Citrus Sinensis ID: 037700

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-------31

MASDLNLPESLYEDYSTPDLPVHGPASVAYWIQALQSHETKERALLILSQNKEIRKDLAPLLWNSIGTISALLQEIISVYRTLSSPNLTETASTRVSNALALFQVTFTSIGSSFAILKVYNCMATFRAIKSSMTRLISVLMVLAKLPLYLYPFLNTKDKEKPHEYLRLTSLGVIGTLVKSDDPEAIRFLLQTEIFPCCLTSMEVGSDLSKQVATFIIYKILLHEEGLKYCCVLADRFFAVARALAQMTEKLVEQPSPRLLKHIICCYHRLSQSPRACDGLRCCLPLWFGDRKFTSQLHVRSSKTPISSS

cccccccccccccccccccccccccHHHHHHHHHHccccHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHcccccccHHEEEcccccHHHHHHHHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHHHcccHHHHHHHHHHHccccHHHHHHccccHHHHHHHHHHHHHHHccccccHHHHccHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHcccHHHHHHHHHHccccccccHHHHHHcccccccccccc

ccccccccHHHHHHcccccccccccHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHcccccccccEEEEEEccccccccccccccHHHHHHccccEEEcccccccccccccHHEEEHHHHHHHHHEccccHHHHHHHHcccHHHHHHHHHHccHHHHHHHHHHHHHHHHHcHccHHHHHccHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcccHHHHHHHHHHccHHHccccHHHHHcccccccccccc

masdlnlpeslyedystpdlpvhgpaSVAYWIQALQSHETKERALLILSQNKEIRKDLAPLLWNSIGTISALLQEIISVYRtlsspnltetASTRVSNALALFQVTFTSIGSSFAILKVYNCMATFRAIKSSMTRLISVLMVLAKlplylypflntkdkekpheylRLTSLGVigtlvksddPEAIRFLLQTEifpccltsmevgsdLSKQVATFIIYKILLHEEGLKYCCVLADRFFAVARALAQMTEKLveqpsprlLKHIICCYhrlsqspracdglrcclplwfgdrkftsqlhvrssktpisss

MASDLNLPESLYEDYSTPDLPVHGPASVAYWIQALQSHETKERALLILSQNKEIRKDLAPLLWNSIGTISALLQEIISVYRTLSSPNLTETASTRVSNALALFQVTFTSIGSSFAILKVYNCMATFRAIKSSMTRLISVLMVLAKLPLYLYPFLNTKDKEKPHEYLRLTSLGVIGTLVKSDDPEAIRFLLQTEIFPCCLTSMEVGSDLSKQVATFIIYKILLHEEGLKYCCVLADRFFAVARALAQMTEklveqpsprLLKHIICCYHRLSQSPRACDGLRCCLPLWFgdrkftsqlhvrssktpisss

*******************LPVHGPASVAYWIQALQSHETKERALLILSQNKEIRKDLAPLLWNSIGTISALLQEIISVYRTLSSPNLTETASTRVSNALALFQVTFTSIGSSFAILKVYNCMATFRAIKSSMTRLISVLMVLAKLPLYLYPFLNTKDKEKPHEYLRLTSLGVIGTLVKSDDPEAIRFLLQTEIFPCCLTSMEVGSDLSKQVATFIIYKILLHEEGLKYCCVLADRFFAVARALAQMTEKLVEQPSPRLLKHIICCYHRLSQSPRACDGLRCCLPLWFGDRKFTS**************

******************************WIQALQSHETKERALLILSQNKEIRKDLAPLLWNSIGTISALLQEIISVYRTLSSPNLTETASTRVSNALALFQVTFTSIGSSFAILKVYNCMATFRAIKSSMTRLISVLMVLAKLPLYLYPFLNTKDKEKPHEYLRLTSLGVIGTLVKSDDPEAIRFLLQTEIFPCCLTSMEVGSDLSKQVATFIIYKILLHEEGLKYCCVLADRFFAVARALAQMTEKLVEQPSPRLLKHIICCYHRLSQSPRACDGLRCCLPLWFGDRKFTSQLHVRSS*******

********ESLYEDYSTPDLPVHGPASVAYWIQALQSHETKERALLILSQNKEIRKDLAPLLWNSIGTISALLQEIISVYRTLSSPNLTETASTRVSNALALFQVTFTSIGSSFAILKVYNCMATFRAIKSSMTRLISVLMVLAKLPLYLYPFLNTKDKEKPHEYLRLTSLGVIGTLVKSDDPEAIRFLLQTEIFPCCLTSMEVGSDLSKQVATFIIYKILLHEEGLKYCCVLADRFFAVARALAQMTEKLVEQPSPRLLKHIICCYHRLSQSPRACDGLRCCLPLWFGDRKFTSQ*************

****LNLPESLYEDYSTPDLPVHGPASVAYWIQALQSHETKERALLILSQNKEIRKDLAPLLWNSIGTISALLQEIISVYRTLSSPNLTETASTRVSNALALFQVTFTSIGSSFAILKVYNCMATFRAIKSSMTRLISVLMVLAKLPLYLYPFLNTKDKEKPHEYLRLTSLGVIGTLVKSDDPEAIRFLLQTEIFPCCLTSMEVGSDLSKQVATFIIYKILLHEEGLKYCCVLADRFFAVARALAQMTEKLVEQPSPRLLKHIICCYHRLSQSPRACDGLRCCLPLWFGDRKFTSQLHVRS********

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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		309	2.2.26 [Sep-21-2011]
Q5R6Z6		299	Cell differentiation prot	yes	no	0.783	0.809	0.498	5e-63
Q92600		299	Cell differentiation prot	yes	no	0.783	0.809	0.498	5e-63
Q5PQL2		299	Cell differentiation prot	yes	no	0.783	0.809	0.498	6e-63
Q9JKY0		299	Cell differentiation prot	yes	no	0.783	0.809	0.498	6e-63
Q4R347		299	Cell differentiation prot	N/A	no	0.783	0.809	0.498	6e-63
A7MB47		299	Cell differentiation prot	yes	no	0.783	0.809	0.498	6e-63
Q6P819		299	Cell differentiation prot	yes	no	0.783	0.809	0.494	1e-62
Q6IP65		299	Cell differentiation prot	N/A	no	0.783	0.809	0.494	1e-62
Q6NWL4		298	Cell differentiation prot	yes	no	0.783	0.812	0.494	9e-62
Q92368		283	Cell differentiation prot	yes	no	0.815	0.890	0.483	2e-59

