Citrus Sinensis ID: 025331

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----

MEKGNEKVMSLVQLPQKAIKDVQFKLKELENGYKSWLAKQPLPVEAAIVTATTAINGAAIGAFLGVMTQDLTSSLPTPPPQSSLNPDAVAPFQQVQAVAGGPLVQARNFAVITGVNAGISCVMKRLRGKEDLQSSVVAAFGSGAAFSLVSGMGGANPAVNAFTSGLLFAIFQGCSFKIGEMWQSTQRPTADDVYYARTRGMLDKLGLQNYTKNFKRGLLTDSTLPLLTDSALRDVRIPPGPRLLILDHIQSFCL

cccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHHccccHHcHHHHHHHHHHccEEEEEEEEcccccHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHcHHHHHHHHHcccccccccccccccccccccccccccHHHHHHHHHHcc

cccccccEEEEccccccHHHHHHHHHHHHHHHHHHHHHcccccEEEEEEEHHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHEHcccccccHHHHHHHHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHcccHHHHHHHHcccccccccccccHHHHHHccccccHHHHHHHHHHHHcc

MEKGNEKVMSLVQLPQKAIKDVQFKLKELENGYKSwlakqplpvEAAIVTATTAINGAAIGAFLGVMtqdltsslptpppqsslnpdavapfqqvqavaggplvqARNFAVITGVNAGISCVMKRLRGKEDLQSSVVAAFGSGAAFSLvsgmgganpavnAFTSGLLFAIFQGCSfkigemwqstqrptaddVYYARTRgmldklglqnytknfkrglltdstlplltdsalrdvrippgprllILDHIQSFCL

MEKGNEKVMSLVQLPQKAIKDVQFKLKELENGYKSWLAKQPLPVEaaivtattaingaaigaFLGVMtqdltsslptpppqsslNPDavapfqqvqavaGGPLVQARNFAVITGVNAGISCVMKRLRGKEDLQssvvaafgsgaafslvsgMGGANPAVNAFTSGLLFAIFQGCSFKIGEMWQSTQRPTADDVYYARTRGMLDKLGLQNYTKNFKRGlltdstlplltdsalRDVRIPPGPRLLILDHIQSFCL

************QLPQKAIKDVQFKLKELENGYKSWLAKQPLPVEAAIVTATTAINGAAIGAFLGVMTQ**********************FQQVQAVAGGPLVQARNFAVITGVNAGISCVMKRLRGKEDLQSSVVAAFGSGAAFSLVSGMGGANPAVNAFTSGLLFAIFQGCSFKIGEMWQSTQRPTADDVYYARTRGMLDKLGLQNYTKNFKRGLLTDSTLPLLTDSALRDVRIPPGPRLLILDHIQSF**

**********************************SWLAKQPLPVEAAIVTATTAINGAAIGAFLGVMTQDLT********************************QARNFAVITGVNAGISCVMKRLRGKEDLQSSVVAAFGSGAAFSLVSGMGG*NPAVNAFTSGLLFAIFQGCSFK****************YYARTRGMLDKLGLQNYTKNFKRGLLTDSTLPLLTDSALRDVRIPPGPRLLILDHIQSFCL

********MSLVQLPQKAIKDVQFKLKELENGYKSWLAKQPLPVEAAIVTATTAINGAAIGAFLGVMTQDLT************NPDAVAPFQQVQAVAGGPLVQARNFAVITGVNAGISCVMKRLRGKEDLQSSVVAAFGSGAAFSLVSGMGGANPAVNAFTSGLLFAIFQGCSFKIGEMWQSTQRPTADDVYYARTRGMLDKLGLQNYTKNFKRGLLTDSTLPLLTDSALRDVRIPPGPRLLILDHIQSFCL

******KVMSLVQLPQKAIKDVQFKLKELENGYKSWLAKQPLPVEAAIVTATTAINGAAIGAFLGVMTQDLTSSLPTPPPQSSLNPDAVAPFQQVQAVAGGPLVQARNFAVITGVNAGISCVMKRLRGKEDLQSSVVAAFGSGAAFSLVSGMGGANPAVNAFTSGLLFAIFQGCSFKIGEMWQSTQRPTADDVYYARTRGMLDKLGLQNYTKNFKRGLLTDSTLPLLTDSALRDVRIPPGPRLLILDHIQSFCL

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

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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

No hits with e-value below 0.001 by BLAST

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		254
224118566		262	predicted protein [Populus trichocarpa]	0.913	0.885	0.714	3e-93
255557172		261	protein translocase, putative [Ricinus c	0.913	0.888	0.710	4e-92
224134921		260	predicted protein [Populus trichocarpa]	0.964	0.942	0.68	2e-91
356509122		260	PREDICTED: uncharacterized protein LOC10	0.972	0.95	0.656	3e-91
356516192		260	PREDICTED: uncharacterized protein LOC10	0.972	0.95	0.648	1e-90
225455153		254	PREDICTED: uncharacterized protein LOC10	0.956	0.956	0.684	8e-88
449456433		253	PREDICTED: uncharacterized protein LOC10	0.956	0.960	0.686	1e-84
449497426		253	PREDICTED: LOW QUALITY PROTEIN: uncharac	0.956	0.960	0.686	2e-84
357464317		263	SAM domain family protein [Medicago trun	0.972	0.939	0.640	2e-83
226494803		270	SAM domain family protein [Zea mays] gi\|	0.877	0.825	0.606	8e-76

>gi\|224118566\|ref\|XP_002317852.1\| predicted protein [Populus trichocarpa] gi\|222858525\|gb\|EEE96072.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

 Score =  347 bits (889), Expect = 3e-93,   Method: Compositional matrix adjust.
 Identities = 168/235 (71%), Positives = 198/235 (84%), Gaps = 3/235 (1%)

Query: 16  QKAIKDVQFKLKELENGYKSWLAKQPLPVEAAIVTATTAINGAAIGAFLGVMTQDLTSSL 75
           Q  IK VQFK KELE+G+KSWL+KQ LPVEAA+VTAT  + GAAIGA +G +T D++SS+
Sbjct: 19  QDPIKLVQFKFKELEDGFKSWLSKQSLPVEAAVVTATGGVQGAAIGAIMGTLTPDISSSM 78

Query: 76  PTPPPQSSLNPDAVAPFQQVQAVAGGPLVQARNFAVITGVNAGISCVMKRLRGKEDLQSS 135
           PTPPPQ+SLNP A+A  +Q QA+AGGPL+QARNFAV+TG NAGI+C+MKRLRGKED+QSS
Sbjct: 79  PTPPPQASLNPQAMASLKQAQALAGGPLIQARNFAVMTGTNAGIACIMKRLRGKEDVQSS 138

Query: 136 VVAAFGSGAAFSLVSGMGGANPAVNAFTSGLLFAIFQGCSFKIGEMWQSTQRPTADDVYY 195
           +VAAFGSGA FSLVSGMGG N A NA TSGL FA+ QG  FK+GE      +P  +D+ Y
Sbjct: 139 MVAAFGSGAMFSLVSGMGGPNLATNAITSGLFFALVQGGLFKLGE---KLSKPPVEDLCY 195

