Citrus Sinensis ID: 047562

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------
MDYIPSLVFPFDRTDPHDDQLPCQQQYHTAGQQNDNQLIFNPLEYGSDLKRPETTNIFAVNDDNSKKMKIMRRDIERHRRQEMSTLYRSLRSLLPLEYLKGKRSMSDHMNEAVNYIKNLQNRIQKLSEKRDELRRLSNSSSSPYYSTTSESECSQTHINLEDSVTVRPCLAGVEVAINTSFRKGIPLSQVVALLAEEGLTVVNCISTKINERLLHNIESEVNDGGRNIDPFELQQKIMKLTSPSSN
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccEEEEEEcccEEEEEEEccccccHHHHHHHHHHHcccEEEEEEEEEEccEEEEEEEEEEccccccccHHHHHHHHHHHHccccc
ccccccEEcccccccccccccccccEEEEccccccccccccccccccccccEEEcccccccccccccccEHHHHHHHHHHHHHHHHHHHHHHcccHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccEEEEEccccEEEEEEEccccccccHHHHHHHHHHcccEEEEEEEEEEccEEEEEEEEEEccccccccHHHHHHHHHHHHccccc
mdyipslvfpfdrtdphddqlpcqqqyhtagqqndnqlifnpleygsdlkrpettnifavnddnskkMKIMRRDIERHRRQEMSTLYRSLRSLlpleylkgkrsmSDHMNEAVNYIKNLQNRIQKLSEKRDELRrlsnsssspyysttsesecsqthinledsvtvrpclaGVEVAINTSFRKGIPLSQVVALLAEEGLTVVNCISTKINERLLHNIEsevndggrnidpfELQQKIMKLTSPSSN
MDYIPSLVFPFDRTDPHDDQLPCQQQYHTagqqndnqLIFNPLEYGSDLKRPETtnifavnddnskkmkiMRRDIERHRRQEMSTLYRSLRSLLPLEYLKGKRSMSDHMNEAVNYIKNLQNRIQKLSEkrdelrrlsnsssspyysttseseCSQTHINLEDSVTVRPCLAGVEVAINTSFRKGIPLSQVVALLAEEGLTVVNCISTKINERLLHNIesevndggrnIDPFElqqkimkltspssn
MDYIPSLVFPFDRTDPHDDQLPCQQQYHTAGQQNDNQLIFNPLEYGSDLKRPETTNIFAVNDDNSKKMKIMRRDIERHRRQEMSTLYRSLRSLLPLEYLKGKRSMSDHMNEAVNYIKNLQNRIQKLSEKRDELRRLsnsssspyysttsesecsQTHINLEDSVTVRPCLAGVEVAINTSFRKGIPLSQVVALLAEEGLTVVNCISTKINERLLHNIESEVNDGGRNIDPFELQQKIMKLTSPSSN
*************************************LIFNPLEY***********IF****************************YRSLRSLLPLEYL*************VNYI*****************************************INLEDSVTVRPCLAGVEVAINTSFRKGIPLSQVVALLAEEGLTVVNCISTKINERLLHNIES***************************
****PSL*********************************************************************RHRRQEMSTLYRSLRSLLPL*********SDHMNEAVNYIKNLQ**********************************************RPCLAGVEVAINTSFRKGIPLSQVVALLAEEGLTVVNCISTKINERLLHNIESEVNDGGRNIDPFELQQKIMKLTS****
MDYIPSLVFPFDRTDPHDDQLPCQQQYHTAGQQNDNQLIFNPLEYGSDLKRPETTNIFAVNDDNSKKMKIMRRDIERHRRQEMSTLYRSLRSLLPLEYLKGKRSMSDHMNEAVNYIKNLQNRIQKL******************************HINLEDSVTVRPCLAGVEVAINTSFRKGIPLSQVVALLAEEGLTVVNCISTKINERLLHNIESEVNDGGRNIDPFELQQKIMKLTSPSSN
*DYIPSLVFPFDRTDPHDDQLPCQQQYHTAGQQNDNQLIFNPLEYGSDLKRPETTNIFAVNDDNSKKMKIMRRDIERHRRQEMSTLYRSLRSLLPLEYLKGKRSMSDHMNEAVNYIKNLQNRIQKLSEKRDELRRLS*********************NLEDSVTVRPCLAGVEVAINTSFRKGIPLSQVVALLAEEGLTVVNCISTKINERLLHNIESEVNDGGRNIDPFELQQKIMKLTS****
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MDYIPSLVFPFDRTDPHDDQLPCQQQYHTAGQQNDNQLIFNPLEYGSDLKRPETTNIFAVNDDNSKKMKIMRRDIERHRRQEMSTLYRSLRSLLPLEYLKGKRSMSDHxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxSSSPYYSTTSESECSQTHINLEDSVTVRPCLAGVEVAINTSFRKGIPLSQVVALLAEEGLTVVNCISTKINERLLHNIESEVNDGGRNIDPFELQQKIMKLTSPSSN
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 ?
Query246 2.2.26 [Sep-21-2011]
Q9LN95257 Transcription factor bHLH yes no 0.898 0.859 0.381 4e-34
Q9FLI1174 Transcription factor bHLH no no 0.691 0.977 0.450 2e-33
Q9STJ6221 Transcription factor bHLH no no 0.686 0.764 0.446 3e-33
Q9LQ08259 Transcription factor bHLH no no 0.922 0.876 0.363 2e-32
Q9FLI0204 Transcription factor bHLH no no 0.691 0.833 0.426 4e-32
Q9STJ7163 Transcription factor bHLH no no 0.585 0.883 0.425 1e-28
Q9ZVB5242 Transcription factor bHLH no no 0.650 0.661 0.265 7e-06
Q9M1K1253 Transcription factor ORG2 no no 0.670 0.652 0.265 2e-05
Q9FYE6240 Transcription factor bHLH no no 0.504 0.516 0.281 9e-05
>sp|Q9LN95|BH055_ARATH Transcription factor bHLH55 OS=Arabidopsis thaliana GN=BHLH55 PE=2 SV=1 Back     alignment and function desciption
 Score =  145 bits (365), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 92/241 (38%), Positives = 145/241 (60%), Gaps = 20/241 (8%)

Query: 6   SLVFPFDRTDPHDDQLPCQQQYHTAGQQNDNQLIFNPLEYGSDLKRPETTNIFAVNDDNS 65
           SL+ P  R    + + PC    H+AG +ND +          + +   T +     DD  
Sbjct: 23  SLITPSTRVSFQEPK-PCNPVIHSAGIENDGR---------QNCETTMTLSEIMKGDDEP 72

Query: 66  KKMKIMRRDIERHRRQEMSTLYRSLRSLLPLEYLKGKRSMSDHMNEAVNYIKNLQNRIQK 125
           K  +   +++ER RRQE ++L++ LR LLP +Y+KGKRS +DH+ EAVNYIK+LQ +I++
Sbjct: 73  KNKRAKHKELERQRRQENTSLFKILRYLLPSQYIKGKRSSADHVLEAVNYIKDLQKKIKE 132

Query: 126 LSEKRDELRR-LSNSSSSPYYSTTS--ESECSQTHINLEDSVTVRPCLAGVEVAINTSFR 182
           +SEKRD ++R +++ SS   +S  S   S CS    +   +V VRPCL G+E+ ++   R
Sbjct: 133 VSEKRDRIKRSITHPSSRGEFSIRSLASSTCSCVG-DTNIAVVVRPCLIGLEIVVSCCNR 191

Query: 183 KGIPLSQVVALLA-EEGLTVVNCISTKINERLLHNIESEVNDGGRNIDPF--ELQQKIMK 239
               LS V+ LLA E+   +V+CIST++++  +H I SEV +G   I+ +  ELQ+KI+K
Sbjct: 192 HESCLSSVLQLLAQEQCFNIVSCISTRLHQGFIHTIASEVEEG---IEVYFSELQEKIIK 248

Query: 240 L 240
           +
Sbjct: 249 I 249

Arabidopsis thaliana (taxid: 3702)
>sp|Q9FLI1|BH036_ARATH Transcription factor bHLH36 OS=Arabidopsis thaliana GN=BHLH36 PE=2 SV=1 Back     alignment and function description
>sp|Q9STJ6|BH126_ARATH Transcription factor bHLH126 OS=Arabidopsis thaliana GN=BHLH126 PE=2 SV=1 Back     alignment and function description
>sp|Q9LQ08|BH125_ARATH Transcription factor bHLH125 OS=Arabidopsis thaliana GN=BHLH125 PE=2 SV=1 Back     alignment and function description
>sp|Q9FLI0|BH120_ARATH Transcription factor bHLH120 OS=Arabidopsis thaliana GN=BHLH120 PE=2 SV=2 Back     alignment and function description
>sp|Q9STJ7|BH118_ARATH Transcription factor bHLH118 OS=Arabidopsis thaliana GN=BHLH118 PE=2 SV=1 Back     alignment and function description
>sp|Q9ZVB5|BH100_ARATH Transcription factor bHLH100 OS=Arabidopsis thaliana GN=BHLH100 PE=2 SV=1 Back     alignment and function description
>sp|Q9M1K1|ORG2_ARATH Transcription factor ORG2 OS=Arabidopsis thaliana GN=ORG2 PE=1 SV=1 Back     alignment and function description
>sp|Q9FYE6|BH101_ARATH Transcription factor bHLH101 OS=Arabidopsis thaliana GN=BHLH101 PE=2 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query246
224058631241 predicted protein [Populus trichocarpa] 0.890 0.908 0.484 2e-46
225455629204 PREDICTED: transcription factor bHLH120 0.760 0.916 0.495 3e-40
224134607246 predicted protein [Populus trichocarpa] 0.719 0.719 0.497 7e-40
359490223195 PREDICTED: transcription factor bHLH120- 0.686 0.866 0.514 3e-39
225426716196 PREDICTED: transcription factor bHLH120- 0.626 0.785 0.539 7e-39
224122516240 predicted protein [Populus trichocarpa] 0.666 0.683 0.525 1e-38
296084086231 unnamed protein product [Vitis vinifera] 0.719 0.766 0.489 2e-38
147810508196 hypothetical protein VITISV_004405 [Viti 0.691 0.867 0.502 2e-38
255539631196 DNA binding protein, putative [Ricinus c 0.691 0.867 0.5 6e-38
147843674254 hypothetical protein VITISV_043103 [Viti 0.707 0.685 0.5 7e-38
>gi|224058631|ref|XP_002299575.1| predicted protein [Populus trichocarpa] gi|222846833|gb|EEE84380.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  191 bits (486), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 123/254 (48%), Positives = 158/254 (62%), Gaps = 35/254 (13%)

Query: 1   MDYIPSLVFPFDRTDPHD-----DQLPCQQQYHTAGQ-----QNDNQLIFNPLEYGSDLK 50
           MDYI S VF  D     D        P QQQ     +       D   + N  ++G   K
Sbjct: 1   MDYISS-VFQIDYNSTDDLVQYFSSFPTQQQTTPKDKVPLRPYEDCHDLANKTQHGRRRK 59

Query: 51  RPETTNIFAVNDDN---SKKMKIMRRDIERHRRQEMSTLYRSLRSLLPLEYLKGKRSMSD 107
            P    + +V D+N   +KK KI+ RDIER RRQEM+ LY SLR LLPL+YLKGKRS SD
Sbjct: 60  SP--IALGSVKDENPNDNKKKKIIHRDIERQRRQEMANLYGSLRCLLPLKYLKGKRSTSD 117

Query: 108 HMNEAVNYIKNLQNRIQKLSEKRDELRRLSNSSSSPYYSTTSESECSQTHINLE----DS 163
           H+++ V YIK+ + +IQKL +K+DEL+R        Y ST+S  E      NLE    D+
Sbjct: 118 HIHQTVYYIKHQEEKIQKLIDKKDELKR--------YLSTSSALE------NLEGCERDT 163

Query: 164 VTVRPCLAGVEVAINTSFRKGIPLSQVVALLAEEGLTVVNCISTKINERLLHNIESEVND 223
           +TVR    GVEV INT+ +KG PLS+V+A+L EEG +VV+CISTK+NER+LHNI SEV D
Sbjct: 164 LTVRTRCVGVEVDINTALKKGFPLSRVLAILIEEGFSVVSCISTKVNERMLHNIISEVTD 223

Query: 224 GGRNIDPFELQQKI 237
            GR++D  ELQQK+
Sbjct: 224 -GRSLDISELQQKL 236

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|225455629|ref|XP_002271172.1| PREDICTED: transcription factor bHLH120 [Vitis vinifera] gi|296084087|emb|CBI24475.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|224134607|ref|XP_002321864.1| predicted protein [Populus trichocarpa] gi|222868860|gb|EEF05991.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|359490223|ref|XP_002271208.2| PREDICTED: transcription factor bHLH120-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|225426716|ref|XP_002275564.1| PREDICTED: transcription factor bHLH120-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|224122516|ref|XP_002318856.1| predicted protein [Populus trichocarpa] gi|222859529|gb|EEE97076.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|296084086|emb|CBI24474.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|147810508|emb|CAN67627.1| hypothetical protein VITISV_004405 [Vitis vinifera] Back     alignment and taxonomy information
>gi|255539631|ref|XP_002510880.1| DNA binding protein, putative [Ricinus communis] gi|223549995|gb|EEF51482.1| DNA binding protein, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|147843674|emb|CAN81995.1| hypothetical protein VITISV_043103 [Vitis vinifera] 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 ?
Query246
TAIR|locus:2165311174 AT5G51780 "AT5G51780" [Arabido 0.691 0.977 0.433 5.4e-31
TAIR|locus:504956298259 AT1G62975 "AT1G62975" [Arabido 0.955 0.907 0.367 6.9e-31
TAIR|locus:2138019163 AT4G25400 "AT4G25400" [Arabido 0.585 0.883 0.406 5.2e-26
TAIR|locus:2040287242 BHLH100 "basic helix-loop-heli 0.711 0.723 0.270 1.8e-08
TAIR|locus:2133089190 AT4G20970 "AT4G20970" [Arabido 0.711 0.921 0.2 7.5e-08
TAIR|locus:2080600253 bHLH38 "basic helix-loop-helix 0.735 0.715 0.236 4.6e-07
TAIR|locus:2146663240 BHLH101 "AT5G04150" [Arabidops 0.605 0.620 0.25 2.2e-06
UNIPROTKB|Q941Z7248 P0431G06.13-1 "BHLH transcript 0.617 0.612 0.253 7.5e-06
TAIR|locus:2080615258 bHLH39 "basic helix-loop-helix 0.886 0.844 0.246 1.5e-05
TAIR|locus:2079512358 AT3G61950 "AT3G61950" [Arabido 0.5 0.343 0.270 0.00027
TAIR|locus:2165311 AT5G51780 "AT5G51780" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 341 (125.1 bits), Expect = 5.4e-31, P = 5.4e-31
 Identities = 75/173 (43%), Positives = 114/173 (65%)

Query:    69 KIMRRDIERHRRQEMSTLYRSLRSLLPLEYLKGKRSMSDHMNEAVNYIKNLQNRIQKLSE 128
             K+M R+ ER RRQEM++LY SLRSLLPL ++KGKRS SD +NEAVNYIK LQ +I++LS 
Sbjct:     3 KMMHRETERQRRQEMASLYASLRSLLPLHFIKGKRSTSDQVNEAVNYIKYLQRKIKELSV 62

Query:   129 KRDELRRLXXXXXXXXXXXXXXXXXXQTHINLEDSVTVRPCLAGVEVAINTSFRKGIP-L 187
             +RD+L  L                     I+ ++ V VR CL GVE+ +++    G P  
Sbjct:    63 RRDDLMVLSRGSLLGSSNGDFKEDVEM--ISGKNHVVVRQCLVGVEIMLSSRCCGGQPRF 120

Query:   188 SQVVALLAEEGLTVVNCISTKINERLLHNIESEVNDGGRNIDPFELQQKIMKL 240
             S V+ +L+E GL ++N IS+ +++RL++ I++EVND    ID  EL+++++++
Sbjct:   121 SSVLQVLSEYGLCLLNSISSIVDDRLVYTIQAEVNDMALMIDLAELEKRLIRM 173
GO:0003677 "DNA binding" evidence=ISS
GO:0005634 "nucleus" evidence=ISM
GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS
GO:0006355 "regulation of transcription, DNA-dependent" evidence=TAS
TAIR|locus:504956298 AT1G62975 "AT1G62975" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2138019 AT4G25400 "AT4G25400" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2040287 BHLH100 "basic helix-loop-helix protein 100" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2133089 AT4G20970 "AT4G20970" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2080600 bHLH38 "basic helix-loop-helix 38" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2146663 BHLH101 "AT5G04150" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|Q941Z7 P0431G06.13-1 "BHLH transcription factor-like" [Oryza sativa Japonica Group (taxid:39947)] Back     alignment and assigned GO terms
TAIR|locus:2080615 bHLH39 "basic helix-loop-helix 39" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2079512 AT3G61950 "AT3G61950" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
Q9LN95BH055_ARATHNo assigned EC number0.38170.89830.8599yesno

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:
fgenesh4_pg.C_LG_I001018
hypothetical protein (241 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 ?
Query246
cd0008360 cd00083, HLH, Helix-loop-helix domain, found in sp 2e-08
pfam0001052 pfam00010, HLH, Helix-loop-helix DNA-binding domai 5e-06
smart0035353 smart00353, HLH, helix loop helix domain 2e-05
>gnl|CDD|238036 cd00083, HLH, Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long Back     alignment and domain information 
 Score = 49.5 bits (119), Expect = 2e-08
 Identities = 20/56 (35%), Positives = 32/56 (57%)

Query: 69  KIMRRDIERHRRQEMSTLYRSLRSLLPLEYLKGKRSMSDHMNEAVNYIKNLQNRIQ 124
           +      ER RR+ ++  +  LRSLLP      K S ++ + +AV+YIK+LQ  +Q
Sbjct: 5   REAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 60

A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins. Length = 60
>gnl|CDD|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain Back     alignment and domain information
>gnl|CDD|197674 smart00353, HLH, helix loop helix domain Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 246
PF0001055 HLH: Helix-loop-helix DNA-binding domain only nucl 99.43
cd0008360 HLH Helix-loop-helix domain, found in specific DNA 99.41
smart0035353 HLH helix loop helix domain. 99.34
KOG1318411 consensus Helix loop helix transcription factor EB 98.95
KOG2483232 consensus Upstream transcription factor 2/L-myc-2 98.67
KOG1319229 consensus bHLHZip transcription factor BIGMAX [Tra 98.49
KOG4029228 consensus Transcription factor HAND2/Transcription 98.25
KOG3561 803 consensus Aryl-hydrocarbon receptor nuclear transl 98.06
KOG4304250 consensus Transcriptional repressors of the hairy/ 98.03
KOG3960284 consensus Myogenic helix-loop-helix transcription 98.01
KOG0561 373 consensus bHLH transcription factor [Transcription 97.87
cd0489572 ACT_ACR_1 ACT domain-containing protein which is c 97.87
PLN0321793 transcription factor ATBS1; Provisional 97.81
cd0489775 ACT_ACR_3 ACT domain-containing protein which is c 97.61
cd0490073 ACT_UUR-like_1 ACT domain family, ACT_UUR-like_1, 97.59
cd0492776 ACT_ACR-like_2 Second ACT domain, of a novel type 97.34
cd0492868 ACT_TyrKc Uncharacterized, N-terminal ACT domain o 97.2
KOG2588 953 consensus Predicted DNA-binding protein [Transcrip 97.18
cd0489970 ACT_ACR-UUR-like_2 C-terminal ACT domains of the b 97.16
cd0489675 ACT_ACR-like_3 ACT domain-containing protein which 97.13
cd0492672 ACT_ACR_4 C-terminal ACT domain, of a novel type o 97.1
cd0492574 ACT_ACR_2 ACT domain-containing protein which is c 96.97
KOG4447173 consensus Transcription factor TWIST [Transcriptio 96.46
PRK05007884 PII uridylyl-transferase; Provisional 96.39
KOG3910632 consensus Helix loop helix transcription factor [T 96.19
cd0487370 ACT_UUR-ACR-like ACT domains of the bacterial sign 95.81
PRK00275895 glnD PII uridylyl-transferase; Provisional 95.73
PRK03381 774 PII uridylyl-transferase; Provisional 95.66
PF1374076 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A. 95.59
PRK01759854 glnD PII uridylyl-transferase; Provisional 95.57
PRK04374869 PII uridylyl-transferase; Provisional 95.56
PF0184266 ACT: ACT domain; InterPro: IPR002912 The ACT domai 95.37
KOG3898254 consensus Transcription factor NeuroD and related 95.36
PRK03059856 PII uridylyl-transferase; Provisional 95.27
PRK05092931 PII uridylyl-transferase; Provisional 95.12
cd0489377 ACT_GcvR_1 ACT domains that comprise the Glycine C 95.1
PRK0019490 hypothetical protein; Validated 95.1
PRK03381774 PII uridylyl-transferase; Provisional 95.06
cd0486981 ACT_GcvR_2 ACT domains that comprise the Glycine C 94.92
PRK01759 854 glnD PII uridylyl-transferase; Provisional 94.85
cd0487288 ACT_1ZPV ACT domain proteins similar to the yet un 94.72
TIGR01693850 UTase_glnD [Protein-PII] uridylyltransferase. This 94.62
TIGR01693 850 UTase_glnD [Protein-PII] uridylyltransferase. This 94.61
PRK05007 884 PII uridylyl-transferase; Provisional 94.6
COG2844867 GlnD UTP:GlnB (protein PII) uridylyltransferase [P 94.47
PF1329180 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A. 94.43
cd0487574 ACT_F4HF-DF N-terminal ACT domain of formyltetrahy 94.43
KOG4395285 consensus Transcription factor Atonal, contains HT 94.28
PRK03059 856 PII uridylyl-transferase; Provisional 93.91
cd0487075 ACT_PSP_1 CT domains found N-terminal of phosphose 93.85
cd0488774 ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-te 93.77
PRK00275 895 glnD PII uridylyl-transferase; Provisional 93.37
cd0488876 ACT_PheB-BS C-terminal ACT domain of a small (~147 92.92
cd0488673 ACT_ThrD-II-like C-terminal ACT domain of biodegra 92.73
PRK04374 869 PII uridylyl-transferase; Provisional 92.68
PRK05092 931 PII uridylyl-transferase; Provisional 92.55
PRK04435147 hypothetical protein; Provisional 91.79
cd0487671 ACT_RelA-SpoT ACT domain found C-terminal of the R 90.75
cd0489469 ACT_ACR-like_1 ACT domain-containing protein which 90.59
cd0211660 ACT ACT domains are commonly involved in specifica 89.66
cd0488075 ACT_AAAH-PDT-like ACT domain of the nonheme iron-d 88.79
cd0487774 ACT_TyrR N-terminal ACT domain of the TyrR protein 87.94
cd0487472 ACT_Af1403 N-terminal ACT domain of the yet unchar 86.57
cd0490580 ACT_CM-PDT C-terminal ACT domain of the bifunction 86.32
PRK08577136 hypothetical protein; Provisional 85.9
cd0493190 ACT_PAH ACT domain of the nonheme iron-dependent a 85.34
PRK06027 286 purU formyltetrahydrofolate deformylase; Reviewed 85.18
cd0488179 ACT_HSDH-Hom ACT_HSDH_Hom CD includes the C-termin 85.04
PRK13011 286 formyltetrahydrofolate deformylase; Reviewed 84.89
cd0490474 ACT_AAAH ACT domain of the nonheme iron-dependent, 83.59
TIGR00655 280 PurU formyltetrahydrofolate deformylase. This mode 83.41
cd0487971 ACT_3PGDH-like ACT_3PGDH-like CD includes the C-te 81.54
PRK13010 289 purU formyltetrahydrofolate deformylase; Reviewed 80.89
>PF00010 HLH: Helix-loop-helix DNA-binding domain only nuclear translocator protein (Arnt) Back     alignment and domain information 
Probab=99.43  E-value=3.7e-13  Score=93.22  Aligned_cols=53  Identities=32%  Similarity=0.465  Sum_probs=48.9

Q ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHhcCCCC--CcCCCCChhHHHHHHHHHHHHHH
Q 047562           68 MKIMRRDIERHRRQEMSTLYRSLRSLLPLE--YLKGKRSMSDHMNEAVNYIKNLQ  120 (246)
Q Consensus        68 ~~~~h~~~ER~RR~~mn~~f~~LrsllP~~--~~~~k~s~~~il~~Ai~YIk~Lq  120 (246)
                      +|..|+..||+||..||..|..|+.+||..  ....|.++++||..||+||++||
T Consensus         1 rR~~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq   55 (55)
T PF00010_consen    1 RRQKHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ   55 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence            578999999999999999999999999996  25678999999999999999997

; InterPro: IPR011598 The helix-loop-helix (HLH) DNA-binding domain consists of a closed bundle of four helices in a left-handed twist with two crossover connections. The HLH domain directs dimerisation, and is juxtaposed to basic regions to create a DNA interaction interface surface that recognises specific DNA sequences. Basic region/HLH (bHLH) proteins regulate diverse biological pathways []. bHLH proteins include MyoD [], SREBPs (sterol regulatory element binding proteins) [], and yeast Pho4 (phosphatase system) []. In certain proteins the bHLH domain contains a leucine-zipper motif. The bHLH/leucine zipper (bHLHZip) domain specifies dimerisation within a network of proteins and determines sequence-specific DNA binding []. bHLHZip domains occur in the transcription factors Myc, Mad, Max and Usf [, ]. This entry is bHLHZip, which covers the bHLH domain and the leucine zipper motif, when present.; PDB: 1NLW_A 1NKP_D 1A93_A 2A93_A 1AM9_C 3U5V_A 1A0A_B 2QL2_C 1UKL_C 1AN4_B ....
>cd00083 HLH Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long Back     alignment and domain information
>smart00353 HLH helix loop helix domain Back     alignment and domain information
>KOG1318 consensus Helix loop helix transcription factor EB [Transcription] Back     alignment and domain information
>KOG2483 consensus Upstream transcription factor 2/L-myc-2 protein [Transcription] Back     alignment and domain information
>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription] Back     alignment and domain information
>KOG4029 consensus Transcription factor HAND2/Transcription factor TAL1/TAL2/LYL1 [Transcription] Back     alignment and domain information
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription] Back     alignment and domain information
>KOG4304 consensus Transcriptional repressors of the hairy/E(spl) family (contains HLH) [Transcription] Back     alignment and domain information
>KOG3960 consensus Myogenic helix-loop-helix transcription factor [Transcription] Back     alignment and domain information
>KOG0561 consensus bHLH transcription factor [Transcription] Back     alignment and domain information
>cd04895 ACT_ACR_1 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein) Back     alignment and domain information
>PLN03217 transcription factor ATBS1; Provisional Back     alignment and domain information
>cd04897 ACT_ACR_3 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein) Back     alignment and domain information
>cd04900 ACT_UUR-like_1 ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains Back     alignment and domain information
>cd04927 ACT_ACR-like_2 Second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein) Back     alignment and domain information
>cd04928 ACT_TyrKc Uncharacterized, N-terminal ACT domain of an Arabidopsis/Oryza predicted tyrosine kinase and other related ACT domains Back     alignment and domain information
>KOG2588 consensus Predicted DNA-binding protein [Transcription] Back     alignment and domain information
>cd04899 ACT_ACR-UUR-like_2 C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains Back     alignment and domain information
>cd04896 ACT_ACR-like_3 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein) Back     alignment and domain information
>cd04926 ACT_ACR_4 C-terminal ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein) Back     alignment and domain information
>cd04925 ACT_ACR_2 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein) Back     alignment and domain information
>KOG4447 consensus Transcription factor TWIST [Transcription] Back     alignment and domain information
>PRK05007 PII uridylyl-transferase; Provisional Back     alignment and domain information
>KOG3910 consensus Helix loop helix transcription factor [Transcription] Back     alignment and domain information
>cd04873 ACT_UUR-ACR-like ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD Back     alignment and domain information
>PRK00275 glnD PII uridylyl-transferase; Provisional Back     alignment and domain information
>PRK03381 PII uridylyl-transferase; Provisional Back     alignment and domain information
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A Back     alignment and domain information
>PRK01759 glnD PII uridylyl-transferase; Provisional Back     alignment and domain information
>PRK04374 PII uridylyl-transferase; Provisional Back     alignment and domain information
>PF01842 ACT: ACT domain; InterPro: IPR002912 The ACT domain is found in a variety of contexts and is proposed to be a conserved regulatory binding fold Back     alignment and domain information
>KOG3898 consensus Transcription factor NeuroD and related HTH proteins [Transcription] Back     alignment and domain information
>PRK03059 PII uridylyl-transferase; Provisional Back     alignment and domain information
>PRK05092 PII uridylyl-transferase; Provisional Back     alignment and domain information
>cd04893 ACT_GcvR_1 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains Back     alignment and domain information
>PRK00194 hypothetical protein; Validated Back     alignment and domain information
>PRK03381 PII uridylyl-transferase; Provisional Back     alignment and domain information
>cd04869 ACT_GcvR_2 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains Back     alignment and domain information
>PRK01759 glnD PII uridylyl-transferase; Provisional Back     alignment and domain information
>cd04872 ACT_1ZPV ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain protein Back     alignment and domain information
>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase Back     alignment and domain information
>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase Back     alignment and domain information
>PRK05007 PII uridylyl-transferase; Provisional Back     alignment and domain information
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A Back     alignment and domain information
>cd04875 ACT_F4HF-DF N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase) Back     alignment and domain information
>KOG4395 consensus Transcription factor Atonal, contains HTH domain [Transcription] Back     alignment and domain information
>PRK03059 PII uridylyl-transferase; Provisional Back     alignment and domain information
>cd04870 ACT_PSP_1 CT domains found N-terminal of phosphoserine phosphatase (PSP, SerB) Back     alignment and domain information
>cd04887 ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI and related domains Back     alignment and domain information
>PRK00275 glnD PII uridylyl-transferase; Provisional Back     alignment and domain information
>cd04888 ACT_PheB-BS C-terminal ACT domain of a small (~147 a Back     alignment and domain information
>cd04886 ACT_ThrD-II-like C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains Back     alignment and domain information
>PRK04374 PII uridylyl-transferase; Provisional Back     alignment and domain information
>PRK05092 PII uridylyl-transferase; Provisional Back     alignment and domain information
>PRK04435 hypothetical protein; Provisional Back     alignment and domain information
>cd04876 ACT_RelA-SpoT ACT domain found C-terminal of the RelA/SpoT domains Back     alignment and domain information
>cd04894 ACT_ACR-like_1 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein) Back     alignment and domain information
>cd02116 ACT ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme Back     alignment and domain information
>cd04880 ACT_AAAH-PDT-like ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH) Back     alignment and domain information
>cd04877 ACT_TyrR N-terminal ACT domain of the TyrR protein Back     alignment and domain information
>cd04874 ACT_Af1403 N-terminal ACT domain of the yet uncharacterized, small (~133 a Back     alignment and domain information
>cd04905 ACT_CM-PDT C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme Back     alignment and domain information
>PRK08577 hypothetical protein; Provisional Back     alignment and domain information
>cd04931 ACT_PAH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH) Back     alignment and domain information
>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed Back     alignment and domain information
>cd04881 ACT_HSDH-Hom ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) and related domains Back     alignment and domain information
>PRK13011 formyltetrahydrofolate deformylase; Reviewed Back     alignment and domain information
>cd04904 ACT_AAAH ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH) Back     alignment and domain information
>TIGR00655 PurU formyltetrahydrofolate deformylase Back     alignment and domain information
>cd04879 ACT_3PGDH-like ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH) Back     alignment and domain information
>PRK13010 purU formyltetrahydrofolate deformylase; Reviewed 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 ?
Query246
1am9_A82 Srebp-1A, protein (sterol regulatory element bindi 3e-08
1nkp_A88 C-MYC, MYC proto-oncogene protein; transcription, 4e-08
1nkp_B83 MAX protein, MYC proto-oncogene protein; transcrip 1e-06
1hlo_A80 Protein (transcription factor MAX); transcriptiona 2e-06
1nlw_A80 MAD protein, MAX dimerizer; transcription factor, 2e-05
1an4_A65 Protein (upstream stimulatory factor); protein-DNA 9e-04
>1am9_A Srebp-1A, protein (sterol regulatory element binding protein 1A); basic-helix-loop- helix-leucine zipper, transcription factor; HET: DNA; 2.30A {Homo sapiens} SCOP: a.38.1.1 PDB: 1ukl_C Length = 82 Back     alignment and structure
 Score = 48.9 bits (117), Expect = 3e-08
 Identities = 20/80 (25%), Positives = 39/80 (48%), Gaps = 6/80 (7%)

Query: 67  KMKIMRRD----IERHRRQEMSTLYRSLRSLLPLEYLKGKRSMSDHMNEAVNYIKNLQNR 122
           + +  +R     IE+  R  ++     L+ L+     + K + S  + +A++YI+ LQ+ 
Sbjct: 1   QSRGEKRTAHNAIEKRYRSSINDKIIELKDLVV--GTEAKLNKSAVLRKAIDYIRFLQHS 58

Query: 123 IQKLSEKRDELRRLSNSSSS 142
            QKL ++   LR   + S S
Sbjct: 59  NQKLKQENLSLRTAVHKSKS 78
>1nkp_A C-MYC, MYC proto-oncogene protein; transcription, DNA, BHLHZ, heterodimer, transcription/DNA complex; 1.80A {Homo sapiens} SCOP: a.38.1.1 Length = 88 Back     alignment and structure
>1nkp_B MAX protein, MYC proto-oncogene protein; transcription, DNA, BHLHZ, heterodimer, transcription/DNA complex; 1.80A {Homo sapiens} SCOP: a.38.1.1 PDB: 1an2_A* 1r05_A 1nlw_B Length = 83 Back     alignment and structure
>1hlo_A Protein (transcription factor MAX); transcriptional regulation, DNA binding, complex (transcription factor MAX/DNA), transcription/DNA complex; HET: DNA; 2.80A {Homo sapiens} SCOP: a.38.1.1 Length = 80 Back     alignment and structure
>1nlw_A MAD protein, MAX dimerizer; transcription factor, DNA, BHLHZ, transcription/DNA complex; 2.00A {Homo sapiens} SCOP: a.38.1.1 Length = 80 Back     alignment and structure
>1an4_A Protein (upstream stimulatory factor); protein-DNA complex, double helix, overhanging base, transcription/DNA complex; HET: DNA; 2.90A {Homo sapiens} SCOP: a.38.1.1 Length = 65 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query246
1nlw_A80 MAD protein, MAX dimerizer; transcription factor, 99.66
1nkp_A88 C-MYC, MYC proto-oncogene protein; transcription, 99.64
1hlo_A80 Protein (transcription factor MAX); transcriptiona 99.63
1am9_A82 Srebp-1A, protein (sterol regulatory element bindi 99.62
1nkp_B83 MAX protein, MYC proto-oncogene protein; transcrip 99.61
3u5v_A76 Protein MAX, transcription factor E2-alpha chimer; 99.53
1a0a_A63 BHLH, protein (phosphate system positive regulator 99.53
1an4_A65 Protein (upstream stimulatory factor); protein-DNA 99.48
4ati_A118 MITF, microphthalmia-associated transcription fact 99.47
4h10_B71 Circadian locomoter output cycles protein kaput; B 99.47
2ql2_B60 Neurod1, neurogenic differentiation factor 1; basi 99.47
1mdy_A68 Protein (MYOD BHLH domain); protein-DNA complex, t 99.39
4h10_A73 ARYL hydrocarbon receptor nuclear translocator-LI 99.27
2lfh_A68 DNA-binding protein inhibitor ID-3; structural gen 99.01
4f3l_A 361 Mclock, circadian locomoter output cycles protein 98.76
4aya_A97 DNA-binding protein inhibitor ID-2; cell cycle; 2. 98.64
4f3l_B 387 BMAL1B; BHLH, PAS, circadian rhythm proteins, tran 98.52
4ath_A83 MITF, microphthalmia-associated transcription fact 98.24
1zpv_A91 ACT domain protein; structural genomics, PSI, prot 96.2
2nyi_A 195 Unknown protein; protein structure initiative, PSI 93.57
1u8s_A 192 Glycine cleavage system transcriptional repressor, 93.47
2ko1_A88 CTR148A, GTP pyrophosphokinase; homodimer, alpha+b 92.64
1u8s_A192 Glycine cleavage system transcriptional repressor, 91.08
2nyi_A195 Unknown protein; protein structure initiative, PSI 90.41
3p96_A 415 Phosphoserine phosphatase SERB; ssgcid, structural 83.26
3he4_B46 Synzip5; heterodimeric coiled-coil, de novo protei 80.99
3o1l_A 302 Formyltetrahydrofolate deformylase; structural gen 80.78
3obi_A 288 Formyltetrahydrofolate deformylase; structural gen 80.49
>1nlw_A MAD protein, MAX dimerizer; transcription factor, DNA, BHLHZ, transcription/DNA complex; 2.00A {Homo sapiens} SCOP: a.38.1.1 Back     alignment and structure
Probab=99.66  E-value=4.6e-16  Score=115.37  Aligned_cols=68  Identities=22%  Similarity=0.345  Sum_probs=63.3

Q ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCcCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 047562           68 MKIMRRDIERHRRQEMSTLYRSLRSLLPLEYLKGKRSMSDHMNEAVNYIKNLQNRIQKLSEKRDELRR  135 (246)
Q Consensus        68 ~~~~h~~~ER~RR~~mn~~f~~LrsllP~~~~~~k~s~~~il~~Ai~YIk~Lq~~v~~L~~~k~~l~~  135 (246)
                      +|..||..||+||..||..|..|+++||......|.|+++||..|++||+.|+++.++|..+++.+..
T Consensus         1 ~R~~HN~~ER~RR~~lk~~f~~Lr~~vP~~~~~~k~sk~~iL~kA~~yI~~L~~~~~~l~~e~~~L~~   68 (80)
T 1nlw_A            1 SRSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQR   68 (80)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcchHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            37899999999999999999999999998877889999999999999999999999999998887764
>1nkp_A C-MYC, MYC proto-oncogene protein; transcription, DNA, BHLHZ, heterodimer, transcription/DNA complex; 1.80A {Homo sapiens} SCOP: a.38.1.1 Back     alignment and structure
>1hlo_A Protein (transcription factor MAX); transcriptional regulation, DNA binding, complex (transcription factor MAX/DNA), transcription/DNA complex; HET: DNA; 2.80A {Homo sapiens} SCOP: a.38.1.1 Back     alignment and structure
>1am9_A Srebp-1A, protein (sterol regulatory element binding protein 1A); basic-helix-loop- helix-leucine zipper, transcription factor; HET: DNA; 2.30A {Homo sapiens} SCOP: a.38.1.1 PDB: 1ukl_C Back     alignment and structure
>1nkp_B MAX protein, MYC proto-oncogene protein; transcription, DNA, BHLHZ, heterodimer, transcription/DNA complex; 1.80A {Homo sapiens} SCOP: a.38.1.1 PDB: 1an2_A* 1r05_A 1nlw_B Back     alignment and structure
>3u5v_A Protein MAX, transcription factor E2-alpha chimer; basic helix-loop-helix (BHLH); 1.70A {Mus musculus} PDB: 2ql2_A* Back     alignment and structure
>1a0a_A BHLH, protein (phosphate system positive regulatory protein PHO4); transcription factor, basic helix loop helix; HET: DNA; 2.80A {Saccharomyces cerevisiae} SCOP: a.38.1.1 Back     alignment and structure
>1an4_A Protein (upstream stimulatory factor); protein-DNA complex, double helix, overhanging base, transcription/DNA complex; HET: DNA; 2.90A {Homo sapiens} SCOP: a.38.1.1 Back     alignment and structure
>4ati_A MITF, microphthalmia-associated transcription factor; DNA-binding protein-DNA complex, melanoma; 2.60A {Mus musculus} PDB: 4atk_A Back     alignment and structure
>4h10_B Circadian locomoter output cycles protein kaput; BHLH, circadian transcription, transcription-DNA complex; 2.40A {Homo sapiens} Back     alignment and structure
>2ql2_B Neurod1, neurogenic differentiation factor 1; basic-helix-loop-helix; HET: DNA; 2.50A {Mus musculus} Back     alignment and structure
>1mdy_A Protein (MYOD BHLH domain); protein-DNA complex, transcription/DNA complex; HET: DNA; 2.80A {Mus musculus} SCOP: a.38.1.1 PDB: 1mdy_B* Back     alignment and structure
>4h10_A ARYL hydrocarbon receptor nuclear translocator-LI 1; BHLH, circadian transcription, transcription-DNA complex; 2.40A {Homo sapiens} Back     alignment and structure
>2lfh_A DNA-binding protein inhibitor ID-3; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens} Back     alignment and structure
>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus} Back     alignment and structure
>4aya_A DNA-binding protein inhibitor ID-2; cell cycle; 2.10A {Homo sapiens} Back     alignment and structure
>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus} Back     alignment and structure
>4ath_A MITF, microphthalmia-associated transcription factor; DNA binding protein, melanoma; HET: MSE; 1.95A {Mus musculus} Back     alignment and structure
>1zpv_A ACT domain protein; structural genomics, PSI, protein structure INIT midwest center for structural genomics, MCSG, unknown funct; 1.90A {Streptococcus pneumoniae} SCOP: d.58.18.7 Back     alignment and structure
>2nyi_A Unknown protein; protein structure initiative, PSI, center for eukaryotic structural genomics, CESG, structural genomics; 1.80A {Galdieria sulphuraria} Back     alignment and structure
>1u8s_A Glycine cleavage system transcriptional repressor, putative; structural genomics, protein structure initiative (PSI), domain swapping; 2.45A {Vibrio cholerae} SCOP: d.58.18.5 d.58.18.5 Back     alignment and structure
>2ko1_A CTR148A, GTP pyrophosphokinase; homodimer, alpha+beta, transferase, structural genomics, PSI-2, protein structure initiative; NMR {Chlorobaculum tepidum} PDB: 3ibw_A Back     alignment and structure
>1u8s_A Glycine cleavage system transcriptional repressor, putative; structural genomics, protein structure initiative (PSI), domain swapping; 2.45A {Vibrio cholerae} SCOP: d.58.18.5 d.58.18.5 Back     alignment and structure
>2nyi_A Unknown protein; protein structure initiative, PSI, center for eukaryotic structural genomics, CESG, structural genomics; 1.80A {Galdieria sulphuraria} Back     alignment and structure
>3p96_A Phosphoserine phosphatase SERB; ssgcid, structural genomics, structural genomics center for infectious disease, hydrolas; 2.05A {Mycobacterium avium} Back     alignment and structure
>3he4_B Synzip5; heterodimeric coiled-coil, de novo protein; 2.46A {Artificial gene} Back     alignment and structure
>3o1l_A Formyltetrahydrofolate deformylase; structural genomics, joint center for structural genomics, J protein structure initiative; HET: MSE; 2.20A {Pseudomonas syringae PV} Back     alignment and structure
>3obi_A Formyltetrahydrofolate deformylase; structural genomics, joint center for structural genomics, J protein structure initiative; HET: MSE; 1.95A {Rhodopseudomonas palustris} 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 246
d1nkpa_88 a.38.1.1 (A:) Myc proto-oncogene protein {Human (H 2e-13
d1nlwa_79 a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T 2e-10
d1nkpb_83 a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T 1e-09
d1a0aa_63 a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa 4e-08
d1am9a_80 a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI 4e-08
d1mdya_68 a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul 2e-06
d1an4a_65 a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien 2e-06
d1uklc_61 a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId 3e-06
>d1nkpa_ a.38.1.1 (A:) Myc proto-oncogene protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88 Back     information, alignment and structure

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Myc proto-oncogene protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.2 bits (151), Expect = 2e-13
 Identities = 19/61 (31%), Positives = 30/61 (49%)

Query: 75  IERHRRQEMSTLYRSLRSLLPLEYLKGKRSMSDHMNEAVNYIKNLQNRIQKLSEKRDELR 134
           +ER RR E+   + +LR  +P      K      + +A  YI ++Q   QKL  + D LR
Sbjct: 13  LERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLR 72

Query: 135 R 135
           +
Sbjct: 73  K 73
>d1nlwa_ a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [TaxId: 9606]} Length = 79 Back     information, alignment and structure
>d1nkpb_ a.38.1.1 (B:) Max protein {Human (Homo sapiens) [TaxId: 9606]} Length = 83 Back     information, alignment and structure
>d1a0aa_ a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 63 Back     information, alignment and structure
>d1am9a_ a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxId: 9606]} Length = 80 Back     information, alignment and structure
>d1mdya_ a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 68 Back     information, alignment and structure
>d1an4a_ a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapiens) [TaxId: 9606]} Length = 65 Back     information, alignment and structure
>d1uklc_ a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId: 9606]} Length = 61 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 ?
Query246
d1nlwa_79 Mad protein {Human (Homo sapiens) [TaxId: 9606]} 99.65
d1nkpa_88 Myc proto-oncogene protein {Human (Homo sapiens) [ 99.63
d1am9a_80 SREBP-1a {Human (Homo sapiens) [TaxId: 9606]} 99.58
d1nkpb_83 Max protein {Human (Homo sapiens) [TaxId: 9606]} 99.57
d1mdya_68 Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10 99.54
d1a0aa_63 Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce 99.51
d1an4a_65 Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960 99.4
d1uklc_61 SREBP-2 {Human (Homo sapiens) [TaxId: 9606]} 99.2
d1zpva183 UPF0237 protein SP0238 {Streptococcus pneumoniae [ 96.21
d1u8sa186 putative transcriptional repressor VC2159 {Vibrio 95.5
d1u8sa293 putative transcriptional repressor VC2159 {Vibrio 94.23
d1y7pa277 Hypothetical protein AF1403, N-terminal domain {Ar 91.21
d2f06a171 Hypothetical protein BT0572 {Bacteroides thetaiota 82.08
>d1nlwa_ a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Mad protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=2.5e-16  Score=114.43  Aligned_cols=67  Identities=22%  Similarity=0.357  Sum_probs=62.5

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHHhcCCCCCcCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 047562           69 KIMRRDIERHRRQEMSTLYRSLRSLLPLEYLKGKRSMSDHMNEAVNYIKNLQNRIQKLSEKRDELRR  135 (246)
Q Consensus        69 ~~~h~~~ER~RR~~mn~~f~~LrsllP~~~~~~k~s~~~il~~Ai~YIk~Lq~~v~~L~~~k~~l~~  135 (246)
                      |..|+.+||+||..||+.|..|+++||......|.|+++||..||+||+.|+++++.|..+++.+..
T Consensus         2 R~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~L~~   68 (79)
T d1nlwa_           2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQR   68 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhCccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999998877789999999999999999999999999988877654
>d1nkpa_ a.38.1.1 (A:) Myc proto-oncogene protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1am9a_ a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1nkpb_ a.38.1.1 (B:) Max protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1mdya_ a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1a0aa_ a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1an4a_ a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1uklc_ a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1zpva1 d.58.18.7 (A:1-83) UPF0237 protein SP0238 {Streptococcus pneumoniae [TaxId: 1313]} Back     information, alignment and structure
>d1u8sa1 d.58.18.5 (A:2-87) putative transcriptional repressor VC2159 {Vibrio cholerae [TaxId: 666]} Back     information, alignment and structure
>d1u8sa2 d.58.18.5 (A:88-180) putative transcriptional repressor VC2159 {Vibrio cholerae [TaxId: 666]} Back     information, alignment and structure
>d1y7pa2 d.58.18.12 (A:2-78) Hypothetical protein AF1403, N-terminal domain {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d2f06a1 d.58.18.11 (A:71-141) Hypothetical protein BT0572 {Bacteroides thetaiotaomicron [TaxId: 818]} Back     information, alignment and structure