>sp\|Q5R6Z6\|RCD1_PONAB Cell differentiation protein RCD1 homolog OS=Pongo abelii GN=RQCD1 PE=2 SV=2	Back alignment and function desciption

 Score =  241 bits (615), Expect = 5e-63,   Method: Compositional matrix adjust.
 Identities = 133/267 (49%), Positives = 168/267 (62%), Gaps = 25/267 (9%)

Query: 31  WIQALQSHETKERALLILSQNKEIRKDLAPLLWNSIGTISALLQEIISVYRTLSSPNLTE 90
           WI  L S ET+E ALL LS+ +E   DLAP+LW+S GTI+ALLQEI+++Y +++ P LT 
Sbjct: 25  WINELSSPETRENALLELSKKRESVPDLAPMLWHSFGTIAALLQEIVNIYPSINPPTLTA 84

Query: 91  TASTRVSNALALFQVTFTSIGSSFAILKVYNCMATFRAIKSSMTRLISVLMVLAKLPLYL 150
             S RV NALAL Q                 C+A+    +S+         + A +PL+L
Sbjct: 85  HQSNRVCNALALLQ-----------------CVASHPETRSAF--------LAAHIPLFL 119

Query: 151 YPFLNTKDKEKPHEYLRLTSLGVIGTLVKSDDPEAIRFLLQTEIFPCCLTSMEVGSDLSK 210
           YPFL+T  K +P EYLRLTSLGVIG LVK+D+ E I FLL TEI P CL  ME GS+LSK
Sbjct: 120 YPFLHTVSKTRPFEYLRLTSLGVIGALVKTDEQEVINFLLTTEIIPLCLRIMESGSELSK 179

Query: 211 QVATFIIYKILLHEEGLKYCCVLADRFFAVARALAQMTEKLVEQPSPRLLKHIICCYHRL 270
            VATFI+ KILL + GL Y C   +RF  VA  L +M  +L ++PS RLLKH++ CY RL
Sbjct: 180 TVATFILQKILLDDTGLAYICQTYERFSHVAMILGKMVLQLSKEPSARLLKHVVRCYLRL 239

Query: 271 SQSPRACDGLRCCLPLWFGDRKFTSQL 297
           S +PRA + LR CLP    D  F   L
Sbjct: 240 SDNPRAREALRQCLPDQLKDTTFAQVL 266

Transcription factor that down-regulates MYB- and JUN-dependent transcription. May play a role in cell differentiation.
Pongo abelii (taxid: 9601)

>sp\|Q92600\|RCD1_HUMAN Cell differentiation protein RCD1 homolog OS=Homo sapiens GN=RQCD1 PE=1 SV=1	Back alignment and function description

>sp\|Q5PQL2\|RCD1_RAT Cell differentiation protein RCD1 homolog OS=Rattus norvegicus GN=Rqcd1 PE=1 SV=1	Back alignment and function description

>sp\|Q9JKY0\|RCD1_MOUSE Cell differentiation protein RCD1 homolog OS=Mus musculus GN=Rqcd1 PE=1 SV=1	Back alignment and function description

>sp\|Q4R347\|RCD1_MACFA Cell differentiation protein RCD1 homolog OS=Macaca fascicularis GN=RQCD1 PE=2 SV=1	Back alignment and function description

>sp\|A7MB47\|RCD1_BOVIN Cell differentiation protein RCD1 homolog OS=Bos taurus GN=RQCD1 PE=2 SV=1	Back alignment and function description

>sp\|Q6P819\|RCD1_XENTR Cell differentiation protein RCD1 homolog OS=Xenopus tropicalis GN=rqcd1 PE=2 SV=1	Back alignment and function description

>sp\|Q6IP65\|RCD1_XENLA Cell differentiation protein RCD1 homolog OS=Xenopus laevis GN=rqcd1 PE=2 SV=1	Back alignment and function description

>sp\|Q6NWL4\|RCD1_DANRE Cell differentiation protein RCD1 homolog OS=Danio rerio GN=rqcd1 PE=2 SV=1	Back alignment and function description

>sp\|Q92368\|RCD1_SCHPO Cell differentiation protein rcd1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rcd1 PE=3 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		309
224128990		316	predicted protein [Populus trichocarpa]	0.825	0.806	0.524	1e-75
449526762		305	PREDICTED: cell differentiation protein	0.867	0.878	0.530	3e-73
449453515		305	PREDICTED: cell differentiation protein	0.867	0.878	0.523	7e-72
255577151		328	Cell differentiation protein rcd1, putat	0.802	0.756	0.542	2e-71
224056413		323	predicted protein [Populus trichocarpa]	0.802	0.767	0.545	2e-71
225460895		319	PREDICTED: cell differentiation protein	0.867	0.840	0.516	2e-71
225460897		319	PREDICTED: cell differentiation protein	0.867	0.840	0.519	3e-71
356567322		325	PREDICTED: cell differentiation protein	0.802	0.763	0.545	3e-71
356527073		325	PREDICTED: cell differentiation protein	0.802	0.763	0.545	4e-71
449444060		319	PREDICTED: cell differentiation protein	0.867	0.840	0.516	5e-71

>gi\|224128990\|ref\|XP_002320473.1\| predicted protein [Populus trichocarpa] gi\|222861246\|gb\|EEE98788.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

 Score =  289 bits (739), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 151/288 (52%), Positives = 191/288 (66%), Gaps = 33/288 (11%)

Query: 26  ASVAYWIQALQSHETKERALLILSQNKEIRKDLAPLLWNSIGTISALLQEIISVYRTLSS 85
           ASV   I++L +  T+ERA+ +LS+N+ IR+++APLLW S+GTIS LLQEIISVYR+L S
Sbjct: 25  ASVVQLIESLNNDATRERAIHLLSKNRAIREEMAPLLWYSVGTISILLQEIISVYRSLHS 84

Query: 86  P--NLTETASTRVSNALALFQVTFTSIGSSFAILKVYNCMATFRAIKSSMTRLISVLMVL 143
           P   LT+  S RV +AL LFQ                 C+A   + K        +  + 
Sbjct: 85  PIPTLTDRVSNRVCDALVLFQ-----------------CVAANPSTK--------MPFIE 119

