort	86.82
2k02_A		87	Ferrous iron transport protein C; FEOC, iron-sulfu	86.71
1yyv_A		131	Putative transcriptional regulator; reductive meth	86.64
3g3z_A		145	NMB1585, transcriptional regulator, MARR family; t	86.59
2cg4_A		152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	86.54
1sd4_A		126	Penicillinase repressor; BLAI, MECI, methicillin,	86.43
2fsw_A		107	PG_0823 protein; alpha-beta structure, helix-turn-	86.24
1okr_A		123	MECI, methicillin resistance regulatory protein ME	86.2
2cfx_A		144	HTH-type transcriptional regulator LRPC; transcrip	86.06
2bv6_A		142	MGRA, HTH-type transcriptional regulator MGRA; mul	86.06
3cdh_A		155	Transcriptional regulator, MARR family; helix-turn	85.68
2l01_A		77	Uncharacterized protein; structural genomics, nort	85.64
3bpv_A		138	Transcriptional regulator; MARR, DNA binding, tran	85.63
3bja_A		139	Transcriptional regulator, MARR family, putative;	85.53
2heo_A		67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	85.48
3bj6_A		152	Transcriptional regulator, MARR family; helix-turn	85.28
2oqg_A		114	Possible transcriptional regulator, ARSR family P;	85.27
3oop_A		143	LIN2960 protein; protein structure initiative, PSI	85.23
1s3j_A		155	YUSO protein; structural genomics, MARR transcript	85.22
3b73_A		111	PHIH1 repressor-like protein; winged-helix-turn-he	85.21
2h09_A		155	Transcriptional regulator MNTR; transcription regu	85.21
2heo_A		67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	85.18
2a61_A		145	Transcriptional regulator TM0710; APC4350, MCSG, m	85.18
2bv6_A		142	MGRA, HTH-type transcriptional regulator MGRA; mul	84.91
1z6r_A		406	MLC protein; transcriptional repressor, ROK family	84.84
3dpl_C		382	Cullin-5; ubiquitin, NEDD8, cullin, HOST-virus int	84.77
2fa5_A		162	Transcriptional regulator MARR/EMRR family; multip	84.69
3bj6_A		152	Transcriptional regulator, MARR family; helix-turn	84.67
1p4x_A		250	Staphylococcal accessory regulator A homologue; wi	84.63
1xn7_A		78	Hypothetical protein YHGG; alpha+beta, GFT structu	84.35
1s3j_A		155	YUSO protein; structural genomics, MARR transcript	84.3
2hoe_A		380	N-acetylglucosamine kinase; TM1224, structural gen	84.26
3bro_A		141	Transcriptional regulator; helix_TURN_helix, multi	84.12
2qww_A		154	Transcriptional regulator, MARR family; YP_013417.	84.06
2ia0_A		171	Putative HTH-type transcriptional regulator PF086;	84.04
1z91_A		147	Organic hydroperoxide resistance transcriptional;	83.97
2nyx_A		168	Probable transcriptional regulatory protein, RV14;	83.92
2p5v_A		162	Transcriptional regulator, LRP/ASNC family; NMB057	83.8
2gxg_A		146	146AA long hypothetical transcriptional regulator;	83.63
3k0l_A		162	Repressor protein; helix-turn-helix, structural ge	83.31
1ub9_A		100	Hypothetical protein PH1061; helix-turn-helix moti	83.2
4a5n_A		131	Uncharacterized HTH-type transcriptional regulato;	83.09
2jt1_A		77	PEFI protein; solution structure, winged helix-tur	82.89
2qww_A		154	Transcriptional regulator, MARR family; YP_013417.	82.8
3hsr_A		140	HTH-type transcriptional regulator SARZ; helix-tur	82.8
3e6m_A		161	MARR family transcriptional regulator; APC88769, s	82.52
2fbi_A		142	Probable transcriptional regulator; MARR, APC5816,	82.49
2k02_A		87	Ferrous iron transport protein C; FEOC, iron-sulfu	82.46
2dk5_A		91	DNA-directed RNA polymerase III 39 kDa polypeptide	82.37
3s2w_A		159	Transcriptional regulator, MARR family; structural	82.28
2f2e_A		146	PA1607; transcription factor, helix-TRUN-helix, AP	82.16
2dbb_A		151	Putative HTH-type transcriptional regulator PH006;	82.14
3eco_A		139	MEPR; mutlidrug efflux pump regulator winged helix	82.06
3k0l_A		162	Repressor protein; helix-turn-helix, structural ge	81.83
2nnn_A		140	Probable transcriptional regulator; structural gen	81.75
3nrv_A		148	Putative transcriptional regulator (MARR/EMRR FAM;	81.58
1t6s_A		162	Conserved hypothetical protein; A winged helix-tur	81.57
4hbl_A		149	Transcriptional regulator, MARR family; HTH, trans	81.29
3cjn_A		162	Transcriptional regulator, MARR family; silicibact	81.2
2rdp_A		150	Putative transcriptional regulator MARR; PFAM PF01	81.15
2hr3_A		147	Probable transcriptional regulator; MCSG, structur	81.12
1z05_A		429	Transcriptional regulator, ROK family; structural	80.83
3s2w_A		159	Transcriptional regulator, MARR family; structural	80.7
1tbx_A		99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	80.68
2y75_A		129	HTH-type transcriptional regulator CYMR; DNA bindi	80.46
3cdh_A		155	Transcriptional regulator, MARR family; helix-turn	80.44
2w25_A		150	Probable transcriptional regulatory protein; trans	80.43
3ech_A		142	MEXR, multidrug resistance operon repressor; winge	80.37
1lj9_A		144	Transcriptional regulator SLYA; HTH DNA binding pr	80.3
3i4p_A		162	Transcriptional regulator, ASNC family; PSI, struc	80.14
1i1g_A		141	Transcriptional regulator LRPA; helix-turn-helix,	80.07

