Citrus Sinensis ID: 021722

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

MEILAIHLQPLLLKRTMSAKEVRASDVRPLPVLEETLNYLLSLLDSTEHPFEVIHDFVFDRTRSVRQDLIMQNIVNDKAINMFEKIVKFHVISHHKLRSSCSSSSISPLHYLNLEQLTKALTSLYNLYEANRSSKPIHEKEAEFRSFYVLLHLDSNGQPVGESLSLWFRHVPSPIIKSKEMWFARQALRYFQMGNYRRFLSTVAAEASYLQYCIIEPYIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEESDVELFCNAYGLQTCIDEVGNKLLPTKQTTFCRPKGGLQNYSFLGFQQLGRQIEL

cccccccccHHHHccccccccccccccccHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHccHHHccEEEEEccHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHcccccccHHHHHHHHHHccHHHHccHHHHHHHHHHHHHHHccHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHccccHHHHHHHHHHccEEcccccccEEEEcccccccccccccccccHHHHHHccccccc

ccEEEEcHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHccccccccHHHHHHHHHHccHHHHccHHHHHHHHHHHHHHcccHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHcccHHHHHHHHHHcccEEEccccccEEEEccccccccccccccEEEEEEEEccccEEEc

MEILAIHLQPLLLKRtmsakevrasdvrplpvLEETLNYLLSLldstehpfevIHDFVFDRTRSVRQDLIMQNIVNDKAINMFEKIVKFHVIShhklrsscssssisplhyLNLEQLTKALTSLYNLyeanrsskpihekeaEFRSFYVLLHldsngqpvgeSLSLWFrhvpspiiksKEMWFARQALRYFQMGNYRRFLSTVAAEASYLQYCIIEPYIDEVRSLALCcihnccyklhpyplghlskVLMMEESDVELFCNAYGLQTCIDevgnkllptkqttfcrpkgglqnysflgFQQLGRQIEL

meilaihlqplllkrtmsakevrasdvrplpvLEETLNYLLSLLDSTEHPFEVIHDFVFDRTRSVRQDLIMQNIVNDKAINMFEKIVKFHVISHHKLRSSCSSSSISPLHYLNLEQLTKALTSLYNLYEANRSSKPIHEKEAEFRSFYVLLHLDSNGQPVGESLSLWFRHVPSPIIKSKEMWFARQALRYFQMGNYRRFLSTVAAEASYLQYCIIEPYIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEESDVELFCNAYGLQTCIDEVGNKLLPTKQTTFcrpkgglqnysflgfqqlgrqiel

MEILAIHLQPLLLKRTMSAKEVRASDVRPLPVleetlnyllslldsteHPFEVIHDFVFDRTRSVRQDLIMQNIVNDKAINMFEKIVKFHVISHHKLRsscssssisPLHYLNLEQLTKALTSLYNLYEANRSSKPIHEKEAEFRSFYVLLHLDSNGQPVGESLSLWFRHVPSPIIKSKEMWFARQALRYFQMGNYRRFLSTVAAEASYLQYCIIEPYIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEESDVELFCNAYGLQTCIDEVGNKLLPTKQTTFCRPKGGLQNYSFLGFQQLGRQIEL

***LAIHLQPLLLKRTMSAKEVRASDVRPLPVLEETLNYLLSLLDSTEHPFEVIHDFVFDRTRSVRQDLIMQNIVNDKAINMFEKIVKFHVISHHKLRSSCSSSSISPLHYLNLEQLTKALTSLYNLYEAN*********EAEFRSFYVLLHLDSNGQPVGESLSLWFRHVPSPIIKSKEMWFARQALRYFQMGNYRRFLSTVAAEASYLQYCIIEPYIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEESDVELFCNAYGLQTCIDEVGNKLLPTKQTTFCRPKGGLQNYSFLGFQQL******

*****IH*QPLLLKRT****EVRASDVRPLPVLEETLNYLLSLLDSTEHPFEVIHDFVFDRTRSVRQDLIMQNIVNDKAINMFEKIVKFHVISHHKLRSSCSSSSISPLHYLNLEQLTKALTSLYNLYEANRSSKPIHEKEAEFRSFYVLLHLDSNGQPVGESLSLWFRHVPSPIIKSKEMWFARQALRYFQMGNYRRFLSTVAAEASYLQYCIIEPYIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEESDVELFCNAYGLQTCIDEVGNKLLP*****************FLGFQQLGR****

MEILAIHLQPLLLKRTMSAKEVRASDVRPLPVLEETLNYLLSLLDSTEHPFEVIHDFVFDRTRSVRQDLIMQNIVNDKAINMFEKIVKFHVISH***********ISPLHYLNLEQLTKALTSLYNLYEANRSSKPIHEKEAEFRSFYVLLHLDSNGQPVGESLSLWFRHVPSPIIKSKEMWFARQALRYFQMGNYRRFLSTVAAEASYLQYCIIEPYIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEESDVELFCNAYGLQTCIDEVGNKLLPTKQTTFCRPKGGLQNYSFLGFQQLGRQIEL

*EILAIHLQPLLLKRTMSAKEVRASDVRPLPVLEETLNYLLSLLDSTEHPFEVIHDFVFDRTRSVRQDLIMQNIVNDKAINMFEKIVKFHVISHHKLRSSCSSSSISPLHYLNLEQLTKALTSLYNLYEANRSSKPIHEKEAEFRSFYVLLHLDSNGQPVGESLSLWFRHVPSPIIKSKEMWFARQALRYFQMGNYRRFLSTVAAEASYLQYCIIEPYIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEESDVELFCNAYGLQTCIDEVGNKLLPTKQTTFCRPKGGLQNYSFLGFQQLGRQIE*

