254781120

254781120

radical SAM protein

GeneID in NCBI database:8210145Locus tag:CLIBASIA_05110
Protein GI in NCBI database:254781120Protein Accession:YP_003065533.1
Gene range:-(1122974, 1124128)Protein Length:384aa
Gene description:radical SAM protein
COG prediction:[R] Predicted Fe-S-cluster redox enzyme
KEGG prediction:radical SAM protein; K06941 ribosomal RNA large subunit methyltransferase N [EC:2.1.1.-]
SEED prediction:Ribosomal RNA large subunit methyltransferase N (EC 2.1.1.-)
Pathway involved in KEGG:not defined
Subsystem involved in SEED:Conserved gene cluster associated with Met-tRNA formyltransferase
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPREDnone TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------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----
MNFLKKESLIGMMREELEEALLKIGIPQRHVRMRTSQIWKWIYVRGIRDFQGMSDISQEVRHLLNQHFSIIYPEIVDEKISCDGTRKWLLRFPARCIGGPVEIETVYIPEKSRGTLCVSSQVGCSLTCSFCYTGTQKLVRNLTAEEILLQVLLARSLLGDFPGCEDIEGMVIPSVGRKISNIVMMGMGEPLCNFDNVKKSLSIASDSMGLSFSKRRITLSTSGFVPNIARVGEEIGVMLAISLHAVSNDLRNILVPINRKYPLEMLIDACRHYPGLSNARRITFEYVMLKGINDSPRDALNLIKILKGIPAKINLIPFNPWPGCEYLCSDQKDIVTFSECIKRSGYSSPIRTPRGLDILAACGQLKSLSKRIPKVPRQEMQITG
cccccccccccccHHHHHHHHHHccccccccccHHHHHHHHHHHHccccHHHHccccHHHHHHHHHcccccccEEEEEEEcccccEEEEEEEcccccccccEEEEEEEEcccccEEEEEcccccccccccEEEccccccccccHHHHHHHHHHHHHHHccccccccccccccccccccccEEEEEccccHHHcHHHHHHHHHHHcccccccccccEEEEEccccHHHHHHHHHHccccEEEEcccccHHHHHHHHcccccccHHHHHHHHHHHHHHHccccEEEEEEEEccccccHHHHHHHHHHHccccccEEEEEcccccccccccccHHHHHHHHHHHHHcccEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHcc
cccccccccccccHHHHHHHHHHcccccccccccHHHHHHHHHHcccccHHHHccHHHHHHHHHHHccEEccccEEEEEEcccccEEEEEEEcccccccccEEEEEEEcccccEEEEEEcccccEEEEcccccccccccccccHHHHHHHHHHHHHHHcccccccccccccccccccEEEEEEEcccccccHHHHHHHHHHHHHHccccccccccEEEEccccccHHHHHHHHHccEEEEEEcccccHHHHHHcccccccccHHHHHHHHHHHHHHccccEEEEEEEEEccccccHHHHHHHHHHHcccccEEEEEccccccccccccccHHHHHHHHHHHHHcccEEEEEccccccHHHHHHHHcccHHHHHHHHHHHHHHcc
MNFLKKESLIGMMREELEEALLKigipqrhvRMRTSQIWKWIYVRGIRDFQGMSDISQEVRHLLNQHFsiiypeivdekiscdgTRKWLLrfparciggpveietvyipeksrgtlcvssqvgcsltcsfcytgTQKLVRNLTAEEILLQVLLARSllgdfpgcediegmvipsvgrkISNIVMMgmgeplcnfdnvkkSLSIASdsmglsfskrritlstsgfvpniaRVGEEIGVMLAISLHAVSNDlrnilvpinrkypLEMLIDACrhypglsnarRITFEYVMLkgindsprDALNLIKILkgipakinlipfnpwpgceylcsdqkDIVTFSEcikrsgysspirtprgLDILAACGQLkslskripkvprqemqitg
mnflkkeslIGMMREELEEALlkigipqrhvrMRTSQIWKWIYVRGIRDFQGMSDISQEVRHLLNQHFSIIYPEIVDEKISCDGTRKWLLRFPARCIGGPVEIETVYIPEKSRGTLCVSSQVGCSLTCSFCYTGTQKLVRNLTAEEILLQVLLARSLLGDFPGCEDIEGMVIPSVGRKISNIVMMGMGEPLCNFDNVKKSLSIASDSMGLSFSKrritlstsgfvpnIARVGEEIGVMLAISLHAVSNDLRNILVPINRKYPLEMLIDACRHYPGLSNARRITFEYVMLKGINDSPRDALNLIKILKGIPAKINLIPFNPWPGCEYLCSDQKDIVTFSECIKRSgysspirtprgLDILAACgqlkslskripkvprqemqitg
MNFLKKESLIGMMREELEEALLKIGIPQRHVRMRTSQIWKWIYVRGIRDFQGMSDISQEVRHLLNQHFSIIYPEIVDEKISCDGTRKWLLRFPARCIGGPVEIETVYIPEKSRGTLCVSSQVGCSLTCSFCYTGTQKLVRNLTAEEILLQVLLARSLLGDFPGCEDIEGMVIPSVGRKISNIVMMGMGEPLCNFDNVKKSLSIASDSMGLSFSKRRITLSTSGFVPNIARVGEEIGVMLAISLHAVSNDLRNILVPINRKYPLEMLIDACRHYPGLSNARRITFEYVMLKGINDSPRDALNLIKILKGIPAKINLIPFNPWPGCEYLCSDQKDIVTFSECIKRSGYSSPIRTPRGLDILAACGQLKSLSKRIPKVPRQEMQITG
****KKE*LIGMMREELEEALLKIGIPQRHVRMRTSQIWKWIYVRGIRDFQGMSDISQEVRHLLNQHFSIIYPEIVDEKISCDGTRKWLLRFPARCIGGPVEIETVYIPEKSRGTLCVSSQVGCSLTCSFCYTGTQKLVRNLTAEEILLQVLLARSLLGDFPGCEDI******SVGRKISNIVMMGMGEPLCNFDNVKKSLSIASDSMGLSFSKRRITLSTSGFVPNIARVGEEIGVMLAISLHAVSNDLRNILVPINRKYPLEMLIDACRHYPGLSNARRITFEYVMLKGINDSPRDALNLIKILKGIPAKINLIPFNPWPGCEYLCSDQKDIVTFSECIKRSGYSSPIRTPRGLDILAACGQL*******************
MNFLKKESLIGMMREELEEALLKIGIPQRHVRMRTSQIWKWIYVRGIRDFQGMSDISQEVRHLLNQHFSIIYPEIVDEKISCDGTRKWLLRFPARCIGGPVEIETVYIPEKSRGTLCVSSQVGCSLTCSFCYTGTQKLVRNLTAEEILLQVLLARSLLGDFPGCEDIEGMVIPSVGRKISNIVMMGMGEPLCNFDNVKKSLSIASDSMGLSFSKRRITLSTSGFVPNIARVGEEIGVMLAISLHAVSNDLRNILVPINRKYPLEMLIDACRHYPGLSNARRITFEYVMLKGINDSPRDALNLIKILKGIPAKINLIPFNPWPGCEYLCSDQKDIVTFSECIKRSGYSSPIRTPRGLDILAACGQLKSLSKRIPKVPRQEMQITG
*****KESLIGMMREELEEALLKIGIPQRHVRMRTSQIWKWIYVRGIRDFQGMSDISQEVRHLLNQHFSIIYPEIVDEKISCDGTRKWLLRFPARCIGGPVEIETVYIPEKSRGTLCVSSQVGCSLTCSFCYTGTQKLVRNLTAEEILLQVLLARSLLGDFPGC***EGMVIPSVGRKISNIVMMGMGEPLCNFDNVKKSLSIASDSMGLSFSKRRITLSTSGFVPNIARVGEEIGVMLAISLHAVSNDLRNILVPINRKYPLEMLIDACRHYPGLSNARRITFEYVMLKGINDSPRDALNLIKILKGIPAKINLIPFNPWPGCEYLCSDQKDIVTFSECIKRSGYSSPIRTPRGLDILAACGQLKSLSK*IPKV*********
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MNFLKKESLIGMMREELEEALLKIGIPQRHVRMRTSQIWKWIYVRGIRDFQGMSDISQEVRHLLNQHFSIIYPEIVDEKISCDGTRKWLLRFPARCIGGPVEIETVYIPEKSRGTLCVSSQVGCSLTCSFCYTGTQKLVRNLTAEEILLQVLLARSLLGDFPGCEDIEGMVIPSVGRKISNIVMMGMGEPLCNFDNVKKSLSIASDSMGLSFSKRRITLSTSGFVPNIARVGEEIGVMLAISLHAVSNDLRNILVPINRKYPLEMLIDACRHYPGLSNARRITFEYVMLKGINDSPRDALNLIKILKGIPAKINLIPFNPWPGCEYLCSDQKDIVTFSECIKRSGYSSPIRTPRGLDILAACGQLKSLSKRIPKVPRQEMQITG
MNFLKKESLIGMMREELEEALLKIGIPQRHVRMRTSQIWKWIYVRGIRDFQGMSDISQEVRHLLNQHFSIIYPEIVDEKISCDGTRKWLLRFPARCIGGPVEIETVYIPEKSRGTLCVSSQVGCSLTCSFCYTGTQKLVRNLTAEEILLQVLLARSLLGDFPGCEDIEGMVIPSVGRKISNIVMMGMGEPLCNFDNVKKSLSIASDSMGLSFSKRRITLSTSGFVPNIARVGEEIGVMLAISLHAVSNDLRNILVPINRKYPLEMLIDACRHYPGLSNARRITFEYVMLKGINDSPRDALNLIKILKGIPAKINLIPFNPWPGCEYLCSDQKDIVTFSECIKRSGYSSPIRTPRGLDILAACGQLKSLSKRIPKVPRQEMQITG
MNFLKKESLIGMMREELEEALLKIGIPQRHVRMRTSQIWKWIYVRGIRDFQGMSDISQEVRHLLNQHFSIIYPEIVDEKISCDGTRKWLLRFPARCIGGPVEIETVYIPEKSRGTLCVSSQVGCSLTCSFCYTGTQKLVRNLTAEEILLQVLLARSLLGDFPGCEDIEGMVIPSVGRKISNIVMMGMGEPLCNFDNVKKSLSIASDSMGLSFSKRRITLSTSGFVPNIARVGEEIGVMLAISLHAVSNDLRNILVPINRKYPLEMLIDACRHYPGLSNARRITFEYVMLKGINDSPRDALNLIKILKGIPAKINLIPFNPWPGCEYLCSDQKDIVTFSECIKRSGYSSPIRTPRGLDILAACGQLKSLSKRIPKVPRQEMQITG

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

IdentityAlignment graphLength Definition E-value
Target384 radical SAM protein [Candidatus Liberibacter asiaticus
254781065352 L-lysine 2,3-aminomutase protein [Candidatus Liber 0.044
>gi|254781065|ref|YP_003065478.1| L-lysine 2,3-aminomutase protein [Candidatus Liberibacter asiaticus str. psy62] Length = 352 Back     alignment
 Score = 30.8 bits (68), Expect = 0.044,   Method: Compositional matrix adjust.
 Identities = 44/193 (22%), Positives = 68/193 (35%), Gaps = 46/193 (23%)

Query: 124 CSLTCSFCY----TGTQKLVRNLTAEEILLQVLLARSLLGDFPGCEDIEG-MVIPSVGRK 178
           C + C FC+     G+QK                     G     +D E  +       +
Sbjct: 105 CPVYCRFCFRREMVGSQK---------------------GTVLSSKDTEAALAYIQEKSQ 143

Query: 179 ISNIVMMGMGEPLC----NFDNVKKSLSIASDSMGLSFSKRRITLSTSGFVPNIARVGEE 234
           I  ++  G G+PL         V K+L        L F  R   +      P + +  +E
Sbjct: 144 IWEVIFTG-GDPLILSHKRLQKVLKTLRYIKHVQILRFHSRVPIVDPQRINPELIQCLKE 202

Query: 235 IGVMLAISLHAVSNDLRNILVPINRKYPLEMLIDACRHYPGLSNARRITF-EYVMLKGIN 293
            G  + I++HA               +P E   +A      L+NA  I   + V+LKGIN
Sbjct: 203 AGKPVYIAIHA--------------NHPYEFSEEAIAAISRLANAGIILLSQSVLLKGIN 248

Query: 294 DSPRDALNLIKIL 306
           D P    NL++  
Sbjct: 249 DDPEILANLMRTF 261

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target384 radical SAM protein [Candidatus Liberibacter asiaticus
315122584389 radical SAM protein [Candidatus Liberibacter solanacear 1 0.0
227823764411 putative radical SAM enzyme, Cfr family [Sinorhizobium 1 1e-153
150398262413 radical SAM protein [Sinorhizobium medicae WSM419] Leng 1 1e-153
205829900409 RecName: Full=Ribosomal RNA large subunit methyltransfe 1 1e-153
110635192408 radical SAM protein [Mesorhizobium sp. BNC1] Length = 4 1 1e-152
15966967411 hypothetical protein SMc03831 [Sinorhizobium meliloti 1 1 1e-152
327190218411 hypothetical protein RHECNPAF_44600102 [Rhizobium etli 1 1e-152
239830929411 radical SAM enzyme, Cfr family [Ochrobactrum intermediu 1 1e-152
153007435411 radical SAM protein [Ochrobactrum anthropi ATCC 49188] 1 1e-152
190893778409 hypothetical protein RHECIAT_CH0004213 [Rhizobium etli 1 1e-151
>gi|315122584|ref|YP_004063073.1| radical SAM protein [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 389 Back     alignment and organism information
 Score =  691 bits (1782), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 328/383 (85%), Positives = 359/383 (93%)

Query: 1   MNFLKKESLIGMMREELEEALLKIGIPQRHVRMRTSQIWKWIYVRGIRDFQGMSDISQEV 60
           MN +KKESLIGM REE+EE+LLKIG+P   VRMRTSQIWKWIYVRG+RDF  MSDIS+E+
Sbjct: 1   MNIVKKESLIGMTREEIEESLLKIGVPPIQVRMRTSQIWKWIYVRGVRDFHFMSDISKEI 60

Query: 61  RHLLNQHFSIIYPEIVDEKISCDGTRKWLLRFPARCIGGPVEIETVYIPEKSRGTLCVSS 120
           R LL+QHF+I+YPEIVDEKISCDGTRKWLLRFPARCIG PV+IETVYIPEKSRGTLCVSS
Sbjct: 61  RCLLDQHFAIVYPEIVDEKISCDGTRKWLLRFPARCIGDPVDIETVYIPEKSRGTLCVSS 120

Query: 121 QVGCSLTCSFCYTGTQKLVRNLTAEEILLQVLLARSLLGDFPGCEDIEGMVIPSVGRKIS 180
           QVGCSLTCSFCYTGTQ+LVRNLT EEILLQ+LL RSLLGDFPGCED+  MV+P VGRK+S
Sbjct: 121 QVGCSLTCSFCYTGTQQLVRNLTVEEILLQILLVRSLLGDFPGCEDMTEMVVPLVGRKVS 180

Query: 181 NIVMMGMGEPLCNFDNVKKSLSIASDSMGLSFSKRRITLSTSGFVPNIARVGEEIGVMLA 240
           NIVMMGMGEPLCNFDNVKK+L IASDSMGLSFSKRRITLSTSGFVPNIARVGEEIGVMLA
Sbjct: 181 NIVMMGMGEPLCNFDNVKKALLIASDSMGLSFSKRRITLSTSGFVPNIARVGEEIGVMLA 240

Query: 241 ISLHAVSNDLRNILVPINRKYPLEMLIDACRHYPGLSNARRITFEYVMLKGINDSPRDAL 300
           ISLHAV NDLRNILVPIN+KYPLEML+DACR+YPGLSN+RRITFEYVMLKGINDSPRDA+
Sbjct: 241 ISLHAVKNDLRNILVPINKKYPLEMLMDACRNYPGLSNSRRITFEYVMLKGINDSPRDAI 300

Query: 301 NLIKILKGIPAKINLIPFNPWPGCEYLCSDQKDIVTFSECIKRSGYSSPIRTPRGLDILA 360
            LIK+LKGIPAKINLIPFNPWPGC+YLCSDQKDI  FSE +K+SGYSSPIRTPRGLDI A
Sbjct: 301 ELIKLLKGIPAKINLIPFNPWPGCDYLCSDQKDIEIFSEYVKKSGYSSPIRTPRGLDIFA 360

