Citrus Sinensis ID: 036786

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-------16
MDKASKLLVLRRLSGAVKPSSPIHRSCSRLLVPSRIINMLPGNSLRHPSSTLITATRNFSSRPSGLDSDFQAPEAIDYRSLLQEDEFHRLANSTIHDLQEKFEEYGDTIQIDGFDVDYGNEVLTLKLGALGTYVLNKQTPNRQIWLSSPVRYYCGRSY
cccHHHHHHHHHHHccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccEEEccccEEEEEEcccEEEEEEccccccEEEEEccccccccccc
ccHHHHHHHHHHHHHHcccccHHHHHHcccccHHHHcccccccccccccHHHcccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccEEEcccEEEEEEccccEEEEEEEHHHcEEEEEEcEEEEccccc
MDKASKLLVLRRLsgavkpsspihrscsrllvpsriinmlpgnslrhpsstlitatrnfssrpsgldsdfqapeaidyRSLLQEDEFHRLANSTIHDLQEKFEEygdtiqidgfdvdygneVLTLKLGALGTyvlnkqtpnrqiwlsspvryycgrsy
mdkaskllVLRRlsgavkpsspihrscsrllVPSRIINMlpgnslrhpsSTLITAtrnfssrpsgldSDFQAPEAIDYRSLLQEDEFHRLANSTIHDLQEKFEEYGDTIQIDGFDVDYGNEVLTLKLGALGTYVlnkqtpnrqiwlsspvryycgrsy
MDKASKLLVLRRLSGAVKPSSPIHRSCSRLLVPSRIINMLPGNSLRHPSSTLITATRNFSSRPSGLDSDFQAPEAIDYRSLLQEDEFHRLANSTIHDLQEKFEEYGDTIQIDGFDVDYGNEVLTLKLGALGTYVLNKQTPNRQIWLSSPVRYYCGRSY
**************************CSRLLVPSRIINML***********************************IDYRSLLQEDEFHRLANSTIHDLQEKFEEYGDTIQIDGFDVDYGNEVLTLKLGALGTYVLNKQTPNRQIWLSSPVRYYCG***
***********R************************************************************************DEFHRLANSTIHDLQEKFEEYGDTIQIDGFDVDYGNEVLTLKLGALGTYVLNKQTPNRQIWLSSPVRYYCGRSY
MDKASKLLVLRRLSGAVKPSSPIHRSCSRLLVPSRIINMLPGNSLRHPSSTLITATRNFSSRPSGLDSDFQAPEAIDYRSLLQEDEFHRLANSTIHDLQEKFEEYGDTIQIDGFDVDYGNEVLTLKLGALGTYVLNKQTPNRQIWLSSPVRYYCGRSY
*****KLLVLRRLSGAVKPSSPIHRSCSRLLVPSRIINMLPGN***********************************RSLLQEDEFHRLANSTIHDLQEKFEEYGDTIQIDGFDVDYGNEVLTLKLGALGTYVLNKQTPNRQIWLSSPVRYYCGRS*
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MDKASKLLVLRRLSGAVKPSSPIHRSCSRLLVPSRIINMLPGNSLRHPSSTLITATRNFSSRPSGLDSDFQAPEAIDYRSLLQEDEFHRLANSTIHDLQEKFEEYGDTIQIDGFDVDYGNEVLTLKLGALGTYVLNKQTPNRQIWLSSPVRYYCGRSY
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 ?
Query158 2.2.26 [Sep-21-2011]
Q9ZR07187 Frataxin, mitochondrial O yes no 0.607 0.513 0.651 5e-34
O35943207 Frataxin, mitochondrial O yes no 0.468 0.357 0.526 5e-14
Q16595210 Frataxin, mitochondrial O no no 0.430 0.323 0.542 2e-13
Q05B87217 Frataxin, mitochondrial O yes no 0.487 0.354 0.488 2e-13
Q8HXX9210 Frataxin, mitochondrial O N/A no 0.430 0.323 0.528 5e-13
O74831158 Frataxin homolog, mitocho yes no 0.575 0.575 0.397 2e-12
Q9W385190 Frataxin homolog, mitocho yes no 0.468 0.389 0.447 3e-10
Q9TY03136 Frataxin, mitochondrial O yes no 0.443 0.514 0.402 9e-10
D3ZYW7208 Frataxin, mitochondrial O yes no 0.449 0.341 0.465 1e-09
Q54C45193 Frataxin, mitochondrial O yes no 0.348 0.284 0.492 2e-09
>sp|Q9ZR07|FRDA_ARATH Frataxin, mitochondrial OS=Arabidopsis thaliana GN=FH PE=2 SV=2 Back     alignment and function desciption
 Score =  143 bits (360), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 71/109 (65%), Positives = 85/109 (77%), Gaps = 13/109 (11%)

Query: 42  GNSLRHPSSTLITATRNFSSRPSGLDSDFQAPEAIDYRSLLQEDEFHRLANSTIHDLQEK 101
           G+ +RH S T    TR+FSS         Q P ++DY S+LQE+EFH+LAN TI+ L EK
Sbjct: 49  GSRIRHDSLT----TRSFSS---------QGPASVDYSSVLQEEEFHKLANFTINHLLEK 95

Query: 102 FEEYGDTIQIDGFDVDYGNEVLTLKLGALGTYVLNKQTPNRQIWLSSPV 150
            E+YGD +QIDGFD+DYGNEVLTLKLG+LGTYVLNKQTPNRQIW+SSPV
Sbjct: 96  IEDYGDNVQIDGFDIDYGNEVLTLKLGSLGTYVLNKQTPNRQIWMSSPV 144
Promotes the biosynthesis of heme as well as the assembly and repair of iron-sulfur clusters by delivering Fe(2+) to proteins involved in these pathways. May play a role in the protection against iron-catalyzed oxidative stress through its ability to catalyze the oxidation of Fe(2+) to Fe(3+). May be able to store large amounts of the metal in the form of a ferrihydrite mineral by oligomerization.
Arabidopsis thaliana (taxid: 3702)
EC: 1EC: .EC: 1EC: 6EC: .EC: 3EC: .EC: 1
>sp|O35943|FRDA_MOUSE Frataxin, mitochondrial OS=Mus musculus GN=Fxn PE=1 SV=1 Back     alignment and function description
>sp|Q16595|FRDA_HUMAN Frataxin, mitochondrial OS=Homo sapiens GN=FXN PE=1 SV=2 Back     alignment and function description
>sp|Q05B87|FRDA_BOVIN Frataxin, mitochondrial OS=Bos taurus GN=FXN PE=2 SV=1 Back     alignment and function description
>sp|Q8HXX9|FRDA_MACFA Frataxin, mitochondrial OS=Macaca fascicularis GN=FXN PE=2 SV=1 Back     alignment and function description
>sp|O74831|FRDA_SCHPO Frataxin homolog, mitochondrial OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPCC1183.03c PE=3 SV=1 Back     alignment and function description
>sp|Q9W385|FRDA_DROME Frataxin homolog, mitochondrial OS=Drosophila melanogaster GN=fh PE=2 SV=1 Back     alignment and function description
>sp|Q9TY03|FRDA_CAEEL Frataxin, mitochondrial OS=Caenorhabditis elegans GN=frh-1 PE=2 SV=1 Back     alignment and function description
>sp|D3ZYW7|FRDA_RAT Frataxin, mitochondrial OS=Rattus norvegicus GN=Fxn PE=1 SV=1 Back     alignment and function description
>sp|Q54C45|FRDA_DICDI Frataxin, mitochondrial OS=Dictyostelium discoideum GN=fxn PE=3 SV=1 Back     alignment and function description

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

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query158
147766885202 hypothetical protein VITISV_004311 [Viti 0.905 0.707 0.620 4e-40
255581048200 Frataxin, mitochondrial precursor, putat 0.930 0.735 0.602 8e-40
225447713197 PREDICTED: frataxin, mitochondrial isofo 0.639 0.512 0.762 9e-39
224124686192 predicted protein [Populus trichocarpa] 0.892 0.734 0.623 4e-38
356571796191 PREDICTED: frataxin, mitochondrial-like 0.905 0.748 0.569 4e-36
124360476155 Frataxin-like [Medicago truncatula] 0.632 0.645 0.72 7e-36
449532278180 PREDICTED: frataxin, mitochondrial-like, 0.886 0.777 0.568 2e-34
356504311191 PREDICTED: frataxin, mitochondrial-like 0.898 0.743 0.552 2e-34
449444405191 PREDICTED: frataxin, mitochondrial-like 0.886 0.732 0.568 4e-34
357499221188 Frataxin-like protein [Medicago truncatu 0.639 0.537 0.702 1e-33
>gi|147766885|emb|CAN67530.1| hypothetical protein VITISV_004311 [Vitis vinifera] Back     alignment and taxonomy information
 Score =  169 bits (428), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 98/158 (62%), Positives = 111/158 (70%), Gaps = 15/158 (9%)

Query: 4   ASKLLVLRRLSGAVKPSSPIH-----------RSCSRLLVPSRIINMLPGNSLRHPSSTL 52
           +SKLL LRRLS A+K SS              R    LL  SR  ++   N LR   S L
Sbjct: 6   SSKLLFLRRLSRALKLSSSSSSSSSSSSSLSVRPYVFLLEASRPSDLAKIN-LR---SFL 61

Query: 53  ITATRNFSSRPSGLDSDFQAPEAIDYRSLLQEDEFHRLANSTIHDLQEKFEEYGDTIQID 112
             A+R+F SR   L+ D Q P AIDY SLLQEDEFH++A+STI DLQEKFEEYGD +QID
Sbjct: 62  SVASRSFCSRTLDLEDDSQGPAAIDYSSLLQEDEFHKVADSTIQDLQEKFEEYGDCVQID 121

Query: 113 GFDVDYGNEVLTLKLGALGTYVLNKQTPNRQIWLSSPV 150
           GFD+DYGN+VLTLKLG LGTYVLNKQTPNRQIWLSSPV
Sbjct: 122 GFDIDYGNQVLTLKLGTLGTYVLNKQTPNRQIWLSSPV 159

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|255581048|ref|XP_002531340.1| Frataxin, mitochondrial precursor, putative [Ricinus communis] gi|223529062|gb|EEF31047.1| Frataxin, mitochondrial precursor, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|225447713|ref|XP_002277091.1| PREDICTED: frataxin, mitochondrial isoform 1 [Vitis vinifera] gi|296081250|emb|CBI17994.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|224124686|ref|XP_002319394.1| predicted protein [Populus trichocarpa] gi|222857770|gb|EEE95317.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|356571796|ref|XP_003554058.1| PREDICTED: frataxin, mitochondrial-like [Glycine max] Back     alignment and taxonomy information
>gi|124360476|gb|ABN08486.1| Frataxin-like [Medicago truncatula] Back     alignment and taxonomy information
>gi|449532278|ref|XP_004173109.1| PREDICTED: frataxin, mitochondrial-like, partial [Cucumis sativus] Back     alignment and taxonomy information
>gi|356504311|ref|XP_003520940.1| PREDICTED: frataxin, mitochondrial-like [Glycine max] Back     alignment and taxonomy information
>gi|449444405|ref|XP_004139965.1| PREDICTED: frataxin, mitochondrial-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|357499221|ref|XP_003619899.1| Frataxin-like protein [Medicago truncatula] gi|355494914|gb|AES76117.1| Frataxin-like protein [Medicago truncatula] 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 ?
Query158
TAIR|locus:2125477187 FH "frataxin homolog" [Arabido 0.854 0.721 0.540 8.5e-33
UNIPROTKB|A8MXJ6196 FXN "Frataxin, mitochondrial" 0.449 0.362 0.547 1.6e-15
MGI|MGI:1096879207 Fxn "frataxin" [Mus musculus ( 0.468 0.357 0.526 2e-15
UNIPROTKB|A6Q0K4211 fxn "Frataxin" [Canis lupus fa 0.430 0.322 0.542 8.8e-15
UNIPROTKB|C9JAX1135 FXN "Frataxin, mitochondrial" 0.430 0.503 0.542 1.8e-14
UNIPROTKB|Q16595210 FXN "Frataxin, mitochondrial" 0.430 0.323 0.542 1.8e-14
UNIPROTKB|I3LTK1215 FXN "Uncharacterized protein" 0.430 0.316 0.528 2.3e-14
UNIPROTKB|Q05B87217 FXN "Frataxin, mitochondrial" 0.487 0.354 0.488 3e-14
ZFIN|ZDB-GENE-070209-286200 fxn "frataxin" [Danio rerio (t 0.778 0.615 0.395 1e-13
UNIPROTKB|F1P1P5122 FXN "Uncharacterized protein" 0.5 0.647 0.476 1.3e-13
TAIR|locus:2125477 FH "frataxin homolog" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 358 (131.1 bits), Expect = 8.5e-33, P = 8.5e-33
 Identities = 86/159 (54%), Positives = 109/159 (68%)

Query:     1 MDKASKLLVLRRLSGAVKPSSPIHRSCSRLLVPSRII--NMLP-------GNSLRHPSST 51
             M  AS+ L LR+L   +K S  + RS + + V S +I  ++ P       G+ +RH S T
Sbjct:     1 MATASRFL-LRKLPRFLKLSPTLLRS-NGVRVSSNLIQDSIEPLDSFWRIGSRIRHDSLT 58

Query:    52 LITATRNFSSRPSGLDSDFQAPEAIDYRSLLQEDEFHRLANSTIHDLQEKFEEYGDTIQI 111
                 TR+FSS         Q P ++DY S+LQE+EFH+LAN TI+ L EK E+YGD +QI
Sbjct:    59 ----TRSFSS---------QGPASVDYSSVLQEEEFHKLANFTINHLLEKIEDYGDNVQI 105

Query:   112 DGFDVDYGNEVLTLKLGALGTYVLNKQTPNRQIWLSSPV 150
             DGFD+DYGNEVLTLKLG+LGTYVLNKQTPNRQIW+SSPV
Sbjct:   106 DGFDIDYGNEVLTLKLGSLGTYVLNKQTPNRQIWMSSPV 144
GO:0004322 "ferroxidase activity" evidence=IEA
GO:0055114 "oxidation-reduction process" evidence=IEA
GO:0005739 "mitochondrion" evidence=ISS
GO:0009060 "aerobic respiration" evidence=IMP
GO:0042542 "response to hydrogen peroxide" evidence=IMP
GO:0006979 "response to oxidative stress" evidence=IMP
GO:0048825 "cotyledon development" evidence=RCA
GO:0051301 "cell division" evidence=RCA
UNIPROTKB|A8MXJ6 FXN "Frataxin, mitochondrial" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
MGI|MGI:1096879 Fxn "frataxin" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|A6Q0K4 fxn "Frataxin" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|C9JAX1 FXN "Frataxin, mitochondrial" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|Q16595 FXN "Frataxin, mitochondrial" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|I3LTK1 FXN "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|Q05B87 FXN "Frataxin, mitochondrial" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-070209-286 fxn "frataxin" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|F1P1P5 FXN "Uncharacterized protein" [Gallus gallus (taxid:9031)] 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 ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer1.16.3.10.914
3rd Layer1.16.30.921

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
GSVIVG00029229001
SubName- Full=Chromosome chr12 scaffold_47, whole genome shotgun sequence; (197 aa)
(Vitis vinifera)
Predicted Functional Partners:
GSVIVG00002729001
SubName- Full=Chromosome chr1 scaffold_135, whole genome shotgun sequence; (155 aa)
   •• • 0.580
GSVIVG00011471001
SubName- Full=Chromosome undetermined scaffold_310, whole genome shotgun sequence; (454 aa)
    • • 0.544
GSVIVG00017707001
SubName- Full=Chromosome chr17 scaffold_16, whole genome shotgun sequence; (381 aa)
    • • 0.497
GSVIVG00027378001
SubName- Full=Chromosome chr19 scaffold_4, whole genome shotgun sequence; (347 aa)
    • • 0.460
GSVIVG00020216001
SubName- Full=Chromosome chr5 scaffold_2, whole genome shotgun sequence; (251 aa)
    • • 0.419
GSVIVG00020593001
SubName- Full=Chromosome chr14 scaffold_21, whole genome shotgun sequence; (276 aa)
    • • 0.409

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 ?
Query158
TIGR0342297 TIGR03422, mito_frataxin, frataxin 8e-31
cd00503105 cd00503, Frataxin, Frataxin is a nuclear-encoded m 1e-26
pfam01491107 pfam01491, Frataxin_Cyay, Frataxin-like domain 3e-23
COG1965106 COG1965, CyaY, Protein implicated in iron transpor 2e-20
TIGR03421102 TIGR03421, FeS_CyaY, iron donor protein CyaY 6e-15
PRK00446105 PRK00446, cyaY, frataxin-like protein; Provisional 8e-10
PRK01379103 PRK01379, cyaY, frataxin-like protein; Provisional 4e-09
>gnl|CDD|132463 TIGR03422, mito_frataxin, frataxin Back     alignment and domain information 
 Score =  106 bits (267), Expect = 8e-31
 Identities = 37/72 (51%), Positives = 53/72 (73%), Gaps = 6/72 (8%)

Query: 86  EFHRLANSTIHDLQEKFEEYGDT-IQIDGFDVDYGNEVLTLKLGALGTYVLNKQTPNRQI 144
           E+H++A+  +  L +K EE G++   +D FDV+Y + VLTL+L ++GTYV+NKQ PN+QI
Sbjct: 1   EYHKVADEYLDHLLDKLEELGESRPDLD-FDVEYSSGVLTLELPSVGTYVINKQPPNKQI 59

Query: 145 WLSSPV----RY 152
           WLSSPV    RY
Sbjct: 60  WLSSPVSGPKRY 71

Frataxin is a mitochondrial protein, mutation of which leads to the disease Friedreich's ataxia. Its orthologs are widely distributed in the bacteria, associated with the ISC system for iron-sulfur cluster assembly, and designated CyaY. This exception-type model allows those examples of frataxin per se that score above the trusted cutoff to the CyaY equivalog-type model (TIGR03421) to be named appropriately. Length = 97
>gnl|CDD|238280 cd00503, Frataxin, Frataxin is a nuclear-encoded mitochondrial protein implicated in Friedreich's ataxia (FRDA), an human autosomal recessive neurodegenerative disease; Frataxin is found in eukaryotes and in purple bacteria; lack of frataxin causes iron to accumulate in the mitochondrial matrix suggesting that frataxin is involved in mitochondrial iron homeostasis and possibly in iron transport; the domain has an alpha-beta fold consisting of two helices flanking an antiparallel beta sheet Back     alignment and domain information
>gnl|CDD|216529 pfam01491, Frataxin_Cyay, Frataxin-like domain Back     alignment and domain information
>gnl|CDD|224876 COG1965, CyaY, Protein implicated in iron transport, frataxin homolog [Inorganic ion transport and metabolism] Back     alignment and domain information
>gnl|CDD|163255 TIGR03421, FeS_CyaY, iron donor protein CyaY Back     alignment and domain information
>gnl|CDD|234765 PRK00446, cyaY, frataxin-like protein; Provisional Back     alignment and domain information
>gnl|CDD|134546 PRK01379, cyaY, frataxin-like protein; Provisional Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 158
PF01491109 Frataxin_Cyay: Frataxin-like domain; InterPro: IPR 99.96
cd00503105 Frataxin Frataxin is a nuclear-encoded mitochondri 99.96
KOG3413156 consensus Mitochondrial matrix protein frataxin, i 99.96
TIGR0342297 mito_frataxin frataxin. Frataxin is a mitochondria 99.96
PRK00446105 cyaY frataxin-like protein; Provisional 99.96
COG1965106 CyaY Protein implicated in iron transport, frataxi 99.96
PRK01379103 cyaY frataxin-like protein; Provisional 99.96
TIGR03421102 FeS_CyaY iron donor protein CyaY. Members of this 99.95
>PF01491 Frataxin_Cyay: Frataxin-like domain; InterPro: IPR002908 The eukaryotic proteins in this entry include frataxin, the protein that is mutated in Friedreich's ataxia [], and related sequences Back     alignment and domain information 
Probab=99.96  E-value=5.1e-30  Score=192.08  Aligned_cols=76  Identities=42%  Similarity=0.707  Sum_probs=70.1

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHhhccCccCCCCcceeecCceEEEEECCCcEEEEeCCCCcceeeeecCCCccCcccC
Q 036786           82 LQEDEFHRLANSTIHDLQEKFEEYGDTIQIDGFDVDYGNEVLTLKLGALGTYVLNKQTPNRQIWLSSPVRYYCGRSY  158 (158)
Q Consensus        82 mte~eF~~lAd~~L~~L~e~lE~~~d~~~~~d~Dve~s~GVLTI~f~d~gtyVINKQ~PnkQIWLSSPisG~~~~~~  158 (158)
                      |++.+||++||++|+.|+++||++.|+.+ .++|+|++||||||+|+++|+||||||+|+||||||||+||..|+.|
T Consensus         1 Mt~~~f~~lad~~l~~i~~~le~~~d~~~-~d~d~e~~~gVLti~~~~~~~~VINkQ~p~~QIWlsSpisG~~hf~~   76 (109)
T PF01491_consen    1 MTESEFHQLADETLDSIEDALEELDDEQD-ADIDVERSGGVLTIEFPDGGQYVINKQPPNRQIWLSSPISGPFHFDY   76 (109)
T ss_dssp             -HHHHHHHHHHHHHHHHHHHHHTCTTSSS-STEEEEEETTEEEEEETTSEEEEEEEECCCTEEEEEETTTEEEEEEE
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHhccCC-CceEEEccCCEEEEEECCCCEEEEeCCCHHHHHHHhcccCCceEEEE
Confidence            88999999999999999999999876543 57999999999999999999999999999999999999999998876

Friedreich's ataxia is a progressive neurodegenerative disorder caused by loss of function mutations in the gene encoding frataxin (FRDA). Frataxin mRNA is predominantly expressed in tissues with a high metabolic rate (including liver, kidney, brown fat and heart). Mouse and yeast frataxin homologues contain a potential N-terminal mitochondrial targeting sequence, and human frataxin has been observed to co-localise with a mitochondrial protein. Furthermore, disruption of the yeast gene has been shown to result in mitochondrial dysfunction. Friedreich's ataxia is thus believed to be a mitochondrial disease caused by a mutation in the nuclear genome (specifically, expansion of an intronic GAA triplet repeat) [, , ]. The bacterial proteins in this entry are iron-sulphur cluster (FeS) metabolism CyaY proteins hmologous to eukaryotic frataxin. Partial Phylogenetic Profiling [] suggests that CyaY most likely functions as part of the ISC system for FeS cluster biosynthesis, and is supported by expermimental data in some species [, ]. ; PDB: 1EW4_A 2P1X_A 1SOY_A 2EFF_A 3T3T_B 3S4M_A 3T3K_A 3S5D_A 1LY7_A 3T3X_B ....
>cd00503 Frataxin Frataxin is a nuclear-encoded mitochondrial protein implicated in Friedreich's ataxia (FRDA), an human autosomal recessive neurodegenerative disease; Frataxin is found in eukaryotes and in purple bacteria; lack of frataxin causes iron to accumulate in the mitochondrial matrix suggesting that frataxin is involved in mitochondrial iron homeostasis and possibly in iron transport; the domain has an alpha-beta fold consisting of two helices flanking an antiparallel beta sheet Back     alignment and domain information
>KOG3413 consensus Mitochondrial matrix protein frataxin, involved in Fe/S protein biosynthesis [Inorganic ion transport and metabolism] Back     alignment and domain information
>TIGR03422 mito_frataxin frataxin Back     alignment and domain information
>PRK00446 cyaY frataxin-like protein; Provisional Back     alignment and domain information
>COG1965 CyaY Protein implicated in iron transport, frataxin homolog [Inorganic ion transport and metabolism] Back     alignment and domain information
>PRK01379 cyaY frataxin-like protein; Provisional Back     alignment and domain information
>TIGR03421 FeS_CyaY iron donor protein CyaY Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query158
1ekg_A127 Mature Human Frataxin Length = 127 3e-14
3s4m_A129 Crystal Structure Of Wild-Type Human Frataxin Lengt 4e-14
3t3x_A129 1.57 A Structure Of Friedreich's Ataxia Frataxin Va 4e-14
1ly7_A121 The Solution Structure Of The The C-Terminal Domain 1e-13
3t3k_A129 1.24 A Structure Of Friedreich's Ataxia Frataxin Va 1e-13
3t3l_A129 1.15 A Structure Of Human Frataxin Variant Q153a Le 2e-13
3t3j_A129 1.70 A Structure Of Friedreich's Ataxia Frataxin Va 2e-13
3t3t_A129 1.38 A Structure Of Human Frataxin Variant Q148g Le 2e-13
3s5f_A129 Crystal Structure Of Human Frataxin Variant W155f L 7e-13
3s5d_A129 Crystal Structure Of Human Frataxin Variant W155a L 2e-12
3s5e_A129 Crystal Structure Of Human Frataxin Variant W155r, 3e-12
2ga5_A123 Yeast Frataxin Length = 123 2e-08
2fql_A123 Crystal Structure Of Trimeric Frataxin From The Yea 7e-08
>pdb|1EKG|A Chain A, Mature Human Frataxin Length = 127 Back     alignment and structure 
Iteration: 1

 Score = 73.9 bits (180), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 38/70 (54%), Positives = 48/70 (68%), Gaps = 2/70 (2%)
Query: 82  LQEDEFHRLANSTIHDLQEKFEEYGDT-IQIDGFDVDYGNEVLTLKLGA-LGTYVLNKQT 139
           L E  + RLA  T+  L E FE+  D     + +DV +G+ VLT+KLG  LGTYV+NKQT
Sbjct: 7   LDETTYERLAEETLDSLAEFFEDLADKPYTFEDYDVSFGSGVLTVKLGGDLGTYVINKQT 66
Query: 140 PNRQIWLSSP 149
           PN+QIWLSSP
Sbjct: 67  PNKQIWLSSP 76
>pdb|3S4M|A Chain A, Crystal Structure Of Wild-Type Human Frataxin Length = 129 Back     alignment and structure
>pdb|3T3X|A Chain A, 1.57 A Structure Of Friedreich's Ataxia Frataxin Variant R165c Length = 129 Back     alignment and structure
>pdb|1LY7|A Chain A, The Solution Structure Of The The C-Terminal Domain Of Frataxin, The Protein Responsible For Friedreich Ataxia Length = 121 Back     alignment and structure
>pdb|3T3K|A Chain A, 1.24 A Structure Of Friedreich's Ataxia Frataxin Variant Q148r Length = 129 Back     alignment and structure
>pdb|3T3L|A Chain A, 1.15 A Structure Of Human Frataxin Variant Q153a Length = 129 Back     alignment and structure
>pdb|3T3J|A Chain A, 1.70 A Structure Of Friedreich's Ataxia Frataxin Variant N146k Length = 129 Back     alignment and structure
>pdb|3T3T|A Chain A, 1.38 A Structure Of Human Frataxin Variant Q148g Length = 129 Back     alignment and structure
>pdb|3S5F|A Chain A, Crystal Structure Of Human Frataxin Variant W155f Length = 129 Back     alignment and structure
>pdb|3S5D|A Chain A, Crystal Structure Of Human Frataxin Variant W155a Length = 129 Back     alignment and structure
>pdb|3S5E|A Chain A, Crystal Structure Of Human Frataxin Variant W155r, One Of The Friedreich's Ataxia Point Mutations Length = 129 Back     alignment and structure
>pdb|2GA5|A Chain A, Yeast Frataxin Length = 123 Back     alignment and structure
>pdb|2FQL|A Chain A, Crystal Structure Of Trimeric Frataxin From The Yeast Saccharomyces Cerevisiae Length = 123 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query158
3oeq_A123 Frataxin homolog, mitochondrial; alpha/beta sandwi 5e-25
3t3l_A129 Frataxin, mitochondrial; Fe-S cluster biosynthesis 2e-22
1ew4_A106 CYAY protein; friedreich ataxia, frataxin family, 1e-21
>3oeq_A Frataxin homolog, mitochondrial; alpha/beta sandwich, metallochaperone, iron-storage, transpo protein; 2.96A {Saccharomyces cerevisiae} PDB: 2fql_A 3oer_A 2ga5_A Length = 123 Back     alignment and structure
 Score = 92.3 bits (229), Expect = 5e-25
 Identities = 28/86 (32%), Positives = 45/86 (52%)

Query: 66  LDSDFQAPEAIDYRSLLQEDEFHRLANSTIHDLQEKFEEYGDTIQIDGFDVDYGNEVLTL 125
           ++S             L  ++ H  A+  +  L +  EE  +       DV+  + V+TL
Sbjct: 1   VESSTDGQVVPQEVLNLPLEKAHEEADDYLDHLLDSLEELSEAHPDCIPDVELSHGVMTL 60

Query: 126 KLGALGTYVLNKQTPNRQIWLSSPVR 151
           ++ A GTYV+NKQ PN+QIWL+SP+ 
Sbjct: 61  EIPAFGTYVINKQPPNKQIWLASPLS 86
>3t3l_A Frataxin, mitochondrial; Fe-S cluster biosynthesis, human mitochondria, oxidoreductas; 1.15A {Homo sapiens} PDB: 3s4m_A 3t3k_A 3t3j_A 3s5f_A 3t3x_A 3t3t_A 3s5e_A 3s5d_A 1ekg_A 1ly7_A Length = 129 Back     alignment and structure
>1ew4_A CYAY protein; friedreich ataxia, frataxin family, iron homeostasis, unknown function; 1.40A {Escherichia coli} SCOP: d.82.2.1 PDB: 2eff_A 2p1x_A 1soy_A Length = 106 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query158
3t3l_A129 Frataxin, mitochondrial; Fe-S cluster biosynthesis 99.97
3oeq_A123 Frataxin homolog, mitochondrial; alpha/beta sandwi 99.97
1ew4_A106 CYAY protein; friedreich ataxia, frataxin family, 99.97
>3t3l_A Frataxin, mitochondrial; Fe-S cluster biosynthesis, human mitochondria, oxidoreductas; 1.15A {Homo sapiens} SCOP: d.82.2.1 PDB: 3s4m_A 3t3k_A 3t3j_A 3s5f_A 3t3x_A 3t3t_A 3s5e_A 3s5d_A 1ekg_A 1ly7_A Back     alignment and structure
Probab=99.97  E-value=5.9e-32  Score=207.88  Aligned_cols=80  Identities=46%  Similarity=0.760  Sum_probs=71.2

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHhhccCcc-CCCCcceeecCceEEEEEC-CCcEEEEeCCCCcceeeeecCCCccCcc
Q 036786           79 RSLLQEDEFHRLANSTIHDLQEKFEEYGDTI-QIDGFDVDYGNEVLTLKLG-ALGTYVLNKQTPNRQIWLSSPVRYYCGR  156 (158)
Q Consensus        79 ~s~mte~eF~~lAd~~L~~L~e~lE~~~d~~-~~~d~Dve~s~GVLTI~f~-d~gtyVINKQ~PnkQIWLSSPisG~~~~  156 (158)
                      ++.|++.|||++||++|+.|+++||++.|+. ...|+|||+++|||||+|+ ++||||||||+||||||||||+||..|+
T Consensus         6 ~~~m~e~ef~~lad~~L~~ie~~le~~~d~~~~~~d~D~e~~~gVLti~f~~~~g~~VINkQ~P~~QIWLASp~SGp~hf   85 (129)
T 3t3l_A            6 PGSLDETTYERLAEETLDSLAEFFEDLADKPYTFEDYDVSFGSGVLTVKLGGDLGTYVINKQTPNKAIWLSSPSSGPKRY   85 (129)
T ss_dssp             ---CCHHHHHHHHHHHHHHHHHHHHHHHTSTTSCTTCEEEEETTEEEEECCTTCCEEEEEEETTTTEEEEECSSSCCEEE
T ss_pred             CCcCCHHHHHHHHHHHHHHHHHHHHhhhcccccccceeeecCCCEEEEEEcCCCCEEEEeCCchhhHhheeCCCCCCeee
Confidence            5679999999999999999999999987652 2367999999999999997 8999999999999999999999999888


Q ss_pred             cC
Q 036786          157 SY  158 (158)
Q Consensus       157 ~~  158 (158)
                      .|
T Consensus        86 d~   87 (129)
T 3t3l_A           86 DW   87 (129)
T ss_dssp             EE
T ss_pred             Ee
Confidence            76
>3oeq_A Frataxin homolog, mitochondrial; alpha/beta sandwich, metallochaperone, iron-storage, transpo protein; 2.96A {Saccharomyces cerevisiae} SCOP: d.82.2.1 PDB: 2fql_A 3oer_A 2ga5_A Back     alignment and structure
>1ew4_A CYAY protein; friedreich ataxia, frataxin family, iron homeostasis, unknown function; 1.40A {Escherichia coli} SCOP: d.82.2.1 PDB: 2eff_A 2p1x_A 1soy_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 158
d2fqla1112 d.82.2.1 (A:61-172) C-terminal domain of frataxin 2e-24
d1ew4a_106 d.82.2.1 (A:) CyaY {Escherichia coli [TaxId: 562]} 6e-23
d1ekga_119 d.82.2.1 (A:) C-terminal domain of frataxin {Human 4e-21
>d2fqla1 d.82.2.1 (A:61-172) C-terminal domain of frataxin {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 112 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: N domain of copper amine oxidase-like
superfamily: Frataxin/Nqo15-like
family: Frataxin-like
domain: C-terminal domain of frataxin
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 88.7 bits (220), Expect = 2e-24
 Identities = 27/70 (38%), Positives = 42/70 (60%)

Query: 82  LQEDEFHRLANSTIHDLQEKFEEYGDTIQIDGFDVDYGNEVLTLKLGALGTYVLNKQTPN 141
           L  ++ H  A+  +  L +  EE  +       DV+  + V+TL++ A GTYV+NKQ PN
Sbjct: 8   LPLEKAHEEADDYLDHLLDSLEELSEAHPDCIPDVELSHGVMTLEIPAFGTYVINKQPPN 67

Query: 142 RQIWLSSPVR 151
           +QIWL+SP+ 
Sbjct: 68  KQIWLASPLS 77
>d1ew4a_ d.82.2.1 (A:) CyaY {Escherichia coli [TaxId: 562]} Length = 106 Back     information, alignment and structure
>d1ekga_ d.82.2.1 (A:) C-terminal domain of frataxin {Human (Homo sapiens) [TaxId: 9606]} Length = 119 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 ?
Query158
d1ekga_119 C-terminal domain of frataxin {Human (Homo sapiens 99.96
d2fqla1112 C-terminal domain of frataxin {Baker's yeast (Sacc 99.96
d1ew4a_106 CyaY {Escherichia coli [TaxId: 562]} 99.96
>d1ekga_ d.82.2.1 (A:) C-terminal domain of frataxin {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: N domain of copper amine oxidase-like
superfamily: Frataxin/Nqo15-like
family: Frataxin-like
domain: C-terminal domain of frataxin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=9.6e-31  Score=196.52  Aligned_cols=77  Identities=49%  Similarity=0.806  Sum_probs=70.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHhhccCccC-CCCcceeecCceEEEEEC-CCcEEEEeCCCCcceeeeecCCCccCcccC
Q 036786           82 LQEDEFHRLANSTIHDLQEKFEEYGDTIQ-IDGFDVDYGNEVLTLKLG-ALGTYVLNKQTPNRQIWLSSPVRYYCGRSY  158 (158)
Q Consensus        82 mte~eF~~lAd~~L~~L~e~lE~~~d~~~-~~d~Dve~s~GVLTI~f~-d~gtyVINKQ~PnkQIWLSSPisG~~~~~~  158 (158)
                      |+|.+||++||++|+.|+++||++.|+.+ .+|+|+|+++|||||+|+ ++|+||||||+||||||||||+|||.|+.|
T Consensus         1 m~e~~f~~~ad~~L~~l~~~le~~~d~~~~~~d~D~e~~~gvLti~f~~~~~~~VINkQ~p~~QIWlASp~sG~~~fd~   79 (119)
T d1ekga_           1 LDETTYERLAEETLDSLAEFFEDLADKPYTFEDYDVSFGSGVLTVKLGGDLGTYVINKQTPNKQIWLSSPSSGPKRYDW   79 (119)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHTTSTTSCTTCEEEEETTEEEEECCTTCCEEEEEEEGGGTEEEEEETTTEEEEEEE
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHhhcccccccceeeeccCCEEEEEECCCCcEEEEeCCCCceeEEEEcCCCCchhcee
Confidence            89999999999999999999999887643 357999999999999995 689999999999999999999999988764
>d2fqla1 d.82.2.1 (A:61-172) C-terminal domain of frataxin {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1ew4a_ d.82.2.1 (A:) CyaY {Escherichia coli [TaxId: 562]} Back     information, alignment and structure