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SSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		308	2.2.26 [Sep-21-2011]
O60318		1980	80 kDa MCM3-associated pr	yes	no	0.805	0.125	0.287	4e-21
Q9WUU9		1971	80 kDa MCM3-associated pr	yes	no	0.805	0.125	0.287	2e-20
O74889		1024	SAC3 family protein 1 OS=	yes	no	0.762	0.229	0.303	2e-18
Q9USI4		458	SAC3 family protein 2 OS=	no	no	0.818	0.550	0.299	1e-15
Q9U3V9		1370	Protein xmas-2 OS=Drosoph	yes	no	0.769	0.172	0.296	1e-13
P46674		1301	Nuclear mRNA export prote	yes	no	0.75	0.177	0.282	2e-12

>sp\|O60318\|MCM3A_HUMAN 80 kDa MCM3-associated protein OS=Homo sapiens GN=MCM3AP PE=1 SV=2	Back alignment and function desciption

 Score =  102 bits (254), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 78/271 (28%), Positives = 135/271 (49%), Gaps = 23/271 (8%)

Query: 26  DVRPLPVLEETLNYLLS-LLDSTEHPFEVIHDFVFDRTRSVRQDLIMQNIVNDKAINMFE 84
           ++RPLPVL  T++YL++ ++D  E      +DFV++RTR +R+D+  Q++ +   +++ E
Sbjct: 690 ELRPLPVLSRTMDYLVTQIMDQKEGSLRDWYDFVWNRTRGIRKDITQQHLCDPLTVSLIE 749

Query: 85  KIVKFHVISHHKLRSSCSSSSISPLHYLNLEQLTKALTSLYNLYEANRSSKPIHEKEAEF 144
           K  +FH+   H +   C     S    +N E +TK L SL  +Y+  R+       EAEF
Sbjct: 750 KCTRFHIHCAHFM---CEEPMSSFDAKINNENMTKCLQSLKEMYQDLRNKGVFCASEAEF 806

Query: 145 RSFYVLLHLDSNGQPVGESLSLWFRHVPSPIIKSKEMWFARQALRYFQMGNYRRFLSTVA 204
           + + VLL L+      G+ L    +  P+ +  S E+ FA QA       N+ RF   V 
Sbjct: 807 QGYNVLLSLNK-----GDILREVQQFHPA-VRNSSEVKFAVQAFAALNSNNFVRFFKLVQ 860

Query: 205 AEASYLQYCIIEPYIDEVRSLALCCIHNCCYKLHP-----YPLGHLSKVLMMEE-SDVEL 258
           + ASYL  C++  Y  ++R  AL  + N  Y +       +PL  + ++L+  +  +   
Sbjct: 861 S-ASYLNACLLHCYFSQIRKDALRAL-NFAYTVSTQRSTIFPLDGVVRMLLFRDCEEATD 918

Query: 259 FCNAYGLQTCIDEVGNKLLPTKQTTFCRPKG 289
           F   +GL      V +  +   ++ F  P+G
Sbjct: 919 FLTCHGLT-----VSDGCVELNRSAFLEPEG 944

May be involved in the nuclear localization pathway of MCM3.
Homo sapiens (taxid: 9606)

>sp\|Q9WUU9\|MCM3A_MOUSE 80 kDa MCM3-associated protein OS=Mus musculus GN=Mcm3ap PE=2 SV=2	Back alignment and function description

>sp\|O74889\|SAC31_SCHPO SAC3 family protein 1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPCC576.05 PE=1 SV=1	Back alignment and function description

>sp\|Q9USI4\|SAC32_SCHPO SAC3 family protein 2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPCC70.06 PE=3 SV=1	Back alignment and function description

>sp\|Q9U3V9\|XMAS2_DROME Protein xmas-2 OS=Drosophila melanogaster GN=xmas-2 PE=1 SV=3	Back alignment and function description

>sp\|P46674\|SAC3_YEAST Nuclear mRNA export protein SAC3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SAC3 PE=1 SV=2	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		308
224057204		357	predicted protein [Populus trichocarpa]	0.935	0.806	0.715	1e-118
255569219		440	leng8 protein, putative [Ricinus communi	0.941	0.659	0.679	1e-114
357515593		403	80 kDa MCM3-associated protein [Medicago	0.941	0.719	0.686	1e-111
388497576		403	unknown [Medicago truncatula]	0.941	0.719	0.672	1e-108
296084674		421	unnamed protein product [Vitis vinifera]	0.935	0.684	0.666	1e-107
225449759		407	PREDICTED: SAC3 family protein 1-like [V	0.935	0.707	0.666	1e-107
298205116		424	unnamed protein product [Vitis vinifera]	0.935	0.679	0.670	1e-107
359494933		407	PREDICTED: SAC3 family protein 1-like [V	0.935	0.707	0.670	1e-107
359494990		407	PREDICTED: LOW QUALITY PROTEIN: SAC3 fam	0.935	0.707	0.666	1e-107
356548802		405	PREDICTED: 80 kDa MCM3-associated protei	0.941	0.716	0.658	1e-107

>gi\|224057204\|ref\|XP_002299171.1\| predicted protein [Populus trichocarpa] gi\|222846429\|gb\|EEE83976.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

 Score =  432 bits (1111), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 206/288 (71%), Positives = 246/288 (85%)

Query: 15  RTMSAKEVRASDVRPLPVLEETLNYLLSLLDSTEHPFEVIHDFVFDRTRSVRQDLIMQNI 74
           RT+SAK ++ASDVRPLPVLE+TL YLL+LLDST+HPFEV+HDF+FDRTRS+RQDL MQNI
Sbjct: 69  RTISAKHMQASDVRPLPVLEDTLAYLLNLLDSTDHPFEVVHDFIFDRTRSIRQDLSMQNI 128