Query: 144 AKLPLYLYPFLNTKDKEKPHEYLRLTSLGVIGTLVKSDDPEAIRFLLQTEIFPCCLTSME 203
           AKLPLYLYPFLN  +KE+PH+++RL SL VIG L K DDP  I FLL++E+FPCC+ SME
Sbjct: 120 AKLPLYLYPFLNNTNKERPHQFIRLASLSVIGALAKVDDPNVINFLLESEVFPCCIRSME 179

Query: 204 VGSDLSKQVATFIIYKILLHEEGLKYCCVLADRFFAVARALAQMTEKLVEQ------PSP 257
           VG  LSK VAT+I+YKIL++EEGL+YCC +A+RFFA+ R L  M  KL E+      PS 
Sbjct: 180 VGDVLSKTVATYIVYKILINEEGLRYCCTVAERFFALVRVLGSMVLKLAEEGQLAENPSI 239

Query: 258 RLLKHIICCYHRLSQSPRACDGLRCCLPLWFGDRKFTSQLHVRSSKTP 305
           RLLKHII CYHRLS+SPR+CDGLRC LP+   D  F        S  P
Sbjct: 240 RLLKHIIWCYHRLSESPRSCDGLRCRLPVILSDAAFIDIFRGDPSAVP 287

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|449526762\|ref\|XP_004170382.1\| PREDICTED: cell differentiation protein RCD1 homolog [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449453515\|ref\|XP_004144502.1\| PREDICTED: cell differentiation protein RCD1 homolog [Cucumis sativus]	Back alignment and taxonomy information

>gi\|255577151\|ref\|XP_002529459.1\| Cell differentiation protein rcd1, putative [Ricinus communis] gi\|223531075\|gb\|EEF32925.1\| Cell differentiation protein rcd1, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|224056413\|ref\|XP_002298844.1\| predicted protein [Populus trichocarpa] gi\|222846102\|gb\|EEE83649.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|225460895\|ref\|XP_002278757.1\| PREDICTED: cell differentiation protein RCD1 homolog isoform 2 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|225460897\|ref\|XP_002278722.1\| PREDICTED: cell differentiation protein RCD1 homolog isoform 1 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356567322\|ref\|XP_003551870.1\| PREDICTED: cell differentiation protein RCD1 homolog [Glycine max]	Back alignment and taxonomy information

>gi\|356527073\|ref\|XP_003532138.1\| PREDICTED: cell differentiation protein RCD1 homolog [Glycine max]	Back alignment and taxonomy information

>gi\|449444060\|ref\|XP_004139793.1\| PREDICTED: cell differentiation protein RCD1 homolog [Cucumis sativus] gi\|449517076\|ref\|XP_004165572.1\| PREDICTED: cell differentiation protein RCD1 homolog [Cucumis sativus]	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		309
UNIPROTKB\|F2Z4M8		299	RQCD1 "Uncharacterized protein	0.572	0.591	0.524	1.4e-60
UNIPROTKB\|A7MB47		299	RQCD1 "Cell differentiation pr	0.572	0.591	0.524	1.4e-60
UNIPROTKB\|Q92600		299	RQCD1 "Cell differentiation pr	0.572	0.591	0.524	1.4e-60
UNIPROTKB\|F2Z5T0		299	RQCD1 "Uncharacterized protein	0.572	0.591	0.524	1.4e-60
UNIPROTKB\|Q4R347		299	RQCD1 "Cell differentiation pr	0.572	0.591	0.524	1.4e-60
UNIPROTKB\|Q5R6Z6		299	RQCD1 "Cell differentiation pr	0.572	0.591	0.524	1.4e-60
MGI\|MGI:1928902		299	Rqcd1 "rcd1 (required for cell	0.572	0.591	0.524	1.4e-60
RGD\|1311495		299	Rqcd1 "Rcd1 required for cell	0.572	0.591	0.524	1.4e-60
ZFIN\|ZDB-GENE-030131-1558		298	rqcd1 "RCD1 required for cell	0.572	0.593	0.519	1.4e-60
UNIPROTKB\|Q6IP65		299	rqcd1 "Cell differentiation pr	0.572	0.591	0.524	2.9e-60

UNIPROTKB\|F2Z4M8 RQCD1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

 Score = 431 (156.8 bits), Expect = 1.4e-60, Sum P(2) = 1.4e-60
 Identities = 95/181 (52%), Positives = 118/181 (65%)

Query:   118 KVYNCMATFRAIKSSM-TRLISVLMVLAKLPLYLYPFLNTKDKEKPHEYLRLTSLGVIGT 176
             +V N +A  + + S   TR  S  +  A +PL+LYPFL+T  K +P EYLRLTSLGVIG 
Sbjct:    89 RVCNALALLQCVASHPETR--SAFLA-AHIPLFLYPFLHTVSKTRPFEYLRLTSLGVIGA 145

Query:   177 LVKSDDPEAIRFLLQTEIFPCCLTSMEVGSDLSKQVATFIIYKILLHEEGLKYCCVLADR 236
             LVK+D+ E I FLL TEI P CL  ME GS+LSK VATFI+ KILL + GL Y C   +R
Sbjct:   146 LVKTDEQEVINFLLTTEIIPLCLRIMESGSELSKTVATFILQKILLDDTGLAYICQTYER 205

Query:   237 FFAVARALAQMTEKLVEQPSPRLLKHIICCYHRLSQSPRACDGLRCCLPLWFGDRKFTSQ 296
             F  VA  L +M  +L ++PS RLLKH++ CY RLS +PRA + LR CLP    D  F   
Sbjct:   206 FSHVAMILGKMVLQLSKEPSARLLKHVVRCYLRLSDNPRAREALRQCLPDQLKDTTFAQV 265

Query:   297 L 297
             L
Sbjct:   266 L 266

GO:0000932 "cytoplasmic mRNA processing body" evidence=IEA

GO:0019221 "cytokine-mediated signaling pathway" evidence=IEA

GO:2000327 "positive regulation of ligand-dependent nuclear receptor transcription coactivator activity" evidence=IEA

UNIPROTKB\|A7MB47 RQCD1 "Cell differentiation protein RCD1 homolog" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|Q92600 RQCD1 "Cell differentiation protein RCD1 homolog" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|F2Z5T0 RQCD1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|Q4R347 RQCD1 "Cell differentiation protein RCD1 homolog" [Macaca fascicularis (taxid:9541)]	Back alignment and assigned GO terms

UNIPROTKB\|Q5R6Z6 RQCD1 "Cell differentiation protein RCD1 homolog" [Pongo abelii (taxid:9601)]	Back alignment and assigned GO terms

MGI\|MGI:1928902 Rqcd1 "rcd1 (required for cell differentiation) homolog 1 (S. pombe)" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

RGD\|1311495 Rqcd1 "Rcd1 required for cell differentiation1 homolog (S. pombe)" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-030131-1558 rqcd1 "RCD1 required for cell differentiation1 homolog (S. pombe)" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|Q6IP65 rqcd1 "Cell differentiation protein RCD1 homolog" [Xenopus laevis (taxid:8355)]	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)
Q92368	RCD1_SCHPO	No assigned EC number	0.4837	0.8155	0.8904	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

Your Input:
	estExt_fgenesh4_pm.C_LG_I1122	hypothetical protein (323 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
		Sorry, there are no predicted associations at the current settings.

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		309
pfam04078		262	pfam04078, Rcd1, Cell differentiation family, Rcd1	1e-112
COG5209		315	COG5209, RCD1, Uncharacterized protein involved in	6e-72

>gnl\|CDD\|190856 pfam04078, Rcd1, Cell differentiation family, Rcd1-like	Back alignment and domain information

 Score =  325 bits (835), Expect = e-112
 Identities = 147/267 (55%), Positives = 171/267 (64%), Gaps = 25/267 (9%)

Query: 31  WIQALQSHETKERALLILSQNKEIRKDLAPLLWNSIGTISALLQEIISVYRTLSSPNLTE 90
            I  L + ET+E ALL LS+ +E   DLAPLLW+S GTI+ALLQEI+S+Y  LS PNLT 
Sbjct: 2   LICDLTNPETRENALLELSKKRESFPDLAPLLWHSFGTIAALLQEIVSIYPLLSPPNLTA 61

Query: 91  TASTRVSNALALFQVTFTSIGSSFAILKVYNCMATFRAIKSSMTRLISVLMVLAKLPLYL 150
             S RV NALAL Q                 C+A+    +    R        A +PLYL
Sbjct: 62  QQSNRVCNALALLQ-----------------CVASHPETRRLFLR--------AHIPLYL 96

Query: 151 YPFLNTKDKEKPHEYLRLTSLGVIGTLVKSDDPEAIRFLLQTEIFPCCLTSMEVGSDLSK 210
           YPFLNT  K +P EYLRLTSLGVIG LVKSDDPE I FLL TEI P CL  ME GS+LSK
Sbjct: 97  YPFLNTTSKSRPFEYLRLTSLGVIGALVKSDDPEVINFLLSTEIIPLCLRIMEFGSELSK 156

Query: 211 QVATFIIYKILLHEEGLKYCCVLADRFFAVARALAQMTEKLVEQPSPRLLKHIICCYHRL 270
            VATFI+ KILL + GL Y C  A+RF+AVA  L +M E+L  QPSPRLLKH+I CY RL
Sbjct: 157 TVATFILQKILLDDVGLNYICQTAERFYAVATVLNKMVEQLTRQPSPRLLKHVIRCYLRL 216

Query: 271 SQSPRACDGLRCCLPLWFGDRKFTSQL 297
           S +PRA + LR CLP    D  F+  L
Sbjct: 217 SDNPRAREALRKCLPEELRDGTFSQLL 243

Two of the members in this family have been characterized as being involved in regulation of Ste11 regulated sex genes. Mammalian Rcd1 is a novel transcriptional cofactor that mediates retinoic acid-induced cell differentiation. Length = 262

>gnl\|CDD\|227534 COG5209, RCD1, Uncharacterized protein involved in cell differentiation/sexual development [General function prediction only]	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		309
PF04078		262	Rcd1: Cell differentiation family, Rcd1-like ; Int	100.0
KOG3036		293	consensus Protein involved in cell differentiation	100.0
COG5209		315	RCD1 Uncharacterized protein involved in cell diff	100.0
cd00020		120	ARM Armadillo/beta-catenin-like repeats. An approx	90.2
cd00020		120	ARM Armadillo/beta-catenin-like repeats. An approx	89.4

>PF04078 Rcd1: Cell differentiation family, Rcd1-like ; InterPro: IPR007216 Rcd1 (Required cell differentiation 1) -like proteins are found among a wide range of organisms []	Back alignment and domain information

Probab=100.00  E-value=6e-117  Score=818.64  Aligned_cols=250  Identities=61%  Similarity=0.934  Sum_probs=232.6

Q ss_pred             HHHHHhcCcchHHHHHHHHHhcccccCchhhHhhhhhchHHHHHHHHHHhhccCCCCCCChhhhhhHHHHHHhhhhhhcc
Q 037700           30 YWIQALQSHETKERALLILSQNKEIRKDLAPLLWNSIGTISALLQEIISVYRTLSSPNLTETASTRVSNALALFQVTFTS  109 (309)
Q Consensus        30 q~I~~L~~~~~Re~AL~eLsk~re~~~dLap~LW~S~Gtia~LLQEIisvYp~Ls~p~Lt~~~SnRVcnaLaLlQ~~~~~  109 (309)
                      |||.||++|++||+||+||||+||++|||||+||||||||++|||||+++||+++||+||+++||||||||||||     
T Consensus         1 q~i~~L~~~~~Re~Al~eLsk~r~~~~~La~~LW~s~G~i~~LLqEIisiYp~l~~~~Lt~~~snRVcnaLaLlQ-----   75 (262)
T PF04078_consen    1 QLILDLCNPETRENALLELSKKRESFPDLAPLLWHSFGTIAALLQEIISIYPALSPPNLTARQSNRVCNALALLQ-----   75 (262)
T ss_dssp             HHHHHTSSHHHHHHHHHHHHHTCCC-TTHHHHHHTSTTHHHHHHHHHHGGGGGTTTT---HHHHHHHHHHHHHHH-----
T ss_pred             ChhHHhcCcchHHHHHHHHHHhhhcccchhHHHHcCCChHHHHHHHHHHHcccCCCcccCHHHHHHHHHHHHHHH-----
Confidence            899999999999999999999999999999999999999999999999999999999999999999999999999     