Query: 196 ARTRGMLDKLGLQNYTKNFKRGLLTDSTLPLLTDSALRDVRIPPGPRLLILDHIQ 250
           ARTR ML+ LGLQNY KNFK+GLLTD+TLPLLTDSALRDVRIPPGPRLLILDH++
Sbjct: 196 ARTRSMLNNLGLQNYEKNFKKGLLTDNTLPLLTDSALRDVRIPPGPRLLILDHLR 250

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|255557172\|ref\|XP_002519617.1\| protein translocase, putative [Ricinus communis] gi\|223541207\|gb\|EEF42762.1\| protein translocase, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|224134921\|ref\|XP_002321938.1\| predicted protein [Populus trichocarpa] gi\|222868934\|gb\|EEF06065.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|356509122\|ref\|XP_003523301.1\| PREDICTED: uncharacterized protein LOC100775460 [Glycine max]	Back alignment and taxonomy information

>gi\|356516192\|ref\|XP_003526780.1\| PREDICTED: uncharacterized protein LOC100813121 [Glycine max]	Back alignment and taxonomy information

>gi\|225455153\|ref\|XP_002267996.1\| PREDICTED: uncharacterized protein LOC100267522 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|449456433\|ref\|XP_004145954.1\| PREDICTED: uncharacterized protein LOC101208652 [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449497426\|ref\|XP_004160398.1\| PREDICTED: LOW QUALITY PROTEIN: uncharacterized LOC101208652 [Cucumis sativus]	Back alignment and taxonomy information

>gi\|357464317\|ref\|XP_003602440.1\| SAM domain family protein [Medicago truncatula] gi\|355491488\|gb\|AES72691.1\| SAM domain family protein [Medicago truncatula]	Back alignment and taxonomy information

>gi\|226494803\|ref\|NP_001146865.1\| SAM domain family protein [Zea mays] gi\|195604410\|gb\|ACG24035.1\| SAM domain family protein [Zea mays] gi\|413922575\|gb\|AFW62507.1\| SAM domain protein [Zea mays]	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		254
TAIR\|locus:2153959		259	AT5G24650 [Arabidopsis thalian	0.909	0.891	0.419	4e-42
TAIR\|locus:2114723		261	AT3G49560 "AT3G49560" [Arabido	0.901	0.877	0.369	5.7e-36

TAIR\|locus:2153959 AT5G24650 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 446 (162.1 bits), Expect = 4.0e-42, P = 4.0e-42
 Identities = 102/243 (41%), Positives = 124/243 (51%)

Query:     8 VMSLVQLPQKAIKDVQFKLKELENGYKSWLAKQPLPVEXXXXXXXXXXXXXXXXXFLGVM 67
             VMSL++  Q  I+  Q K KE+E G+KSWL+KQ LPVE                  +G +
Sbjct:    16 VMSLMKDQQNPIQQFQVKFKEIETGFKSWLSKQKLPVEAAVVTAMGGVQGAFIGGLMGTL 75

Query:    68 XXXXXXXXXXXXXXXXXNPDXXXXXXXXXXXXGGPLVQARNFAVITGVNAGISCVMKRLR 127
                              +P             GGPLVQARNFA ITGVNAGI+CVMKR+R
Sbjct:    76 SPEMPQAGI--------DPQAMASLKQTQALVGGPLVQARNFAAITGVNAGIACVMKRIR 127

Query:   128 GKEDLQXXXXXXXXXXXXXXXXXXMGGANPAVNAFTSGLLFAIFQGCSFKIGEMWQSTQR 187
             GKEDL+                   G     +NA T+   FA+FQG  FK+GE +    +
Sbjct:   128 GKEDLESAVVAAFGSGVAYSLVSA-GLQGQPMNAITTAAGFAVFQGVFFKLGERFS---K 183

Query:   188 PTADDVYYARTRGMLDKLGLQNYTKNFKRGXXXXXXXXXXXXXXXRDVRIPPGPRLLILD 247
             P+ +D YY R R ML KLGL+ Y KNFK+G               RDV IPPGPRLLILD
Sbjct:   184 PSVEDPYYTRGRSMLLKLGLEKYEKNFKKGLLADPTLPLLTDSALRDVSIPPGPRLLILD 243

Query:   248 HIQ 250
             HIQ
Sbjct:   244 HIQ 246

GO:0005739 "mitochondrion" evidence=ISM

GO:0005744 "mitochondrial inner membrane presequence translocase complex" evidence=ISS

GO:0015031 "protein transport" evidence=ISS

GO:0015450 "P-P-bond-hydrolysis-driven protein transmembrane transporter activity" evidence=ISS

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0005773 "vacuole" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0005774 "vacuolar membrane" evidence=IDA

GO:0009507 "chloroplast" evidence=IDA

GO:0009536 "plastid" evidence=IDA

TAIR\|locus:2114723 AT3G49560 "AT3G49560" [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

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	grail3.0031027502	hypothetical protein (263 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		254
pfam02466		128	pfam02466, Tim17, Tim17/Tim22/Tim23/Pmp24 family	3e-14
cd09487		56	cd09487, SAM_superfamily, SAM (Sterile alpha motif	1e-10
pfam00536		62	pfam00536, SAM_1, SAM domain (Sterile alpha motif)	1e-07
cd09585		69	cd09585, SAM_DDHD2, SAM domain of DDHD2	2e-06
PTZ00236		164	PTZ00236, PTZ00236, mitochondrial import inner mem	5e-06
TIGR00980		170	TIGR00980, 3a0801so1tim17, mitochondrial import in	3e-05
smart00454		68	smart00454, SAM, Sterile alpha motif	4e-05
TIGR00983		149	TIGR00983, 3a0801s02tim23, mitochondrial import in	2e-04
pfam07647		66	pfam07647, SAM_2, SAM domain (Sterile alpha motif)	6e-04
cd09508		70	cd09508, SAM_HD, SAM domain of HD-phosphohydrolase	0.001
cd09516		69	cd09516, SAM_sec23ip-like, SAM domain of sec23ip-l	0.002
COG5596		191	COG5596, TIM22, Mitochondrial import inner membran	0.003

>gnl\|CDD\|217053 pfam02466, Tim17, Tim17/Tim22/Tim23/Pmp24 family	Back alignment and domain information

 Score = 67.3 bits (165), Expect = 3e-14
 Identities = 38/129 (29%), Positives = 53/129 (41%), Gaps = 10/129 (7%)

Query: 43  PVEAAIVTATTAINGAAIGAFLGVMTQDLTSSLPTPPPQSSLNPDAVAPFQQVQAVAGGP 102
           P      T    + GA  G F G     L ++L + P +  LN         + A     
Sbjct: 3   PERIVYDTGGGFLMGAVYGGFFGAP-HGLVNALRSGPLKLRLN-------GVLNATGRRG 54

Query: 103 LVQARNFAVITGVNAGISCVMKRLRGKEDLQSSVVAAFGSGAAFSLVSGMGGANPAVNAF 162
                NFAV  G+ +GI C +++LRGKED  +S++A   +GA   L  G   A  AV A 
Sbjct: 55  PSHGNNFAVFGGLYSGIECALEKLRGKEDPWNSIIAGALTGAVLGLRGGPKAA--AVGAA 112

Query: 163 TSGLLFAIF 171
                 A  
Sbjct: 113 VGAAFSAAI 121

The pre-protein translocase of the mitochondrial outer membrane (Tom) allows the import of pre-proteins from the cytoplasm. Tom forms a complex with a number of proteins, including Tim17. Tim17 and Tim23 are thought to form the translocation channel of the inner membrane. This family includes Tim17, Tim22 and Tim23. This family also includes Pmp24 a peroxisomal protein. The involvement of this domain in the targeting of PMP24 remains to be proved. PMP24 was known as Pmp27 in. Length = 128

>gnl\|CDD\|188886 cd09487, SAM_superfamily, SAM (Sterile alpha motif )	Back alignment and domain information

>gnl\|CDD\|215981 pfam00536, SAM_1, SAM domain (Sterile alpha motif)	Back alignment and domain information

>gnl\|CDD\|188984 cd09585, SAM_DDHD2, SAM domain of DDHD2	Back alignment and domain information

>gnl\|CDD\|173487 PTZ00236, PTZ00236, mitochondrial import inner membrane translocase subunit tim17; Provisional	Back alignment and domain information

>gnl\|CDD\|130053 TIGR00980, 3a0801so1tim17, mitochondrial import inner membrane translocase subunit tim17	Back alignment and domain information

>gnl\|CDD\|197735 smart00454, SAM, Sterile alpha motif	Back alignment and domain information

>gnl\|CDD\|130056 TIGR00983, 3a0801s02tim23, mitochondrial import inner membrane translocase subunit tim23	Back alignment and domain information

>gnl\|CDD\|203706 pfam07647, SAM_2, SAM domain (Sterile alpha motif)	Back alignment and domain information

>gnl\|CDD\|188907 cd09508, SAM_HD, SAM domain of HD-phosphohydrolase	Back alignment and domain information

>gnl\|CDD\|188915 cd09516, SAM_sec23ip-like, SAM domain of sec23ip-like subfamily	Back alignment and domain information

>gnl\|CDD\|227883 COG5596, TIM22, Mitochondrial import inner membrane translocase, subunit TIM22 [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		254
KOG3225		168	consensus Mitochondrial import inner membrane tran	99.94
TIGR00980		170	3a0801so1tim17 mitochondrial import inner membrane	99.87
PTZ00236		164	mitochondrial import inner membrane translocase su	99.87
TIGR00983		149	3a0801s02tim23 mitochondrial import inner membrane	99.87
PF02466		128	Tim17: Tim17/Tim22/Tim23/Pmp24 family; InterPro: I	99.86
KOG1652		183	consensus Mitochondrial import inner membrane tran	99.77
COG5596		191	TIM22 Mitochondrial import inner membrane transloc	99.63
KOG3324		206	consensus Mitochondrial import inner membrane tran	99.59
PF00536		64	SAM_1: SAM domain (Sterile alpha motif); InterPro:	99.31
KOG4374		216	consensus RNA-binding protein Bicaudal-C [RNA proc	99.19
cd00166		63	SAM Sterile alpha motif.; Widespread domain in sig	99.1
PF07647		66	SAM_2: SAM domain (Sterile alpha motif); InterPro:	99.0
smart00454		68	SAM Sterile alpha motif. Widespread domain in sign	98.96
KOG3678		832	consensus SARM protein (with sterile alpha and arm	98.04
PF09597		57	IGR: IGR protein motif; InterPro: IPR019083 This e	97.41
COG5596		191	TIM22 Mitochondrial import inner membrane transloc	97.33
KOG4608		270	consensus Uncharacterized conserved protein [Funct	97.21
KOG4384		361	consensus Uncharacterized SAM domain protein [Gene	96.99
TIGR00980		170	3a0801so1tim17 mitochondrial import inner membrane	92.63
KOG1170		1099	consensus Diacylglycerol kinase [Lipid transport a	91.88
KOG4375		272	consensus Scaffold protein Shank and related SAM d	90.51
KOG0196		996	consensus Tyrosine kinase, EPH (ephrin) receptor f	89.85
KOG4374		216	consensus RNA-binding protein Bicaudal-C [RNA proc	84.76
PF10247		67	Romo1: Reactive mitochondrial oxygen species modul	83.7
KOG1398		460	consensus Uncharacterized conserved protein [Funct	81.15

>KOG3225 consensus Mitochondrial import inner membrane translocase, subunit TIM22 [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

Probab=99.94  E-value=5.8e-28  Score=204.42  Aligned_cols=125  Identities=19%  Similarity=0.290  Sum_probs=109.2

Q ss_pred             hhHHH-HHHHHHHHHHHHHHHHHhhhhcccCCCCCCC-CCCCCchhhhhhhhhhhhhhCCchHHHHHHHHHHHHHHHHHH
Q 025331           44 VEAAI-VTATTAINGAAIGAFLGVMTQDLTSSLPTPP-PQSSLNPDAVAPFQQVQAVAGGPLVQARNFAVITGVNAGISC  121 (254)
Q Consensus        44 ~E~cv-~T~~gav~Gg~lG~~~G~~~~~~~~~~~~~~-~~~~~~~~~~~~~k~~~~~~~~~~~~a~nFAviggvysg~ec  121 (254)
                      +++|+ |+++++|+|+++|+.+|+|.++++.+..+|. ...++++|+   +|+   |+.+++++++|||++|++|+++||
T Consensus        39 ~n~c~~Ka~~sgV~GfglG~~~GlFlas~d~~~~dP~i~~~~ar~q~---~kd---Mg~r~~s~~knF~~iGlvfsg~Ec  112 (168)
T KOG3225|consen   39 ENSCAVKAVKSGVTGFGLGGAFGLFLASLDTQPNDPTIYRMPARKQV---AKD---MGQRSGSYAKNFAIIGLVFSGVEC  112 (168)
T ss_pred             hcchhHHHHHhhccccchhhhHHhhhhhcccCCCCCchhhhhhHHHH---HHH---HHhhhcchhhhhhhhhhhehhHHH
Confidence            34888 9999999999999999999999986522221 123455555   666   889999999999999999999999


Q ss_pred             HHHHhhcccchhhHHHHHHHHhHHhhhccCCCCCChhHHHHHHHHHHHHHHHHHHHhhh
Q 025331          122 VMKRLRGKEDLQSSVVAAFGSGAAFSLVSGMGGANPAVNAFTSGLLFAIFQGCSFKIGE  180 (254)
Q Consensus       122 ~ie~~Rgk~D~~Nsi~AG~~TGail~~~~G~~~~~~~~~ai~gga~fA~~sga~~~~g~  180 (254)
                      ++|++|.|+||+|++++||+||+.++.|+||      ++++.+|++|++||++|++.-+
T Consensus       113 ~iE~~RAK~D~~NgaiaG~vtGg~l~~raGp------~a~~~G~agfa~fS~~id~y~~  165 (168)
T KOG3225|consen  113 LIESFRAKSDWYNGAIAGCVTGGSLGYRAGP------KAAAIGCAGFAAFSAAIDKYMR  165 (168)
T ss_pred             HHHHHHhhhchhcceeeeeeeccchhhcccc------hhhhhchhHHHHHHHHHHHhhh
Confidence            9999999999999999999999999999998      9999999999999999987643

>TIGR00980 3a0801so1tim17 mitochondrial import inner membrane translocase subunit tim17	Back alignment and domain information

>PTZ00236 mitochondrial import inner membrane translocase subunit tim17; Provisional	Back alignment and domain information

>TIGR00983 3a0801s02tim23 mitochondrial import inner membrane translocase subunit tim23	Back alignment and domain information

>PF02466 Tim17: Tim17/Tim22/Tim23/Pmp24 family; InterPro: IPR003397 The membrane-embedded multi-protein complexes of mitochondria mediate the transport of nuclear-encoded proteins across and into the outer or inner mitochondrial membranes []	Back alignment and domain information

>KOG1652 consensus Mitochondrial import inner membrane translocase, subunit TIM17 [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>COG5596 TIM22 Mitochondrial import inner membrane translocase, subunit TIM22 [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG3324 consensus Mitochondrial import inner membrane translocase, subunit TIM23 [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>PF00536 SAM_1: SAM domain (Sterile alpha motif); InterPro: IPR021129 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes	Back alignment and domain information

>KOG4374 consensus RNA-binding protein Bicaudal-C [RNA processing and modification]	Back alignment and domain information

>cd00166 SAM Sterile alpha motif	Back alignment and domain information

>PF07647 SAM_2: SAM domain (Sterile alpha motif); InterPro: IPR011510 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes	Back alignment and domain information

>smart00454 SAM Sterile alpha motif	Back alignment and domain information

>KOG3678 consensus SARM protein (with sterile alpha and armadillo motifs) [Extracellular structures]	Back alignment and domain information

>PF09597 IGR: IGR protein motif; InterPro: IPR019083 This entry is found in fungal and plant proteins and contains a conserved IGR motif	Back alignment and domain information

>COG5596 TIM22 Mitochondrial import inner membrane translocase, subunit TIM22 [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG4608 consensus Uncharacterized conserved protein [Function unknown]	Back alignment and domain information

>KOG4384 consensus Uncharacterized SAM domain protein [General function prediction only]	Back alignment and domain information

>TIGR00980 3a0801so1tim17 mitochondrial import inner membrane translocase subunit tim17	Back alignment and domain information

>KOG1170 consensus Diacylglycerol kinase [Lipid transport and metabolism]	Back alignment and domain information

>KOG4375 consensus Scaffold protein Shank and related SAM domain proteins [Signal transduction mechanisms]	Back alignment and domain information

>KOG0196 consensus Tyrosine kinase, EPH (ephrin) receptor family [Signal transduction mechanisms]	Back alignment and domain information

>KOG4374 consensus RNA-binding protein Bicaudal-C [RNA processing and modification]	Back alignment and domain information

>PF10247 Romo1: Reactive mitochondrial oxygen species modulator 1; InterPro: IPR018450 The majority of endogenous reactive oxygen species (ROS) in cells are produced by the mitochondrial respiratory chain	Back alignment and domain information

>KOG1398 consensus Uncharacterized conserved protein [Function unknown]	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		254
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-12
3k1r_B		74	Usher syndrome type-1G protein; protein-protein co	6e-10
2kg5_A		100	ARF-GAP, RHO-GAP domain, ANK repeat and PH domain-	2e-06
2f3n_A		76	SH3 and multiple ankyrin repeat domains 3; postsyn	6e-06
2kso_A		82	Ephrin type-A receptor 2; SAM domain, heterodimer,	6e-06
3bq7_A		81	Diacylglycerol kinase delta; SAM domain, polymeriz	6e-06
3kka_C		86	Ephrin type-A receptor 2; ATP-binding, kinase, nuc	9e-06
3h8m_A		90	Ephrin type-A receptor 7; SAM domain, kinase,struc	9e-06
3hil_A		82	Ephrin type-A receptor 1; ATP-binding, kinase, nuc	2e-05
1b4f_A		82	EPHB2; SAM domain, EPH receptor, signal transducti	4e-05
2k4p_A		86	Phosphatidylinositol-3,4,5-trisphosphate 5- phosph	4e-05
1ucv_A		81	Ephrin type-A receptor 8; receptor oligomerization	6e-05
2gle_A		74	Neurabin-1; SAM domain, scaffold, protein protein	7e-05
2qkq_A		83	Ephrin type-B receptor 4; ATP-binding, glycoprotei	8e-05
2lmr_A		101	ODIN, ankyrin repeat and SAM domain-containing pro	9e-05
2eao_A		99	Ephrin type-B receptor 1; cell-free protein synthe	1e-04
1b0x_A		94	Protein (EPHA4 receptor tyrosine kinase); protein	1e-04
2e8n_A		88	Ephrin type-A receptor 2; cell-free protein synthe	1e-04
1kw4_A		89	Polyhomeotic; SAM domain, polycomb group, polymer,	1e-04
2ke7_A		103	Ankyrin repeat and sterIle alpha motif domain- con	2e-04
2eam_A		80	Putative 47 kDa protein; cell-free protein synthes	4e-04
3sei_A		149	Caskin-1; SAM domain, protein-protein interaction,	5e-04
1x40_A		91	ARAP2; ASAP-related protein2, GTPase activity, sig	6e-04

>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

 Score = 66.4 bits (161), Expect = 1e-12
 Identities = 48/279 (17%), Positives = 93/279 (33%), Gaps = 65/279 (23%)

Query: 1   MEKGNEKVMSLVQLPQKAIKDVQFKLKELENGYKSWLAK--------QPLPVEAA--IVT 50
            +   + ++S+ +     + +  F  K++++  KS L+K            V     +  
Sbjct: 14  HQYQYKDILSVFE--DAFVDN--FDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFW 69

Query: 51  ATTAINGAAIGAFLG-VMTQD---LTSSLPTPPPQSSLNPDAVAPFQQVQAVAGGPLVQA 106
              +     +  F+  V+  +   L S + T   Q S+        +Q   +     V A
Sbjct: 70  TLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYI--EQRDRLYNDNQVFA 127

Query: 107 RNFAVITGVNAGISCVMKRLRGKEDLQSSVVAAFGSGAAFSLVSGMGG------ANPAVN 160
           +       V+        RL+    L+ +++      A   L+ G+ G      A     
Sbjct: 128 KYN-----VS--------RLQPYLKLRQALLEL--RPAKNVLIDGVLGSGKTWVALDVCL 172

Query: 161 A--FTSGLLFAIFQGCSFKIGEMWQS-TQRPTADDVYYARTRGMLDKLGLQNYTKNFKRG 217
           +      + F IF          W +     + + V       ML KL  Q    N+   
Sbjct: 173 SYKVQCKMDFKIF----------WLNLKNCNSPETVL-----EMLQKLLYQI-DPNWTSR 216

Query: 218 LLTDSTLPLLTDSA---LRD-VRIPPGPR-LLILDHIQS 251
               S + L   S    LR  ++  P    LL+L ++Q+
Sbjct: 217 SDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQN 255

PyMOL of 1vt4

>3k1r_B Usher syndrome type-1G protein; protein-protein complex, alternative splicing, coiled coil, deafness, hearing, non-syndromic deafness, polymorphism; 2.30A {Homo sapiens} Length = 74	Back alignment and structure

>2kg5_A ARF-GAP, RHO-GAP domain, ANK repeat and PH domain-containing protein 3; SAM domain, helix bundle, cell membrane, cell projection, cytoplasm; NMR {Homo sapiens} Length = 100	Back alignment and structure

>2f3n_A SH3 and multiple ankyrin repeat domains 3; postsynaptic density, SAM domain, shank, scaffolding protein, structural protein; 2.10A {Rattus norvegicus} SCOP: a.60.1.2 PDB: 2f44_A Length = 76	Back alignment and structure

>2kso_A Ephrin type-A receptor 2; SAM domain, heterodimer, cell signaling, angiogenesis, apopt ATP-binding, cataract; NMR {Homo sapiens} Length = 82	Back alignment and structure

>3bq7_A Diacylglycerol kinase delta; SAM domain, polymerization domain, alternative splicing, cytoplasm, membrane, metal-binding, phorbol-ester binding; 2.90A {Homo sapiens} Length = 81	Back alignment and structure

>3kka_C Ephrin type-A receptor 2; ATP-binding, kinase, nucleotide-binding, transferase, tyrosine-protein kinase, signal, sterIle alpha motif; 2.40A {Homo sapiens} Length = 86	Back alignment and structure

>3h8m_A Ephrin type-A receptor 7; SAM domain, kinase,structural genomics, structural genomics consortium, SGC, alternative splicing, ATP-binding; 2.10A {Homo sapiens} Length = 90	Back alignment and structure

>3hil_A Ephrin type-A receptor 1; ATP-binding, kinase, nucleotide-binding, transferase, tyrosine-protein kinase, signal, sterIle alpha motif; 2.00A {Homo sapiens} PDB: 3kka_A Length = 82	Back alignment and structure

>1b4f_A EPHB2; SAM domain, EPH receptor, signal transduction, oligomer; 1.95A {Homo sapiens} SCOP: a.60.1.2 PDB: 1f0m_A 1sgg_A Length = 82	Back alignment and structure

>2k4p_A Phosphatidylinositol-3,4,5-trisphosphate 5- phosphatase 2; helix bundle, signaling protein, actin-binding, alternative splicing, cell adhesion; NMR {Homo sapiens} PDB: 2kso_B Length = 86	Back alignment and structure

>1ucv_A Ephrin type-A receptor 8; receptor oligomerization, developmental regulation, tyrosine kinase, riken structural genomics/proteomics initiative; NMR {Homo sapiens} SCOP: a.60.1.2 Length = 81	Back alignment and structure

>2gle_A Neurabin-1; SAM domain, scaffold, protein protein interaction, protein binding; NMR {Rattus norvegicus} Length = 74	Back alignment and structure

>2qkq_A Ephrin type-B receptor 4; ATP-binding, glycoprotein, kinase, membrane, nucleotide- binding, phosphorylation, repeat, signal, transferase; 2.10A {Homo sapiens} Length = 83	Back alignment and structure

>2lmr_A ODIN, ankyrin repeat and SAM domain-containing protein; signaling protein; NMR {Homo sapiens} Length = 101	Back alignment and structure

>2eao_A Ephrin type-B receptor 1; cell-free protein synthesis, protein regulation, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 99	Back alignment and structure

>1b0x_A Protein (EPHA4 receptor tyrosine kinase); protein interaction module, dimerization domain, transferase; 2.00A {Mus musculus} SCOP: a.60.1.2 Length = 94	Back alignment and structure

>2e8n_A Ephrin type-A receptor 2; cell-free protein synthesis, protein regulation, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 88	Back alignment and structure

>1kw4_A Polyhomeotic; SAM domain, polycomb group, polymer, DNA binding protein; 1.75A {Drosophila melanogaster} SCOP: a.60.1.2 PDB: 1pk1_A Length = 89	Back alignment and structure

>2ke7_A Ankyrin repeat and sterIle alpha motif domain- containing protein 1B; SAM domain, alternative splicing, ANK repeat, cell junction, cell membrane; NMR {Homo sapiens} Length = 103	Back alignment and structure

>2eam_A Putative 47 kDa protein; cell-free protein synthesis, protein regulation, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80	Back alignment and structure

>3sei_A Caskin-1; SAM domain, protein-protein interaction, signaling protein; 2.40A {Homo sapiens} PDB: 3sen_A Length = 149	Back alignment and structure

>1x40_A ARAP2; ASAP-related protein2, GTPase activity, signal transduction, SAM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.60.1.2 Length = 91	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		254
3k1r_B		74	Usher syndrome type-1G protein; protein-protein co	99.68
2f3n_A		76	SH3 and multiple ankyrin repeat domains 3; postsyn	99.41
1kw4_A		89	Polyhomeotic; SAM domain, polycomb group, polymer,	99.39
2e8n_A		88	Ephrin type-A receptor 2; cell-free protein synthe	99.37
2qkq_A		83	Ephrin type-B receptor 4; ATP-binding, glycoprotei	99.37
2kso_A		82	Ephrin type-A receptor 2; SAM domain, heterodimer,	99.36
1b4f_A		82	EPHB2; SAM domain, EPH receptor, signal transducti	99.35
1ucv_A		81	Ephrin type-A receptor 8; receptor oligomerization	99.33
3hil_A		82	Ephrin type-A receptor 1; ATP-binding, kinase, nuc	99.32
2gle_A		74	Neurabin-1; SAM domain, scaffold, protein protein	99.32
3bq7_A		81	Diacylglycerol kinase delta; SAM domain, polymeriz	99.31
2eao_A		99	Ephrin type-B receptor 1; cell-free protein synthe	99.29
1b0x_A		94	Protein (EPHA4 receptor tyrosine kinase); protein	99.29
3h8m_A		90	Ephrin type-A receptor 7; SAM domain, kinase,struc	99.28
2eam_A		80	Putative 47 kDa protein; cell-free protein synthes	99.28
3kka_C		86	Ephrin type-A receptor 2; ATP-binding, kinase, nuc	99.26
2kg5_A		100	ARF-GAP, RHO-GAP domain, ANK repeat and PH domain-	99.24
1x40_A		91	ARAP2; ASAP-related protein2, GTPase activity, sig	99.16
2lmr_A		101	ODIN, ankyrin repeat and SAM domain-containing pro	99.15
3bs5_B		80	Connector enhancer of kinase suppressor of RAS 2;	99.13
2e8o_A		103	SAM domain and HD domain-containing protein 1; cel	99.13
2ean_A		83	Connector enhancer of kinase suppressor of RAS 2;	99.12
2k4p_A		86	Phosphatidylinositol-3,4,5-trisphosphate 5- phosph	99.1
2d3d_A		88	VTS1 protein; RNA binding, SAM domain, SRE hairpin	99.01
1pk1_B		89	Sex COMB on midleg CG9495-PA; hetero SAM domain, p	98.99
2ke7_A		103	Ankyrin repeat and sterIle alpha motif domain- con	98.98
3sei_A		149	Caskin-1; SAM domain, protein-protein interaction,	98.97
1v38_A		78	SAM-domain protein samsn-1; structural genomics, h	98.95
2dl0_A		97	SAM and SH3 domain-containing protein 1; cell-free	98.95
2b6g_A		119	VTS1P; alpha-helix, pentaloop, hairpin, RNA bindin	98.95
3bs7_A		78	Protein aveugle; sterIle alpha motif (SAM) domain,	98.9
2es6_A		101	VTS1P; SAM domain, protein structure, gene regulat	98.86
3sei_A		149	Caskin-1; SAM domain, protein-protein interaction,	98.85
2kiv_A		148	Ankyrin repeat and sterIle alpha motif domain- con	98.77
1v85_A		91	Similar to ring finger protein 36; apoptosis, neur	98.74
1ow5_A		85	Serine/threonine-protein kinase STE11; MAP kinase,	98.74
3bs5_A		106	Protein aveugle; sterIle alpha motif, SAM domain,	98.73
2kiv_A		148	Ankyrin repeat and sterIle alpha motif domain- con	98.68
2d8c_A		97	Phosphatidylcholine:ceramide cholinephosphotransfe	98.61
2y9u_A		69	Tumor protein 63; apoptosis, sterIle alpha motif,	98.5
2y9t_A		82	Tumor protein 63; apoptosis, sterIle alpha motif,	98.5
1oxj_A		173	RNA-binding protein smaug; SAM domain, PHAT domain	98.47
1wwv_A		91	Connector enhancer of kinase suppressor of RAS 1;	98.24
3tad_C		265	Liprin-beta-1; protein binding; 2.90A {Mus musculu	97.8
3idw_A		72	Actin cytoskeleton-regulatory complex protein SLA;	97.37
3tad_C		265	Liprin-beta-1; protein binding; 2.90A {Mus musculu	97.17
2dkz_A		84	Hypothetical protein LOC64762; cell-free protein s	96.83
1dxs_A		80	P53-like transcription factor; P73 SAM-like domain	95.35
2l5y_A		150	Stromal interaction molecule 2; EF-hand, SAM domai	95.24
3tac_B		334	Liprin-alpha-2; transferase-protein binding comple	94.55
2k60_A		150	Protein (stromal interaction molecule 1); EF-hand,	93.94
3tac_B		334	Liprin-alpha-2; transferase-protein binding comple	93.75
2eap_A		90	Lymphocyte cytosolic protein 2; cell-free protein	92.98
1uqv_A		85	STE50 protein; SAM, sterIle alpha motif, helical,	91.23

>3k1r_B Usher syndrome type-1G protein; protein-protein complex, alternative splicing, coiled coil, deafness, hearing, non-syndromic deafness, polymorphism; 2.30A {Homo sapiens}	Back alignment and structure

Probab=99.68  E-value=7e-18  Score=125.90  Aligned_cols=58  Identities=22%  Similarity=0.385  Sum_probs=55.2

Q ss_pred             HHHHHHHhhcCchhhHHHHhhccCCCccccCCChhhhhhCCCCCChhHHHHHHHhhcc
Q 025331          196 ARTRGMLDKLGLQNYTKNFKRGLLTDSTLPLLTDSALRDVRIPPGPRLLILDHIQSFC  253 (254)
Q Consensus       196 a~~~~~l~~Lgl~~y~~~f~~e~~~~~~l~~~~~~~Lk~~giP~gpr~~il~~~~~~~  253 (254)
                      ..+..+|++|||++|..+|+++++|+++|.+||++|||+||||+|||+|||++|++++
T Consensus         3 ~~v~~wL~~lgL~~Y~~~F~~~~id~e~l~~lt~~DL~~lGI~~G~RkkIl~ai~~~~   60 (74)
T 3k1r_B            3 SPLETFLASLHMEDFAALLRQEKIDLEALMLCSDLDLRSISVPLGPREKILGAVRRRR   60 (74)
T ss_dssp             CHHHHHHHTTTCGGGHHHHHHTTCCHHHHTTCCHHHHHHTTCCHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHCCCHHHHHHHHHcCcCHHHHhHCCHHHHHHcCCCcchHHHHHHHHHHHH
Confidence            4689999999999999999999999999999999999999999999999999998763

PyMOL of 3k1r

>2f3n_A SH3 and multiple ankyrin repeat domains 3; postsynaptic density, SAM domain, shank, scaffolding protein, structural protein; 2.10A {Rattus norvegicus} SCOP: a.60.1.2 PDB: 2f44_A	Back alignment and structure

>1kw4_A Polyhomeotic; SAM domain, polycomb group, polymer, DNA binding protein; 1.75A {Drosophila melanogaster} SCOP: a.60.1.2 PDB: 1pk1_A	Back alignment and structure

>2e8n_A Ephrin type-A receptor 2; cell-free protein synthesis, protein regulation, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2qkq_A Ephrin type-B receptor 4; ATP-binding, glycoprotein, kinase, membrane, nucleotide- binding, phosphorylation, repeat, signal, transferase; 2.10A {Homo sapiens}	Back alignment and structure

>2kso_A Ephrin type-A receptor 2; SAM domain, heterodimer, cell signaling, angiogenesis, apopt ATP-binding, cataract; NMR {Homo sapiens}	Back alignment and structure

>1b4f_A EPHB2; SAM domain, EPH receptor, signal transduction, oligomer; 1.95A {Homo sapiens} SCOP: a.60.1.2 PDB: 1f0m_A 1sgg_A	Back alignment and structure

>1ucv_A Ephrin type-A receptor 8; receptor oligomerization, developmental regulation, tyrosine kinase, riken structural genomics/proteomics initiative; NMR {Homo sapiens} SCOP: a.60.1.2	Back alignment and structure

>3hil_A Ephrin type-A receptor 1; ATP-binding, kinase, nucleotide-binding, transferase, tyrosine-protein kinase, signal, sterIle alpha motif; 2.00A {Homo sapiens} PDB: 3kka_A	Back alignment and structure

>2gle_A Neurabin-1; SAM domain, scaffold, protein protein interaction, protein binding; NMR {Rattus norvegicus}	Back alignment and structure

>3bq7_A Diacylglycerol kinase delta; SAM domain, polymerization domain, alternative splicing, cytoplasm, membrane, metal-binding, phorbol-ester binding; 2.90A {Homo sapiens}	Back alignment and structure

>2eao_A Ephrin type-B receptor 1; cell-free protein synthesis, protein regulation, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>1b0x_A Protein (EPHA4 receptor tyrosine kinase); protein interaction module, dimerization domain, transferase; 2.00A {Mus musculus} SCOP: a.60.1.2	Back alignment and structure

>3h8m_A Ephrin type-A receptor 7; SAM domain, kinase,structural genomics, structural genomics consortium, SGC, alternative splicing, ATP-binding; 2.10A {Homo sapiens}	Back alignment and structure

>2eam_A Putative 47 kDa protein; cell-free protein synthesis, protein regulation, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>3kka_C Ephrin type-A receptor 2; ATP-binding, kinase, nucleotide-binding, transferase, tyrosine-protein kinase, signal, sterIle alpha motif; 2.40A {Homo sapiens} SCOP: a.60.1.0	Back alignment and structure

>2kg5_A ARF-GAP, RHO-GAP domain, ANK repeat and PH domain-containing protein 3; SAM domain, helix bundle, cell membrane, cell projection, cytoplasm; NMR {Homo sapiens}	Back alignment and structure

>1x40_A ARAP2; ASAP-related protein2, GTPase activity, signal transduction, SAM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.60.1.2	Back alignment and structure

>2lmr_A ODIN, ankyrin repeat and SAM domain-containing protein; signaling protein; NMR {Homo sapiens}	Back alignment and structure

>3bs5_B Connector enhancer of kinase suppressor of RAS 2; sterIle alpha motif, SAM domain, SAM domain dimer, SAM domain complex, cytoplasm, membrane; 2.00A {Homo sapiens}	Back alignment and structure

>2e8o_A SAM domain and HD domain-containing protein 1; cell-free protein synthesis, protein regulation, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2ean_A Connector enhancer of kinase suppressor of RAS 2; cell-free protein synthesis, protein regulation, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2k4p_A Phosphatidylinositol-3,4,5-trisphosphate 5- phosphatase 2; helix bundle, signaling protein, actin-binding, alternative splicing, cell adhesion; NMR {Homo sapiens} PDB: 2kso_B	Back alignment and structure

>2d3d_A VTS1 protein; RNA binding, SAM domain, SRE hairpin binding, RNA binding protein; 1.60A {Saccharomyces cerevisiae} PDB: 2f8k_A 2fe9_A	Back alignment and structure

>1pk1_B Sex COMB on midleg CG9495-PA; hetero SAM domain, polymers, transcriptional repression, transcription repression; 1.80A {Drosophila melanogaster} SCOP: a.60.1.2 PDB: 1pk3_A	Back alignment and structure

>2ke7_A Ankyrin repeat and sterIle alpha motif domain- containing protein 1B; SAM domain, alternative splicing, ANK repeat, cell junction, cell membrane; NMR {Homo sapiens}	Back alignment and structure

>3sei_A Caskin-1; SAM domain, protein-protein interaction, signaling protein; 2.40A {Homo sapiens} PDB: 3sen_A	Back alignment and structure

>1v38_A SAM-domain protein samsn-1; structural genomics, hypothetical protein, riken structural genomics/proteomics initiative, RSGI, signaling protein; NMR {Mus musculus} SCOP: a.60.1.2	Back alignment and structure

>2dl0_A SAM and SH3 domain-containing protein 1; cell-free protein synthesis, protein regulation, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2b6g_A VTS1P; alpha-helix, pentaloop, hairpin, RNA binding protein; NMR {Saccharomyces cerevisiae}	Back alignment and structure

>3bs7_A Protein aveugle; sterIle alpha motif (SAM) domain, cytoplasm, membrane, sensory transduction, vision, signaling protein; 1.90A {Drosophila melanogaster}	Back alignment and structure

>2es6_A VTS1P; SAM domain, protein structure, gene regulation; NMR {Saccharomyces cerevisiae} PDB: 2ese_A	Back alignment and structure

>3sei_A Caskin-1; SAM domain, protein-protein interaction, signaling protein; 2.40A {Homo sapiens} PDB: 3sen_A	Back alignment and structure

>2kiv_A Ankyrin repeat and sterIle alpha motif domain- containing protein 1B; SAM domain, tandem, signaling protein, alternative splicing, ANK repeat; NMR {Homo sapiens}	Back alignment and structure

>1v85_A Similar to ring finger protein 36; apoptosis, neuron, cell death, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus}	Back alignment and structure

>1ow5_A Serine/threonine-protein kinase STE11; MAP kinase, MAPKKK, SAM domain, pointed domain, SCM domain, STE50 regulator, transferase; NMR {Saccharomyces cerevisiae} SCOP: a.60.1.2 PDB: 1x9x_A	Back alignment and structure

>3bs5_A Protein aveugle; sterIle alpha motif, SAM domain, SAM domain dimer, SAM domain complex, cytoplasm, membrane; 2.00A {Drosophila melanogaster}	Back alignment and structure

>2kiv_A Ankyrin repeat and sterIle alpha motif domain- containing protein 1B; SAM domain, tandem, signaling protein, alternative splicing, ANK repeat; NMR {Homo sapiens}	Back alignment and structure

>2d8c_A Phosphatidylcholine:ceramide cholinephosphotransferase 1; cell-free protein synthesis, protein regulation, lipid metabolism, structural genomics; NMR {Mus musculus} SCOP: a.60.1.2	Back alignment and structure

>2y9u_A Tumor protein 63; apoptosis, sterIle alpha motif, 5-helix bundle, mutations, A syndrome; 1.60A {Homo sapiens} PDB: 1rg6_A	Back alignment and structure

>2y9t_A Tumor protein 63; apoptosis, sterIle alpha motif, 5-helix bundle; NMR {Homo sapiens}	Back alignment and structure

>1oxj_A RNA-binding protein smaug; SAM domain, PHAT domain; 1.80A {Drosophila melanogaster} SCOP: a.60.1.2 a.118.1.13	Back alignment and structure

>1wwv_A Connector enhancer of kinase suppressor of RAS 1; structural genomics, protein regulation, transcription; NMR {Homo sapiens} SCOP: a.60.1.2	Back alignment and structure

>3tad_C Liprin-beta-1; protein binding; 2.90A {Mus musculus}	Back alignment and structure

>3idw_A Actin cytoskeleton-regulatory complex protein SLA; clathrin adaptor, endocytosis, SAM domain, yeast, actin-BIND membrane, endosome; 1.85A {Saccharomyces cerevisiae}	Back alignment and structure

>3tad_C Liprin-beta-1; protein binding; 2.90A {Mus musculus}	Back alignment and structure

>2dkz_A Hypothetical protein LOC64762; cell-free protein synthesis, protein regulation, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>1dxs_A P53-like transcription factor; P73 SAM-like domain, gene regulation, P53 P63 homologue, sterIle alpha motif, tumour supressor; 2.54A {Homo sapiens} SCOP: a.60.1.2 PDB: 1cok_A	Back alignment and structure

>2l5y_A Stromal interaction molecule 2; EF-hand, SAM domain, store OPE calcium entry, signaling protein; NMR {Homo sapiens}	Back alignment and structure

>3tac_B Liprin-alpha-2; transferase-protein binding complex; 2.20A {Homo sapiens} PDB: 3tad_A	Back alignment and structure

>2k60_A Protein (stromal interaction molecule 1); EF-hand, SAM domain, EF-SAM, STIM1, store operated calcium entry regulator, SOCE; NMR {Homo sapiens}	Back alignment and structure

>3tac_B Liprin-alpha-2; transferase-protein binding complex; 2.20A {Homo sapiens} PDB: 3tad_A	Back alignment and structure

>2eap_A Lymphocyte cytosolic protein 2; cell-free protein synthesis, protein regulation, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>1uqv_A STE50 protein; SAM, sterIle alpha motif, helical, protein-protein interaction domain, growth arrest, signaling protein; NMR {Saccharomyces cerevisiae} SCOP: a.60.1.2 PDB: 1z1v_A	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Alignment Graph	Length	Definition	E-value
Query		254
d2f3na1		64	a.60.1.2 (A:2-65) Sh3 and multiple ankyrin repeat	6e-07
d1ucva_		81	a.60.1.2 (A:) Ephrin type-A receptor 8, C-terminal	2e-05
d1b0xa_		72	a.60.1.2 (A:) EphA4 receptor tyrosine kinases {Mou	2e-05
d1dxsa_		57	a.60.1.2 (A:) C-terminal domain of p73 {Human (Hom	2e-04
d1oxja1		62	a.60.1.2 (A:594-655) RNA-binding protein Smaug {Dr	5e-04
d1kw4a_		70	a.60.1.2 (A:) Polyhomeotic {Drosophila melanogaste	0.001

>d2f3na1 a.60.1.2 (A:2-65) Sh3 and multiple ankyrin repeat domains 3 (Shank3) {Rat(Rattus norvegicus) [TaxId: 10116]} Length = 64	Back information, alignment and structure


class: All alpha proteins
fold: SAM domain-like
superfamily: SAM/Pointed domain
family: SAM (sterile alpha motif) domain
domain: Sh3 and multiple ankyrin repeat domains 3 (Shank3)
species: Rat(Rattus norvegicus) [TaxId: 10116]

 Score = 43.7 bits (103), Expect = 6e-07
 Identities = 12/63 (19%), Positives = 24/63 (38%), Gaps = 6/63 (9%)

Query: 189 TADDVYYARTRGMLDKLGLQNYTKNFKRGLLTDSTLPLLTDSALRDVRI-PPGPRLLILD 247
           +  DV        L+ + L  +   F+   +  + LP LT     ++ +   G R  I  
Sbjct: 5   SKFDVG-----DWLESIHLGEHRDRFEDHEIEGAHLPALTKEDFVELGVTRVGHRENIER 59

Query: 248 HIQ 250
            ++
Sbjct: 60  ALR 62

PyMOL of d2f3na1

>d1ucva_ a.60.1.2 (A:) Ephrin type-A receptor 8, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 81	Back information, alignment and structure

>d1b0xa_ a.60.1.2 (A:) EphA4 receptor tyrosine kinases {Mouse (Mus musculus) [TaxId: 10090]} Length = 72	Back information, alignment and structure

>d1dxsa_ a.60.1.2 (A:) C-terminal domain of p73 {Human (Homo sapiens) [TaxId: 9606]} Length = 57	Back information, alignment and structure

>d1oxja1 a.60.1.2 (A:594-655) RNA-binding protein Smaug {Drosophila melanogaster [TaxId: 7227]} Length = 62	Back information, alignment and structure

>d1kw4a_ a.60.1.2 (A:) Polyhomeotic {Drosophila melanogaster [TaxId: 7227]} Length = 70	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		254
d1dxsa_		57	C-terminal domain of p73 {Human (Homo sapiens) [Ta	99.38
d1oxja1		62	RNA-binding protein Smaug {Drosophila melanogaster	99.35
d1ow5a_		60	Serine/threonine-protein kinase ste11 {Baker's yea	99.31
d2f3na1		64	Sh3 and multiple ankyrin repeat domains 3 (Shank3)	99.3
d1pk3a1		63	Polycomb protein Scm {Fruit fly (Drosophila melano	99.18
d1b0xa_		72	EphA4 receptor tyrosine kinases {Mouse (Mus muscul	99.18
d1v38a_		78	Sam-domain protein samsn-1 {Mouse (Mus musculus) [	99.17
d1ucva_		81	Ephrin type-A receptor 8, C-terminal domain {Human	99.13
d1b4fa_		74	EphB2 receptor {Human (Homo sapiens) [TaxId: 9606]	99.12
d1x40a1		78	Centaurin-delta 1 (Arap2) {Human(Homo sapiens) [Ta	99.11
d1kw4a_		70	Polyhomeotic {Drosophila melanogaster [TaxId: 7227	98.91
d1wwva1		78	Connector enhancer of kinase suppressor of Ras 1,	98.89
d2d8ca1		85	Sphingomyelin synthase 1, SMS1 {Mouse (Mus musculu	98.48
d1rg6a_		67	C-terminal domain of p63 {Human (Homo sapiens) [Ta	97.21

>d1dxsa_ a.60.1.2 (A:) C-terminal domain of p73 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

class: All alpha proteins
fold: SAM domain-like
superfamily: SAM/Pointed domain
family: SAM (sterile alpha motif) domain
domain: C-terminal domain of p73
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.38  E-value=6.8e-14  Score=97.82  Aligned_cols=54  Identities=28%  Similarity=0.273  Sum_probs=51.2

Q ss_pred             HHHHHhhcCchhhHHHHhhccCC-CccccCCChhhhhhCCCCCChhHHHHHHHhh
Q 025331          198 TRGMLDKLGLQNYTKNFKRGLLT-DSTLPLLTDSALRDVRIPPGPRLLILDHIQS  251 (254)
Q Consensus       198 ~~~~l~~Lgl~~y~~~f~~e~~~-~~~l~~~~~~~Lk~~giP~gpr~~il~~~~~  251 (254)
                      +.++|++|||++|..+|.+..+| ++.+..+|++||++||||.|+|+||+..|+.
T Consensus         2 v~~wL~~lgL~~Y~~~F~~~G~~~l~~l~~lt~eDL~~lGI~~~hr~kilk~i~~   56 (57)
T d1dxsa_           2 LVSFLTGLGCPNCIEYFTSQGLQSIYHLQNLTIEDLGALKIPEQYRMTIWRGLQD   56 (57)
T ss_dssp             HHHHHHHTTCTTSHHHHHTTTCCCHHHHHTCCHHHHHHTTCCTTTHHHHHHHHHH
T ss_pred             HHHHHHHCCcHHHHHHHHHccCCcHHHHHHhhHHHHHHcCCCHHHHHHHHHHHHh
Confidence            68899999999999999999996 8999999999999999999999999998864

PyMOL of d1dxsa_

>d1oxja1 a.60.1.2 (A:594-655) RNA-binding protein Smaug {Drosophila melanogaster [TaxId: 7227]}	Back information, alignment and structure

>d1ow5a_ a.60.1.2 (A:) Serine/threonine-protein kinase ste11 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d2f3na1 a.60.1.2 (A:2-65) Sh3 and multiple ankyrin repeat domains 3 (Shank3) {Rat(Rattus norvegicus) [TaxId: 10116]}	Back information, alignment and structure

>d1pk3a1 a.60.1.2 (A:17-79) Polycomb protein Scm {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}	Back information, alignment and structure

>d1b0xa_ a.60.1.2 (A:) EphA4 receptor tyrosine kinases {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1v38a_ a.60.1.2 (A:) Sam-domain protein samsn-1 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1ucva_ a.60.1.2 (A:) Ephrin type-A receptor 8, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1b4fa_ a.60.1.2 (A:) EphB2 receptor {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x40a1 a.60.1.2 (A:8-85) Centaurin-delta 1 (Arap2) {Human(Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1kw4a_ a.60.1.2 (A:) Polyhomeotic {Drosophila melanogaster [TaxId: 7227]}	Back information, alignment and structure

>d1wwva1 a.60.1.2 (A:8-85) Connector enhancer of kinase suppressor of Ras 1, CNK1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2d8ca1 a.60.1.2 (A:7-91) Sphingomyelin synthase 1, SMS1 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1rg6a_ a.60.1.2 (A:) C-terminal domain of p63 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure