Citrus Sinensis ID: 028700

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-----

MGEPLNNYAALVEAVRIMTGLPFQVSPKRITVSTVGIVHAINKFHSDLPGLNLAVSLHAPVQDVRCQIMPAARAFPLEKLMNALKEYQKNSQQKIFIEYIMLDGVNDEEQHAHQLGKLLETFQVVVNLIPFNPIGSVSQFRTSSDDKVSSFQKILRGSYNIRTTVRKQMGQDISGACGQLVVNLPDKISAKSTPPVTDIEDLCIR

cccccccHHHHHHHHHHccccccccccccEEEEccccHHHHHHHHHcccccEEEEEcccccHHHHHHcccccccccHHHHHHHHHHHHHHcccEEEEEEEEEccccccHHHHHHHHHHHcccccEEEEEcccccccccccccccHHHHHHHHHHHHHccccEEEEcccccccHHHHHHHccccccccccccccccccccccHHcc

cccccccHHHHHHHHHHHcccccccccEEEEEEcccHHHHHHHHHHccccEEEEEEEccccHHHHHHccHHHccccHHHHHHHHHHHHHHcccEEEEEEEEEccccccHHHHHHHHHHHcccccEEEEEEccccccccccccccHHHHHHHHHHHHHHcccEEEEEEcccccHHHHHHHHHHHHHcHHHHHHHHHHHcccccEcc

MGEPLNNYAALVEAVRImtglpfqvspkritvSTVGIVHAINKFhsdlpglnlavslhapvqdvrcqimpaaraFPLEKLMNALKEYQKNSQQKIFIEYIMldgvndeeQHAHQLGKLLETFQVVVNLipfnpigsvsqfrtssddkvsSFQKILRGSYNIRTTVRKQMgqdisgacgqlvvnlpdkisakstppvtdiedlcir

******NYAALVEAVRIMTGLPFQVSPKRITVSTVGIVHAINKFHSDLPGLNLAVSLHAPVQDVRCQIMPAARAFPLEKLMNALKEYQKNSQQKIFIEYIMLDGVNDEEQHAHQLGKLLETFQVVVNLIPFNPIGSVSQF*********SFQKILRGSYNIRTTVRKQMGQDISGACGQLVVNLP********************

MGEPLNNYAALVEAVRIMTGLPFQVSPKRITVSTVGIVHAINKFHSDLPGLNLAVSLHAPVQDVRCQIMPAARAFPLEKLMNALKEYQKNSQQKIFIEYIMLDGVNDEEQHAHQLGKLLETFQVVVNLIPFNPIGSVSQ***********FQKILRGSYNIRTTVRKQMGQDISGACGQLVVNLPDKISAKSTPPVTDIEDLCIR

**EPLNNYAALVEAVRIMTGLPFQVSPKRITVSTVGIVHAINKFHSDLPGLNLAVSLHAPVQDVRCQIMPAARAFPLEKLMNALKEYQKNSQQKIFIEYIMLDGVNDEEQHAHQLGKLLETFQVVVNLIPFNPIGSVSQFRTSSDDKVSSFQKILRGSYNIRTTVRKQMGQDISGACGQLVVNLPDKI*****************

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		205	2.2.26 [Sep-21-2011]
Q6MDD0		358	Probable dual-specificity	yes	no	0.878	0.502	0.415	7e-37
Q8R9T4		342	Probable dual-specificity	yes	no	0.863	0.517	0.416	3e-36
Q0VND7		381	Dual-specificity RNA meth	yes	no	0.897	0.482	0.455	3e-35
Q67PQ7		371	Probable dual-specificity	yes	no	0.858	0.474	0.412	1e-34
A0LQM1		342	Dual-specificity RNA meth	yes	no	0.863	0.517	0.443	3e-34
A8AD69		388	Dual-specificity RNA meth	yes	no	0.897	0.474	0.413	9e-34
B0K1Y9		342	Probable dual-specificity	yes	no	0.853	0.511	0.395	1e-33
B0KA06		342	Probable dual-specificity	yes	no	0.853	0.511	0.395	1e-33
A1WE19		391	Dual-specificity RNA meth	yes	no	0.897	0.470	0.434	2e-33
Q6D273		398	Dual-specificity RNA meth	yes	no	0.897	0.462	0.408	2e-33

>sp\|Q6MDD0\|RLMN2_PARUW Probable dual-specificity RNA methyltransferase RlmN 2 OS=Protochlamydia amoebophila (strain UWE25) GN=rlmN2 PE=3 SV=2	Back alignment and function desciption

 Score =  153 bits (387), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 76/183 (41%), Positives = 116/183 (63%), Gaps = 3/183 (1%)

Query: 1   MGEPLNNYAALVEAVRIMTGLPF-QVSPKRITVSTVGIVHAINKFHSDLPGLNLAVSLHA 59
           MGEPL NY ++V ++R+++   F  +S +RITVSTVG+V  I +   +   +NL +SLHA
Sbjct: 159 MGEPLKNYESVVASIRVLSHPDFCNISQRRITVSTVGVVEGIKRLSKEGLKVNLVLSLHA 218

Query: 60  PVQDVRCQIMPAARAFPLEKLMNALKEYQKNSQQKIFIEYIMLDGVNDEEQHAHQLGKLL 119
           P Q +R +I+P AR +PLE+++ ++ EY + +++ I  EY +L G+ND   HAH+L  LL
Sbjct: 219 PNQHIRKKIIPYARKYPLEEILESMDEYAQKTKRDITFEYTLLAGINDHPDHAHELAHLL 278

Query: 120 ETFQVVVNLIPFNPIGSVSQFRTSSDDKVSSFQKILRGSYNIRTTVRKQMGQDISGACGQ 179
           +  Q  VNLIP+NPI  + + +      +  F+ +L GS+ I  T R   G DI  ACGQ
Sbjct: 279 KGKQCTVNLIPYNPIPGL-RLKRPEKKAIKQFRSVLYGSH-IVNTCRYTKGDDIGAACGQ 336

Query: 180 LVV 182
           L +
Sbjct: 337 LAL 339

Specifically methylates position 2 of adenine 2503 in 23S rRNA.
Protochlamydia amoebophila (strain UWE25) (taxid: 264201)
EC: 2EC: .EC: 1EC: .EC: 1EC: .EC: 1EC: 9EC: 2

>sp\|Q8R9T4\|RLMN_THETN Probable dual-specificity RNA methyltransferase RlmN OS=Thermoanaerobacter tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4) GN=rlmN PE=3 SV=1	Back alignment and function description

>sp\|Q0VND7\|RLMN_ALCBS Dual-specificity RNA methyltransferase RlmN OS=Alcanivorax borkumensis (strain SK2 / ATCC 700651 / DSM 11573) GN=rlmN PE=3 SV=1	Back alignment and function description