Query: 361 ACGQLKSLSKRIPKVPRQEMQIT 383
           ACGQLKSLSKR+P++  ++ QIT
Sbjct: 361 ACGQLKSLSKRVPRISSKQAQIT 383


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|227823764|ref|YP_002827737.1| putative radical SAM enzyme, Cfr family [Sinorhizobium fredii NGR234] Length = 411 Back     alignment and organism information
>gi|150398262|ref|YP_001328729.1| radical SAM protein [Sinorhizobium medicae WSM419] Length = 413 Back     alignment and organism information
>gi|205829900|sp|Q2K3B1|RLMN_RHIEC RecName: Full=Ribosomal RNA large subunit methyltransferase N; AltName: Full=23S rRNA m2A2503 methyltransferase Length = 409 Back     alignment and organism information
>gi|110635192|ref|YP_675400.1| radical SAM protein [Mesorhizobium sp. BNC1] Length = 408 Back     alignment and organism information
>gi|15966967|ref|NP_387320.1| hypothetical protein SMc03831 [Sinorhizobium meliloti 1021] Length = 411 Back     alignment and organism information
>gi|327190218|gb|EGE57323.1| hypothetical protein RHECNPAF_44600102 [Rhizobium etli CNPAF512] Length = 411 Back     alignment and organism information
>gi|239830929|ref|ZP_04679258.1| radical SAM enzyme, Cfr family [Ochrobactrum intermedium LMG 3301] Length = 411 Back     alignment and organism information
>gi|153007435|ref|YP_001368650.1| radical SAM protein [Ochrobactrum anthropi ATCC 49188] Length = 411 Back     alignment and organism information
>gi|190893778|ref|YP_001980320.1| hypothetical protein RHECIAT_CH0004213 [Rhizobium etli CIAT 652] Length = 409 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target384 radical SAM protein [Candidatus Liberibacter asiaticus
PRK11194372 PRK11194, PRK11194, ribosomal RNA large subunit methylt 2e-97
TIGR00048355 TIGR00048, TIGR00048, radical SAM enzyme, Cfr family 7e-97
PRK14463349 PRK14463, PRK14463, ribosomal RNA large subunit methylt 2e-92
PRK14460354 PRK14460, PRK14460, ribosomal RNA large subunit methylt 3e-87
PRK14454342 PRK14454, PRK14454, ribosomal RNA large subunit methylt 3e-85
PRK14462356 PRK14462, PRK14462, ribosomal RNA large subunit methylt 9e-84
PRK14467348 PRK14467, PRK14467, ribosomal RNA large subunit methylt 2e-79
PRK14455356 PRK14455, PRK14455, ribosomal RNA large subunit methylt 3e-79
PRK14469343 PRK14469, PRK14469, ribosomal RNA large subunit methylt 5e-77
PRK14466345 PRK14466, PRK14466, ribosomal RNA large subunit methylt 1e-73
PRK14468343 PRK14468, PRK14468, ribosomal RNA large subunit methylt 2e-70
PRK14457345 PRK14457, PRK14457, ribosomal RNA large subunit methylt 2e-69
PRK14461371 PRK14461, PRK14461, ribosomal RNA large subunit methylt 2e-64
PRK14459373 PRK14459, PRK14459, ribosomal RNA large subunit methylt 4e-62
PRK14456368 PRK14456, PRK14456, ribosomal RNA large subunit methylt 6e-58
PRK14465342 PRK14465, PRK14465, ribosomal RNA large subunit methylt 5e-49
PRK14453347 PRK14453, PRK14453, chloramphenicol/florfenicol resista 2e-46
COG0820349 COG0820, COG0820, Predicted Fe-S-cluster redox enzyme [ 1e-115
PRK14470336 PRK14470, PRK14470, ribosomal RNA large subunit methylt 8e-44
PRK14464344 PRK14464, PRK14464, ribosomal RNA large subunit methylt 8e-35
pfam04055165 pfam04055, Radical_SAM, Radical SAM superfamily 1e-11
cd01335204 cd01335, Radical_SAM, Radical SAM superfamily 8e-06
>gnl|CDD|183031 PRK11194, PRK11194, ribosomal RNA large subunit methyltransferase N; Provisional Back     alignment and domain information
>gnl|CDD|161680 TIGR00048, TIGR00048, radical SAM enzyme, Cfr family Back     alignment and domain information
>gnl|CDD|172938 PRK14463, PRK14463, 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|184690 PRK14462, PRK14462, 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|184687 PRK14455, PRK14455, 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|184692 PRK14466, PRK14466, 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|184688 PRK14457, PRK14457, ribosomal RNA large subunit methyltransferase N; Provisional Back     alignment and domain information
>gnl|CDD|172936 PRK14461, PRK14461, 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|172940 PRK14465, PRK14465, 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|31162 COG0820, COG0820, Predicted Fe-S-cluster redox enzyme [General function prediction only] 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|146602 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

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 384 radical SAM protein [Candidatus Liberibacter asiaticus
PRK11194372 hypothetical protein; Provisional 100.0
TIGR00048378 TIGR00048 radical SAM enzyme, Cfr family; InterPro: IPR 100.0
COG0820349 Predicted Fe-S-cluster redox enzyme [General function p 100.0
PRK11145246 pflA pyruvate formate lyase-activating enzyme 1; Provis 99.68
TIGR02493243 PFLA pyruvate formate-lyase 1-activating enzyme; InterP 99.38
COG0731296 Fe-S oxidoreductases [Energy production and conversion] 99.32
PRK00164334 moaA molybdenum cofactor biosynthesis protein A; Review 99.11
COG1180260 PflA Pyruvate-formate lyase-activating enzyme [Posttran 99.06
PRK13361329 molybdenum cofactor biosynthesis protein A; Provisional 99.06
cd01335204 Radical_SAM Radical SAM superfamily. Enzymes of this fa 99.01
TIGR02668324 moaA_archaeal probable molybdenum cofactor biosynthesis 98.99
COG2896322 MoaA Molybdenum cofactor biosynthesis enzyme [Coenzyme 98.91
smart00729216 Elp3 Elongator protein 3, MiaB family, Radical SAM. Thi 98.86
PRK05301 375 pyrroloquinoline quinone biosynthesis protein PqqE; Pro 98.8
TIGR03470318 HpnH hopanoid biosynthesis associated radical SAM prote 98.75
COG2100414 Predicted Fe-S oxidoreductase [General function predict 98.73
) of Arabidopsis thaliana (Mouse-ear cress), mammalian Gephryin (e.g. Q9NQX3 from SWISSPROT) and Drosophila melanogaster (Fruit fly) Cinnamon (P39205 from SWISSPROT) . This entry represents the bacterial form of MoaA (molybdenum cofactor biosynthesis protein A). The MoaA protein is a member of the wider S-adenosylmethionine(SAM)-dependent enzyme family which catalyze the formation of protein and/or substrate radicals by reductive cleavage of SAM via a [4Fe-4S] cluster. Monomeric and homodimeric forms of MoaA have been observed in vivo, and it is not clear what the physiologically relevant form of the enzyme is . The core of each monomer consists of an incomplete TIM barrel, formed by the N-terminal region of the protein, containing a [4Fe-4S] cluster. The C-terminal region of the protein, which also contains a [4Fe-4S] cluster consists of a beta-sheet covering the lateral opening of the barrel, an extended loop and three alpha helices. The N-terminal [4Fe-4S] cluster is coordinated with 3 cysteines and an exchangeable SAM molecule, while the C-terminal [4Fe-4S], also coordinated with 3 cysteines, is the binding and activation site for GTP .; GO: 0046872 metal ion binding, 0006777 Mo-molybdopterin cofactor biosynthetic process." target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=TIGR02666">TIGR02666346 moaA molybdenum cofactor biosynthesis protein A; InterP 98.65
PRK07094323 biotin synthase; Provisional 98.38
COG1032490 Fe-S oxidoreductase [Energy production and conversion] 98.31
COG1625 414 Fe-S oxidoreductase, related to NifB/MoaA family [Energ 98.25
TIGR03471472 HpnJ hopanoid biosynthesis associated radical SAM prote 98.22
PRK06256325 biotin synthase; Validated 98.19
TIGR01290 461 nifB nitrogenase cofactor biosynthesis protein NifB; In 98.13
PRK06267324 hypothetical protein; Provisional 98.05
COG0621437 MiaB 2-methylthioadenine synthetase [Translation, ribos 97.43
COG0502335 BioB Biotin synthase and related enzymes [Coenzyme meta 97.29
PRK08508279 biotin synthase; Provisional 97.25
TIGR03278 404 methan_mark_10 putative methanogenesis marker protein 1 96.98
TIGR01579492 MiaB-like-C MiaB-like tRNA modifying enzyme; InterPro: 96.55
PRK06245336 cofG FO synthase subunit 1; Reviewed 96.23
TIGR03550322 F420_cofG 7,8-didemethyl-8-hydroxy-5-deazariboflavin sy 95.96
TIGR02109 363 PQQ_syn_pqqE coenzyme PQQ biosynthesis protein E; Inter 95.36
TIGR00238357 TIGR00238 lysine 2,3-aminomutase YodO family protein; I 95.01
KOG2876323 consensus 94.8
PRK05927350 hypothetical protein; Provisional 94.18
COG1060370 ThiH Thiamine biosynthesis enzyme ThiH and related unch 91.98
PRK10076213 pyruvate formate lyase II activase; Provisional 99.48
TIGR02494305 PFLE_PFLC glycyl-radical enzyme activating protein fami 98.6
COG2108353 Uncharacterized conserved protein related to pyruvate f 93.04
pfam04055165 Radical_SAM Radical SAM superfamily. Radical SAM protei 98.86
PRK13758 370 anaerobic sulfatase-maturase; Provisional 98.31
COG0535347 Predicted Fe-S oxidoreductases [General function predic 98.14
COG0641 378 AslB Arylsulfatase regulator (Fe-S oxidoreductase) [Gen 98.09
TIGR03365238 Bsubt_queE 7-cyano-7-deazaguanosine (preQ0) biosynthesi 97.84
PRK13745 412 anaerobic sulfatase-maturase; Provisional 97.74
COG1533297 SplB DNA repair photolyase [DNA replication, recombinat 97.36
TIGR03551343 F420_cofH 7,8-didemethyl-8-hydroxy-5-deazariboflavin sy 97.17
PRK07360375 FO synthase subunit 2; Reviewed 96.96
PRK08444353 hypothetical protein; Provisional 96.73
COG5014228 Predicted Fe-S oxidoreductase [General function predict 96.68
TIGR02495220 NrdG2 anaerobic ribonucleoside-triphosphate reductase a 96.66
PRK08445348 hypothetical protein; Provisional 95.82
PRK05926371 hypothetical protein; Provisional 92.25
PRK09234846 fbiC FO synthase; Reviewed 91.32
PRK13762321 tRNA-modifying enzyme; Provisional 98.77
COG1509369 KamA Lysine 2,3-aminomutase [Amino acid transport and m 98.64
TIGR03279 433 cyano_FeS_chp putative FeS-containing Cyanobacterial-sp 97.58
COG0602212 NrdG Organic radical activating enzymes [Posttranslatio 96.71
TIGR02826165 RNR_activ_nrdG3 anaerobic ribonucleoside-triphosphate r 96.5
PRK11121154 nrdG anaerobic ribonucleotide reductase-activating prot 93.7
COG2516339 Biotin synthase-related enzyme [General function predic 90.63
>PRK11194 hypothetical protein; Provisional Back     alignment and domain information
>TIGR00048 TIGR00048 radical SAM enzyme, Cfr family; InterPro: IPR004383 This family of conserved hypothetical proteins groups bacterial proteins of unknown function Back     alignment and domain information
>COG0820 Predicted Fe-S-cluster redox enzyme [General function prediction only] Back     alignment and domain information
>PRK11145 pflA pyruvate formate lyase-activating enzyme 1; Provisional Back     alignment and domain information
>TIGR02493 PFLA pyruvate formate-lyase 1-activating enzyme; InterPro: IPR012838 Members of this family are iron-sulphur proteins with a radical-SAM domain Back     alignment and domain information
>COG0731 Fe-S oxidoreductases [Energy production and conversion] Back     alignment and domain information
>PRK00164 moaA molybdenum cofactor biosynthesis protein A; Reviewed Back     alignment and domain information
>COG1180 PflA Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>PRK13361 molybdenum cofactor biosynthesis protein A; Provisional Back     alignment and domain information
>cd01335 Radical_SAM Radical SAM superfamily Back     alignment and domain information
>TIGR02668 moaA_archaeal probable molybdenum cofactor biosynthesis protein A; InterPro: IPR013485 This entry consists of archaeal proteins which are predicted to be functionally equivalent to MoaA (molybdenum cofactor biosynthesis protein A) from bacteria (see IPR013483 from INTERPRO) Back     alignment and domain information
>COG2896 MoaA Molybdenum cofactor biosynthesis enzyme [Coenzyme metabolism] Back     alignment and domain information
>smart00729 Elp3 Elongator protein 3, MiaB family, Radical SAM 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
>COG2100 Predicted Fe-S oxidoreductase [General function prediction only] Back     alignment and domain information
>TIGR02666 moaA molybdenum cofactor biosynthesis protein A; InterPro: IPR013483 The majority of molybdenum-containing enzymes utilise a molybdenum cofactor (MoCF or Moco) consisting of a Mo atom coordinated via a cisdithiolene moiety to molybdopterin (MPT) Back     alignment and domain information
>PRK07094 biotin synthase; Provisional Back     alignment and domain information
>COG1032 Fe-S oxidoreductase [Energy production and conversion] Back     alignment and domain information
>COG1625 Fe-S oxidoreductase, related to NifB/MoaA family [Energy production and conversion] Back     alignment and domain information
>TIGR03471 HpnJ hopanoid biosynthesis associated radical SAM protein HpnJ Back     alignment and domain information
>PRK06256 biotin synthase; Validated Back     alignment and domain information
>TIGR01290 nifB nitrogenase cofactor biosynthesis protein NifB; InterPro: IPR005980 NifB is a protein required for the biosynthesis of the iron-molybdenum (or iron-vanadium) cofactor used by the nitrogen-fixing enzyme nitrogenase Back     alignment and domain information
>PRK06267 hypothetical protein; Provisional Back     alignment and domain information
>COG0621 MiaB 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>COG0502 BioB Biotin synthase and related enzymes [Coenzyme metabolism] Back     alignment and domain information
>PRK08508 biotin synthase; Provisional Back     alignment and domain information
>TIGR03278 methan_mark_10 putative methanogenesis marker protein 10 Back     alignment and domain information
>TIGR01579 MiaB-like-C MiaB-like tRNA modifying enzyme; InterPro: IPR006467 This clade of sequences is closely related to MiaB, a modifier of isopentenylated adenosine-37 of certain eukaryotic and bacterial tRNAs (see IPR006463 from INTERPRO) Back     alignment and domain information
>PRK06245 cofG FO synthase subunit 1; Reviewed Back     alignment and domain information
>TIGR03550 F420_cofG 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofG subunit Back     alignment and domain information
>TIGR02109 PQQ_syn_pqqE coenzyme PQQ biosynthesis protein E; InterPro: IPR011843 This entry describes coenzyme PQQ biosynthesis protein E, a gene required for the biosynthesis of pyrrolo-quinoline-quinone (coenzyme PQQ) Back     alignment and domain information
>TIGR00238 TIGR00238 lysine 2,3-aminomutase YodO family protein; InterPro: IPR003739 This family represents essentially the whole of the Escherichia coli YjeK family and of some of its apparent orthologs Back     alignment and domain information
>KOG2876 consensus Back     alignment and domain information
>PRK05927 hypothetical protein; Provisional 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
>PRK10076 pyruvate formate lyase II activase; Provisional Back     alignment and domain information
>TIGR02494 PFLE_PFLC glycyl-radical enzyme activating protein family; InterPro: IPR012839 This subset of the radical-SAM domain includes a number of probable activating proteins acting on different enzymes all requiring an amino-acid-centred radical 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
>pfam04055 Radical_SAM Radical SAM superfamily Back     alignment and domain information
>PRK13758 anaerobic sulfatase-maturase; Provisional Back     alignment and domain information
>COG0535 Predicted Fe-S oxidoreductases [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
>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
>COG1533 SplB DNA repair photolyase [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR03551 F420_cofH 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofH subunit Back     alignment and domain information
>PRK07360 FO synthase subunit 2; Reviewed Back     alignment and domain information
>PRK08444 hypothetical protein; Provisional Back     alignment and domain information
>COG5014 Predicted Fe-S oxidoreductase [General function prediction only] Back     alignment and domain information
>TIGR02495 NrdG2 anaerobic ribonucleoside-triphosphate reductase activating protein; InterPro: IPR012840 This enzyme is a member of the radical-SAM family Back     alignment and domain information
>PRK08445 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
>PRK13762 tRNA-modifying enzyme; Provisional Back     alignment and domain information
>COG1509 KamA Lysine 2,3-aminomutase [Amino acid transport and metabolism] Back     alignment and domain information
>TIGR03279 cyano_FeS_chp putative FeS-containing Cyanobacterial-specific oxidoreductase Back     alignment and domain information
>COG0602 NrdG Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>TIGR02826 RNR_activ_nrdG3 anaerobic ribonucleoside-triphosphate reductase activating protein; InterPro: IPR014191 Members of this entry represent a set of proteins related to, yet architecturally different from, the activating protein for the glycine radical-containing, oxygen-sensitive ribonucleoside-triphosphate reductase (RNR, see IPR012837 from INTERPRO) Back     alignment and domain information
>PRK11121 nrdG anaerobic ribonucleotide reductase-activating protein; Provisional Back     alignment and domain information
>COG2516 Biotin synthase-related enzyme [General function prediction only] Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target384 radical SAM protein [Candidatus Liberibacter asiaticus
3rf9_A404 X-Ray Structure Of Rlmn From Escherichia Coli Lengt 1e-106
3rfa_A404 X-Ray Structure Of Rlmn From Escherichia Coli In Co 1e-103
>gi|332639897|pdb|3RF9|A Chain A, X-Ray Structure Of Rlmn From Escherichia Coli Length = 404 Back     alignment and structure
 Score =  388 bits (997), Expect = e-106,   Method: Composition-based stats.
 Identities = 159/379 (41%), Positives = 217/379 (57%), Gaps = 23/379 (6%)

Query: 6   KESLIGMMREELEEALLKIGIPQRHVRMRTSQIWKWIYVRGIRDFQGMSDISQEVRHLLN 65
           K +L+ + R+++ E    +G        R  Q+ KW+Y     +F  M+DI++ +R  L 
Sbjct: 17  KINLLDLNRQQMREFFKDLG----EKPFRADQVMKWMYHYCCDNFDEMTDINKVLRGKLK 72

Query: 66  QHFSIIYPEIVDEKISCDGTRKWLLRFPARCIGGPVEIETVYIPEKSRGTLCVSSQVGCS 125
           +   I  PE+V+E+ S DGT KW +            +ETVYIPE  R TLCVSSQVGC+
Sbjct: 73  EVAEIRAPEVVEEQRSSDGTIKWAIAVGD------QRVETVYIPEDDRATLCVSSQVGCA 126

Query: 126 LTCSFCYTGTQKLVRNLTAEEILLQVLLARSLLGDFPGCEDIEGMVIPSVGRKISNIVMM 185
           L C FC T  Q   RNL   EI+ QV  A  ++G              +  R I+N+VMM
Sbjct: 127 LECKFCSTAQQGFNRNLRVSEIIGQVWRAAKIVG----------AAKVTGQRPITNVVMM 176

Query: 186 GMGEPLCNFDNVKKSLSIASDSMGLSFSKRRITLSTSGFVPNIARVGEEIGVMLAISLHA 245
           GMGEPL N +NV  ++ I  D  G   SKRR+TLSTSG VP + ++G+ I V LAISLHA
Sbjct: 177 GMGEPLLNLNNVVPAMEIMLDDFGFGLSKRRVTLSTSGVVPALDKLGDMIDVALAISLHA 236

Query: 246 VSNDLRNILVPINRKYPLEMLIDACRHYPGLSNAR--RITFEYVMLKGINDSPRDALNLI 303
            ++++R+ +VPIN+KY +E  + A R Y   SNA   R+T EYVML  +ND    A  L 
Sbjct: 237 PNDEIRDEIVPINKKYNIETFLAAVRRYLEKSNANQGRVTIEYVMLDHVNDGTEHAHQLA 296

Query: 304 KILKGIPAKINLIPFNPWPGCEYLCSDQKDIVTFSECIKRSGYSSPIRTPRGLDILAACG 363
           ++LK  P KINLIP+NP+PG  Y  S    I  FS+ +   G+++ +R  RG DI AACG
Sbjct: 297 ELLKDTPCKINLIPWNPFPGAPYGRSSNSRIDRFSKVLMSYGFTTIVRKTRGDDIDAACG 356

Query: 364 QLKSLS-KRIPKVPRQEMQ 381
           QL      R  +  R+ MQ
Sbjct: 357 QLAGDVIDRTKRTLRKRMQ 375


>gi|332639899|pdb|3RFA|A Chain A, X-Ray Structure Of Rlmn From Escherichia Coli In Complex With S- Adenosylmethionine Length = 404 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target384 radical SAM protein [Candidatus Liberibacter asiaticus
3c8f_A245 Pyruvate formate-lyase 1-activating enzyme; adoMet radi 1e-06
2yx0_A342 Radical SAM enzyme; predicted tRNA modification enzyme, 2e-04
2z2u_A311 UPF0026 protein MJ0257; metal binding protein; 2.40A {M 8e-04
>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
 Score = 49.2 bits (116), Expect = 1e-06
 Identities = 36/206 (17%), Positives = 74/206 (35%), Gaps = 38/206 (18%)

Query: 123 GCSLTCSFCY---TGTQKLVRNLTAEEILLQVLLARSLLGDFPGCEDIEGMVIPSVGRKI 179
           GC + C +C+   T      + +T E+++ +V+  R  +    G                
Sbjct: 28  GCLMRCLYCHNRDTWDTHGGKEVTVEDLMKEVVTYRHFMNASGGG--------------- 72

Query: 180 SNIVMMGMGEPLCNFDNVKKSLSIASDSMGLSFSKRRITLSTSGFVPNIARVGEE---IG 236
              V    GE +   + V+                    L T+GFV     V +E   + 
Sbjct: 73  ---VTASGGEAILQAEFVRDWFRACKKEG------IHTCLDTNGFVRRYDPVIDELLEVT 123

Query: 237 VMLAISLHAVSNDLRNILVPINRKYPLEMLIDACRHYPGLSNARRITFEYVMLKGINDSP 296
            ++ + L  +++++   LV ++    LE                ++   YV++ G +D  
Sbjct: 124 DLVMLDLKQMNDEIHQNLVGVSNHRTLEFAKYLANKNV------KVWIRYVVVPGWSDDD 177

Query: 297 RDALNLIKILKGIPA--KINLIPFNP 320
             A  L +  + +    KI L+P++ 
Sbjct: 178 DSAHRLGEFTRDMGNVEKIELLPYHE 203


>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
>2z2u_A UPF0026 protein MJ0257; metal binding protein; 2.40A {Methanocaldococcus jannaschii} Length = 311 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target384 radical SAM protein [Candidatus Liberibacter asiaticus
3c8f_A245 Pyruvate formate-lyase 1-activating enzyme; adoMet radi 99.87
3iix_A348 Biotin synthetase, putative; adoMet radical, SAM radica 98.78
2qgq_A304 Protein TM_1862; alpha-beta protein, structural genomic 98.68
1r30_A369 Biotin synthase; SAM radical protein, TIM barrel, FES c 98.28
1olt_A 457 Oxygen-independent coproporphyrinogen III oxidase; heme 94.24
3can_A182 Pyruvate-formate lyase-activating enzyme; structural ge 99.6
2yx0_A342 Radical SAM enzyme; predicted tRNA modification enzyme, 99.39
2z2u_A311 UPF0026 protein MJ0257; metal binding protein; 2.40A {M 99.16
2a5h_A416 L-lysine 2,3-aminomutase; radical SAM, four-iron-four-s 99.16
1tv8_A340 MOAA, molybdenum cofactor biosynthesis protein A; TIM b 99.0
>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
Probab=99.87  E-value=5.1e-20  Score=167.64  Aligned_cols=205  Identities=19%  Similarity=0.326  Sum_probs=159.3

Q ss_pred             CCEEEEEECCCCHHCCCCCC---CCCCHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEECCCC
Q ss_conf             73389884065100486132---244111027898999999999999722203444434344454586110144101454
Q gi|254781120|r  113 RGTLCVSSQVGCSLTCSFCY---TGTQKLVRNLTAEEILLQVLLARSLLGDFPGCEDIEGMVIPSVGRKISNIVMMGMGE  189 (384)
Q Consensus       113 r~T~CvSSQvGC~m~C~FCa---Tg~~G~~RNLt~~EIv~Qv~~~~~~l~~~~~~~~~~~~~~~~~~~~i~NiVfMGmGE  189 (384)
                      +...+|-+| ||.+.|.||.   |......+.++..|+++++........                 ..+..|.|+| ||
T Consensus        19 G~r~~vf~~-GCN~~C~~C~n~~~~~~~~~~~~~~~e~~~ei~~~~~~~~-----------------~~~~~v~~sG-GE   79 (245)
T 3c8f_A           19 GIRFITFFQ-GCLMRCLYCHNRDTWDTHGGKEVTVEDLMKEVVTYRHFMN-----------------ASGGGVTASG-GE   79 (245)
T ss_dssp             SEEEEEEES-CCSCCCTTCSCGGGCCTTCSEEECHHHHHHHHGGGHHHHT-----------------STTCEEEEEE-SC
T ss_pred             CCEEEEECC-CCCCCCCCCCCHHHHCCCCCCCCCHHHHHHHHHHHHHHHC-----------------CCCCEEECCC-CC
T ss_conf             638999878-7478898999713418679918899999999999999752-----------------5787585355-56


Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEECCCCHH----HHHHHCCCCCCEEEEEECCCCHHHHHHCCCCCCCCHHH
Q ss_conf             45428999999603768457787753688851387414----78860125651799840455113444123312578999
Q gi|254781120|r  190 PLCNFDNVKKSLSIASDSMGLSFSKRRITLSTSGFVPN----IARVGEEIGVMLAISLHAVSNDLRNILVPINRKYPLEM  265 (384)
Q Consensus       190 Pl~N~d~v~~ai~~l~~~~g~~~~~r~ITvST~Gi~p~----I~~la~~~~~~LAiSLha~~~~~R~~lmPi~~~~~l~~  265 (384)
                      |++++|.+...++.+.+ .|+     ++.++|.|..+.    ++++... -....+|+++++++...+++..    +.+.
T Consensus        80 P~l~~~~l~~l~~~~k~-~g~-----~~~l~TnG~~~~~~~~~~~l~~~-~d~v~id~~~~~~~~~~~~~g~----~~~~  148 (245)
T 3c8f_A           80 AILQAEFVRDWFRACKK-EGI-----HTCLDTNGFVRRYDPVIDELLEV-TDLVMLDLKQMNDEIHQNLVGV----SNHR  148 (245)
T ss_dssp             GGGGHHHHHHHHHHHHT-TTC-----CEEEEECCCCCCCCHHHHHHHHT-CSEEEEECCCSSHHHHHHHHSS----CSHH
T ss_pred             CCCCHHHHHHHHHHHHH-HCC-----CEEEECCCCCCCCHHHHHHHHCC-CCEEEEECCCCCHHHHHHHHCC----CCHH
T ss_conf             53469999999998886-438-----47997788655534566665235-7579984354678899987386----5089


Q ss_pred             HHHHHHHHHHHCCCCEEEEEEEEECCCCCCHHHHHHHHHHHCCCC--CEEEEEECCCCC-------CCC-----CCCCCH
Q ss_conf             999999998625894599999872699988899999999832545--316675127788-------798-----868898
Q gi|254781120|r  266 LIDACRHYPGLSNARRITFEYVMLKGINDSPRDALNLIKILKGIP--AKINLIPFNPWP-------GCE-----YLCSDQ  331 (384)
Q Consensus       266 l~~a~~~y~~~~~~rrit~EYvli~gvNDs~e~a~~L~~ll~~~~--~~vNLIp~N~~~-------~~~-----~~~~~~  331 (384)
                      +++.++...+ . +.++.++++++.|+||+.++..+++++++.++  ..|+++||++..       +.+     .++|+.
T Consensus       149 vl~~l~~l~~-~-g~~v~i~~~~i~g~~d~~e~i~~i~~~i~~l~~~~~v~l~py~~~g~~k~~~~~~~y~~~~~~~p~~  226 (245)
T 3c8f_A          149 TLEFAKYLAN-K-NVKVWIRYVVVPGWSDDDDSAHRLGEFTRDMGNVEKIELLPYHELGKHKWVAMGEEYKLDGVKPPKK  226 (245)
T ss_dssp             HHHHHHHHHH-H-TCCEEEEEEECTTTTCCHHHHHHHHHHHHHHCCEEEEEEEECCCCSHHHHHHTTCCCTTTTCCCCCH
T ss_pred             HHHHHHHHHH-C-CCCEEEEEEEECCCCCCHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCHHHHCCCCCCCCCCCCCCH
T ss_conf             9999999997-8-9989999999899489999999999999857997558884476166411665185454457899999


Q ss_pred             HHHHHHHHHHHHCCCEEE
Q ss_conf             999999999998798785
Q gi|254781120|r  332 KDIVTFSECIKRSGYSSP  349 (384)
Q Consensus       332 ~~i~~F~~~L~~~Gi~~t  349 (384)
                      +.++++.+++++.|+.|.
T Consensus       227 e~l~~~~~~~~~~G~~V~  244 (245)
T 3c8f_A          227 ETMERVKGILEQYGHKVM  244 (245)
T ss_dssp             HHHHHHHHHHHTTTCCBC
T ss_pred             HHHHHHHHHHHHCCCEEE
T ss_conf             999999999998599067



>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
>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
>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
>1olt_A Oxygen-independent coproporphyrinogen III oxidase; heme biosynthesis, decarboxylase, radical SAM enzyme, 4Fe- 4S cluster; HET: SAM; 2.07A {Escherichia coli} SCOP: c.1.28.2 Back     alignment and structure
>3can_A Pyruvate-formate lyase-activating enzyme; structural genomics, PSI, MCSG, APC20359.1; 1.80A {Bacteroides vulgatus atcc 8482} 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
>2a5h_A L-lysine 2,3-aminomutase; radical SAM, four-iron-four-sulfur cluster, 4Fe4S, FS4, SAM, S-adenosylmethionine, alpha-beta channel; HET: SAM LYS PLP; 2.10A {Clostridium subterminale} 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

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

No hit with e-value below 0.005

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target384 radical SAM protein [Candidatus Liberibacter asiaticus
d1tv8a_327 Molybdenum cofactor biosynthesis protein A MoaA {Staphy 98.48
d1r30a_312 Biotin synthase {Escherichia coli [TaxId: 562]} 98.17
d1olta_ 441 Oxygen-independent coproporphyrinogen III oxidase HemN 90.77
>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=98.48  E-value=3.3e-05  Score=56.23  Aligned_cols=176  Identities=19%  Similarity=0.275  Sum_probs=110.5

Q ss_pred             EEEEEECCCCHHCCCCCCCCC-----CHH---HCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEEC
Q ss_conf             389884065100486132244-----111---027898999999999999722203444434344454586110144101
Q gi|254781120|r  115 TLCVSSQVGCSLTCSFCYTGT-----QKL---VRNLTAEEILLQVLLARSLLGDFPGCEDIEGMVIPSVGRKISNIVMMG  186 (384)
Q Consensus       115 T~CvSSQvGC~m~C~FCaTg~-----~G~---~RNLt~~EIv~Qv~~~~~~l~~~~~~~~~~~~~~~~~~~~i~NiVfMG  186 (384)
                      +++|+----|.+.|+||....     ..+   .+-|+.+++..-+   ++ +.+              .  .+..|.|.|
T Consensus        13 ~l~ieiT~~CNlrC~~C~~~~~~~~~~~~~~~~~~ls~e~~~~li---~~-~~~--------------~--g~~~v~~~G   72 (327)
T d1tv8a_          13 DLRLSVTDRCNFRCDYCMPKEVFGDDFVFLPKNELLTFDEMARIA---KV-YAE--------------L--GVKKIRITG   72 (327)
T ss_dssp             EEEEECCSCCSCCCTTTSCTTTSSTTCCCCCGGGSCCHHHHHHHH---HH-HHH--------------T--TCCEEEEES
T ss_pred             CEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHH---HH-HHH--------------C--CCEEEEECC
T ss_conf             579972210089694789760167777647721459999999999---99-987--------------5--983897379


Q ss_pred             CCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEECCCC--HHHHHHHCCCCCCEEEEEECCCCHHHHHHCCCCCCCCHH
Q ss_conf             454454289999996037684577877536888513874--147886012565179984045511344412331257899
Q gi|254781120|r  187 MGEPLCNFDNVKKSLSIASDSMGLSFSKRRITLSTSGFV--PNIARVGEEIGVMLAISLHAVSNDLRNILVPINRKYPLE  264 (384)
Q Consensus       187 mGEPl~N~d~v~~ai~~l~~~~g~~~~~r~ITvST~Gi~--p~I~~la~~~~~~LAiSLha~~~~~R~~lmPi~~~~~l~  264 (384)
                       |||+++.|-+-....... . +   ....+.++|-++.  ..+++|.+..-..+.+||.+.+++.-+.+.-.+  ...+
T Consensus        73 -GEp~l~~~~~e~i~~~~~-~-~---~~~~~~~Tng~ll~~~~~~~l~~~g~~~i~iSldg~~~e~~~~~rg~~--g~~~  144 (327)
T d1tv8a_          73 -GEPLMRRDLDVLIAKLNQ-I-D---GIEDIGLTTNGLLLKKHGQKLYDAGLRRINVSLDAIDDTLFQSINNRN--IKAT  144 (327)
T ss_dssp             -SCGGGSTTHHHHHHHHTT-C-T---TCCEEEEEECSTTHHHHHHHHHHHTCCEEEEECCCSSHHHHHHHHSSC--CCHH
T ss_pred             -CCCCCCCCHHHHHHHHHH-H-C---CCCCCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCHHHHHHHEEEC--CCCC
T ss_conf             -861246647999998754-2-1---222013444311120679999983998786202568787764510203--5421


Q ss_pred             HHHHHHHHHHHHCCCCEEEEEEEEECCCCCCHHHHHHHHHHHCCCCCEEEEEECCCCC
Q ss_conf             9999999998625894599999872699988899999999832545316675127788
Q gi|254781120|r  265 MLIDACRHYPGLSNARRITFEYVMLKGINDSPRDALNLIKILKGIPAKINLIPFNPWP  322 (384)
Q Consensus       265 ~l~~a~~~y~~~~~~rrit~EYvli~gvNDs~e~a~~L~~ll~~~~~~vNLIp~N~~~  322 (384)
                      ..+.+++... .. +-++.+..+++.+.|+..-  ..+.++++.....+.++++.+..
T Consensus       145 ~~~~~~~~~~-~~-g~~~~~~~~v~~~~n~~~~--~~~~~~~~~~~~~~~~~~~~~~~  198 (327)
T d1tv8a_         145 TILEQIDYAT-SI-GLNVKVNVVIQKGINDDQI--IPMLEYFKDKHIEIRFIEFMDVG  198 (327)
T ss_dssp             HHHHHHHHHH-HT-TCEEEEEEEECTTTTGGGH--HHHHHHHHHTTCCEEEEECCCBC
T ss_pred             HHHHHHHHHH-HC-CCCCCEEEEEECCCCCCCC--HHHHHHHHHHCCCCCEEEEECCC
T ss_conf             1236899999-85-9986325898568353100--89999997406541013531146



>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

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 384 radical SAM protein [Candidatus Liberibacter asiat
2yx0_A_342 (A:) Radical SAM enzyme; predicted tRNA modificati 9e-27
2z2u_A_311 (A:) UPF0026 protein MJ0257; metal binding protein 2e-20
3c8f_A_245 (A:) Pyruvate formate-lyase 1-activating enzyme; a 2e-15
1tv8_A_1-313313 (A:1-313) MOAA, molybdenum cofactor biosynthesis p 0.002
3can_A_182 (A:) Pyruvate-formate lyase-activating enzyme; str 1e-14
2a5h_A_95-342248 (A:95-342) L-lysine 2,3-aminomutase; radical SAM, 5e-14
>2yx0_A (A:) Radical SAM enzyme; predicted tRNA modification enzyme, metal binding protein, structural genomics, NPPSFA; 2.21A {Pyrococcus horikoshii}Length = 342 Back     alignment and structure
 Score =  115 bits (288), Expect = 9e-27
 Identities = 44/346 (12%), Positives = 88/346 (25%), Gaps = 36/346 (10%)

Query: 38  IWKWIYV-RGIRDFQGMSDISQEVRHLLNQHFSIIYPEIVDEKISCDGTRKWLLRFP-AR 95
           + + I +  G    Q   ++ +EV  L  +       EIV          K       + 
Sbjct: 1   MMEMITIKPGKITVQANPNMPKEVAELFRKQH----YEIVGR----HSGVKLCHWLKKSL 52

Query: 96  CIGGPVEIETVYIPEKSRGTLCVSSQVGCSLTCSFCY------TGTQKLVRNLTAEEILL 149
             G     +  Y     R          C+  C FC+       GT+          I+ 
Sbjct: 53  TEGRFCYKQKFYGIHSHRCLQMTPVLAWCTHNCIFCWRPMENFLGTELPQPWDDPAFIVE 112

Query: 150 QVLLARSLLGDFPGCEDIEGMVIPSVGRKISNIVMMGMGEPLCNFDNVKKSLSIASDSMG 209
           + + A+  L                     ++  +   GEP   +  +   +        
Sbjct: 113 ESIKAQRKLLIGYKGNPKVDKKKFEEAWNPTHAAISLSGEP-MLYPYMGDLVEEFHK--- 168

Query: 210 LSFSKRRITLSTSGFVPNIARVGEEIG---VMLAISLHAVSNDLRNILVPINRKYPLEML 266
                    + T+G +P       +       L +S+ A   +  N +         E +
Sbjct: 169 ---RGFTTFIVTNGTIPERLEEMIKEDKLPTQLYVSITAPDIETYNSVNIPMIPDGWERI 225

Query: 267 IDACRHYPGLSNARRITFEYVMLKGINDSPRDALNLIKILKGI-PAKINLIPFNPWPGCE 325
           +             R      ++KG N          K++    P  +    +       
Sbjct: 226 LRFLELM--RDLPTRTVVRLTLVKGENM--HSPEKYAKLILKARPMFVEAKAYMFVGYSR 281

Query: 326 Y-----LCSDQKDIVTFSECIKRSGYSSPIRTPRGLDILAACGQLK 366
                      +DI  F+E + +      I        +    +  
Sbjct: 282 NRLTINNMPSHQDIREFAEALVKHLPGYHIEDEYEPSRVVLIMRDD 327


>2z2u_A (A:) UPF0026 protein MJ0257; metal binding protein; 2.40A {Methanocaldococcus jannaschii}Length = 311 Back     alignment and structure
>3c8f_A (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
>1tv8_A (A:1-313) MOAA, molybdenum cofactor biosynthesis protein A; TIM barrel, ligand binding protein; HET: SAM; 2.20A {Staphylococcus aureus}Length = 313 Back     alignment and structure
>3can_A (A:) Pyruvate-formate lyase-activating enzyme; structural genomics, PSI, MCSG, APC20359.1; 1.80A {Bacteroides vulgatus atcc 8482}Length = 182 Back     alignment and structure
>2a5h_A (A:95-342) L-lysine 2,3-aminomutase; radical SAM, four-iron-four-sulfur cluster, 4Fe4S, FS4, SAM, S-adenosylmethionine, alpha-beta channel; HET: SAM LYS PLP; 2.10A {Clostridium subterminale}Length = 248 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target384 radical SAM protein [Candidatus Liberibacter asiaticus
2yx0_A_342 Radical SAM enzyme; predicted tRNA modification en 99.88
2z2u_A_311 UPF0026 protein MJ0257; metal binding protein; 2.4 99.83
3c8f_A_245 Pyruvate formate-lyase 1-activating enzyme; adoMet 99.68
2a5h_A_95-342248 L-lysine 2,3-aminomutase; radical SAM, four-iron-f 99.6
3iix_A_348 Biotin synthetase, putative; adoMet radical, SAM r 99.18
1r30_A_369 Biotin synthase; SAM radical protein, TIM barrel, 98.91
1olt_A_1-364364 Oxygen-independent coproporphyrinogen III oxidase; 98.83
3can_A_182 Pyruvate-formate lyase-activating enzyme; structur 99.46
1tv8_A_1-313313 MOAA, molybdenum cofactor biosynthesis protein A; 99.15
2qgq_A_1-112112 Protein TM_1862; alpha-beta protein, structural ge 96.63
2qgq_A_113-234122 Protein TM_1862; alpha-beta protein, structural ge 92.13
>2yx0_A (A:) Radical SAM enzyme; predicted tRNA modification enzyme, metal binding protein, structural genomics, NPPSFA; 2.21A {Pyrococcus horikoshii} Back     alignment and structure
Probab=99.88  E-value=2.2e-21  Score=178.86  Aligned_cols=307  Identities=12%  Similarity=0.037  Sum_probs=232.9

Q ss_pred             HHHHH-HHCCCCCHHHHCCCCHHHHHHHHHCCCCCCCCEEEEEECCCCCCCEEEECCCCCCCCCEEEEEEECC------C
Q ss_conf             99999-8717999678334788999998620225787023465314544303775247777898155443023------4
Q gi|254781120|r   38 IWKWI-YVRGIRDFQGMSDISQEVRHLLNQHFSIIYPEIVDEKISCDGTRKWLLRFPARCIGGPVEIETVYIP------E  110 (384)
Q Consensus        38 I~~wi-y~k~v~~f~~MtnLpk~lR~~L~e~~~i~~l~iv~~~~S~DGT~K~L~~l~d~~~~dg~~IEsVlip------~  110 (384)
                      ||+|+ +++++.+|++|++||+..++.|.+...        .....|++.|++..+.+     ...++...+.      .
T Consensus         1 ~~~~~~~~~~~~~~~~~~~l~~~~~e~l~~~~~--------~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~   67 (342)
T 2yx0_A            1 MMEMITIKPGKITVQANPNMPKEVAELFRKQHY--------EIVGRHSGVKLCHWLKK-----SLTEGRFCYKQKFYGIH   67 (342)
T ss_dssp             ----------CCCCCBCCSSCHHHHHHHHHTTC--------EEEBTTEEECCCTTHHH-----HHHHCCCCHHHHHHCCC
T ss_pred             CCCCEEECCCCCHHHHCCCCCHHHHHHHHHCCC--------EEEECCCCEEECHHHHH-----HHCCCCCCCCCCCCCCC
T ss_conf             965255334400353088999899999987798--------78715766677540398-----83779964550012634


Q ss_pred             CCCCEEEEEECCCCHHCCCCCCCCC------CHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEE
Q ss_conf             6773389884065100486132244------1110278989999999999997222034444343444545861101441
Q gi|254781120|r  111 KSRGTLCVSSQVGCSLTCSFCYTGT------QKLVRNLTAEEILLQVLLARSLLGDFPGCEDIEGMVIPSVGRKISNIVM  184 (384)
Q Consensus       111 ~~r~T~CvSSQvGC~m~C~FCaTg~------~G~~RNLt~~EIv~Qv~~~~~~l~~~~~~~~~~~~~~~~~~~~i~NiVf  184 (384)
                      ..+..+++...-||+++|.||....      .+-.|..+..++++++..+.+...................+..+..+++
T Consensus        68 ~~~~~~~i~~t~gCn~~C~yC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (342)
T 2yx0_A           68 SHRCLQMTPVLAWCTHNCIFCWRPMENFLGTELPQPWDDPAFIVEESIKAQRKLLIGYKGNPKVDKKKFEEAWNPTHAAI  147 (342)
T ss_dssp             GGGEEEEESCSSCCSBCCTTCCCSSSSCSCSSCCSSCCCHHHHHHHHHHHHHHHHTTCC--CCSCHHHHHHHTSCCEEEE
T ss_pred             CCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCEEEE
T ss_conf             64448876841252777988999887777755545557989999999999999876532675302677775148757999


Q ss_pred             ECCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEECCCCHHHHHHH---CCCCCCEEEEEECCCCHHHHHHCCCCCCC
Q ss_conf             014544542899999960376845778775368885138741478860---12565179984045511344412331257
Q gi|254781120|r  185 MGMGEPLCNFDNVKKSLSIASDSMGLSFSKRRITLSTSGFVPNIARVG---EEIGVMLAISLHAVSNDLRNILVPINRKY  261 (384)
Q Consensus       185 MGmGEPl~N~d~v~~ai~~l~~~~g~~~~~r~ITvST~Gi~p~I~~la---~~~~~~LAiSLha~~~~~R~~lmPi~~~~  261 (384)
                      .+.|||+++ ..+...++.+.. .|     .++.+.|.|.........   ......+.+|+.+++++.+..+.....+.
T Consensus       148 ~~~gep~~~-~~~~~~~~~~~~-~~-----~~~~~~tn~~~~~~~~~~~~~~~~~~~v~isl~~~~~~~~~~~~~~~~~~  220 (342)
T 2yx0_A          148 SLSGEPMLY-PYMGDLVEEFHK-RG-----FTTFIVTNGTIPERLEEMIKEDKLPTQLYVSITAPDIETYNSVNIPMIPD  220 (342)
T ss_dssp             CSSSCGGGS-TTHHHHHHHHHH-TT-----CEEEEEECSCCHHHHHHHHHTTCCCSEEEEEECCSSHHHHHHHHCBSSSC
T ss_pred             ECCCCCCCC-HHHHHHHHHHHH-CC-----CEEEEECCCCCHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHCCCCCC
T ss_conf             468775454-409999999986-39-----72899548877258999886425775799627899989999871877777


Q ss_pred             CHHHHHHHHHHHHHHCCCCEEEEEEEEECCCCCCHHHHHHHHHHHCCCCC-EEEEEECCCCCCCC-----CCCCCHHHHH
Q ss_conf             89999999999986258945999998726999888999999998325453-16675127788798-----8688989999
Q gi|254781120|r  262 PLEMLIDACRHYPGLSNARRITFEYVMLKGINDSPRDALNLIKILKGIPA-KINLIPFNPWPGCE-----YLCSDQKDIV  335 (384)
Q Consensus       262 ~l~~l~~a~~~y~~~~~~rrit~EYvli~gvNDs~e~a~~L~~ll~~~~~-~vNLIp~N~~~~~~-----~~~~~~~~i~  335 (384)
                      ++++++++++.+. .. +-++.+..+++.|.||.  +..++++++..+.+ .|++.||.|.++.+     ..+++.+.+.
T Consensus       221 ~~~~~~~~i~~l~-~~-g~~v~~~~~~~~g~n~~--~~~~~~~~~~~lg~~~v~~~~~~p~~~~~~~~~~~~~~~~~~~~  296 (342)
T 2yx0_A          221 GWERILRFLELMR-DL-PTRTVVRLTLVKGENMH--SPEKYAKLILKARPMFVEAKAYMFVGYSRNRLTINNMPSHQDIR  296 (342)
T ss_dssp             HHHHHHHHHHHHT-TC-SSEEEEEEEECTTTTCC--CHHHHHHHHHHHCCSEEEEEECC------CCCCGGGSCCHHHHH
T ss_pred             HHHHHHHHHHHHH-HC-CCCEEEEEEEECCCCHH--HHHHHHHHHHHCCCCEEEEECCEECCCCCHHCCCCCCCCHHHHH
T ss_conf             8999999999999-66-99889999986898878--89999999987499889986525568860112401499889999


Q ss_pred             HHHHHHHHCCCEEEECCCCCCCCCCCCCCCHHH
Q ss_conf             999999987987854158777100112002102
Q gi|254781120|r  336 TFSECIKRSGYSSPIRTPRGLDILAACGQLKSL  368 (384)
Q Consensus       336 ~F~~~L~~~Gi~~tiR~srG~DI~aACGQL~~~  368 (384)
                      +|.+.+.+.+....++...|.++.++|++.+-.
T Consensus       297 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  329 (342)
T 2yx0_A          297 EFAEALVKHLPGYHIEDEYEPSRVVLIMRDDVD  329 (342)
T ss_dssp             HHHHHHHTTCTTEEEEEEEGGGTEEEEEETTSE
T ss_pred             HHHHHHHHHCCCCEEECCCCCCEEEEEEECCCC
T ss_conf             999999987269664226676518997741415



>2z2u_A (A:) UPF0026 protein MJ0257; metal binding protein; 2.40A {Methanocaldococcus jannaschii} Back     alignment and structure
>3c8f_A (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
>2a5h_A (A:95-342) L-lysine 2,3-aminomutase; radical SAM, four-iron-four-sulfur cluster, 4Fe4S, FS4, SAM, S-adenosylmethionine, alpha-beta channel; HET: SAM LYS PLP; 2.10A {Clostridium subterminale} Back     alignment and structure
>3iix_A (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 (A:) Biotin synthase; SAM radical protein, TIM barrel, FES cluster, transferase; HET: SAM DTB; 3.40A {Escherichia coli} Back     alignment and structure
>1olt_A (A:1-364) Oxygen-independent coproporphyrinogen III oxidase; heme biosynthesis, decarboxylase, radical SAM enzyme, 4Fe- 4S cluster; HET: SAM; 2.07A {Escherichia coli} Back     alignment and structure
>3can_A (A:) Pyruvate-formate lyase-activating enzyme; structural genomics, PSI, MCSG, APC20359.1; 1.80A {Bacteroides vulgatus atcc 8482} Back     alignment and structure
>1tv8_A (A:1-313) MOAA, molybdenum cofactor biosynthesis protein A; TIM barrel, ligand binding protein; HET: SAM; 2.20A {Staphylococcus aureus} Back     alignment and structure
>2qgq_A (A:1-112) 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
>2qgq_A (A:113-234) 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