Citrus Sinensis ID: 009017

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

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

MVCTANDLSAWKDFPKGLRVLLLDQDSSAAAELKFKLEAMDYIVSTFYNENEALSAFSDKPENFHVAIVEVTTSNTDGSFKFLETAKDLPTIITSNIHCLSTMMKCIALGAVEFLRKPLSEDKLRNLWQHVVHKAFNAGGSALSDSLKPVKESVVSMLHLKLENGESKNEKSENTEYVLVPQQSDNEQSVPNDKYPAPSTPQLKQGGRLLDDIDCQDNTNFSTEKESAEQDGESKFVETTCGNSIAEGTLQEDKPQRPRETIVKEEHDPTNGSKTECNMLPLPYEKDNLKGSNCVIENPSKASGLQNSCGNKANRKKMKAVEQLGVDQAIPSRILELMKVEGLTRHNVASHLQKYRMHRRHILPKEDDRKWPHARDQMLRNYYPHKPIMAFPPYHSNHLVPTGPVYPVWGAPSNHLAAVQMWAPPGYPPWQQAESWNWKPYPGMPADAWGCPVMPLPNGPYSSFPQGASGYHNSGVDDNSYAMPQNSVDLHPAEEVIDKVVKEAISKPWLPLPLGLKPPSADSVLAELSRQGISTIPPRINGSHPC

ccccccccccccccccccEEEEEcccHHHHHHHHHHHHccccEEEEEccHHHHHHHHHcccccccEEEEEcccccccHHHHHHHHcccccEEEEcccccHHHHHHHHHccccHHccccccHHHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccccHHHHHHHcccccccHHHHHHHHHHHHHHcccccccccccccccHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHcccccccccccccccc

ccEcccccEEHHHcccccEEEEEcccHHHHHHHHHHHHHcccEEEEccHHHHHHHHHHHccccccEEEEEcccccccHHHHHHHHHccccEEEEEccccccHHHHHHHHcHHHHEEccccHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEcccccEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEccHHHHHHHHHHHHHHccccccHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHccccHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHcccccccccccccccc

mvctandlsawkdfpkGLRVLLLDQDSSAAAELKFKLEAMDYIVSTFYNenealsafsdkpenFHVAIVEVttsntdgsfkfletakdlptiitSNIHCLSTMMKCIALGAVEFLrkplsedklRNLWQHVVHKAFNaggsalsdslkpVKESVVSMLHLKLengeskneksenteyvlvpqqsdneqsvpndkypapstpqlkqggrllddidcqdntnfstekesaeqdgeskfvettcgnsiaegtlqedkpqrpretivkeehdptngsktecnmlplpyekdnlkgsncvienpskasglqnscgnkanrKKMKAVEQLGVDQAIPSRILELMKVEGLTRHNVASHLQKYRMHrrhilpkeddrkwpharDQMLRnyyphkpimafppyhsnhlvptgpvypvwgapsnhlaavqmwappgyppwqqaeswnwkpypgmpadawgcpvmplpngpyssfpqgasgyhnsgvddnsyampqnsvdlhpaEEVIDKVVKEAiskpwlplplglkppsaDSVLAELSRqgistippringshpc

mvctandlsawkdfpkGLRVLLLDQDSSAAAELKFKLEAMDYIVSTFYNENEALSAFSDKPENFHVAIVEVttsntdgsFKFLETAKDLPTIITSNIHCLSTMMKCIALGAVEFLRKPLSEDKLRNLWQHVVHKAFNAggsalsdslKPVKESVVSMLHLKlengeskneksenTEYVLVPQQsdneqsvpndkyPAPSTPQLKQGGRLLDDIDCQDNTNFStekesaeqdgeskfVETTCGNsiaegtlqedkpqrpretivkeehdptngsktecnMLPLPYEKDNLKGSNCVIEnpskasglqnSCGNKANRKKMKAVEqlgvdqaipSRILELMKVEGLTRHNVASHLQKYRMHrrhilpkeddrkwphaRDQMLRNYYPHKPIMAFPPYHSNHLVPTGPVYPVWGAPSNHLAAVQMWAPPGYPPWQQAESWNWKPYPGMPADAWGCPVMPLPNGPYSSFPQGASGYHNSGVDDNSYAMPQNSVDLHPAEEVIDKVVKEAISKPWLPLPLGLKPPSADSVLAELSrqgistippringshpc

MVCTANDLSAWKDFPKGLRVLLLDQDSSAAAELKFKLEAMDYIVSTFYNENEALSAFSDKPENFHVAIVEVTTSNTDGSFKFLETAKDLPTIITSNIHCLSTMMKCIALGAVEFLRKPLSEDKLRNLWQHVVHKAFNAGGSALSDSLKPVKESVVSMLHlklengeskneksenteYVLVPQQSDNEQSVPNDKYPAPSTPQLKQGGRLLDDIDCQDNTNFSTEKESAEQDGESKFVETTCGNSIAEGTLQEDKPQRPRETIVKEEHDPTNGSKTECNMLPLPYEKDNLKGSNCVIENPSKASGLQNSCGNKANRKKMKAVEQLGVDQAIPSRILELMKVEGLTRHNVASHLQKYRMHRRHILPKEDDRKWPHARDQMLRNYYPHKPIMAFPPYHSNHLVPTGPVYPVWGAPSNHLAAVQMWAPPGYPPWQQAESWNWKPYPGMPADAWGCPVMPLPNGPYSSFPQGASGYHNSGVDDNSYAMPQNSVDLHPAEEVIDKVVKEAISkpwlplplglkppSADSVLAELSRQGISTIPPRINGSHPC

*****NDLSAWKDFPKGLRVLLLDQDSSAAAELKFKLEAMDYIVSTFYNENEALSAFSDKPENFHVAIVEVTTSNTDGSFKFLETAKDLPTIITSNIHCLSTMMKCIALGAVEFLRKPLSEDKLRNLWQHVVHKAFNAGG***************************************************************************************************************************************************************************************LGVDQAIPSRILELMKVEGLTRHNVASHLQKYRMHRRHILP*****KWPHARDQMLRNYYPHKPIMAFPPYHSNHLVPTGPVYPVWGAPSNHLAAVQMWAPPGYPPWQQAESWNWKPYPGMPADAWGCPVMPL**************************************EVIDKVVKEAISKPWLPLPLG*******************************

*************FPKGLRVLLLDQDSSAAAELKFKLEAMDYIVSTFYNENEALSAFSDKPENFHVAIVEVTTSNTDGSFKFLETAKDLPTIITSNIHCLSTMMKCIALGAVEFLRKPLSEDKLRNLWQHVVHKAFNAGGS**************************************************************KQGGRLLDDIDCQDNTNFST**************************************************KTECNMLPLPYEKDNLKGSNCVIEN******************KM**VEQLGV**AIPSRILELMKVEGLTRHNVASHLQKY*********************************************************************************************************************************************IDKVVKEAISKPWLPLPLGLKPPSADSVLAELSRQGIST***********

MVCTANDLSAWKDFPKGLRVLLLDQDSSAAAELKFKLEAMDYIVSTFYNENEALSAFSDKPENFHVAIVEVTTSNTDGSFKFLETAKDLPTIITSNIHCLSTMMKCIALGAVEFLRKPLSEDKLRNLWQHVVHKAFNAGGSALSDSLKPVKESVVSMLHLKLEN**********TEYVLVPQQ**************PSTPQLKQGGRLLDDIDCQDNTNF***************VETTCGNSIAEGTLQEDKPQRPRETIVKEEHDPTNGSKTECNMLPLPYEKDNLKGSNCVIENPSKASGLQNSCGNKANRKKMKAVEQLGVDQAIPSRILELMKVEGLTRHNVASHLQKYRMHRRHILPKEDDRKWPHARDQMLRNYYPHKPIMAFPPYHSNHLVPTGPVYPVWGAPSNHLAAVQMWAPPGYPPWQQAESWNWKPYPGMPADAWGCPVMPLPNGPYSSFPQGASGYHNSGVDDNSYAMPQNSVDLHPAEEVIDKVVKEAISKPWLPLPLGLKPPSADSVLAELSRQGISTIPPRINGSHPC

**C**NDLSAWKDFPKGLRVLLLDQDSSAAAELKFKLEAMDYIVSTFYNENEALSAFSDKPENFHVAIVEVTTSNTDGSFKFLETAKDLPTIITSNIHCLSTMMKCIALGAVEFLRKPLSEDKLRNLWQHVVHKAFN************************************************************************************************SKFVE*****SI***********************************************************LQNSCGNKANRKKMKAVEQLGVDQAIPSRILELMKVEGLTRHNVASHLQKYRMHRRHILPKEDDRKWPHARDQMLRNYYPHKPIMAFPPYHSNHLVPTGPVYPVWGAPSNHLAAVQMWAPPGYPPWQQAESWNWKPYPGMPADAWGCPVMPLPNGPYSSFPQGASGYHNSGVDDNSYAMPQNSVDLHPAEEVIDKVVKEAISKPWLPLPLGLKPPSADSVLAELSRQGISTIPP********

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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		546	2.2.26 [Sep-21-2011]
Q6LA43		535	Two-component response re	yes	no	0.890	0.908	0.501	1e-118
Q9FFH0		386	Transcription activator G	no	no	0.351	0.497	0.383	5e-23
Q9SIV3		420	Transcription activator G	no	no	0.401	0.521	0.355	1e-19
Q5Z5I4		455	Probable transcription fa	yes	no	0.401	0.481	0.345	6e-18
Q5NAN5		539	Probable transcription fa	no	no	0.097	0.098	0.660	2e-15
Q940D0		690	Two-component response re	no	no	0.219	0.173	0.370	4e-13
P62598		596	Two-component response re	no	no	0.238	0.218	0.343	5e-13
Q9ZWJ9		664	Two-component response re	no	no	0.225	0.185	0.362	2e-12
Q7Y0W5		341	Two-component response re	no	no	0.221	0.354	0.333	2e-11
Q7Y0W3		341	Two-component response re	N/A	no	0.221	0.354	0.333	2e-11

>sp\|Q6LA43\|APRR2_ARATH Two-component response regulator-like APRR2 OS=Arabidopsis thaliana GN=APRR2 PE=2 SV=2	Back alignment and function desciption

 Score =  426 bits (1095), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 296/590 (50%), Positives = 365/590 (61%), Gaps = 104/590 (17%)

Query: 1   MVCTANDLSAWKDFPKGLRVLLL------DQDSSAAAELKFKLEAMDYIVSTFYNENEAL 54
           MV TANDLS W++FPKGL+VLLL      D D S+AAE + +LE+MDYIV+TF +E EAL
Sbjct: 1   MVITANDLSKWENFPKGLKVLLLLNGCDSDGDGSSAAETRSELESMDYIVTTFTDETEAL 60

Query: 55  SAFSDKPENFHVAIVEVTTSNTDGSFKFLETAKD-LPTIITSNIHCLSTMMKCIALGAVE 113
           SA    PE+FH+AIVEV  S    SFKFLE AKD LPTI+ S  HC++T MKCIALGAVE
Sbjct: 61  SAVVKNPESFHIAIVEVNMSAESESFKFLEAAKDVLPTIMISTDHCITTTMKCIALGAVE 120

Query: 114 FLRKPLSEDKLRNLWQHVVHKAFNAGGSALSDSLKPVKESVVSMLHLKLENGESKNEKSE 173
           FL+KPLS +KL+N+WQHVVHKAFN GGS +S SLKPVKESVVSMLHL+            
Sbjct: 121 FLQKPLSPEKLKNIWQHVVHKAFNDGGSNVSISLKPVKESVVSMLHLE------------ 168

Query: 174 NTEYVLVPQQSDNEQSVPNDKYPAPSTPQLKQGGRLLDDIDCQDNTNF-------STEKE 226
            T+  +             +K PAPSTPQLKQ  RLLD  DCQ+N NF       STEK+
Sbjct: 169 -TDMTI------------EEKDPAPSTPQLKQDSRLLDG-DCQENINFSMENVNSSTEKD 214

Query: 227 SAE--QD-GESKFVETTCGNSIAEGTLQEDK--PQRPRETIVKEEHDPTNGSKTE-CNML 280
           + E  QD GESK V+TT         L +DK   +  R    KEE   T    +E  + +
Sbjct: 215 NMEDHQDIGESKSVDTT------NRKLDDDKVVVKEERGDSEKEEEGETGDLISEKTDSV 268

Query: 281 PLPYEKDNLKGSNCVIENPSKASGLQNSCGNKANRKK-----------MKAVEQLGVDQA 329
            +  ++D  K  N       K+SG++N  GNK +RKK           ++AVEQLGVDQA
Sbjct: 269 DIHKKEDETKPIN-------KSSGIKNVSGNKTSRKKVDWTPELHKKFVQAVEQLGVDQA 321

Query: 330 IPSRILELMKVEGLTRHNVASHLQKYRMHRRHILPKED-DRKWPHARDQML---RNY--- 382
           IPSRILELMKV  LTRHNVASHLQK+R HR++ILPK+D + +W  +R+      RNY   
Sbjct: 322 IPSRILELMKVGTLTRHNVASHLQKFRQHRKNILPKDDHNHRWIQSRENHRPNQRNYNVF 381

Query: 383 -YPHKPIMAFPPYHSNHLVPTGPVYPVWGAPSNHLAAVQMWAPPGYPPWQQAESWNWK-P 440
              H+P+MA+P +    + P G + P+W  P   +         G PP      W+WK P
Sbjct: 382 QQQHRPVMAYPVWGLPGVYPPGAIPPLWPPPLQSI---------GQPP-----PWHWKPP 427

Query: 441 YPGMPADAWGCPVMPLPNGPY---SSFPQGASGYHNSGVDDNSYAMPQNSVDLHPAEEVI 497
           YP +  +AWGCPV P   G Y   S+   G   Y N G +     MP +     P EE++
Sbjct: 428 YPTVSGNAWGCPVGPPVTGSYITPSNTTAGGFQYPN-GAETGFKIMPAS----QPDEEML 482

Query: 498 DKVVKEAISKPWLPLPLGLKPPSADSVLAELSRQGISTIPPR---INGSH 544
           D+VVKEAISKPWLPLPLGLKPPSA+SVLAEL+RQGIS +P     INGSH
Sbjct: 483 DQVVKEAISKPWLPLPLGLKPPSAESVLAELTRQGISAVPSSSCLINGSH 532

Transcriptional activator that binds specifically to the DNA sequence 5'-[AG]GATT-3'.
Arabidopsis thaliana (taxid: 3702)

>sp\|Q9FFH0\|GLK2_ARATH Transcription activator GLK2 OS=Arabidopsis thaliana GN=GLK2 PE=2 SV=1	Back alignment and function description

>sp\|Q9SIV3\|GLK1_ARATH Transcription activator GLK1 OS=Arabidopsis thaliana GN=GLK1 PE=2 SV=2	Back alignment and function description

>sp\|Q5Z5I4\|GLK1_ORYSJ Probable transcription factor GLK1 OS=Oryza sativa subsp. japonica GN=GLK1 PE=2 SV=1	Back alignment and function description

>sp\|Q5NAN5\|GLK2_ORYSJ Probable transcription factor GLK2 OS=Oryza sativa subsp. japonica GN=GLK2 PE=2 SV=1	Back alignment and function description

>sp\|Q940D0\|ARR1_ARATH Two-component response regulator ARR1 OS=Arabidopsis thaliana GN=ARR1 PE=1 SV=2	Back alignment and function description

>sp\|P62598\|ARR12_ARATH Two-component response regulator ARR12 OS=Arabidopsis thaliana GN=ARR12 PE=2 SV=2	Back alignment and function description

>sp\|Q9ZWJ9\|ARR2_ARATH Two-component response regulator ARR2 OS=Arabidopsis thaliana GN=ARR2 PE=1 SV=1	Back alignment and function description

>sp\|Q7Y0W5\|EHD1_ORYSJ Two-component response regulator EHD1 OS=Oryza sativa subsp. japonica GN=EHD1 PE=1 SV=1	Back alignment and function description