>2xub_A DNA-directed RNA polymerase III subunit RPC3; transcription, winged helix; 2.80A {Homo sapiens} PDB: 2xv4_S	Back alignment and structure

Probab=100.00  E-value=8e-89  Score=733.50  Aligned_cols=474  Identities=21%  Similarity=0.387  Sum_probs=362.8

Q ss_pred             ccHHHHHHHHHHHHhhhchhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCC
Q 010353            2 LTEYGTKHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKA   81 (512)
Q Consensus         2 ~s~~~~~Lc~~iv~~~FG~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~   81 (512)
                      ||+++++||+.||++||||+|++||++|+++|++||++|++.|++++++||+||++|||||||.|+..+.  |       
T Consensus         1 Ms~~~~~L~~~li~~~FG~~~~~V~~~Ll~~G~ltL~~I~~~t~L~~~~Vk~~L~vLIQh~lV~~~~~~~--~-------   71 (534)
T 2xub_A            1 MTQAEIKLCSLLLQEHFGEIVEKIGVHLIRTGSQPLRVIAHDTGTSLDQVKKALCVLVQHNLVSYQVHKR--G-------   71 (534)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETT--T-------
T ss_pred             CCHHHHHHHHHHHHHhcChHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHHHHHhcCCeeEEeCCC--C-------
Confidence            7999999999999999999999999999999999999999999999999999999999999998765431  1       


Q ss_pred             ccEEEechhhHHHHhchhhHHHHHHHHhhhhHHHHHHHHHHcccCCHHHHHHHHhhccc----CCCccCHHHHHHHHHHH
Q 010353           82 NTQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEK----EGNLVDLDSLRETLVKL  157 (512)
Q Consensus        82 ~~~Y~~~~~~il~rlR~pr~l~~i~~~~G~~a~~Iv~~lL~~G~l~~~~li~~~~~~~~----~~~~~~~~~l~~~f~~L  157 (512)
                      .++|++|+++||+|+|||+||.+|+++||++|+.|+++||.+|++|+++++..+.++.+    +++..+...++++|.+|
T Consensus        72 ~~~Y~~~~~~il~~lR~pk~l~~i~~~~G~~a~~I~~~ll~~G~~t~~~ll~~~~~~~~~~~~~~~~~~~~~l~~~f~~L  151 (534)
T 2xub_A           72 VVEYEAQCSRVLRMLRYPRYIYTTKTLYSDTGELIVEELLLNGKLTMSAVVKKVADRLTETMEDGKTMDYAEVSNTFVRL  151 (534)
T ss_dssp             EEEEEECHHHHHGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHCCBCHHHHHHHHHHHHHHTSSSSCCCCHHHHHHHHHHH
T ss_pred             cEEEEEChhhHHHHHhhHHHHHHHHHHhcHHHHHHHHHHHHcCCccHHHHHHHHHhhcccccccccccCHHHHHHHHHHH
Confidence            58999999999999999999999999999999999999999999999999999876532    22334788999999999


Q ss_pred             HhcccccccCCCCCCCCCCCccCCcccccCCCCCcccCCchhhHHHHHHhhCchhhhhhhhhc-ccccccccccc-CCCC
Q 010353          158 VTAHYVERCPASEPLLMPISEEEGPARKKGSKSAKKIGEPETIEQQVVEAALPMEAMRFSVVT-NVESDVGEKEK-NSNN  235 (512)
Q Consensus       158 v~~~fi~rv~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~a~~~~~~r~~~~~-~~~~~~~~~~~-~~~~  235 (512)
                      +++|||+|||+..+...  ++...   ..|.+.   +..              .+.+.|..|. +.....+++.. .+..
T Consensus       152 v~~~fI~rv~~~~~~~~--~~~~~---~~~~~~---~~~--------------~~~~~~~~p~~~~~~~~k~~~~~~~~~  209 (534)
T 2xub_A          152 ADTHFVQRCPSVPTTEN--SDPGP---PPPAPT---LVI--------------NEKDMYLVPKLSLIGKGKRRRSSDEDA  209 (534)
T ss_dssp             HHTTSEEECCCC--------------------------------------------------------------------
T ss_pred             HhCCCEEeCCCCCcccc--ccccc---ccCCch---hhh--------------cchhhhccchhhhHHHhhhccccCCcc
Confidence            99999999986432111  11110   011110   000              0011111111 00000111100 1111


Q ss_pred             CCCCCcccCCcccccccCCCCCCccEEEecHHHHHHHHHHHHHHHHHHhhcChhHHHHHHHHHhccccccccccccCCCc
Q 010353          236 VTPGEKRKHDVLELDECGVADEQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQATSSAEKKVKTKNSVP  315 (512)
Q Consensus       236 ~~~~~Krk~~~~~~d~~~~~~~~~v~wrvN~~rf~~~lR~~~iv~~v~~r~g~~a~~v~~~~L~~~~~~~~~~~~~~s~p  315 (512)
                      +.+++|++.+...+|+ +...+++++|||||++|+++|||++|+++|++|+|+.||.||++||++.+.++ ++|++.|.|
T Consensus       210 ~~~~~~k~~~~~~~~~-~~~~d~~~~wrvN~erf~~~lR~~~lv~~v~~r~~~~a~~V~~~lL~~~e~~~-~~~~~~s~~  287 (534)
T 2xub_A          210 AGEPKAKRPKYTTDNK-EPIPDDGIYWQANLDRFHQHFRDQAIVSAVANRMDQTSSEIVRTMLRMSEITT-SSSAPFTQP  287 (534)
T ss_dssp             ----------------------CTTSEEECHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHTTTTTS-CTTCSBCCC
T ss_pred             ccccccccccCCCccc-cccCCCCceEEeeHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHhhccC-CccccCCCc
Confidence            2233444443332222 34467899999999999999999999999999999999999999999988655 567788999