>sp\|Q67PQ7\|RLMN_SYMTH Probable dual-specificity RNA methyltransferase RlmN OS=Symbiobacterium thermophilum (strain T / IAM 14863) 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\|A8AD69\|RLMN_CITK8 Dual-specificity RNA methyltransferase RlmN OS=Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696) GN=rlmN PE=3 SV=1	Back alignment and function description

>sp\|B0K1Y9\|RLMN_THEPX Probable dual-specificity RNA methyltransferase RlmN OS=Thermoanaerobacter sp. (strain X514) GN=rlmN PE=3 SV=1	Back alignment and function description

>sp\|B0KA06\|RLMN_THEP3 Probable dual-specificity RNA methyltransferase RlmN OS=Thermoanaerobacter pseudethanolicus (strain ATCC 33223 / 39E) GN=rlmN PE=3 SV=1	Back alignment and function description

>sp\|A1WE19\|RLMN_VEREI Dual-specificity RNA methyltransferase RlmN OS=Verminephrobacter eiseniae (strain EF01-2) GN=rlmN PE=3 SV=1	Back alignment and function description

>sp\|Q6D273\|RLMN_ERWCT Dual-specificity RNA methyltransferase RlmN OS=Erwinia carotovora subsp. atroseptica (strain SCRI 1043 / ATCC BAA-672) 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		205
224060769		373	predicted protein [Populus trichocarpa]	0.980	0.538	0.846	8e-96
449438321		384	PREDICTED: dual-specificity RNA methyltr	0.985	0.526	0.821	1e-95
225428987		372	PREDICTED: ribosomal RNA large subunit m	0.985	0.543	0.821	8e-93
357480659		380	Ribosomal RNA large subunit methyltransf	0.990	0.534	0.794	7e-92
356539162		378	PREDICTED: ribosomal RNA large subunit m	0.990	0.537	0.794	2e-91
255632735		245	unknown [Glycine max]	0.990	0.828	0.784	1e-90
388521505		385	unknown [Lotus japonicus]	0.990	0.527	0.779	2e-88
357113533		382	PREDICTED: ribosomal RNA large subunit m	0.995	0.534	0.754	7e-88
15230899		372	radical SAM domain-containing protein [A	0.995	0.548	0.764	9e-88
9294428		382	unnamed protein product [Arabidopsis tha	0.995	0.534	0.764	1e-87

>gi\|224060769\|ref\|XP_002300266.1\| predicted protein [Populus trichocarpa] gi\|222847524\|gb\|EEE85071.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

 Score =  355 bits (910), Expect = 8e-96,   Method: Compositional matrix adjust.
 Identities = 176/208 (84%), Positives = 187/208 (89%), Gaps = 7/208 (3%)

Query: 1   MGEPLNNYAALVEAVRIMTGLPFQVSPKRITVSTVGIVHAINKFHSDLPGLNLAVSLHAP 60
           MGEPLNNY+ALVEAVR M+G+PFQ+SPKRITVSTVGI+HAINK H DLPGLNLAVSLHAP
Sbjct: 169 MGEPLNNYSALVEAVRAMSGVPFQLSPKRITVSTVGIIHAINKLHKDLPGLNLAVSLHAP 228

Query: 61  VQDVRCQIMPAARAFPLEKLMNALKEYQKNSQQKIFIEYIMLDGVNDEEQHAHQLGKLLE 120
           VQDVRCQIMPAARAFPLEKLM+AL+ YQKNS QKIFIEYIMLDGVNDEEQHAHQLGKLLE
Sbjct: 229 VQDVRCQIMPAARAFPLEKLMDALQVYQKNSMQKIFIEYIMLDGVNDEEQHAHQLGKLLE 288

Query: 121 TFQVVVNLIPFNPIGSVSQFRTSSDDKVSSFQKILRGSYNIRTTVRKQMGQDISGACGQL 180
           TF VVVNLIPFNPIGS+SQFRTSS++KV  FQKILRG  NIRTTVRKQMGQDISGACGQL
Sbjct: 289 TFDVVVNLIPFNPIGSLSQFRTSSEEKVLRFQKILRGVNNIRTTVRKQMGQDISGACGQL 348

Query: 181 VVNLPDKISAKSTPP---VTDIEDLCIR 205
           VVNLPD    +  PP   VTDIEDL  R
Sbjct: 349 VVNLPD----EKKPPNLGVTDIEDLVSR 372

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|449438321\|ref\|XP_004136937.1\| PREDICTED: dual-specificity RNA methyltransferase RlmN 1-like [Cucumis sativus] gi\|449495695\|ref\|XP_004159917.1\| PREDICTED: dual-specificity RNA methyltransferase RlmN 1-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|225428987\|ref\|XP_002265287.1\| PREDICTED: ribosomal RNA large subunit methyltransferase N [Vitis vinifera] gi\|147817733\|emb\|CAN60150.1\| hypothetical protein VITISV_044331 [Vitis vinifera] gi\|296083052\|emb\|CBI22456.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|357480659\|ref\|XP_003610615.1\| Ribosomal RNA large subunit methyltransferase N [Medicago truncatula] gi\|355511950\|gb\|AES93573.1\| Ribosomal RNA large subunit methyltransferase N [Medicago truncatula]	Back alignment and taxonomy information

>gi\|356539162\|ref\|XP_003538069.1\| PREDICTED: ribosomal RNA large subunit methyltransferase N 1-like [Glycine max]	Back alignment and taxonomy information

>gi\|255632735\|gb\|ACU16719.1\| unknown [Glycine max]	Back alignment and taxonomy information

>gi\|388521505\|gb\|AFK48814.1\| unknown [Lotus japonicus]	Back alignment and taxonomy information

>gi\|357113533\|ref\|XP_003558557.1\| PREDICTED: ribosomal RNA large subunit methyltransferase N 2-like [Brachypodium distachyon]	Back alignment and taxonomy information

>gi\|15230899\|ref\|NP_188597.1\| radical SAM domain-containing protein [Arabidopsis thaliana] gi\|28393068\|gb\|AAO41968.1\| unknown protein [Arabidopsis thaliana] gi\|28827394\|gb\|AAO50541.1\| unknown protein [Arabidopsis thaliana] gi\|332642748\|gb\|AEE76269.1\| radical SAM domain-containing protein [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|9294428\|dbj\|BAB02548.1\| 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
Query		205
TAIR\|locus:2091161		372	AT3G19630 [Arabidopsis thalian	0.995	0.548	0.764	1.8e-80
DICTYBASE\|DDB_G0288255		407	DDB_G0288255 "putative ribosom	0.951	0.479	0.417	1.5e-35
UNIPROTKB\|Q603C0		366	rlmN "Dual-specificity RNA met	0.897	0.502	0.407	3.7e-32
UNIPROTKB\|P36979		384	rlmN "23S rRNA m2A2503 methylt	0.897	0.479	0.413	6e-32
UNIPROTKB\|Q8EC29		373	rlmN "Dual-specificity RNA met	0.897	0.493	0.376	1.8e-30
TIGR_CMR\|SO_3315		373	SO_3315 "conserved hypothetica	0.897	0.493	0.376	1.8e-30
UNIPROTKB\|Q9KTX3		373	rlmN "Dual-specificity RNA met	0.897	0.493	0.392	3.8e-30
TIGR_CMR\|VC_0757		373	VC_0757 "conserved hypothetica	0.897	0.493	0.392	3.8e-30
UNIPROTKB\|Q47WB7		386	rlmN "Dual-specificity RNA met	0.897	0.476	0.373	6.4e-28
TIGR_CMR\|CPS_4255		386	CPS_4255 "radical SAM enzyme,	0.897	0.476	0.373	6.4e-28

TAIR\|locus:2091161 AT3G19630 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 808 (289.5 bits), Expect = 1.8e-80, P = 1.8e-80
 Identities = 156/204 (76%), Positives = 178/204 (87%)

Query:     1 MGEPLNNYAALVEAVRIMTGLPFQVSPKRITVSTVGIVHAINKFHSDLPGLNLAVSLHAP 60
             MGEPLNNY A+VEAVR+M   PFQ+SPKRIT+STVGIVHAINK H+DLPG++LAVSLHAP
Sbjct:   169 MGEPLNNYNAVVEAVRVMLNQPFQLSPKRITISTVGIVHAINKLHNDLPGVSLAVSLHAP 228

Query:    61 VQDVRCQIMPAARAFPLEKLMNALKEYQKNSQQKIFIEYIMLDGVNDEEQHAHQLGKLLE 120
             VQ++RCQIMPAARAFPL+KLM+AL+ +QKNSQQKIFIEYIMLDGVND+EQHAH LG+LL+
Sbjct:   229 VQEIRCQIMPAARAFPLQKLMDALQTFQKNSQQKIFIEYIMLDGVNDQEQHAHLLGELLK 288

Query:   121 TFQVVVNLIPFNPIGSVSQFRTSSDDKVSSFQKILRGSYNIRTTVRKQMGQDISGACGQL 180
             TFQVV+NLIPFNPIGS SQF TSS   VS FQKILR +Y IRTT+RK+MGQDISGACGQL
Sbjct:   289 TFQVVINLIPFNPIGSTSQFETSSIQGVSRFQKILRETYKIRTTIRKEMGQDISGACGQL 348

Query:   181 VVNLPDKISAKSTPPVTDIEDLCI 204
             VVN PD      T  + DIEDL +
Sbjct:   349 VVNQPDIKKTPGTVELRDIEDLLL 372

GO:0003824 "catalytic activity" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM;IEA

GO:0008173 "RNA methyltransferase activity" evidence=IEA

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

GO:0000278 "mitotic cell cycle" evidence=RCA

GO:0006396 "RNA processing" evidence=RCA

DICTYBASE\|DDB_G0288255 DDB_G0288255 "putative ribosomal RNA large subunit methyltransferase N" [Dictyostelium discoideum (taxid:44689)]	Back alignment and assigned GO terms

UNIPROTKB\|Q603C0 rlmN "Dual-specificity RNA methyltransferase RlmN" [Methylococcus capsulatus str. Bath (taxid:243233)]	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

TIGR_CMR\|VC_0757 VC_0757 "conserved hypothetical protein" [Vibrio cholerae O1 biovar El Tor (taxid:686)]	Back alignment and assigned GO terms

UNIPROTKB\|Q47WB7 rlmN "Dual-specificity RNA methyltransferase RlmN" [Colwellia psychrerythraea 34H (taxid:167879)]	Back alignment and assigned GO terms

TIGR_CMR\|CPS_4255 CPS_4255 "radical SAM enzyme, Cfr family" [Colwellia psychrerythraea 34H (taxid:167879)]	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	LOW CONFIDENCE prediction!

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		205
COG0820		349	COG0820, COG0820, Predicted Fe-S-cluster redox enz	4e-65
TIGR00048		355	TIGR00048, TIGR00048, 23S rRNA m2A2503 methyltrans	1e-56
PRK14455		356	PRK14455, PRK14455, ribosomal RNA large subunit me	6e-52
PRK14460		354	PRK14460, PRK14460, ribosomal RNA large subunit me	7e-52
PRK14454		342	PRK14454, PRK14454, ribosomal RNA large subunit me	1e-50
PRK14453		347	PRK14453, PRK14453, chloramphenicol/florfenicol re	6e-48
PRK14468		343	PRK14468, PRK14468, ribosomal RNA large subunit me	7e-48
PRK14457		345	PRK14457, PRK14457, ribosomal RNA large subunit me	2e-47
PRK11194		372	PRK11194, PRK11194, ribosomal RNA large subunit me	2e-47
PRK14467		348	PRK14467, PRK14467, ribosomal RNA large subunit me	4e-47
PRK14469		343	PRK14469, PRK14469, ribosomal RNA large subunit me	1e-45
PRK14463		349	PRK14463, PRK14463, ribosomal RNA large subunit me	3e-44
PRK14462		356	PRK14462, PRK14462, ribosomal RNA large subunit me	4e-43
PRK14459		373	PRK14459, PRK14459, ribosomal RNA large subunit me	6e-42
PRK14466		345	PRK14466, PRK14466, ribosomal RNA large subunit me	3e-41
PRK14461		371	PRK14461, PRK14461, ribosomal RNA large subunit me	6e-40
PRK14456		368	PRK14456, PRK14456, ribosomal RNA large subunit me	3e-34
PRK14465		342	PRK14465, PRK14465, ribosomal RNA large subunit me	2e-30
PRK14470		336	PRK14470, PRK14470, ribosomal RNA large subunit me	3e-25
PRK14464		344	PRK14464, PRK14464, ribosomal RNA large subunit me	2e-18
pfam04055		165	pfam04055, Radical_SAM, Radical SAM superfamily	0.001

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

 Score =  204 bits (520), Expect = 4e-65
 Identities = 79/184 (42%), Positives = 114/184 (61%), Gaps = 3/184 (1%)

Query: 1   MGEPLNNYAALVEAVRIMTG-LPFQVSPKRITVSTVGIVHAINKFHSDLPGLNLAVSLHA 59
           MGEPL N   +V+A+ I+       +S +RITVST GIV  I K   +  G+ LA+SLHA
Sbjct: 161 MGEPLLNLDNVVKALEIINDDEGLGLSKRRITVSTSGIVPRIRKLADEQLGVALAISLHA 220

Query: 60  PVQDVRCQIMPAARAFPLEKLMNALKEYQKNSQQKIFIEYIMLDGVNDEEQHAHQLGKLL 119
           P  ++R Q+MP  + +P+E+L+ A++ Y + S +++  EY++LDGVND  +HA +L KLL
Sbjct: 221 PNDELRDQLMPINKKYPIEELLEAIRYYPEKSGRRVTFEYVLLDGVNDSLEHAKELAKLL 280

Query: 120 ETFQVVVNLIPFNPIGSVSQFRTSSDDKVSSFQKILRGSYNIRTTVRKQMGQDISGACGQ 179
           +     VNLIP+NP+   S +  SS +++  F KIL     +  TVRK  G DI  ACGQ
Sbjct: 281 KGIPCKVNLIPYNPV-PGSDYERSSKERIRKFLKIL-KKAGVLVTVRKTRGDDIDAACGQ 338

Query: 180 LVVN 183
           L   
Sbjct: 339 LRGK 342

Length = 349

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

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

>gnl\|CDD\|172935 PRK14460, PRK14460, 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\|184685 PRK14453, PRK14453, chloramphenicol/florfenicol resistance protein; 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\|184688 PRK14457, PRK14457, 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\|172944 PRK14469, PRK14469, ribosomal RNA large subunit methyltransferase N; Provisional	Back alignment and domain information

>gnl\|CDD\|237720 PRK14463, PRK14463, 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\|184689 PRK14459, PRK14459, 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\|237718 PRK14461, PRK14461, 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\|172940 PRK14465, PRK14465, 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\|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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		205
PRK14462		356	ribosomal RNA large subunit methyltransferase N; P	100.0
PRK14454		342	ribosomal RNA large subunit methyltransferase N; P	100.0
PRK14461		371	ribosomal RNA large subunit methyltransferase N; P	100.0
PRK14459		373	ribosomal RNA large subunit methyltransferase N; P	100.0
PRK14467		348	ribosomal RNA large subunit methyltransferase N; P	100.0
PRK14457		345	ribosomal RNA large subunit methyltransferase N; P	100.0
PRK11194		372	ribosomal RNA large subunit methyltransferase N; P	100.0
TIGR00048		355	radical SAM enzyme, Cfr family. A Staphylococcus s	100.0
PRK14455		356	ribosomal RNA large subunit methyltransferase N; P	100.0
PRK14466		345	ribosomal RNA large subunit methyltransferase N; P	100.0
PRK14460		354	ribosomal RNA large subunit methyltransferase N; P	100.0
PRK14453		347	chloramphenicol/florfenicol resistance protein; Pr	100.0
PRK14465		342	ribosomal RNA large subunit methyltransferase N; P	100.0
PRK14456		368	ribosomal RNA large subunit methyltransferase N; P	100.0
PRK14468		343	ribosomal RNA large subunit methyltransferase N; P	100.0
PRK14463		349	ribosomal RNA large subunit methyltransferase N; P	100.0
COG0820		349	Predicted Fe-S-cluster redox enzyme [General funct	100.0
PRK14470		336	ribosomal RNA large subunit methyltransferase N; P	100.0
PRK14469		343	ribosomal RNA large subunit methyltransferase N; P	100.0
PRK14464		344	ribosomal RNA large subunit methyltransferase N; P	100.0
PRK10076		213	pyruvate formate lyase II activase; Provisional	100.0
PRK11145		246	pflA pyruvate formate lyase-activating enzyme 1; P	99.93
TIGR01290		442	nifB nitrogenase cofactor biosynthesis protein Nif	99.92
COG1180		260	PflA Pyruvate-formate lyase-activating enzyme [Pos	99.9
TIGR02494		295	PFLE_PFLC glycyl-radical enzyme activating protein	99.88
COG2896		322	MoaA Molybdenum cofactor biosynthesis enzyme [Coen	99.87
PRK13762		322	tRNA-modifying enzyme; Provisional	99.87
TIGR03278		404	methan_mark_10 putative methanogenesis marker prot	99.83
TIGR02493		235	PFLA pyruvate formate-lyase 1-activating enzyme. A	99.82
PRK00164		331	moaA molybdenum cofactor biosynthesis protein A; R	99.8
PLN02951		373	Molybderin biosynthesis protein CNX2	99.77
PRK13361		329	molybdenum cofactor biosynthesis protein A; Provis	99.75
TIGR02668		302	moaA_archaeal probable molybdenum cofactor biosynt	99.74
TIGR02666		334	moaA molybdenum cofactor biosynthesis protein A, b	99.72
COG0731		296	Fe-S oxidoreductases [Energy production and conver	99.71
COG2100		414	Predicted Fe-S oxidoreductase [General function pr	99.57
TIGR02495		191	NrdG2 anaerobic ribonucleoside-triphosphate reduct	99.49
PRK05301		378	pyrroloquinoline quinone biosynthesis protein PqqE	99.38
TIGR02109		358	PQQ_syn_pqqE coenzyme PQQ biosynthesis protein E.	99.33
TIGR03470		318	HpnH hopanoid biosynthesis associated radical SAM	99.32
smart00729		216	Elp3 Elongator protein 3, MiaB family, Radical SAM	99.14
COG1625		414	Fe-S oxidoreductase, related to NifB/MoaA family [	98.95
PF04055		166	Radical_SAM: Radical SAM superfamily; InterPro: IP	98.94
COG0535		347	Predicted Fe-S oxidoreductases [General function p	98.93
PRK13758		370	anaerobic sulfatase-maturase; Provisional	98.93
cd01335		204	Radical_SAM Radical SAM superfamily. Enzymes of th	98.92
KOG2876		323	consensus Molybdenum cofactor biosynthesis pathway	98.88
PRK13745		412	anaerobic sulfatase-maturase; Provisional	98.76
TIGR03822		321	AblA_like_2 lysine-2,3-aminomutase-related protein	98.72
PRK09240		371	thiH thiamine biosynthesis protein ThiH; Reviewed	98.64
TIGR03821		321	AblA_like_1 lysine-2,3-aminomutase-related protein	98.64
TIGR03279		433	cyano_FeS_chp putative FeS-containing Cyanobacteri	98.59
TIGR00238		331	KamA family protein. Note that the E. coli homolog	98.53
PRK07094		323	biotin synthase; Provisional	98.44
PLN02389		379	biotin synthase	98.39
COG5014		228	Predicted Fe-S oxidoreductase [General function pr	98.35
COG0641		378	AslB Arylsulfatase regulator (Fe-S oxidoreductase)	98.3
COG1964		475	Predicted Fe-S oxidoreductases [General function p	98.29
TIGR03365		238	Bsubt_queE 7-cyano-7-deazaguanosine (preQ0) biosyn	98.29
PRK08508		279	biotin synthase; Provisional	98.28
TIGR02491		154	NrdG anaerobic ribonucleoside-triphosphate reducta	98.23
TIGR00433		296	bioB biotin synthetase. Catalyzes the last step of	98.19
TIGR00539		360	hemN_rel putative oxygen-independent coproporphyri	98.18
PRK06256		336	biotin synthase; Validated	98.18
PRK15108		345	biotin synthase; Provisional	98.13
COG1313		335	PflX Uncharacterized Fe-S protein PflX, homolog of	98.09
PRK05660		378	HemN family oxidoreductase; Provisional	98.07
PRK08446		350	coproporphyrinogen III oxidase; Provisional	98.01
TIGR02351		366	thiH thiazole biosynthesis protein ThiH. Members t	98.01
PRK05799		374	coproporphyrinogen III oxidase; Provisional	97.96
PRK09249		453	coproporphyrinogen III oxidase; Provisional	97.94
TIGR03820		417	lys_2_3_AblA lysine-2,3-aminomutase. This model de	97.93
PRK05628		375	coproporphyrinogen III oxidase; Validated	97.89
PRK08599		377	coproporphyrinogen III oxidase; Provisional	97.85
TIGR00538		455	hemN oxygen-independent coproporphyrinogen III oxi	97.74
PRK08208		430	coproporphyrinogen III oxidase; Validated	97.72
TIGR03551		343	F420_cofH 7,8-didemethyl-8-hydroxy-5-deazariboflav	97.72
TIGR01212		302	radical SAM protein, TIGR01212 family. This unchar	97.68
PRK13347		453	coproporphyrinogen III oxidase; Provisional	97.65
PRK08207		488	coproporphyrinogen III oxidase; Provisional	97.6
COG2108		353	Uncharacterized conserved protein related to pyruv	97.58
TIGR03699		340	mena_SCO4550 menaquinone biosynthesis protein, SCO	97.55
PRK14862		440	rimO ribosomal protein S12 methylthiotransferase;	97.42
COG1533		297	SplB DNA repair photolyase [DNA replication, recom	97.41
PRK07379		400	coproporphyrinogen III oxidase; Provisional	97.4
TIGR01125		430	MiaB-like tRNA modifying enzyme YliG, TIGR01125. T	97.39
PRK06294		370	coproporphyrinogen III oxidase; Provisional	97.36
PRK09057		380	coproporphyrinogen III oxidase; Provisional	97.34
PRK08898		394	coproporphyrinogen III oxidase; Provisional	97.33
TIGR00510		302	lipA lipoate synthase. The family shows strong seq	97.32
PRK06582		390	coproporphyrinogen III oxidase; Provisional	97.3
TIGR00423		309	radical SAM domain protein, CofH subfamily. This p	97.29
PLN02428		349	lipoic acid synthase	97.28
PRK06267		350	hypothetical protein; Provisional	97.23
PRK12928		290	lipoyl synthase; Provisional	97.2
PRK05904		353	coproporphyrinogen III oxidase; Provisional	97.17
PTZ00413		398	lipoate synthase; Provisional	97.13
PF13394		119	Fer4_14: 4Fe-4S single cluster domain; PDB: 1TV8_B	97.11
PRK05481		289	lipoyl synthase; Provisional	97.11
TIGR02026		497	BchE magnesium-protoporphyrin IX monomethyl ester	96.97
COG0502		335	BioB Biotin synthase and related enzymes [Coenzyme	96.91
TIGR01210		313	conserved hypothetical protein TIGR01210. This fam	96.8
KOG1160		601	consensus Fe-S oxidoreductase [Energy production a	96.78
TIGR03471		472	HpnJ hopanoid biosynthesis associated radical SAM	96.77
PRK14338		459	(dimethylallyl)adenosine tRNA methylthiotransferas	96.74
PRK09058		449	coproporphyrinogen III oxidase; Provisional	96.72
TIGR03700		351	mena_SCO4494 putative menaquinone biosynthesis pro	96.67
TIGR00089		429	RNA modification enzyme, MiaB family. This subfami	96.45
PRK07360		371	FO synthase subunit 2; Reviewed	96.18
PRK14334		440	(dimethylallyl)adenosine tRNA methylthiotransferas	95.94
PRK08629		433	coproporphyrinogen III oxidase; Provisional	95.84
PF13353		139	Fer4_12: 4Fe-4S single cluster domain; PDB: 3C8F_A	95.82
TIGR01579		414	MiaB-like-C MiaB-like tRNA modifying enzyme. This	95.62
PRK11121		154	nrdG anaerobic ribonucleotide reductase-activating	95.58
COG1509		369	KamA Lysine 2,3-aminomutase [Amino acid transport	95.55
PRK06245		336	cofG FO synthase subunit 1; Reviewed	95.4
TIGR02826		147	RNR_activ_nrdG3 anaerobic ribonucleoside-triphosph	95.31
COG0602		212	NrdG Organic radical activating enzymes [Posttrans	95.23
PRK14332		449	(dimethylallyl)adenosine tRNA methylthiotransferas	95.16
PRK14326		502	(dimethylallyl)adenosine tRNA methylthiotransferas	95.14
TIGR01211		522	ELP3 histone acetyltransferase, ELP3 family. The S	95.03
TIGR01574		438	miaB-methiolase tRNA-N(6)-(isopentenyl)adenosine-3	94.96
PRK08444		353	hypothetical protein; Provisional	94.95
PRK09613		469	thiH thiamine biosynthesis protein ThiH; Reviewed	94.64
PRK14331		437	(dimethylallyl)adenosine tRNA methylthiotransferas	94.63
PRK08445		348	hypothetical protein; Provisional	94.58
PRK14328		439	(dimethylallyl)adenosine tRNA methylthiotransferas	94.56
PRK14327		509	(dimethylallyl)adenosine tRNA methylthiotransferas	94.41
cd03174		265	DRE_TIM_metallolyase DRE-TIM metallolyase superfam	94.3
TIGR03550		322	F420_cofG 7,8-didemethyl-8-hydroxy-5-deazariboflav	94.25
COG2516		339	Biotin synthase-related enzyme [General function p	94.01
COG1856		275	Uncharacterized homolog of biotin synthetase [Func	93.88
PRK14325		444	(dimethylallyl)adenosine tRNA methylthiotransferas	93.83
PRK14329		467	(dimethylallyl)adenosine tRNA methylthiotransferas	93.47
TIGR01578		420	MiaB-like-B MiaB-like tRNA modifying enzyme, archa	93.28
PRK14335		455	(dimethylallyl)adenosine tRNA methylthiotransferas	93.27
PRK14340		445	(dimethylallyl)adenosine tRNA methylthiotransferas	93.01
PRK14333		448	(dimethylallyl)adenosine tRNA methylthiotransferas	92.37
PF06463		128	Mob_synth_C: Molybdenum Cofactor Synthesis C; Inte	91.97
PRK14337		446	(dimethylallyl)adenosine tRNA methylthiotransferas	91.79
PRK01254		707	hypothetical protein; Provisional	91.57
PRK05926		370	hypothetical protein; Provisional	91.57
PRK09234		843	fbiC FO synthase; Reviewed	91.56
PRK14339		420	(dimethylallyl)adenosine tRNA methylthiotransferas	90.68
PRK14330		434	(dimethylallyl)adenosine tRNA methylthiotransferas	90.51
PRK00955		620	hypothetical protein; Provisional	90.17
PRK14336		418	(dimethylallyl)adenosine tRNA methylthiotransferas	87.68
PRK05927		350	hypothetical protein; Provisional	85.92
COG1243		515	ELP3 Histone acetyltransferase [Transcription / Ch	85.49
COG0621		437	MiaB 2-methylthioadenine synthetase [Translation,	83.82

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

Probab=100.00  E-value=2.6e-47  Score=332.92  Aligned_cols=183  Identities=36%  Similarity=0.605  Sum_probs=172.7

Q ss_pred             CCccCCCHHHHHHHHHHhhcC-CCCCCCCcEEEEcCCcHHHHHHHhhcCCCceEEEeecCCCHHhhhhhcCCCCCCCHHH
Q 028700            1 MGEPLNNYAALVEAVRIMTGL-PFQVSPKRITVSTVGIVHAINKFHSDLPGLNLAVSLHAPVQDVRCQIMPAARAFPLEK   79 (205)
Q Consensus         1 mGEPllq~~~l~~~l~~lk~~-~i~~~~~~~~v~T~G~~~~~~~l~~~~~~~~l~~slk~~d~~~~~~i~~~~~~~~~~~   79 (205)
                      |||||+|++|+.++++.|++. |++++.+|+||||+|+.+.++++.+..+.+.|.+||||+|++.|+++||+++.+++++
T Consensus       169 mGEPL~N~d~v~~~l~~l~~~~Gl~~~~r~itVsTsG~~~~i~~L~~~dl~v~LaiSLha~d~e~r~~l~pv~~~~~l~~  248 (356)
T PRK14462        169 MGEPLDNLDNVSKAIKIFSENDGLAISPRRQTISTSGLASKIKKLGEMNLGVQLAISLHAVDDELRSELMPINKAYNIES  248 (356)
T ss_pred             CcccccCHHHHHHHHHHhcCccCCCcCCCceEEECCCChHHHHHHHhcCCCeEEEEECCCCCHHHHHHhCCCCccCCHHH
Confidence            899999999999999999996 9999999999999999999999887643356889999999999999999999999999


Q ss_pred             HHHHHHHHHHhcCCcEEEEEEEeCCCCCCHHHHHHHHHHHhcCCceEEEeecCCCCCCCCccCCcHHHHHHHHHHHHhcC
Q 028700           80 LMNALKEYQKNSQQKIFIEYIMLDGVNDEEQHAHQLGKLLETFQVVVNLIPFNPIGSVSQFRTSSDDKVSSFQKILRGSY  159 (205)
Q Consensus        80 i~~~l~~~~~~~~~~V~ir~~lIpGiNDs~e~i~~l~~~l~~~~~~v~lip~~~~g~~~~~~~~~~e~l~~~~~~l~~~~  159 (205)
                      +++++++|....+.+|++|||||||+||++|++++|++|+++++++||||||||++ ..+|++|+++++++|+++|+ ++
T Consensus       249 ll~~l~~y~~~~~~~i~ieyvLI~GvNDs~e~a~~La~llk~l~~~VnLIPyn~~~-~~~~~~ps~e~i~~f~~~l~-~~  326 (356)
T PRK14462        249 IIDAVRKFPIDQRKRVMFEYLVIKDVNDDLKSAKKLVKLLNGIKAKVNLILFNPHE-GSKFERPSLEDMIKFQDYLN-SK  326 (356)
T ss_pred             HHHHHHHHHHHhCCeEEEEEEEECCCCCCHHHHHHHHHHHhhcCcEEEEEeCCCCC-CCCCCCCCHHHHHHHHHHHH-HC
Confidence            99999989877899999999999999999999999999999998999999999997 88999999999999999999 79


Q ss_pred             CceEEecccccccccccccccccccc
Q 028700          160 NIRTTVRKQMGQDISGACGQLVVNLP  185 (205)
Q Consensus       160 Gi~~~i~~~~g~d~~~~Cgql~~~~~  185 (205)
                      |+.+++|.++|+||.||||||+.+..
T Consensus       327 gi~vtvR~~~G~dI~aACGQL~~~~~  352 (356)
T PRK14462        327 GLLCTIRESKGLDISAACGQLREKKL  352 (356)
T ss_pred             CCcEEEeCCCCCchhhcCccchhhhc
Confidence            99999999999999999999987543

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

>PRK14461 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

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

>PRK14457 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

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

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

>PRK14466 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

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

>PRK14465 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

>PRK14468 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

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

>PRK14470 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

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

>PRK10076 pyruvate formate lyase II activase; 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

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

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

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

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

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

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

>PLN02951 Molybderin biosynthesis protein CNX2	Back alignment and domain information

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

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

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

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

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

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

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

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

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

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

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

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

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

>cd01335 Radical_SAM Radical SAM superfamily	Back alignment and domain information

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

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

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

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

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

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

>TIGR00238 KamA family protein	Back alignment and domain information

>PRK07094 biotin synthase; Provisional	Back alignment and domain information

>PLN02389 biotin synthase	Back alignment and domain information

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

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

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

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

>PRK08508 biotin synthase; Provisional	Back alignment and domain information

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

>TIGR00433 bioB biotin synthetase	Back alignment and domain information

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

>PRK06256 biotin synthase; Validated	Back alignment and domain information

>PRK15108 biotin synthase; Provisional	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

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

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

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

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

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

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

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

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

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

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

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

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

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

>PRK08207 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

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

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

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

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

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

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

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

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

>TIGR00510 lipA lipoate synthase	Back alignment and domain information

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

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

>PLN02428 lipoic acid synthase	Back alignment and domain information

>PRK06267 hypothetical protein; Provisional	Back alignment and domain information

>PRK12928 lipoyl synthase; Provisional	Back alignment and domain information

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

>PTZ00413 lipoate synthase; Provisional	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

>PRK05481 lipoyl synthase; Provisional	Back alignment and domain information

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

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

>TIGR01210 conserved hypothetical protein TIGR01210	Back alignment and domain information

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

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

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

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

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

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

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

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

>PRK08629 coproporphyrinogen III oxidase; Provisional	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

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

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

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

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

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

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

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

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

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

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

>PRK08444 hypothetical protein; Provisional	Back alignment and domain information

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

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

>PRK08445 hypothetical protein; Provisional	Back alignment and domain information

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

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

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

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

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

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

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

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

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

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

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

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

>PF06463 Mob_synth_C: Molybdenum Cofactor Synthesis C; InterPro: IPR010505 The majority of molybdenum-containing enzymes utilise a molybdenum cofactor (MoCF or Moco) consisting of a Mo atom coordinated via a cis-dithiolene moiety to molybdopterin (MPT)	Back alignment and domain information

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

>PRK01254 hypothetical protein; Provisional	Back alignment and domain information

>PRK05926 hypothetical protein; Provisional	Back alignment and domain information

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

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

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

>PRK00955 hypothetical protein; Provisional	Back alignment and domain information

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

>PRK05927 hypothetical protein; Provisional	Back alignment and domain information

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

>COG0621 MiaB 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]	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		205
3rf9_A		404	X-Ray Structure Of Rlmn From Escherichia Coli Lengt		6e-34
3rfa_A		404	X-Ray Structure Of Rlmn From Escherichia Coli In Co		1e-32

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

Back alignment and structure

Iteration: 1

Score = 140 bits (352), Expect = 6e-34, Method: Compositional matrix adjust. Identities = 79/191 (41%), Positives = 117/191 (61%), Gaps = 7/191 (3%) Query: 1 MGEPLNNYAALVEAVRIM-TGLPFQVSPKRITVSTVGIVHAINKFHSDLPGLNLAVSLHA 59 MGEPL N +V A+ IM F +S +R+T+ST G+V A++K D+ + LA+SLHA Sbjct: 178 MGEPLLNLNNVVPAMEIMLDDFGFGLSKRRVTLSTSGVVPALDKL-GDMIDVALAISLHA 236 Query: 60 PVQDVRCQIMPAARAFPLEKLMNALKEYQKNS---QQKIFIEYIMLDGVNDEEQHAHQLG 116 P ++R +I+P + + +E + A++ Y + S Q ++ IEY+MLD VND +HAHQL Sbjct: 237 PNDEIRDEIVPINKKYNIETFLAAVRRYLEKSNANQGRVTIEYVMLDHVNDGTEHAHQLA 296 Query: 117 KLLETFQVVVNLIPFNPIGSVSQFRTSSDDKVSSFQKILRGSYNIRTTVRKQMGQDISGA 176 +LL+ +NLIP+NP R SS+ ++ F K+L SY T VRK G DI A Sbjct: 297 ELLKDTPCKINLIPWNPFPGAPYGR-SSNSRIDRFSKVLM-SYGFTTIVRKTRGDDIDAA 354 Query: 177 CGQLVVNLPDK 187 CGQL ++ D+ Sbjct: 355 CGQLAGDVIDR 365

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		205
3rfa_A		404	Ribosomal RNA large subunit methyltransferase N; r	6e-77
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-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 =  235 bits (602), Expect = 6e-77
 Identities = 77/191 (40%), Positives = 117/191 (61%), Gaps = 7/191 (3%)

Query: 1   MGEPLNNYAALVEAVRIMT-GLPFQVSPKRITVSTVGIVHAINKFHSDLPGLNLAVSLHA 59
           MGEPL N   +V A+ IM     F +S +R+T+ST G+V A++K    +  + LA+SLHA
Sbjct: 178 MGEPLLNLNNVVPAMEIMLDDFGFGLSKRRVTLSTSGVVPALDKLGDMID-VALAISLHA 236

Query: 60  PVQDVRCQIMPAARAFPLEKLMNALKEYQKNS---QQKIFIEYIMLDGVNDEEQHAHQLG 116
           P  ++R +I+P  + + +E  + A++ Y + S   Q ++ IEY+MLD VND  +HAHQL 
Sbjct: 237 PNDEIRDEIVPINKKYNIETFLAAVRRYLEKSNANQGRVTIEYVMLDHVNDGTEHAHQLA 296

Query: 117 KLLETFQVVVNLIPFNPIGSVSQFRTSSDDKVSSFQKILRGSYNIRTTVRKQMGQDISGA 176
           +LL+     +NLIP+NP    + +  SS+ ++  F K+L  SY   T VRK  G DI  A
Sbjct: 297 ELLKDTPCKINLIPWNPFPG-APYGRSSNSRIDRFSKVLM-SYGFTTIVRKTRGDDIDAA 354

Query: 177 CGQLVVNLPDK 187
           CGQL  ++ D+
Sbjct: 355 CGQLAGDVIDR 365

PyMOL of 3rfa

>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
Query		205
3rfa_A		404	Ribosomal RNA large subunit methyltransferase N; r	100.0
3can_A		182	Pyruvate-formate lyase-activating enzyme; structur	99.92
3c8f_A		245	Pyruvate formate-lyase 1-activating enzyme; adoMet	99.82
2yx0_A		342	Radical SAM enzyme; predicted tRNA modification en	99.78
2z2u_A		311	UPF0026 protein MJ0257; metal binding protein; 2.4	99.77
1tv8_A		340	MOAA, molybdenum cofactor biosynthesis protein A;	99.64
2a5h_A		416	L-lysine 2,3-aminomutase; radical SAM, four-iron-f	99.25
3iix_A		348	Biotin synthetase, putative; adoMet radical, SAM r	99.23
1r30_A		369	Biotin synthase; SAM radical protein, TIM barrel,	99.02
3t7v_A		350	Methylornithine synthase PYLB; TIM-barrel fold, mu	98.87
1olt_A		457	Oxygen-independent coproporphyrinogen III oxidase;	98.15
2qgq_A		304	Protein TM_1862; alpha-beta protein, structural ge	98.1
1hfe_L		421	Protein (Fe-only hydrogenase (E.C.1.18.99.1) (larg	95.84
4fhd_A		368	Spore photoproduct lyase; partial TIM-barrel, DNA	92.81

>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=1e-41  Score=301.72  Aligned_cols=184  Identities=41%  Similarity=0.709  Sum_probs=158.6

Q ss_pred             CCccCCCHHHHHHHHHHhhcC-CCCCCCCcEEEEcCCcHHHHHHHhhcCCCceEEEeecCCCHHhhhhhcCCCCCCCHHH
Q 028700            1 MGEPLNNYAALVEAVRIMTGL-PFQVSPKRITVSTVGIVHAINKFHSDLPGLNLAVSLHAPVQDVRCQIMPAARAFPLEK   79 (205)
Q Consensus         1 mGEPllq~~~l~~~l~~lk~~-~i~~~~~~~~v~T~G~~~~~~~l~~~~~~~~l~~slk~~d~~~~~~i~~~~~~~~~~~   79 (205)
                      |||||+|++++.++++.+++. |++++.++++|+|||+.+.+++++++. ++.+++|||++|++.|++++|+++.+++++
T Consensus       178 gGEPLln~d~v~~~i~~lk~~~Gl~~s~r~itlsTnG~~p~i~~L~~~~-d~~LaiSLka~d~e~~~~i~pv~~~~~le~  256 (404)
T 3rfa_A          178 MGEPLLNLNNVVPAMEIMLDDFGFGLSKRRVTLSTSGVVPALDKLGDMI-DVALAISLHAPNDEIRDEIVPINKKYNIET  256 (404)
T ss_dssp             SSCGGGCHHHHHHHHHHHHSTTTTCCCGGGEEEEESCCHHHHHHHHHHC-CCEEEEECCCSSHHHHHHHSGGGGTSCHHH
T ss_pred             CCCcccCHHHHHHHHHHHHhhcCcCcCCCceEEECCCcHHHHHHHHHhh-cceEEecccCCCHHHHHHhcCCccCCCHHH
Confidence            699999999999999999995 999999999999999999999999886 457889999999999999999988999999


Q ss_pred             HHHHHHHHHHhcCC---cEEEEEEEeCCCCCCHHHHHHHHHHHhcCCceEEEeecCCCCCCCCccCCcHHHHHHHHHHHH
Q 028700           80 LMNALKEYQKNSQQ---KIFIEYIMLDGVNDEEQHAHQLGKLLETFQVVVNLIPFNPIGSVSQFRTSSDDKVSSFQKILR  156 (205)
Q Consensus        80 i~~~l~~~~~~~~~---~V~ir~~lIpGiNDs~e~i~~l~~~l~~~~~~v~lip~~~~g~~~~~~~~~~e~l~~~~~~l~  156 (205)
                      +++++++|....+.   +|++||+||||+||+++++.+|++|+++++++|+||||||++ ...|.+|+.+++++|+++++
T Consensus       257 vl~ai~~~~~~~g~~~~~V~ie~vLI~GvNDs~e~~~~La~ll~~l~~~VnLIpynP~~-~~~~~~ps~e~i~~f~~iL~  335 (404)
T 3rfa_A          257 FLAAVRRYLEKSNANQGRVTIEYVMLDHVNDGTEHAHQLAELLKDTPCKINLIPWNPFP-GAPYGRSSNSRIDRFSKVLM  335 (404)
T ss_dssp             HHHHHHHHHHHCTTTTTCEEEEEEEBTTTTCSHHHHHHHHHHTTTSCEEEEEEECCCCT-TCCCCBCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCcccEEEEEEEecCCCCCHHHHHHHHHHHHcCCCcEEEEeccCCC-CCCCCCCCHHHHHHHHHHHH
Confidence            99999888877777   899999999999999999999999999998899999999996 78899999999999999999


Q ss_pred             hcCCceEEecccccccccccccccccccccc
Q 028700          157 GSYNIRTTVRKQMGQDISGACGQLVVNLPDK  187 (205)
Q Consensus       157 ~~~Gi~~~i~~~~g~d~~~~Cgql~~~~~~~  187 (205)
                       ++|+.+++|.++|+||+||||||+....+.
T Consensus       336 -~~Gi~vtiR~~~G~di~aaCGQL~~~~~~~  365 (404)
T 3rfa_A          336 -SYGFTTIVRKTRGDDIDAACGQLAGDVIDR  365 (404)
T ss_dssp             -HTTCEEEECCCCCC----------------
T ss_pred             -HcCCcEEEcCCCCcccccccccchhhhhhh
Confidence             799999999999999999999999776544

PyMOL of 3rfa

>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

>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

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

>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

>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

>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

>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

>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

>1hfe_L Protein (Fe-only hydrogenase (E.C.1.18.99.1) (larger subunit)); hydrogene metabolism, periplasm; 1.60A {Desulfovibrio vulgaris subsp} SCOP: c.96.1.1 d.58.1.5 PDB: 1e08_A* 1gx7_A*	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

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		205
d1tv8a_		327	Molybdenum cofactor biosynthesis protein A MoaA {S	99.07
d1r30a_		312	Biotin synthase {Escherichia coli [TaxId: 562]}	95.46
d1olta_		441	Oxygen-independent coproporphyrinogen III oxidase	95.08

>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=99.07  E-value=4.1e-09  Score=86.81  Aligned_cols=123  Identities=15%  Similarity=0.188  Sum_probs=93.1

Q ss_pred             CccCCCHHHHHHHHHHhhcCCCCCCCCcEE-EEcCCcH--HHHHHHhhcCCCceEEEeecCCCHHhhhhhcCCCCCCCHH
Q 028700            2 GEPLNNYAALVEAVRIMTGLPFQVSPKRIT-VSTVGIV--HAINKFHSDLPGLNLAVSLHAPVQDVRCQIMPAARAFPLE   78 (205)
Q Consensus         2 GEPllq~~~l~~~l~~lk~~~i~~~~~~~~-v~T~G~~--~~~~~l~~~~~~~~l~~slk~~d~~~~~~i~~~~~~~~~~   78 (205)
                      |||+++.++ .+.+..+...+.    .... ++|++..  ..++++.+.+++ .+.+|+++.+++.|.++.|..  ..++
T Consensus        73 GEp~l~~~~-~e~i~~~~~~~~----~~~~~~Tng~ll~~~~~~~l~~~g~~-~i~iSldg~~~e~~~~~rg~~--g~~~  144 (327)
T d1tv8a_          73 GEPLMRRDL-DVLIAKLNQIDG----IEDIGLTTNGLLLKKHGQKLYDAGLR-RINVSLDAIDDTLFQSINNRN--IKAT  144 (327)
T ss_dssp             SCGGGSTTH-HHHHHHHTTCTT----CCEEEEEECSTTHHHHHHHHHHHTCC-EEEEECCCSSHHHHHHHHSSC--CCHH
T ss_pred             CcccccccH-HHHHHHHhhhcc----ccccccccccccchhHHHHHHHcCCC-EEeeecccCCHHHhhhheeec--cccc
Confidence            999999774 445554544432    1344 4555554  368888888874 899999999999999998764  3588


Q ss_pred             HHHHHHHHHHHhcCCcEEEEEEEeCCCCCCHHHHHHHHHHHhcCCceEEEeecCCCC
Q 028700           79 KLMNALKEYQKNSQQKIFIEYIMLDGVNDEEQHAHQLGKLLETFQVVVNLIPFNPIG  135 (205)
Q Consensus        79 ~i~~~l~~~~~~~~~~V~ir~~lIpGiNDs~e~i~~l~~~l~~~~~~v~lip~~~~g  135 (205)
                      .+..+++...+ .+.++.+.+++++|.|..  ++.++.++++..+..+.++++.+.+
T Consensus       145 ~~~~~~~~~~~-~g~~~~~~~~v~~~~n~~--~~~~~~~~~~~~~~~~~~~~~~~~~  198 (327)
T d1tv8a_         145 TILEQIDYATS-IGLNVKVNVVIQKGINDD--QIIPMLEYFKDKHIEIRFIEFMDVG  198 (327)
T ss_dssp             HHHHHHHHHHH-TTCEEEEEEEECTTTTGG--GHHHHHHHHHHTTCCEEEEECCCBC
T ss_pred             hhhhHHHHHHH-cCCCcceeEEEecCcccc--ccHHHHHHHHhhccccceeeeeccc
Confidence            88888885554 788999999999999987  6788999999888766677776654

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