>sp\|Q7Y0W3\|EHD1_ORYSI Two-component response regulator EHD1 OS=Oryza sativa subsp. indica PE=2 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		546
225427316		557	PREDICTED: two-component response regula	0.992	0.973	0.703	0.0
147794999		563	hypothetical protein VITISV_001044 [Viti	0.990	0.960	0.678	0.0
224126555		549	predicted protein [Populus trichocarpa]	0.979	0.974	0.663	0.0
449513573		559	PREDICTED: LOW QUALITY PROTEIN: two-comp	0.989	0.966	0.639	0.0
449464910		560	PREDICTED: two-component response regula	0.989	0.964	0.638	0.0
356540587		570	PREDICTED: two-component response regula	0.987	0.945	0.613	1e-179
419193836		560	APRR2-like protein [Solanum lycopersicum	0.990	0.966	0.584	1e-179
357482307		543	Two-component response regulator-like pr	0.963	0.968	0.587	1e-175
356495556		533	PREDICTED: two-component response regula	0.930	0.953	0.612	1e-174
224138036		448	pseudo response regulator [Populus trich	0.787	0.959	0.682	1e-174

>gi\|225427316\|ref\|XP_002279150.1\| PREDICTED: two-component response regulator-like APRR2 [Vitis vinifera] gi\|297742160\|emb\|CBI33947.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

 Score =  780 bits (2013), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 393/559 (70%), Positives = 441/559 (78%), Gaps = 17/559 (3%)

Query: 1   MVCTANDLSAWKDFPKGLRVLLLDQDSSAAAELKFKLEAMDYIVSTFYNENEALSAFSDK 60
           MVCTANDL  WKDFPKGLRVLLLD D+++AAE++ KLE MDYIVSTF NENEALSA S K
Sbjct: 1   MVCTANDLQEWKDFPKGLRVLLLDDDTTSAAEIRSKLEEMDYIVSTFCNENEALSAISSK 60

Query: 61  PENFHVAIVEVTTSNTDGSFKFLETAKDLPTIITSNIHCLSTMMKCIALGAVEFLRKPLS 120
           PE+FHVAIVEV+T N +GSFKFLETAKDLPTI+ S+IHCLSTMMKCIALGAVEFLRKPLS
Sbjct: 61  PESFHVAIVEVSTGN-NGSFKFLETAKDLPTIMISSIHCLSTMMKCIALGAVEFLRKPLS 119

Query: 121 EDKLRNLWQHVVHKAFNAGGSALSDSLKPVKESVVSMLHLKLENGESKNEKSENTEYVLV 180
           EDKLRN+WQHVVHKAFNAGGS L +SLKPVKESV SML L++EN E +NE S  T  V  
Sbjct: 120 EDKLRNIWQHVVHKAFNAGGSVLPESLKPVKESVASMLQLQMENEEPRNESSAETLNVSN 179

Query: 181 PQQSDNEQSVPNDKYPAPSTPQLKQGGRLLDDIDCQDNTNFSTEKESAEQDGESKFVETT 240
             ++D+ QS   DKYPAPSTPQLKQGGR LDD DC D TN STEKES EQDGESK VETT
Sbjct: 180 VHENDHMQSAGTDKYPAPSTPQLKQGGRSLDDGDCLDQTNCSTEKESGEQDGESKSVETT 239

Query: 241 CGNSIAEGTLQEDKPQRPRETIVKEEHDPTNGSKTECNMLPLPYEKDNLKGSNCVIENPS 300
           CG S+AE T Q   PQ   E+++KEE D  +G K+E NM P P  KD+L        NP 
Sbjct: 240 CGTSVAEVTAQVSPPQGLGESVIKEEDDSADGCKSESNMSPHPQNKDSLSEFGGDARNPR 299

Query: 301 KASGLQNSCGNKANRKKMK-------------AVEQLGVDQAIPSRILELMKVEGLTRHN 347
           KASG+ + CG +ANRKKMK             AVEQLGVDQAIPSRILELMKVEGLTRHN
Sbjct: 300 KASGVHSPCGTRANRKKMKVDWTPELHKKFVQAVEQLGVDQAIPSRILELMKVEGLTRHN 359

Query: 348 VASHLQKYRMHRRHILPKEDDRKWPHARDQMLRNYYPHKPIMAFPPYHSNHLVPTGPVYP 407
           VASHLQKYRMHRRHILPKEDDR+WPH RD M RNYYP KP+MAFPPYHS+H +P   +YP
Sbjct: 360 VASHLQKYRMHRRHILPKEDDRRWPHQRDPMQRNYYPQKPVMAFPPYHSSHTLPAAQLYP 419

Query: 408 VWGAPSNHLAAVQMWAPPGYPPWQQAESWNWKPYPGMPADAWGCPVMPLPNGPYSSFPQG 467
           VWG PS+H A  QMW+ PGY  WQ AESW WKPYPGM ADAWGCPVM   + P SSFPQ 
Sbjct: 420 VWGQPSSHPA--QMWSTPGYHTWQPAESWIWKPYPGMNADAWGCPVMTPTHTPCSSFPQN 477

Query: 468 ASGY-HNSGVDDNSYAMPQNSVDLHPAEEVIDKVVKEAISKPWLPLPLGLKPPSADSVLA 526
            SG+ HN+G    +  +PQ+ +DL+PAEE+ID+VVKEAISKPW+PLPLGLKPP+ +SVLA
Sbjct: 478 PSGFDHNNGSGIYNTGIPQSPIDLYPAEELIDRVVKEAISKPWMPLPLGLKPPATESVLA 537

Query: 527 ELSRQGISTIPPRINGSHP 545
           ELSRQGISTIPP IN   P
Sbjct: 538 ELSRQGISTIPPHINTPRP 556

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|147794999\|emb\|CAN71929.1\| hypothetical protein VITISV_001044 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|224126555\|ref\|XP_002329583.1\| predicted protein [Populus trichocarpa] gi\|222870292\|gb\|EEF07423.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|449513573\|ref\|XP_004164360.1\| PREDICTED: LOW QUALITY PROTEIN: two-component response regulator-like APRR2-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449464910\|ref\|XP_004150172.1\| PREDICTED: two-component response regulator-like APRR2-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|356540587\|ref\|XP_003538769.1\| PREDICTED: two-component response regulator-like APRR2-like [Glycine max]	Back alignment and taxonomy information

>gi\|419193836\|gb\|AFX68729.1\| APRR2-like protein [Solanum lycopersicum]	Back alignment and taxonomy information

>gi\|357482307\|ref\|XP_003611439.1\| Two-component response regulator-like protein [Medicago truncatula] gi\|355512774\|gb\|AES94397.1\| Two-component response regulator-like protein [Medicago truncatula]	Back alignment and taxonomy information

>gi\|356495556\|ref\|XP_003516642.1\| PREDICTED: two-component response regulator-like APRR2-like [Glycine max]	Back alignment and taxonomy information

>gi\|224138036\|ref\|XP_002326502.1\| pseudo response regulator [Populus trichocarpa] gi\|222833824\|gb\|EEE72301.1\| pseudo response regulator [Populus trichocarpa]	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		546
TAIR\|locus:2141020		535	APRR2 [Arabidopsis thaliana (t	0.890	0.908	0.477	1.1e-108
TAIR\|locus:2167639		386	GLK2 "AT5G44190" [Arabidopsis	0.391	0.554	0.384	1.3e-28
UNIPROTKB\|Q7Y0W3		341	Q7Y0W3 "Two-component response	0.221	0.354	0.349	7e-24
UNIPROTKB\|Q7Y0W5		341	EHD1 "Two-component response r	0.221	0.354	0.349	7e-24
TAIR\|locus:2130095		664	RR2 "response regulator 2" [Ar	0.225	0.185	0.362	2.6e-21
TAIR\|locus:2093668		690	RR1 "response regulator 1" [Ar	0.219	0.173	0.370	7.1e-21
TAIR\|locus:2040194		596	RR12 "response regulator 12" [	0.252	0.231	0.340	8.3e-21
TAIR\|locus:2116587		552	RR10 "response regulator 10" [	0.234	0.231	0.333	2.7e-20
TAIR\|locus:2065398		382	RR14 "response regulator 14" [	0.219	0.314	0.312	1.5e-19
TAIR\|locus:2155954		292	APRR4 "pseudo-response regulat	0.217	0.407	0.346	2.4e-17

TAIR\|locus:2141020 APRR2 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1074 (383.1 bits), Expect = 1.1e-108, P = 1.1e-108
 Identities = 282/590 (47%), Positives = 353/590 (59%)

Query:     1 MVCTANDLSAWKDFPKGLRVLLL------DQDSSAAAELKFKLEAMDYIVSTFYNENEAL 54
             MV TANDLS W++FPKGL+VLLL      D D S+AAE + +LE+MDYIV+TF +E EAL
Sbjct:     1 MVITANDLSKWENFPKGLKVLLLLNGCDSDGDGSSAAETRSELESMDYIVTTFTDETEAL 60

Query:    55 SAFSDKPENFHVAIVEVTTSNTDGSFKFLETAKD-LPTIITSNIHCLSTMMKCIALGAVE 113
             SA    PE+FH+AIVEV  S    SFKFLE AKD LPTI+ S  HC++T MKCIALGAVE
Sbjct:    61 SAVVKNPESFHIAIVEVNMSAESESFKFLEAAKDVLPTIMISTDHCITTTMKCIALGAVE 120

Query:   114 FLRKPLSEDKLRNLWQHVVHKAFNAGGSALSDSLKPVKESVVSMLHXXXXXXXXXXXXXX 173
             FL+KPLS +KL+N+WQHVVHKAFN GGS +S SLKPVKESVVSMLH              
Sbjct:   121 FLQKPLSPEKLKNIWQHVVHKAFNDGGSNVSISLKPVKESVVSMLHL------------- 167

Query:   174 XXXYVLVPQQSDNEQSVPNDKYPAPSTPQLKQGGRLLDDIDCQDNTNFS-------TEKE 226
                        + + ++  +K PAPSTPQLKQ  RLLD  DCQ+N NFS       TEK+
Sbjct:   168 -----------ETDMTI-EEKDPAPSTPQLKQDSRLLDG-DCQENINFSMENVNSSTEKD 214

Query:   227 SAE--QD-GESKFVETTCGNSIAEGTLQEDKP--QRPRETIVKEEHDPTNGSKTE-CNML 280
             + E  QD GESK V+TT         L +DK   +  R    KEE   T    +E  + +
Sbjct:   215 NMEDHQDIGESKSVDTT------NRKLDDDKVVVKEERGDSEKEEEGETGDLISEKTDSV 268

Query:   281 PLPYEKDNLKGSNCVIENPSKASGLQNSCGNKANRKKM-----------KAVEQLGVDQA 329
              +  ++D  K  N       K+SG++N  GNK +RKK+           +AVEQLGVDQA
Sbjct:   269 DIHKKEDETKPIN-------KSSGIKNVSGNKTSRKKVDWTPELHKKFVQAVEQLGVDQA 321

Query:   330 IPSRILELMKVEGLTRHNVASHLQKYRMHRRHILPKED-DRKWPHARDQML---RNY--- 382
             IPSRILELMKV  LTRHNVASHLQK+R HR++ILPK+D + +W  +R+      RNY   
Sbjct:   322 IPSRILELMKVGTLTRHNVASHLQKFRQHRKNILPKDDHNHRWIQSRENHRPNQRNYNVF 381

Query:   383 -YPHKPIMAFPPYHSNHLVPTGPVYPVWGAPSNHLAAVQMWAPPGYPPWQQAESWNWKP- 440
                H+P+MA+P +    + P G + P+W  P   L ++      G PP      W+WKP 
Sbjct:   382 QQQHRPVMAYPVWGLPGVYPPGAIPPLWPPP---LQSI------GQPP-----PWHWKPP 427

Query:   441 YPGMPADAWGCPVMPLPNGPY---SSFPQGASGYHNSGVDDNSYAMPQNSVDLHPAEEVI 497
             YP +  +AWGCPV P   G Y   S+   G   Y N G +     MP +     P EE++
Sbjct:   428 YPTVSGNAWGCPVGPPVTGSYITPSNTTAGGFQYPN-GAETGFKIMPASQ----PDEEML 482

Query:   498 DKVVKEAISXXXXXXXXXXXXXSADSVLAELSRQGISTIPPR---INGSH 544
             D+VVKEAIS             SA+SVLAEL+RQGIS +P     INGSH
Sbjct:   483 DQVVKEAISKPWLPLPLGLKPPSAESVLAELTRQGISAVPSSSCLINGSH 532

GO:0000156 "phosphorelay response regulator activity" evidence=IEA;ISS

GO:0000160 "phosphorelay signal transduction system" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0007623 "circadian rhythm" evidence=RCA;TAS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0005515 "protein binding" evidence=IPI

GO:0009736 "cytokinin mediated signaling pathway" evidence=RCA

TAIR\|locus:2167639 GLK2 "AT5G44190" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

UNIPROTKB\|Q7Y0W3 Q7Y0W3 "Two-component response regulator EHD1" [Oryza sativa Indica Group (taxid:39946)]	Back alignment and assigned GO terms

UNIPROTKB\|Q7Y0W5 EHD1 "Two-component response regulator EHD1" [Oryza sativa Japonica Group (taxid:39947)]	Back alignment and assigned GO terms

TAIR\|locus:2130095 RR2 "response regulator 2" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2093668 RR1 "response regulator 1" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2040194 RR12 "response regulator 12" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2116587 RR10 "response regulator 10" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2065398 RR14 "response regulator 14" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2155954 APRR4 "pseudo-response regulator 4" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q6LA43	APRR2_ARATH	No assigned EC number	0.5016	0.8901	0.9084	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		546
PLN03162		526	PLN03162, PLN03162, golden-2 like transcription fa	1e-35
TIGR01557		57	TIGR01557, myb_SHAQKYF, myb-like DNA-binding domai	1e-13
cd00156		113	cd00156, REC, Signal receiver domain; originally t	2e-08
COG0784		130	COG0784, CheY, FOG: CheY-like receiver [Signal tra	5e-07
pfam00072		111	pfam00072, Response_reg, Response regulator receiv	1e-05
COG0745		229	COG0745, OmpR, Response regulators consisting of a	4e-05
COG2204		464	COG2204, AtoC, Response regulator containing CheY-	5e-04
COG3706		435	COG3706, PleD, Response regulator containing a Che	0.001
PRK10365		441	PRK10365, PRK10365, transcriptional regulatory pro	0.004

>gnl\|CDD\|178707 PLN03162, PLN03162, golden-2 like transcription factor; Provisional	Back alignment and domain information

 Score =  139 bits (352), Expect = 1e-35
 Identities = 99/280 (35%), Positives = 135/280 (48%), Gaps = 56/280 (20%)

Query: 314 NRKKMKAVEQLGVDQAIPSRILELMKVEGLTRHNVASHLQKYRMHRRHILPKE-DDRKWP 372
           +R+ + AVEQLGV++A PSRILELM V+ LTRHN+ASHLQKYR HRRH+  +E +   W 
Sbjct: 245 HRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQKYRSHRRHLAAREAEAASWT 304

Query: 373 HAR--DQM------LRNYYP-----HKP--------IMAFPPYHSNHLVPTGPVYPVWGA 411
           H R   Q        R+  P     H P         MA  P       P      VWG 
Sbjct: 305 HRRAYTQAPWPRSSRRDGLPYLVPIHTPHIQPRPSMAMAMQPQLQTPHHPISTPLKVWGY 364

Query: 412 PSNHLAAVQMWAPPGYPP---WQQAESWNWKPYPGMPADAW---GCPVMPLPNGPYSS-- 463
           P+   + V MW  P       WQ A+   W+ +P    DA+    C   P+   P  +  
Sbjct: 365 PTVDHSNVHMWQQPAVATPSYWQAADGSYWQ-HPATGYDAFSARACYPHPMQRVPLGTTH 423

Query: 464 ---------FPQGASGYHNSGVDDNSYAMPQN----------------SVDLHPAEEVID 498
                    FP  +  Y +  +  + Y   Q+                 ++ H ++EV+D
Sbjct: 424 AGLPIMAPGFPDESCYYGDDMLAASMYLCNQSYDSEIGRAAGVAACSKPIETHLSKEVLD 483

Query: 499 KVVKEAISKPWLPLPLGLKPPSADSVLAELSRQGISTIPP 538
             + EA++ PW P PLGLKPPS + V+AEL RQGI+T+PP
Sbjct: 484 AAIGEALANPWTPPPLGLKPPSMEGVIAELQRQGINTVPP 523

Length = 526

>gnl\|CDD\|130620 TIGR01557, myb_SHAQKYF, myb-like DNA-binding domain, SHAQKYF class	Back alignment and domain information

>gnl|CDD|238088 cd00156, REC, Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; contains a phosphoacceptor site that is phosphorylated by histidine kinase homologs; usually found N-terminal to a DNA binding effector domain; forms homodimers