Q ss_pred             cChHHHHHHhhhhhcCCCCcHHHHHHHHhhc---------------------CHHHHHHHHHHHHHHHHHHHHhCchHHH
Q 010353          316 LSLSSIYEEVIKSEAGRNMTLDHVRASLVQL---------------------DFEKIIEIAQNEEVESVVSKRYGRDAYR  374 (512)
Q Consensus       316 is~~~i~~~l~~~~~~~~~~~~~i~~~L~~l---------------------~~~~~~~~lr~~~le~~v~~~~G~~~~R  374 (512)
                      +++++|.+.+   +.+.+++.+.+++||..|                     ||+++++.||+.+++++|.++||..|+|
T Consensus       288 is~~~I~~~l---~~~~~l~~~~l~~~L~lL~~~~~~fv~~~g~~g~g~y~V~~~~~~~~lr~~~ie~ii~~~~G~~a~R  364 (534)
T 2xub_A          288 LSSNEIFRSL---PVGYNISKQVLDQYLTLLADDPLEFVGKSGDSGGGMYVINLHKALASLATATLESVVQERFGSRCAR  364 (534)
T ss_dssp             EEHHHHHHTS---CTTCCCCHHHHHHHHHHHHSCTTCCEEECCCCSSCEEEEBHHHHHHHHHHHHHHHHHHHHHCHHHHH
T ss_pred             ccHHHHHHHc---CCcccccHHHHHHHHHHHhCCcHHhhhccccCCCceEEEeHHHHHHHHHHHHHHHHHHHHhChHHHH
Confidence            9999999999   346788899999999875                     8999999999999999999999999999


Q ss_pred             HHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCC--CCCceEEEEEEehHHHHHHHHHHHHHHH
Q 010353          375 IFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTG--ARQSQFLLWKVNRQILWKHVLDEMFHAA  452 (512)
Q Consensus       375 i~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~--~~~~t~~lw~v~~~~~~~~~l~~~~k~~  452 (512)
                      |||+|..+|++ ||++|++.+|||.||+|++||+|+++|||++||+||++  +|+|+||||++|.+++..++++++||++
T Consensus       365 I~r~L~~~~~l-~d~~ia~~a~i~~k~vR~~Ly~L~~~g~v~~qevp~~~d~~~~~~~ylW~~~~~~~~~~l~~~~~k~l  443 (534)
T 2xub_A          365 IFRLVLQKKHI-EQKQVEDFAMIPAKEAKDMLYKMLSENFMSLQEIPKTPDHAPSRTFYLYTVNILSAARMLLHRCYKSI  443 (534)
T ss_dssp             HHHHHHHC----CHHHHHHHHCSCHHHHHHHHHHHHHTTCC---------------------CCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCC-CHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEEEccCCCCCCCcceEEEEEEcHHHHHHHHHHHHHHHH
Confidence            99999999998 99999999999999999999999999999999999987  8999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhhhhccccc-----------------------ccCChhHHHHHHHHHHHHHHHHHHHhhhhhhhhcc
Q 010353          453 LNLSLRVSYELDREKELLNLPA-----------------------DKRTGPLQDRYNRIRKVRILLESSQMKLDDAILLF  509 (512)
Q Consensus       453 ~nl~~R~~~e~~~~k~ll~k~~-----------------------~~~~~~e~~~l~~~~~~~~~L~~~~~rlD~~l~ll  509 (512)
                      .||++|+++|+++++.||+|.+                       +..+|+|+++|++|++++++|+++++|||++||+|
T Consensus       444 ~nl~~Rl~~E~~~~~~lL~k~eR~d~~~~~vk~~~~~~~~~~e~~e~lt~~e~~~l~~~~~~~~~L~~~~~~lD~~i~vl  523 (534)
T 2xub_A          444 ANLIERRQFETKENKRLLEKSQRVEAIIASMQATGAEEAQLQEIEEMITAPERQQLETLKRNVNKLDASEIQVDETIFLL  523 (534)
T ss_dssp             HHHHHHHHHHHHHTHHHHHHHHHHHHHHHCCC--------CHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHhhhhHHHHhhccccchhhhHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHhHHhHHHHH
Confidence            9999999999999999999943                       35679999999999999999999999999999999


Q ss_pred             ccC
Q 010353          510 HDF  512 (512)
Q Consensus       510 ~d~  512 (512)
                      +||
T Consensus       524 ~dy  526 (534)
T 2xub_A          524 ESY  526 (534)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            997

PyMOL of 2xub

>2xub_A DNA-directed RNA polymerase III subunit RPC3; transcription, winged helix; 2.80A {Homo sapiens} PDB: 2xv4_S	Back alignment and structure

>1q1h_A TFE, transcription factor E, TFE; TFIIE, transcription initiation, preinitiation complex, RNA polymerase II, transcription bubble; 2.90A {Sulfolobus solfataricus} SCOP: a.4.5.41	Back alignment and structure

>1q1h_A TFE, transcription factor E, TFE; TFIIE, transcription initiation, preinitiation complex, RNA polymerase II, transcription bubble; 2.90A {Sulfolobus solfataricus} SCOP: a.4.5.41	Back alignment and structure

>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A	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

>2oqg_A Possible transcriptional regulator, ARSR family P; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.54A {Rhodococcus SP}	Back alignment and structure

>1r1u_A CZRA, repressor protein; zinc, DNA binding, transcriptional regulation, winged HTH protein, transcription repressor; 2.00A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 1r1v_A 2kjb_A 2kjc_A	Back alignment and structure

>3pqk_A Biofilm growth-associated repressor; helix-turn-helix motif, winged-helix fold, transcriptional R DNA binding, transcription; 2.09A {Xylella fastidiosa} PDB: 3pqj_A	Back alignment and structure

>3bz6_A UPF0502 protein pspto_2686; APC84902, conserved domain, pseudomonas syringae PV. tomato DC3000, structural genomics, PSI-2; 2.21A {Pseudomonas syringae PV} SCOP: a.4.5.75 a.4.5.75	Back alignment and structure

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73	Back alignment and structure

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}	Back alignment and structure

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}	Back alignment and structure

>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A	Back alignment and structure

>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12}	Back alignment and structure

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}	Back alignment and structure

>1u2w_A CADC repressor, cadmium efflux system accessory protein; LEAD, SOFT metal ION resistance, ARSR/SM family, DNA binding protein; 1.90A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 3f72_A	Back alignment and structure

>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A	Back alignment and structure

>1ku9_A Hypothetical protein MJ223; putative transcription factor, homodimeric winged-helix fold, structural genomics, PSI; 2.80A {Methanocaldococcus jannaschii} SCOP: a.4.5.36	Back alignment and structure

>2d1h_A ST1889, 109AA long hypothetical transcriptional regulator; helix-turn-helix, intermolecular and intramolecular S-S bond structural genomics; 2.05A {Sulfolobus tokodaii} SCOP: a.4.5.50	Back alignment and structure

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19	Back alignment and structure

>3bdd_A Regulatory protein MARR; putative multiple antibiotic-resistance repressor, structura genomics, joint center for structural genomics, JCSG; 2.20A {Streptococcus suis}	Back alignment and structure

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}	Back alignment and structure

>1r1t_A Transcriptional repressor SMTB; zinc, transcriptional regulation, winged HTH protein, DNA binding, transcription repressor; 1.70A {Synechococcus elongatus pcc 7942} SCOP: a.4.5.5 PDB: 1r23_A 1smt_A 1r22_A	Back alignment and structure

>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19	Back alignment and structure

>1ub9_A Hypothetical protein PH1061; helix-turn-helix motif, winged helix motif, structural genom transcription; 2.05A {Pyrococcus horikoshii} SCOP: a.4.5.28	Back alignment and structure

>1ldj_A Cullin homolog 1, CUL-1; cullin, ROC1, HRT1, zinc ring finger, ligase, ubiquitin, ubiquitination, SCF; 3.00A {Homo sapiens} SCOP: a.4.5.34 a.118.17.1 e.40.1.1 PDB: 1u6g_A 1ldk_A 1ldk_B 3rtr_A	Back alignment and structure

>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19	Back alignment and structure

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}	Back alignment and structure

>1sfx_A Conserved hypothetical protein AF2008; structural genomics, HTH MOT protein structure initiative, midwest center for structural genomics; 1.55A {Archaeoglobus fulgidus} SCOP: a.4.5.50	Back alignment and structure

>3eyi_A Z-DNA-binding protein 1; alternative splicing, DNA-binding, polymorphism, DNA binding protein/Z-DNA complex, DNA binding protein/DNA complex; 1.45A {Homo sapiens} PDB: 2l4m_A	Back alignment and structure

>1sfx_A Conserved hypothetical protein AF2008; structural genomics, HTH MOT protein structure initiative, midwest center for structural genomics; 1.55A {Archaeoglobus fulgidus} SCOP: a.4.5.50	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

>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP}	Back alignment and structure

>2lnb_A Z-DNA-binding protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, immune system; NMR {Homo sapiens}	Back alignment and structure

>1sfu_A 34L protein; protein/Z-DNA complex, DNA binding protein/DNA complex; 2.00A {Yaba-like disease virus} SCOP: a.4.5.19	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

>2fu4_A Ferric uptake regulation protein; DNA binding domain, helix-turn-helix, DNA binding protein; 1.80A {Escherichia coli}	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

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19	Back alignment and structure

>1ku9_A Hypothetical protein MJ223; putative transcription factor, homodimeric winged-helix fold, structural genomics, PSI; 2.80A {Methanocaldococcus jannaschii} SCOP: a.4.5.36	Back alignment and structure

>3f6v_A Possible transcriptional regulator, ARSR family protein; probable transcriptional repressor ARSR family, structural genomics, PSI-2; 1.48A {Rhodococcus SP}	Back alignment and structure

>2l02_A Uncharacterized protein; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative; NMR {Bacteroides thetaiotaomicron}	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

>2pex_A Transcriptional regulator OHRR; transcription regulator; 1.90A {Xanthomonas campestris} PDB: 2pfb_A	Back alignment and structure

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73	Back alignment and structure

>2hzt_A Putative HTH-type transcriptional regulator YTCD; DNA-binding protein, HTH-type transcription regulators, structural genomics, PSI-2; HET: CSU MSE; 2.00A {Bacillus subtilis} SCOP: a.4.5.69	Back alignment and structure

>2vxz_A Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Pyrobaculum spherical virus}	Back alignment and structure

>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62	Back alignment and structure

>2l02_A Uncharacterized protein; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative; NMR {Bacteroides thetaiotaomicron}	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

>3bro_A Transcriptional regulator; helix_TURN_helix, multiple antibiotic resistance protein (MA structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.04A {Oenococcus oeni} SCOP: a.4.5.28	Back alignment and structure

>1lj9_A Transcriptional regulator SLYA; HTH DNA binding protein, structural genomics, PSI, protein structure initiative; 1.60A {Enterococcus faecalis} SCOP: a.4.5.28	Back alignment and structure

>2p4w_A Transcriptional regulatory protein ARSR family; archaea, PHR, heat shock, transcriptional regulation, winged DNA binding; 2.60A {Pyrococcus furiosus} SCOP: a.4.5.64	Back alignment and structure

>2vxz_A Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Pyrobaculum spherical virus}	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

>2eth_A Transcriptional regulator, putative, MAR family; MARR family, structural genomics, joint center for structura genomics, JCSG; 2.30A {Thermotoga maritima} SCOP: a.4.5.28	Back alignment and structure

>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A*	Back alignment and structure

>1y0u_A Arsenical resistance operon repressor, putative; structural genomics, protein structure initiative, PSI; HET: MSE; 1.60A {Archaeoglobus fulgidus} SCOP: a.4.5.5	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

>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A	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

>3lmm_A Uncharacterized protein; multi-domained alpha-beta protein, structural genomics, PSI- 2, protein structure initiative; 3.00A {Corynebacterium diphtheriae}	Back alignment and structure

>3cjn_A Transcriptional regulator, MARR family; silicibacter pomeroy structural genomics, PSI-2, protein structure initiative; 1.95A {Silicibacter pomeroyi dss-3}	Back alignment and structure

>3tgn_A ADC operon repressor ADCR; helix-turn-helix, transcriptional regulator, transcription; 2.00A {Streptococcus pneumoniae}	Back alignment and structure

>2xvc_A ESCRT-III, SSO0910; cell cycle, cell division, cytokinesis, winged-helix; 2.15A {Sulfolobus solfataricus}	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

>2a61_A Transcriptional regulator TM0710; APC4350, MCSG, midwest center for structural genomics, PSI, protein structure initiative, MARR; 1.80A {Thermotoga maritima} SCOP: a.4.5.28	Back alignment and structure

>2fbi_A Probable transcriptional regulator; MARR, APC5816, structural genomic protein structure initiative; 2.10A {Pseudomonas aeruginosa} SCOP: a.4.5.28	Back alignment and structure

>2d1h_A ST1889, 109AA long hypothetical transcriptional regulator; helix-turn-helix, intermolecular and intramolecular S-S bond structural genomics; 2.05A {Sulfolobus tokodaii} SCOP: a.4.5.50	Back alignment and structure

>2hye_C Cullin-4A, CUL-4A; beta propeller, ring finger, zinc finger, propeller cluster, helical repeats, cullin repeats, protein binding; HET: DNA; 3.10A {Homo sapiens} SCOP: a.4.5.34 a.118.17.1 e.40.1.1 PDB: 4a0k_A* 4a0c_C 4a0l_E*	Back alignment and structure

>2l01_A Uncharacterized protein; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative; NMR {Bacteroides vulgatus}	Back alignment and structure

>2k02_A Ferrous iron transport protein C; FEOC, iron-sulfur, metal-binding, metal binding protein; NMR {Klebsiella pneumoniae subsp}	Back alignment and structure

>1yyv_A Putative transcriptional regulator; reductive methylation, D lysine, structural genomics, PSI; HET: MLY; 2.35A {Salmonella typhimurium} SCOP: a.4.5.69	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

>2cg4_A Regulatory protein ASNC; DNA binding, FFRP, LRP family, transcription, DNA- binding, transcription regulation; 2.4A {Escherichia coli} SCOP: a.4.5.32 d.58.4.2	Back alignment and structure

>1sd4_A Penicillinase repressor; BLAI, MECI, methicillin, B-lactam, DNA binding PR; 2.00A {Staphylococcus aureus} SCOP: a.4.5.39 PDB: 1xsd_A	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

>1okr_A MECI, methicillin resistance regulatory protein MECI; bacterial antibiotic resistance, MECI protein, transcriptional regulatory element; 2.4A {Staphylococcus aureus} SCOP: a.4.5.39 PDB: 1sax_A 1sd7_A 2d45_A 1sd6_A	Back alignment and structure

>2cfx_A HTH-type transcriptional regulator LRPC; transcriptional regulation, DNA binding, FFRP; 2.4A {Bacillus subtilis} SCOP: a.4.5.32 d.58.4.2	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

>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

>2l01_A Uncharacterized protein; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative; NMR {Bacteroides vulgatus}	Back alignment and structure

>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A*	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

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A	Back alignment and structure

>3bj6_A Transcriptional regulator, MARR family; helix-turn-helix, trasnscription regulator, STR genomics, PSI-2, protein structure initiative; 2.01A {Silicibacter pomeroyi dss-3}	Back alignment and structure

>2oqg_A Possible transcriptional regulator, ARSR family P; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.54A {Rhodococcus SP}	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

>1s3j_A YUSO protein; structural genomics, MARR transcriptional regulator family, PSI, protein structure initiative; HET: MSE; 2.25A {Bacillus subtilis} SCOP: a.4.5.28	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

>2h09_A Transcriptional regulator MNTR; transcription regulator, diphtheria toxin, manganese transport, structural genomics, NPPSFA; 2.10A {Escherichia coli}	Back alignment and structure

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A	Back alignment and structure

>2a61_A Transcriptional regulator TM0710; APC4350, MCSG, midwest center for structural genomics, PSI, protein structure initiative, MARR; 1.80A {Thermotoga maritima} SCOP: a.4.5.28	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

>1z6r_A MLC protein; transcriptional repressor, ROK family protein, DNA binding P helix-turn-helix, phosphotransferase system; 2.70A {Escherichia coli} SCOP: a.4.5.63 c.55.1.10 c.55.1.10 PDB: 3bp8_A	Back alignment and structure

>3dpl_C Cullin-5; ubiquitin, NEDD8, cullin, HOST-virus interaction, receptor, UBL conjugation, UBL conjugation pathway, acetylation, cytoplasm; 2.60A {Homo sapiens} PDB: 3dqv_C	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

>3bj6_A Transcriptional regulator, MARR family; helix-turn-helix, trasnscription regulator, STR genomics, PSI-2, protein structure initiative; 2.01A {Silicibacter pomeroyi dss-3}	Back alignment and structure

>1p4x_A Staphylococcal accessory regulator A homologue; winged-helix protein, transcription; 2.20A {Staphylococcus aureus} SCOP: a.4.5.28 a.4.5.28	Back alignment and structure

>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62	Back alignment and structure

>1s3j_A YUSO protein; structural genomics, MARR transcriptional regulator family, PSI, protein structure initiative; HET: MSE; 2.25A {Bacillus subtilis} SCOP: a.4.5.28	Back alignment and structure

>2hoe_A N-acetylglucosamine kinase; TM1224, structural genomics, PSI-2, protein structure initiative, joint center structural genomics, JCSG; 2.46A {Thermotoga maritima} SCOP: a.4.5.63 c.55.1.10 c.55.1.10	Back alignment and structure

>3bro_A Transcriptional regulator; helix_TURN_helix, multiple antibiotic resistance protein (MA structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.04A {Oenococcus oeni} SCOP: a.4.5.28	Back alignment and structure

>2qww_A Transcriptional regulator, MARR family; YP_013417.1, multiple antibiotic-resistance repressor (MARR) structural genomics; HET: MSE; 2.07A {Listeria monocytogenes str}	Back alignment and structure

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}	Back alignment and structure

>1z91_A Organic hydroperoxide resistance transcriptional; OHRR, MARR family, bacterial transcription factor, DNA bindi protein; 2.50A {Bacillus subtilis} SCOP: a.4.5.28 PDB: 1z9c_A*	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

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A	Back alignment and structure

>2gxg_A 146AA long hypothetical transcriptional regulator; winged helix; 1.45A {Sulfolobus tokodaii} PDB: 2eb7_A 2yr2_A 3gez_A 3gf2_A* 3gfi_A 3gfm_A 3gfj_A 3gfl_A	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

>1ub9_A Hypothetical protein PH1061; helix-turn-helix motif, winged helix motif, structural genom transcription; 2.05A {Pyrococcus horikoshii} SCOP: a.4.5.28	Back alignment and structure

>4a5n_A Uncharacterized HTH-type transcriptional regulato; activator, DNA binding, MARR-like; 1.81A {Bacillus subtilis} PDB: 4a5m_A	Back alignment and structure

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}	Back alignment and structure

>2qww_A Transcriptional regulator, MARR family; YP_013417.1, multiple antibiotic-resistance repressor (MARR) structural genomics; HET: MSE; 2.07A {Listeria monocytogenes str}	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

>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

>2fbi_A Probable transcriptional regulator; MARR, APC5816, structural genomic protein structure initiative; 2.10A {Pseudomonas aeruginosa} SCOP: a.4.5.28	Back alignment and structure

>2k02_A Ferrous iron transport protein C; FEOC, iron-sulfur, metal-binding, metal binding protein; NMR {Klebsiella pneumoniae subsp}	Back alignment and structure

>2dk5_A DNA-directed RNA polymerase III 39 kDa polypeptide; structural genomics, winged helix domain, NPPSFA; NMR {Homo sapiens} SCOP: a.4.5.85	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

>2f2e_A PA1607; transcription factor, helix-TRUN-helix, APC5613, structural genomics, PSI, protein structure initiative; HET: GLC; 1.85A {Pseudomonas aeruginosa} SCOP: a.4.5.69	Back alignment and structure

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}	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

>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

>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

>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

>1t6s_A Conserved hypothetical protein; A winged helix-turn-helix, structural genomics, BSGC structu by NIH, protein structure initiative, PSI; 1.95A {Chlorobium tepidum tls} SCOP: a.4.5.60 a.4.5.60	Back alignment and structure

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

>3cjn_A Transcriptional regulator, MARR family; silicibacter pomeroy structural genomics, PSI-2, protein structure initiative; 1.95A {Silicibacter pomeroyi dss-3}	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

>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

>1z05_A Transcriptional regulator, ROK family; structural genomics, protein structure initiative, midwest center for structural genomics; 2.00A {Vibrio cholerae o1 biovar eltor} SCOP: a.4.5.63 c.55.1.10 c.55.1.10	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

>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

>2y75_A HTH-type transcriptional regulator CYMR; DNA binding protein; 2.00A {Bacillus subtilis}	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

>2w25_A Probable transcriptional regulatory protein; transcription regulation, mutant, RV3291C, Glu104Ala, DNA-binding; 2.15A {Mycobacterium tuberculosis} PDB: 2vbw_A* 2vbx_A* 2vby_A* 2vbz_A* 2vc0_A 2vc1_A 2w24_A 2ivm_A 2w29_A 2qz8_A	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

>1lj9_A Transcriptional regulator SLYA; HTH DNA binding protein, structural genomics, PSI, protein structure initiative; 1.60A {Enterococcus faecalis} SCOP: a.4.5.28	Back alignment and structure

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}	Back alignment and structure

>1i1g_A Transcriptional regulator LRPA; helix-turn-helix, LRP/ASNC family; 2.90A {Pyrococcus furiosus} SCOP: a.4.5.32 d.58.4.2	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		512
d1q1ha_		88	Transcription factor E/IIe-alpha, N-terminal domai	98.81
d1q1ha_		88	Transcription factor E/IIe-alpha, N-terminal domai	96.92
d1sfxa_		109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	96.73
d1z05a1		71	Transcriptional regulator VC2007 N-terminal domain	96.04
d1sfxa_		109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	95.99
d1ub9a_		100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	95.77
d1z6ra1		70	Mlc protein N-terminal domain {Escherichia coli [T	95.25
d2d1ha1		109	Hypothetical transcriptional regulator ST1889 {Sul	95.23
d1ku9a_		151	DNA-binding protein Mj223 {Archaeon Methanococcus	94.62
d1u2wa1		108	Cadmium efflux system accessory protein CadC {Stap	94.52
d2hoea1		62	N-acetylglucosamine kinase {Thermotoga maritima [T	94.33
d1ku9a_		151	DNA-binding protein Mj223 {Archaeon Methanococcus	93.96
d2d1ha1		109	Hypothetical transcriptional regulator ST1889 {Sul	93.69
d1r1ta_		98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	92.96
d1z05a1		71	Transcriptional regulator VC2007 N-terminal domain	92.8
d1r1ua_		94	Metal-sensing transcriptional repressor CzrA {Stap	91.86
d1sd4a_		122	Penicillinase repressor BlaI {Staphylococcus aureu	91.79
d2cfxa1		63	Transcriptional regulator LrpC {Bacillus subtilis	91.46
d1okra_		120	Methicillin resistance regulatory protein MecI {St	90.97
d1mkma1		75	Transcriptional regulator IclR, N-terminal domain	90.8
d1s3ja_		143	Putative transcriptional regulator YusO {Bacillus	90.37
d2cg4a1		63	Regulatory protein AsnC {Escherichia coli [TaxId:	90.35
d1ulya_		190	Hypothetical protein PH1932 {Pyrococcus horikoshii	89.76
d1z6ra1		70	Mlc protein N-terminal domain {Escherichia coli [T	89.69
d1i1ga1		60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	89.6
d1j75a_		57	Dlm-1 {Mouse (Mus musculus) [TaxId: 10090]}	89.02
d1i1ga1		60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	89.01
d2a61a1		139	Transcriptional regulator TM0710 {Thermotoga marit	88.74
d2p4wa1		194	Transcriptional regulatory protein PF1790 {Pyrococ	88.67
d2cyya1		60	Putative transcriptional regulator PH1519 {Archaeo	88.26
d1mkma1		75	Transcriptional regulator IclR, N-terminal domain	87.78
d1lnwa_		141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	87.7
d2cfxa1		63	Transcriptional regulator LrpC {Bacillus subtilis	87.01
d2hoea1		62	N-acetylglucosamine kinase {Thermotoga maritima [T	85.79
d1ub9a_		100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	85.79
d1ulya_		190	Hypothetical protein PH1932 {Pyrococcus horikoshii	85.61
d2cg4a1		63	Regulatory protein AsnC {Escherichia coli [TaxId:	85.48
d1xmka1		73	Z-alpha domain of dsRNA-specific adenosine deamina	84.18
d2p4wa1		194	Transcriptional regulatory protein PF1790 {Pyrococ	83.98
d2cyya1		60	Putative transcriptional regulator PH1519 {Archaeo	83.37
d2etha1		140	Putative transcriptional regulator TM0816 {Thermot	83.05
d1p6ra_		82	Penicillinase repressor BlaI {Bacillus licheniform	82.97
d1xmka1		73	Z-alpha domain of dsRNA-specific adenosine deamina	81.79
d1jgsa_		138	Multiple antibiotic resistance repressor, MarR {Es	81.78
d1u2wa1		108	Cadmium efflux system accessory protein CadC {Stap	81.4
d2g9wa1		122	Hypothetical protein Rv1846c {Mycobacterium tuberc	81.37
d1xd7a_		127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	81.14

>d1q1ha_ a.4.5.41 (A:) Transcription factor E/IIe-alpha, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}	Back information, alignment and structure

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcription factor E/IIe-alpha, N-terminal domain
domain: Transcription factor E/IIe-alpha, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=98.81  E-value=4.4e-09  Score=81.10  Aligned_cols=82  Identities=18%  Similarity=0.279  Sum_probs=69.3

Q ss_pred             HHHHHHHHHHhCchHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCCceEEEEEEeh
Q 010353          358 EEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNR  437 (512)
Q Consensus       358 ~~le~~v~~~~G~~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~~lw~v~~  437 (512)
                      ..+..++.+-.|+.|.+|++.|.++|.-+++++||+...+..+++|++||.|+..|++..-..... ..++..|+|+++.
T Consensus         6 ~ll~~~~~~i~Ge~~~~v~~~L~~~~~evtDe~iA~~tgi~in~VRk~Ly~L~~~~L~~y~R~kd~-~~gw~~Y~W~~~~   84 (88)
T d1q1ha_           6 DLFINLAKSLLGDDVIDVLRILLDKGTEMTDEEIANQLNIKVNDVRKKLNLLEEQGFVSYRKTRDK-DSGWFIYYWKPNI   84 (88)
T ss_dssp             THHHHHHHTTSCSTTHHHHHHHHHHCSCBCHHHHHHTTTSCHHHHHHHHHHHHHHTSCEEEEEC----CCCCEEEEECTH
T ss_pred             HHHHHHHHHHccHHHHHHHHHHHhccCcCCHHHHHHHhCCcHHHHHHHHHHHHhCCceEEEEeecC-CCCcEEEEEEech
Confidence            457788999999999999999987654339999999999999999999999999999966544333 5799999999998


Q ss_pred             HHH
Q 010353          438 QIL  440 (512)
Q Consensus       438 ~~~  440 (512)
                      +++
T Consensus        85 e~i   87 (88)
T d1q1ha_          85 DQI   87 (88)
T ss_dssp             HHH
T ss_pred             hcC
Confidence            865

PyMOL of d1q1ha_

>d1q1ha_ a.4.5.41 (A:) Transcription factor E/IIe-alpha, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}	Back information, alignment and structure

>d1sfxa_ a.4.5.50 (A:) Hypothetical protein AF2008 {Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]}	Back information, alignment and structure

>d1sfxa_ a.4.5.50 (A:) Hypothetical protein AF2008 {Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

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

>d1z6ra1 a.4.5.63 (A:12-81) Mlc protein N-terminal domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d2d1ha1 a.4.5.50 (A:1-109) Hypothetical transcriptional regulator ST1889 {Sulfolobus tokodaii [TaxId: 111955]}	Back information, alignment and structure

>d1ku9a_ a.4.5.36 (A:) DNA-binding protein Mj223 {Archaeon Methanococcus jannaschii [TaxId: 2190]}	Back information, alignment and structure

>d1u2wa1 a.4.5.5 (A:12-119) Cadmium efflux system accessory protein CadC {Staphylococcus aureus [TaxId: 1280]}	Back information, alignment and structure

>d2hoea1 a.4.5.63 (A:10-71) N-acetylglucosamine kinase {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d1ku9a_ a.4.5.36 (A:) DNA-binding protein Mj223 {Archaeon Methanococcus jannaschii [TaxId: 2190]}	Back information, alignment and structure

>d2d1ha1 a.4.5.50 (A:1-109) Hypothetical transcriptional regulator ST1889 {Sulfolobus tokodaii [TaxId: 111955]}	Back information, alignment and structure

>d1r1ta_ a.4.5.5 (A:) SmtB repressor {Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]}	Back information, alignment and structure

>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]}	Back information, alignment and structure

>d1r1ua_ a.4.5.5 (A:) Metal-sensing transcriptional repressor CzrA {Staphylococcus aureus [TaxId: 1280]}	Back information, alignment and structure

>d1sd4a_ a.4.5.39 (A:) Penicillinase repressor BlaI {Staphylococcus aureus [TaxId: 1280]}	Back information, alignment and structure

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}	Back information, alignment and structure

>d1okra_ a.4.5.39 (A:) Methicillin resistance regulatory protein MecI {Staphylococcus aureus [TaxId: 1280]}	Back information, alignment and structure

>d1mkma1 a.4.5.33 (A:1-75) Transcriptional regulator IclR, N-terminal domain {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d1s3ja_ a.4.5.28 (A:) Putative transcriptional regulator YusO {Bacillus subtilis [TaxId: 1423]}	Back information, alignment and structure

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1ulya_ a.4.5.58 (A:) Hypothetical protein PH1932 {Pyrococcus horikoshii [TaxId: 53953]}	Back information, alignment and structure

>d1z6ra1 a.4.5.63 (A:12-81) Mlc protein N-terminal domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	Back information, alignment and structure

>d1j75a_ a.4.5.19 (A:) Dlm-1 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	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

>d2p4wa1 a.4.5.64 (A:1-194) Transcriptional regulatory protein PF1790 {Pyrococcus furiosus [TaxId: 2261]}	Back information, alignment and structure

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}	Back information, alignment and structure

>d1mkma1 a.4.5.33 (A:1-75) Transcriptional regulator IclR, N-terminal domain {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d1lnwa_ a.4.5.28 (A:) MexR repressor {Pseudomonas aeruginosa [TaxId: 287]}	Back information, alignment and structure

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}	Back information, alignment and structure

>d2hoea1 a.4.5.63 (A:10-71) N-acetylglucosamine kinase {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

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

>d1ulya_ a.4.5.58 (A:) Hypothetical protein PH1932 {Pyrococcus horikoshii [TaxId: 53953]}	Back information, alignment and structure

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1xmka1 a.4.5.19 (A:294-366) Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2p4wa1 a.4.5.64 (A:1-194) Transcriptional regulatory protein PF1790 {Pyrococcus furiosus [TaxId: 2261]}	Back information, alignment and structure

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}	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

>d1p6ra_ a.4.5.39 (A:) Penicillinase repressor BlaI {Bacillus licheniformis [TaxId: 1402]}	Back information, alignment and structure

>d1xmka1 a.4.5.19 (A:294-366) Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1 {Human (Homo sapiens) [TaxId: 9606]}	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

>d1u2wa1 a.4.5.5 (A:12-119) Cadmium efflux system accessory protein CadC {Staphylococcus aureus [TaxId: 1280]}	Back information, alignment and structure

>d2g9wa1 a.4.5.39 (A:3-124) Hypothetical protein Rv1846c {Mycobacterium tuberculosis [TaxId: 1773]}	Back information, alignment and structure

>d1xd7a_ a.4.5.55 (A:) Hypothetical protein ywnA {Bacillus subtilis [TaxId: 1423]}	Back information, alignment and structure