Q ss_pred             cCchhhhhhhcccccccccccchhhHHHHHHHHHhcCccccccccccccCCCCCcchhhhhhhhhhhhccCChhHHHHHH
Q 037700          110 IGSSFAILKVYNCMATFRAIKSSMTRLISVLMVLAKLPLYLYPFLNTKDKEKPHEYLRLTSLGVIGTLVKSDDPEAIRFL  189 (309)
Q Consensus       110 ~~~~~~~~~~~~cvAshp~~~~~eTR~~~~~Fl~A~iplYLyPfLntt~k~rp~EyLRLtSLGVIgaLvK~dd~evI~fL  189 (309)
                                  ||||||     |||.   +||+||||+||||||||++|+|||||||||||||||||||+||+|||+||
T Consensus        76 ------------~vAshp-----etr~---~Fl~a~iplyLyPfL~tt~k~r~~E~LRLtsLGVIgaLvK~d~~evi~fL  135 (262)
T PF04078_consen   76 ------------CVASHP-----ETRM---PFLKAHIPLYLYPFLNTTSKTRPFEYLRLTSLGVIGALVKTDDPEVISFL  135 (262)
T ss_dssp             ------------HHHH-T-----TTHH---HHHHTTGGGGGHHHHH----SHHHHHHHHHHHHHHHHHHTT--HHHHHHH
T ss_pred             ------------HHHcCh-----HHHH---HHHHcCchhhehhhhhccccccccchhhHhHHHHHHHHHcCCcHHHHHHH
Confidence                        999999     9999   99999999999999999999999999999999999999999999999999


Q ss_pred             hhccccccccccccccchhhHHHHHHHHHHHhcccccchhhhhhhhhHHHHHHHHHHHHHHHhhCCCchhHHHHHHHHHH
Q 037700          190 LQTEIFPCCLTSMEVGSDLSKQVATFIIYKILLHEEGLKYCCVLADRFFAVARALAQMTEKLVEQPSPRLLKHIICCYHR  269 (309)
Q Consensus       190 L~tEiiPlCLriME~GSelSKtvAtfIlqKIL~~d~GL~YiC~t~eRF~aV~~vL~~mv~~l~~~ps~RLLKhIIrCY~R  269 (309)
                      ++|||||+|||+||.|||+||||||||+||||+||+||+|+|+|+|||+||+++|++||++|+++||+||||||||||+|
T Consensus       136 l~tEiiplcLr~me~GselSKtvAtfIlqKIL~dd~GL~yiC~t~eRf~av~~vL~~mV~~l~~~pS~RLLKhIIrCYlR  215 (262)
T PF04078_consen  136 LQTEIIPLCLRIMEFGSELSKTVATFILQKILLDDVGLNYICQTAERFFAVAMVLNKMVEQLVKQPSPRLLKHIIRCYLR  215 (262)
T ss_dssp             HCTTHHHHHHHHHHHS-HHHHHHHHHHHHHHHHSHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHH
T ss_pred             HhhchHHHHHHHHHhccHHHHHHHHHHHHHHHcchhHHHHHhcCHHHHHHHHHHHHHHHHHHccCCChhHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hcCChhhHhhhhhcCCccccchhhhhhhccCCCCC
Q 037700          270 LSQSPRACDGLRCCLPLWFGDRKFTSQLHVRSSKT  304 (309)
Q Consensus       270 Ls~n~rar~aLr~~LP~~Lrd~~f~~~l~~d~~~~  304 (309)
                      ||||||||++|++|||++|||++|.+++++|++++
T Consensus       216 Lsdnprar~aL~~~LP~~Lrd~~f~~~l~~D~~~k  250 (262)
T PF04078_consen  216 LSDNPRAREALRQCLPDQLRDGTFSNILKDDPSTK  250 (262)
T ss_dssp             HTTSTTHHHHHHHHS-GGGTSSTTTTGGCS-HHHH
T ss_pred             HccCHHHHHHHHHhCcHHHhcHHHHHHHhcCHHHH
Confidence            99999999999999999999999999999999765

Rcd1 was initially identified as an essential factor in nitrogen starvation-invoked differentiation in fission yeast. This results largely from a defect in nitrogen starvation-invoked induction of ste11+, a key transcriptional factor gene required for the onset of sexual development. It is one of the most conserved proteins in eukaryotes, and its mammalian homologue is expressed in a variety of differentiating tissues [, ]. The mammalian Rcd1 is a novel transcriptional cofactor and is critical for retinoic acid-induced differentiation of F9 mouse teratocarcinoma cells, at least in part, via forming complexes with retinoic acid receptor and activation transcription factor-2 (ATF-2) []. Two of the members in this family have been characterised as being involved in regulation of Ste11 regulated sex genes [, ].; PDB: 2FV2_B.

>KOG3036 consensus Protein involved in cell differentiation/sexual development [General function prediction only]	Back alignment and domain information

>COG5209 RCD1 Uncharacterized protein involved in cell differentiation/sexual development [General function prediction only]	Back alignment and domain information

>cd00020 ARM Armadillo/beta-catenin-like repeats	Back alignment and domain information

>cd00020 ARM Armadillo/beta-catenin-like repeats	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		309
2fv2_A		268	Crystal Structure Analysis Of Human Rcd-1 Conserved		7e-64

>pdb|2FV2|A Chain A, Crystal Structure Analysis Of Human Rcd-1 Conserved Region Length = 268

Back alignment and structure

Iteration: 1

Score = 240 bits (612), Expect = 7e-64, Method: Compositional matrix adjust. Identities = 133/267 (49%), Positives = 168/267 (62%), Gaps = 25/267 (9%) Query: 31 WIQALQSHETKERALLILSQNKEIRKDLAPLLWNSIGTISALLQEIISVYRTLSSPNLTE 90 WI L S ET+E ALL LS+ +E DLAP+LW+S GTI+ALLQEI+++Y +++ P LT Sbjct: 8 WINELSSPETRENALLELSKKRESVPDLAPMLWHSFGTIAALLQEIVNIYPSINPPTLTA 67 Query: 91 TASTRVSNALALFQVTFTSIGSSFAILKVYNCMATFRAIKSSMTRLISVLMVLAKLPLYL 150 S RV NALAL Q C+A+ +S+ + A +PL+L Sbjct: 68 HQSNRVCNALALLQ-----------------CVASHPETRSAF--------LAAHIPLFL 102 Query: 151 YPFLNTKDKEKPHEYLRLTSLGVIGTLVKSDDPEAIRFLLQTEIFPCCLTSMEVGSDLSK 210 YPFL+T K +P EYLRLTSLGVIG LVK+D+ E I FLL TEI P CL ME GS+LSK Sbjct: 103 YPFLHTVSKTRPFEYLRLTSLGVIGALVKTDEQEVINFLLTTEIIPLCLRIMESGSELSK 162 Query: 211 QVATFIIYKILLHEEGLKYCCVLADRFFAVARALAQMTEKLVEQPSPRLLKHIICCYHRL 270 VATFI+ KILL + GL Y C +RF VA L +M +L ++PS RLLKH++ CY RL Sbjct: 163 TVATFILQKILLDDTGLAYICQTYERFSHVAMILGKMVLQLSKEPSARLLKHVVRCYLRL 222 Query: 271 SQSPRACDGLRCCLPLWFGDRKFTSQL 297 S +PRA + LR CLP D F L Sbjct: 223 SDNPRAREALRQCLPDQLKDTTFAQVL 249

PyMOL of 2fv2

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		309
2fv2_A		268	RCD1 required for cell differentiation1 homolog; a	5e-91
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-07

>2fv2_A RCD1 required for cell differentiation1 homolog; armadillo-repeat, transcription; 2.20A {Homo sapiens} Length = 268	Back alignment and structure

 Score =  271 bits (693), Expect = 5e-91
 Identities = 133/272 (48%), Positives = 168/272 (61%), Gaps = 25/272 (9%)

Query: 27  SVAYWIQALQSHETKERALLILSQNKEIRKDLAPLLWNSIGTISALLQEIISVYRTLSSP 86
            +  WI  L S ET+E ALL LS+ +E   DLAP+LW+S GTI+ALLQEI+++Y +++ P
Sbjct: 4   KIYQWINELSSPETRENALLELSKKRESVPDLAPMLWHSFGTIAALLQEIVNIYPSINPP 63

Query: 87  NLTETASTRVSNALALFQVTFTSIGSSFAILKVYNCMATFRAIKSSMTRLISVLMVLAKL 146
            LT   S RV NALAL Q                 C+A+    +S          + A +
Sbjct: 64  TLTAHQSNRVCNALALLQ-----------------CVASHPETRS--------AFLAAHI 98

Query: 147 PLYLYPFLNTKDKEKPHEYLRLTSLGVIGTLVKSDDPEAIRFLLQTEIFPCCLTSMEVGS 206
           PL+LYPFL+T  K +P EYLRLTSLGVIG LVK+D+ E I FLL TEI P CL  ME GS
Sbjct: 99  PLFLYPFLHTVSKTRPFEYLRLTSLGVIGALVKTDEQEVINFLLTTEIIPLCLRIMESGS 158

Query: 207 DLSKQVATFIIYKILLHEEGLKYCCVLADRFFAVARALAQMTEKLVEQPSPRLLKHIICC 266
           +LSK VATFI+ KILL + GL Y C   +RF  VA  L +M  +L ++PS RLLKH++ C
Sbjct: 159 ELSKTVATFILQKILLDDTGLAYICQTYERFSHVAMILGKMVLQLSKEPSARLLKHVVRC 218

Query: 267 YHRLSQSPRACDGLRCCLPLWFGDRKFTSQLH 298
           Y RLS +PRA + LR CLP    D  F   L 
Sbjct: 219 YLRLSDNPRAREALRQCLPDQLKDTTFAQVLK 250

PyMOL of 2fv2

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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		309
2fv2_A		268	RCD1 required for cell differentiation1 homolog; a	100.0
4db6_A		210	Armadillo repeat protein; solenoid repeat, armadil	96.76
4hxt_A		252	De novo protein OR329; structural genomics, PSI-bi	96.58
1xqr_A		296	HSPBP1 protein; armadillo repeat, superhelical twi	95.91
4db8_A		252	Armadillo-repeat protein; solenoid repeat, de novo	95.75
4db6_A		210	Armadillo repeat protein; solenoid repeat, armadil	95.18
4db8_A		252	Armadillo-repeat protein; solenoid repeat, de novo	95.13
4hxt_A		252	De novo protein OR329; structural genomics, PSI-bi	95.02
4b8j_A		528	Importin subunit alpha-1A; transport protein, nucl	94.57
4b8j_A		528	Importin subunit alpha-1A; transport protein, nucl	93.78
1wa5_B		530	Importin alpha subunit; nuclear transport/complex,	92.01
2jdq_A		450	Importin alpha-1 subunit; transport, PB2 subunit,	91.25
2z6h_A		644	Catenin beta-1, beta-catenin; C-terminal domain, a	90.82
2jdq_A		450	Importin alpha-1 subunit; transport, PB2 subunit,	89.04
1jdh_A		529	Beta-catenin; beta-catenin, protein-protein comple	86.18
1xm9_A		457	Plakophilin 1; armadillo repeat, cell adhesion; 2.	86.04
1wa5_B		530	Importin alpha subunit; nuclear transport/complex,	83.75
2z6h_A		644	Catenin beta-1, beta-catenin; C-terminal domain, a	82.23
1xqr_A		296	HSPBP1 protein; armadillo repeat, superhelical twi	80.16

>2fv2_A RCD1 required for cell differentiation1 homolog; armadillo-repeat, transcription; 2.20A {Homo sapiens}	Back alignment and structure

Probab=100.00  E-value=7.5e-120  Score=838.44  Aligned_cols=256  Identities=52%  Similarity=0.851  Sum_probs=253.2

Q ss_pred             ChhHHHHHHHHhcCcchHHHHHHHHHhcccccCchhhHhhhhhchHHHHHHHHHHhhccCCCCCCChhhhhhHHHHHHhh
Q 037700           24 GPASVAYWIQALQSHETKERALLILSQNKEIRKDLAPLLWNSIGTISALLQEIISVYRTLSSPNLTETASTRVSNALALF  103 (309)
Q Consensus        24 ~~~~v~q~I~~L~~~~~Re~AL~eLsk~re~~~dLap~LW~S~Gtia~LLQEIisvYp~Ls~p~Lt~~~SnRVcnaLaLl  103 (309)
                      |+++++|||.||++|++||+||+||||+||++|||||+||||||||++|||||+++||+++||+||+++|||||||||||
T Consensus         1 ~~~~i~qli~~L~~p~~Re~AL~eLsk~Re~~~~La~~LW~S~Gtia~LLQEIisiYp~lspp~Lt~~~SnRVcnaLaLl   80 (268)
T 2fv2_A            1 DREKIYQWINELSSPETRENALLELSKKRESVPDLAPMLWHSFGTIAALLQEIVNIYPSINPPTLTAHQSNRVCNALALL   80 (268)
T ss_dssp             -CHHHHHHHHHTSSTTTHHHHHHHHHHHTTTCTTHHHHHHHSTTHHHHHHHHHHHTGGGBTTBCCCHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHhcCchhHHHHHHHHHHhhhccccHHHHHHhccCHHHHHHHHHHHHcccCCCcccCHHHHhHHHHHHHHH
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhcccCchhhhhhhcccccccccccchhhHHHHHHHHHhcCccccccccccccCCCCCcchhhhhhhhhhhhccCChh
Q 037700          104 QVTFTSIGSSFAILKVYNCMATFRAIKSSMTRLISVLMVLAKLPLYLYPFLNTKDKEKPHEYLRLTSLGVIGTLVKSDDP  183 (309)
Q Consensus       104 Q~~~~~~~~~~~~~~~~~cvAshp~~~~~eTR~~~~~Fl~A~iplYLyPfLntt~k~rp~EyLRLtSLGVIgaLvK~dd~  183 (309)
                      |                 ||||||     |||.   +||+||||+||||||||++|+|||||||||||||||||||+||+
T Consensus        81 Q-----------------cvAshp-----etr~---~Fl~a~iplyLyPfL~t~sk~r~fE~LRLtsLGVIgaLvK~dd~  135 (268)
T 2fv2_A           81 Q-----------------CVASHP-----ETRS---AFLAAHIPLFLYPFLHTVSKTRPFEYLRLTSLGVIGALVKTDEQ  135 (268)
T ss_dssp             H-----------------HHHHCT-----TTHH---HHHHTTGGGGTHHHHHCCCCSHHHHHHHHHHHHHHHHHGGGCCH
T ss_pred             H-----------------HHHcCc-----chhh---HHHHccchHHhhhhhccccCCCcchhhhhhHHHHHHHHhccCcH
Confidence            9                 999999     9999   99999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhccccccccccccccchhhHHHHHHHHHHHhcccccchhhhhhhhhHHHHHHHHHHHHHHHhhCCCchhHHHH
Q 037700          184 EAIRFLLQTEIFPCCLTSMEVGSDLSKQVATFIIYKILLHEEGLKYCCVLADRFFAVARALAQMTEKLVEQPSPRLLKHI  263 (309)
Q Consensus       184 evI~fLL~tEiiPlCLriME~GSelSKtvAtfIlqKIL~~d~GL~YiC~t~eRF~aV~~vL~~mv~~l~~~ps~RLLKhI  263 (309)
                      |||+||++|||||+|||+||.|||+||||||||+||||+||+||+|+|+|+|||+||++||++||++++++||+||||||
T Consensus       136 eVi~fLL~tEiiplCLrime~GselSKtvAtfIlqKIL~dd~GL~YiC~t~eRF~av~~vL~~mV~~l~~~ps~RLLKhi  215 (268)
T 2fv2_A          136 EVINFLLTTEIIPLCLRIMESGSELSKTVATFILQKILLDDTGLAYICQTYERFSHVAMILGKMVLQLSKEPSARLLKHV  215 (268)
T ss_dssp             HHHHHHHHTTHHHHHHHHHHHSCHHHHHHHHHHHHHHHHSHHHHHHHTSSHHHHHHHHHHHHHHHHHTTTSCCHHHHHHH
T ss_pred             HHHHHHHhhhHHHHHHHHHhhccHHHHHHHHHHHHHHhccchhHHHHHccHHHHHHHHHHHHHHHHHHhcCCChHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcCChhhHhhhhhcCCccccchhhhhhhccCCCCC
Q 037700          264 ICCYHRLSQSPRACDGLRCCLPLWFGDRKFTSQLHVRSSKT  304 (309)
Q Consensus       264 IrCY~RLs~n~rar~aLr~~LP~~Lrd~~f~~~l~~d~~~~  304 (309)
                      ||||+|||||||||++|++|||++|||++|++++++|+.++
T Consensus       216 ircYlRLsdn~rar~aL~~~LP~~Lrd~tf~~~l~~D~~~k  256 (268)
T 2fv2_A          216 VRCYLRLSDNPRAREALRQCLPDQLKDTTFAQVLKDDTTTK  256 (268)
T ss_dssp             HHHHHHHTTSHHHHHHHHHHSCGGGTSSTTHHHHTSCHHHH
T ss_pred             HHHHHHHhcCHHHHHHHHHhCcHHhhChHHHHHHhcCHHHH
Confidence            99999999999999999999999999999999999999775

PyMOL of 2fv2

>4db6_A Armadillo repeat protein; solenoid repeat, armadillo repeat motif, de novo protein; 1.80A {Synthetic construct} PDB: 4db9_A 4dba_A	Back alignment and structure

>4hxt_A De novo protein OR329; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; 1.95A {Artificial gene}	Back alignment and structure

>1xqr_A HSPBP1 protein; armadillo repeat, superhelical twist, chaperone; 2.10A {Homo sapiens} SCOP: a.118.1.21 PDB: 1xqs_A*	Back alignment and structure

>4db8_A Armadillo-repeat protein; solenoid repeat, de novo protein; 2.50A {Synthetic construct}	Back alignment and structure

>4db6_A Armadillo repeat protein; solenoid repeat, armadillo repeat motif, de novo protein; 1.80A {Synthetic construct} PDB: 4db9_A 4dba_A	Back alignment and structure

>4db8_A Armadillo-repeat protein; solenoid repeat, de novo protein; 2.50A {Synthetic construct}	Back alignment and structure

>4hxt_A De novo protein OR329; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; 1.95A {Artificial gene}	Back alignment and structure

>4b8j_A Importin subunit alpha-1A; transport protein, nuclear localization signal; 2.00A {Oryza sativa japonica group} PDB: 4b8o_A 2yns_A 4b8p_A	Back alignment and structure

>4b8j_A Importin subunit alpha-1A; transport protein, nuclear localization signal; 2.00A {Oryza sativa japonica group} PDB: 4b8o_A 2yns_A 4b8p_A	Back alignment and structure

>1wa5_B Importin alpha subunit; nuclear transport/complex, nuclear transport, exportin, RAN GTPase, protein transport; HET: GTP; 2.0A {Saccharomyces cerevisiae} SCOP: a.118.1.1 PDB: 1un0_A 2c1t_A 1bk5_A 1ee5_A 1bk6_A 1ee4_A	Back alignment and structure

>2jdq_A Importin alpha-1 subunit; transport, PB2 subunit, nuclear protein, protein transport, armadillo repeats; 2.2A {Homo sapiens} PDB: 3tj3_A	Back alignment and structure

>2z6h_A Catenin beta-1, beta-catenin; C-terminal domain, activator, alternative splicing, cell adhesion, cytoplasm, cytoskeleton, disease mutation, nucleus; 2.20A {Homo sapiens}	Back alignment and structure

>2jdq_A Importin alpha-1 subunit; transport, PB2 subunit, nuclear protein, protein transport, armadillo repeats; 2.2A {Homo sapiens} PDB: 3tj3_A	Back alignment and structure

>1jdh_A Beta-catenin; beta-catenin, protein-protein complex, transcription; 1.90A {Homo sapiens} SCOP: a.118.1.1 PDB: 1qz7_A 1g3j_A 1th1_A* 1i7w_A* 1i7x_A 1jpp_A 1m1e_A 1v18_A* 3oux_A 3ouw_A 1jpw_A 3tx7_A* 2gl7_A 1t08_A 1luj_A 2bct_A 3bct_A* 3ifq_A* 3sla_A 3sl9_A	Back alignment and structure

>1xm9_A Plakophilin 1; armadillo repeat, cell adhesion; 2.80A {Homo sapiens} SCOP: a.118.1.24	Back alignment and structure

>1wa5_B Importin alpha subunit; nuclear transport/complex, nuclear transport, exportin, RAN GTPase, protein transport; HET: GTP; 2.0A {Saccharomyces cerevisiae} SCOP: a.118.1.1 PDB: 1un0_A 2c1t_A 1bk5_A 1ee5_A 1bk6_A 1ee4_A	Back alignment and structure

>2z6h_A Catenin beta-1, beta-catenin; C-terminal domain, activator, alternative splicing, cell adhesion, cytoplasm, cytoskeleton, disease mutation, nucleus; 2.20A {Homo sapiens}	Back alignment and structure

>1xqr_A HSPBP1 protein; armadillo repeat, superhelical twist, chaperone; 2.10A {Homo sapiens} SCOP: a.118.1.21 PDB: 1xqs_A*	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		309
d1xqra1		264	Hsp70-binding protein 1 (HspBP1) {Human (Homo sapi	94.57
d1wa5b_		503	Karyopherin alpha {Baker's yeast (Saccharomyces ce	92.21
d1xqra1		264	Hsp70-binding protein 1 (HspBP1) {Human (Homo sapi	91.24
d1q1sc_		434	Importin alpha {Mouse (Mus musculus) [TaxId: 10090	91.24
d1q1sc_		434	Importin alpha {Mouse (Mus musculus) [TaxId: 10090	85.38
d1wa5b_		503	Karyopherin alpha {Baker's yeast (Saccharomyces ce	84.81

>d1xqra1 a.118.1.21 (A:87-350) Hsp70-binding protein 1 (HspBP1) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: HspBP1 domain
domain: Hsp70-binding protein 1 (HspBP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.57  E-value=0.22  Score=40.60  Aligned_cols=131  Identities=15%  Similarity=0.199  Sum_probs=92.8

Q ss_pred             hhHHHHHHHHHhcCccccccccccccCCCCCcchhhhhhhhhhhhccCChhHHHHHHhhccccccccccccccchhhHHH
Q 037700          133 MTRLISVLMVLAKLPLYLYPFLNTKDKEKPHEYLRLTSLGVIGTLVKSDDPEAIRFLLQTEIFPCCLTSMEVGSDLSKQV  212 (309)
Q Consensus       133 eTR~~~~~Fl~A~iplYLyPfLntt~k~rp~EyLRLtSLGVIgaLvK~dd~evI~fLL~tEiiPlCLriME~GSelSKtv  212 (309)
                      ..+.   .++..+..-.|-..|+..    +...+|-..++.++.+++.+++-. .-+.....+|..++.+..+++-.+..
T Consensus        92 ~~~~---~~~~~~~i~~Lv~lL~~~----~~~~v~~~a~~aL~~l~~~~~~~~-~~~~~~~gi~~L~~lL~~~~~~~~~~  163 (264)
T d1xqra1          92 AIQE---QVLGLGALRKLLRLLDRD----ACDTVRVKALFAISCLVREQEAGL-LQFLRLDGFSVLMRAMQQQVQKLKVK  163 (264)
T ss_dssp             HHHH---HHHHTTHHHHHHHHHHHC----SCHHHHHHHHHHHHHHHTTCHHHH-HHHHHTTHHHHHHHHHHSSCHHHHHH
T ss_pred             HHHH---HHHHcCchHHHHHHhhcC----CCHHHHHHHHHHHHHHhccchhhH-HHHHHhhhhhHHHHHHhcCchHHHHH
Confidence            7777   888888666677777532    234588899999999998666544 44456778899999999999999999


Q ss_pred             HHHHHHHHhcccccchhhhhhhhhHHHHHHHHHHHHHHHhhCCCchhHHHHHHHHHHhcC-ChhhHhh
Q 037700          213 ATFIIYKILLHEEGLKYCCVLADRFFAVARALAQMTEKLVEQPSPRLLKHIICCYHRLSQ-SPRACDG  279 (309)
Q Consensus       213 AtfIlqKIL~~d~GL~YiC~t~eRF~aV~~vL~~mv~~l~~~ps~RLLKhIIrCY~RLs~-n~rar~a  279 (309)
                      |...+..++..+.+..-.      +.. ..++..++ .+.+.+++.+-++..++-..|+. +|..+..
T Consensus       164 a~~~L~~l~~~~~~~~~~------~~~-~~~v~~L~-~lL~~~~~~~~~~a~~aL~~L~~~~~~~~~~  223 (264)
T d1xqra1         164 SAFLLQNLLVGHPEHKGT------LCS-MGMVQQLV-ALVRTEHSPFHEHVLGALCSLVTDFPQGVRE  223 (264)
T ss_dssp             HHHHHHHHHHHCGGGHHH------HHH-TTHHHHHH-HHHTSCCSTHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHhccHHHHHH------HHH-hhhHHHHH-HHHcCCCHHHHHHHHHHHHHHHhcCHHHHHH
Confidence            999999987654332211      111 12344444 34578899999999999998886 4444443

PyMOL of d1xqra1

>d1wa5b_ a.118.1.1 (B:) Karyopherin alpha {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1xqra1 a.118.1.21 (A:87-350) Hsp70-binding protein 1 (HspBP1) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1q1sc_ a.118.1.1 (C:) Importin alpha {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1q1sc_ a.118.1.1 (C:) Importin alpha {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1wa5b_ a.118.1.1 (B:) Karyopherin alpha {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure