Citrus Sinensis ID: 024072

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270---
MSFSIRIAEKLPLLSSRVSLIGVPKLWFVSFLHLNRRFPKKMAFSLENGQVSVENKAGLVRPATEAHAEEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINRFAVTDHLPHGLLDSLLPGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIARGLESALALTSANLTGQPSSVSVKDFENLWERCACVYDGGVLPSGRAGSTVVDLTRLGKFKILRPGSAKEETIAILEKHSLVEEPAAG
ccHHHHHHHHccccccccccccccEEEEEEccccccccccccccccccccEEEEccccccccccHHHHHHHHHHHHccccEEEccccccccccccccHHHHHHHHHHccccccccEEEEEccHHHHHHccccccHHHHHHHcccccccEEEEEcccccccccccccccccEEEEccccHHHHHHHHHccccccccccccccccccccHHHHccccccccEEEEcccccccccccEEEEcccccccEEEccccccHHHHHHHHccccccccccc
ccccHHHHHHcccccHHHHHccccHEHEHHHHHHcccHHHHEEEcccccEEEEEEEEEEEccccHHHHHHHHHHHHcccEEEccccEEEccccccccHHHHHHHHHHccccccccEEEEEccHHHHHHHHcccHHHHHHHHHcccccEEEEEEccccccccccEcccccEEEEEccccHHHHHHHHHccccEEccccccccccccccHHHHHHHcccEEEEEcccccccEEEEEEEEEcccccccEEEccccccHHHHHHHHcccEccHcccc
MSFSIRiaeklpllssrvsligvpklwFVSFLhlnrrfpkkmafslengqvsvenkaglvrpatEAHAEEAIQALKTgkviavptdtlygfacdacssEAVNRIYEIkgrkhtsplaicvgdvsdinrfavtdhlphglldsllpgpvtvvlsrgessnlekslnpglesigvrvpdsnFVRVIARGLESALALTsanltgqpssvsvkDFENLWERCACvydggvlpsgragstvvdltrlgkfkilrpgsakeETIAILEKhslveepaag
msfsiriaeklpllssrvslIGVPKLWFVSFLHLNRRFPKKMAFSLENGQVSVENKAGLVRPATEAHAEEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEikgrkhtsplAICVGDVSDINRFAVTDHLPHGLLDSLLPGPVTVVLSRgessnlekslnpglesigvrvpDSNFVRVIARGLESALALtsanltgqpssvSVKDFENLWERCACVYDggvlpsgragstvvdltrlgkfkilrpgsakeeTIAIlekhslveepaag
MSFSIRIAEKLPLLSSRVSLIGVPKLWFVSFLHLNRRFPKKMAFSLENGQVSVENKAGLVRPATEAHAEEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINRFAVTDHLPHGLLDSLLPGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIARGLESALALTSANLTGQPSSVSVKDFENLWERCACVYDGGVLPSGRAGSTVVDLTRLGKFKILRPGSAKEETIAILEKHSLVEEPAAG
*****RIAEKLPLLSSRVSLIGVPKLWFVSFLHLNRRFPKKMAFSLENGQVSVENKAGLVRPATEAHAEEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINRFAVTDHLPHGLLDSLLPGPVTVVLS****************SIGVRVPDSNFVRVIARGLESALALTSANLTGQPSSVSVKDFENLWERCACVYDGGVLPSGRAGSTVVDLTRLGKFKILRPG*****TIAI*************
**********LPLLSSRVSLIGVPKLWFVSF*******************VSVENKAGLVRPATEAHAEEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINRFAVTDHLPHGLLDSLLPGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIARGLESALALTSANLTGQPSSVSVKDFENLWERCACVYDGGVLPSGRAGSTVVDLTRLGKFKILRPGSAKEETIAILEKHSLVE*****
MSFSIRIAEKLPLLSSRVSLIGVPKLWFVSFLHLNRRFPKKMAFSLENGQVSVENKAGLVRPATEAHAEEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINRFAVTDHLPHGLLDSLLPGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIARGLESALALTSANLTGQPSSVSVKDFENLWERCACVYDGGVLPSGRAGSTVVDLTRLGKFKILRPGSAKEETIAILEKHSLVEEPAAG
***SIRIAEKLPLLSSRVSLIGVPKLWFVSFLHLNRRFPKKMAFSLENGQVSVENKAGLVRPATEAHAEEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINRFAVTDHLPHGLLDSLLPGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIARGLESALALTSANLTGQPSSVSVKDFENLWERCACVYDGGVLPSGRAGSTVVDLTRLGKFKILRPGSAKEETIAILEKHSLVEE****
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MSFSIRIAEKLPLLSSRVSLIGVPKLWFVSFLHLNRRFPKKMAFSLENGQVSVENKAGLVRPATEAHAEEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINRFAVTDHLPHGLLDSLLPGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIARGLESALALTSANLTGQPSSVSVKDFENLWERCACVYDGGVLPSGRAGSTVVDLTRLGKFKILRPGSAKEETIAILEKHSLVEEPAAG
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 ?
Query273 2.2.26 [Sep-21-2011]
Q499R4280 YrdC domain-containing pr yes no 0.710 0.692 0.472 2e-43
Q86U90279 YrdC domain-containing pr yes no 0.699 0.684 0.487 5e-43
Q0VC80276 YrdC domain-containing pr yes no 0.710 0.702 0.485 3e-42
Q3U5F4280 YrdC domain-containing pr yes no 0.699 0.682 0.477 2e-40
Q60369207 Uncharacterized protein M yes no 0.545 0.719 0.302 6e-19
P39153 346 Probable tRNA threonylcar yes no 0.673 0.531 0.310 1e-15
Q10618217 Uncharacterized protein R yes no 0.663 0.834 0.319 3e-14
A7N129185 tRNA threonylcarbamoylade yes no 0.648 0.956 0.294 2e-13
P32579 426 tRNA threonylcarbamoylade yes no 0.736 0.471 0.295 4e-13
P45831220 Uncharacterized protein M yes no 0.659 0.818 0.323 1e-12
>sp|Q499R4|YRDC_RAT YrdC domain-containing protein, mitochondrial OS=Rattus norvegicus GN=Yrdc PE=2 SV=1 Back     alignment and function desciption
 Score =  175 bits (444), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 96/203 (47%), Positives = 131/203 (64%), Gaps = 9/203 (4%)

Query: 71  AIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINRFA 130
           A+  L+ G V+AVPTDTLYG AC A  S A++ +Y +KGR    PLA+C+G V+D+ R+ 
Sbjct: 74  AVAELRAGAVVAVPTDTLYGLACSASCSAALSCVYRLKGRSEAKPLAVCLGRVADVYRYC 133

Query: 131 VTDHLPHGLLDSLLPGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIARGLES 190
               +P  LL+ L PGPVT+V+ R E   L K LNP    +G+R+PD  F+  +A+    
Sbjct: 134 QV-RVPRELLEDLFPGPVTLVMERSE--ELNKDLNPFTPLVGIRIPDHAFMLDLAQMFGG 190

Query: 191 ALALTSANLTGQPSSVSVKDFENLWERCACVYDGGVL-----PSGRAGSTVVDLTRLGKF 245
            LALTSANL+ Q SS+SV++F++LW   + V DGG +     P  R GSTVVDL+  GKF
Sbjct: 191 PLALTSANLSSQASSLSVEEFQDLWPHLSLVIDGGPIGDSESPECRLGSTVVDLSVPGKF 250

Query: 246 KILRPGSAKEETIAILE-KHSLV 267
            I+R G A E T AIL+ K+ L+
Sbjct: 251 GIIRSGCALENTTAILQGKYGLL 273
May regulate the activity of some transporters.
Rattus norvegicus (taxid: 10116)
>sp|Q86U90|YRDC_HUMAN YrdC domain-containing protein, mitochondrial OS=Homo sapiens GN=YRDC PE=1 SV=1 Back     alignment and function description
>sp|Q0VC80|YRDC_BOVIN YrdC domain-containing protein, mitochondrial OS=Bos taurus GN=YRDC PE=2 SV=1 Back     alignment and function description
>sp|Q3U5F4|YRDC_MOUSE YrdC domain-containing protein, mitochondrial OS=Mus musculus GN=Yrdc PE=1 SV=1 Back     alignment and function description
>sp|Q60369|Y062_METJA Uncharacterized protein MJ0062 OS=Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) GN=MJ0062 PE=3 SV=1 Back     alignment and function description
>sp|P39153|YWLC_BACSU Probable tRNA threonylcarbamoyladenosine biosynthesis protein YwlC OS=Bacillus subtilis (strain 168) GN=ywlC PE=3 SV=1 Back     alignment and function description
>sp|Q10618|Y1301_MYCTU Uncharacterized protein Rv1301/MT1340 OS=Mycobacterium tuberculosis GN=Rv1301 PE=3 SV=1 Back     alignment and function description
>sp|A7N129|RIMN_VIBHB tRNA threonylcarbamoyladenosine biosynthesis protein RimN OS=Vibrio harveyi (strain ATCC BAA-1116 / BB120) GN=rimN PE=3 SV=1 Back     alignment and function description
>sp|P32579|SUA5_YEAST tRNA threonylcarbamoyladenosine biosynthesis protein SUA5 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SUA5 PE=1 SV=1 Back     alignment and function description
>sp|P45831|Y1136_MYCLE Uncharacterized protein ML1136 OS=Mycobacterium leprae (strain TN) GN=ML1136 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 ?
Query273
225435305272 PREDICTED: yrdC domain-containing protei 0.970 0.974 0.730 1e-107
224104509232 predicted protein [Populus trichocarpa] 0.846 0.995 0.800 1e-104
255578866233 Protein SUA5, putative [Ricinus communis 0.835 0.978 0.803 1e-101
356539446290 PREDICTED: yrdC domain-containing protei 0.838 0.789 0.765 1e-97
449462123281 PREDICTED: yrdC domain-containing protei 0.970 0.943 0.667 8e-96
297793617284 hypothetical protein ARALYDRAFT_358267 [ 0.974 0.936 0.664 5e-95
42573748288 DHBP synthase RibB-like alpha/beta domai 0.952 0.902 0.671 9e-94
357472217 462 YrdC domain-containing protein [Medicago 0.769 0.454 0.790 1e-92
356544602227 PREDICTED: LOW QUALITY PROTEIN: yrdC dom 0.798 0.960 0.773 1e-91
9759323239 unnamed protein product [Arabidopsis tha 0.802 0.916 0.739 3e-89
>gi|225435305|ref|XP_002285123.1| PREDICTED: yrdC domain-containing protein, mitochondrial [Vitis vinifera] gi|297746251|emb|CBI16307.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
 Score =  394 bits (1011), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 203/278 (73%), Positives = 228/278 (82%), Gaps = 13/278 (4%)

Query: 1   MSFSIRIAEKLPLLSSRVSL--IGVPKLWFVSFLHLNRRF----PKKMAFSLENGQVSVE 54
           M+   + AE+  LL+ R  L  +GV K  FV  L  NRRF    PKKM       +  + 
Sbjct: 1   MNIPAKFAERSLLLTFRSPLRALGVAKFGFVQILKQNRRFRVSFPKKM-------EAVMG 53

Query: 55  NKAGLVRPATEAHAEEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTS 114
           ++ G+VRPAT+AHAEEAI+A+K GKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTS
Sbjct: 54  SELGVVRPATDAHAEEAIEAIKAGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTS 113

Query: 115 PLAICVGDVSDINRFAVTDHLPHGLLDSLLPGPVTVVLSRGESSNLEKSLNPGLESIGVR 174
           PLAICVGDV DI RFAVTDHLP GLL SLLPGPVTVVL RGE S +EKSLNPGL+SIGVR
Sbjct: 114 PLAICVGDVLDIQRFAVTDHLPDGLLGSLLPGPVTVVLRRGELSIIEKSLNPGLDSIGVR 173

Query: 175 VPDSNFVRVIARGLESALALTSANLTGQPSSVSVKDFENLWERCACVYDGGVLPSGRAGS 234
           VPD +F+RVIA G E+ALALTSANL+GQPSSV +KDFENLWE CA VYDGGVLPSGRAGS
Sbjct: 174 VPDCDFIRVIAHGSETALALTSANLSGQPSSVCIKDFENLWEHCAYVYDGGVLPSGRAGS 233

Query: 235 TVVDLTRLGKFKILRPGSAKEETIAILEKHSLVEEPAA 272
           TVVDL+RLGK+KILRPGSA EET+AILE+HSL+ E AA
Sbjct: 234 TVVDLSRLGKYKILRPGSAMEETVAILERHSLMPEAAA 271

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|224104509|ref|XP_002313460.1| predicted protein [Populus trichocarpa] gi|222849868|gb|EEE87415.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|255578866|ref|XP_002530287.1| Protein SUA5, putative [Ricinus communis] gi|223530185|gb|EEF32094.1| Protein SUA5, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|356539446|ref|XP_003538209.1| PREDICTED: yrdC domain-containing protein, mitochondrial-like [Glycine max] Back     alignment and taxonomy information
>gi|449462123|ref|XP_004148791.1| PREDICTED: yrdC domain-containing protein, mitochondrial-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|297793617|ref|XP_002864693.1| hypothetical protein ARALYDRAFT_358267 [Arabidopsis lyrata subsp. lyrata] gi|297310528|gb|EFH40952.1| hypothetical protein ARALYDRAFT_358267 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|42573748|ref|NP_974970.1| DHBP synthase RibB-like alpha/beta domain-containing protein [Arabidopsis thaliana] gi|332009969|gb|AED97352.1| DHBP synthase RibB-like alpha/beta domain-containing protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|357472217|ref|XP_003606393.1| YrdC domain-containing protein [Medicago truncatula] gi|355507448|gb|AES88590.1| YrdC domain-containing protein [Medicago truncatula] Back     alignment and taxonomy information
>gi|356544602|ref|XP_003540738.1| PREDICTED: LOW QUALITY PROTEIN: yrdC domain-containing protein, mitochondrial-like [Glycine max] Back     alignment and taxonomy information
>gi|9759323|dbj|BAB09832.1| unnamed protein product [Arabidopsis thaliana] 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 ?
Query273
TAIR|locus:2175173288 AT5G60590 "AT5G60590" [Arabido 0.985 0.934 0.675 3.1e-90
UNIPROTKB|Q0VC80276 YRDC "YrdC domain-containing p 0.747 0.739 0.479 3.8e-46
ZFIN|ZDB-GENE-070410-65263 zgc:162301 "zgc:162301" [Danio 0.717 0.745 0.497 6.2e-46
UNIPROTKB|Q86U90279 YRDC "YrdC domain-containing p 0.750 0.734 0.479 2.7e-45
UNIPROTKB|E2R8D0274 YRDC "Uncharacterized protein" 0.754 0.751 0.476 3.4e-45
UNIPROTKB|F1NJF5259 YRDC "Uncharacterized protein" 0.717 0.756 0.497 3.1e-44
MGI|MGI:2387201280 Yrdc "yrdC domain containing ( 0.747 0.728 0.472 5e-44
RGD|708492280 Yrdc "yrdC domain containing ( 0.747 0.728 0.467 7.3e-43
FB|FBgn0061361248 CG33786 [Drosophila melanogast 0.739 0.814 0.435 2.3e-39
UNIPROTKB|Q2GG33194 ECH_0802 "Sua5/YciO/YrdC/YwlC 0.666 0.938 0.356 6.8e-24
TAIR|locus:2175173 AT5G60590 "AT5G60590" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 900 (321.9 bits), Expect = 3.1e-90, P = 3.1e-90
 Identities = 187/277 (67%), Positives = 221/277 (79%)

Query:     1 MSFSIRIAEKLP-LL---SSRVSLIGVPKLWFVSFLHLNRRF----PKKMAFSLENGQVS 52
             M+ S R+AEKLP +L   SS +   GV +L   S  + +RR      KKM +SLE  +  
Sbjct:     1 MNLSTRLAEKLPGILPAPSSPLLRKGVSELRCFSIANQSRRLRWGLQKKMVWSLERAETC 60

Query:    53 VENKAGLVRPATEAHAEEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKH 112
             V +K+ LV PATEA+A+EAI+A+K+ KVIAVPTDTLYGFACDACS EAV+RIYEIKGRK 
Sbjct:    61 VVSKSCLVHPATEAYAQEAIEAIKSEKVIAVPTDTLYGFACDACSLEAVSRIYEIKGRKL 120

Query:   113 TSPLAICVGDVSDINRFAVTDHLPHGLLDSLLPGPVTVVLSRGESSNLEKSLNPGLESIG 172
             TSPLAICVGDV DI R A T HLPHGLLDSLLPGPVT+VL RGESS LEKSLNPG+ +IG
Sbjct:   121 TSPLAICVGDVLDIKRVATTSHLPHGLLDSLLPGPVTLVLQRGESSILEKSLNPGIGTIG 180

Query:   173 VRVPDSNFVRVIARGLESALALTSANLTGQPSSVSVKDFENLWERCACVYDGGVLPSGRA 232
             VRVPD  F+R ++RG  S LALTSANL+G  SSV VKDFENLW+ CA VYDGG+LPSGRA
Sbjct:   181 VRVPDCEFIREVSRGSGSVLALTSANLSGDRSSVCVKDFENLWQHCAYVYDGGLLPSGRA 240

Query:   233 GSTVVDLTRLGKFKILRPGSAKEETIAILEKHSLVEE 269
             GST+VDLT++GK+KI+RPGSAK+ T+AILEK+ L EE
Sbjct:   241 GSTIVDLTKVGKYKIIRPGSAKQATVAILEKYLLEEE 277
GO:0003674 "molecular_function" evidence=ND
GO:0008150 "biological_process" evidence=ND
UNIPROTKB|Q0VC80 YRDC "YrdC domain-containing protein, mitochondrial" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-070410-65 zgc:162301 "zgc:162301" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|Q86U90 YRDC "YrdC domain-containing protein, mitochondrial" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|E2R8D0 YRDC "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|F1NJF5 YRDC "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
MGI|MGI:2387201 Yrdc "yrdC domain containing (E.coli)" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|708492 Yrdc "yrdC domain containing (E.coli)" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
FB|FBgn0061361 CG33786 [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
UNIPROTKB|Q2GG33 ECH_0802 "Sua5/YciO/YrdC/YwlC family protein" [Ehrlichia chaffeensis str. Arkansas (taxid:205920)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query273
pfam01300178 pfam01300, Sua5_yciO_yrdC, Telomere recombination 1e-50
COG0009211 COG0009, SUA5, Putative translation factor (SUA5) 6e-46
TIGR00057201 TIGR00057, TIGR00057, tRNA threonylcarbamoyl adeno 6e-42
COG0068 750 COG0068, HypF, Hydrogenase maturation factor [Post 3e-13
TIGR00143 711 TIGR00143, hypF, [NiFe] hydrogenase maturation pro 8e-13
PRK10634190 PRK10634, PRK10634, tRNA(ANN) t(6)A37 threonylcarb 2e-12
PRK11630206 PRK11630, PRK11630, hypothetical protein; Provisio 9e-10
>gnl|CDD|216422 pfam01300, Sua5_yciO_yrdC, Telomere recombination Back     alignment and domain information 
 Score =  164 bits (417), Expect = 1e-50
 Identities = 75/181 (41%), Positives = 107/181 (59%), Gaps = 5/181 (2%)

Query: 73  QALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINRFAVT 132
           +AL+ G ++A PTDT+YG  CDA + EAV R+ EIKGR    PLA+ V D+  + ++A  
Sbjct: 1   EALRQGGIVAYPTDTVYGLGCDATNEEAVERLREIKGRPRDKPLAVMVSDLEQLKKYADE 60

Query: 133 -DHLPHGLLDSLLPGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIARGLESA 191
            +     L +   PGP+T++L     S+L K + PGL ++GVR+PD    R++   L   
Sbjct: 61  LEEAALKLAERFWPGPITLIL-PASKSSLPKLVTPGLGTVGVRLPDHPLARLLLEALGEP 119

Query: 192 LALTSANLTGQPSSVSVKD-FENLWERCACVYDGGVLPSGRAGSTVVDLTRLGKFKILRP 250
           L  TSANL+G+PS+   ++  E L      + DGG +P     STVVDLT  GK +ILR 
Sbjct: 120 LVATSANLSGEPSATDAEEVLEELGGIVDLILDGGRIP-VGVDSTVVDLTD-GKPRILRR 177

Query: 251 G 251
           G
Sbjct: 178 G 178

This domain has been shown to bind preferentially to dsRNA. The domain is found in SUA5 as well as HypF and YrdC. It has also been shown to be required for telomere recombniation in yeast. Length = 178
>gnl|CDD|223088 COG0009, SUA5, Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|232802 TIGR00057, TIGR00057, tRNA threonylcarbamoyl adenosine modification protein, Sua5/YciO/YrdC/YwlC family Back     alignment and domain information
>gnl|CDD|223146 COG0068, HypF, Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>gnl|CDD|232844 TIGR00143, hypF, [NiFe] hydrogenase maturation protein HypF Back     alignment and domain information
>gnl|CDD|182603 PRK10634, PRK10634, tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein; Provisional Back     alignment and domain information
>gnl|CDD|183245 PRK11630, PRK11630, hypothetical 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 273
TIGR00143 711 hypF [NiFe] hydrogenase maturation protein HypF. A 100.0
COG0068 750 HypF Hydrogenase maturation factor [Posttranslatio 100.0
TIGR00057201 Sua5/YciO/YrdC/YwlC family protein. partial match 100.0
COG0009211 SUA5 Putative translation factor (SUA5) [Translati 100.0
PRK11630206 hypothetical protein; Provisional 100.0
PRK10634190 tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modif 100.0
PF01300179 Sua5_yciO_yrdC: Telomere recombination; InterPro: 100.0
KOG3051261 consensus RNA binding/translational regulation pro 99.95
PF0750335 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc fin 98.31
COG2192555 Predicted carbamoyl transferase, NodU family [Post 96.77
TIGR00143 711 hypF [NiFe] hydrogenase maturation protein HypF. A 80.25
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF Back     alignment and domain information 
Probab=100.00  E-value=2.6e-53  Score=429.50  Aligned_cols=231  Identities=26%  Similarity=0.371  Sum_probs=201.1

Q ss_pred             cCcCCC-CCCCCCCCCceeEEEcCCCcccCCCHHHHHHHHHHHhcCceEEEecCceEEEEeecCCHHHHHHHHHHhCCCC
Q 024072           34 LNRRFP-KKMAFSLENGQVSVENKAGLVRPATEAHAEEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKH  112 (273)
Q Consensus        34 ~~RRfh-~~~ac~~cgp~~~~~~~~~~~~~~~~~~i~~a~~~L~~G~IvaiptdtgYgL~cda~n~~AV~rLr~~K~R~~  112 (273)
                      .||||| |+++|+.|||++++.+..|. . ..++.+++|+++|++|+|||+||+|||||+|||+|++||+|||++|+|| 
T Consensus       132 ~~rr~h~~~~~C~~Cgp~l~l~~~~g~-~-~~~~~i~~aa~~L~~G~IVaipt~ggy~L~cda~n~~AV~rLr~~K~Rp-  208 (711)
T TIGR00143       132 LDRRFHAQPIACPRCGPQLNFVSRGGH-A-EQDDALLEAAKLLKKGKIIAIKGIGGFHLACDARNDEVVERLRLRKNRP-  208 (711)
T ss_pred             ccccCCCCCccCCCCCcEEEEEeCCCC-c-cchHHHHHHHHHHhCCCEEEEEcCCcceeecCCCCHHHHHHHHHHhCCC-
Confidence            599999 99999999999999998876 2 2457899999999999999999999999999999999999999999998 


Q ss_pred             CCCcEEEECCHHHHhhhhccCCchHHHHhccCCCCeEEEEccCCCCccccccCCCCCeEEEEcCCcHHHHHHHHhCCCeE
Q 024072          113 TSPLAICVGDVSDINRFAVTDHLPHGLLDSLLPGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIARGLESAL  192 (273)
Q Consensus       113 ~KPfavm~~dl~~l~~~~~v~~~~~~ll~~~~PgpiTvIl~~~~~~~l~~~l~~~~~tiGvrlP~~p~~~~Ll~~~g~PL  192 (273)
                      +|||+||++|++++++|+++++.++++|.+ |++|++ |+++++...+++.++++.+|||||+||||+|++|++.+|.||
T Consensus       209 ~KPlavmv~d~~~~~~~~~~~~~e~~lL~~-~~~Piv-ll~~~~~~~l~~~v~~~~~tiGvrlP~~pl~~~Ll~~~g~PL  286 (711)
T TIGR00143       209 LKPFAVMSPDLESAEQHAELNNLECELLTS-PAAPIV-LLRKKPDIKLAPNIAPNLPTIGVMLPYTPLHHLLLQLLAFPL  286 (711)
T ss_pred             CCCEEEEECCHHHHHHHhcCCHHHHHHHHc-CCCCEE-EEECCCCCCCChhhcCCCCEEEEEcCCCHHHHHHHHHcCCcE
Confidence            699999999999999999998888888876 688875 588764324788999999999999999999999999999999


Q ss_pred             EEecCCCCCCCCCCCHHHH-HhhhhcccEEEcCcccCCCCCCCeeEEcccCCcc-----------------------EEE
Q 024072          193 ALTSANLTGQPSSVSVKDF-ENLWERCACVYDGGVLPSGRAGSTVVDLTRLGKF-----------------------KIL  248 (273)
Q Consensus       193 v~TSAN~SGep~~~~~~~~-~~~~~~vd~ivd~g~~~~~~~~STVVdl~~~~~~-----------------------~Il  248 (273)
                      ||||||+||+|++++.+++ +++.+.+|+++++++...++.+||||+++. +++                       .||
T Consensus       287 v~TSAN~SGep~~~~~~e~~~~l~~~~D~~L~~~r~i~~~~dsSVV~~~~-~~~~ilR~~RG~aP~~~~l~~~~~~~~vl  365 (711)
T TIGR00143       287 VMTSANLPGLPMAIDNAEILDKLQGIADGFLVHNRRIVNRVDDSVVQHVA-GEILFLRRSRGFAPQPLTLPPNGNPKKIL  365 (711)
T ss_pred             EECccCCCCCCCCCCHHHHHHHhcCCccEEEeCCCCcCCCCCCceEEEEC-CeeEEEeccCCCCCcccccCCcCCCCcEE
Confidence            9999999999999999885 567788999998887666778999999874 222                       377


Q ss_pred             ecCCChHHHHHHHhcCCccccC
Q 024072          249 RPGSAKEETIAILEKHSLVEEP  270 (273)
Q Consensus       249 R~G~~~k~~~~l~~~~~~~~~~  270 (273)
                      +.|+.+|||+|+.+++..+-.|
T Consensus       366 a~G~~lknt~~l~~~~~~~~S~  387 (711)
T TIGR00143       366 ALGAELKNTFSLLKGGQAYLSQ  387 (711)
T ss_pred             EechhhcceEEEEeCCEEEEcC
Confidence            7777788888887776655444

A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>TIGR00057 Sua5/YciO/YrdC/YwlC family protein Back     alignment and domain information
>COG0009 SUA5 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK11630 hypothetical protein; Provisional Back     alignment and domain information
>PRK10634 tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein; Provisional Back     alignment and domain information
>PF01300 Sua5_yciO_yrdC: Telomere recombination; InterPro: IPR006070 The YrdC family of hypothetical proteins are widely distributed in eukaryotes and prokaryotes and occur as: (i) independent proteins, (ii) with C-terminal extensions, and (iii) as domains in larger proteins, some of which are implicated in regulation [] Back     alignment and domain information
>KOG3051 consensus RNA binding/translational regulation protein of the SUA5 family [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule Back     alignment and domain information
>COG2192 Predicted carbamoyl transferase, NodU family [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF 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 ?
Query273
1jcu_A208 Solution Structure Of Mth1692 Protein From Methanob 4e-22
3aje_A 352 Crystal Structure Of S. Tokodaii Sua5 Complexed Wit 2e-14
2eqa_A 352 Crystal Structure Of The Hypothetical Sua5 Protein 3e-14
1hru_A188 The Structure Of The Yrdc Gene Product From E.Coli 3e-09
1k7j_A206 Structural Genomics, Protein Tf1 Length = 206 6e-09
1kk9_A221 Crystal Structure Of E. Coli Ycio Length = 221 6e-09
3vth_A 761 Crystal Structure Of Full-Length Hypf In The Phosph 5e-06
3tsq_A 658 Crystal Structure Of E. Coli Hypf With Atp And Carb 2e-05
3tsp_A 657 Crystal Structure Of E. Coli Hypf Length = 657 2e-05
4g9i_A 772 Crystal Structure Of T.Kodakarensis Hypf Length = 7 7e-05
>pdb|1JCU|A Chain A, Solution Structure Of Mth1692 Protein From Methanobacterium Thermoautotrophicum Length = 208 Back     alignment and structure 
Iteration: 1

 Score =  101 bits (252), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 65/185 (35%), Positives = 98/185 (52%), Gaps = 6/185 (3%)
Query: 69  EEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINR 128
           EEAI  ++ G ++  PTDT+YG   +A   +AV R++ +KGR    P++ICV  V +I R
Sbjct: 17  EEAISVMEGGGIVIYPTDTIYGLGVNALDEDAVRRLFRVKGRSPHKPVSICVSCVDEIPR 76
Query: 129 FAVTDHLPHGLLDSLLPGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIARGL 188
           F+        L++ +LPGP TVVL R E   +   +  G   +G+RVPD    R IA   
Sbjct: 77  FSRPSGDAMELMERILPGPYTVVLERNEL--IPDVITGGSSRVGIRVPDDEICRRIAARF 134
Query: 189 ESALALTSANLTGQPSSVSVKDFENLWERCACVYDGGVLPSGRAGSTVVDLTRLGKFKIL 248
              +  TSAN++G+P S  +++     +    V D G        STV+DLT +   ++L
Sbjct: 135 --PVTATSANISGKPPSPRLEEIVRDLDAVDLVLDAGDC-LDMEPSTVIDLT-VNPPRVL 190
Query: 249 RPGSA 253
           R G  
Sbjct: 191 RRGKG 195
>pdb|3AJE|A Chain A, Crystal Structure Of S. Tokodaii Sua5 Complexed With L-Threonine And Amppnp Length = 352 Back     alignment and structure
>pdb|2EQA|A Chain A, Crystal Structure Of The Hypothetical Sua5 Protein From Sulfolobus Tokodaii Length = 352 Back     alignment and structure
>pdb|1HRU|A Chain A, The Structure Of The Yrdc Gene Product From E.Coli Length = 188 Back     alignment and structure
>pdb|1K7J|A Chain A, Structural Genomics, Protein Tf1 Length = 206 Back     alignment and structure
>pdb|1KK9|A Chain A, Crystal Structure Of E. Coli Ycio Length = 221 Back     alignment and structure
>pdb|3VTH|A Chain A, Crystal Structure Of Full-Length Hypf In The Phosphate- And Nucleotide-Bound Form Length = 761 Back     alignment and structure
>pdb|3TSQ|A Chain A, Crystal Structure Of E. Coli Hypf With Atp And Carbamoyl Phosphate Length = 658 Back     alignment and structure
>pdb|3TSP|A Chain A, Crystal Structure Of E. Coli Hypf Length = 657 Back     alignment and structure
>pdb|4G9I|A Chain A, Crystal Structure Of T.Kodakarensis Hypf Length = 772 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 ?
Query273
1k7j_A206 Protein YCIO, protein TF1; structural genomics, X- 2e-47
1jcu_A208 Conserved protein MTH1692; mixed alpha-beta struct 8e-47
1hru_A188 YRDC gene product; protein folding, structural gen 2e-35
2eqa_A 352 Hypothetical protein ST1526; YRDC/RIBB fold, YRDC 4e-35
3vth_A 761 Hydrogenase maturation factor; carbamoyltransfer, 1e-26
3l7v_A295 Putative uncharacterized protein SMU.1377C; transc 4e-25
3ttc_A 657 HYPF, transcriptional regulatory protein; Zn finge 5e-25
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 1e-05
>1k7j_A Protein YCIO, protein TF1; structural genomics, X-RAY crystallography, putative translation factor, PSI, protein structure initiative; 1.40A {Escherichia coli} SCOP: d.115.1.1 PDB: 1kk9_A Length = 206 Back     alignment and structure
 Score =  156 bits (396), Expect = 2e-47
 Identities = 44/185 (23%), Positives = 84/185 (45%), Gaps = 6/185 (3%)

Query: 69  EEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINR 128
            +A++ ++ G VI  PTD+ Y   C      A+ RI  I+         +   D+S+++ 
Sbjct: 18  NQAVEIVRKGGVIVYPTDSGYALGCKIEDKNAMERICRIRQLPDGHNFTLMCRDLSELST 77

Query: 129 FAVTDHLPHGLLDSLLPGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIARGL 188
           ++  D++   L+ +  PG  T +L   +     + L    ++IG+RVP +   + +   L
Sbjct: 78  YSFVDNVAFRLMKNNTPGNYTFILKGTKEV-PRRLLQEKRKTIGMRVPSNPIAQALLEAL 136

Query: 189 ESALALTSANLTGQPSSVSVKD--FENLWERCACVYDGGVLPSGRAGSTVVDLTRLGKFK 246
              +  TS  L G   + S  +   + L ++   +  GG    G+  +TV+DLT      
Sbjct: 137 GEPMLSTSLMLPGSEFTESDPEEIKDRLEKQVDLIIHGG--YLGQKPTTVIDLTD-DTPV 193

Query: 247 ILRPG 251
           ++R G
Sbjct: 194 VVREG 198
>1jcu_A Conserved protein MTH1692; mixed alpha-beta structure, structural genomics; NMR {Methanothermobacterthermautotrophicus} SCOP: d.115.1.1 Length = 208 Back     alignment and structure
>1hru_A YRDC gene product; protein folding, structural genomics, RNA, SUA5, PSI, protein structure initiative, midwest center for structural genomics; 2.00A {Escherichia coli} SCOP: d.115.1.1 Length = 188 Back     alignment and structure
>2eqa_A Hypothetical protein ST1526; YRDC/RIBB fold, YRDC domain, SUA5 domain, structural genomics, NPPSFA; HET: AMP; 1.80A {Sulfolobus tokodaii} PDB: 3aje_A* 4e1b_A* Length = 352 Back     alignment and structure
>3vth_A Hydrogenase maturation factor; carbamoyltransfer, maturation of [NIFE]-hydrogenase, carbamoylphosphate, iron, HYPE; HET: APC AP2; 2.00A {Thermoanaerobacter tengcongensis} PDB: 3vti_A Length = 761 Back     alignment and structure
>3l7v_A Putative uncharacterized protein SMU.1377C; transcription; 2.26A {Streptococcus mutans} Length = 295 Back     alignment and structure
>3ttc_A HYPF, transcriptional regulatory protein; Zn finger, nucleotide binding, hydrogenase maturation factor transferase; HET: ADP; 1.86A {Escherichia coli} PDB: 3tsp_A* 3tsu_A* 3ttf_A* 3ttd_A 3tsq_A Length = 657 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query273
3vth_A 761 Hydrogenase maturation factor; carbamoyltransfer, 100.0
4g9i_A 772 Hydrogenase maturation protein HYPF; zinc finger, 100.0
3ttc_A 657 HYPF, transcriptional regulatory protein; Zn finge 100.0
1k7j_A206 Protein YCIO, protein TF1; structural genomics, X- 100.0
2eqa_A 352 Hypothetical protein ST1526; YRDC/RIBB fold, YRDC 100.0
1jcu_A208 Conserved protein MTH1692; mixed alpha-beta struct 100.0
1hru_A188 YRDC gene product; protein folding, structural gen 100.0
3l7v_A295 Putative uncharacterized protein SMU.1377C; transc 100.0
3ven_A576 O-carbamoyltransferase TOBZ; antibiotic biosynthes 97.36
>3vth_A Hydrogenase maturation factor; carbamoyltransfer, maturation of [NIFE]-hydrogenase, carbamoylphosphate, iron, HYPE; HET: APC AP2; 2.00A {Thermoanaerobacter tengcongensis} PDB: 3vti_A Back     alignment and structure
Probab=100.00  E-value=9.3e-57  Score=456.23  Aligned_cols=228  Identities=21%  Similarity=0.275  Sum_probs=202.5

Q ss_pred             cCcCCC-CCCCCCCCCceeEEEcCCCcccCCCHHHHHHHHHHHhcCceEEEecCceEEEEeecCCHHHHHHHHHHhCCCC
Q 024072           34 LNRRFP-KKMAFSLENGQVSVENKAGLVRPATEAHAEEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKH  112 (273)
Q Consensus        34 ~~RRfh-~~~ac~~cgp~~~~~~~~~~~~~~~~~~i~~a~~~L~~G~IvaiptdtgYgL~cda~n~~AV~rLr~~K~R~~  112 (273)
                      .||||| ||+||+.|||++++.+..|     ..+.+++|+++|++|+|||+||||||||+|||+|++||+|||++|+|| 
T Consensus       175 ~~RRfhAqp~aC~~CGP~l~l~~~~~-----~~~~i~~aa~~L~~G~IVa~pt~t~YgL~cda~n~~AV~rL~~~K~Rp-  248 (761)
T 3vth_A          175 HDRRFHAQPVACFDCGPSLSFVGEGC-----FDDEIKCVAKALKEGKIVAIKGIGGFHLAVNALDDEAVATLRRRKKRY-  248 (761)
T ss_dssp             TSTTTTCTTCCCTTTSCCEEEESSCC-----CSCHHHHHHHHHHTTCCEEEECSSSEEEECBTTCHHHHHHHHHHHTCC-
T ss_pred             ccccccCCCCcCCccCCeeEEeCCCC-----chHHHHHHHHHHHcCCEEEEECCcEEEEEecCCCHHHHHHHHHHhCCC-
Confidence            499999 9999999999999998776     346799999999999999999999999999999999999999999999 


Q ss_pred             CCCcEEEECCHHHHhhhhccCCchHHHHhccCCCCeEEEEccCCCCccccccCCCCCeEEEEcCCcHHHHHHHHhCCCeE
Q 024072          113 TSPLAICVGDVSDINRFAVTDHLPHGLLDSLLPGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIARGLESAL  192 (273)
Q Consensus       113 ~KPfavm~~dl~~l~~~~~v~~~~~~ll~~~~PgpiTvIl~~~~~~~l~~~l~~~~~tiGvrlP~~p~~~~Ll~~~g~PL  192 (273)
                      +|||+||++|++++++|+++++.+++++++ ||||+| ||++++. .+++.++++.+|||||+||||+|++|++.+|.||
T Consensus       249 ~KPl~vmv~dl~~l~~~~~v~~~~~~ll~~-~pgPit-lL~~~~~-~lp~~v~~~~~tvGvRlP~~pl~~~Ll~~~g~PL  325 (761)
T 3vth_A          249 GKPFAVMMRDVEEVKKYCIVSPEEERLLLS-QRRPIV-LLKKKGE-KLAKGIADDLDTLGVMLPYAPIHYLLMEEIDFPI  325 (761)
T ss_dssp             SSCCCEECSSHHHHHHHBCCCHHHHHHHHS-TTCCEE-EEEBCSS-CCCTTSSTTCSEEEEECCCSHHHHHHHHHCSSCE
T ss_pred             CCCeEEEeCCHHHHHHHccCCHHHHHHHhC-CCCCEE-EEECCCC-CCCHhHcCCCCeEEEEecCCHHHHHHHHHcCCeE
Confidence            899999999999999999999888999998 999998 5777643 5889999999999999999999999999999999


Q ss_pred             EEecCCCCCCCCCCCHHHH-HhhhhcccEEEcCcccCCCCCCCeeEEcccC---------------------CccEEEec
Q 024072          193 ALTSANLTGQPSSVSVKDF-ENLWERCACVYDGGVLPSGRAGSTVVDLTRL---------------------GKFKILRP  250 (273)
Q Consensus       193 v~TSAN~SGep~~~~~~~~-~~~~~~vd~ivd~g~~~~~~~~STVVdl~~~---------------------~~~~IlR~  250 (273)
                      +|||||+||+|++++.+++ +++.+.+|+|+|+++....+.+|||||++.+                     ....||+.
T Consensus       326 v~TSAN~SG~p~~~~~~e~~~~l~~~vD~iLd~~r~i~~~~~STVvd~~~~~~~iLR~grG~~P~~~~l~~~~~~~vla~  405 (761)
T 3vth_A          326 VMTSGNVSEEPICKDNEEALEKLKDIADVFLLNNRDIVNRIDDSVTSFNAGAERIIRRARGYAPQPILLKKEVKASILAV  405 (761)
T ss_dssp             ECEESSSTTSCCCCSHHHHHHHTTTTCSEEEEESSCCSSCCCCCEECEETTEECCSBCCTTTTTCCEECSSCCSSCEEEC
T ss_pred             EEcCcccCCCCCCCCHHHHHHHccCcCCEEEECCCCccCCCCCeEEEEECCcEEEEecCCCCCCCccccCCCCCCcEEEe
Confidence            9999999999999999986 5677889999998754446689999998642                     01258888


Q ss_pred             CCChHHHHHHHhcCCccccC
Q 024072          251 GSAKEETIAILEKHSLVEEP  270 (273)
Q Consensus       251 G~~~k~~~~l~~~~~~~~~~  270 (273)
                      |+.+|||+|+++++..+-.|
T Consensus       406 G~~lknt~~l~~~~~~~~s~  425 (761)
T 3vth_A          406 GGFYKNTFCMTKGHYAFISH  425 (761)
T ss_dssp             CCSTTBCCEEEETTEEEECC
T ss_pred             ChhhcceEEEEECCEEEEec
Confidence            88899999988877665444
>4g9i_A Hydrogenase maturation protein HYPF; zinc finger, ATP binding, carbamoyla transferase; 4.50A {Thermococcus kodakarensis} Back     alignment and structure
>3ttc_A HYPF, transcriptional regulatory protein; Zn finger, nucleotide binding, hydrogenase maturation factor transferase; HET: ADP; 1.86A {Escherichia coli} PDB: 3tsp_A* 3tsu_A* 3ttf_A* 3ttd_A 3tsq_A Back     alignment and structure
>1k7j_A Protein YCIO, protein TF1; structural genomics, X-RAY crystallography, putative translation factor, PSI, protein structure initiative; 1.40A {Escherichia coli} SCOP: d.115.1.1 PDB: 1kk9_A Back     alignment and structure
>2eqa_A Hypothetical protein ST1526; YRDC/RIBB fold, YRDC domain, SUA5 domain, structural genomics, NPPSFA; HET: AMP; 1.80A {Sulfolobus tokodaii} PDB: 3aje_A* 4e1b_A* Back     alignment and structure
>1jcu_A Conserved protein MTH1692; mixed alpha-beta structure, structural genomics; NMR {Methanothermobacterthermautotrophicus} SCOP: d.115.1.1 Back     alignment and structure
>1hru_A YRDC gene product; protein folding, structural genomics, RNA, SUA5, PSI, protein structure initiative, midwest center for structural genomics; 2.00A {Escherichia coli} SCOP: d.115.1.1 Back     alignment and structure
>3l7v_A Putative uncharacterized protein SMU.1377C; transcription; 2.26A {Streptococcus mutans} Back     alignment and structure
>3ven_A O-carbamoyltransferase TOBZ; antibiotic biosynthesis, substrate assisted catalysis, subst channeling, adenylation; HET: TLA; 1.57A {Streptoalloteichus tenebrarius} PDB: 3veo_A 3ves_A* 3vet_A* 3vew_A* 3ver_A* 3vf4_A* 3vf2_A* 3vex_A* 3vez_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 273
d1k7ja_206 d.115.1.1 (A:) Hypothetical protein YciO {Escheric 3e-26
d1hrua_186 d.115.1.1 (A:) Hypothetical protein YrdC {Escheric 5e-26
d1jcua_208 d.115.1.1 (A:) Hypothetical protein MTH1692 {Archa 6e-26
>d1k7ja_ d.115.1.1 (A:) Hypothetical protein YciO {Escherichia coli [TaxId: 562]} Length = 206 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: YrdC/RibB
superfamily: YrdC/RibB
family: YrdC-like
domain: Hypothetical protein YciO
species: Escherichia coli [TaxId: 562]

 Score =   99 bits (248), Expect = 3e-26
 Identities = 41/185 (22%), Positives = 78/185 (42%), Gaps = 6/185 (3%)

Query: 69  EEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINR 128
            +A++ ++ G VI  PTD+ Y   C      A+ RI  I+         +   D+S+++ 
Sbjct: 18  NQAVEIVRKGGVIVYPTDSGYALGCKIEDKNAMERICRIRQLPDGHNFTLMCRDLSELST 77

Query: 129 FAVTDHLPHGLLDSLLPGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIARGL 188
           ++  D+     L           + +G      + L    ++IG+RVP +   + +   L
Sbjct: 78  YSFVDN-VAFRLMKNNTPGNYTFILKGTKEVPRRLLQEKRKTIGMRVPSNPIAQALLEAL 136

Query: 189 ESALALTSANLTGQPSSVSVKD--FENLWERCACVYDGGVLPSGRAGSTVVDLTRLGKFK 246
              +  TS  L G   + S  +   + L ++   +  GG    G+  +TV+DLT      
Sbjct: 137 GEPMLSTSLMLPGSEFTESDPEEIKDRLEKQVDLIIHGG--YLGQKPTTVIDLTD-DTPV 193

Query: 247 ILRPG 251
           ++R G
Sbjct: 194 VVREG 198
>d1hrua_ d.115.1.1 (A:) Hypothetical protein YrdC {Escherichia coli [TaxId: 562]} Length = 186 Back     information, alignment and structure
>d1jcua_ d.115.1.1 (A:) Hypothetical protein MTH1692 {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Length = 208 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 ?
Query273
d1k7ja_206 Hypothetical protein YciO {Escherichia coli [TaxId 100.0
d1jcua_208 Hypothetical protein MTH1692 {Archaeon Methanobact 100.0
d1hrua_186 Hypothetical protein YrdC {Escherichia coli [TaxId 100.0
>d1k7ja_ d.115.1.1 (A:) Hypothetical protein YciO {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: YrdC/RibB
superfamily: YrdC/RibB
family: YrdC-like
domain: Hypothetical protein YciO
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=4.1e-49  Score=343.04  Aligned_cols=187  Identities=24%  Similarity=0.420  Sum_probs=168.0

Q ss_pred             HHHHHHHHHHHhcCceEEEecCceEEEEeecCCHHHHHHHHHHhCCCCCCCcEEEECCHHHHhhhhccCCchHHHHhccC
Q 024072           65 EAHAEEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINRFAVTDHLPHGLLDSLL  144 (273)
Q Consensus        65 ~~~i~~a~~~L~~G~IvaiptdtgYgL~cda~n~~AV~rLr~~K~R~~~KPfavm~~dl~~l~~~~~v~~~~~~ll~~~~  144 (273)
                      .+.+++|++.|++||||++||||+|||+|||+|++||+|||++|+|+.+|||++|++|++++++|+++++...++++++|
T Consensus        14 ~~~i~~a~~~L~~G~vv~~PTdTvYgl~~da~~~~av~~i~~iK~R~~~kpl~vlv~~~~~~~~~~~~~~~~~~l~~~~w   93 (206)
T d1k7ja_          14 QRLINQAVEIVRKGGVIVYPTDSGYALGCKIEDKNAMERICRIRQLPDGHNFTLMCRDLSELSTYSFVDNVAFRLMKNNT   93 (206)
T ss_dssp             HHHHHHHHHHHHTTCCEEEEETTEEEEEEETTCHHHHHHHHHHHTCCTTCCCEEECSSHHHHHHHBCCCHHHHHHHHTSC
T ss_pred             HHHHHHHHHHHHcCCEEEEECCceeEEEEeCCChHHHHHHHHhhccccccccccccCCHHHHHHHhhhhhhhhhhhcccc
Confidence            56799999999999999999999999999999999999999999999999999999999999999988888889999999


Q ss_pred             CCCeEEEEccCCCCccccccCCCCCeEEEEcCCcHHHHHHHHhCCCeEEEecCCCCCCCC-CCCHHHHHh-hhhcccEEE
Q 024072          145 PGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIARGLESALALTSANLTGQPS-SVSVKDFEN-LWERCACVY  222 (273)
Q Consensus       145 PgpiTvIl~~~~~~~l~~~l~~~~~tiGvrlP~~p~~~~Ll~~~g~PLv~TSAN~SGep~-~~~~~~~~~-~~~~vd~iv  222 (273)
                      |||+|+|+++++. .....+.++.++||||+|+||+++.|++.+|.||++||||+||++. .++.+++.+ +.+.+|+++
T Consensus        94 PgplT~i~~~~~~-~~~~~~~~~~~tv~iRip~~~~~~~Ll~~~~~Pl~sTSAN~sG~~~~~~~~~~i~~~~~~~vd~ii  172 (206)
T d1k7ja_          94 PGNYTFILKGTKE-VPRRLLQEKRKTIGMRVPSNPIAQALLEALGEPMLSTSLMLPGSEFTESDPEEIKDRLEKQVDLII  172 (206)
T ss_dssp             SSSEEEEEEBCTT-SCGGGSCTTTCEEEEECCCSHHHHHHHHHHCSCEEEEECBCTTCSSBCCCHHHHHHHHTTTCSEEE
T ss_pred             ccceeeeecCCcc-ccchhhccccceeeeeecccchhHHHHHhhcCceeeecccccccccccCCHHHHHHHhCCCceEEE
Confidence            9999999998653 3446777888999999999999999999999999999999999875 456777654 557899999


Q ss_pred             cCcccCCCCCCCeeEEcccCCccEEEecCCChH
Q 024072          223 DGGVLPSGRAGSTVVDLTRLGKFKILRPGSAKE  255 (273)
Q Consensus       223 d~g~~~~~~~~STVVdl~~~~~~~IlR~G~~~k  255 (273)
                      |+|..  .+.+|||||++. ++++|+|+|++..
T Consensus       173 d~g~~--~~~pSTIid~~~-~~~~ilR~Ga~~~  202 (206)
T d1k7ja_         173 HGGYL--GQKPTTVIDLTD-DTPVVVREGVGDV  202 (206)
T ss_dssp             ECCCC--CSCCCEEEECGG-GCCEEEECCSSCS
T ss_pred             eCCCc--CCCCCeEEEEEC-CCeEEEecCCCCc
Confidence            99886  347999999986 5789999999853
>d1jcua_ d.115.1.1 (A:) Hypothetical protein MTH1692 {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Back     information, alignment and structure
>d1hrua_ d.115.1.1 (A:) Hypothetical protein YrdC {Escherichia coli [TaxId: 562]} Back     information, alignment and structure