Query: 75  VNDKAINMFEKIVKFHVISHHKLRSSCSSSSISPLHYLNLEQLTKALTSLYNLYEANRSS 134
           V+DK+I M+EK+VKFHVISH KL+   SSS IS +HYLN+EQLTKALTSLYNLY+ANR S
Sbjct: 129 VDDKSIYMYEKMVKFHVISHLKLQRCRSSSDISSVHYLNMEQLTKALTSLYNLYDANRDS 188

Query: 135 KPIHEKEAEFRSFYVLLHLDSNGQPVGESLSLWFRHVPSPIIKSKEMWFARQALRYFQMG 194
             ++  EAEFRS YVLLHLDSN QP+GESLSLWFR V  PII+SKEM FAR  LR++QMG
Sbjct: 189 GTVYGNEAEFRSLYVLLHLDSNTQPMGESLSLWFRFVLHPIIRSKEMCFARSVLRFYQMG 248

Query: 195 NYRRFLSTVAAEASYLQYCIIEPYIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEES 254
           NY RF ST++AEASYLQYCI+E YI++VR+L+L  I+N  YKLHPYPL HLSK+L M+ES
Sbjct: 249 NYMRFFSTISAEASYLQYCILERYINKVRALSLSYINNAGYKLHPYPLVHLSKLLKMKES 308

Query: 255 DVELFCNAYGLQTCIDEVGNKLLPTKQTTFCRPKGGLQNYSFLGFQQL 302
           D+E+ CNA GL+TC D++GNKLLPTKQTTFC PK G Q+Y F G +Q 
Sbjct: 309 DLEVLCNACGLETCADDMGNKLLPTKQTTFCCPKEGFQSYIFTGLEQF 356

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|255569219\|ref\|XP_002525578.1\| leng8 protein, putative [Ricinus communis] gi\|223535157\|gb\|EEF36837.1\| leng8 protein, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|357515593\|ref\|XP_003628085.1\| 80 kDa MCM3-associated protein [Medicago truncatula] gi\|355522107\|gb\|AET02561.1\| 80 kDa MCM3-associated protein [Medicago truncatula]	Back alignment and taxonomy information

>gi\|388497576\|gb\|AFK36854.1\| unknown [Medicago truncatula]	Back alignment and taxonomy information

>gi\|296084674\|emb\|CBI25811.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|225449759\|ref\|XP_002269431.1\| PREDICTED: SAC3 family protein 1-like [Vitis vinifera]	Back alignment and taxonomy information

>gi\|298205116\|emb\|CBI40637.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|359494933\|ref\|XP_003634875.1\| PREDICTED: SAC3 family protein 1-like [Vitis vinifera]	Back alignment and taxonomy information

>gi\|359494990\|ref\|XP_003634893.1\| PREDICTED: LOW QUALITY PROTEIN: SAC3 family protein 1-like [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356548802\|ref\|XP_003542788.1\| PREDICTED: 80 kDa MCM3-associated protein-like [Glycine max]	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		308
TAIR\|locus:2096189		406	SAC3C "AT3G54380" [Arabidopsis	0.944	0.716	0.510	1.5e-76
TAIR\|locus:2082485		1697	SAC3B "AT3G06290" [Arabidopsis	0.844	0.153	0.293	2.8e-25
UNIPROTKB\|F1NVG3		1659	MCM3AP "Uncharacterized protei	0.642	0.119	0.319	2.3e-18
ZFIN\|ZDB-GENE-040715-1		2118	mcm3ap "MCM3 minichromosome ma	0.642	0.093	0.305	4.5e-17
MGI\|MGI:1930089		1971	Mcm3ap "minichromosome mainten	0.711	0.111	0.278	2.3e-16
RGD\|1306834		1908	Mcm3ap "minichromosome mainten	0.711	0.114	0.273	4.6e-16
UNIPROTKB\|E1BJE7		1979	MCM3AP "Uncharacterized protei	0.711	0.110	0.269	6.2e-16
UNIPROTKB\|I3LCF4		1990	MCM3AP "Uncharacterized protei	0.704	0.109	0.288	6.2e-16
UNIPROTKB\|O60318		1980	MCM3AP "80 kDa MCM3-associated	0.805	0.125	0.258	2.1e-15
POMBASE\|SPCC70.06		458	SPCC70.06 "nuclear export fact	0.467	0.314	0.343	8.2e-14

TAIR\|locus:2096189 SAC3C "AT3G54380" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 771 (276.5 bits), Expect = 1.5e-76, P = 1.5e-76
 Identities = 149/292 (51%), Positives = 200/292 (68%)

Query:    15 RTMSAKEVRASDVRPLPVXXXXXXXXXXXXXXXXHPFEVIHDFVFDRTRSVRQDLIMQNI 74
             RT+SA +V+ASDVRPLPV                HPFEV+HDF+FDRTRS+RQDL +QN+
Sbjct:   116 RTLSAADVQASDVRPLPVLEETLRYLLSLLDSKEHPFEVVHDFIFDRTRSIRQDLSIQNL 175

Query:    75 VNDKAINMFEKIVKFHVISHHKLRXXXXXXXXXPLHYLNLEQLTKALTSLYNLYEANRSS 134
              N++ I ++E++VKFHVISH +L+          +H+LN+EQL K LTSLYN+Y+ANR  
Sbjct:   176 ANERVIYLYEEMVKFHVISHERLQSCSGTSISS-MHHLNMEQLAKTLTSLYNIYDANRKP 234