Back alignment and domain information

>gnl\|CDD\|223855 COG0784, CheY, FOG: CheY-like receiver [Signal transduction mechanisms]	Back alignment and domain information

>gnl\|CDD\|200976 pfam00072, Response_reg, Response regulator receiver domain	Back alignment and domain information

>gnl\|CDD\|223816 COG0745, OmpR, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]	Back alignment and domain information

>gnl\|CDD\|225114 COG2204, AtoC, Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]	Back alignment and domain information

>gnl\|CDD\|226229 COG3706, PleD, Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal transduction mechanisms]	Back alignment and domain information

>gnl\|CDD\|182412 PRK10365, PRK10365, transcriptional regulatory protein ZraR; Provisional	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		546
PLN03162		526	golden-2 like transcription factor; Provisional	100.0
COG0745		229	OmpR Response regulators consisting of a CheY-like	99.85
COG4566		202	TtrR Response regulator [Signal transduction mecha	99.84
COG2204		464	AtoC Response regulator containing CheY-like recei	99.76
COG4753		475	Response regulator containing CheY-like receiver d	99.75
TIGR01557		57	myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF c	99.75
PF00072		112	Response_reg: Response regulator receiver domain;	99.72
COG2197		211	CitB Response regulator containing a CheY-like rec	99.72
COG4565		224	CitB Response regulator of citrate/malate metaboli	99.71
PRK10529		225	DNA-binding transcriptional activator KdpE; Provis	99.66
PRK10816		223	DNA-binding transcriptional regulator PhoP; Provis	99.65
COG3437		360	Response regulator containing a CheY-like receiver	99.65
PRK11083		228	DNA-binding response regulator CreB; Provisional	99.64
PRK10840		216	transcriptional regulator RcsB; Provisional	99.64
PRK10046		225	dpiA two-component response regulator DpiA; Provis	99.64
PRK10766		221	DNA-binding transcriptional regulator TorR; Provis	99.63
PRK10643		222	DNA-binding transcriptional regulator BasR; Provis	99.63
TIGR02154		226	PhoB phosphate regulon transcriptional regulatory	99.63
PRK09836		227	DNA-binding transcriptional activator CusR; Provis	99.63
PRK10336		219	DNA-binding transcriptional regulator QseB; Provis	99.63
PRK10161		229	transcriptional regulator PhoB; Provisional	99.62
PRK11517		223	transcriptional regulatory protein YedW; Provision	99.62
COG3706		435	PleD Response regulator containing a CheY-like rec	99.61
COG0784		130	CheY FOG: CheY-like receiver [Signal transduction	99.61
PRK10955		232	DNA-binding transcriptional regulator CpxR; Provis	99.61
PRK11173		237	two-component response regulator; Provisional	99.6
PRK09483		217	response regulator; Provisional	99.6
PRK10360		196	DNA-binding transcriptional activator UhpA; Provis	99.59
PRK09468		239	ompR osmolarity response regulator; Provisional	99.59
TIGR03787		227	marine_sort_RR proteobacterial dedicated sortase s	99.58
PRK09958		204	DNA-binding transcriptional activator EvgA; Provis	99.58
CHL00148		240	orf27 Ycf27; Reviewed	99.57
TIGR01387		218	cztR_silR_copR heavy metal response regulator. Mem	99.57
PLN03029		222	type-a response regulator protein; Provisional	99.57
PRK10701		240	DNA-binding transcriptional regulator RstA; Provis	99.57
PRK13856		241	two-component response regulator VirG; Provisional	99.56
COG4567		182	Response regulator consisting of a CheY-like recei	99.56
PRK15479		221	transcriptional regulatory protein TctD; Provision	99.53
PRK10430		239	DNA-binding transcriptional activator DcuR; Provis	99.53
PRK10710		240	DNA-binding transcriptional regulator BaeR; Provis	99.52
PRK09935		210	transcriptional regulator FimZ; Provisional	99.52
PRK10841		924	hybrid sensory kinase in two-component regulatory	99.47
PRK09390		202	fixJ response regulator FixJ; Provisional	99.46
KOG0519		786	consensus Sensory transduction histidine kinase [S	99.46
PRK11107		919	hybrid sensory histidine kinase BarA; Provisional	99.46
PRK10923		469	glnG nitrogen regulation protein NR(I); Provisiona	99.45
COG3947		361	Response regulator containing CheY-like receiver a	99.45
PRK15347		921	two component system sensor kinase SsrA; Provision	99.45
TIGR02875		262	spore_0_A sporulation transcription factor Spo0A.	99.44
PRK15115		444	response regulator GlrR; Provisional	99.44
PRK11697		238	putative two-component response-regulatory protein	99.44
PRK15369		211	two component system sensor kinase SsrB; Provision	99.44
PRK15411		207	rcsA colanic acid capsular biosynthesis activation	99.44
PRK10651		216	transcriptional regulator NarL; Provisional	99.43
PRK11361		457	acetoacetate metabolism regulatory protein AtoC; P	99.43
PRK11475		207	DNA-binding transcriptional activator BglJ; Provis	99.43
PRK10365		441	transcriptional regulatory protein ZraR; Provision	99.43
PRK14084		246	two-component response regulator; Provisional	99.43
PRK10403		215	transcriptional regulator NarP; Provisional	99.42
PRK09581		457	pleD response regulator PleD; Reviewed	99.41
PRK10100		216	DNA-binding transcriptional regulator CsgD; Provis	99.4
PRK13435		145	response regulator; Provisional	99.4
PRK11466		914	hybrid sensory histidine kinase TorS; Provisional	99.39
TIGR02956		968	TMAO_torS TMAO reductase sytem sensor TorS. This p	99.39
TIGR02915		445	PEP_resp_reg putative PEP-CTERM system response re	99.38
PRK10610		129	chemotaxis regulatory protein CheY; Provisional	99.38
PRK09959		1197	hybrid sensory histidine kinase in two-component r	99.38
PRK09581		457	pleD response regulator PleD; Reviewed	99.38
TIGR01818		463	ntrC nitrogen regulation protein NR(I). This model	99.37
PRK12555		337	chemotaxis-specific methylesterase; Provisional	99.36
PRK11091		779	aerobic respiration control sensor protein ArcB; P	99.36
PRK00742		354	chemotaxis-specific methylesterase; Provisional	99.32
COG2201		350	CheB Chemotaxis response regulator containing a Ch	99.27
PRK13558		665	bacterio-opsin activator; Provisional	99.27
COG3707		194	AmiR Response regulator with putative antiterminat	99.18
PRK09191		261	two-component response regulator; Provisional	99.16
cd00156		113	REC Signal receiver domain; originally thought to	99.13
PRK13837		828	two-component VirA-like sensor kinase; Provisional	99.09
PRK13557		540	histidine kinase; Provisional	99.01
PRK10693		303	response regulator of RpoS; Provisional	98.98
PRK15029		755	arginine decarboxylase; Provisional	98.89
COG3279		244	LytT Response regulator of the LytR/AlgR family [T	98.81
PRK11107		919	hybrid sensory histidine kinase BarA; Provisional	98.13
COG3706		435	PleD Response regulator containing a CheY-like rec	97.64
smart00448		55	REC cheY-homologous receiver domain. CheY regulate	97.56
PF06490		109	FleQ: Flagellar regulatory protein FleQ; InterPro:	97.26
cd02071		122	MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 bin	96.69
PRK02261		137	methylaspartate mutase subunit S; Provisional	96.69
TIGR00640		132	acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal	96.66
PF00249		48	Myb_DNA-binding: Myb-like DNA-binding domain; Inte	96.3
PLN03162		526	golden-2 like transcription factor; Provisional	96.0
PF03709		115	OKR_DC_1_N: Orn/Lys/Arg decarboxylase, N-terminal	95.89
cd02067		119	B12-binding B12 binding domain (B12-BD). This doma	95.43
PRK10618		894	phosphotransfer intermediate protein in two-compon	94.89
PRK15399		713	lysine decarboxylase LdcC; Provisional	94.72
TIGR01501		134	MthylAspMutase methylaspartate mutase, S subunit.	94.6
COG2185		143	Sbm Methylmalonyl-CoA mutase, C-terminal domain/su	94.29
PRK15400		714	lysine decarboxylase CadA; Provisional	94.07
TIGR03815		322	CpaE_hom_Actino helicase/secretion neighborhood Cp	94.04
cd02072		128	Glm_B12_BD B12 binding domain of glutamate mutase	92.28
COG4999		140	Uncharacterized domain of BarA-like signal transdu	91.04
PRK09426		714	methylmalonyl-CoA mutase; Reviewed	91.02
PF02310		121	B12-binding: B12 binding domain; InterPro: IPR0061	90.99
KOG1924		1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	89.75
cd04728		248	ThiG Thiazole synthase (ThiG) is the tetrameric en	88.97
cd02070		201	corrinoid_protein_B12-BD B12 binding domain of cor	87.23
cd02069		213	methionine_synthase_B12_BD B12 binding domain of m	86.54
PF10087		97	DUF2325: Uncharacterized protein conserved in bact	86.5
PRK00208		250	thiG thiazole synthase; Reviewed	85.98
PRK01130		221	N-acetylmannosamine-6-phosphate 2-epimerase; Provi	85.37
PRK15320		251	transcriptional activator SprB; Provisional	84.16
PRK05749		425	3-deoxy-D-manno-octulosonic-acid transferase; Revi	83.79
PF07688		283	KaiA: KaiA domain; InterPro: IPR011648 KaiA is a c	83.53
PRK00043		212	thiE thiamine-phosphate pyrophosphorylase; Reviewe	83.31
PF01408		120	GFO_IDH_MocA: Oxidoreductase family, NAD-binding R	82.19
COG0512		191	PabA Anthranilate/para-aminobenzoate synthases com	81.59
TIGR02370		197	pyl_corrinoid methyltransferase cognate corrinoid	80.33

>PLN03162 golden-2 like transcription factor; Provisional	Back alignment and domain information

Probab=100.00  E-value=5.5e-71  Score=558.59  Aligned_cols=238  Identities=39%  Similarity=0.640  Sum_probs=184.6

Q ss_pred             ccCCCCcCccchhhhhhHHHHHHHhcCCCCChHHHHHHhCCCCccHHHHHHHHHHHHhhhcccCCccc-CCCCccccccc
Q 009017          300 SKASGLQNSCGNKANRKKMKAVEQLGVDQAIPSRILELMKVEGLTRHNVASHLQKYRMHRRHILPKED-DRKWPHARDQM  378 (546)
Q Consensus       300 ~~~~~~~~~~~~~lh~~f~~av~~lg~~~a~p~~i~~~m~v~~l~~~~v~shlqkyr~~~~~~~~~~~-~~~~~~~~~~~  378 (546)
                      .-.|+.|++||+|||+|||+||++||.||||||+||++|||+||||+||||||||||+++|+.+.++. .++|+++|+..
T Consensus       231 ~g~KKpRLrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHLQKYRl~rk~l~~rEaEa~swt~kr~~~  310 (526)
T PLN03162        231 PGKKKAKVDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQKYRSHRRHLAAREAEAASWTHRRAYT  310 (526)
T ss_pred             CCCCCCcccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHHHHHHHhcccccchhhhhccchhhhhhc
Confidence            34567889999999999999999999999999999999999999999999999999999999999998 79999999865


Q ss_pred             cc-----CCCCCCCc---ccCCCC-------------CCCCCCCCCCCCcccCCCCCCCCccccCCCCC---CCCCCCCC
Q 009017          379 LR-----NYYPHKPI---MAFPPY-------------HSNHLVPTGPVYPVWGAPSNHLAAVQMWAPPG---YPPWQQAE  434 (546)
Q Consensus       379 ~~-----~~~~~~~~---~~~~~~-------------~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~---~~~~~~~~  434 (546)
                      ..     +.....|+   ++|||.             .++||.|-..++||||||+++++.|||||++.   .++|++.+
T Consensus       311 ~~P~~rs~~~~g~p~~~pigfP~~~P~P~~~~~~~P~~~~~Hhpf~rPLhVWGhPtvd~s~v~mWp~h~~~~p~pW~~~D  390 (526)
T PLN03162        311 QAPWPRSSRRDGLPYLVPIHTPHIQPRPSMAMAMQPQLQTPHHPISTPLKVWGYPTVDHSNVHMWQQPAVATPSYWQAAD  390 (526)
T ss_pred             cCCcccCCCCCCCccccccCCCCCCCCCCccCCCCCCcccccccccccceeccCCCCCCcccccccccccCCCCCCCCCC
Confidence            42     11111111   455542             22233233346799999999999999999844   46799975


Q ss_pred             --CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC------CCCCCCCCCC---CCCC--------------------CCCCC
Q 009017          435 --SWNWKPYPGMPADAWGCPVMPLPNGPYSSF------PQGASGYHNS---GVDD--------------------NSYAM  483 (546)
Q Consensus       435 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~---~~~~--------------------~~~~~  483 (546)
                        ||| +||.+..|. -|+||||.|...+...      |+-.|+|..+   |+.|                    .+...
T Consensus       391 p~fW~-h~~~~~~a~-~gtpc~p~pm~Rfp~ppv~~G~p~~~P~~p~~~~yy~~d~~a~~~~~~~~~~~~~~~~~~~~~~  468 (526)
T PLN03162        391 GSYWQ-HPATGYDAF-SARACYPHPMQRVPLGTTHAGLPIMAPGFPDESCYYGDDMLAASMYLCNQSYDSEIGRAAGVAA  468 (526)
T ss_pred             cchhh-cccccCccc-cCCcccCchhhhCCCCCCCCCCccccCCCCchhhcccccchhhcccccccccccccccccchhh
Confidence              886 478876543 3999999776321111      2212233221   1222                    11222


Q ss_pred             CCCcccCCCchHHHHHHHHHHhhCCCccCCCCCCCCchhHHHHHHHHcCCCCCCCC
Q 009017          484 PQNSVDLHPAEEVIDKVVKEAISKPWLPLPLGLKPPSADSVLAELSRQGISTIPPR  539 (546)
Q Consensus       484 ~~~~~~~~~~~e~~d~~~~~~~~~p~~p~p~glk~p~~~~v~~el~~~g~~~~p~~  539 (546)
                      .++++++|||||+|||||||||+||||||||||||||+||||+|||||||++|||+
T Consensus       469 ~~~~~~~hpSkEsiDAAIgdvLskPWlPlPLGLKpPSldsVm~ELqRQGi~~vpp~  524 (526)
T PLN03162        469 CSKPIETHLSKEVLDAAIGEALANPWTPPPLGLKPPSMEGVIAELQRQGINTVPPS  524 (526)
T ss_pred             cccccccCccHHHHHHHHHHHhhCCCCCCCcCCCCccHHHHHHHHHHcccCCCCCC
Confidence            45899999999999999999999999999999999999999999999999999996

>COG0745 OmpR Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]	Back alignment and domain information

>COG4566 TtrR Response regulator [Signal transduction mechanisms]	Back alignment and domain information

>COG2204 AtoC Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]	Back alignment and domain information

>COG4753 Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms]	Back alignment and domain information

>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class	Back alignment and domain information

>PF00072 Response_reg: Response regulator receiver domain; InterPro: IPR001789 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []	Back alignment and domain information

>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]	Back alignment and domain information

>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]	Back alignment and domain information

>PRK10529 DNA-binding transcriptional activator KdpE; Provisional	Back alignment and domain information

>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional	Back alignment and domain information

>COG3437 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]	Back alignment and domain information

>PRK11083 DNA-binding response regulator CreB; Provisional	Back alignment and domain information

>PRK10840 transcriptional regulator RcsB; Provisional	Back alignment and domain information

>PRK10046 dpiA two-component response regulator DpiA; Provisional	Back alignment and domain information

>PRK10766 DNA-binding transcriptional regulator TorR; Provisional	Back alignment and domain information

>PRK10643 DNA-binding transcriptional regulator BasR; Provisional	Back alignment and domain information

>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB	Back alignment and domain information

>PRK09836 DNA-binding transcriptional activator CusR; Provisional	Back alignment and domain information

>PRK10336 DNA-binding transcriptional regulator QseB; Provisional	Back alignment and domain information

>PRK10161 transcriptional regulator PhoB; Provisional	Back alignment and domain information

>PRK11517 transcriptional regulatory protein YedW; Provisional	Back alignment and domain information

>COG3706 PleD Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal transduction mechanisms]	Back alignment and domain information

>COG0784 CheY FOG: CheY-like receiver [Signal transduction mechanisms]	Back alignment and domain information

>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional	Back alignment and domain information

>PRK11173 two-component response regulator; Provisional	Back alignment and domain information

>PRK09483 response regulator; Provisional	Back alignment and domain information

>PRK10360 DNA-binding transcriptional activator UhpA; Provisional	Back alignment and domain information

>PRK09468 ompR osmolarity response regulator; Provisional	Back alignment and domain information

>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator	Back alignment and domain information

>PRK09958 DNA-binding transcriptional activator EvgA; Provisional	Back alignment and domain information

>CHL00148 orf27 Ycf27; Reviewed	Back alignment and domain information

>TIGR01387 cztR_silR_copR heavy metal response regulator	Back alignment and domain information

>PLN03029 type-a response regulator protein; Provisional	Back alignment and domain information

>PRK10701 DNA-binding transcriptional regulator RstA; Provisional	Back alignment and domain information

>PRK13856 two-component response regulator VirG; Provisional	Back alignment and domain information

>COG4567 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]	Back alignment and domain information

>PRK15479 transcriptional regulatory protein TctD; Provisional	Back alignment and domain information

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional	Back alignment and domain information

>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional	Back alignment and domain information

>PRK09935 transcriptional regulator FimZ; Provisional	Back alignment and domain information

>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional	Back alignment and domain information

>PRK09390 fixJ response regulator FixJ; Provisional	Back alignment and domain information

>KOG0519 consensus Sensory transduction histidine kinase [Signal transduction mechanisms]	Back alignment and domain information

>PRK11107 hybrid sensory histidine kinase BarA; Provisional	Back alignment and domain information

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional	Back alignment and domain information

>COG3947 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]	Back alignment and domain information

>PRK15347 two component system sensor kinase SsrA; Provisional	Back alignment and domain information

>TIGR02875 spore_0_A sporulation transcription factor Spo0A	Back alignment and domain information

>PRK15115 response regulator GlrR; Provisional	Back alignment and domain information

>PRK11697 putative two-component response-regulatory protein YehT; Provisional	Back alignment and domain information

>PRK15369 two component system sensor kinase SsrB; Provisional	Back alignment and domain information

>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional	Back alignment and domain information

>PRK10651 transcriptional regulator NarL; Provisional	Back alignment and domain information

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional	Back alignment and domain information

>PRK11475 DNA-binding transcriptional activator BglJ; Provisional	Back alignment and domain information

>PRK10365 transcriptional regulatory protein ZraR; Provisional	Back alignment and domain information

>PRK14084 two-component response regulator; Provisional	Back alignment and domain information

>PRK10403 transcriptional regulator NarP; Provisional	Back alignment and domain information

>PRK09581 pleD response regulator PleD; Reviewed	Back alignment and domain information

>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional	Back alignment and domain information

>PRK13435 response regulator; Provisional	Back alignment and domain information

>PRK11466 hybrid sensory histidine kinase TorS; Provisional	Back alignment and domain information

>TIGR02956 TMAO_torS TMAO reductase sytem sensor TorS	Back alignment and domain information

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator	Back alignment and domain information

>PRK10610 chemotaxis regulatory protein CheY; Provisional	Back alignment and domain information

>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional	Back alignment and domain information

>PRK09581 pleD response regulator PleD; Reviewed	Back alignment and domain information

>TIGR01818 ntrC nitrogen regulation protein NR(I)	Back alignment and domain information

>PRK12555 chemotaxis-specific methylesterase; Provisional	Back alignment and domain information

>PRK11091 aerobic respiration control sensor protein ArcB; Provisional	Back alignment and domain information

>PRK00742 chemotaxis-specific methylesterase; Provisional	Back alignment and domain information

>COG2201 CheB Chemotaxis response regulator containing a CheY-like receiver domain and a methylesterase domain [Cell motility and secretion / Signal transduction mechanisms]	Back alignment and domain information

>PRK13558 bacterio-opsin activator; Provisional	Back alignment and domain information

>COG3707 AmiR Response regulator with putative antiterminator output domain [Signal transduction mechanisms]	Back alignment and domain information

>PRK09191 two-component response regulator; Provisional	Back alignment and domain information

>cd00156 REC Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; contains a phosphoacceptor site that is phosphorylated by histidine kinase homologs; usually found N-terminal to a DNA binding effector domain; forms homodimers

Back alignment and domain information

>PRK13837 two-component VirA-like sensor kinase; Provisional	Back alignment and domain information

>PRK13557 histidine kinase; Provisional	Back alignment and domain information

>PRK10693 response regulator of RpoS; Provisional	Back alignment and domain information

>PRK15029 arginine decarboxylase; Provisional	Back alignment and domain information

>COG3279 LytT Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]	Back alignment and domain information

>PRK11107 hybrid sensory histidine kinase BarA; Provisional	Back alignment and domain information

>COG3706 PleD Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal transduction mechanisms]	Back alignment and domain information

>smart00448 REC cheY-homologous receiver domain	Back alignment and domain information

>PF06490 FleQ: Flagellar regulatory protein FleQ; InterPro: IPR010518 This domain is found at the N terminus of a subset of sigma54-dependent transcriptional activators that are involved in regulation of flagellar motility e	Back alignment and domain information

>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain	Back alignment and domain information

>PRK02261 methylaspartate mutase subunit S; Provisional	Back alignment and domain information

>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain	Back alignment and domain information

>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins	Back alignment and domain information

>PLN03162 golden-2 like transcription factor; Provisional	Back alignment and domain information

>PF03709 OKR_DC_1_N: Orn/Lys/Arg decarboxylase, N-terminal domain; InterPro: IPR005308 This domain has a flavodoxin-like fold, and is termed the "wing" domain because of its position in the overall 3D structure	Back alignment and domain information

>cd02067 B12-binding B12 binding domain (B12-BD)	Back alignment and domain information

>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional	Back alignment and domain information

>PRK15399 lysine decarboxylase LdcC; Provisional	Back alignment and domain information

>TIGR01501 MthylAspMutase methylaspartate mutase, S subunit	Back alignment and domain information

>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]	Back alignment and domain information

>PRK15400 lysine decarboxylase CadA; Provisional	Back alignment and domain information

>TIGR03815 CpaE_hom_Actino helicase/secretion neighborhood CpaE-like protein	Back alignment and domain information

>cd02072 Glm_B12_BD B12 binding domain of glutamate mutase (Glm)	Back alignment and domain information

>COG4999 Uncharacterized domain of BarA-like signal transduction histidine kinases [Signal transduction mechanisms]	Back alignment and domain information

>PRK09426 methylmalonyl-CoA mutase; Reviewed	Back alignment and domain information

>PF02310 B12-binding: B12 binding domain; InterPro: IPR006158 The cobalamin (vitamin B12) binding domain can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin)	Back alignment and domain information

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]	Back alignment and domain information

>cd04728 ThiG Thiazole synthase (ThiG) is the tetrameric enzyme that is involved in the formation of the thiazole moiety of thiamin pyrophosphate, an essential ubiquitous cofactor that plays an important role in carbohydrate and amino acid metabolism	Back alignment and domain information

>cd02070 corrinoid_protein_B12-BD B12 binding domain of corrinoid proteins	Back alignment and domain information

>cd02069 methionine_synthase_B12_BD B12 binding domain of methionine synthase	Back alignment and domain information

>PF10087 DUF2325: Uncharacterized protein conserved in bacteria (DUF2325); InterPro: IPR016772 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function	Back alignment and domain information

>PRK00208 thiG thiazole synthase; Reviewed	Back alignment and domain information

>PRK01130 N-acetylmannosamine-6-phosphate 2-epimerase; Provisional	Back alignment and domain information

>PRK15320 transcriptional activator SprB; Provisional	Back alignment and domain information

>PRK05749 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed	Back alignment and domain information

>PF07688 KaiA: KaiA domain; InterPro: IPR011648 KaiA is a component of the kaiABC clock protein complex, which constitutes the main circadian regulator in cyanobacteria	Back alignment and domain information

>PRK00043 thiE thiamine-phosphate pyrophosphorylase; Reviewed	Back alignment and domain information

>PF01408 GFO_IDH_MocA: Oxidoreductase family, NAD-binding Rossmann fold; InterPro: IPR000683 This group of enzymes utilise NADP or NAD, and is known as the GFO/IDH/MOCA family in UniProtKB/Swiss-Prot	Back alignment and domain information

>COG0512 PabA Anthranilate/para-aminobenzoate synthases component II [Amino acid transport and metabolism / Coenzyme metabolism]	Back alignment and domain information

>TIGR02370 pyl_corrinoid methyltransferase cognate corrinoid proteins, Methanosarcina family	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		546
1irz_A		64	Solution Structure Of Arr10-B Belonging To The Garp		4e-08
3cg0_A		140	Crystal Structure Of Signal Receiver Domain Of Modu		4e-04
1l5y_A		155	Crystal Structure Of Mg2+ / Bef3-bound Receiver Dom		4e-04
1qkk_A		155	Crystal Structure Of The Receiver Domain And Linker		4e-04

>pdb|1IRZ|A Chain A, Solution Structure Of Arr10-B Belonging To The Garp Family Of Plant Myb-Related Dna Binding Motifs Of The Arabidopsis Response Regulators Length = 64

Back alignment and structure

Iteration: 1
 Score = 56.6 bits (135), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 25/49 (51%), Positives = 38/49 (77%)
Query: 314 NRKKMKAVEQLGVDQAIPSRILELMKVEGLTRHNVASHLQKYRMHRRHI 362
           + K + AV+ LGV++A+P +IL+LM V+ LTR NVASHLQK+R+  + +
Sbjct: 15  HNKFLAAVDHLGVERAVPKKILDLMNVDKLTRENVASHLQKFRVALKKV 63

PyMOL of 1irz

>pdb|3CG0|A Chain A, Crystal Structure Of Signal Receiver Domain Of Modulated Diguanylate Cyclase From Desulfovibrio Desulfuricans G20, An Example Of Alternate Folding Length = 140

Back alignment and structure

>pdb|1L5Y|A Chain A, Crystal Structure Of Mg2+ / Bef3-bound Receiver Domain Of Sinorhizobium Meliloti Dctd Length = 155

Back alignment and structure

>pdb|1QKK|A Chain A, Crystal Structure Of The Receiver Domain And Linker Region Of Dctd From Sinorhizobium Meliloti Length = 155

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		546
1irz_A		64	ARR10-B; helix-turn-helix, DNA binding protein; NM	2e-15
1w25_A		459	Stalked-cell differentiation controlling protein;	2e-10
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-09
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-08
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-06
3jte_A		143	Response regulator receiver protein; structural ge	2e-08
3eq2_A		394	Probable two-component response regulator; adaptor	3e-07
1ny5_A		387	Transcriptional regulator (NTRC family); AAA+ ATPa	3e-07
1srr_A		124	SPO0F, sporulation response regulatory protein; as	3e-07
3dzd_A		368	Transcriptional regulator (NTRC family); sigma43 a	4e-07
3crn_A		132	Response regulator receiver domain protein, CHEY-;	8e-07
2qr3_A		140	Two-component system response regulator; structura	3e-06
1dc7_A		124	NTRC, nitrogen regulation protein; receiver domain	4e-06
3hdg_A		137	Uncharacterized protein; two-component sensor acti	5e-06
1qkk_A		155	DCTD, C4-dicarboxylate transport transcriptional r	9e-06
3cfy_A		137	Putative LUXO repressor protein; structural genomi	1e-05
2rjn_A		154	Response regulator receiver:metal-dependent phosph	1e-05
3hzh_A		157	Chemotaxis response regulator (CHEY-3); phosphatas	1e-05
3bre_A		358	Probable two-component response regulator; protein	1e-05
4dad_A		146	Putative pilus assembly-related protein; response	2e-05
3hv2_A		153	Response regulator/HD domain protein; PSI-2, NYSGX	7e-05
1s8n_A		205	Putative antiterminator; RV1626, structural genomi	1e-04
1qo0_D		196	AMIR; binding protein, gene regulator, receptor; 2	1e-04
3kto_A		136	Response regulator receiver protein; PSI-II,struct	2e-04
3luf_A		259	Two-component system response regulator/ggdef doma	2e-04
3r0j_A		250	Possible two component system response transcript	3e-04
3hdv_A		136	Response regulator; PSI-II, structural genomics, P	4e-04
3rqi_A		184	Response regulator protein; structural genomics, s	6e-04
1yio_A		208	Response regulatory protein; transcription regulat	8e-04

>1irz_A ARR10-B; helix-turn-helix, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: a.4.1.11 Length = 64	Back alignment and structure

 Score = 69.6 bits (170), Expect = 2e-15
 Identities = 25/49 (51%), Positives = 38/49 (77%)

Query: 314 NRKKMKAVEQLGVDQAIPSRILELMKVEGLTRHNVASHLQKYRMHRRHI 362
           + K + AV+ LGV++A+P +IL+LM V+ LTR NVASHLQK+R+  + +
Sbjct: 15  HNKFLAAVDHLGVERAVPKKILDLMNVDKLTRENVASHLQKFRVALKKV 63

PyMOL of 1irz

>1w25_A Stalked-cell differentiation controlling protein; two-component system, ggdef domain, cyclic dinucleotide, cyclic-digmp; HET: C2E; 2.70A {Caulobacter vibrioides} SCOP: c.23.1.1 c.23.1.1 d.58.29.2 PDB: 2v0n_A* 2wb4_A* Length = 459	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

>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

>3jte_A Response regulator receiver protein; structural genomics, nysgrc, response regulator receiver domain, target 11226E, PSI-2; 1.90A {Clostridium thermocellum atcc 27405} Length = 143	Back alignment and structure

>3eq2_A Probable two-component response regulator; adaptor sigmas, signaling protein; 3.40A {Pseudomonas aeruginosa} PDB: 3f7a_A Length = 394	Back alignment and structure

>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54 activator, bacterial transcription, DIM transcription; HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1 c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A* Length = 387	Back alignment and structure

>1srr_A SPO0F, sporulation response regulatory protein; aspartate pocket, two component system; 1.90A {Bacillus subtilis} SCOP: c.23.1.1 PDB: 1pey_A 3q15_C 2ftk_E* 1fsp_A 1nat_A 1pux_A 2fsp_A 2jvj_A 2jvk_A 2jvi_A 1f51_E Length = 124	Back alignment and structure

>3dzd_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; HET: ADP; 2.40A {Aquifex aeolicus} PDB: 1zit_A 2jrl_A Length = 368	Back alignment and structure

>3crn_A Response regulator receiver domain protein, CHEY-; structural genomics, signal regulator receiver domain; HET: PHD; 1.58A {Methanospirillum hungatei jf-1} Length = 132	Back alignment and structure

>2qr3_A Two-component system response regulator; structural genomics, signal receiver, PSI-2, protein structu initiative; 1.80A {Bacteroides fragilis} Length = 140	Back alignment and structure

>1dc7_A NTRC, nitrogen regulation protein; receiver domain, phosphorylation, signal transduction, conformational rearrangement; NMR {Salmonella typhimurium} SCOP: c.23.1.1 PDB: 1j56_A 1krw_A 1krx_A 1ntr_A 1dc8_A* Length = 124	Back alignment and structure

>3hdg_A Uncharacterized protein; two-component sensor activity, response regulator, PSI-II, 11227F, NYSGXRC, structural genomics; 2.27A {Wolinella succinogenes} Length = 137	Back alignment and structure

>1qkk_A DCTD, C4-dicarboxylate transport transcriptional regulatory protein; receiver domain, 2-component signal transduction; 1.7A {Sinorhizobium meliloti} SCOP: c.23.1.1 PDB: 1l5z_A 1l5y_A Length = 155	Back alignment and structure

>3cfy_A Putative LUXO repressor protein; structural genomics, unknown function, uncharacterized protein, signal receiver domain; 2.50A {Vibrio parahaemolyticus rimd 2210633} Length = 137	Back alignment and structure

>2rjn_A Response regulator receiver:metal-dependent phosphohydrolase, HD subdomain; structural genomics, oceanospirillum SP. MED92; 2.10A {Neptuniibacter caesariensis} Length = 154	Back alignment and structure

>3hzh_A Chemotaxis response regulator (CHEY-3); phosphatase, complex, response regulator, receiver domain, two-component signal transduction; HET: BFD; 1.96A {Borrelia burgdorferi} Length = 157	Back alignment and structure

>3bre_A Probable two-component response regulator; protein-nucleotide complex, signaling protein; HET: C2E; 2.40A {Pseudomonas aeruginosa} PDB: 3i5a_A* Length = 358	Back alignment and structure

>4dad_A Putative pilus assembly-related protein; response regulator receiver domain, CHEY-related protein, ST genomics; 2.50A {Burkholderia pseudomallei} PDB: 4dn6_A Length = 146	Back alignment and structure

>3hv2_A Response regulator/HD domain protein; PSI-2, NYSGXRC, structural genomics, protein structure initiative; 1.50A {Pseudomonas fluorescens pf-5} Length = 153	Back alignment and structure

>1s8n_A Putative antiterminator; RV1626, structural genomics, transcriptional antiterminator, component system, PSI; 1.48A {Mycobacterium tuberculosis} SCOP: c.23.1.1 PDB: 1sd5_A Length = 205	Back alignment and structure

>1qo0_D AMIR; binding protein, gene regulator, receptor; 2.25A {Pseudomonas aeruginosa} SCOP: c.23.1.3 Length = 196	Back alignment and structure

>3kto_A Response regulator receiver protein; PSI-II,structural genomics, protein structure initiative; 1.98A {Pseudoalteromonas atlantica T6C} Length = 136	Back alignment and structure

>3luf_A Two-component system response regulator/ggdef domain protein; structural genomics, ASA_2441, PSI-2, protein structure initiative; HET: MSE; 1.76A {Aeromonas salmonicida} PDB: 3mf4_A* Length = 259	Back alignment and structure

>3r0j_A Possible two component system response transcript positive regulator PHOP; beta-alpha fold, winged helix-turn-helix; 2.50A {Mycobacterium tuberculosis} Length = 250	Back alignment and structure

>3hdv_A Response regulator; PSI-II, structural genomics, Pro structure initiative, NEW YORK SGX research center for STRU genomics, nysgxrc; 2.09A {Pseudomonas putida} Length = 136	Back alignment and structure

>3rqi_A Response regulator protein; structural genomics, seattle structural genomics center for infectious disease, ssgcid; HET: PHD CIT; 1.70A {Burkholderia pseudomallei} Length = 184	Back alignment and structure

>1yio_A Response regulatory protein; transcription regulation, DNA binding protein; 2.20A {Pseudomonas fluorescens} SCOP: a.4.6.2 c.23.1.1 PDB: 1zn2_A Length = 208	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		546
1irz_A		64	ARR10-B; helix-turn-helix, DNA binding protein; NM	99.94
3to5_A		134	CHEY homolog; alpha(5)beta(5), chemotaxis, FLIM, p	99.9
3gl9_A		122	Response regulator; beta-sheet, surrounded by alph	99.84
3t6k_A		136	Response regulator receiver; flavodoxin-like, stru	99.83
3f6p_A		120	Transcriptional regulatory protein YYCF; unphospho	99.83
3r0j_A		250	Possible two component system response transcript	99.82
3rqi_A		184	Response regulator protein; structural genomics, s	99.81
3crn_A		132	Response regulator receiver domain protein, CHEY-;	99.81
3jte_A		143	Response regulator receiver protein; structural ge	99.81
2lpm_A		123	Two-component response regulator; transcription re	99.8
3gt7_A		154	Sensor protein; structural genomics, signal receiv	99.8
1dbw_A		126	Transcriptional regulatory protein FIXJ; doubly wo	99.8
1yio_A		208	Response regulatory protein; transcription regulat	99.8
3hv2_A		153	Response regulator/HD domain protein; PSI-2, NYSGX	99.8
3m6m_D		143	Sensory/regulatory protein RPFC; RPFF, REC, enoyl-	99.8
1kgs_A		225	DRRD, DNA binding response regulator D; DNA-bindin	99.79
3h1g_A		129	Chemotaxis protein CHEY homolog; sulfate-bound CHE	99.79
2pl1_A		121	Transcriptional regulatory protein PHOP; CHEY-like	99.79
3q9s_A		249	DNA-binding response regulator; DNA binding protei	99.79
2qzj_A		136	Two-component response regulator; 11017X, PSI-II,	99.79
3cfy_A		137	Putative LUXO repressor protein; structural genomi	99.79
1zgz_A		122	Torcad operon transcriptional regulatory protein;	99.79
1srr_A		124	SPO0F, sporulation response regulatory protein; as	99.79
3heb_A		152	Response regulator receiver domain protein (CHEY);	99.79
1xhf_A		123	DYE resistance, aerobic respiration control protei	99.79
2a9o_A		120	Response regulator; essential protein, YYCF/YYCG h	99.79
3grc_A		140	Sensor protein, kinase; protein structure initiati	99.79
3kht_A		144	Response regulator; PSI-II, 11023K, structural gen	99.78
3nhm_A		133	Response regulator; protein structure initiative I	99.78
3kto_A		136	Response regulator receiver protein; PSI-II,struct	99.78
1tmy_A		120	CHEY protein, TMY; chemotaxis, phosphoryl transfer	99.78
1jbe_A		128	Chemotaxis protein CHEY; signaling protein; 1.08A	99.78
2r25_B		133	Osmosensing histidine protein kinase SLN1; alpha5-	99.78
3eod_A		130	Protein HNR; response regulator, phosphoprotein, t	99.78
3snk_A		135	Response regulator CHEY-like protein; P-loop conta	99.78
1a04_A		215	Nitrate/nitrite response regulator protein NARL; s	99.78
3hdv_A		136	Response regulator; PSI-II, structural genomics, P	99.78
3hdg_A		137	Uncharacterized protein; two-component sensor acti	99.77
3b2n_A		133	Uncharacterized protein Q99UF4; structural genomic	99.77
3i42_A		127	Response regulator receiver domain protein (CHEY-	99.77
4e7p_A		150	Response regulator; DNA binding, cytosol, transcri	99.77
3kcn_A		151	Adenylate cyclase homolog; SGX, PSI 2, structural	99.77
3lua_A		140	Response regulator receiver protein; two-component	99.77
2qxy_A		142	Response regulator; regulation of transcription, N	99.77
3hzh_A		157	Chemotaxis response regulator (CHEY-3); phosphatas	99.77
1zh2_A		121	KDP operon transcriptional regulatory protein KDPE	99.77
1p6q_A		129	CHEY2; chemotaxis, signal transduction, response r	99.77
2qr3_A		140	Two-component system response regulator; structura	99.77
3cnb_A		143	DNA-binding response regulator, MERR family; signa	99.77
1ys7_A		233	Transcriptional regulatory protein PRRA; response	99.77
3h5i_A		140	Response regulator/sensory box protein/ggdef domai	99.76
1i3c_A		149	Response regulator RCP1; phytochrome, signaling pr	99.76
1mvo_A		136	PHOP response regulator; phosphate regulon, transc	99.76
2oqr_A		230	Sensory transduction protein REGX3; response regul	99.76
2jba_A		127	Phosphate regulon transcriptional regulatory PROT;	99.76
1dz3_A		130	Stage 0 sporulation protein A; response regulator,	99.76
3luf_A		259	Two-component system response regulator/ggdef doma	99.76
3c3m_A		138	Response regulator receiver protein; structural ge	99.76
2zay_A		147	Response regulator receiver protein; structural ge	99.76
2rjn_A		154	Response regulator receiver:metal-dependent phosph	99.75
1mb3_A		124	Cell division response regulator DIVK; signal tran	99.75
3cg0_A		140	Response regulator receiver modulated diguanylate	99.75
3f6c_A		134	Positive transcription regulator EVGA; structural	99.75
1k68_A		140	Phytochrome response regulator RCPA; phosphorylate	99.75
3n53_A		140	Response regulator receiver modulated diguanylate;	99.75
1k66_A		149	Phytochrome response regulator RCPB; CHEY homologu	99.75
2gwr_A		238	DNA-binding response regulator MTRA; two-component	99.75
3cu5_A		141	Two component transcriptional regulator, ARAC FAM;	99.75
3cg4_A		142	Response regulator receiver domain protein (CHEY-;	99.75
3lte_A		132	Response regulator; structural genomics, PSI, prot	99.75
3mm4_A		206	Histidine kinase homolog; receiver domain, CKI1, c	99.74
1dcf_A		136	ETR1 protein; beta-alpha five sandwich, transferas	99.74
1qkk_A		155	DCTD, C4-dicarboxylate transport transcriptional r	99.74
3a10_A		116	Response regulator; phosphoacceptor, signaling pro	99.74
3n0r_A		286	Response regulator; sigma factor, receiver, two-co	99.73
1p2f_A		220	Response regulator; DRRB, OMPR/PHOB, transcription	99.73
3c3w_A		225	Two component transcriptional regulatory protein;	99.73
2ayx_A		254	Sensor kinase protein RCSC; two independent struct	99.73
3eul_A		152	Possible nitrate/nitrite response transcriptional	99.73
1s8n_A		205	Putative antiterminator; RV1626, structural genomi	99.73
3cz5_A		153	Two-component response regulator, LUXR family; str	99.73
2gkg_A		127	Response regulator homolog; social motility, recei	99.73
3ilh_A		146	Two component response regulator; NYSGXRC, PSI-II,	99.73
4dad_A		146	Putative pilus assembly-related protein; response	99.72
3eqz_A		135	Response regulator; structural genomics, unknown f	99.72
3dzd_A		368	Transcriptional regulator (NTRC family); sigma43 a	99.72
2jk1_A		139	HUPR, hydrogenase transcriptional regulatory prote	99.71
3eq2_A		394	Probable two-component response regulator; adaptor	99.71
2qvg_A		143	Two component response regulator; NYSGXRC, PSI-2,	99.71
2qv0_A		143	Protein MRKE; structural genomics, transcription,	99.7
2qsj_A		154	DNA-binding response regulator, LUXR family; struc	99.68
1ny5_A		387	Transcriptional regulator (NTRC family); AAA+ ATPa	99.68
2rdm_A		132	Response regulator receiver protein; structural ge	99.68
1w25_A		459	Stalked-cell differentiation controlling protein;	99.68
3klo_A		225	Transcriptional regulator VPST; REC domain, HTH do	99.68
2pln_A		137	HP1043, response regulator; signaling protein; 1.8	99.68
3t8y_A		164	CHEB, chemotaxis response regulator protein-glutam	99.67
3kyj_B		145	CHEY6 protein, putative histidine protein kinase;	99.67
3c97_A		140	Signal transduction histidine kinase; structural g	99.66
2hqr_A		223	Putative transcriptional regulator; phosporylation	99.66
1dc7_A		124	NTRC, nitrogen regulation protein; receiver domain	99.65
3bre_A		358	Probable two-component response regulator; protein	99.65
2j48_A		119	Two-component sensor kinase; pseudo-receiver, circ	99.64
3sy8_A		400	ROCR; TIM barrel phosphodiesterase-A, transcriptio	99.63
1qo0_D		196	AMIR; binding protein, gene regulator, receptor; 2	99.6
2b4a_A		138	BH3024; flavodoxin-like fold, structural genomics,	99.6
3luf_A		259	Two-component system response regulator/ggdef doma	99.57
1a2o_A		349	CHEB methylesterase; bacterial chemotaxis, adaptat	99.57
2vyc_A		755	Biodegradative arginine decarboxylase; pyridoxal p	99.47
1w25_A		459	Stalked-cell differentiation controlling protein;	98.96
3cwo_X		237	Beta/alpha-barrel protein based on 1THF and 1TMY;	98.77
3q7r_A		121	Transcriptional regulatory protein; CHXR, receiver	96.96
2ayx_A		254	Sensor kinase protein RCSC; two independent struct	96.75
3n75_A		715	LDC, lysine decarboxylase, inducible; pyridoxal-5'	96.72
2yxb_A		161	Coenzyme B12-dependent mutase; alpha/beta, structu	95.72
1ccw_A		137	Protein (glutamate mutase); coenzyme B12, radical	93.95
3cwo_X		237	Beta/alpha-barrel protein based on 1THF and 1TMY;	93.91
3fkq_A		373	NTRC-like two-domain protein; RER070207001320, str	92.35
3q58_A		229	N-acetylmannosamine-6-phosphate 2-epimerase; TIM b	90.12
2xij_A		762	Methylmalonyl-COA mutase, mitochondrial; isomerase	89.6
1wv2_A		265	Thiazole moeity, thiazole biosynthesis protein THI	88.19
3igs_A		232	N-acetylmannosamine-6-phosphate 2-epimerase 2; ene	88.14
2i2x_B		258	MTAC, methyltransferase 1; TIM barrel and helix bu	86.7
2yum_A		75	ZZZ3 protein, zinc finger ZZ-type-containing prote	86.39
1req_A		727	Methylmalonyl-COA mutase; isomerase, intramolecula	86.11
1r8j_A		289	KAIA; circadian clock protein; 2.03A {Synechococcu	85.6
2yus_A		79	SWI/SNF-related matrix-associated actin- dependent	85.3
3qja_A		272	IGPS, indole-3-glycerol phosphate synthase; struct	81.82
1y80_A		210	Predicted cobalamin binding protein; corrinoid, fa	81.63
2bfw_A		200	GLGA glycogen synthase; glycosyltransferase family	81.47
2cqr_A		73	RSGI RUH-043, DNAJ homolog subfamily C member 1; m	81.16

>1irz_A ARR10-B; helix-turn-helix, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: a.4.1.11	Back alignment and structure

Probab=99.94  E-value=4.3e-27  Score=187.26  Aligned_cols=61  Identities=41%  Similarity=0.652  Sum_probs=58.0

Q ss_pred             CCCCcCccchhhhhhHHHHHHHhcCCCCChHHHHHHhCCCCccHHHHHHHHHHHHhhhccc
Q 009017          302 ASGLQNSCGNKANRKKMKAVEQLGVDQAIPSRILELMKVEGLTRHNVASHLQKYRMHRRHI  362 (546)
Q Consensus       302 ~~~~~~~~~~~lh~~f~~av~~lg~~~a~p~~i~~~m~v~~l~~~~v~shlqkyr~~~~~~  362 (546)
                      .+++|++||+|||++||+||++||.|+||||.||++|||+|||++||||||||||+++++.
T Consensus         3 ~~k~r~~WT~elH~~Fv~Av~~LG~~~AtPk~Il~~M~v~gLT~~~VkSHLQKYR~~l~r~   63 (64)
T 1irz_A            3 QKKPRVLWTHELHNKFLAAVDHLGVERAVPKKILDLMNVDKLTRENVASHLQKFRVALKKV   63 (64)
T ss_dssp             CCCSSCSSCHHHHHHHHHHHHHHCTTTCCHHHHHHHHCCTTCCHHHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHhCCCCCCcHHHHHHcCCCCCCHHHHHHHHHHHHHHHHcc
Confidence            4677889999999999999999999999999999999999999999999999999998874

PyMOL of 1irz

>3to5_A CHEY homolog; alpha(5)beta(5), chemotaxis, FLIM, phosphorylation, motor AC signaling protein; 1.65A {Vibrio cholerae}	Back alignment and structure

>3gl9_A Response regulator; beta-sheet, surrounded by alpha helices, BOTH sides, signaling protein; HET: BFD; 1.80A {Thermotoga maritima} SCOP: c.23.1.0 PDB: 3dgf_C 3dge_C	Back alignment and structure

>3t6k_A Response regulator receiver; flavodoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: MSE; 1.86A {Chloroflexus aurantiacus} SCOP: c.23.1.0	Back alignment and structure

>3f6p_A Transcriptional regulatory protein YYCF; unphosphorelated, receiver domain, cytoplasm, DNA-binding, phosphoprotein, transcription regulation; 1.95A {Bacillus subtilis} SCOP: c.23.1.1 PDB: 2zwm_A	Back alignment and structure

>3r0j_A Possible two component system response transcript positive regulator PHOP; beta-alpha fold, winged helix-turn-helix; 2.50A {Mycobacterium tuberculosis}	Back alignment and structure

>3rqi_A Response regulator protein; structural genomics, seattle structural genomics center for infectious disease, ssgcid; HET: PHD CIT; 1.70A {Burkholderia pseudomallei}	Back alignment and structure

>3crn_A Response regulator receiver domain protein, CHEY-; structural genomics, signal regulator receiver domain; HET: PHD; 1.58A {Methanospirillum hungatei jf-1}	Back alignment and structure

>3jte_A Response regulator receiver protein; structural genomics, nysgrc, response regulator receiver DOM target 11226E, PSI-2; 1.90A {Clostridium thermocellum atcc 27405}	Back alignment and structure

>2lpm_A Two-component response regulator; transcription regulator; NMR {Sinorhizobium meliloti}	Back alignment and structure

>3gt7_A Sensor protein; structural genomics, signal receiver domain, kinase, PSI-2, protein structure initiative; 2.30A {Syntrophus aciditrophicus SB}	Back alignment and structure

>1dbw_A Transcriptional regulatory protein FIXJ; doubly wound five-stranded beta/alpha fold, nitrogen fixatio regulation; HET: 15P; 1.60A {Sinorhizobium meliloti} SCOP: c.23.1.1 PDB: 1dck_A* 1dcm_A 1d5w_A*	Back alignment and structure

>1yio_A Response regulatory protein; transcription regulation, DNA binding protein; 2.20A {Pseudomonas fluorescens} SCOP: a.4.6.2 c.23.1.1 PDB: 1zn2_A	Back alignment and structure

>3hv2_A Response regulator/HD domain protein; PSI-2, NYSGXRC, structural genomics, protein structure initiative; 1.50A {Pseudomonas fluorescens pf-5}	Back alignment and structure

>3m6m_D Sensory/regulatory protein RPFC; RPFF, REC, enoyl-COA hydratase, lyase-transferase COMP; 2.50A {Xanthomonas campestris PV}	Back alignment and structure

>1kgs_A DRRD, DNA binding response regulator D; DNA-binding protein, ALPH-beta sandwich, winged-helix, helix helix, DNA binding protein; HET: DNA MSE; 1.50A {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB: 3nnn_A*	Back alignment and structure

>3h1g_A Chemotaxis protein CHEY homolog; sulfate-bound CHEY, cytoplasm, flagellar rotatio magnesium, metal-binding, phosphoprotein; 1.70A {Helicobacter pylori} SCOP: c.23.1.1 PDB: 3gwg_A 3h1e_A 3h1f_A	Back alignment and structure

>2pl1_A Transcriptional regulatory protein PHOP; CHEY-like fold, response regulator, beryllium fluoride, transcription factor, activated, virulence; 1.90A {Escherichia coli} SCOP: c.23.1.1 PDB: 2pkx_A	Back alignment and structure

>3q9s_A DNA-binding response regulator; DNA binding protein; 2.40A {Deinococcus radiodurans}	Back alignment and structure

>2qzj_A Two-component response regulator; 11017X, PSI-II, structural genomics; 2.89A {Clostridium difficile}	Back alignment and structure

>3cfy_A Putative LUXO repressor protein; structural genomics, unknown function, uncharacterized protein, signal receiver domain; 2.50A {Vibrio parahaemolyticus rimd 2210633}	Back alignment and structure

>1zgz_A Torcad operon transcriptional regulatory protein; two-component system, gene regulation, transcription factor, respiratory system; 1.80A {Escherichia coli} SCOP: c.23.1.1	Back alignment and structure

>1srr_A SPO0F, sporulation response regulatory protein; aspartate pocket, two component system; 1.90A {Bacillus subtilis} SCOP: c.23.1.1 PDB: 1pey_A 3q15_C 2ftk_E* 1fsp_A 1nat_A 1pux_A 2fsp_A 2jvj_A 2jvk_A 2jvi_A 1f51_E	Back alignment and structure

>3heb_A Response regulator receiver domain protein (CHEY); NYSGXRC, PSI-II, respose regulator, structure initiative, structural genomics; 2.40A {Rhodospirillum rubrum} SCOP: c.23.1.0	Back alignment and structure

>1xhf_A DYE resistance, aerobic respiration control protein ARCA; two-component system, gene regulation, transcription factor, anoxic redox control; 2.15A {Escherichia coli} SCOP: c.23.1.1 PDB: 1xhe_A	Back alignment and structure

>2a9o_A Response regulator; essential protein, YYCF/YYCG homolog, signaling protein; 1.65A {Streptococcus pneumoniae} SCOP: c.23.1.1 PDB: 1nxo_A 1nxs_A 1nxv_A 1nxw_A 1nxx_A 1nxp_A 2a9p_A 2a9q_A 1nxt_A* 2a9r_A*	Back alignment and structure

>3grc_A Sensor protein, kinase; protein structure initiative II(PSI II), NYSGXRC, 11025B, structural genomics; 2.21A {Polaromonas SP}	Back alignment and structure

>3kht_A Response regulator; PSI-II, 11023K, structural genomics, Pro structure initiative, NEW YORK SGX research center for STRU genomics, nysgxrc; 2.10A {Hahella chejuensis} SCOP: c.23.1.0	Back alignment and structure

>3nhm_A Response regulator; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.19A {Myxococcus xanthus}	Back alignment and structure

>3kto_A Response regulator receiver protein; PSI-II,structural genomics, protein structure initiative; 1.98A {Pseudoalteromonas atlantica T6C} SCOP: c.23.1.0	Back alignment and structure

>1tmy_A CHEY protein, TMY; chemotaxis, phosphoryl transfer, signal transduction; 1.90A {Thermotoga maritima} SCOP: c.23.1.1 PDB: 2tmy_A 3tmy_A 4tmy_A 1u0s_Y	Back alignment and structure

>1jbe_A Chemotaxis protein CHEY; signaling protein; 1.08A {Escherichia coli} SCOP: c.23.1.1 PDB: 3chy_A 1a0o_A 1cey_A 1bdj_A 1eay_A 1f4v_A 1ffg_A 1ffs_A 1ffw_A 1fqw_A 2b1j_A 1chn_A 1djm_A 1kmi_Y* 1d4z_A 3olx_A 3olw_A 1cye_A 2che_A 2chf_A ...	Back alignment and structure

>2r25_B Osmosensing histidine protein kinase SLN1; alpha5-BETA5, response regulator, four helix bundle, histidine phosphotransfer (HPT) protein; 1.70A {Saccharomyces cerevisiae} SCOP: c.23.1.1 PDB: 1oxk_B 1oxb_B	Back alignment and structure

>3eod_A Protein HNR; response regulator, phosphoprotein, two-component regulatory system, signaling protein; 1.75A {Escherichia coli K12}	Back alignment and structure

>3snk_A Response regulator CHEY-like protein; P-loop containing nucleoside triphosphate hydrolases, struct genomics; 2.02A {Mesorhizobium loti}	Back alignment and structure

>1a04_A Nitrate/nitrite response regulator protein NARL; signal transduction protein, response regulators, two- component systems; 2.20A {Escherichia coli} SCOP: a.4.6.2 c.23.1.1 PDB: 1rnl_A	Back alignment and structure

>3hdv_A Response regulator; PSI-II, structural genomics, Pro structure initiative, NEW YORK SGX research center for STRU genomics, nysgxrc; 2.09A {Pseudomonas putida} SCOP: c.23.1.0	Back alignment and structure

>3hdg_A Uncharacterized protein; two-component sensor activity, response regulator, PSI-II, 11227F, NYSGXRC, structural genomics; 2.27A {Wolinella succinogenes} SCOP: c.23.1.0	Back alignment and structure

>3b2n_A Uncharacterized protein Q99UF4; structural genomics, PSI-2, protein structure initiative, NE SGX research center for structural genomics; 2.04A {Staphylococcus aureus}	Back alignment and structure

>3i42_A Response regulator receiver domain protein (CHEY- like); structural genomics, PSI-2, protein structure initiative; 2.15A {Methylobacillus flagellatus KT} SCOP: c.23.1.0	Back alignment and structure

>4e7p_A Response regulator; DNA binding, cytosol, transcription regulator; 1.89A {Streptococcus pneumoniae} PDB: 4e7o_A	Back alignment and structure

>3kcn_A Adenylate cyclase homolog; SGX, PSI 2, structural genomics, protein structure initiative; 2.45A {Rhodopirellula baltica}	Back alignment and structure

>3lua_A Response regulator receiver protein; two-component signal transduction system, histidine kinase, phosphorelay, receiver domain, nysgxrc; 2.40A {Clostridium thermocellum}	Back alignment and structure

>2qxy_A Response regulator; regulation of transcription, NYSGXRC, protein structure initiative II (PSI II), structural genomics; 1.95A {Thermotoga maritima}	Back alignment and structure

>3hzh_A Chemotaxis response regulator (CHEY-3); phosphatase, complex, response regulator, receiver domain, two-component signal transduction; HET: BFD; 1.96A {Borrelia burgdorferi}	Back alignment and structure

>1zh2_A KDP operon transcriptional regulatory protein KDPE; two-component system, gene regulation, transcription factor, KDP potassium transport system; 2.00A {Escherichia coli} SCOP: c.23.1.1 PDB: 1zh4_A	Back alignment and structure

>1p6q_A CHEY2; chemotaxis, signal transduction, response regulator, structural proteomics in europe, spine, structural genomics; NMR {Sinorhizobium meliloti} SCOP: c.23.1.1 PDB: 1p6u_A	Back alignment and structure

>2qr3_A Two-component system response regulator; structural genomics, signal receiver, PSI-2, protein structu initiative; 1.80A {Bacteroides fragilis}	Back alignment and structure

>3cnb_A DNA-binding response regulator, MERR family; signal receiver domain, DNA binding protein, protein structu initiative, PSI-2; 2.00A {Colwellia psychrerythraea}	Back alignment and structure

>1ys7_A Transcriptional regulatory protein PRRA; response regulator, DNA binding domain, phosphorylation; 1.58A {Mycobacterium tuberculosis} SCOP: a.4.6.1 c.23.1.1 PDB: 1ys6_A	Back alignment and structure

>3h5i_A Response regulator/sensory box protein/ggdef domain protein; structural genomics, transcription, PSI-2; 1.90A {Carboxydothermus hydrogenoformans z-2901}	Back alignment and structure

>1i3c_A Response regulator RCP1; phytochrome, signaling protein; 1.90A {Synechocystis SP} SCOP: c.23.1.1 PDB: 1jlk_A	Back alignment and structure

>1mvo_A PHOP response regulator; phosphate regulon, transcriptional regulatory protein, alpha/beta doubly wound fold, phosphorylation; 1.60A {Bacillus subtilis} SCOP: c.23.1.1	Back alignment and structure

>2oqr_A Sensory transduction protein REGX3; response regulator, winged-helix-turn-helix, DNA-binding, 3D swapping, two component system; 2.03A {Mycobacterium tuberculosis H37RV}	Back alignment and structure

>2jba_A Phosphate regulon transcriptional regulatory PROT; transcription factor, sensory transduction, phosphate regula transcription regulation; 1.45A {Escherichia coli} PDB: 2jba_B 1b00_A 2iyn_A 2jb9_A 1zes_A	Back alignment and structure

>1dz3_A Stage 0 sporulation protein A; response regulator, domain swapping; 1.65A {Bacillus stearothermophilus} SCOP: c.23.1.1 PDB: 1qmp_A*	Back alignment and structure

>3luf_A Two-component system response regulator/ggdef domain protein; structural genomics, ASA_2441, PSI-2, protein structure initiative; HET: MSE; 1.76A {Aeromonas salmonicida} PDB: 3mf4_A*	Back alignment and structure

>3c3m_A Response regulator receiver protein; structural genomics, unknown function, PSI-2, protein struct initiative; HET: MSE; 1.70A {Methanoculleus marisnigri JR1}	Back alignment and structure

>2zay_A Response regulator receiver protein; structural genomics, NYSGXRC, target 11006U, protein structure initiative; 2.00A {Desulfuromonas acetoxidans}	Back alignment and structure

>2rjn_A Response regulator receiver:metal-dependent phosphohydrolase, HD subdomain; structural genomics, oceanospirillum SP. MED92; 2.10A {Neptuniibacter caesariensis}	Back alignment and structure

>1mb3_A Cell division response regulator DIVK; signal transduction protein, structural proteomics in europe, spine, structural genomics; 1.41A {Caulobacter vibrioides} SCOP: c.23.1.1 PDB: 1m5u_A 1mav_A 1mb0_A 1m5t_A	Back alignment and structure

>3cg0_A Response regulator receiver modulated diguanylate with PAS/PAC sensor; signal receiver domain, diguanylate cyclase; 2.15A {Desulfovibrio desulfuricans subsp}	Back alignment and structure

>3f6c_A Positive transcription regulator EVGA; structural genomics, PSI-2, protein structure initiative, PO transcription regulator EVGA; 1.45A {Escherichia coli k-12}	Back alignment and structure

>1k68_A Phytochrome response regulator RCPA; phosphorylated aspartate, CHEY homologue, homodimer, (beta/alpha)5, signaling protein; HET: PHD; 1.90A {Tolypothrix SP} SCOP: c.23.1.1	Back alignment and structure

>3n53_A Response regulator receiver modulated diguanylate; diguanylate cyclase, protein structure I II(PSI II), NYSGXRC, structural genomics; 2.20A {Pelobacter carbinolicus} SCOP: c.23.1.0	Back alignment and structure

>1k66_A Phytochrome response regulator RCPB; CHEY homologue, homodimer, APO-protein, (beta/alpha)5, signaling protein; 1.75A {Tolypothrix SP} SCOP: c.23.1.1	Back alignment and structure

>2gwr_A DNA-binding response regulator MTRA; two-component regulatory system, transcription regulation, phosphorylation, OMPR family; 2.10A {Mycobacterium tuberculosis} PDB: 3nhz_A	Back alignment and structure

>3cu5_A Two component transcriptional regulator, ARAC FAM; structural genomics, protein structure initiative; 2.60A {Clostridium phytofermentans isdg}	Back alignment and structure

>3cg4_A Response regulator receiver domain protein (CHEY-; structural genomics, unknown function; HET: MSE; 1.61A {Methanospirillum hungatei jf-1}	Back alignment and structure

>3lte_A Response regulator; structural genomics, PSI, protein structure initiative, NYSG YORK structural genomix research consortium, nysgxrc; 2.00A {Bermanella marisrubri}	Back alignment and structure

>3mm4_A Histidine kinase homolog; receiver domain, CKI1, cytokinin signaling, ROS fold, CHEY-like, transferase; 2.00A {Arabidopsis thaliana} PDB: 3mmn_A	Back alignment and structure

>1dcf_A ETR1 protein; beta-alpha five sandwich, transferase; 2.50A {Arabidopsis thaliana} SCOP: c.23.1.2	Back alignment and structure

>1qkk_A DCTD, C4-dicarboxylate transport transcriptional regulatory protein; receiver domain, 2-component signal transduction; 1.7A {Sinorhizobium meliloti} SCOP: c.23.1.1 PDB: 1l5z_A 1l5y_A	Back alignment and structure

>3a10_A Response regulator; phosphoacceptor, signaling protein; HET: MSE PG4; 1.63A {Thermotoga maritima} PDB: 3a0r_B* 3a0u_A*	Back alignment and structure

>3n0r_A Response regulator; sigma factor, receiver, two-component SI transduction, signaling protein; HET: MSE GOL; 1.25A {Caulobacter vibrioides} PDB: 3t0y_A	Back alignment and structure

>1p2f_A Response regulator; DRRB, OMPR/PHOB, transcription; HET: MSE; 1.80A {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB: 3nns_A*	Back alignment and structure

>3c3w_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 2.20A {Mycobacterium tuberculosis}	Back alignment and structure

>2ayx_A Sensor kinase protein RCSC; two independent structural domains, transferase; NMR {Escherichia coli} SCOP: c.23.1.1 c.23.1.6 PDB: 2ayz_A 2ayy_A	Back alignment and structure

>3eul_A Possible nitrate/nitrite response transcriptional regulatory protein NARL (DNA-binding...; central beta strand flanked by alpha helices; 1.90A {Mycobacterium tuberculosis}	Back alignment and structure

>1s8n_A Putative antiterminator; RV1626, structural genomics, transcriptional antiterminator, component system, PSI; 1.48A {Mycobacterium tuberculosis} SCOP: c.23.1.1 PDB: 1sd5_A	Back alignment and structure

>3cz5_A Two-component response regulator, LUXR family; structural genomics, protein structure initiative; 2.70A {Aurantimonas SP}	Back alignment and structure

>2gkg_A Response regulator homolog; social motility, receiver domain, signalling, high resolutio signaling protein; 1.00A {Myxococcus xanthus} PDB: 2i6f_A 2nt4_A 2nt3_A	Back alignment and structure

>3ilh_A Two component response regulator; NYSGXRC, PSI-II, protein S initiative, structural genomics; 2.59A {Cytophaga hutchinsonii}	Back alignment and structure

>4dad_A Putative pilus assembly-related protein; response regulator receiver domain, CHEY-related protein, ST genomics; 2.50A {Burkholderia pseudomallei} PDB: 4dn6_A	Back alignment and structure

>3eqz_A Response regulator; structural genomics, unknown function, PSI-2, protein struct initiative; 2.15A {Colwellia psychrerythraea} SCOP: c.23.1.0	Back alignment and structure

>3dzd_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; HET: ADP; 2.40A {Aquifex aeolicus} PDB: 1zit_A 2jrl_A	Back alignment and structure

>2jk1_A HUPR, hydrogenase transcriptional regulatory protein HU; nucleotide-binding, transcription regulation; 2.10A {Rhodobacter capsulatus} PDB: 2vui_B 2vuh_B	Back alignment and structure

>3eq2_A Probable two-component response regulator; adaptor sigmas, signaling protein; 3.40A {Pseudomonas aeruginosa} PDB: 3f7a_A	Back alignment and structure

>2qvg_A Two component response regulator; NYSGXRC, PSI-2, structural genomics, protein structure initiative; 1.50A {Legionella pneumophila subsp}	Back alignment and structure

>2qv0_A Protein MRKE; structural genomics, transcription, PSI-2, protein structure initiative; 2.40A {Klebsiella pneumoniae}	Back alignment and structure

>2qsj_A DNA-binding response regulator, LUXR family; structural genomics, PSI-2, protein structure initiative; 2.10A {Silicibacter pomeroyi dss-3}	Back alignment and structure

>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54 activator, bacterial transcription, DIM transcription; HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1 c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A*	Back alignment and structure

>2rdm_A Response regulator receiver protein; structural genomics, unknown function, PSI-2, protein struct initiative; HET: MSE; 1.76A {Sinorhizobium medicae}	Back alignment and structure

>1w25_A Stalked-cell differentiation controlling protein; two-component system, ggdef domain, cyclic dinucleotide, cyclic-digmp; HET: C2E; 2.70A {Caulobacter vibrioides} SCOP: c.23.1.1 c.23.1.1 d.58.29.2 PDB: 2v0n_A* 2wb4_A*	Back alignment and structure

>3klo_A Transcriptional regulator VPST; REC domain, HTH domain, DNA-binding, transcription regulation; HET: C2E TAR; 2.80A {Vibrio cholerae} PDB: 3kln_A*	Back alignment and structure

>2pln_A HP1043, response regulator; signaling protein; 1.80A {Helicobacter pylori} PDB: 2hqo_A	Back alignment and structure

>3t8y_A CHEB, chemotaxis response regulator protein-glutamate methylesterase; CHEA, hydrolase; 1.90A {Thermotoga maritima}	Back alignment and structure

>3kyj_B CHEY6 protein, putative histidine protein kinase; protein-protein interaction, histidine kinase, response regulator, phosphorylation; 1.40A {Rhodobacter sphaeroides} PDB: 3kyi_B*	Back alignment and structure

>3c97_A Signal transduction histidine kinase; structural genomics, signaling, PSI-2, protein structure initiative; 1.70A {Aspergillus oryzae RIB40}	Back alignment and structure

>2hqr_A Putative transcriptional regulator; phosporylation-independent response regulator, H. pylori, SY dimer, signaling protein; NMR {Helicobacter pylori}	Back alignment and structure

>1dc7_A NTRC, nitrogen regulation protein; receiver domain, phosphorylation, signal transduction, conformational rearrangement; NMR {Salmonella typhimurium} SCOP: c.23.1.1 PDB: 1j56_A 1krw_A 1krx_A 1ntr_A 1dc8_A*	Back alignment and structure

>3bre_A Probable two-component response regulator; protein-nucleotide complex, signaling protein; HET: C2E; 2.40A {Pseudomonas aeruginosa} PDB: 3i5a_A*	Back alignment and structure

>2j48_A Two-component sensor kinase; pseudo-receiver, circadian clock, transferase, response regulator, histidine protein kinase; NMR {Synechococcus elongatus}	Back alignment and structure

>3sy8_A ROCR; TIM barrel phosphodiesterase-A, transcription regulator; HET: EPE; 2.50A {Pseudomonas aeruginosa}	Back alignment and structure

>1qo0_D AMIR; binding protein, gene regulator, receptor; 2.25A {Pseudomonas aeruginosa} SCOP: c.23.1.3	Back alignment and structure

>2b4a_A BH3024; flavodoxin-like fold, structural genomics, joint center for structural genomics, JCSG, protein structure initiative; 2.42A {Bacillus halodurans} SCOP: c.23.1.1	Back alignment and structure

>3luf_A Two-component system response regulator/ggdef domain protein; structural genomics, ASA_2441, PSI-2, protein structure initiative; HET: MSE; 1.76A {Aeromonas salmonicida} PDB: 3mf4_A*	Back alignment and structure

>1a2o_A CHEB methylesterase; bacterial chemotaxis, adaptation, serine hydrolase; 2.40A {Salmonella typhimurium} SCOP: c.23.1.1 c.40.1.1	Back alignment and structure

>2vyc_A Biodegradative arginine decarboxylase; pyridoxal phosphate, PLP-dependent E lyase, acid resistance; HET: LLP; 2.4A {Escherichia coli}	Back alignment and structure

>1w25_A Stalked-cell differentiation controlling protein; two-component system, ggdef domain, cyclic dinucleotide, cyclic-digmp; HET: C2E; 2.70A {Caulobacter vibrioides} SCOP: c.23.1.1 c.23.1.1 d.58.29.2 PDB: 2v0n_A* 2wb4_A*	Back alignment and structure

>3cwo_X Beta/alpha-barrel protein based on 1THF and 1TMY; XRAY, CHEY, HISF, half barrel, de novo protein; 3.10A {Thermotoga maritima} PDB: 2lle_A	Back alignment and structure

>3q7r_A Transcriptional regulatory protein; CHXR, receiver domain, transcription factor, OMPR, chlamydia transcription; 1.60A {Chlamydia trachomatis} PDB: 3q7s_A* 3q7t_A	Back alignment and structure

>2ayx_A Sensor kinase protein RCSC; two independent structural domains, transferase; NMR {Escherichia coli} SCOP: c.23.1.1 c.23.1.6 PDB: 2ayz_A 2ayy_A	Back alignment and structure

>3n75_A LDC, lysine decarboxylase, inducible; pyridoxal-5'-phosphate dependent decarboxylase, acid stress stringent response; HET: LLP G4P P6G; 2.00A {Escherichia coli} PDB: 3q16_A*	Back alignment and structure

>2yxb_A Coenzyme B12-dependent mutase; alpha/beta, structural genomics, NPPSFA, national project on structural and functional analyses; 1.80A {Aeropyrum pernix}	Back alignment and structure

>1ccw_A Protein (glutamate mutase); coenzyme B12, radical reaction, TIM-barrel rossman-fold, isomerase; HET: CNC TAR; 1.60A {Clostridium cochlearium} SCOP: c.23.6.1 PDB: 1cb7_A* 1b1a_A 1i9c_A* 1be1_A 1fmf_A 1id8_A*	Back alignment and structure

>3cwo_X Beta/alpha-barrel protein based on 1THF and 1TMY; XRAY, CHEY, HISF, half barrel, de novo protein; 3.10A {Thermotoga maritima} PDB: 2lle_A	Back alignment and structure

>3fkq_A NTRC-like two-domain protein; RER070207001320, structural GE joint center for structural genomics, JCSG, protein structu initiative, PSI-2; HET: ATP 2PE; 2.10A {Eubacterium rectale}	Back alignment and structure

>3q58_A N-acetylmannosamine-6-phosphate 2-epimerase; TIM beta/alpha barrel, ribulose-phosphate binding barrel, carbohydrate metabolic process; HET: BTB; 1.80A {Salmonella enterica subsp}	Back alignment and structure

>2xij_A Methylmalonyl-COA mutase, mitochondrial; isomerase, organic aciduria, vitamin B12; HET: B12 5AD BTB; 1.95A {Homo sapiens} PDB: 2xiq_A* 3bic_A	Back alignment and structure

>1wv2_A Thiazole moeity, thiazole biosynthesis protein THIG; structural genomics, protein structure initiative, PSI; 2.90A {Pseudomonas aeruginosa} SCOP: c.1.31.1	Back alignment and structure

>3igs_A N-acetylmannosamine-6-phosphate 2-epimerase 2; energy metabolism, sugars, csgid, carbohydrate metabolism, isomerase; HET: MSE 16G; 1.50A {Salmonella enterica subsp} SCOP: c.1.2.0	Back alignment and structure

>2i2x_B MTAC, methyltransferase 1; TIM barrel and helix bundle (MTAB), rossman fold and helix B (MTAC); HET: B13; 2.50A {Methanosarcina barkeri}	Back alignment and structure

>2yum_A ZZZ3 protein, zinc finger ZZ-type-containing protein 3; transcription, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>1req_A Methylmalonyl-COA mutase; isomerase, intramolecular transferase; HET: B12 DCA; 2.00A {Propionibacterium freudenreichii subspshermanii} SCOP: c.1.19.1 c.23.6.1 PDB: 2req_A* 3req_A* 4req_A* 6req_A* 7req_A* 5req_A* 1e1c_A*	Back alignment and structure

>1r8j_A KAIA; circadian clock protein; 2.03A {Synechococcus elongatus pcc 7942} SCOP: a.186.1.1 c.23.1.5 PDB: 1m2e_A 1m2f_A	Back alignment and structure

>2yus_A SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily...; SWI/SNF complex 155 kDa subunit, BRG1-associated factor 155; NMR {Homo sapiens}	Back alignment and structure

>3qja_A IGPS, indole-3-glycerol phosphate synthase; structural genomics, T structural genomics consortium, TBSGC, lyase; 1.29A {Mycobacterium tuberculosis} PDB: 3t40_A* 3t44_A* 3t55_A* 3t78_A* 4fb7_A*	Back alignment and structure

>1y80_A Predicted cobalamin binding protein; corrinoid, factor IIIM, methyl transferase, structural genomics, PSI, protein structure initiative; HET: B1M; 1.70A {Moorella thermoacetica}	Back alignment and structure

>2bfw_A GLGA glycogen synthase; glycosyltransferase family 5 UDP/ADP-glucose-glycogen syntha rossman folds, transferase; 1.8A {Pyrococcus abyssi} SCOP: c.87.1.8	Back alignment and structure

>2cqr_A RSGI RUH-043, DNAJ homolog subfamily C member 1; membrane protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.3	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Alignment Graph	Length	Definition	E-value
Query		546
d1irza_		64	a.4.1.11 (A:) Arr10-B {Thale cress (Arabidopsis th	1e-14
d1dcfa_		134	c.23.1.2 (A:) Receiver domain of the ethylene rece	4e-11
d1ny5a1		137	c.23.1.1 (A:1-137) Transcriptional activator sigm5	2e-10
d2a9pa1		117	c.23.1.1 (A:2-118) DNA-binding response regulator	3e-10
d1a04a2		138	c.23.1.1 (A:5-142) Nitrate/nitrite response regula	3e-09
d1dbwa_		123	c.23.1.1 (A:) Transcriptional regulatory protein F	4e-09
d1peya_		119	c.23.1.1 (A:) Sporulation response regulator Spo0F	8e-09
d1dz3a_		123	c.23.1.1 (A:) Sporulation response regulator Spo0A	9e-09
d1u0sy_		118	c.23.1.1 (Y:) CheY protein {Thermotoga maritima [T	2e-08
d1zgza1		120	c.23.1.1 (A:2-121) TorCAD operon transcriptional r	3e-08
d1p6qa_		129	c.23.1.1 (A:) CheY protein {Sinorhizobium meliloti	3e-08
d1krwa_		123	c.23.1.1 (A:) NTRC receiver domain {Salmonella typ	3e-08
d1zesa1		121	c.23.1.1 (A:3-123) PhoB receiver domain {Escherich	4e-08
d1p2fa2		120	c.23.1.1 (A:1-120) Response regulator DrrB {Thermo	4e-08
d1xhfa1		121	c.23.1.1 (A:2-122) Aerobic respiration control pro	4e-08
d1jbea_		128	c.23.1.1 (A:) CheY protein {Escherichia coli [TaxI	6e-08
d1k68a_		140	c.23.1.1 (A:) Response regulator for cyanobacteria	7e-08
d1mb3a_		123	c.23.1.1 (A:) Cell division response regulator Div	7e-08
d1zh2a1		119	c.23.1.1 (A:2-120) Transcriptional regulatory prot	1e-07
d1kgsa2		122	c.23.1.1 (A:2-123) PhoB receiver domain {Thermotog	1e-07
d1ys7a2		121	c.23.1.1 (A:7-127) Transcriptional regulatory prot	2e-07
d1mvoa_		121	c.23.1.1 (A:) PhoP receiver domain {Bacillus subti	2e-07
d2pl1a1		119	c.23.1.1 (A:1-119) PhoP receiver domain {Escherich	5e-07
d2r25b1		128	c.23.1.1 (B:1087-1214) Response regulator Sin1 {Ba	6e-07
d1yioa2		128	c.23.1.1 (A:3-130) Response regulatory protein Sty	6e-07
d1a2oa1		140	c.23.1.1 (A:1-140) Methylesterase CheB, N-terminal	2e-06
d1w25a1		139	c.23.1.1 (A:2-140) Response regulator PleD, receiv	2e-06
d1s8na_		190	c.23.1.1 (A:) Probable two-component system transc	4e-06
d2ayxa1		133	c.23.1.1 (A:817-949) Sensor kinase protein RcsC, C	4e-06
d1i3ca_		144	c.23.1.1 (A:) Response regulator for cyanobacteria	1e-05
d1w25a2		153	c.23.1.1 (A:141-293) Response regulator PleD, rece	2e-05
d1qkka_		140	c.23.1.1 (A:) Transcriptional regulatory protein D	2e-05
d1k66a_		149	c.23.1.1 (A:) Response regulator for cyanobacteria	3e-04
d1qo0d_		189	c.23.1.3 (D:) Positive regulator of the amidase op	0.002

>d1irza_ a.4.1.11 (A:) Arr10-B {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 64	Back information, alignment and structure


class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: GARP response regulators
domain: Arr10-B
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 66.1 bits (161), Expect = 1e-14
 Identities = 25/49 (51%), Positives = 38/49 (77%)

Query: 314 NRKKMKAVEQLGVDQAIPSRILELMKVEGLTRHNVASHLQKYRMHRRHI 362
           + K + AV+ LGV++A+P +IL+LM V+ LTR NVASHLQK+R+  + +
Sbjct: 15  HNKFLAAVDHLGVERAVPKKILDLMNVDKLTRENVASHLQKFRVALKKV 63

PyMOL of d1irza_

>d1dcfa_ c.23.1.2 (A:) Receiver domain of the ethylene receptor {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 134	Back information, alignment and structure

>d1ny5a1 c.23.1.1 (A:1-137) Transcriptional activator sigm54 (NtrC1), N-terminal domain {Aquifex aeolicus [TaxId: 63363]} Length = 137	Back information, alignment and structure

>d2a9pa1 c.23.1.1 (A:2-118) DNA-binding response regulator MicA, N-terminal domain {Streptococcus pneumoniae [TaxId: 1313]} Length = 117	Back information, alignment and structure

>d1a04a2 c.23.1.1 (A:5-142) Nitrate/nitrite response regulator (NarL), receiver domain {Escherichia coli [TaxId: 562]} Length = 138	Back information, alignment and structure

>d1dbwa_ c.23.1.1 (A:) Transcriptional regulatory protein FixJ, receiver domain {Rhizobium meliloti [TaxId: 382]} Length = 123	Back information, alignment and structure

>d1peya_ c.23.1.1 (A:) Sporulation response regulator Spo0F {Bacillus subtilis [TaxId: 1423]} Length = 119	Back information, alignment and structure

>d1dz3a_ c.23.1.1 (A:) Sporulation response regulator Spo0A {Bacillus stearothermophilus [TaxId: 1422]} Length = 123	Back information, alignment and structure

>d1u0sy_ c.23.1.1 (Y:) CheY protein {Thermotoga maritima [TaxId: 2336]} Length = 118	Back information, alignment and structure

>d1zgza1 c.23.1.1 (A:2-121) TorCAD operon transcriptional regulator TorD, N-terminal domain {Escherichia coli [TaxId: 562]} Length = 120	Back information, alignment and structure

>d1p6qa_ c.23.1.1 (A:) CheY protein {Sinorhizobium meliloti, CheY2 [TaxId: 382]} Length = 129	Back information, alignment and structure

>d1krwa_ c.23.1.1 (A:) NTRC receiver domain {Salmonella typhimurium [TaxId: 90371]} Length = 123	Back information, alignment and structure

>d1zesa1 c.23.1.1 (A:3-123) PhoB receiver domain {Escherichia coli [TaxId: 562]} Length = 121	Back information, alignment and structure

>d1p2fa2 c.23.1.1 (A:1-120) Response regulator DrrB {Thermotoga maritima [TaxId: 2336]} Length = 120	Back information, alignment and structure

>d1xhfa1 c.23.1.1 (A:2-122) Aerobic respiration control protein ArcA, N-terminal domain {Escherichia coli [TaxId: 562]} Length = 121	Back information, alignment and structure

>d1k68a_ c.23.1.1 (A:) Response regulator for cyanobacterial phytochrome {Calothrix sp. pcc 7601, RcpA [TaxId: 1188]} Length = 140	Back information, alignment and structure

>d1mb3a_ c.23.1.1 (A:) Cell division response regulator DivK {Caulobacter crescentus [TaxId: 155892]} Length = 123	Back information, alignment and structure

>d1zh2a1 c.23.1.1 (A:2-120) Transcriptional regulatory protein KdpE, N-terminal domain {Escherichia coli [TaxId: 562]} Length = 119	Back information, alignment and structure

>d1kgsa2 c.23.1.1 (A:2-123) PhoB receiver domain {Thermotoga maritima [TaxId: 2336]} Length = 122	Back information, alignment and structure

>d1ys7a2 c.23.1.1 (A:7-127) Transcriptional regulatory protein PrrA, N-terminal domain {Mycobacterium tuberculosis [TaxId: 1773]} Length = 121	Back information, alignment and structure

>d1mvoa_ c.23.1.1 (A:) PhoP receiver domain {Bacillus subtilis [TaxId: 1423]} Length = 121	Back information, alignment and structure

>d2pl1a1 c.23.1.1 (A:1-119) PhoP receiver domain {Escherichia coli [TaxId: 562]} Length = 119	Back information, alignment and structure

>d2r25b1 c.23.1.1 (B:1087-1214) Response regulator Sin1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 128	Back information, alignment and structure

>d1yioa2 c.23.1.1 (A:3-130) Response regulatory protein StyR, N-terminal domain {Pseudomonas fluorescens [TaxId: 294]} Length = 128	Back information, alignment and structure

>d1a2oa1 c.23.1.1 (A:1-140) Methylesterase CheB, N-terminal domain {Salmonella typhimurium [TaxId: 90371]} Length = 140	Back information, alignment and structure

>d1w25a1 c.23.1.1 (A:2-140) Response regulator PleD, receiver domain {Caulobacter crescentus [TaxId: 155892]} Length = 139	Back information, alignment and structure

>d1s8na_ c.23.1.1 (A:) Probable two-component system transcriptional regulator Rv1626 {Mycobacterium tuberculosis [TaxId: 1773]} Length = 190	Back information, alignment and structure

>d2ayxa1 c.23.1.1 (A:817-949) Sensor kinase protein RcsC, C-terminal domain {Escherichia coli [TaxId: 562]} Length = 133	Back information, alignment and structure

>d1i3ca_ c.23.1.1 (A:) Response regulator for cyanobacterial phytochrome {Synechocystis sp. PCC 6803, RCP1 [TaxId: 1148]} Length = 144	Back information, alignment and structure

>d1w25a2 c.23.1.1 (A:141-293) Response regulator PleD, receiver domain {Caulobacter crescentus [TaxId: 155892]} Length = 153	Back information, alignment and structure

>d1qkka_ c.23.1.1 (A:) Transcriptional regulatory protein DctD, receiver domain {Sinorhizobium meliloti [TaxId: 382]} Length = 140	Back information, alignment and structure

>d1k66a_ c.23.1.1 (A:) Response regulator for cyanobacterial phytochrome {Calothrix sp. pcc 7601, RcpB [TaxId: 1188]} Length = 149	Back information, alignment and structure

>d1qo0d_ c.23.1.3 (D:) Positive regulator of the amidase operon AmiR {Pseudomonas aeruginosa [TaxId: 287]} Length = 189	Back information, alignment and structure

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		546
d2pl1a1		119	PhoP receiver domain {Escherichia coli [TaxId: 562	99.91
d1dbwa_		123	Transcriptional regulatory protein FixJ, receiver	99.9
d1kgsa2		122	PhoB receiver domain {Thermotoga maritima [TaxId:	99.9
d1zesa1		121	PhoB receiver domain {Escherichia coli [TaxId: 562	99.89
d2a9pa1		117	DNA-binding response regulator MicA, N-terminal do	99.89
d1ys7a2		121	Transcriptional regulatory protein PrrA, N-termina	99.89
d1mvoa_		121	PhoP receiver domain {Bacillus subtilis [TaxId: 14	99.89
d1irza_		64	Arr10-B {Thale cress (Arabidopsis thaliana) [TaxId	99.89
d1zh2a1		119	Transcriptional regulatory protein KdpE, N-termina	99.89
d1krwa_		123	NTRC receiver domain {Salmonella typhimurium [TaxI	99.89
d1xhfa1		121	Aerobic respiration control protein ArcA, N-termin	99.89
d1peya_		119	Sporulation response regulator Spo0F {Bacillus sub	99.89
d1zgza1		120	TorCAD operon transcriptional regulator TorD, N-te	99.89
d1qkka_		140	Transcriptional regulatory protein DctD, receiver	99.89
d1ny5a1		137	Transcriptional activator sigm54 (NtrC1), N-termin	99.89
d2ayxa1		133	Sensor kinase protein RcsC, C-terminal domain {Esc	99.88
d1u0sy_		118	CheY protein {Thermotoga maritima [TaxId: 2336]}	99.88
d1w25a1		139	Response regulator PleD, receiver domain {Caulobac	99.87
d1jbea_		128	CheY protein {Escherichia coli [TaxId: 562]}	99.87
d1mb3a_		123	Cell division response regulator DivK {Caulobacter	99.87
d1p2fa2		120	Response regulator DrrB {Thermotoga maritima [TaxI	99.87
d1p6qa_		129	CheY protein {Sinorhizobium meliloti, CheY2 [TaxId	99.87
d1s8na_		190	Probable two-component system transcriptional regu	99.87
d1yioa2		128	Response regulatory protein StyR, N-terminal domai	99.87
d2r25b1		128	Response regulator Sin1 {Baker's yeast (Saccharomy	99.86
d1dz3a_		123	Sporulation response regulator Spo0A {Bacillus ste	99.85
d1dcfa_		134	Receiver domain of the ethylene receptor {Thale cr	99.85
d1i3ca_		144	Response regulator for cyanobacterial phytochrome	99.85
d1k68a_		140	Response regulator for cyanobacterial phytochrome	99.85
d1k66a_		149	Response regulator for cyanobacterial phytochrome	99.85
d1a04a2		138	Nitrate/nitrite response regulator (NarL), receive	99.85
d1w25a2		153	Response regulator PleD, receiver domain {Caulobac	99.85
d2b4aa1		118	Hypothetical protein BH3024 {Bacillus halodurans [	99.81
d1a2oa1		140	Methylesterase CheB, N-terminal domain {Salmonella	99.79
d1qo0d_		189	Positive regulator of the amidase operon AmiR {Pse	99.74
d1ccwa_		137	Glutamate mutase, small subunit {Clostridium cochl	95.54
d7reqa2		168	Methylmalonyl-CoA mutase alpha subunit, C-terminal	94.81
d1xrsb1		160	D-lysine 5,6-aminomutase beta subunit KamE, C-term	91.81
d1r8ja2		135	N-terminal domain of the circadian clock protein K	89.24
d1xi3a_		206	Thiamin phosphate synthase {Archaeon (Pyrococcus f	83.45
d7reqb2		163	Methylmalonyl-CoA mutase beta subunit, C-terminal	81.82
d1kzyc2		106	53BP1 {Human (Homo sapiens) [TaxId: 9606]}	81.21

>d2pl1a1 c.23.1.1 (A:1-119) PhoP receiver domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoP receiver domain
species: Escherichia coli [TaxId: 562]

Probab=99.91  E-value=6.7e-24  Score=186.55  Aligned_cols=114  Identities=16%  Similarity=0.322  Sum_probs=110.2

Q ss_pred             CEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhhcCCCCeeEEEEecCCCCCCCHHHHHHHhC----CCcEEE
Q 009017           18 LRVLLLDQDSSAAAELKFKLEAMDYIVSTFYNENEALSAFSDKPENFHVAIVEVTTSNTDGSFKFLETAK----DLPTII   93 (546)
Q Consensus        18 ~rILIVDDD~~~~~~L~~~Le~~Gy~V~~ass~~eALe~L~~~~~~pDLVIlDl~mp~~~dGlellr~Lr----~iPIIv   93 (546)
                      ||||||||++.++..++.+|+..||+|.++.++++|++.+.+  ..||+||+|+.||+ ++|++++++|+    .+|||+
T Consensus         1 mrILvVDDd~~~~~~l~~~L~~~G~~v~~a~~g~eal~~l~~--~~~dliilD~~mP~-~~G~e~~~~i~~~~~~~pvi~   77 (119)
T d2pl1a1           1 MRVLVVEDNALLRHHLKVQIQDAGHQVDDAEDAKEADYYLNE--HIPDIAIVDLGLPD-EDGLSLIRRWRSNDVSLPILV   77 (119)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHH--SCCSEEEECSCCSS-SCHHHHHHHHHHTTCCSCEEE
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHh--cccceeehhccCCC-chhHHHHHHHHhcCcccceEe
Confidence            589999999999999999999999999999999999999999  78999999999999 99999999997    799999


Q ss_pred             EecCCChHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHHH
Q 009017           94 TSNIHCLSTMMKCIALGAVEFLRKPLSEDKLRNLWQHVVHK  134 (546)
Q Consensus        94 LSs~~d~e~i~~Al~aGAdDYL~KP~~~eeL~~~I~~vlrr  134 (546)
                      +|+..+.+...+|+++||+|||.||++.++|..+|+++++|
T Consensus        78 lt~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~v~~~lrR  118 (119)
T d2pl1a1          78 LTARESWQDKVEVLSAGADDYVTKPFHIEEVMARMQALMRR  118 (119)
T ss_dssp             EESCCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHHH
T ss_pred             eeccCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHcc
Confidence            99999999999999999999999999999999999999875

PyMOL of d2pl1a1

>d1dbwa_ c.23.1.1 (A:) Transcriptional regulatory protein FixJ, receiver domain {Rhizobium meliloti [TaxId: 382]}	Back information, alignment and structure

>d1kgsa2 c.23.1.1 (A:2-123) PhoB receiver domain {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d1zesa1 c.23.1.1 (A:3-123) PhoB receiver domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d2a9pa1 c.23.1.1 (A:2-118) DNA-binding response regulator MicA, N-terminal domain {Streptococcus pneumoniae [TaxId: 1313]}	Back information, alignment and structure

>d1ys7a2 c.23.1.1 (A:7-127) Transcriptional regulatory protein PrrA, N-terminal domain {Mycobacterium tuberculosis [TaxId: 1773]}	Back information, alignment and structure

>d1mvoa_ c.23.1.1 (A:) PhoP receiver domain {Bacillus subtilis [TaxId: 1423]}	Back information, alignment and structure

>d1irza_ a.4.1.11 (A:) Arr10-B {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}	Back information, alignment and structure

>d1zh2a1 c.23.1.1 (A:2-120) Transcriptional regulatory protein KdpE, N-terminal domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1krwa_ c.23.1.1 (A:) NTRC receiver domain {Salmonella typhimurium [TaxId: 90371]}	Back information, alignment and structure

>d1xhfa1 c.23.1.1 (A:2-122) Aerobic respiration control protein ArcA, N-terminal domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1peya_ c.23.1.1 (A:) Sporulation response regulator Spo0F {Bacillus subtilis [TaxId: 1423]}	Back information, alignment and structure

>d1zgza1 c.23.1.1 (A:2-121) TorCAD operon transcriptional regulator TorD, N-terminal domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1qkka_ c.23.1.1 (A:) Transcriptional regulatory protein DctD, receiver domain {Sinorhizobium meliloti [TaxId: 382]}	Back information, alignment and structure

>d1ny5a1 c.23.1.1 (A:1-137) Transcriptional activator sigm54 (NtrC1), N-terminal domain {Aquifex aeolicus [TaxId: 63363]}	Back information, alignment and structure

>d2ayxa1 c.23.1.1 (A:817-949) Sensor kinase protein RcsC, C-terminal domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1u0sy_ c.23.1.1 (Y:) CheY protein {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d1w25a1 c.23.1.1 (A:2-140) Response regulator PleD, receiver domain {Caulobacter crescentus [TaxId: 155892]}	Back information, alignment and structure

>d1mb3a_ c.23.1.1 (A:) Cell division response regulator DivK {Caulobacter crescentus [TaxId: 155892]}	Back information, alignment and structure

>d1p2fa2 c.23.1.1 (A:1-120) Response regulator DrrB {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d1p6qa_ c.23.1.1 (A:) CheY protein {Sinorhizobium meliloti, CheY2 [TaxId: 382]}	Back information, alignment and structure

>d1s8na_ c.23.1.1 (A:) Probable two-component system transcriptional regulator Rv1626 {Mycobacterium tuberculosis [TaxId: 1773]}	Back information, alignment and structure

>d1yioa2 c.23.1.1 (A:3-130) Response regulatory protein StyR, N-terminal domain {Pseudomonas fluorescens [TaxId: 294]}	Back information, alignment and structure

>d2r25b1 c.23.1.1 (B:1087-1214) Response regulator Sin1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1dz3a_ c.23.1.1 (A:) Sporulation response regulator Spo0A {Bacillus stearothermophilus [TaxId: 1422]}	Back information, alignment and structure

>d1dcfa_ c.23.1.2 (A:) Receiver domain of the ethylene receptor {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}	Back information, alignment and structure

>d1i3ca_ c.23.1.1 (A:) Response regulator for cyanobacterial phytochrome {Synechocystis sp. PCC 6803, RCP1 [TaxId: 1148]}	Back information, alignment and structure

>d1k68a_ c.23.1.1 (A:) Response regulator for cyanobacterial phytochrome {Calothrix sp. pcc 7601, RcpA [TaxId: 1188]}	Back information, alignment and structure

>d1k66a_ c.23.1.1 (A:) Response regulator for cyanobacterial phytochrome {Calothrix sp. pcc 7601, RcpB [TaxId: 1188]}	Back information, alignment and structure

>d1a04a2 c.23.1.1 (A:5-142) Nitrate/nitrite response regulator (NarL), receiver domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1w25a2 c.23.1.1 (A:141-293) Response regulator PleD, receiver domain {Caulobacter crescentus [TaxId: 155892]}	Back information, alignment and structure

>d2b4aa1 c.23.1.1 (A:2-119) Hypothetical protein BH3024 {Bacillus halodurans [TaxId: 86665]}	Back information, alignment and structure

>d1a2oa1 c.23.1.1 (A:1-140) Methylesterase CheB, N-terminal domain {Salmonella typhimurium [TaxId: 90371]}	Back information, alignment and structure

>d1qo0d_ c.23.1.3 (D:) Positive regulator of the amidase operon AmiR {Pseudomonas aeruginosa [TaxId: 287]}	Back information, alignment and structure

>d1ccwa_ c.23.6.1 (A:) Glutamate mutase, small subunit {Clostridium cochlearium [TaxId: 1494]}	Back information, alignment and structure

>d7reqa2 c.23.6.1 (A:561-728) Methylmalonyl-CoA mutase alpha subunit, C-terminal domain {Propionibacterium freudenreichii, subsp. shermanii [TaxId: 1744]}	Back information, alignment and structure

>d1xrsb1 c.23.6.1 (B:102-261) D-lysine 5,6-aminomutase beta subunit KamE, C-terminal domain {Clostridium sticklandii [TaxId: 1511]}	Back information, alignment and structure

>d1r8ja2 c.23.1.5 (A:1-135) N-terminal domain of the circadian clock protein KaiA {Synechococcus elongatus [TaxId: 32046]}	Back information, alignment and structure

>d1xi3a_ c.1.3.1 (A:) Thiamin phosphate synthase {Archaeon (Pyrococcus furiosus) [TaxId: 2261]}	Back information, alignment and structure

>d7reqb2 c.23.6.1 (B:476-638) Methylmalonyl-CoA mutase beta subunit, C-terminal domain {Propionibacterium freudenreichii, subsp. shermanii [TaxId: 1744]}	Back information, alignment and structure

>d1kzyc2 c.15.1.4 (C:1867-1972) 53BP1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure