Citrus Sinensis ID: 011810

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------

MRTLAIANMEVGSVWMRLVRVRGGAPSVFLMKPSAVSSSSKTTRTIRYKNHLSTFFPSSNPPPITFLSPVSPTRRPLSTATCSPQIPLATIEDYCSDAGGGDNINVLPKKGSRVLLKGMSFTELQQWVRSHAFRPGQALMLWKRLYGDDIWAHCTDELEGLNKDFKKMLSEHAEFRALSLKDILTSSDGTRKILFMLDDGLVIETVVIPCNRGRTTVCVSSQVGCAMNCQFCYTGRMGLKRHLTAAEIVEQAVFARRLLSSEVGSITNVVFMGMGEPLHNVENVIKAANIMVHEQGLHFSPRKVTVSTSGLVPQLKQFLNESNCALAVSLNATTDEVRNWIMPINRKYKLGLLIETLREELHFKNNYKVLFEYVMLAGVNDSFDDAKRLIGLVQGIPCKINLISFNPHCGSQFTPTTDEKMIEFRNILAGAGCTVFLRLSRGDDQMAACGQLGNPGAIQAPLLRVPEKFQTAINASI

ccccEEEcccccEEEEEEEEEccccccccccccccccccccccccEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHcccccHHHHHHHHHHHcccccccccHHHccccHHHHHHHHcccccccccEEEEEEcccccEEEEEEcccccEEEEEEEcccccccEEEEcccccccccccccccccccccccccHHHHHHHHHHHHHHHccccccccEEEEcccccccccHHHHHHHHHHHcccccccccccEEEEcccccHHHHHHHHHccccEEEEEcccccHHHHHHcccccccccHHHHHHHHHHHHccccccEEEEEEEEcccccccHHHHHHHHHHHcccccEEEEEccccccccccccccHHHHHHHHHHHHHcccEEEEcccccccHHHccccccccccccccccccHHHHHHHHHHcc

ccEEEEEEcccccEEEEEEEEccccccccEccccccccccccccccccHHHHHHcccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccHHHHHHHHHHccccccHHHHHHHHHHHcccccccHHHHcHHHHHHHHHHHHcEEEcccEEEEEEEcccccEEEEEEEccccEEEEEEEEccccccEEEEEccccccEcccEcccccccccccccHHHHHHHHHHHHHHHccccccEEEEEEEccccccccHHHHHHHHHHHHHccccccccEEEEEEcccHHHHHHHHHHHccEEEEEEEccccHHHHHHccHHcccccHHHHHHHHHHHHHHccccEEEEEEEEcccccccHHHHHHHHHHHcccccEEEEEEcccccccccccccHHHHHHHHHHHHHcccEEEEEccccccHHHHHHHHHHccccHcHHHHHHHHHHHcccccc

MRTLAIANMEVGSVWMRLVRVrggapsvflmkpsavsssskttrtiryknhlstffpssnpppitflspvsptrrplstatcspqiplatiedycsdagggdninvlpkkgsrvllkgmsFTELQQWVRSHAFRPGQALMLWKRLYGDDIWAHCTDELEGLNKDFKKMLSEHAEFRALSLKdiltssdgTRKILFMLDDGLVIETVVipcnrgrttVCVSsqvgcamncqfcytgrmglkrHLTAAEIVEQAVFARRLLSSEVGSITNVVFMGMGEPLHNVENVIKAANIMVHeqglhfsprkvtvstsglvpqLKQFLNESNCALAVSLNATTDEVRNWIMPINRKYKLGLLIETLREELHFKNNYKVLFEYVMLAGVNDSFDDAKRLIGlvqgipckinlisfnphcgsqftpttdEKMIEFRNILAGAGCTVFLRlsrgddqmaacgqlgnpgaiqapllrvpEKFQTAINASI

MRTLAIANMEVGSVWMRLVRVRGGApsvflmkpsavsssskttrTIRYKNHlstffpssnpppITFLSPVSPTRRPLStatcspqiplATIEDYCSDAGGGDNINVLPKKGSRVLLKGMSFTELQQWVRSHAFRPGQALMLWKRLYGDDIWAHCTDELEGLNKDFKKMLSEHAEFRALSLKDILTSSDGTRKILFMLDDGLVIETVVIPCNRGRTTVCVSSQVGCAMNCQFCYTGRMGLKRHLTAAEIVEQAVFARRLLSSEVGSITNVVFMGMGEPLHNVENVIKAANIMVHEQGLHFSPRKVTVSTSGLVPQLKQFLNESNCALAVSLNattdevrnwimpINRKYKLGLLIETLREELHFKNNYKVLFEYVMLAGVNDSFDDAKRLIGLVQGIPCKINLISFNPHCGSQFTPTTDEKMIEFRNILAGAGCTVFLRLSRGDDQMAACGQLGNpgaiqapllrVPEKFQTAINASI

****AIANMEVGSVWMRLVRVRGGAPSVFLM**************************************************CSPQIPLATIEDYCSDAGGGDNINVLPKKGSRVLLKGMSFTELQQWVRSHAFRPGQALMLWKRLYGDDIWAHCTDELEGLNKDFKKMLSEHAEFRALSLKDILTSSDGTRKILFMLDDGLVIETVVIPCNRGRTTVCVSSQVGCAMNCQFCYTGRMGLKRHLTAAEIVEQAVFARRLLSSEVGSITNVVFMGMGEPLHNVENVIKAANIMVHEQGLHFSPRKVTVSTSGLVPQLKQFLNESNCALAVSLNATTDEVRNWIMPINRKYKLGLLIETLREELHFKNNYKVLFEYVMLAGVNDSFDDAKRLIGLVQGIPCKINLISFNPHCGSQFTPTTDEKMIEFRNILAGAGCTVFLRLSRGDDQMAACGQLGNPGAIQAPLLRV************

****A*ANMEVGSVWMRLVRVRGGAPSVFLMKPSAVSSSSKTTRTIRYKNHLSTFFPSSNPPPITFL************************************************LKGMSFTELQQWVRSHAFRPGQALMLWKRLYGDDIWAHCTDELEGLNKDFKKMLSEHAEFRALSLKDILTSSDGTRKILFMLDDGLVIETVVIPCNRGRTTVCVSSQVGCAMNCQFCYTGRMGLKRHLTAAEIVEQAVFARRLLSSEVGSITNVVFMGMGEPLHNVENVIKAANIMVHEQGLHFSPRKVTVSTSGLVPQLKQFLNESNCALAVSLNATTDEVRNWIMPINRKYKLGLLIETLREELHFKNNYKVLFEYVMLAGVNDSFDDAKRLIGLVQGIPCKINLISFNPHCGSQFTPTTDEKMIEFRNILAGAGCTVFLRLSRGDDQMAACGQ**************************

MRTLAIANMEVGSVWMRLVRVRGGAPSVFLMKP**********RTIRYKNHLSTFFPSSNPPPITFLSPVSPTRRPLSTATCSPQIPLATIEDYCSDAGGGDNINVLPKKGSRVLLKGMSFTELQQWVRSHAFRPGQALMLWKRLYGDDIWAHCTDELEGLNKDFKKMLSEHAEFRALSLKDILTSSDGTRKILFMLDDGLVIETVVIPCNRGRTTVCVSSQVGCAMNCQFCYTGRMGLKRHLTAAEIVEQAVFARRLLSSEVGSITNVVFMGMGEPLHNVENVIKAANIMVHEQGLHFSPRKVTVSTSGLVPQLKQFLNESNCALAVSLNATTDEVRNWIMPINRKYKLGLLIETLREELHFKNNYKVLFEYVMLAGVNDSFDDAKRLIGLVQGIPCKINLISFNPHCGSQFTPTTDEKMIEFRNILAGAGCTVFLRLSRGDDQMAACGQLGNPGAIQAPLLRVPEKFQTAINASI

MRTLAIANMEVGSVWMRLVRVRGGAPSVFLMKPSAVSSSSKTTRTIRYKNHLSTFFPSSNPPPITFLSPVSPTRRPLSTATCS*****************************RVLLKGMSFTELQQWVRSHAFRPGQALMLWKRLYGDDIWAHCTDELEGLNKDFKKMLSEHAEFRALSLKDILTSSDGTRKILFMLDDGLVIETVVIPCNRGRTTVCVSSQVGCAMNCQFCYTGRMGLKRHLTAAEIVEQAVFARRLLSSEVGSITNVVFMGMGEPLHNVENVIKAANIMVHEQGLHFSPRKVTVSTSGLVPQLKQFLNESNCALAVSLNATTDEVRNWIMPINRKYKLGLLIETLREELHFKNNYKVLFEYVMLAGVNDSFDDAKRLIGLVQGIPCKINLISFNPHCGSQFTPTTDEKMIEFRNILAGAGCTVFLRLSRGDDQMAACGQLGNPGA********************

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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		477	2.2.26 [Sep-21-2011]
Q74E53		360	Dual-specificity RNA meth	yes	no	0.683	0.905	0.469	7e-77
Q3A2Z4		371	Dual-specificity RNA meth	yes	no	0.723	0.929	0.429	2e-75
Q39S71		346	Dual-specificity RNA meth	yes	no	0.693	0.956	0.458	5e-74
A0LQM1		342	Dual-specificity RNA meth	yes	no	0.696	0.970	0.434	2e-73
A5GEC2		343	Dual-specificity RNA meth	yes	no	0.693	0.965	0.45	3e-73
A1AL40		347	Dual-specificity RNA meth	yes	no	0.706	0.971	0.456	1e-72
B9KQP1		392	Dual-specificity RNA meth	yes	no	0.714	0.869	0.413	1e-70
Q3IY22		392	Dual-specificity RNA meth	yes	no	0.714	0.869	0.413	1e-70
A3PFQ4		392	Dual-specificity RNA meth	yes	no	0.714	0.869	0.413	1e-70
A4WNI9		392	Dual-specificity RNA meth	yes	no	0.716	0.872	0.409	4e-70

>sp\|Q74E53\|RLMN_GEOSL Dual-specificity RNA methyltransferase RlmN OS=Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA) GN=rlmN PE=3 SV=1	Back alignment and function desciption

 Score =  288 bits (736), Expect = 7e-77,   Method: Compositional matrix adjust.
 Identities = 159/339 (46%), Positives = 210/339 (61%), Gaps = 13/339 (3%)

Query: 116 LKGMSFTELQQWVRSHAFRPGQALMLWKRLY--GDDIWAHCTDELEGLNKDFKKMLSEHA 173
           +KG+S  EL++++        +A  ++K LY  G   +A  TD    L K+ ++ L E A
Sbjct: 7   IKGLSIDELERFLLGKGKERYRARQIFKWLYQRGATSFAEMTD----LAKELRRDLEETA 62

Query: 174 EFRALSLKDILTSSDGTRKILFMLDDGLVIETVVIPCNRGRTTVCVSSQVGCAMNCQFCY 233
               LS + +  S DGTRK LF LDDG  +E+V+IP    R T+C+SSQVGCAM C+FC 
Sbjct: 63  RISTLSPEALEISRDGTRKYLFRLDDGCSVESVLIP-EEDRNTLCISSQVGCAMACEFCL 121

Query: 234 TGRMGLKRHLTAAEIVEQAVFARRLLSSEVGSITNVVFMGMGEPLHNVENVIKAANIMVH 293
           TG   L R+LT AEIV Q    +R +      + N+VFMGMGEPL N++NVI+A  IM+H
Sbjct: 122 TGTFRLTRNLTTAEIVNQVCAVQRDVP-----VRNIVFMGMGEPLANLDNVIRALQIMLH 176

Query: 294 EQGLHFSPRKVTVSTSGLVPQLKQFLNESNCALAVSLNATTDEVRNWIMPINRKYKLGLL 353
           + GL FS R++TVST+GLVP++++        LAVSLNATTDE+R+ IMPINRKY L +L
Sbjct: 177 DDGLQFSTRRITVSTAGLVPEMERLGRSVTVNLAVSLNATTDELRDRIMPINRKYPLAVL 236

Query: 354 IETLREELHFKNNYKVLFEYVMLAGVNDSFDDAKRLIGLVQGIPCKINLISFNPHCGSQF 413
           ++  R         K+  EYV+L GVND+ DDAKRL+ L+  IP KINLI FN H G  F
Sbjct: 237 LDACR-RFPLPGRRKITIEYVLLGGVNDTLDDAKRLVRLLSDIPSKINLIPFNEHEGCSF 295

Query: 414 TPTTDEKMIEFRNILAGAGCTVFLRLSRGDDQMAACGQL 452
              + + +  F   L     TV  R SRG D  AACGQL
Sbjct: 296 RSPSQDAIDRFHRYLLDKHFTVITRSSRGADISAACGQL 334

Specifically methylates position 2 of adenine 2503 in 23S rRNA.
Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA) (taxid: 243231)
EC: 2EC: .EC: 1EC: .EC: 1EC: .EC: 1EC: 9EC: 2

>sp\|Q3A2Z4\|RLMN_PELCD Dual-specificity RNA methyltransferase RlmN OS=Pelobacter carbinolicus (strain DSM 2380 / Gra Bd 1) GN=rlmN PE=3 SV=1	Back alignment and function description

>sp\|Q39S71\|RLMN_GEOMG Dual-specificity RNA methyltransferase RlmN OS=Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210) GN=rlmN PE=3 SV=1	Back alignment and function description

>sp\|A0LQM1\|RLMN_SYNFM Dual-specificity RNA methyltransferase RlmN OS=Syntrophobacter fumaroxidans (strain DSM 10017 / MPOB) GN=rlmN PE=3 SV=1	Back alignment and function description

>sp\|A5GEC2\|RLMN_GEOUR Dual-specificity RNA methyltransferase RlmN OS=Geobacter uraniireducens (strain Rf4) GN=rlmN PE=3 SV=1	Back alignment and function description

>sp\|A1AL40\|RLMN_PELPD Dual-specificity RNA methyltransferase RlmN OS=Pelobacter propionicus (strain DSM 2379) GN=rlmN PE=3 SV=1	Back alignment and function description

>sp\|B9KQP1\|RLMN_RHOSK Dual-specificity RNA methyltransferase RlmN OS=Rhodobacter sphaeroides (strain KD131 / KCTC 12085) GN=rlmN PE=3 SV=1	Back alignment and function description

>sp\|Q3IY22\|RLMN_RHOS4 Dual-specificity RNA methyltransferase RlmN OS=Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158) GN=rlmN1 PE=3 SV=1	Back alignment and function description

>sp\|A3PFQ4\|RLMN_RHOS1 Dual-specificity RNA methyltransferase RlmN OS=Rhodobacter sphaeroides (strain ATCC 17029 / ATH 2.4.9) GN=rlmN PE=3 SV=1	Back alignment and function description

>sp\|A4WNI9\|RLMN_RHOS5 Dual-specificity RNA methyltransferase RlmN OS=Rhodobacter sphaeroides (strain ATCC 17025 / ATH 2.4.3) GN=rlmN 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
Query		477
296086557		439	unnamed protein product [Vitis vinifera]	0.865	0.940	0.772	0.0
359473450		907	PREDICTED: uncharacterized protein LOC10	0.836	0.439	0.772	0.0
449455661		482	PREDICTED: dual-specificity RNA methyltr	0.758	0.751	0.845	0.0
356524059		445	PREDICTED: ribosomal RNA large subunit m	0.870	0.932	0.741	0.0
18406673		458	radical SAM domain-containing protein [A	0.807	0.840	0.766	1e-179
297837501		458	radical SAM domain-containing protein [A	0.807	0.840	0.766	1e-178
3249072		454	Contains similarity to hypothetical 43.1	0.807	0.848	0.766	1e-178
255568836		861	catalytic, putative [Ricinus communis] g	0.893	0.494	0.686	1e-178
115438803		405	Os01g0640800 [Oryza sativa Japonica Grou	0.811	0.955	0.711	1e-172
194700820		409	unknown [Zea mays] gi\|413950759\|gb\|AFW83	0.765	0.892	0.761	1e-170

>gi\|296086557\|emb\|CBI32146.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

 Score =  671 bits (1730), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 320/414 (77%), Positives = 355/414 (85%), Gaps = 1/414 (0%)

Query: 61  PPPITFLSPV-SPTRRPLSTATCSPQIPLATIEDYCSDAGGGDNINVLPKKGSRVLLKGM 119
           P P   L P+ S   R LS A  S  IP+ +   +        + N  P KGS+VLLKGM
Sbjct: 25  PIPFPHLKPLLSLHHRSLSIAASSSTIPVYSTYHHHHHPSSAADENGNPIKGSKVLLKGM 84

Query: 120 SFTELQQWVRSHAFRPGQALMLWKRLYGDDIWAHCTDELEGLNKDFKKMLSEHAEFRALS 179
            + ELQ WV+SH +RPGQALMLWKRLYG++IWAHC DELEGLNKDFK MLSEHAEF+AL+
Sbjct: 85  RYFELQNWVQSHGYRPGQALMLWKRLYGNNIWAHCIDELEGLNKDFKSMLSEHAEFKALT 144

Query: 180 LKDILTSSDGTRKILFMLDDGLVIETVVIPCNRGRTTVCVSSQVGCAMNCQFCYTGRMGL 239
           LKD + +SDGTRKILF LDDGLVIETV+IPC+RGR TVCVSSQVGCAMNCQFCYTGRMGL
Sbjct: 145 LKDSIKASDGTRKILFTLDDGLVIETVIIPCDRGRNTVCVSSQVGCAMNCQFCYTGRMGL 204

Query: 240 KRHLTAAEIVEQAVFARRLLSSEVGSITNVVFMGMGEPLHNVENVIKAANIMVHEQGLHF 299
            RHLTAAEIVEQAV+ARRL SSEVGSITNVVFMGMGEP HN+E+VIKAA+IMVH+QGLHF
Sbjct: 205 TRHLTAAEIVEQAVYARRLFSSEVGSITNVVFMGMGEPFHNIESVIKAADIMVHDQGLHF 264

Query: 300 SPRKVTVSTSGLVPQLKQFLNESNCALAVSLNATTDEVRNWIMPINRKYKLGLLIETLRE 359
           SPRKVTVSTSGLVPQLK FL ESNCALAVSLNATTDEVRNW+MPINRKY L LL++TLRE
Sbjct: 265 SPRKVTVSTSGLVPQLKHFLRESNCALAVSLNATTDEVRNWVMPINRKYNLSLLLQTLRE 324

Query: 360 ELHFKNNYKVLFEYVMLAGVNDSFDDAKRLIGLVQGIPCKINLISFNPHCGSQFTPTTDE 419
           EL  K+NYKVLFEYVMLAGVNDS +DA+RLI LVQGIPCK+NLISFNPHCGSQF PT++E
Sbjct: 325 ELRSKHNYKVLFEYVMLAGVNDSLEDARRLIDLVQGIPCKVNLISFNPHCGSQFKPTSEE 384

Query: 420 KMIEFRNILAGAGCTVFLRLSRGDDQMAACGQLGNPGAIQAPLLRVPEKFQTAI 473
           K+IEFRNILA AGC VFLR SRGDDQMAACGQLG PG +QAPLLRVP KFQ+A+
Sbjct: 385 KIIEFRNILAEAGCIVFLRPSRGDDQMAACGQLGKPGQVQAPLLRVPAKFQSAL 438

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|359473450\|ref\|XP_002264209.2\| PREDICTED: uncharacterized protein LOC100267261 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|449455661\|ref\|XP_004145570.1\| PREDICTED: dual-specificity RNA methyltransferase RlmN-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|356524059\|ref\|XP_003530650.1\| PREDICTED: ribosomal RNA large subunit methyltransferase N-like [Glycine max]	Back alignment and taxonomy information

>gi\|18406673\|ref\|NP_564755.1\| radical SAM domain-containing protein [Arabidopsis thaliana] gi\|15451230\|gb\|AAK96886.1\| Unknown protein [Arabidopsis thaliana] gi\|20148295\|gb\|AAM10038.1\| unknown protein [Arabidopsis thaliana] gi\|332195547\|gb\|AEE33668.1\| radical SAM domain-containing protein [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|297837501\|ref\|XP_002886632.1\| radical SAM domain-containing protein [Arabidopsis lyrata subsp. lyrata] gi\|297332473\|gb\|EFH62891.1\| radical SAM domain-containing protein [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|3249072\|gb\|AAC24056.1\| Contains similarity to hypothetical 43.1 KD protein in NDK-GCPE intergenic region gb\|493519 from E. coli sequence gb\|U02965 [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|255568836\|ref\|XP_002525389.1\| catalytic, putative [Ricinus communis] gi\|223535352\|gb\|EEF37027.1\| catalytic, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|115438803\|ref\|NP_001043681.1\| Os01g0640800 [Oryza sativa Japonica Group] gi\|113533212\|dbj\|BAF05595.1\| Os01g0640800 [Oryza sativa Japonica Group] gi\|218188735\|gb\|EEC71162.1\| hypothetical protein OsI_03021 [Oryza sativa Indica Group] gi\|222618932\|gb\|EEE55064.1\| hypothetical protein OsJ_02780 [Oryza sativa Japonica Group]	Back alignment and taxonomy information

>gi\|194700820\|gb\|ACF84494.1\| unknown [Zea mays] gi\|413950759\|gb\|AFW83408.1\| hypothetical protein ZEAMMB73_769953 [Zea mays]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		477
TAIR\|locus:2195608		458	AT1G60230 [Arabidopsis thalian	0.958	0.997	0.675	1.7e-160
UNIPROTKB\|Q74E53		360	rlmN "Dual-specificity RNA met	0.683	0.905	0.471	9.9e-71
TIGR_CMR\|GSU_1111		360	GSU_1111 "conserved hypothetic	0.683	0.905	0.471	9.9e-71
UNIPROTKB\|Q83C77		370	rlmN "Dual-specificity RNA met	0.698	0.9	0.443	3.3e-63
TIGR_CMR\|CBU_1252		370	CBU_1252 "radical SAM enzyme,	0.698	0.9	0.443	3.3e-63
TIGR_CMR\|SPO_3346		393	SPO_3346 "radical SAM enzyme,	0.725	0.880	0.385	7.3e-59
UNIPROTKB\|P36979		384	rlmN "23S rRNA m2A2503 methylt	0.714	0.888	0.401	1.2e-56
UNIPROTKB\|Q8EC29		373	rlmN "Dual-specificity RNA met	0.687	0.879	0.412	1.2e-56
TIGR_CMR\|SO_3315		373	SO_3315 "conserved hypothetica	0.687	0.879	0.412	1.2e-56
UNIPROTKB\|Q9KTX3		373	rlmN "Dual-specificity RNA met	0.687	0.879	0.421	1.6e-56

TAIR\|locus:2195608 AT1G60230 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1563 (555.3 bits), Expect = 1.7e-160, P = 1.7e-160
 Identities = 314/465 (67%), Positives = 371/465 (79%)

Query:    13 SVWMRLVRVRGGAPSVFLMKPSAVSSSSKTTRTIRYKNHLSTFFPSSNPPPITFLSPVSP 72
             S  MR + +     S  ++ PS +SS++    T+   + L +   +++   I F    S 
Sbjct:     2 STTMRRLGIITLTNSAAVVTPSLLSSTAAFPGTLTLPSPLLSDRLTNS---ILFHESRSL 58

Query:    73 TRRPLSTATCSPQIPLATIEDYCSDAGGGDNINVLPKKGSRVLLKGMSFTELQQWVRSHA 132
             +    S+++ S    L ++E+Y S  G     +V      +V+LKGM++  LQ+WV+SH 
Sbjct:    59 SFSCFSSSSSSSAAYLPSLEEYPSAKG-----SVKRDDNQKVVLKGMTYASLQEWVQSHG 113

Query:   133 FRPGQALMLWKRLYGDDIWAHCTDELEGLNKDFKKMLSEHAEFRALSLKDILTSSDGTRK 192
             FRPGQALMLWKRLY D+IWA+  DELEGLNKD K+M+SEHAEF ALS KDI ++SDGTRK
Sbjct:   114 FRPGQALMLWKRLYKDNIWANNVDELEGLNKDLKRMISEHAEFGALSFKDIRSASDGTRK 173

Query:   193 ILFMLDDGLVIETVVIPCNRGRTTVCVSSQVGCAMNCQFCYTGRMGLKRHLTAAEIVEQA 252
             ILF LDDGLVIETVVIPC+RGRTTVCVSSQVGCAMNCQFCYTGRMGLKR+LT AEIVEQA
Sbjct:   174 ILFTLDDGLVIETVVIPCDRGRTTVCVSSQVGCAMNCQFCYTGRMGLKRNLTTAEIVEQA 233

Query:   253 VFARRLLSSEVGSITNVVFMGMGEPLHNVENVIKAANIMVHEQGLHFSPRKVTVSTSGLV 312
             V+ARRLLS EVGSITNVVFMGMGEP HN++NVIKAANIMV E GLHFSPRKVTVSTSGLV
Sbjct:   234 VYARRLLSHEVGSITNVVFMGMGEPFHNIDNVIKAANIMVDENGLHFSPRKVTVSTSGLV 293

Query:   313 PQLKQFLNESNCALAVSLNATTDEVRNWIMPINRKYKLGLLIETLREELHFKNNYKVLFE 372
             PQLK+FL ESNCALAVSLNATTDEVRNWIMPINRKYKL LL+ETLRE L  ++ YKVLFE
Sbjct:   294 PQLKRFLRESNCALAVSLNATTDEVRNWIMPINRKYKLSLLLETLREGLSSRHKYKVLFE 353

Query:   373 YVMLAGVNDSFDDAKRLIGLVQGIPCKINLISFNPHCGSQFTPTTDEKMIEFRNILAGAG 432
             YVMLAGVNDS DDA+RL+ LVQGIPCKINLI FNPH GSQF  T ++KMI+FRN+LA  G
Sbjct:   354 YVMLAGVNDSMDDARRLVELVQGIPCKINLIQFNPHSGSQFIQTEEDKMIKFRNVLAEGG 413

Query:   433 CTVFLRLSRGDDQMAACGQLGNPGAIQAPLLRVPEKFQTAINASI 477
             CTV +R SRG+DQMAACGQLG  GA+QAP++RVPE+F+TA+ AS+
Sbjct:   414 CTVLMRFSRGNDQMAACGQLGMIGAVQAPVMRVPEQFRTALKASV 458

GO:0003824 "catalytic activity" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0008173 "RNA methyltransferase activity" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

GO:0051536 "iron-sulfur cluster binding" evidence=IEA

UNIPROTKB\|Q74E53 rlmN "Dual-specificity RNA methyltransferase RlmN" [Geobacter sulfurreducens PCA (taxid:243231)]	Back alignment and assigned GO terms

TIGR_CMR\|GSU_1111 GSU_1111 "conserved hypothetical protein TIGR00048" [Geobacter sulfurreducens PCA (taxid:243231)]	Back alignment and assigned GO terms

UNIPROTKB\|Q83C77 rlmN "Dual-specificity RNA methyltransferase RlmN" [Coxiella burnetii RSA 493 (taxid:227377)]	Back alignment and assigned GO terms

TIGR_CMR\|CBU_1252 CBU_1252 "radical SAM enzyme, Cfr family" [Coxiella burnetii RSA 493 (taxid:227377)]	Back alignment and assigned GO terms

TIGR_CMR\|SPO_3346 SPO_3346 "radical SAM enzyme, Cfr family" [Ruegeria pomeroyi DSS-3 (taxid:246200)]	Back alignment and assigned GO terms

UNIPROTKB\|P36979 rlmN "23S rRNA m2A2503 methyltransferase and tRNA m2A37 methyltransferase" [Escherichia coli K-12 (taxid:83333)]	Back alignment and assigned GO terms

UNIPROTKB\|Q8EC29 rlmN "Dual-specificity RNA methyltransferase RlmN" [Shewanella oneidensis MR-1 (taxid:211586)]	Back alignment and assigned GO terms

TIGR_CMR\|SO_3315 SO_3315 "conserved hypothetical protein TIGR00048" [Shewanella oneidensis MR-1 (taxid:211586)]	Back alignment and assigned GO terms

UNIPROTKB\|Q9KTX3 rlmN "Dual-specificity RNA methyltransferase RlmN" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)]	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 Level	EC number	Confidence of Prediction
3rd Layer	2.1.1	0.691

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		477
PRK14463		349	PRK14463, PRK14463, ribosomal RNA large subunit me	1e-117
COG0820		349	COG0820, COG0820, Predicted Fe-S-cluster redox enz	1e-111
TIGR00048		355	TIGR00048, TIGR00048, 23S rRNA m2A2503 methyltrans	1e-103
PRK14460		354	PRK14460, PRK14460, ribosomal RNA large subunit me	3e-96
PRK14462		356	PRK14462, PRK14462, ribosomal RNA large subunit me	4e-94
PRK11194		372	PRK11194, PRK11194, ribosomal RNA large subunit me	4e-90
PRK14467		348	PRK14467, PRK14467, ribosomal RNA large subunit me	8e-90
PRK14455		356	PRK14455, PRK14455, ribosomal RNA large subunit me	2e-86
PRK14454		342	PRK14454, PRK14454, ribosomal RNA large subunit me	1e-84
PRK14466		345	PRK14466, PRK14466, ribosomal RNA large subunit me	1e-84
PRK14457		345	PRK14457, PRK14457, ribosomal RNA large subunit me	2e-81
PRK14468		343	PRK14468, PRK14468, ribosomal RNA large subunit me	7e-75
PRK14469		343	PRK14469, PRK14469, ribosomal RNA large subunit me	1e-71
PRK14461		371	PRK14461, PRK14461, ribosomal RNA large subunit me	1e-67
PRK14465		342	PRK14465, PRK14465, ribosomal RNA large subunit me	2e-65
PRK14459		373	PRK14459, PRK14459, ribosomal RNA large subunit me	1e-64
PRK14456		368	PRK14456, PRK14456, ribosomal RNA large subunit me	5e-64
PRK14470		336	PRK14470, PRK14470, ribosomal RNA large subunit me	1e-61
PRK14453		347	PRK14453, PRK14453, chloramphenicol/florfenicol re	3e-54
PRK14464		344	PRK14464, PRK14464, ribosomal RNA large subunit me	8e-43
pfam04055		165	pfam04055, Radical_SAM, Radical SAM superfamily	1e-14
cd01335		204	cd01335, Radical_SAM, Radical SAM superfamily	2e-07
TIGR02493		235	TIGR02493, PFLA, pyruvate formate-lyase 1-activati	5e-07
TIGR04038		191	TIGR04038, tatD_link_rSAM, radical SAM protein, Ta	8e-05
pfam13394		116	pfam13394, Fer4_14, 4Fe-4S single cluster domain	3e-04
TIGR00238		331	TIGR00238, TIGR00238, KamA family protein	3e-04
TIGR04100		197	TIGR04100, rSAM_pair_X, radical SAM enzyme, TIGR04	5e-04
COG1509		369	COG1509, KamA, Lysine 2,3-aminomutase [Amino acid	0.001
COG1032		490	COG1032, COG1032, Fe-S oxidoreductase [Energy prod	0.004

>gnl\|CDD\|237720 PRK14463, PRK14463, ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

 Score =  347 bits (892), Expect = e-117
 Identities = 158/344 (45%), Positives = 204/344 (59%), Gaps = 17/344 (4%)

Query: 113 RVLLKGMSFTELQQWVRSHA---FRPGQALMLWKRLYGDDIWAHCTDELEGLNKDFKKML 169
           +  +K ++  EL+ ++       FR  Q   ++K LY  D  A    E+  L+KD +  L
Sbjct: 4   KTDIKNLTLQELEAFLAGQGKERFRAKQ---IFKWLYQRD--ARSFAEMTNLSKDLRAEL 58

Query: 170 SEHAEFRALSLKDILTSSDGTRKILFMLDDGLVIETVVIPCNRGRTTVCVSSQVGCAMNC 229
            E A    L  + +  S DGTRK LF L+DG  +E+V+IP +  R T+C+SSQVGCAM C
Sbjct: 59  EETARISNLEPEAVEVSRDGTRKYLFRLEDGNAVESVLIP-DEDRNTLCISSQVGCAMGC 117

Query: 230 QFCYTGRMGLKRHLTAAEIVEQAVFARRLLSSEVGSITNVVFMGMGEPLHNVENVIKAAN 289
            FC TG   L R+LT AEIV Q    +R        + N+VFMGMGEPL N++NVI A  
Sbjct: 118 AFCLTGTFRLTRNLTTAEIVNQVCAVKR-----DVPVRNIVFMGMGEPLANLDNVIPALQ 172

Query: 290 IMVHEQGLHFSPRKVTVSTSGLVPQLKQFLNESNCALAVSLNATTDEVRNWIMPINRKYK 349
           I+    GL FS RKVTVSTSGLVP++++   E    LAVSLNATTDEVR+ IMP+NR+Y 
Sbjct: 173 ILTDPDGLQFSTRKVTVSTSGLVPEMEELGREVTVNLAVSLNATTDEVRDRIMPVNRRYP 232

Query: 350 LGLLIETLRE-ELHFKNNYKVLFEYVMLAGVNDSFDDAKRLIGLVQGIPCKINLISFNPH 408
           L  L+   +   L  +   K+  EYVM+ G+NDS +DAKRL+ L+  IP K+NLI FN H
Sbjct: 233 LAELLAACKAFPLPGRR--KITIEYVMIRGLNDSLEDAKRLVRLLSDIPSKVNLIPFNEH 290

Query: 409 CGSQFTPTTDEKMIEFRNILAGAGCTVFLRLSRGDDQMAACGQL 452
            G  F   T E +  F   L     TV  R SRG D  AACGQL
Sbjct: 291 EGCDFRSPTQEAIDRFHKYLLDKHVTVITRSSRGSDISAACGQL 334

Length = 349

>gnl\|CDD\|223890 COG0820, COG0820, Predicted Fe-S-cluster redox enzyme [General function prediction only]	Back alignment and domain information

>gnl\|CDD\|232798 TIGR00048, TIGR00048, 23S rRNA m2A2503 methyltransferase	Back alignment and domain information

>gnl\|CDD\|172935 PRK14460, PRK14460, ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>gnl\|CDD\|237719 PRK14462, PRK14462, ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>gnl\|CDD\|183031 PRK11194, PRK11194, ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>gnl\|CDD\|184693 PRK14467, PRK14467, ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>gnl\|CDD\|237717 PRK14455, PRK14455, ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>gnl\|CDD\|184686 PRK14454, PRK14454, ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>gnl\|CDD\|237721 PRK14466, PRK14466, ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>gnl\|CDD\|184688 PRK14457, PRK14457, ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>gnl\|CDD\|184694 PRK14468, PRK14468, ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>gnl\|CDD\|172944 PRK14469, PRK14469, ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>gnl\|CDD\|237718 PRK14461, PRK14461, ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>gnl\|CDD\|172940 PRK14465, PRK14465, ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>gnl\|CDD\|184689 PRK14459, PRK14459, ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>gnl\|CDD\|172932 PRK14456, PRK14456, ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>gnl\|CDD\|172945 PRK14470, PRK14470, ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>gnl\|CDD\|184685 PRK14453, PRK14453, chloramphenicol/florfenicol resistance protein; Provisional	Back alignment and domain information

>gnl\|CDD\|184691 PRK14464, PRK14464, ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>gnl\|CDD\|217866 pfam04055, Radical_SAM, Radical SAM superfamily	Back alignment and domain information

>gnl\|CDD\|100105 cd01335, Radical_SAM, Radical SAM superfamily	Back alignment and domain information

>gnl\|CDD\|131546 TIGR02493, PFLA, pyruvate formate-lyase 1-activating enzyme	Back alignment and domain information

>gnl\|CDD\|188553 TIGR04038, tatD_link_rSAM, radical SAM protein, TatD family-associated	Back alignment and domain information

>gnl\|CDD\|222098 pfam13394, Fer4_14, 4Fe-4S single cluster domain	Back alignment and domain information

>gnl\|CDD\|232891 TIGR00238, TIGR00238, KamA family protein	Back alignment and domain information

>gnl\|CDD\|188615 TIGR04100, rSAM_pair_X, radical SAM enzyme, TIGR04100 family	Back alignment and domain information

>gnl\|CDD\|224426 COG1509, KamA, Lysine 2,3-aminomutase [Amino acid transport and metabolism]	Back alignment and domain information

>gnl\|CDD\|223963 COG1032, COG1032, Fe-S oxidoreductase [Energy production and conversion]	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		477
PRK14461		371	ribosomal RNA large subunit methyltransferase N; P	100.0
PRK14465		342	ribosomal RNA large subunit methyltransferase N; P	100.0
PRK14459		373	ribosomal RNA large subunit methyltransferase N; P	100.0
COG0820		349	Predicted Fe-S-cluster redox enzyme [General funct	100.0
PRK14466		345	ribosomal RNA large subunit methyltransferase N; P	100.0
PRK11194		372	ribosomal RNA large subunit methyltransferase N; P	100.0
PRK14462		356	ribosomal RNA large subunit methyltransferase N; P	100.0
PRK14467		348	ribosomal RNA large subunit methyltransferase N; P	100.0
TIGR00048		355	radical SAM enzyme, Cfr family. A Staphylococcus s	100.0
PRK14457		345	ribosomal RNA large subunit methyltransferase N; P	100.0
PRK14454		342	ribosomal RNA large subunit methyltransferase N; P	100.0
PRK14455		356	ribosomal RNA large subunit methyltransferase N; P	100.0
PRK14460		354	ribosomal RNA large subunit methyltransferase N; P	100.0
PRK14463		349	ribosomal RNA large subunit methyltransferase N; P	100.0
PRK14470		336	ribosomal RNA large subunit methyltransferase N; P	100.0
PRK14456		368	ribosomal RNA large subunit methyltransferase N; P	100.0
PRK14464		344	ribosomal RNA large subunit methyltransferase N; P	100.0
PRK14453		347	chloramphenicol/florfenicol resistance protein; Pr	100.0
PRK14468		343	ribosomal RNA large subunit methyltransferase N; P	100.0
PRK14469		343	ribosomal RNA large subunit methyltransferase N; P	100.0
PRK11145		246	pflA pyruvate formate lyase-activating enzyme 1; P	99.98
TIGR01290		442	nifB nitrogenase cofactor biosynthesis protein Nif	99.95
COG1180		260	PflA Pyruvate-formate lyase-activating enzyme [Pos	99.94
TIGR02493		235	PFLA pyruvate formate-lyase 1-activating enzyme. A	99.94
TIGR02494		295	PFLE_PFLC glycyl-radical enzyme activating protein	99.93
PRK00164		331	moaA molybdenum cofactor biosynthesis protein A; R	99.93
PRK10076		213	pyruvate formate lyase II activase; Provisional	99.93
PRK13762		322	tRNA-modifying enzyme; Provisional	99.91
TIGR03821		321	AblA_like_1 lysine-2,3-aminomutase-related protein	99.9
PLN02951		373	Molybderin biosynthesis protein CNX2	99.9
COG2896		322	MoaA Molybdenum cofactor biosynthesis enzyme [Coen	99.89
TIGR02668		302	moaA_archaeal probable molybdenum cofactor biosynt	99.89
PRK13361		329	molybdenum cofactor biosynthesis protein A; Provis	99.88
TIGR02666		334	moaA molybdenum cofactor biosynthesis protein A, b	99.87
TIGR02495		191	NrdG2 anaerobic ribonucleoside-triphosphate reduct	99.86
COG0731		296	Fe-S oxidoreductases [Energy production and conver	99.86
TIGR03278		404	methan_mark_10 putative methanogenesis marker prot	99.82
PRK05301		378	pyrroloquinoline quinone biosynthesis protein PqqE	99.79
TIGR03470		318	HpnH hopanoid biosynthesis associated radical SAM	99.79
TIGR02109		358	PQQ_syn_pqqE coenzyme PQQ biosynthesis protein E.	99.77
COG2100		414	Predicted Fe-S oxidoreductase [General function pr	99.76
smart00729		216	Elp3 Elongator protein 3, MiaB family, Radical SAM	99.75
TIGR03822		321	AblA_like_2 lysine-2,3-aminomutase-related protein	99.72
PRK13758		370	anaerobic sulfatase-maturase; Provisional	99.71
TIGR00238		331	KamA family protein. Note that the E. coli homolog	99.69
COG1313		335	PflX Uncharacterized Fe-S protein PflX, homolog of	99.67
TIGR03820		417	lys_2_3_AblA lysine-2,3-aminomutase. This model de	99.67
TIGR03365		238	Bsubt_queE 7-cyano-7-deazaguanosine (preQ0) biosyn	99.67
PRK13745		412	anaerobic sulfatase-maturase; Provisional	99.66
PF04055		166	Radical_SAM: Radical SAM superfamily; InterPro: IP	99.63
COG0641		378	AslB Arylsulfatase regulator (Fe-S oxidoreductase)	99.62
cd01335		204	Radical_SAM Radical SAM superfamily. Enzymes of th	99.61
COG1509		369	KamA Lysine 2,3-aminomutase [Amino acid transport	99.57
COG0535		347	Predicted Fe-S oxidoreductases [General function p	99.57
TIGR02491		154	NrdG anaerobic ribonucleoside-triphosphate reducta	99.53
PRK07094		323	biotin synthase; Provisional	99.52
COG5014		228	Predicted Fe-S oxidoreductase [General function pr	99.51
PRK09240		371	thiH thiamine biosynthesis protein ThiH; Reviewed	99.47
TIGR00433		296	bioB biotin synthetase. Catalyzes the last step of	99.44
PF13353		139	Fer4_12: 4Fe-4S single cluster domain; PDB: 3C8F_A	99.38
PRK06256		336	biotin synthase; Validated	99.36
TIGR01125		430	MiaB-like tRNA modifying enzyme YliG, TIGR01125. T	99.35
PRK08508		279	biotin synthase; Provisional	99.31
PRK14338		459	(dimethylallyl)adenosine tRNA methylthiotransferas	99.29
PRK14862		440	rimO ribosomal protein S12 methylthiotransferase;	99.28
TIGR02351		366	thiH thiazole biosynthesis protein ThiH. Members t	99.28
PRK05481		289	lipoyl synthase; Provisional	99.24
TIGR02826		147	RNR_activ_nrdG3 anaerobic ribonucleoside-triphosph	99.19
PRK15108		345	biotin synthase; Provisional	99.19
TIGR00089		429	RNA modification enzyme, MiaB family. This subfami	99.18
PRK05660		378	HemN family oxidoreductase; Provisional	99.18
TIGR03471		472	HpnJ hopanoid biosynthesis associated radical SAM	99.18
PRK11121		154	nrdG anaerobic ribonucleotide reductase-activating	99.17
TIGR00539		360	hemN_rel putative oxygen-independent coproporphyri	99.17
PF13394		119	Fer4_14: 4Fe-4S single cluster domain; PDB: 1TV8_B	99.17
PRK09249		453	coproporphyrinogen III oxidase; Provisional	99.17
TIGR03551		343	F420_cofH 7,8-didemethyl-8-hydroxy-5-deazariboflav	99.16
PRK14332		449	(dimethylallyl)adenosine tRNA methylthiotransferas	99.16
PLN02389		379	biotin synthase	99.15
PRK08446		350	coproporphyrinogen III oxidase; Provisional	99.15
TIGR02026		497	BchE magnesium-protoporphyrin IX monomethyl ester	99.15
TIGR01579		414	MiaB-like-C MiaB-like tRNA modifying enzyme. This	99.15
PRK14334		440	(dimethylallyl)adenosine tRNA methylthiotransferas	99.14
PRK05799		374	coproporphyrinogen III oxidase; Provisional	99.14
PRK06245		336	cofG FO synthase subunit 1; Reviewed	99.13
PRK12928		290	lipoyl synthase; Provisional	99.12
KOG2876		323	consensus Molybdenum cofactor biosynthesis pathway	99.12
PRK14326		502	(dimethylallyl)adenosine tRNA methylthiotransferas	99.1
PRK13347		453	coproporphyrinogen III oxidase; Provisional	99.1
PRK14331		437	(dimethylallyl)adenosine tRNA methylthiotransferas	99.09
TIGR00423		309	radical SAM domain protein, CofH subfamily. This p	99.09
PRK08599		377	coproporphyrinogen III oxidase; Provisional	99.08
PRK14330		434	(dimethylallyl)adenosine tRNA methylthiotransferas	99.08
COG0602		212	NrdG Organic radical activating enzymes [Posttrans	99.08
TIGR00538		455	hemN oxygen-independent coproporphyrinogen III oxi	99.08
TIGR00510		302	lipA lipoate synthase. The family shows strong seq	99.07
PRK14328		439	(dimethylallyl)adenosine tRNA methylthiotransferas	99.07
PRK14340		445	(dimethylallyl)adenosine tRNA methylthiotransferas	99.06
PRK14337		446	(dimethylallyl)adenosine tRNA methylthiotransferas	99.06
PRK05628		375	coproporphyrinogen III oxidase; Validated	99.06
PRK06267		350	hypothetical protein; Provisional	99.06
TIGR03699		340	mena_SCO4550 menaquinone biosynthesis protein, SCO	99.06
TIGR01574		438	miaB-methiolase tRNA-N(6)-(isopentenyl)adenosine-3	99.05
PRK14325		444	(dimethylallyl)adenosine tRNA methylthiotransferas	99.05
PRK14339		420	(dimethylallyl)adenosine tRNA methylthiotransferas	99.05
PRK08207		488	coproporphyrinogen III oxidase; Provisional	99.03
TIGR01578		420	MiaB-like-B MiaB-like tRNA modifying enzyme, archa	99.03
PRK14336		418	(dimethylallyl)adenosine tRNA methylthiotransferas	99.03
COG0621		437	MiaB 2-methylthioadenine synthetase [Translation,	99.02
TIGR01212		302	radical SAM protein, TIGR01212 family. This unchar	99.0
PRK14335		455	(dimethylallyl)adenosine tRNA methylthiotransferas	99.0
PRK14327		509	(dimethylallyl)adenosine tRNA methylthiotransferas	98.99
PRK14329		467	(dimethylallyl)adenosine tRNA methylthiotransferas	98.98
PRK14333		448	(dimethylallyl)adenosine tRNA methylthiotransferas	98.97
PRK08208		430	coproporphyrinogen III oxidase; Validated	98.96
PLN02428		349	lipoic acid synthase	98.92
PRK07379		400	coproporphyrinogen III oxidase; Provisional	98.9
COG2108		353	Uncharacterized conserved protein related to pyruv	98.9
TIGR01210		313	conserved hypothetical protein TIGR01210. This fam	98.86
COG1964		475	Predicted Fe-S oxidoreductases [General function p	98.81
PRK06582		390	coproporphyrinogen III oxidase; Provisional	98.79
PRK05904		353	coproporphyrinogen III oxidase; Provisional	98.78
PRK08898		394	coproporphyrinogen III oxidase; Provisional	98.76
TIGR03700		351	mena_SCO4494 putative menaquinone biosynthesis pro	98.76
COG0502		335	BioB Biotin synthase and related enzymes [Coenzyme	98.74
PRK09057		380	coproporphyrinogen III oxidase; Provisional	98.73
PRK09058		449	coproporphyrinogen III oxidase; Provisional	98.73
PRK06294		370	coproporphyrinogen III oxidase; Provisional	98.73
PRK08445		348	hypothetical protein; Provisional	98.73
PRK09613		469	thiH thiamine biosynthesis protein ThiH; Reviewed	98.72
TIGR03550		322	F420_cofG 7,8-didemethyl-8-hydroxy-5-deazariboflav	98.71
COG1625		414	Fe-S oxidoreductase, related to NifB/MoaA family [	98.68
PRK07360		371	FO synthase subunit 2; Reviewed	98.64
PRK08629		433	coproporphyrinogen III oxidase; Provisional	98.59
TIGR03279		433	cyano_FeS_chp putative FeS-containing Cyanobacteri	98.57
COG1533		297	SplB DNA repair photolyase [DNA replication, recom	98.56
PRK00955		620	hypothetical protein; Provisional	98.56
COG1032		490	Fe-S oxidoreductase [Energy production and convers	98.51
PRK08444		353	hypothetical protein; Provisional	98.51
PRK01254		707	hypothetical protein; Provisional	98.41
PRK05927		350	hypothetical protein; Provisional	98.37
PTZ00413		398	lipoate synthase; Provisional	98.35
PRK09234		843	fbiC FO synthase; Reviewed	98.22
PRK05926		370	hypothetical protein; Provisional	98.2
TIGR01211		522	ELP3 histone acetyltransferase, ELP3 family. The S	98.09
COG0635		416	HemN Coproporphyrinogen III oxidase and related Fe	98.04
COG1856		275	Uncharacterized homolog of biotin synthetase [Func	98.01
PRK09234		843	fbiC FO synthase; Reviewed	97.93
COG1243		515	ELP3 Histone acetyltransferase [Transcription / Ch	97.6
COG1060		370	ThiH Thiamine biosynthesis enzyme ThiH and related	97.54
COG2516		339	Biotin synthase-related enzyme [General function p	97.53
COG1244		358	Predicted Fe-S oxidoreductase [General function pr	97.45
COG1242		312	Predicted Fe-S oxidoreductase [General function pr	97.25
KOG1160		601	consensus Fe-S oxidoreductase [Energy production a	97.23
COG0320		306	LipA Lipoate synthase [Coenzyme metabolism]	96.95
COG1031		560	Uncharacterized Fe-S oxidoreductase [Energy produc	96.84
cd03174		265	DRE_TIM_metallolyase DRE-TIM metallolyase superfam	95.98
KOG2672		360	consensus Lipoate synthase [Coenzyme transport and	94.69
COG4277		404	Predicted DNA-binding protein with the Helix-hairp	93.94
KOG2900		380	consensus Biotin synthase [Coenzyme transport and	91.29
KOG4355		547	consensus Predicted Fe-S oxidoreductase [General f	87.98

>PRK14461 ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

Probab=100.00  E-value=1.6e-94  Score=737.43  Aligned_cols=342  Identities=36%  Similarity=0.588  Sum_probs=327.3

Q ss_pred             CCccccCCCCHHHHHHHHHHCCCCcchHHHHHHHHhcCCCccCCchhhcCCCHHHHHHHHHHhccccceEeEEeecCCC-
Q 011810          111 GSRVLLKGMSFTELQQWVRSHAFRPGQALMLWKRLYGDDIWAHCTDELEGLNKDFKKMLSEHAEFRALSLKDILTSSDG-  189 (477)
Q Consensus       111 ~~~~~~~~l~~~el~~~~~~~g~~~~ra~qi~~~l~~~~~~~~~~~~~~~l~~~~r~~L~~~~~~~~~~~~~~~~s~Dg-  189 (477)
                      .++.+|++|+++||++++.++|+|+|||+|||+|+|+++  +.+|++|+||||++|++|+++|.+..+++...+.|.|| 
T Consensus         5 ~~~~~l~~l~~~el~~~~~~~g~~~fRa~Qi~~wiy~~~--~~~~~~mtnlpk~lR~~L~~~~~i~~l~~~~~~~S~Dg~   82 (371)
T PRK14461          5 MEQRNLYDLNLAELTELLTAWGQPAFRARQLYRHLYVNL--ADSVLAMTDLPLALRERLTAELPLSTLRLEQVQIGDNGL   82 (371)
T ss_pred             cCCcCcccCCHHHHHHHHHHcCCCchHHHHHHHHHHHcC--CCCHHHccccCHHHHHHHhhccccCCcceEEEEECCCCC
Confidence            467889999999999999999999999999999999999  67999999999999999999999999999999999999 


Q ss_pred             ceEEEEEecCCCeeEEEEeccCCCceeEEEEecCccCCCCCCCCCCCCCCCcCCCHHHHHHHHHHHHHHhcccC------
Q 011810          190 TRKILFMLDDGLVIETVVIPCNRGRTTVCVSSQVGCAMNCQFCYTGRMGLKRHLTAAEIVEQAVFARRLLSSEV------  263 (477)
Q Consensus       190 t~K~l~~l~DG~~IEtVlip~~~~r~tlCVSsq~GCnl~C~FC~tg~~g~~r~Lt~eEIv~qv~~~~~~~~~~~------  263 (477)
                      |+||||+++||..||||+||+ .+|+|+|||||+||+|+|.||+||++|+.|||+++||++|+..+.+.++..+      
T Consensus        83 T~K~L~~l~DG~~IEtVli~~-~~r~TlCvSSQvGC~mgC~FCaTG~~G~~RNLt~~EIv~Qv~~~~~~l~~~~~~~~~~  161 (371)
T PRK14461         83 TRKALFRLPDGAVVETVLMIY-PDRATVCVSTQAGCGMGCVFCATGTLGLLRNLSSGEIVAQVIWASRELRAMGAAISKR  161 (371)
T ss_pred             eEEEEEEcCCCCEEEEEEEec-CCCceEEEEccCCccCCCCcccCCCCCcccCCCHHHHHHHHHHHHHHhhhcccccccc
Confidence            999999999999999999998 5899999999999999999999999999999999999999998876653211      


Q ss_pred             -----CCeeEEEEecCCcccCCHHHHHHHHHHHHHhcCCCCCCCeEEEEcCCchHHHHHHHhcC-CeEEEEeeCCCCHHH
Q 011810          264 -----GSITNVVFMGMGEPLHNVENVIKAANIMVHEQGLHFSPRKVTVSTSGLVPQLKQFLNES-NCALAVSLNATTDEV  337 (477)
Q Consensus       264 -----~~v~nIvF~GmGEPLln~d~vi~~i~~l~~~~Gl~i~~r~ItvsTNGi~p~i~~L~~~~-d~~LaISL~a~~~e~  337 (477)
                           ..|+|||||||||||+|||+|+++++++.++.|++||.|+|||||+|++|.|++|+++. +++|||||||++++.
T Consensus       162 ~~~~~~~i~NIVfMGMGEPL~NydnV~~ai~il~d~~g~~is~R~ITVST~Givp~I~~la~~~~~v~LAiSLHA~~~e~  241 (371)
T PRK14461        162 HAGPVGRVTNLVFMGMGEPFANYDRWWQAVERLHDPQGFNLGARSMTVSTVGLVKGIRRLANERLPINLAISLHAPDDAL  241 (371)
T ss_pred             cccccCceeeEEEEccCCchhhHHHHHHHHHHhcCccccCcCCCceEEEeecchhHHHHHHhcccCceEEEEeCCCCHHH
Confidence                 45999999999999999999999999999999999999999999999999999999976 899999999999999


Q ss_pred             HhhHcCCCCCCcHHHHHHHHHHHHHhhcCCeEEEEEEEeCCCCCCHHHHHHHHHHHhcC------CCeEEEEeecCCCCC
Q 011810          338 RNWIMPINRKYKLGLLIETLREELHFKNNYKVLFEYVMLAGVNDSFDDAKRLIGLVQGI------PCKINLISFNPHCGS  411 (477)
Q Consensus       338 r~~I~pi~~~~~le~ile~l~~~l~~~~~~~V~ieyvLI~GvNDs~ed~~~La~ll~~l------~~~VnLipynp~~~~  411 (477)
                      |++|||+|++|+++++++++++| ..+++++|+|||+||+|+||+++++++|+++++++      +++||||||||+++.
T Consensus       242 R~~lmPin~~ypl~eLl~a~~~y-~~~t~rrit~EYvLi~gvNDs~e~A~~L~~llk~~~~~~~l~~~VNLIp~Np~~~~  320 (371)
T PRK14461        242 RSELMPVNRRYPIADLMAATRDY-IAKTRRRVSFEYVLLQGKNDHPEQAAALARLLRGEAPPGPLLVHVNLIPWNPVPGT  320 (371)
T ss_pred             HHHhcCcccCCCHHHHHHHHHHH-HHhhCCEEEEEEEEECCCCCCHHHHHHHHHHHcCCccccCCceEEEEecCCCCCCC
Confidence            99999999999999999999995 78999999999999999999999999999999999      789999999999999


Q ss_pred             CCCCCcHHHHHHHHHHHHhCCCeEEecCCCCCcccccccccccCC
Q 011810          412 QFTPTTDEKMIEFRNILAGAGCTVFLRLSRGDDQMAACGQLGNPG  456 (477)
Q Consensus       412 ~~~~ps~e~l~~f~~~L~~~Gi~v~vR~s~G~di~aaCGQL~~~~  456 (477)
                      .|++|+.+++++|+++|.++|+.|++|.++|+||+||||||+.++
T Consensus       321 ~~~~ps~~~i~~F~~~L~~~gi~vtiR~s~G~DI~AACGQL~~~~  365 (371)
T PRK14461        321 PLGRSERERVTTFQRILTDYGIPCTVRVERGVEIAAACGQLAGRH  365 (371)
T ss_pred             CCCCCCHHHHHHHHHHHHHCCceEEEeCCCCcChhhcCcccccCC
Confidence            999999999999999999999999999999999999999999865

>PRK14465 ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>PRK14459 ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>COG0820 Predicted Fe-S-cluster redox enzyme [General function prediction only]	Back alignment and domain information

>PRK14466 ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>PRK11194 ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>PRK14462 ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>PRK14467 ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>TIGR00048 radical SAM enzyme, Cfr family	Back alignment and domain information

>PRK14457 ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>PRK14454 ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>PRK14455 ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>PRK14460 ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>PRK14463 ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>PRK14470 ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>PRK14456 ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>PRK14464 ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>PRK14453 chloramphenicol/florfenicol resistance protein; Provisional	Back alignment and domain information

>PRK14468 ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>PRK14469 ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>PRK11145 pflA pyruvate formate lyase-activating enzyme 1; Provisional	Back alignment and domain information

>TIGR01290 nifB nitrogenase cofactor biosynthesis protein NifB	Back alignment and domain information

>COG1180 PflA Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>TIGR02493 PFLA pyruvate formate-lyase 1-activating enzyme	Back alignment and domain information

>TIGR02494 PFLE_PFLC glycyl-radical enzyme activating protein family	Back alignment and domain information

>PRK00164 moaA molybdenum cofactor biosynthesis protein A; Reviewed	Back alignment and domain information

>PRK10076 pyruvate formate lyase II activase; Provisional	Back alignment and domain information

>PRK13762 tRNA-modifying enzyme; Provisional	Back alignment and domain information

>TIGR03821 AblA_like_1 lysine-2,3-aminomutase-related protein	Back alignment and domain information

>PLN02951 Molybderin biosynthesis protein CNX2	Back alignment and domain information

>COG2896 MoaA Molybdenum cofactor biosynthesis enzyme [Coenzyme metabolism]	Back alignment and domain information

>TIGR02668 moaA_archaeal probable molybdenum cofactor biosynthesis protein A, archaeal	Back alignment and domain information

>PRK13361 molybdenum cofactor biosynthesis protein A; Provisional	Back alignment and domain information

>TIGR02666 moaA molybdenum cofactor biosynthesis protein A, bacterial	Back alignment and domain information

>TIGR02495 NrdG2 anaerobic ribonucleoside-triphosphate reductase activating protein	Back alignment and domain information

>COG0731 Fe-S oxidoreductases [Energy production and conversion]	Back alignment and domain information

>TIGR03278 methan_mark_10 putative methanogenesis marker protein 10	Back alignment and domain information

>PRK05301 pyrroloquinoline quinone biosynthesis protein PqqE; Provisional	Back alignment and domain information

>TIGR03470 HpnH hopanoid biosynthesis associated radical SAM protein HpnH	Back alignment and domain information

>TIGR02109 PQQ_syn_pqqE coenzyme PQQ biosynthesis protein E	Back alignment and domain information

>COG2100 Predicted Fe-S oxidoreductase [General function prediction only]	Back alignment and domain information

>smart00729 Elp3 Elongator protein 3, MiaB family, Radical SAM	Back alignment and domain information

>TIGR03822 AblA_like_2 lysine-2,3-aminomutase-related protein	Back alignment and domain information

>PRK13758 anaerobic sulfatase-maturase; Provisional	Back alignment and domain information

>TIGR00238 KamA family protein	Back alignment and domain information

>COG1313 PflX Uncharacterized Fe-S protein PflX, homolog of pyruvate formate lyase activating proteins [General function prediction only]	Back alignment and domain information

>TIGR03820 lys_2_3_AblA lysine-2,3-aminomutase	Back alignment and domain information

>TIGR03365 Bsubt_queE 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE	Back alignment and domain information

>PRK13745 anaerobic sulfatase-maturase; Provisional	Back alignment and domain information

>PF04055 Radical_SAM: Radical SAM superfamily; InterPro: IPR007197 Radical SAM proteins catalyze diverse reactions, including unusual methylations, isomerization, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation	Back alignment and domain information

>COG0641 AslB Arylsulfatase regulator (Fe-S oxidoreductase) [General function prediction only]	Back alignment and domain information

>cd01335 Radical_SAM Radical SAM superfamily	Back alignment and domain information

>COG1509 KamA Lysine 2,3-aminomutase [Amino acid transport and metabolism]	Back alignment and domain information

>COG0535 Predicted Fe-S oxidoreductases [General function prediction only]	Back alignment and domain information

>TIGR02491 NrdG anaerobic ribonucleoside-triphosphate reductase activating protein	Back alignment and domain information

>PRK07094 biotin synthase; Provisional	Back alignment and domain information

>COG5014 Predicted Fe-S oxidoreductase [General function prediction only]	Back alignment and domain information

>PRK09240 thiH thiamine biosynthesis protein ThiH; Reviewed	Back alignment and domain information

>TIGR00433 bioB biotin synthetase	Back alignment and domain information

>PF13353 Fer4_12: 4Fe-4S single cluster domain; PDB: 3C8F_A 3CB8_A 3T7V_A 2YX0_A 3CAN_A	Back alignment and domain information

>PRK06256 biotin synthase; Validated	Back alignment and domain information

>TIGR01125 MiaB-like tRNA modifying enzyme YliG, TIGR01125	Back alignment and domain information

>PRK08508 biotin synthase; Provisional	Back alignment and domain information

>PRK14338 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>PRK14862 rimO ribosomal protein S12 methylthiotransferase; Provisional	Back alignment and domain information

>TIGR02351 thiH thiazole biosynthesis protein ThiH	Back alignment and domain information

>PRK05481 lipoyl synthase; Provisional	Back alignment and domain information

>TIGR02826 RNR_activ_nrdG3 anaerobic ribonucleoside-triphosphate reductase activating protein	Back alignment and domain information

>PRK15108 biotin synthase; Provisional	Back alignment and domain information

>TIGR00089 RNA modification enzyme, MiaB family	Back alignment and domain information

>PRK05660 HemN family oxidoreductase; Provisional	Back alignment and domain information

>TIGR03471 HpnJ hopanoid biosynthesis associated radical SAM protein HpnJ	Back alignment and domain information

>PRK11121 nrdG anaerobic ribonucleotide reductase-activating protein; Provisional	Back alignment and domain information

>TIGR00539 hemN_rel putative oxygen-independent coproporphyrinogen III oxidase	Back alignment and domain information

>PF13394 Fer4_14: 4Fe-4S single cluster domain; PDB: 1TV8_B 1TV7_A 2FB2_A 2FB3_A	Back alignment and domain information

>PRK09249 coproporphyrinogen III oxidase; Provisional	Back alignment and domain information

>TIGR03551 F420_cofH 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofH subunit	Back alignment and domain information

>PRK14332 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>PLN02389 biotin synthase	Back alignment and domain information

>PRK08446 coproporphyrinogen III oxidase; Provisional	Back alignment and domain information

>TIGR02026 BchE magnesium-protoporphyrin IX monomethyl ester anaerobic oxidative cyclase	Back alignment and domain information

>TIGR01579 MiaB-like-C MiaB-like tRNA modifying enzyme	Back alignment and domain information

>PRK14334 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>PRK05799 coproporphyrinogen III oxidase; Provisional	Back alignment and domain information

>PRK06245 cofG FO synthase subunit 1; Reviewed	Back alignment and domain information

>PRK12928 lipoyl synthase; Provisional	Back alignment and domain information

>KOG2876 consensus Molybdenum cofactor biosynthesis pathway protein [Coenzyme transport and metabolism]	Back alignment and domain information

>PRK14326 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>PRK13347 coproporphyrinogen III oxidase; Provisional	Back alignment and domain information

>PRK14331 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>TIGR00423 radical SAM domain protein, CofH subfamily	Back alignment and domain information

>PRK08599 coproporphyrinogen III oxidase; Provisional	Back alignment and domain information

>PRK14330 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>COG0602 NrdG Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>TIGR00538 hemN oxygen-independent coproporphyrinogen III oxidase	Back alignment and domain information

>TIGR00510 lipA lipoate synthase	Back alignment and domain information

>PRK14328 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>PRK14340 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>PRK14337 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>PRK05628 coproporphyrinogen III oxidase; Validated	Back alignment and domain information

>PRK06267 hypothetical protein; Provisional	Back alignment and domain information

>TIGR03699 mena_SCO4550 menaquinone biosynthesis protein, SCO4550 family	Back alignment and domain information

>TIGR01574 miaB-methiolase tRNA-N(6)-(isopentenyl)adenosine-37 thiotransferase enzyme MiaB	Back alignment and domain information

>PRK14325 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>PRK14339 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>PRK08207 coproporphyrinogen III oxidase; Provisional	Back alignment and domain information

>TIGR01578 MiaB-like-B MiaB-like tRNA modifying enzyme, archaeal-type	Back alignment and domain information

>PRK14336 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>COG0621 MiaB 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>TIGR01212 radical SAM protein, TIGR01212 family	Back alignment and domain information

>PRK14335 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>PRK14327 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>PRK14329 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>PRK14333 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>PRK08208 coproporphyrinogen III oxidase; Validated	Back alignment and domain information

>PLN02428 lipoic acid synthase	Back alignment and domain information

>PRK07379 coproporphyrinogen III oxidase; Provisional	Back alignment and domain information

>COG2108 Uncharacterized conserved protein related to pyruvate formate-lyase activating enzyme [General function prediction only]	Back alignment and domain information

>TIGR01210 conserved hypothetical protein TIGR01210	Back alignment and domain information

>COG1964 Predicted Fe-S oxidoreductases [General function prediction only]	Back alignment and domain information

>PRK06582 coproporphyrinogen III oxidase; Provisional	Back alignment and domain information

>PRK05904 coproporphyrinogen III oxidase; Provisional	Back alignment and domain information

>PRK08898 coproporphyrinogen III oxidase; Provisional	Back alignment and domain information

>TIGR03700 mena_SCO4494 putative menaquinone biosynthesis protein, SCO4494 family	Back alignment and domain information

>COG0502 BioB Biotin synthase and related enzymes [Coenzyme metabolism]	Back alignment and domain information

>PRK09057 coproporphyrinogen III oxidase; Provisional	Back alignment and domain information

>PRK09058 coproporphyrinogen III oxidase; Provisional	Back alignment and domain information

>PRK06294 coproporphyrinogen III oxidase; Provisional	Back alignment and domain information

>PRK08445 hypothetical protein; Provisional	Back alignment and domain information

>PRK09613 thiH thiamine biosynthesis protein ThiH; Reviewed	Back alignment and domain information

>TIGR03550 F420_cofG 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofG subunit	Back alignment and domain information

>COG1625 Fe-S oxidoreductase, related to NifB/MoaA family [Energy production and conversion]	Back alignment and domain information

>PRK07360 FO synthase subunit 2; Reviewed	Back alignment and domain information

>PRK08629 coproporphyrinogen III oxidase; Provisional	Back alignment and domain information

>TIGR03279 cyano_FeS_chp putative FeS-containing Cyanobacterial-specific oxidoreductase	Back alignment and domain information

>COG1533 SplB DNA repair photolyase [DNA replication, recombination, and repair]	Back alignment and domain information

>PRK00955 hypothetical protein; Provisional	Back alignment and domain information

>COG1032 Fe-S oxidoreductase [Energy production and conversion]	Back alignment and domain information

>PRK08444 hypothetical protein; Provisional	Back alignment and domain information

>PRK01254 hypothetical protein; Provisional	Back alignment and domain information

>PRK05927 hypothetical protein; Provisional	Back alignment and domain information

>PTZ00413 lipoate synthase; Provisional	Back alignment and domain information

>PRK09234 fbiC FO synthase; Reviewed	Back alignment and domain information

>PRK05926 hypothetical protein; Provisional	Back alignment and domain information

>TIGR01211 ELP3 histone acetyltransferase, ELP3 family	Back alignment and domain information

>COG0635 HemN Coproporphyrinogen III oxidase and related Fe-S oxidoreductases [Coenzyme metabolism]	Back alignment and domain information

>COG1856 Uncharacterized homolog of biotin synthetase [Function unknown]	Back alignment and domain information

>PRK09234 fbiC FO synthase; Reviewed	Back alignment and domain information

>COG1243 ELP3 Histone acetyltransferase [Transcription / Chromatin structure and dynamics]	Back alignment and domain information

>COG1060 ThiH Thiamine biosynthesis enzyme ThiH and related uncharacterized enzymes [Coenzyme metabolism / General function prediction only]	Back alignment and domain information

>COG2516 Biotin synthase-related enzyme [General function prediction only]	Back alignment and domain information

>COG1244 Predicted Fe-S oxidoreductase [General function prediction only]	Back alignment and domain information

>COG1242 Predicted Fe-S oxidoreductase [General function prediction only]	Back alignment and domain information

>KOG1160 consensus Fe-S oxidoreductase [Energy production and conversion]	Back alignment and domain information

>COG0320 LipA Lipoate synthase [Coenzyme metabolism]	Back alignment and domain information

>COG1031 Uncharacterized Fe-S oxidoreductase [Energy production and conversion]	Back alignment and domain information

>cd03174 DRE_TIM_metallolyase DRE-TIM metallolyase superfamily	Back alignment and domain information

>KOG2672 consensus Lipoate synthase [Coenzyme transport and metabolism]	Back alignment and domain information

>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]	Back alignment and domain information

>KOG2900 consensus Biotin synthase [Coenzyme transport and metabolism]	Back alignment and domain information

>KOG4355 consensus Predicted Fe-S oxidoreductase [General function prediction only]	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		477
3rf9_A		404	X-Ray Structure Of Rlmn From Escherichia Coli Lengt		5e-61
3rfa_A		404	X-Ray Structure Of Rlmn From Escherichia Coli In Co		7e-60

>pdb|3RF9|A Chain A, X-Ray Structure Of Rlmn From Escherichia Coli Length = 404

Back alignment and structure

Iteration: 1

Score = 231 bits (590), Expect = 5e-61, Method: Compositional matrix adjust. Identities = 140/358 (39%), Positives = 209/358 (58%), Gaps = 17/358 (4%) Query: 105 NVLPKKGSRVLLKGMSFTELQQWVRSHAFRPGQALMLWKRLYGDDIWAHCTD---ELEGL 161 NV K G ++ L ++ +++++ + +P +A + K +Y +C D E+ + Sbjct: 10 NVTTKDG-KINLLDLNRQQMREFFKDLGEKPFRADQVMKWMY-----HYCCDNFDEMTDI 63 Query: 162 NKDFKKMLSEHAEFRALSLKDILTSSDGTRKILFMLDDGLVIETVVIPCNRGRTTVCVSS 221 NK + L E AE RA + + SSDGT K + D V ETV IP + R T+CVSS Sbjct: 64 NKVLRGKLKEVAEIRAPEVVEEQRSSDGTIKWAIAVGDQRV-ETVYIPED-DRATLCVSS 121 Query: 222 QVGCAMNCQFCYTGRMGLKRHLTAAEIVEQAVFARRLLSSEVGS----ITNVVFMGMGEP 277 QVGCA+ C+FC T + G R+L +EI+ Q A +++ + + ITNVV MGMGEP Sbjct: 122 QVGCALECKFCSTAQQGFNRNLRVSEIIGQVWRAAKIVGAAKVTGQRPITNVVMMGMGEP 181 Query: 278 LHNVENVIKAANIMVHEQGLHFSPRKVTVSTSGLVPQLKQFLNESNCALAVSLNATTDEV 337 L N+ NV+ A IM+ + G S R+VT+STSG+VP L + + + ALA+SL+A DE+ Sbjct: 182 LLNLNNVVPAMEIMLDDFGFGLSKRRVTLSTSGVVPALDKLGDMIDVALAISLHAPNDEI 241 Query: 338 RNWIMPINRKYKLGLLIETLREELHFK--NNYKVLFEYVMLAGVNDSFDDAKRLIGLVQG 395 R+ I+PIN+KY + + +R L N +V EYVML VND + A +L L++ Sbjct: 242 RDEIVPINKKYNIETFLAAVRRYLEKSNANQGRVTIEYVMLDHVNDGTEHAHQLAELLKD 301 Query: 396 IPCKINLISFNPHCGSQFTPTTDEKMIEFRNILAGAGCTVFLRLSRGDDQMAACGQLG 453 PCKINLI +NP G+ + +++ ++ F +L G T +R +RGDD AACGQL Sbjct: 302 TPCKINLIPWNPFPGAPYGRSSNSRIDRFSKVLMSYGFTTIVRKTRGDDIDAACGQLA 359

PyMOL of 3rf9

>pdb|3RFA|A Chain A, X-Ray Structure Of Rlmn From Escherichia Coli In Complex With S- Adenosylmethionine Length = 404

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
Query		477
3rfa_A		404	Ribosomal RNA large subunit methyltransferase N; r	1e-150
3c8f_A		245	Pyruvate formate-lyase 1-activating enzyme; adoMet	2e-11
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-10
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-06
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-05
2yx0_A		342	Radical SAM enzyme; predicted tRNA modification en	8e-04

>3rfa_A Ribosomal RNA large subunit methyltransferase N; radical SAM, S-adenosylmethionine, iron sulfur cluster, oxidoreductase; HET: SAM; 2.05A {Escherichia coli} PDB: 3rf9_A* Length = 404	Back alignment and structure

 Score =  434 bits (1118), Expect = e-150
 Identities = 137/358 (38%), Positives = 205/358 (57%), Gaps = 22/358 (6%)

Query: 107 LPKKGSRVLLKGMSFTELQQWVRSH---AFRPGQALMLWKRLYG---DDIWAHCTDELEG 160
           +  K  ++ L  ++  +++++ +      FR  Q   + K +Y    D+      DE+  
Sbjct: 11  VTTKDGKINLLDLNRQQMREFFKDLGEKPFRADQ---VMKWMYHYCCDNF-----DEMTD 62

Query: 161 LNKDFKKMLSEHAEFRALSLKDILTSSDGTRKILFMLDDGLVIETVVIPCNRGRTTVCVS 220
           +NK  +  L E AE RA  + +   SSDGT K    + D   +ETV IP    R T+CVS
Sbjct: 63  INKVLRGKLKEVAEIRAPEVVEEQRSSDGTIKWAIAVGDQR-VETVYIP-EDDRATLCVS 120

Query: 221 SQVGCAMNCQFCYTGRMGLKRHLTAAEIVEQAVFARRLLSSEVGS----ITNVVFMGMGE 276
           SQVGCA+ C+FC T + G  R+L  +EI+ Q   A +++ +   +    ITNVV MGMGE
Sbjct: 121 SQVGCALECKFCSTAQQGFNRNLRVSEIIGQVWRAAKIVGAAKVTGQRPITNVVMMGMGE 180

Query: 277 PLHNVENVIKAANIMVHEQGLHFSPRKVTVSTSGLVPQLKQFLNESNCALAVSLNATTDE 336
           PL N+ NV+ A  IM+ + G   S R+VT+STSG+VP L +  +  + ALA+SL+A  DE
Sbjct: 181 PLLNLNNVVPAMEIMLDDFGFGLSKRRVTLSTSGVVPALDKLGDMIDVALAISLHAPNDE 240

Query: 337 VRNWIMPINRKYKLGLLIETLRE--ELHFKNNYKVLFEYVMLAGVNDSFDDAKRLIGLVQ 394
           +R+ I+PIN+KY +   +  +R   E    N  +V  EYVML  VND  + A +L  L++
Sbjct: 241 IRDEIVPINKKYNIETFLAAVRRYLEKSNANQGRVTIEYVMLDHVNDGTEHAHQLAELLK 300

Query: 395 GIPCKINLISFNPHCGSQFTPTTDEKMIEFRNILAGAGCTVFLRLSRGDDQMAACGQL 452
             PCKINLI +NP  G+ +  +++ ++  F  +L   G T  +R +RGDD  AACGQL
Sbjct: 301 DTPCKINLIPWNPFPGAPYGRSSNSRIDRFSKVLMSYGFTTIVRKTRGDDIDAACGQL 358

PyMOL of 3rfa

>3c8f_A Pyruvate formate-lyase 1-activating enzyme; adoMet radical, SAM radical, activase, glycyl radical, 4Fe- 4S, carbohydrate metabolism, cytoplasm; HET: MT2 PGE; 2.25A {Escherichia coli} PDB: 3cb8_A* Length = 245	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

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

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

>2yx0_A Radical SAM enzyme; predicted tRNA modification enzyme, metal binding protein, structural genomics, NPPSFA; 2.21A {Pyrococcus horikoshii} Length = 342	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		477
3rfa_A		404	Ribosomal RNA large subunit methyltransferase N; r	100.0
2yx0_A		342	Radical SAM enzyme; predicted tRNA modification en	99.97
3c8f_A		245	Pyruvate formate-lyase 1-activating enzyme; adoMet	99.94
2z2u_A		311	UPF0026 protein MJ0257; metal binding protein; 2.4	99.94
1tv8_A		340	MOAA, molybdenum cofactor biosynthesis protein A;	99.87
3can_A		182	Pyruvate-formate lyase-activating enzyme; structur	99.84
2a5h_A		416	L-lysine 2,3-aminomutase; radical SAM, four-iron-f	99.79
3t7v_A		350	Methylornithine synthase PYLB; TIM-barrel fold, mu	99.78
3iix_A		348	Biotin synthetase, putative; adoMet radical, SAM r	99.77
1r30_A		369	Biotin synthase; SAM radical protein, TIM barrel,	99.62
2qgq_A		304	Protein TM_1862; alpha-beta protein, structural ge	99.54
1olt_A		457	Oxygen-independent coproporphyrinogen III oxidase;	99.35
4fhd_A		368	Spore photoproduct lyase; partial TIM-barrel, DNA	98.04
2l69_A		134	Rossmann 2X3 fold protein; structural genomics, no	85.32

>3rfa_A Ribosomal RNA large subunit methyltransferase N; radical SAM, S-adenosylmethionine, iron sulfur cluster, oxidoreductase; HET: SAM; 2.05A {Escherichia coli} PDB: 3rf9_A*	Back alignment and structure

Probab=100.00  E-value=4.6e-83  Score=666.37  Aligned_cols=342  Identities=39%  Similarity=0.614  Sum_probs=308.7

Q ss_pred             CccccCCCCHHHHHHHHHHCCCCcchHHHHHHHHhcCCCccCCchhhcCCCHHHHHHHHHHhccccceEeEEeecCCCce
Q 011810          112 SRVLLKGMSFTELQQWVRSHAFRPGQALMLWKRLYGDDIWAHCTDELEGLNKDFKKMLSEHAEFRALSLKDILTSSDGTR  191 (477)
Q Consensus       112 ~~~~~~~l~~~el~~~~~~~g~~~~ra~qi~~~l~~~~~~~~~~~~~~~l~~~~r~~L~~~~~~~~~~~~~~~~s~Dgt~  191 (477)
                      ++++|++|+++||++|+.++|+|+|||+|||+|+|+++  +.+|++||||||++|++|++.|.+..++++..+.|.|||+
T Consensus        16 ~~~~l~~~~~~~l~~~~~~~g~~~fra~qi~~w~~~~~--~~~~~~mt~l~k~~r~~l~~~~~~~~~~~~~~~~s~dgt~   93 (404)
T 3rfa_A           16 GKINLLDLNRQQMREFFKDLGEKPFRADQVMKWMYHYC--CDNFDEMTDINKVLRGKLKEVAEIRAPEVVEEQRSSDGTI   93 (404)
T ss_dssp             -CEEGGGCCHHHHHHHHHHTTCCHHHHHHHHHHHHHSC--CCCGGGCTTSCHHHHHHHHHHEECCCCEEEEEEECTTSCE
T ss_pred             CCCCcccCCHHHHHHHHHHcCCcchHHHHHHHHHHhcC--CCChHHhcccCHHHHHHHHhcCCCCCCceEEEEECCCCCE
Confidence            46899999999999999999999999999999999999  6799999999999999999999999999999999999999


Q ss_pred             EEEEEecCCCeeEEEEeccCCCceeEEEEecCccCCCCCCCCCCCCCCCcCCCHHHHHHHHHHHHHHhccc----CCCee
Q 011810          192 KILFMLDDGLVIETVVIPCNRGRTTVCVSSQVGCAMNCQFCYTGRMGLKRHLTAAEIVEQAVFARRLLSSE----VGSIT  267 (477)
Q Consensus       192 K~l~~l~DG~~IEtVlip~~~~r~tlCVSsq~GCnl~C~FC~tg~~g~~r~Lt~eEIv~qv~~~~~~~~~~----~~~v~  267 (477)
                      ||||++ ||..||||+||+ ++|.|+|||+|+|||++|.||+++..++.++++++||++|+..+..++...    +.+++
T Consensus        94 K~l~~l-dg~~iEtV~i~~-~~r~tlcVSsq~GCnl~C~fC~tg~~g~~r~Lt~eEIv~qv~~~~~~~~~~g~~gg~~i~  171 (404)
T 3rfa_A           94 KWAIAV-GDQRVETVYIPE-DDRATLCVSSQVGCALECKFCSTAQQGFNRNLRVSEIIGQVWRAAKIVGAAKVTGQRPIT  171 (404)
T ss_dssp             EEEEEE-TTEEEEEEEEEC-SSCEEEECCCEEECSSCCTTCGGGTTCEEEECCHHHHHHHHHHHHHHHCCHHHHSSCSCS
T ss_pred             EEEEEc-CCceEEEEEEec-CCCceEEEEeCCCCCCcCCCCCCCCCCCCCcCCHHHHHHHHHHHHHHhhhcccccCCCcc
Confidence            999999 999999999998 589999999999999999999999998999999999999999887766421    24699


Q ss_pred             EEEEecCCcccCCHHHHHHHHHHHHHhcCCCCCCCeEEEEcCCchHHHHHHHhcCCeEEEEeeCCCCHHHHhhHcCCCCC
Q 011810          268 NVVFMGMGEPLHNVENVIKAANIMVHEQGLHFSPRKVTVSTSGLVPQLKQFLNESNCALAVSLNATTDEVRNWIMPINRK  347 (477)
Q Consensus       268 nIvF~GmGEPLln~d~vi~~i~~l~~~~Gl~i~~r~ItvsTNGi~p~i~~L~~~~d~~LaISL~a~~~e~r~~I~pi~~~  347 (477)
                      +|+||||||||+|++++.++++.+.+..|++++.++++|+|||+.|.+++|++..++.|+||||+++++.|++|+|++++
T Consensus       172 ~Ivf~GgGEPLln~d~v~~~i~~lk~~~Gl~~s~r~itlsTnG~~p~i~~L~~~~d~~LaiSLka~d~e~~~~i~pv~~~  251 (404)
T 3rfa_A          172 NVVMMGMGEPLLNLNNVVPAMEIMLDDFGFGLSKRRVTLSTSGVVPALDKLGDMIDVALAISLHAPNDEIRDEIVPINKK  251 (404)
T ss_dssp             EEEECSSSCGGGCHHHHHHHHHHHHSTTTTCCCGGGEEEEESCCHHHHHHHHHHCCCEEEEECCCSSHHHHHHHSGGGGT
T ss_pred             EEEEeCCCCcccCHHHHHHHHHHHHhhcCcCcCCCceEEECCCcHHHHHHHHHhhcceEEecccCCCHHHHHHhcCCccC
Confidence            99999999999999999999997766579999999999999999999999999888899999999999999999999999


Q ss_pred             CcHHHHHHHHHHHHHhhcCC---eEEEEEEEeCCCCCCHHHHHHHHHHHhcCCCeEEEEeecCCCCCCCCCCcHHHHHHH
Q 011810          348 YKLGLLIETLREELHFKNNY---KVLFEYVMLAGVNDSFDDAKRLIGLVQGIPCKINLISFNPHCGSQFTPTTDEKMIEF  424 (477)
Q Consensus       348 ~~le~ile~l~~~l~~~~~~---~V~ieyvLI~GvNDs~ed~~~La~ll~~l~~~VnLipynp~~~~~~~~ps~e~l~~f  424 (477)
                      ++++++++++++| ..+.+.   +|+++|+||+|+||+++++++|++|+++++++||||||||.++.++++|+.+++++|
T Consensus       252 ~~le~vl~ai~~~-~~~~g~~~~~V~ie~vLI~GvNDs~e~~~~La~ll~~l~~~VnLIpynP~~~~~~~~ps~e~i~~f  330 (404)
T 3rfa_A          252 YNIETFLAAVRRY-LEKSNANQGRVTIEYVMLDHVNDGTEHAHQLAELLKDTPCKINLIPWNPFPGAPYGRSSNSRIDRF  330 (404)
T ss_dssp             SCHHHHHHHHHHH-HHHCTTTTTCEEEEEEEBTTTTCSHHHHHHHHHHTTTSCEEEEEEECCCCTTCCCCBCCHHHHHHH
T ss_pred             CCHHHHHHHHHHH-HHHhCCCcccEEEEEEEecCCCCCHHHHHHHHHHHHcCCCcEEEEeccCCCCCCCCCCCHHHHHHH
Confidence            9999999999874 667777   999999999999999999999999999999999999999999889999999999999


Q ss_pred             HHHHHhCCCeEEecCCCCCcccccccccccCCCC
Q 011810          425 RNILAGAGCTVFLRLSRGDDQMAACGQLGNPGAI  458 (477)
Q Consensus       425 ~~~L~~~Gi~v~vR~s~G~di~aaCGQL~~~~~~  458 (477)
                      +++|+++|+.+++|.++|+||+||||||+.+...
T Consensus       331 ~~iL~~~Gi~vtiR~~~G~di~aaCGQL~~~~~~  364 (404)
T 3rfa_A          331 SKVLMSYGFTTIVRKTRGDDIDAACGQLAGDVID  364 (404)
T ss_dssp             HHHHHHTTCEEEECCCCCC---------------
T ss_pred             HHHHHHcCCcEEEcCCCCcccccccccchhhhhh
Confidence            9999999999999999999999999999877543

PyMOL of 3rfa

>2yx0_A Radical SAM enzyme; predicted tRNA modification enzyme, metal binding protein, structural genomics, NPPSFA; 2.21A {Pyrococcus horikoshii}	Back alignment and structure

>3c8f_A Pyruvate formate-lyase 1-activating enzyme; adoMet radical, SAM radical, activase, glycyl radical, 4Fe- 4S, carbohydrate metabolism, cytoplasm; HET: MT2 PGE; 2.25A {Escherichia coli} PDB: 3cb8_A*	Back alignment and structure

>2z2u_A UPF0026 protein MJ0257; metal binding protein; 2.40A {Methanocaldococcus jannaschii}	Back alignment and structure

>1tv8_A MOAA, molybdenum cofactor biosynthesis protein A; TIM barrel, ligand binding protein; HET: SAM; 2.20A {Staphylococcus aureus} SCOP: c.1.28.3 PDB: 1tv7_A* 2fb3_A* 2fb2_A*	Back alignment and structure

>3can_A Pyruvate-formate lyase-activating enzyme; structural genomics, pyruvate-formate lyase-activating enzym MCSG, APC20359.1; 1.80A {Bacteroides vulgatus atcc 8482}	Back alignment and structure

>2a5h_A L-lysine 2,3-aminomutase; radical SAM, four-iron-four-sulfur cluster, 4Fe4S, FS4, SAM, adenosylmethionine, alpha-beta channel; HET: SAM LYS PLP; 2.10A {Clostridium subterminale}	Back alignment and structure

>3t7v_A Methylornithine synthase PYLB; TIM-barrel fold, mutase, [4Fe-4S]-cluster, SAM, lysine, transferase; HET: SAM MD0; 1.50A {Methanosarcina barkeri}	Back alignment and structure

>3iix_A Biotin synthetase, putative; adoMet radical, SAM radical, adoMet cleavage, Fe4S4 cluster, HYDE, hydrogenase, maturation, beta barrel; HET: OTY CSO 5AD CPS; 1.25A {Thermotoga maritima} PDB: 3ciw_A* 3iiz_A* 3cix_A*	Back alignment and structure

>1r30_A Biotin synthase; SAM radical protein, TIM barrel, FES cluster, transferase; HET: SAM DTB; 3.40A {Escherichia coli} SCOP: c.1.28.1	Back alignment and structure

>2qgq_A Protein TM_1862; alpha-beta protein, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium; HET: CXS; 2.00A {Thermotoga maritima MSB8}	Back alignment and structure

>1olt_A Oxygen-independent coproporphyrinogen III oxidase; heme biosynthesis, decarboxylase, radical SAM enzyme, 4Fe- 4 cluster; HET: SAM; 2.07A {Escherichia coli} SCOP: c.1.28.2	Back alignment and structure

>4fhd_A Spore photoproduct lyase; partial TIM-barrel, DNA repair, damaged DNA; HET: EEM 0TT; 2.00A {Geobacillus thermodenitrificans} PDB: 4fhc_A* 4fhg_A* 4fhe_A* 4fhf_A*	Back alignment and structure

>2l69_A Rossmann 2X3 fold protein; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Artificial gene}	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	Probability
Query		477
d1tv8a_		327	Molybdenum cofactor biosynthesis protein A MoaA {S	99.72
d1r30a_		312	Biotin synthase {Escherichia coli [TaxId: 562]}	98.88
d1olta_		441	Oxygen-independent coproporphyrinogen III oxidase	98.49

>d1tv8a_ c.1.28.3 (A:) Molybdenum cofactor biosynthesis protein A MoaA {Staphylococcus aureus [TaxId: 1280]}	Back information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Radical SAM enzymes
family: MoCo biosynthesis proteins
domain: Molybdenum cofactor biosynthesis protein A MoaA
species: Staphylococcus aureus [TaxId: 1280]

Probab=99.72  E-value=4e-16  Score=152.70  Aligned_cols=174  Identities=18%  Similarity=0.234  Sum_probs=128.0

Q ss_pred             eeEEEEecCccCCCCCCCCCCCC-----C---CCcCCCHHHHHHHHHHHHHHhcccCCCeeEEEEecCCcccCCHHHHHH
Q 011810          215 TTVCVSSQVGCAMNCQFCYTGRM-----G---LKRHLTAAEIVEQAVFARRLLSSEVGSITNVVFMGMGEPLHNVENVIK  286 (477)
Q Consensus       215 ~tlCVSsq~GCnl~C~FC~tg~~-----g---~~r~Lt~eEIv~qv~~~~~~~~~~~~~v~nIvF~GmGEPLln~d~vi~  286 (477)
                      .++.|+.+..||++|.||+....     .   ....|+.+++...+..+.+      .++..|.|+| |||+++.+. .+
T Consensus        12 ~~l~ieiT~~CNlrC~~C~~~~~~~~~~~~~~~~~~ls~e~~~~li~~~~~------~g~~~v~~~G-GEp~l~~~~-~e   83 (327)
T d1tv8a_          12 RDLRLSVTDRCNFRCDYCMPKEVFGDDFVFLPKNELLTFDEMARIAKVYAE------LGVKKIRITG-GEPLMRRDL-DV   83 (327)
T ss_dssp             CEEEEECCSCCSCCCTTTSCTTTSSTTCCCCCGGGSCCHHHHHHHHHHHHH------TTCCEEEEES-SCGGGSTTH-HH
T ss_pred             CcEEEEeccccCCcCcCCCCccccCCCCccCCccccCCHHHHHHHHHHHHH------cCCeEEEeCC-CcccccccH-HH
Confidence            45888999999999999985421     1   1345888888776655443      3678899999 999999764 45


Q ss_pred             HHHHHHHhcCCCCCCCeEEEEcCCc-h--HHHHHHHhcCCeEEEEeeCCCCHHHHhhHcCCCCCCcHHHHHHHHHHHHHh
Q 011810          287 AANIMVHEQGLHFSPRKVTVSTSGL-V--PQLKQFLNESNCALAVSLNATTDEVRNWIMPINRKYKLGLLIETLREELHF  363 (477)
Q Consensus       287 ~i~~l~~~~Gl~i~~r~ItvsTNGi-~--p~i~~L~~~~d~~LaISL~a~~~e~r~~I~pi~~~~~le~ile~l~~~l~~  363 (477)
                      .+....+..+..     ..+.|||. +  +.+.+|.+.+...+.|||++.+++.++++++.+  ..++.++++++.  ..
T Consensus        84 ~i~~~~~~~~~~-----~~~~Tng~ll~~~~~~~l~~~g~~~i~iSldg~~~e~~~~~rg~~--g~~~~~~~~~~~--~~  154 (327)
T d1tv8a_          84 LIAKLNQIDGIE-----DIGLTTNGLLLKKHGQKLYDAGLRRINVSLDAIDDTLFQSINNRN--IKATTILEQIDY--AT  154 (327)
T ss_dssp             HHHHHTTCTTCC-----EEEEEECSTTHHHHHHHHHHHTCCEEEEECCCSSHHHHHHHHSSC--CCHHHHHHHHHH--HH
T ss_pred             HHHHHhhhcccc-----ccccccccccchhHHHHHHHcCCCEEeeecccCCHHHhhhheeec--cccchhhhHHHH--HH
Confidence            554343333332     44556554 3  467888888766678999999999999999864  457899999996  57


Q ss_pred             hcCCeEEEEEEEeCCCCCCHHHHHHHHHHHhcCCCeEEEEeecC
Q 011810          364 KNNYKVLFEYVMLAGVNDSFDDAKRLIGLVQGIPCKINLISFNP  407 (477)
Q Consensus       364 ~~~~~V~ieyvLI~GvNDs~ed~~~La~ll~~l~~~VnLipynp  407 (477)
                      +.+.++.+.++++++.|..  ++.++.++++..+..+.+.++.+
T Consensus       155 ~~g~~~~~~~~v~~~~n~~--~~~~~~~~~~~~~~~~~~~~~~~  196 (327)
T d1tv8a_         155 SIGLNVKVNVVIQKGINDD--QIIPMLEYFKDKHIEIRFIEFMD  196 (327)
T ss_dssp             HTTCEEEEEEEECTTTTGG--GHHHHHHHHHHTTCCEEEEECCC
T ss_pred             HcCCCcceeEEEecCcccc--ccHHHHHHHHhhccccceeeeec
Confidence            7899999999999987754  67788888887777666655543

PyMOL of d1tv8a_

>d1r30a_ c.1.28.1 (A:) Biotin synthase {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1olta_ c.1.28.2 (A:) Oxygen-independent coproporphyrinogen III oxidase HemN {Escherichia coli [TaxId: 562]}	Back information, alignment and structure