Query:   135 KPIHEKEAEFRSFYVLLHLDSNGQPVGESLSLWFRHVPSPIIKSKEMWFARQALRYFQMG 194
               I+E EAEFRS YVLLHL+ +   +GE LSLWFR +   ++KSKE+ F R  LR ++MG
Sbjct:   235 DYIYENEAEFRSLYVLLHLNPSSGVMGEPLSLWFRKLTFALVKSKEICFVRNLLRLYRMG 294

Query:   195 NYRRFLSTVAAEASYLQYCIIEPYIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEES 254
             NY+ FLS  A+EA+YLQYCI E +I E+R +A+  I+N CYKL PYPL  LS+ L M+E 
Sbjct:   295 NYKNFLSRTASEATYLQYCISEHHIREMRLVAVQYINNVCYKLQPYPLLRLSQNLKMKEL 354

Query:   255 DVELFCNAYGLQTCIDEVGNKLLPTKQTTFCRPKGGLQNYSFLGFQQLGRQI 306
             DVE  C+  GL+TC D  G  +LP KQ+TF  P+   + Y  +G +++   I
Sbjct:   355 DVESLCHECGLETCTDPDGFTVLPVKQSTFRSPEDKFKVYDLIGIERIKMSI 406

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0048573 "photoperiodism, flowering" evidence=RCA

TAIR\|locus:2082485 SAC3B "AT3G06290" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

UNIPROTKB\|F1NVG3 MCM3AP "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-040715-1 mcm3ap "MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

MGI\|MGI:1930089 Mcm3ap "minichromosome maintenance deficient 3 (S. cerevisiae) associated protein" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

RGD\|1306834 Mcm3ap "minichromosome maintenance complex component 3 associated protein" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|E1BJE7 MCM3AP "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|I3LCF4 MCM3AP "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|O60318 MCM3AP "80 kDa MCM3-associated protein" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

POMBASE\|SPCC70.06 SPCC70.06 "nuclear export factor (predicted)" [Schizosaccharomyces pombe (taxid:4896)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

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		308
COG5079		646	COG5079, SAC3, Nuclear protein export factor [Intr	8e-30
pfam03399		155	pfam03399, SAC3_GANP, SAC3/GANP/Nin1/mts3/eIF-3 p2	5e-11

>gnl\|CDD\|227411 COG5079, SAC3, Nuclear protein export factor [Intracellular trafficking and secretion / Cell division and chromosome partitioning]	Back alignment and domain information

 Score =  118 bits (298), Expect = 8e-30
 Identities = 83/268 (30%), Positives = 119/268 (44%), Gaps = 33/268 (12%)

Query: 25  SDVRPLPVLEETLNYLLSLLDSTEHPFEVIHDFVFDRTRSVRQDLIMQNIVNDKAINMFE 84
           SDVRP  VL +T++YL+ L          +H FV DRTR+VRQD  +QN     A+   E
Sbjct: 129 SDVRPPEVLVKTIDYLVKLCAG--DQLIEMHRFVRDRTRAVRQDFTIQNEKGKDAVECHE 186

Query: 85  KIVKFHVISHHKLRSSCSSSSISPLHYLNLEQLTKALTSLYNLYEANRSSKPIHEKEAEF 144
           +I +FH++  H L      S         LEQL K+L SL  LY+  R+ K     EAEF
Sbjct: 187 RIARFHILFLHLLHDHPHFSK-----QQELEQLKKSLASLIELYDDGRAGKKECPNEAEF 241

Query: 145 RSFYVLLHLDSNGQP-VGESLSLWFRHVPSPIIKSKEMWFARQALRYFQMGNYR------ 197
           R++ +L  L   G P     +  W    P  I     +  A + ++  Q  N+R      
Sbjct: 242 RAYAILASL---GDPRYVAGIQGW----PGGIFCDLPVQIALKLMQLAQSNNFRLLGRRN 294

Query: 198 ---------RFLSTVAAEA-SYLQYCIIEPYIDEVRSLALCCIHNCCYKLH-PYPLGHLS 246
                    RF   + + +  YL  C++E +   +R  AL  +       H   P   LS
Sbjct: 295 TEACFNLYTRFFKLIQSPSVQYLMGCLLEKHNISIRGGALKAMEKEIESAHKNIPFVDLS 354

Query: 247 KVLMMEESD-VELFCNAYGLQTCIDEVG 273
            +L  EE    E FC  YGL+  I++  
Sbjct: 355 GILDFEEKGEGEEFCKYYGLEIRIEDSV 382

Length = 646

>gnl\|CDD\|217534 pfam03399, SAC3_GANP, SAC3/GANP/Nin1/mts3/eIF-3 p25 family	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		308
KOG1860		927	consensus Nuclear protein export factor [Intracell	100.0
COG5079		646	SAC3 Nuclear protein export factor [Intracellular	100.0
KOG1861		540	consensus Leucine permease transcriptional regulat	100.0
PF03399		204	SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; I	100.0
PF10075		143	PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro	99.24
KOG3151		260	consensus 26S proteasome regulatory complex, subun	98.39
KOG4414		197	consensus COP9 signalosome, subunit CSN8 [Posttran	97.9
PF01399		105	PCI: PCI domain; InterPro: IPR000717 A homology do	96.37
KOG3252		217	consensus Uncharacterized conserved protein [Funct	95.9
KOG1464		440	consensus COP9 signalosome, subunit CSN2 [Posttran	94.74
smart00088		88	PINT motif in proteasome subunits, Int-6, Nip-1 an	87.59
smart00753		88	PAM PCI/PINT associated module.	87.59
KOG0687		393	consensus 26S proteasome regulatory complex, subun	87.35
KOG2581		493	consensus 26S proteasome regulatory complex, subun	84.39

>KOG1860 consensus Nuclear protein export factor [Intracellular trafficking, secretion, and vesicular transport; Cell cycle control, cell division, chromosome partitioning]	Back alignment and domain information

Probab=100.00  E-value=8.5e-57  Score=450.81  Aligned_cols=259  Identities=34%  Similarity=0.555  Sum_probs=232.9

Q ss_pred             CCccccccccCCCCCC-CCCCCCCCCHHHHHHHHHHHHHH-HcCCCCCcchhhhhhhhhhhhhhhhhhhhhcCCchhHHH
Q 021722            5 AIHLQPLLLKRTMSAK-EVRASDVRPLPVLEETLNYLLSL-LDSTEHPFEVIHDFVFDRTRSVRQDLIMQNIVNDKAINM   82 (308)
Q Consensus         5 ~~~~~VK~Y~RsaA~~-~~~P~~vRp~~vL~kT~~yL~~~-~~~~~~~~~~~y~Fi~DRlRaIRQDl~vQ~i~~~~~v~v   82 (308)
                      +|.+|||+|.|+|||+ .|.|++||||+||.+||+||+.+ +...+.++..+|+|+|||+||||||+|+||+.+..||.+
T Consensus       140 ~~~~aVK~ysRPAAgke~pLPsdvRP~~VL~~T~dYLl~~v~~~~~~sl~~~y~FvwDRtRAVR~D~t~Q~~~d~~Av~l  219 (927)
T KOG1860|consen  140 SPSLAVKEYSRPAAGKERPLPSDVRPPPVLVKTVDYLLGKVLCDKDISLREMYDFVWDRTRAVRQDFTIQNYSDQEAVEL  219 (927)
T ss_pred             CHHHHHHHhcCcccCCCCCCccccCCHHHHHHHHHHHHHHhhccccccHHHHHHHHHHHHHHHHHHHHHhccCChHHHHH
Confidence            7899999999999998 45899999999999999999974 455666899999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhhhhcCCCCCCChhhhhcHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHhhcCCCCchhh
Q 021722           83 FEKIVKFHVISHHKLRSSCSSSSISPLHYLNLEQLTKALTSLYNLYEANRSSKPIHEKEAEFRSFYVLLHLDSNGQPVGE  162 (308)
Q Consensus        83 lE~~~Rf~i~~~~~l~~~~~~~~f~~~~~~n~~ql~~cl~~L~~lY~~~~~~~~~~~ne~Ef~~Y~iL~~l~~~~~~~~~  162 (308)
                      +|+|+||||++.|+||+++.  .|+  .++|+|||++|+.+|.++|++++++|+.|+||+||+||++|++|++++.  .+
T Consensus       220 lE~i~RfhI~~~h~Lce~~~--~Fd--a~~nlEQL~K~l~sL~elYdD~r~~g~~cpnE~EFR~Y~vLl~Lgd~~~--~~  293 (927)
T KOG1860|consen  220 LERIARFHILFRHRLCEEPE--QFD--AQQNLEQLQKCLQSLGELYDDLRKGGIPCPNEPEFRGYYVLLSLGDPQV--VR  293 (927)
T ss_pred             HHHHHHHHHHHHHHhccCcc--cCC--hhHHHHHHHHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHhcCCchH--HH
Confidence            99999999999999999874  675  7899999999999999999999999999999999999999999999862  22


Q ss_pred             hHHHHhhhCChhhhcCHhHHHHHHHHHHHHhCCHHHHHH------------------HHHh-cccHHHHHHHhHhHHHHH
Q 021722          163 SLSLWFRHVPSPIIKSKEMWFARQALRYFQMGNYRRFLS------------------TVAA-EASYLQYCIIEPYIDEVR  223 (308)
Q Consensus       163 ~l~~~l~~l~~~i~~s~~v~~Al~v~~a~~~~Ny~rfFk------------------Ll~~-~~~~L~~cl~~~~~~~vR  223 (308)
                          -++.+|++++++++|++|+.+++++++|||.+||+                  +..+ ..++|+.|+++.||+.+|
T Consensus       294 ----~iq~~~~evr~~~~Vk~al~~~~a~~~nn~~~~~r~~~~~t~a~~~l~~~~~~l~q~p~~~~L~~~v~~~~f~~ir  369 (927)
T KOG1860|consen  294 ----DIQAWPDEVRQDSEVKLALCLRRAFQSNNFRRFFRLSSLRTEALQNLYTRFFKLMQSPALPYLMGCVLELFFPDIR  369 (927)
T ss_pred             ----HHHhcCcccccchhHHHHHHHHHHhccCCeeeeeeccchhHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHH
Confidence                23467999999999999999999999999988864                  4332 578899999999999999


Q ss_pred             HHHHHHHHhhhcC--CCCcCHHHHHHHhcCCc-hHHHHHHHHhCCeecccCCCc
Q 021722          224 SLALCCIHNCCYK--LHPYPLGHLSKVLMMEE-SDVELFCNAYGLQTCIDEVGN  274 (308)
Q Consensus       224 ~~aL~~i~~a~yk--~~~ipl~~L~~~L~f~~-~e~~~f~~~~Gl~~~~d~~g~  274 (308)
                      ..|++.|.+ +|+  ..+||+.++..+|+|+. ++...+|..|||+++.|+.+.
T Consensus       370 ~~al~~~~~-~~~~~~~~vp~~~l~~~l~f~~~e~~~~~~~~y~Leis~~~~~~  422 (927)
T KOG1860|consen  370 WAALRAMSH-AYNSKHVPVPLGKLDRILLFDGEEELKVVCNYYGLEISVDDKIV  422 (927)
T ss_pred             HHHHHHHHH-HHhccCCCcchhHHHHHHhcCChhhhHhhhhheeeEeecccccc
Confidence            999999998 573  45899999999999995 779999999999997665444

>COG5079 SAC3 Nuclear protein export factor [Intracellular trafficking and secretion / Cell division and chromosome partitioning]	Back alignment and domain information

>KOG1861 consensus Leucine permease transcriptional regulator [Transcription]	Back alignment and domain information

>PF03399 SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; InterPro: IPR005062 This large family includes diverse proteins involved in large complexes [, , ]	Back alignment and domain information

>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8	Back alignment and domain information

>KOG3151 consensus 26S proteasome regulatory complex, subunit RPN12/PSMD8 [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG4414 consensus COP9 signalosome, subunit CSN8 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]	Back alignment and domain information

>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins	Back alignment and domain information

>KOG3252 consensus Uncharacterized conserved protein [Function unknown]	Back alignment and domain information

>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]	Back alignment and domain information

>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15	Back alignment and domain information

>smart00753 PAM PCI/PINT associated module	Back alignment and domain information

>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG2581 consensus 26S proteasome regulatory complex, subunit RPN3/PSMD3 [Posttranslational modification, protein turnover, chaperones]	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		308
3t5v_A		316	Sac3:thp1:sem1 Complex Length = 316		5e-10

>pdb|3T5V|A Chain A, Sac3:thp1:sem1 Complex Length = 316

Back alignment and structure

Iteration: 1

Score = 61.6 bits (148), Expect = 5e-10, Method: Compositional matrix adjust. Identities = 59/226 (26%), Positives = 104/226 (46%), Gaps = 24/226 (10%) Query: 57 FVFDRTRSVRQDLIMQNIVNDKAINMFEKIVKFHVISHHKLRXXXXXXXXXPLHYLNLEQ 116 F++DR RS+RQD QN +A++ E+IV+ H++ H + LEQ Sbjct: 35 FLWDRMRSIRQDFTYQNYSGPEAVDCNERIVRIHLLILHIMVKSNVEFSLQQ----ELEQ 90 Query: 117 LTKALTSLYNLYEANRSSKPIHEKEAEFRSFYVLLHL-----DSNGQPVGE--------S 163 L K+L +L +Y+ RSS EAEFR++ +L + D N Q + + Sbjct: 91 LHKSLITLSEIYDDVRSSGGTCPNEAEFRAYALLSKIRDPQYDENIQRLPKHIFQDKLVQ 150 Query: 164 LSLWFRHVPSPIIKSKEMWFARQALRYFQMGNYRRFLSTVAAEA-SYLQYCIIEPYIDEV 222 ++L FR V S ++ + + F Y RF + + + L ++ ++ ++ Sbjct: 151 MALCFRRVISNSAYTERGFVKTENCLNF----YARFFQLMQSPSLPLLMGFFLQMHLTDI 206 Query: 223 RSLALCCIHNCCYKLH-PYPLGHLSKVLMMEE-SDVELFCNAYGLQ 266 R AL + + K H P P +L +L+ ++ FCN Y ++ Sbjct: 207 RFYALRALSHTLNKKHKPIPFIYLENMLLFNNRQEIIEFCNYYSIE 252

PyMOL of 3t5v

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		308
3t5v_A		316	Nuclear mRNA export protein SAC3; PCI, mRNA nuclea	2e-48
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-06
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05

>3t5v_A Nuclear mRNA export protein SAC3; PCI, mRNA nuclear export, mRNA, nuclear, transcription; 2.90A {Saccharomyces cerevisiae} Length = 316	Back alignment and structure

 Score =  163 bits (413), Expect = 2e-48
 Identities = 68/283 (24%), Positives = 118/283 (41%), Gaps = 31/283 (10%)

Query: 24  ASDVRPLPVLEETLNYLLSLLDSTEHPFEVIHDFVFDRTRSVRQDLIMQNIVNDKAINMF 83
            SDVRP  +L +TL+Y++  L +T         F++DR RS+RQD   QN    +A++  
Sbjct: 5   PSDVRPPHILVKTLDYIVDNLLTT---LPESEGFLWDRMRSIRQDFTYQNYSGPEAVDCN 61

Query: 84  EKIVKFHVISHHKLRSSCSSSSISPLHYLNLEQLTKALTSLYNLYEANRSSKPIHEKEAE 143
           E+IV+ H++  H +  S    S        LEQL K+L +L  +Y+  RSS      EAE
Sbjct: 62  ERIVRIHLLILHIMVKSNVEFS----LQQELEQLHKSLITLSEIYDDVRSSGGTCPNEAE 117

Query: 144 FRSFYVLLHLDSNGQPVGESLSLWFRHVPSPIIKSKEMWFARQALRYFQ----------- 192
           FR++ +L  +               + +P  I + K +  A    R              
Sbjct: 118 FRAYALLSKIRDP------QYDENIQRLPKHIFQDKLVQMALCFRRVISNSAYTERGFVK 171

Query: 193 ----MGNYRRFLSTV-AAEASYLQYCIIEPYIDEVRSLALCCIHNCCYKLH-PYPLGHLS 246
               +  Y RF   + +     L    ++ ++ ++R  AL  + +   K H P P  +L 
Sbjct: 172 TENCLNFYARFFQLMQSPSLPLLMGFFLQMHLTDIRFYALRALSHTLNKKHKPIPFIYLE 231

Query: 247 KVLMME-ESDVELFCNAYGLQTCIDEVGNKLLPTKQTTFCRPK 288
            +L+     ++  FCN Y ++    +  +       +      
Sbjct: 232 NMLLFNNRQEIIEFCNYYSIEIINGDAADLKTLQHYSHKLSET 274

PyMOL of 3t5v

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

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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		308
3t5v_A		316	Nuclear mRNA export protein SAC3; PCI, mRNA nuclea	100.0
4b0z_A		229	RPN12, 26S proteasome regulatory subunit RPN12; pr	99.96
4b4t_T		274	26S proteasome regulatory subunit RPN12; hydrolase	99.95
1rz4_A		226	Eukaryotic translation initiation factor 3 subuni;	98.91
3txn_A		394	26S proteasome regulatory complex subunit P42B; PC	96.29
4b4t_O		393	26S proteasome regulatory subunit RPN9; hydrolase,	93.54
4b4t_R		429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	93.33
3t5x_A		203	PCI domain-containing protein 2; PCI, mRNA nuclear	93.25
3chm_A		169	COP9 signalosome complex subunit 7; heat/ARM repea	87.19
4b4t_Q		434	26S proteasome regulatory subunit RPN6; hydrolase,	85.98
3t5v_B		455	Nuclear mRNA export protein THP1; PCI, mRNA nuclea	83.65

>3t5v_A Nuclear mRNA export protein SAC3; PCI, mRNA nuclear export, mRNA, nuclear, transcription; 2.90A {Saccharomyces cerevisiae}	Back alignment and structure

Probab=100.00  E-value=6.4e-64  Score=466.48  Aligned_cols=257  Identities=26%  Similarity=0.389  Sum_probs=220.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHcCCCCCcchhhhhhhhhhhhhhhhhhhhhcCCchhHHHHHHHHHHHHHHHhhhhhc
Q 021722           21 EVRASDVRPLPVLEETLNYLLSLLDSTEHPFEVIHDFVFDRTRSVRQDLIMQNIVNDKAINMFEKIVKFHVISHHKLRSS  100 (308)
Q Consensus        21 ~~~P~~vRp~~vL~kT~~yL~~~~~~~~~~~~~~y~Fi~DRlRaIRQDl~vQ~i~~~~~v~vlE~~~Rf~i~~~~~l~~~  100 (308)
                      +|+|++||||+||++||+||++++...   +..+|+|+|||||||||||||||+.++++|.|||+|+||||++.|+||..
T Consensus         2 ~P~P~~vRP~~vL~~Tl~yL~~~~~~~---~~~~y~fi~Dr~RsIRqDltvQ~i~~~~~v~v~E~~aRf~i~~~~~L~~~   78 (316)
T 3t5v_A            2 SPLPSDVRPPHILVKTLDYIVDNLLTT---LPESEGFLWDRMRSIRQDFTYQNYSGPEAVDCNERIVRIHLLILHIMVKS   78 (316)
T ss_dssp             ----CCCCCHHHHHHHHHHHHHHTGGG---TTTCHHHHHHHHHHHHHHHHHTTCCSHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             CCChhhcCCHHHHHHHHHHHHHHHHhc---chhhhHHHHhhhhhhccCceeeccCCchHHHHHHHHHHHHHHHHHHHhhC
Confidence            578999999999999999999988653   44689999999999999999999999999999999999999999999976


Q ss_pred             CCCCCCChhhhhcHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHhhcCCCCchhhhHHHHhhhCChhhhcCHh
Q 021722          101 CSSSSISPLHYLNLEQLTKALTSLYNLYEANRSSKPIHEKEAEFRSFYVLLHLDSNGQPVGESLSLWFRHVPSPIIKSKE  180 (308)
Q Consensus       101 ~~~~~f~~~~~~n~~ql~~cl~~L~~lY~~~~~~~~~~~ne~Ef~~Y~iL~~l~~~~~~~~~~l~~~l~~l~~~i~~s~~  180 (308)
                      +.  +|+  +++|.+|+++||++|+++|++.++.|+.++||+||+||+||+++++.+      +...+..+|++++++|.
T Consensus        79 ~~--~f~--~~~~~eQl~~~L~sL~~lY~d~~~~~~~~~ne~EF~aY~lL~~l~~~~------~~~~l~~Lp~~i~~~p~  148 (316)
T 3t5v_A           79 NV--EFS--LQQELEQLHKSLITLSEIYDDVRSSGGTCPNEAEFRAYALLSKIRDPQ------YDENIQRLPKHIFQDKL  148 (316)
T ss_dssp             CC--CCC--HHHHHHHHHHHHHHHHHHHHHHHHTTCCCTTHHHHHHHHHHHSTTCTH------HHHHHTTSCHHHHTSHH
T ss_pred             CC--ccc--hHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHhccch------HHHHHHhCCHHHhcCHH
Confidence            43  564  789999999999999999999988788899999999999999998753      22356789999999999


Q ss_pred             HHHHHHHHHHHH---------------hCCHHHHHHHHHh-cccHHHHHHHhHhHHHHHHHHHHHHHhhhcC--CCCcCH
Q 021722          181 MWFARQALRYFQ---------------MGNYRRFLSTVAA-EASYLQYCIIEPYIDEVRSLALCCIHNCCYK--LHPYPL  242 (308)
Q Consensus       181 v~~Al~v~~a~~---------------~~Ny~rfFkLl~~-~~~~L~~cl~~~~~~~vR~~aL~~i~~a~yk--~~~ipl  242 (308)
                      ||+|+++.+|+.               .|||++||+++++ ++|||++|+|+.||+++|..||++|++ +|+  ..++|+
T Consensus       149 Vq~AL~l~~a~~~~~~~e~~~~~~~~~~gNY~rFFrL~~~~~~pyL~aclle~~~~~vR~~AL~~i~k-ay~~k~~~~pl  227 (316)
T 3t5v_A          149 VQMALCFRRVISNSAYTERGFVKTENCLNFYARFFQLMQSPSLPLLMGFFLQMHLTDIRFYALRALSH-TLNKKHKPIPF  227 (316)
T ss_dssp             HHHHHHHHHHHCCTTCCCTTCCCCSSCCCCHHHHHHHHTCTTSCHHHHHHHGGGHHHHHHHHHHHHHH-HSCTTCCCEEH
T ss_pred             HHHHHHHHHHHHhcccccccccccccccchHHHHHHHHhccCCChHHHHHHHHHHHHHHHHHHHHHHH-HhccCCCCcCH
Confidence            999999999986               4899999998753 389999999999999999999999999 574  247999


Q ss_pred             HHHHHHhcCCc-hHHHHHHHHhCCeecccCCCccc-ccCCCCcccCCCCCCc
Q 021722          243 GHLSKVLMMEE-SDVELFCNAYGLQTCIDEVGNKL-LPTKQTTFCRPKGGLQ  292 (308)
Q Consensus       243 ~~L~~~L~f~~-~e~~~f~~~~Gl~~~~d~~g~~~-l~~k~~~f~~~~~~~~  292 (308)
                      ++|+++|+|++ +|+.+||++|||+++++ +|... ..+.++.|.+++..+.
T Consensus       228 ~~L~~~L~Fds~ee~~~F~~~~gl~~~~~-~~~~~~~~~~~~~~~~~~~p~~  278 (316)
T 3t5v_A          228 IYLENMLLFNNRQEIIEFCNYYSIEIING-DAADLKTLQHYSHKLSETQPLK  278 (316)
T ss_dssp             HHHHHHTTCSSHHHHHHHHHHTTCCEETT-TEECGGGCCCSSSSCTTSCCCC
T ss_pred             HHHHHHhCCCCHHHHHHHHHHCCCeEeCC-CCchHHhhcchhccccccCCCc
Confidence            99999999985 78999999999999753 34332 2456677776665444

PyMOL of 3t5v

>4b0z_A RPN12, 26S proteasome regulatory subunit RPN12; protein binding, proteasome ubitquitin; HET: SGM GOL; 1.58A {Schizosaccharomyces pombe}	Back alignment and structure

>4b4t_T 26S proteasome regulatory subunit RPN12; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}	Back alignment and structure

>1rz4_A Eukaryotic translation initiation factor 3 subuni; heat analogous motif, winged-helix, biosynthetic protein; 2.10A {Homo sapiens} SCOP: a.4.5.53 a.118.1.18	Back alignment and structure

>3txn_A 26S proteasome regulatory complex subunit P42B; PCI domain, alpha solenoid, regulatory PART LID, hydrolase, protein binding; 2.50A {Drosophila melanogaster} PDB: 3txm_A	Back alignment and structure

>4b4t_O 26S proteasome regulatory subunit RPN9; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}	Back alignment and structure

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}	Back alignment and structure

>3t5x_A PCI domain-containing protein 2; PCI, mRNA nuclear export, transcription; 2.12A {Homo sapiens}	Back alignment and structure

>3chm_A COP9 signalosome complex subunit 7; heat/ARM repeats, winged helix motif, developmental protein, phosphoprotein; 1.50A {Arabidopsis thaliana}	Back alignment and structure

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}	Back alignment and structure

>3t5v_B Nuclear mRNA export protein THP1; PCI, mRNA nuclear export, mRNA, nuclear, transcription; 2.90A {Saccharomyces cerevisiae}	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		308
d1rz4a1		85	Eukaryotic translation initiation factor 3 subunit	96.72
d1ufma_		84	COP9 signalosome complex subunit 4, GSN4 {Mouse (M	82.2

>d1rz4a1 a.4.5.53 (A:132-216) Eukaryotic translation initiation factor 3 subunit 12, eIF3k, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Eukaryotic translation initiation factor 3 subunit 12, eIF3k, C-terminal domain
domain: Eukaryotic translation initiation factor 3 subunit 12, eIF3k, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.72  E-value=0.0019  Score=46.14  Aligned_cols=66  Identities=21%  Similarity=0.294  Sum_probs=50.6

Q ss_pred             hHHHHHHHHHHHHHhhhcCCCCcCHHHHHHHhcCC-chHHHHHHHHhCCeecccCCCcccccCCCCcccCCCC
Q 021722          218 YIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMME-ESDVELFCNAYGLQTCIDEVGNKLLPTKQTTFCRPKG  289 (308)
Q Consensus       218 ~~~~vR~~aL~~i~~a~yk~~~ipl~~L~~~L~f~-~~e~~~f~~~~Gl~~~~d~~g~~~l~~k~~~f~~~~~  289 (308)
                      |-..+|..+...+.. +|.  .||.+.|+++||.. +.+...+++.+||+..  ++|.+ ++..+-...-|+.
T Consensus         3 FedsIR~~i~~vv~i-Tyq--~I~~~~L~e~LG~~~d~~L~~~i~~~gW~~~--~~g~v-~v~nqe~~iK~kn   69 (85)
T d1rz4a1           3 FEDSVRKFICHVVGI-TYQ--HIDRWLLAEMLGDLSDSQLKVWMSKYGWSAD--ESGQI-FICSQEESIKPKN   69 (85)
T ss_dssp             HHHHHHHHHHHHHHH-HCS--EECHHHHHHHTTSCCHHHHHHHHHHHTCEEC--C--CE-ECCCHHHHTSCCC
T ss_pred             HHHHHHHHHHhheee-eee--EEcHHHHHHHhCCCCHHHHHHHHHHcCCEEc--CCCEE-EecChhhhcCccc
Confidence            456799999999987 586  79999999999976 5779999999999983  34555 4556655665543

PyMOL of d1rz4a1

>d1ufma_ a.4.5.47 (A:) COP9 signalosome complex subunit 4, GSN4 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure