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Conserved domains on  [gi|499240617|ref|WP_010938157|]
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12,18-didecarboxysiroheme deacetylase [Desulfovibrio vulgaris]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rSAM_ahbC_deAc super family cl37468
12,18-didecarboxysiroheme deacetylase; This model describes one of a pair of radical SAM ...
 2-391 0e+00

12,18-didecarboxysiroheme deacetylase; This model describes one of a pair of radical SAM enzymes involved in the alternative heme biosynthesis (ahb) pathway for heme b biosynthesis from siroheme. This anaerobic pathway occurs in sulfate-reducing bacteria and methanogens. A very similar pair of radical SAM enzymes (TIGR04054, TIGR04055) is involved in heme d1 biosynthesis in species such as Heliobacillus mobilis and Heliophilum fasciatum. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]


The actual alignment was detected with superfamily member TIGR04546:

Pssm-ID: 275339 [Multi-domain]  Cd Length: 390  Bit Score: 809.04  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617    2 IGISKLYCGQVEPSDALRYGRNSGQLPSHLLQFSKDKKPVVVWNMTRRCNLKCVHCYAKAVDPEGKDEISTEQAKTIIDD 81
Cdd:TIGR04546   1 IGISKLYCGTVEPSDALRYGRHSGKLPSHLLQFSKDKKPVVVWNMTRRCNLKCVHCYAHAQDEEFKDEMSTEEGKALIDD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617   82 LAQYGAPVMLFSGGEPLVRQDLVELAKHATGRGMRAVISTNGTLITKEKARELKEVGLSYVGISLDGGEEVHDKFRAVPG 161
Cdd:TIGR04546  81 LAAFGAPVLLFSGGEPLMRKDLPELAAYAVSKGMRAVISTNGTLITKEKARELKEVGLSYVGISLDGGEEVHDRFRGVPG 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  162 SYRRALQGIENCKAEGLKVGLRFTINKRNQSEVPKLFQLLRDLEVPRICFYHLVYSGRGSELIKEDLDHAETRAIVDLIM 241
Cdd:TIGR04546 161 AFDAALKGIENCREEGIKVGLRFTINKRNVADIPAIFDLLEAEDIPRVCFYHLVYSGRGSKLVKEDLSHEETRATVDLIM 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  242 DKTRELFDAGLPKEVLTVDNHADGPYVWMRMLREDPKRAEEVFELLQYNEGNNSGRGIGCISWDGQVHADQFWRNHTFGN 321
Cdd:TIGR04546 241 DRTRDLFERGLPKEVLTVDNHADGPYLYLRMLKEDPKRAAEVLELLQMNEGNSSGRGIGCVSWDGEVHADQFWRHHSFGN 320

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  322 VLERPFSEIWDDPNIELLHKLKDKKKHVGGRCATCRYLNICGGNFRARAEAYYGDEWAQDPACYLTDDEI 391
Cdd:TIGR04546 321 VRERPFSEIWTDPSNELLARLKDKKPHVQGRCAACRWLDVCGGNFRARAEAVTGDLWAPDPACYLTDEEI 390
 
Name Accession Description Interval E-value
rSAM_ahbC_deAc TIGR04546
12,18-didecarboxysiroheme deacetylase; This model describes one of a pair of radical SAM ...
 2-391 0e+00

12,18-didecarboxysiroheme deacetylase; This model describes one of a pair of radical SAM enzymes involved in the alternative heme biosynthesis (ahb) pathway for heme b biosynthesis from siroheme. This anaerobic pathway occurs in sulfate-reducing bacteria and methanogens. A very similar pair of radical SAM enzymes (TIGR04054, TIGR04055) is involved in heme d1 biosynthesis in species such as Heliobacillus mobilis and Heliophilum fasciatum. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]


Pssm-ID: 275339 [Multi-domain]  Cd Length: 390  Bit Score: 809.04  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617    2 IGISKLYCGQVEPSDALRYGRNSGQLPSHLLQFSKDKKPVVVWNMTRRCNLKCVHCYAKAVDPEGKDEISTEQAKTIIDD 81
Cdd:TIGR04546   1 IGISKLYCGTVEPSDALRYGRHSGKLPSHLLQFSKDKKPVVVWNMTRRCNLKCVHCYAHAQDEEFKDEMSTEEGKALIDD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617   82 LAQYGAPVMLFSGGEPLVRQDLVELAKHATGRGMRAVISTNGTLITKEKARELKEVGLSYVGISLDGGEEVHDKFRAVPG 161
Cdd:TIGR04546  81 LAAFGAPVLLFSGGEPLMRKDLPELAAYAVSKGMRAVISTNGTLITKEKARELKEVGLSYVGISLDGGEEVHDRFRGVPG 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  162 SYRRALQGIENCKAEGLKVGLRFTINKRNQSEVPKLFQLLRDLEVPRICFYHLVYSGRGSELIKEDLDHAETRAIVDLIM 241
Cdd:TIGR04546 161 AFDAALKGIENCREEGIKVGLRFTINKRNVADIPAIFDLLEAEDIPRVCFYHLVYSGRGSKLVKEDLSHEETRATVDLIM 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  242 DKTRELFDAGLPKEVLTVDNHADGPYVWMRMLREDPKRAEEVFELLQYNEGNNSGRGIGCISWDGQVHADQFWRNHTFGN 321
Cdd:TIGR04546 241 DRTRDLFERGLPKEVLTVDNHADGPYLYLRMLKEDPKRAAEVLELLQMNEGNSSGRGIGCVSWDGEVHADQFWRHHSFGN 320

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  322 VLERPFSEIWDDPNIELLHKLKDKKKHVGGRCATCRYLNICGGNFRARAEAYYGDEWAQDPACYLTDDEI 391
Cdd:TIGR04546 321 VRERPFSEIWTDPSNELLARLKDKKPHVQGRCAACRWLDVCGGNFRARAEAVTGDLWAPDPACYLTDEEI 390
SkfB COG0535
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
 41-184 6.78e-63

Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, chromosome partitioning, Coenzyme transport and metabolism];


Pssm-ID: 440301 [Multi-domain]  Cd Length: 159  Bit Score: 198.97  E-value: 6.78e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  41 VVVWNMTRRCNLKCVHCYAKAvDPEGKDEISTEQAKTIIDDLAQYGAPVMLFSGGEPLVRQDLVELAKHATGRGMRAVIS 120
Cdd:COG0535    1 RLQIELTNRCNLRCKHCYADA-GPKRPGELSTEEAKRILDELAELGVKVVGLTGGEPLLRPDLFELVEYAKELGIRVNLS 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 499240617 121 TNGTLITKEKARELKEVGLSYVGISLDGGE-EVHDKFRAVPGSYRRALQGIENCKAEGLKVGLRF 184
Cdd:COG0535   80 TNGTLLTEELAERLAEAGLDHVTISLDGVDpETHDKIRGVPGAFDKVLEAIKLLKEAGIPVGINT 144
Radical_SAM pfam04055
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
 46-186 2.34e-27

Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual methylations, isomerization, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation.


Pssm-ID: 427681 [Multi-domain]  Cd Length: 159  Bit Score: 106.07  E-value: 2.34e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617   46 MTRRCNLKCVHCYAKAVDPEGK-DEISTEQAKTIIDDLAQYGAPVMLFSGGEPLVRQDLVE----LAKHATGRGMRAVIS 120
Cdd:pfam04055   1 ITRGCNLRCTYCAFPSIRARGKgRELSPEEILEEAKELKRLGVEVVILGGGEPLLLPDLVEllerLLKLELAEGIRITLE 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 499240617  121 TNGTLITKEKARELKEVGLSYVGISLDGGEEVHDKFRAVPGSYRRALQGIENCKAEGLKVGLRFTI 186
Cdd:pfam04055  81 TNGTLLDEELLELLKEAGLDRVSIGLESGDDEVLKLINRGHTFEEVLEALELLREAGIPVVTDNIV 146
SPASM_MftC-like cd21123
Iron-sulfur cluster-binding SPASM domain of mycofactocin radical SAM maturase MftC and similar ...
 290-385 3.21e-26

Iron-sulfur cluster-binding SPASM domain of mycofactocin radical SAM maturase MftC and similar proteins; This group is composed of Mycobacterium tuberculosis putative mycofactocin radical SAM maturase MftC and similar proteins. MftC is a radical S-adenosylmethionine (SAM) enzyme that may function to modify mycofactocin, a conserved polypeptide that might serve as an electron carrier. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster. This group appears to contain one auxillary Fe-S cluster that is similar to the second auxillary 4Fe-4S cluster (AuxII) of Clostridium perfringens anaerobic sulfatase-maturating enzyme (anSME).


Pssm-ID: 410614 [Multi-domain]  Cd Length: 91  Bit Score: 100.79  E-value: 3.21e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617 290 NEGNNSGRGIGCISWDGQVHADQFWrNHTFGNVLERPFSEIWDDpniELLHKLKDKKKHVGGRCATCRYLNICGGnFRAR 369
Cdd:cd21123    1 TGGCGAGRGIAFISPDGDVYPCGFL-PFSAGNVREDSFKDIWEN---SELFKKLRDREFLKGKCGKCKYRNVCGG-CRAR 75

                         90
                 ....*....|....*.
gi 499240617 370 AEAYYGDEWAQDPACY 385
Cdd:cd21123   76 AYAYTGDPLGEDPGCI 91
moaA PRK00164
GTP 3',8-cyclase MoaA;
47-179 4.33e-13

GTP 3',8-cyclase MoaA;


Pssm-ID: 234672 [Multi-domain]  Cd Length: 331  Bit Score: 69.40  E-value: 4.33e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  47 TRRCNLKCVHCYAKAVDP--EGKDEISTEQAKTIIDDLAQYGAPVMLFSGGEPLVRQDLVELAK--HATGRGMRAVISTN 122
Cdd:PRK00164  24 TDRCNFRCTYCMPEGYLPflPKEELLSLEEIERLVRAFVALGVRKVRLTGGEPLLRKDLEDIIAalAALPGIRDLALTTN 103

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 499240617 123 GTLITKeKARELKEVGLSYVGISLDGGEEvhDKFRAVPGSYR--RALQGIENCKAEGLK 179
Cdd:PRK00164 104 GYLLAR-RAAALKDAGLDRVNVSLDSLDP--ERFKAITGRDRldQVLAGIDAALAAGLT 159
Elp3 smart00729
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
 40-215 1.51e-09

Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases.


Pssm-ID: 214792 [Multi-domain]  Cd Length: 216  Bit Score: 57.41  E-value: 1.51e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617    40 PVVVWNMTRRCNLKCVHCYAKAVDPEGKDEiSTEQAKTIIDDLAQYGAPVML-----FSGGEPLVRQ-----DLVELAKH 109
Cdd:smart00729   1 PLALYIITRGCPRRCTFCSFPSLRGKLRSR-YLEALVREIELLAEKGEKEGLvgtvfIGGGTPTLLSpeqleELLEAIRE 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617   110 ATGRGMRA--VISTNGTLITKEKARELKEVGLSYVGISLDGG-EEVHDKFRAvPGSYRRALQGIENCKAEG-LKVGLRFT 185
Cdd:smart00729  80 ILGLAKDVeiTIETRPDTLTEELLEALKEAGVNRVSLGVQSGdDEVLKAINR-GHTVEDVLEAVELLREAGpIKVSTDLI 158

                          170       180       190
                   ....*....|....*....|....*....|..
gi 499240617   186 IN--KRNQSEVPKLFQLLRDLEVPRICFYHLV 215
Cdd:smart00729 159 VGlpGETEEDFEETLKLLKELGPDRVSIFPLS 190
rSAM_mat_DarW NF041300
radical SAM/SPASM peptide maturase DarW; DarW is a radical SAM/SPASM domain-containing peptide ...
 35-215 1.73e-09

radical SAM/SPASM peptide maturase DarW; DarW is a radical SAM/SPASM domain-containing peptide maturase most closely related to the darobactin maturase DarE.


Pssm-ID: 469197 [Multi-domain]  Cd Length: 415  Bit Score: 59.13  E-value: 1.73e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  35 SKDKKPVVVWNMTRRCNLKCVHCYAKAvdpEGKDEISTEQ--AKTIIDDLAQYGAPVMLF--SGGE-----PLVRQDLVE 105
Cdd:NF041300  36 SPARWLVVVLKATRLCNLRCTYCRSWA---EGPNQTMTFDvlARAVREALSMPGLHGVEFvwHGGEvtllkPKVFKKLIW 112

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617 106 LAKH--ATGRGMRAVISTNGTLITKEKARELKEVGLSyVGISLDGGEEVHDKFRAVPG---SYRRALQGIENCKAEGLKV 180
Cdd:NF041300 113 LQQQfrQPGQEVRNSIQTNATHLTDEWIEFLSELGMG-VGVSIDGPPEVHDRRRLDKDgrpTSSRVAGGIARLRQAGIPH 191

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 499240617 181 GLRFTINKRNQSEVP-KLFQLLRDLEVPRICFYHLV 215
Cdd:NF041300 192 GALVVVDRELIDAGAeRLLGYLAEIGLDKISFLNVL 227
N_Twi_rSAM NF033640
twitch domain-containing radical SAM protein; Members of this family are unusual among radical ...
 50-213 1.64e-07

twitch domain-containing radical SAM protein; Members of this family are unusual among radical SAM proteins in several ways. First, the N-terminal region consists of an iron-sulfur cluster-binding twitch domain (half of a SPASM domain), something usually found C-terminal to the radical SAM domain. Second, the radical SAM domains in many of the members of this family score poorly vs. the Pfam HMM, PF04055 (version 19), used to identify radical SAM. Lastly, the majority of members sequenced to date come from uncultured bacteria from marine or aquifer sources rather than from conventionally cultured bacterial isolates. The function is unknown.


Pssm-ID: 468123 [Multi-domain]  Cd Length: 396  Bit Score: 52.66  E-value: 1.64e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  50 CNLKCVHCYA-------------KAVDPEGKDEISTEQAKTIIDDLAQYgAP---VMLFSGGEPLVR-------QDLVE- 105
Cdd:NF033640 120 CNLKCRMCGPhsssswakeakklGGPKLGDKKKISWFEDEEFWKWLEEL-LPslkEIYFAGGEPLLIkehykllEKLVEk 198

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617 106 -LAKHatgrgMRAVISTNGTLITK------EKARELKEVGLSyvgISLDGGEEVHDKFRAvPGSYRRALQGIENCKAEGL 178
Cdd:NF033640 199 gRAKN-----IELRYNTNLTVLPDklkdllDLWKKFKSVSIS---ASIDGVGERNEYIRY-GSKWDEIEKNLKKLKEECP 269

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 499240617 179 KVGLRF--TINKRNQSEVPKLFQLLRDLEVPRICFYH 213
Cdd:NF033640 270 NVELRInpTVSALNVLHLPELLDWLLELGLGPIDIYL 306
 
Name Accession Description Interval E-value
rSAM_ahbC_deAc TIGR04546
12,18-didecarboxysiroheme deacetylase; This model describes one of a pair of radical SAM ...
 2-391 0e+00

12,18-didecarboxysiroheme deacetylase; This model describes one of a pair of radical SAM enzymes involved in the alternative heme biosynthesis (ahb) pathway for heme b biosynthesis from siroheme. This anaerobic pathway occurs in sulfate-reducing bacteria and methanogens. A very similar pair of radical SAM enzymes (TIGR04054, TIGR04055) is involved in heme d1 biosynthesis in species such as Heliobacillus mobilis and Heliophilum fasciatum. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]


Pssm-ID: 275339 [Multi-domain]  Cd Length: 390  Bit Score: 809.04  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617    2 IGISKLYCGQVEPSDALRYGRNSGQLPSHLLQFSKDKKPVVVWNMTRRCNLKCVHCYAKAVDPEGKDEISTEQAKTIIDD 81
Cdd:TIGR04546   1 IGISKLYCGTVEPSDALRYGRHSGKLPSHLLQFSKDKKPVVVWNMTRRCNLKCVHCYAHAQDEEFKDEMSTEEGKALIDD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617   82 LAQYGAPVMLFSGGEPLVRQDLVELAKHATGRGMRAVISTNGTLITKEKARELKEVGLSYVGISLDGGEEVHDKFRAVPG 161
Cdd:TIGR04546  81 LAAFGAPVLLFSGGEPLMRKDLPELAAYAVSKGMRAVISTNGTLITKEKARELKEVGLSYVGISLDGGEEVHDRFRGVPG 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  162 SYRRALQGIENCKAEGLKVGLRFTINKRNQSEVPKLFQLLRDLEVPRICFYHLVYSGRGSELIKEDLDHAETRAIVDLIM 241
Cdd:TIGR04546 161 AFDAALKGIENCREEGIKVGLRFTINKRNVADIPAIFDLLEAEDIPRVCFYHLVYSGRGSKLVKEDLSHEETRATVDLIM 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  242 DKTRELFDAGLPKEVLTVDNHADGPYVWMRMLREDPKRAEEVFELLQYNEGNNSGRGIGCISWDGQVHADQFWRNHTFGN 321
Cdd:TIGR04546 241 DRTRDLFERGLPKEVLTVDNHADGPYLYLRMLKEDPKRAAEVLELLQMNEGNSSGRGIGCVSWDGEVHADQFWRHHSFGN 320

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  322 VLERPFSEIWDDPNIELLHKLKDKKKHVGGRCATCRYLNICGGNFRARAEAYYGDEWAQDPACYLTDDEI 391
Cdd:TIGR04546 321 VRERPFSEIWTDPSNELLARLKDKKPHVQGRCAACRWLDVCGGNFRARAEAVTGDLWAPDPACYLTDEEI 390
rSAM_NirJ1 TIGR04054
putative heme d1 biosynthesis radical SAM protein NirJ1; Members of this radical SAM protein ...
 2-391 1.04e-180

putative heme d1 biosynthesis radical SAM protein NirJ1; Members of this radical SAM protein subfamily, designated NirJ1, occur in genomic contexts with a paralog NirJ2 and with other nitrite reductase operon genes associated with heme d1 biosynthesis, as in Heliobacillus mobilis and Heliophilum fasciatum. NirJ1 is presumed by bioinformatics analysis (Xiong, et al.) to be a heme d1 biosynthesis protein by context, perhaps involved in conversions of acetate groups to methyl groups in conversion from uroporphyrinogen III. A very closely related protein, involved in alternative heme b biosynthesis, occurs in Desulfovibrio and in methanogens. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]


Pssm-ID: 274946 [Multi-domain]  Cd Length: 387  Bit Score: 507.34  E-value: 1.04e-180
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617    2 IGISKLYCGQVEPSDALRYGRNSGQLPSHLlqfSKDKKPVVVWNMTRRCNLKCVHCYAKAVDPEGKDEISTEQAKTIIDD 81
Cdd:TIGR04054   1 ISITKLLCNTENFGDSLRYVHGAKGQKHGA---SPGHGPVVVWNCTRTCNLRCIHCYADSDNKKYEGELTTEEAKRFIDD 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617   82 LAQYGAPVMLFSGGEPLVRQDLVELAKHATGRGMRAVISTNGTLITKEKARELKEVGLSYVGISLDGGEEVHDKFRAVPG 161
Cdd:TIGR04054  78 LADFKVPVLLFSGGEPLMREDIFELAEYAKKRNIRSTISTNGTLIDKDVAKRLKKIGVGYVGISLDGIGENNDKFRGKKG 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  162 SYRRALQGIENCKAEGLKVGLRFTINKRNQSEVPKLFQLLRDLEVPRICFYHLVYSGRGSELIKEDLDHAETRAIVDLIM 241
Cdd:TIGR04054 158 AFDAALAGIRNCVAVGQKVGLRFTINRHNYKELEDIFDLIEEENIPRVCFYHLVYSGRGSKMVAEDISHEESRQAMDLIM 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  242 DKTRELFDAGLPKEVLTVDNHADGPYVWMRMLREDPKRAEEVFELLQYNEGNNSGRGIGCISWDGQVHADQFWRNHTFGN 321
Cdd:TIGR04054 238 ERTLDFHRRGLDKEILTVDNHADAVYLYLKLKKKDPDKADKILKLLKTNGGNRSGIAFANVDFKGNVHPDQFTQNHTFGN 317

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  322 VLERPFSEIWDDPNIELLHKLKDKKKHVGGRCATCRYLNICGGNFRARAEAYYGDEWAQDPACYLTDDEI 391
Cdd:TIGR04054 318 VRERKFGEIWTDLSNPILAGLKNRKPLLKGRCASCKWLNVCNGNFRTRAEAVTGDFWESDPACYLTDEEI 387
pseudo_SAM_Halo TIGR04347
pseudo-rSAM protein/SPASM domain protein; Members of this family all have a C-terminal SPASM ...
 2-391 5.82e-138

pseudo-rSAM protein/SPASM domain protein; Members of this family all have a C-terminal SPASM domain (see model TIGR04085), a region usually found as a C-terminal second 4Fe-4S domain of radical SAM domain (see pfam04055) proteins. A majority of rSAM/SPASM proteins modify ribosomally produced peptides. In a few members of this family, the key Cys residues of the radical SAM domain have been lost, making this a pseudo-rSAM family. Members of this family are restricted so far to Haloarchaea, always occur next a member of family TIGR04031, and are often accompanied by another rSAM/SPASM domain protein. The function of this two or three gene cassette is unknown.


Pssm-ID: 275143 [Multi-domain]  Cd Length: 390  Bit Score: 399.20  E-value: 5.82e-138
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617    2 IGISKLYCGQVEPSDALRYGRNSGQLPSHLLQfSKDKKPVVVWNMTRRCNLKCVHCYAKAvDPEGKD-EISTEQAKTIID 80
Cdd:TIGR04347   1 ISVSKLLCDLGAEGDGLRYDAADGADSEQITE-EKQRRPVVVWNTTRRCNLYCEHCYAGA-DTEAAPgELSTAEAKALLD 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617   81 DLAQYGAPVMLFSGGEPLVRQDLVELAKHATGRGMRAVISTNGTLITKEKARELKEVGLSYVGISLDGGEEVHDKFRAVP 160
Cdd:TIGR04347  79 DLADYGVPVILFSGGEPLVRDDLEELVAYAADAGIRPVLSTNGTLLTEERAEALRDAGLDYAGVSVDGLPERNDEFRGKD 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  161 GSYRRALQGIENCKAEGLKVGLRFTINKRNQSEVPKLFQLLRDLEVPRICFYHLVYSGRGSELIKEDLDHAETRAIVDLI 240
Cdd:TIGR04347 159 GAFDAAVRGIENCLDVGLKTGLRYTITEANAPDLEEVVDLLADVGLDRFCFYHLDYGGRGAEISDLDLDPAAQRRAVRRV 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  241 MDKTRELFDAGLPKEVLTVDNHADGPYVWMRMLRE-DPKRAEEVFELLQYNEGNNSGRGIGCISWDGQVHADQFWRNHTF 319
Cdd:TIGR04347 239 CDLTLEYHDRGEEIETLLVGNYADAAYIVEYAREElGEDRAEAIYRYLESNGGDPTGERVADVDYQGNVHLTQFWQGYSL 318

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 499240617  320 GNVLERPFSEIWDDPNIELLHKLKDKKKHVGGRCATCRYLNICGGNFRARAEAYYGDEWAQDPACYLTDDEI 391
Cdd:TIGR04347 319 GNVRDRPFGDIWEDESNPLLAKLRDREEHLTGKCADCQYKSICRGGSRLRALAAGGDLFAPDPQCYLTDEER 390
sam_11 TIGR04053
radical SAM protein, BA_1875 family; Members of this subfamily of the radical SAM domain ...
 37-384 4.14e-72

radical SAM protein, BA_1875 family; Members of this subfamily of the radical SAM domain superfamily show closer sequence relationships to peptide-modifying proteins of bacteriocin and PQQ biosynthesis than to other characterized radical SAM proteins. Within this subfamily, targets are likely to be diverse. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 274945 [Multi-domain]  Cd Length: 365  Bit Score: 229.87  E-value: 4.14e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617   37 DKKP-VVVWNMTRRCNLKCVHCYAKAVDPEGKDEISTEQAKTIIDDLAQYG--APVMLFSGGEPLVRQDLVELAKHATGR 113
Cdd:TIGR04053   4 NERPlIVIWEVTRACALACKHCRASAQPKPLPGELTTEEGKALLDQIAEFGdpYPLLVLTGGDPLMRPDLFELVDYATSL 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  114 GMRAVISTNGT-LITKEKARELKEVGLSYVGISLDGGE-EVHDKFRAVPGSYRRALQGIENCKAEGLKVGLRFTINKRNQ 191
Cdd:TIGR04053  84 GLRVSLSPSVTpNLTREAIAALKEAGVSAVSLSLDGATaETHDAFRGVPGSFDRTVNAIRAALELGIPVQINTTVTAENV 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  192 SEVPKLFQLLRDLEVPRICFYHLVYSGRGSELikEDLDHAETRAIVDLIMD-KTRELFD-----------AGLPKEVLTV 259
Cdd:TIGR04053 164 HELPDVAKLLKDLGVKLWSVFFLVPTGRGQAL--DDLTPEEAEDVLHWLYDvSDRYGFDvktteaphyrrVALQRKGLEK 241

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  260 DNHADGPYvwMRMLREDPKRA--EEVFELLQYNEGNNSGRGIGCISWDGQVHADQFWRNHTfGNVLERPFSEIW-DDPNI 336
Cdd:TIGR04053 242 DELRGGEL--YRQLTEKLTELlgEPVGRPPRRPMGTRDGNGFIFVSHTGDVYPSGFLPLSA-GNVREESLVEIYrESPLF 318

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*...
gi 499240617  337 ELLHKLKDkkkhVGGRCATCRYLNICGGNfRARAEAYYGDEWAQDPAC 384
Cdd:TIGR04053 319 KSLRDPDE----FKGKCGRCEFRHVCGGS-RARAYAVTGDPLAEDPAC 361
SkfB COG0535
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
 41-184 6.78e-63

Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, chromosome partitioning, Coenzyme transport and metabolism];


Pssm-ID: 440301 [Multi-domain]  Cd Length: 159  Bit Score: 198.97  E-value: 6.78e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  41 VVVWNMTRRCNLKCVHCYAKAvDPEGKDEISTEQAKTIIDDLAQYGAPVMLFSGGEPLVRQDLVELAKHATGRGMRAVIS 120
Cdd:COG0535    1 RLQIELTNRCNLRCKHCYADA-GPKRPGELSTEEAKRILDELAELGVKVVGLTGGEPLLRPDLFELVEYAKELGIRVNLS 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 499240617 121 TNGTLITKEKARELKEVGLSYVGISLDGGE-EVHDKFRAVPGSYRRALQGIENCKAEGLKVGLRF 184
Cdd:COG0535   80 TNGTLLTEELAERLAEAGLDHVTISLDGVDpETHDKIRGVPGAFDKVLEAIKLLKEAGIPVGINT 144
AslB COG0641
Sulfatase maturation enzyme AslB, radical SAM superfamily [Posttranslational modification, ...
 42-387 6.09e-50

Sulfatase maturation enzyme AslB, radical SAM superfamily [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440406 [Multi-domain]  Cd Length: 349  Bit Score: 171.71  E-value: 6.09e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  42 VVWNMTRRCNLKCVHCYAKAVDPEGKDEISTEQAKTIIDDLAQY---GAPVML-FSGGEPLVRQDL----VELAKHATGR 113
Cdd:COG0641    3 LVLKPTSRCNLRCSYCYYSEGDEGSRRRMSEETAEKAIDFLIESsgpGKELTItFFGGEPLLNFDFikeiVEYARKYAKK 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617 114 GM--RAVISTNGTLITKEKARELKEVGLSyVGISLDGGEEVHDKFRAVP---GSYRRALQGIENCKAEGLKVGLRFTINK 188
Cdd:COG0641   83 GKkiRFSIQTNGTLLDDEWIDFLKENGFS-VGISLDGPKEIHDRNRVTKngkGSFDRVMRNIKLLKEHGVEVNIRCTVTR 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617 189 RNQSEVPKLFQLLRDLEVPRICFYHLVYSGRGSELIK-EDLDHAEtraivdlimdktRELFDAGLpkevltvdnHADGPY 267
Cdd:COG0641  162 ENLDDPEELYDFLKELGFRSIQFNPVVEEGEADYSLTpEDYGEFL------------IELFDEWL---------ERDGGK 220

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617 268 VWMRMLREDPKRaeevfeLLQYNEGNNSGRGIG--CISWDGQVHA-DQFWRNHTF--GNVLERPFSEIWDDPNIELLHKL 342
Cdd:COG0641  221 IFVREFDILLAG------LLPPCSSPCVGAGGNylVVDPDGDIYPcDEFVGDPEFrlGNVFDGSLAELLDSPKLRAFGRE 294

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*.
gi 499240617 343 KDKKKHVGgrCATCRYLNICGGNFRARAEAYYGDEWA-QDPACYLT 387
Cdd:COG0641  295 KNVLLDEE--CRSCPYLPLCGGGCPANRYAETGDGFKpYSYYCELY 338
COG4001 COG4001
Uncharacterized conserved protein [Function unknown];
40-385 6.37e-39

Uncharacterized conserved protein [Function unknown];


Pssm-ID: 443181 [Multi-domain]  Cd Length: 491  Bit Score: 145.56  E-value: 6.37e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  40 PVVVWNMTRRCNLKCVHCYAKAVDPEgKDEISTEQAKTIIDDLAQYGAPVMLFSGGEPLVRQDLVELAKHATGRGMRAVI 119
Cdd:COG4001  120 FFVVWWNTTMCNLRCCHCYQEAGKPL-PDELTTEEKLKVIDDLDRAGVVAIALSGGEPTIHPDFFRILYAAASRGIYVAA 198

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617 120 STNGTLITKEKARELKEVGLSYVGISLDG--GEEVHDKFRAVPGSYRRALQGIENCKAEGLKVGLRFTINKRNQSEVPKL 197
Cdd:COG4001  199 ATNGTLIAAEKALEKKKAGGGYVVISSDGdaAPHEHDDFRRGGGGWRRAAVAANNAAVLGMNVAATTTTTTNNEDEVIDL 278

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617 198 FQLLRDLEVPRICFYHLVYSGRGSELIKEDLDHAETRA---IVDLIMDKTREL------FDAGLPKEVLTVDNHADGPYV 268
Cdd:COG4001  279 LLLAEEIGGKRVVFFFFVPGGGGKENIDDDLPPVEEEEfmrKIAYEMKRRPMIqvtttaPQYVVVAESESGGKSVAPHHH 358

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617 269 WMRmlreDPKRAEEVFELlqynEGNNSGRGIGCISWDGQVHADQFWRNhTFGNVLERPFSEIWDDPNIELLHKLKDKKKH 348
Cdd:COG4001  359 GGS----EEIIREAIAEF----GGGGGGGRIYAIIPEGGVVPPCFFPP-PVVGLRRIEFDDIWETWEKEFLLLRRRNLLL 429

                        330       340       350
                 ....*....|....*....|....*....|....*..
gi 499240617 349 VGGRCatCRYLNICGGNfRARAEAYYGDEWAQDPACY 385
Cdd:COG4001  430 GNCCC--CCYRCRCGGG-RRRAAYYYYDDLTDPPGCI 463
mycofact_rSAM TIGR03962
mycofactocin radical SAM maturase; Members of this family are uncharacterized radical SAM ...
 44-369 2.49e-34

mycofactocin radical SAM maturase; Members of this family are uncharacterized radical SAM proteins from the Mycobacterium tuberculosis and many other Actinobacteria, as well as some deltaproteobacteria (e.g. Geobacter uraniireducens), firmicutes (Pelotomaculum thermopropionicum and Desulfotomaculum acetoxidans), and Chloroflexi (Thermomicrobium roseum DSM 5159 and Sphaerobacter thermophilus DSM 20745). They resemble several characterized radical SAM enzymes of peptide modification (PqqE, AlbA), and are always found next to the proposed target, TIGR03969, the putative mycofactocin precursor. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 188477 [Multi-domain]  Cd Length: 339  Bit Score: 129.97  E-value: 2.49e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617   44 WNMTRRCNLKCVHCYAKA--VDPegkDEISTEQAKTIIDDLAQYGAPVMLFSGGEPLVRQDLVELAKHATGRGMRAVIST 121
Cdd:TIGR03962  16 WELTYACNLACVHCLSSSgkRDP---RELTTAECKRLIDELAAMQVFYVNIGGGEPTVRPDFWELMDYATAHGVGVKFST 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  122 NGTLITKEKARELKEVGLSYVGISLDGG-EEVHDKFRAvPGSYRRALQGIENCKAEGLK-VGLRFTINKRNQSEVPKLFQ 199
Cdd:TIGR03962  93 NGVRIDPEVADRLAATDYVDVQISLDGAtAEVNDAVRG-AGSFDLARRAMDNLAAAGFRgFKISVVLTRRNFGQLDEFYA 171

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  200 LLRD----LEVPRicfyhLVYSGRGSELIKEdldhaetraiVDLIMDKTRELFD--AGLPKEVLTVDNhadgpyvwmrml 273
Cdd:TIGR03962 172 LADRygaqLRLTR-----LRPSGRGADVWDE----------LHPTAAQQRQLYDwlVAHGERVLTGDS------------ 224

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  274 redpkraeeVFELLQYNE---GNN---SGRGIGCISWDGQVHADQFWRNHTF--GNVLERP-FSEIWDDPNIellhKLKD 344
Cdd:TIGR03962 225 ---------FFHLAALGQplpGLNmcgAGRVVCLIDPVGDVYACPFVIHEEFlaGNVREDGgFAGVWRTSPL----FRRL 291

                         330       340
                  ....*....|....*....|....*.
gi 499240617  345 KKKHVGGRCATCRYLNIC-GGNFRAR 369
Cdd:TIGR03962 292 REPQSGGACQSCSAYDSCrGGCMAAK 317
Radical_SAM pfam04055
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
 46-186 2.34e-27

Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual methylations, isomerization, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation.


Pssm-ID: 427681 [Multi-domain]  Cd Length: 159  Bit Score: 106.07  E-value: 2.34e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617   46 MTRRCNLKCVHCYAKAVDPEGK-DEISTEQAKTIIDDLAQYGAPVMLFSGGEPLVRQDLVE----LAKHATGRGMRAVIS 120
Cdd:pfam04055   1 ITRGCNLRCTYCAFPSIRARGKgRELSPEEILEEAKELKRLGVEVVILGGGEPLLLPDLVEllerLLKLELAEGIRITLE 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 499240617  121 TNGTLITKEKARELKEVGLSYVGISLDGGEEVHDKFRAVPGSYRRALQGIENCKAEGLKVGLRFTI 186
Cdd:pfam04055  81 TNGTLLDEELLELLKEAGLDRVSIGLESGDDEVLKLINRGHTFEEVLEALELLREAGIPVVTDNIV 146
SPASM_MftC-like cd21123
Iron-sulfur cluster-binding SPASM domain of mycofactocin radical SAM maturase MftC and similar ...
 290-385 3.21e-26

Iron-sulfur cluster-binding SPASM domain of mycofactocin radical SAM maturase MftC and similar proteins; This group is composed of Mycobacterium tuberculosis putative mycofactocin radical SAM maturase MftC and similar proteins. MftC is a radical S-adenosylmethionine (SAM) enzyme that may function to modify mycofactocin, a conserved polypeptide that might serve as an electron carrier. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster. This group appears to contain one auxillary Fe-S cluster that is similar to the second auxillary 4Fe-4S cluster (AuxII) of Clostridium perfringens anaerobic sulfatase-maturating enzyme (anSME).


Pssm-ID: 410614 [Multi-domain]  Cd Length: 91  Bit Score: 100.79  E-value: 3.21e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617 290 NEGNNSGRGIGCISWDGQVHADQFWrNHTFGNVLERPFSEIWDDpniELLHKLKDKKKHVGGRCATCRYLNICGGnFRAR 369
Cdd:cd21123    1 TGGCGAGRGIAFISPDGDVYPCGFL-PFSAGNVREDSFKDIWEN---SELFKKLRDREFLKGKCGKCKYRNVCGG-CRAR 75

                         90
                 ....*....|....*.
gi 499240617 370 AEAYYGDEWAQDPACY 385
Cdd:cd21123   76 AYAYTGDPLGEDPGCI 91
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
 44-214 9.23e-26

Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and MoaA, an enzyme of the biosynthesis of molybdopterin.


Pssm-ID: 100105 [Multi-domain]  Cd Length: 204  Bit Score: 103.18  E-value: 9.23e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  44 WNMTRRCNLKCVHCYAKA-VDPEGKDEISTEQAKTIIDDLAQYGAPVMLFSGGEPLVRQDLVELAKHA--TGRGMRAVIS 120
Cdd:cd01335    1 LELTRGCNLNCGFCSNPAsKGRGPESPPEIEEILDIVLEAKERGVEVVILTGGEPLLYPELAELLRRLkkELPGFEISIE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617 121 TNGTLITKEKARELKEVGLSYVGISLDGG-EEVHDKFRAVPGSYRRALQGIENCKAEGLKVGLRFTINKRNQSEVPKLFQ 199
Cdd:cd01335   81 TNGTLLTEELLKELKELGLDGVGVSLDSGdEEVADKIRGSGESFKERLEALKELREAGLGLSTTLLVGLGDEDEEDDLEE 160

                        170
                 ....*....|....*
gi 499240617 200 LLRDLEVPRICFYHL 214
Cdd:cd01335  161 LELLAEFRSPDRVSL 175
SCM_rSAM_ScmE TIGR04250
SynChlorMet cassette radical SAM/SPASM protein ScmE; A biosynthesis cassette found in ...
 45-384 7.92e-24

SynChlorMet cassette radical SAM/SPASM protein ScmE; A biosynthesis cassette found in Syntrophobacter fumaroxidans MPOB, Chlorobium limicola DSM 245, Methanocella paludicola SANAE, and delta proteobacterium NaphS2 contains two PqqE-like radical SAM/SPASM domain proteins, a PqqD homolog, and a conserved hypothetical protein. These components suggest modification of a ribosomally produced peptide precursor, but the precursor has not been identified. Of the two PqqE homologs of the cassette, this family is the closer in sequence.


Pssm-ID: 211973 [Multi-domain]  Cd Length: 358  Bit Score: 101.09  E-value: 7.92e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617   45 NMTRRCNLKCVHCYAKAVDPEGKDEISTEQAKTIIDDLAQYGAPVMLFSGGEPLVRQDLVELAKHATGRGMRAVISTNGT 124
Cdd:TIGR04250   8 DITGRCNLRCRYCSHFSSAAETPTDLETAEWLRFFRELNRCSVLRVVLSGGEPFMRSDFREIIDGIVKNRMRFSILSNGT 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  125 LITKEKARELKEVG-LSYVGISLDGG-EEVHDKFRAvPGSYRRALQGIENCKAEGLKVGLRFTINKRNQSEVPKLFQ-LL 201
Cdd:TIGR04250  88 LITDAIASFLAATRrCDYVQVSIDGStPGTHDRLRG-TGSFLQAVEGIELLRKHAIPVVVRVTIHRWNVDDLRPIAAlLL 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  202 RDLEVPRICFYHLVYSGrgseLIKEDLDHAE-TRAIVDLIMDKTRELfDAGLPKEVltvdNHADGPYvwmrmlrEDPKRA 280
Cdd:TIGR04250 167 DDLGLPAFSTNAASYMG----LCRSNTDDVQlDTAERTLAMEILLEL-EKEYPGRI----SASAGPL-------ADARTW 230

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  281 EEVFELLQYNEGNNSGRGI----GCISWDGQVHAD------QFWRNHTFGNVLERPFSEIW-DDPNIELLHKLKDKKKHV 349
Cdd:TIGR04250 231 ASMEQARIDQQGNMPGRGYlsgcGGIFMSLAVRADgvivpcNQLSHIELGRINRDSLRELWqNHPVLLQLRNRVTIPLTD 310

                         330       340       350
                  ....*....|....*....|....*....|....*.
gi 499240617  350 GGRCATCRYLNICGGNFRARAEAYYGDEWAQDP-AC 384
Cdd:TIGR04250 311 FEFCKDCDYIPYCTGNCPALAYTTFGEINHPSPdAC 346
SCM_rSAM_ScmF TIGR04251
SynChlorMet cassette radical SAM/SPASM protein ScmF; A biosynthesis cassette found in ...
 46-240 2.60e-21

SynChlorMet cassette radical SAM/SPASM protein ScmF; A biosynthesis cassette found in Syntrophobacter fumaroxidans MPOB, Chlorobium limicola DSM 245, Methanocella paludicola SANAE, and delta proteobacterium NaphS2 contains two PqqE-like radical SAM/SPASM domain proteins, a PqqD homolog, and a conserved hypothetical protein. These components suggest modification of a ribosomally produced peptide precursor, but the precursor has not been identified. Of the two PqqE homologs of the cassette, this family is the more distant in sequence.


Pssm-ID: 211974 [Multi-domain]  Cd Length: 353  Bit Score: 94.13  E-value: 2.60e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617   46 MTRRCNLKCVHCYakaVDPEGKDEISTEQA------KTIIDDLAQYGAPVMLFSGGEPLVRQDLVELAKHATGRGMRAVI 119
Cdd:TIGR04251  10 LTEGCNLKCRHCW---IDPKYQGEGEQHPSldpslfRSIIRQAIPLGLTSVKLTGGEPLLHPAIGEILECIGENNLQLSV 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  120 STNGTLITKEKARELKEVGLSYVGISLDGGE-EVHDKFRAVPGSYRRALQGIENCKAEGLKVGLRFTINKRNQSEVPKLF 198
Cdd:TIGR04251  87 ETNGLLCTPQTARDLASCETPFVSVSLDGVDaATHDWMRGVKGAFDKAVRGIHNLVEAGIHPQIIMTVTRRNVGQMEQIV 166

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 499240617  199 QLLRDLEVPRICFYHLVYSGRGSELIKEdldhAETRAIVDLI 240
Cdd:TIGR04251 167 RLAESLGAESVKFNHVQPTSRGSKMHEN----GETLSIGELV 204
MoaA2 COG1964
C-terminal domain of the GTP 3',8'-cyclase MoaA, radical SAM superfamily (molybdenum cofactor ...
 47-188 2.99e-16

C-terminal domain of the GTP 3',8'-cyclase MoaA, radical SAM superfamily (molybdenum cofactor biosynthesis) [Coenzyme transport and metabolism];


Pssm-ID: 441567 [Multi-domain]  Cd Length: 473  Bit Score: 79.92  E-value: 2.99e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  47 TRRCNLKCVHCYAKAvDPEGKDEISTEQAKTIIDDL-AQYG-APVMLFSGGEPLVRQDLVELAKHATGRGMRAV-ISTNG 123
Cdd:COG1964  102 TNRCNLNCPICFANS-GPGYGYEPSLEEIEKMLDALvREEGePDVVQFSGGEPTVHPDLFEILDLAKERPIKHVmINTNG 180

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499240617 124 TLITK--EKARELKEVG-LSYVGISLDG-GEEVHDKFRAVPGSYRRaLQGIENCKAEGLKVGLRFTINK 188
Cdd:COG1964  181 IRIAKdpDFAERLAEAGpLFEVYLQFDGlSDEPYRRLRGADLLEVK-LKAIENLRKAGISTTLVPTLVK 248
MoaA COG2896
GTP 3',8-cyclase (molybdenum cofactor biosynthesis protein MoaA) [Coenzyme transport and ...
 47-179 5.89e-14

GTP 3',8-cyclase (molybdenum cofactor biosynthesis protein MoaA) [Coenzyme transport and metabolism]; GTP 3',8-cyclase (molybdenum cofactor biosynthesis protein MoaA) is part of the Pathway/BioSystem: Molybdopterin biosynthesis


Pssm-ID: 442141 [Multi-domain]  Cd Length: 329  Bit Score: 72.02  E-value: 5.89e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  47 TRRCNLKCVHCYAK-AVDPEGKDEI-STEQaktiIDDLAQygapvmLFS----------GGEPLVRQDLVELAK--HATG 112
Cdd:COG2896   21 TDRCNFRCTYCMPEeGYQFLPKEELlSFEE----IERLVR------AFVelgvrkirltGGEPLLRKDLPELIArlAALP 90

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499240617 113 RGMRAVISTNGTLItKEKARELKEVGLSYVGISLDGGEEvhDKFRAVP--GSYRRALQGIENCKAEGLK 179
Cdd:COG2896   91 GIEDLALTTNGSLL-ARYAEALKAAGLDRVNVSLDSLDP--ERFRRITrrDDLDKVLAGIDAALAAGLT 156
moaA PRK00164
GTP 3',8-cyclase MoaA;
47-179 4.33e-13

GTP 3',8-cyclase MoaA;


Pssm-ID: 234672 [Multi-domain]  Cd Length: 331  Bit Score: 69.40  E-value: 4.33e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  47 TRRCNLKCVHCYAKAVDP--EGKDEISTEQAKTIIDDLAQYGAPVMLFSGGEPLVRQDLVELAK--HATGRGMRAVISTN 122
Cdd:PRK00164  24 TDRCNFRCTYCMPEGYLPflPKEELLSLEEIERLVRAFVALGVRKVRLTGGEPLLRKDLEDIIAalAALPGIRDLALTTN 103

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 499240617 123 GTLITKeKARELKEVGLSYVGISLDGGEEvhDKFRAVPGSYR--RALQGIENCKAEGLK 179
Cdd:PRK00164 104 GYLLAR-RAAALKDAGLDRVNVSLDSLDP--ERFKAITGRDRldQVLAGIDAALAAGLT 159
rSAM_skfB TIGR04403
sporulation killing factor system radical SAM maturase; Members of this family are a radical ...
 46-194 7.33e-12

sporulation killing factor system radical SAM maturase; Members of this family are a radical SAM enzyme of post-translational modification of ribosomally translated peptides. In Bacillus subtilis, the enzyme SkfB creates a sactipeptide (sulfur-to-alpha-carbon) crosslink of Cys-4 to Met-12 of the mature form of sporulation killing factor (SkfA). In Paenibacillus larvae subsp. larvae B-3650, the Met is replaced by Leu, so the modification must be different. SkfB has 2 4Fe-4S clusters, one in its radical SAM domain (pfam04055) and one in a region that somewhat resembles the SPASM domain (TIGR04085).


Pssm-ID: 275196 [Multi-domain]  Cd Length: 402  Bit Score: 66.49  E-value: 7.33e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617   46 MTRRCNLKCVHCYAKAVDPEgKDEISTEQAKTIIDDLAQYGAPVMLFSGGEPLVRQDLVELAKHATGRGMRAVISTNGTL 125
Cdd:TIGR04403 110 LTNACNLSCSFCYASSGKPY-PEELATDQWIQVMQKLAAVGVADVTLTGGEAKLIKGFKEIVTVASSLFTNVNVFSNGLN 188

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499240617  126 ITKEKARELKEVGLSYVGISLDGGEEVHDKFRAVPGSYRRALQGIENCKAEGLKVGLRFTINKRNQSEV 194
Cdd:TIGR04403 189 WRDEEVELLSHLGNVSVQISIDGTPETHNLLRGRKGAFEESMNTIKRLAEANIPVIVAMTINEKNADTV 257
PRK13745 PRK13745
anaerobic sulfatase-maturation protein;
50-215 9.07e-12

anaerobic sulfatase-maturation protein;


Pssm-ID: 237489 [Multi-domain]  Cd Length: 412  Bit Score: 66.04  E-value: 9.07e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  50 CNLKCVHCY----AKAVDPEGKDEISTEQAKTIIDDLAQYGA-PVMLFS--GGEPLVR-----QDLVELA-KHATGRGMR 116
Cdd:PRK13745  24 CNLACDYCYylekSKLYQENPKHVMSDELLEKFIKEYINSQTmPQVLFTwhGGETLMRplsfyKKALELQkKYARGRQID 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617 117 AVISTNGTLITKEKARELKEVGLsYVGISLDGGEEVHDKFR----AVPgSYRRALQGIENCKAEGLKVGLRFTINKRNQS 192
Cdd:PRK13745 104 NCIQTNGTLLTDEWCEFFRENNF-LVGVSIDGPQEFHDEYRknkmGKP-SFVKVMKGINLLKKHGVEWNAMAVVNDFNAD 181

                        170       180
                 ....*....|....*....|...
gi 499240617 193 EVPKLFQLLRDLEVPRICFYHLV 215
Cdd:PRK13745 182 YPLDFYHFFKELDCHYIQFAPIV 204
PLN02951 PLN02951
Molybderin biosynthesis protein CNX2
 46-156 1.92e-11

Molybderin biosynthesis protein CNX2


Pssm-ID: 215513 [Multi-domain]  Cd Length: 373  Bit Score: 64.78  E-value: 1.92e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  46 MTRRCNLKCVHCY-AKAVDPEGKDEI-STEQAKTIIDDLAQYGAPVMLFSGGEPLVRQDLVELAKHATG-RGMRAV-IST 121
Cdd:PLN02951  64 LTERCNLRCQYCMpEEGVELTPKSHLlSQDEIVRLAGLFVAAGVDKIRLTGGEPTLRKDIEDICLQLSSlKGLKTLaMTT 143

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 499240617 122 NGTLITKeKARELKEVGLSYVGISLDggEEVHDKF 156
Cdd:PLN02951 144 NGITLSR-KLPRLKEAGLTSLNISLD--TLVPAKF 175
SAM_SPASM_FxsB TIGR04269
radical SAM/SPASM domain protein, FxsB family; This model describes a radical SAM (pfam04055) ...
 49-211 3.02e-11

radical SAM/SPASM domain protein, FxsB family; This model describes a radical SAM (pfam04055)/SPASM domain (TIGR04085) fusion subfamily distinct from PqqE, MftC, anaerobic sulfatase maturases, and other peptide maturases. The combined region described in this model can itself be fused to another domain, such as TIGR04267, or stand alone. Members occurring in the same cassette as a member of family TIGR04268 should be designated FxsB.


Pssm-ID: 275093 [Multi-domain]  Cd Length: 363  Bit Score: 64.37  E-value: 3.02e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617   49 RCNLKCVHCYAKavdpEGKDE--------ISTEQAKTIIDDLAQYGAPVML------FSGGEPL------VRQDLVELAK 108
Cdd:TIGR04269  11 RCDLACDHCYVY----EHADQswrarpkvMSAETRRAFARRLAEHAAAHDLpsvaviLHGGEPLlagaerLRAFAAELRS 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  109 HATGR-GMRAVISTNGTLITKEKARELKEVGLSyVGISLDGGEEVHDK---FRAVPGSYRRALQGIENCKAE---GLKVG 181
Cdd:TIGR04269  87 ALDPVtALDLRLQTNGVLLDDEALDLLVEHDIG-VGVSLDGDRAANDRhrlTRDGRSSHDQVLRALELLRRPeyrHLFAG 165

                         170       180       190
                  ....*....|....*....|....*....|
gi 499240617  182 LRFTINKRNQSEVpkLFQLLRDLEVPRICF 211
Cdd:TIGR04269 166 LLCTVDVANDPVA--VYEALAALDPPRIDF 193
PflA COG1180
Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, ...
 50-213 4.01e-11

Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440793 [Multi-domain]  Cd Length: 242  Bit Score: 62.51  E-value: 4.01e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  50 CNLKCVHCY----AKAVDPEGKDEISTEQaktIIDDLAQY-----GAPVMLFSGGEPLVRQD-LVELAKHATGRGMRAVI 119
Cdd:COG1180   31 CNLRCPYCHnpeiSQGRPDAAGRELSPEE---LVEEALKDrgfldSCGGVTFSGGEPTLQPEfLLDLAKLAKELGLHTAL 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617 120 STNGTlITKEKARELKEVgLSYVGISLDGGEEvhDKFRAVPG-SYRRALQGIENCKAEGLKVGLRFT-INKRNQS--EVP 195
Cdd:COG1180  108 DTNGY-IPEEALEELLPY-LDAVNIDLKAFDD--EFYRKLTGvSLEPVLENLELLAESGVHVEIRTLvIPGLNDSeeELE 183

                        170       180
                 ....*....|....*....|.
gi 499240617 196 KLFQLLRDL-EVPRICF--YH 213
Cdd:COG1180  184 AIARFIAELgDVIPVHLlpFH 204
TM0948 COG5014
Uncharacterized conserved protein TM0948, MoaA-related, radical SAM superfamily [General ...
 50-184 3.97e-10

Uncharacterized conserved protein TM0948, MoaA-related, radical SAM superfamily [General function prediction only];


Pssm-ID: 444038  Cd Length: 261  Bit Score: 60.00  E-value: 3.97e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  50 CNLKCVHCYA---KAVDPEGKDEISTEQAKTIIDDLA-QYGAPVMLFSGGEP-LVRQDLVELAKHATGRGMRAVISTNGT 124
Cdd:COG5014   50 CNLRCGFCWSwrfRDFPLTIGKFYSPEEVAERLIEIArERGYRQVRLSGGEPtIGFEHLLKVLELFSERGLTFILETNGI 129

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 499240617 125 LIT--KEKARELKEVGLSYVGISLDG--GEEVHDKFRAVPGSYRRALQGIENCKAEGLKVGLRF 184
Cdd:COG5014  130 LIGydRELARELASFRNIVVRVSIKGctPEEFSMLTGADPEFFELQLRALKNLVDAGLEPGREV 193
NrdG2 TIGR02495
anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of ...
 24-189 6.61e-10

anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of the radical-SAM family (pfam04055). It is often gene clustered with the class III (anaerobic) ribonucleotide triphosphate reductase (NrdD, TIGR02487) and presumably fulfills the identical function as NrdG, which utilizes S-adenosyl methionine, an iron-sulfur cluster and a reductant (dihydroflavodoxin) to produce a glycine-centered radical in NrdD. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism, Protein fate, Protein modification and repair]


Pssm-ID: 274164 [Multi-domain]  Cd Length: 192  Bit Score: 58.14  E-value: 6.61e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617   24 SGQLPSHLLQFSkDKKPVVVWnmTRRCNLKCVHCYAKAV-DPEGKDEISTEQaktIIDDLAQYGAPV--MLFSGGEPLVR 100
Cdd:TIGR02495   3 AGLVPFSTVDYP-GKLAFTIF--LQGCNLKCPYCHNPLLiPRRGSGEIEVEE---LLEFLRRRRGLLdgVVITGGEPTLQ 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  101 QDLVELAKHATGRGMRAVISTNGTliTKEKARELKEVGL-SYVGISLDGGEEVHDKFRAVPGSY--RRALQGIENCKAEG 177
Cdd:TIGR02495  77 AGLPDFLREVRELGFEVKLDTNGS--NPRRLEELLEEGLvDYVAMDVKAPPEKYGELYGLEKNGaaKNILKSLEILLESG 154

                         170
                  ....*....|..
gi 499240617  178 LKVGLRFTINKR 189
Cdd:TIGR02495 155 IPFELRTTVVRG 166
Fer4_12 pfam13353
4Fe-4S single cluster domain; This family includes proteins containing domains which bind to ...
 50-148 6.73e-10

4Fe-4S single cluster domain; This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich.


Pssm-ID: 433138 [Multi-domain]  Cd Length: 137  Bit Score: 56.80  E-value: 6.73e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617   50 CNLKCVHCYAKAV-DPEGKDEISTEQAKTIIDDLAQYGAPVMLFSGGEPLVRQD-LVELAKHATGRGMRAVI-STNGTLI 126
Cdd:pfam13353  15 CNHHCKGCFNPETwDFKYGKPFTEELEDEIIEDLAKPYIQGLTLSGGEPLLNAEaLLELVKRVREECPEKDIwLWTGYTF 94

                          90       100
                  ....*....|....*....|..
gi 499240617  127 TKEKARELKEVgLSYVGISLDG 148
Cdd:pfam13353  95 EELQSKDQLEL-LKLIDVLVDG 115
PRK13758 PRK13758
anaerobic sulfatase-maturase; Provisional
 50-203 1.19e-09

anaerobic sulfatase-maturase; Provisional


Pssm-ID: 172296 [Multi-domain]  Cd Length: 370  Bit Score: 59.54  E-value: 1.19e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  50 CNLKCVHCY------AKAVDPEG--KDEISTEQAKTIIDDLAQYGApvMLFSGGEPLVR-----QDLVELAKHATGRGMR 116
Cdd:PRK13758  15 CNLKCTYCFyhslsdNRNVKSYGimRDEVLESMVKRVLNEAEGHCS--FAFQGGEPTLAgleffEELMELQRKHNYKNLK 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617 117 AV--ISTNGTLITKEKARELKEVGLsYVGISLDGGEEVHDKFR---AVPGSYRRALQGIENCKAEGLKVGLRFTINKRNQ 191
Cdd:PRK13758  93 IYnsLQTNGTLIDESWAKFLSENKF-LVGLSMDGPKEIHNLNRkdcCGLDTFSKVERAAELFKKYKVEFNILCVVTSNTA 171

                        170
                 ....*....|..
gi 499240617 192 SEVPKLFQLLRD 203
Cdd:PRK13758 172 RHVNKIYKYFKE 183
Elp3 smart00729
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
 40-215 1.51e-09

Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases.


Pssm-ID: 214792 [Multi-domain]  Cd Length: 216  Bit Score: 57.41  E-value: 1.51e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617    40 PVVVWNMTRRCNLKCVHCYAKAVDPEGKDEiSTEQAKTIIDDLAQYGAPVML-----FSGGEPLVRQ-----DLVELAKH 109
Cdd:smart00729   1 PLALYIITRGCPRRCTFCSFPSLRGKLRSR-YLEALVREIELLAEKGEKEGLvgtvfIGGGTPTLLSpeqleELLEAIRE 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617   110 ATGRGMRA--VISTNGTLITKEKARELKEVGLSYVGISLDGG-EEVHDKFRAvPGSYRRALQGIENCKAEG-LKVGLRFT 185
Cdd:smart00729  80 ILGLAKDVeiTIETRPDTLTEELLEALKEAGVNRVSLGVQSGdDEVLKAINR-GHTVEDVLEAVELLREAGpIKVSTDLI 158

                          170       180       190
                   ....*....|....*....|....*....|..
gi 499240617   186 IN--KRNQSEVPKLFQLLRDLEVPRICFYHLV 215
Cdd:smart00729 159 VGlpGETEEDFEETLKLLKELGPDRVSIFPLS 190
rSAM_mat_DarW NF041300
radical SAM/SPASM peptide maturase DarW; DarW is a radical SAM/SPASM domain-containing peptide ...
 35-215 1.73e-09

radical SAM/SPASM peptide maturase DarW; DarW is a radical SAM/SPASM domain-containing peptide maturase most closely related to the darobactin maturase DarE.


Pssm-ID: 469197 [Multi-domain]  Cd Length: 415  Bit Score: 59.13  E-value: 1.73e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  35 SKDKKPVVVWNMTRRCNLKCVHCYAKAvdpEGKDEISTEQ--AKTIIDDLAQYGAPVMLF--SGGE-----PLVRQDLVE 105
Cdd:NF041300  36 SPARWLVVVLKATRLCNLRCTYCRSWA---EGPNQTMTFDvlARAVREALSMPGLHGVEFvwHGGEvtllkPKVFKKLIW 112

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617 106 LAKH--ATGRGMRAVISTNGTLITKEKARELKEVGLSyVGISLDGGEEVHDKFRAVPG---SYRRALQGIENCKAEGLKV 180
Cdd:NF041300 113 LQQQfrQPGQEVRNSIQTNATHLTDEWIEFLSELGMG-VGVSIDGPPEVHDRRRLDKDgrpTSSRVAGGIARLRQAGIPH 191

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 499240617 181 GLRFTINKRNQSEVP-KLFQLLRDLEVPRICFYHLV 215
Cdd:NF041300 192 GALVVVDRELIDAGAeRLLGYLAEIGLDKISFLNVL 227
rSAM_more_4Fe4S TIGR04085
radical SAM additional 4Fe4S-binding SPASM domain; This domain contains regions binding ...
 296-384 3.20e-08

radical SAM additional 4Fe4S-binding SPASM domain; This domain contains regions binding additional 4Fe4S clusters found in various radical SAM proteins C-terminal to the domain described by model pfam04055. Radical SAM enzymes with this domain tend to be involved in protein modification, including anaerobic sulfatase maturation proteins, a quinohemoprotein amine dehydrogenase biogenesis protein, the Pep1357-cyclizing radical SAM enzyme, and various bacteriocin biosynthesis proteins. The motif CxxCxxxxxCxxxC is nearly invariant for members of this family, although PqqE has a variant form. We name this domain SPASM for Subtilosin, PQQ, Anaerobic Sulfatase, and Mycofactocin.


Pssm-ID: 274968 [Multi-domain]  Cd Length: 93  Bit Score: 50.65  E-value: 3.20e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  296 GRGIGCISWDGQVHADQFW--RNHTFGNVLERPFSEIWDDPNIELLHKLKDKKKHvgGRCATCRYLNICGGNFRARAEAY 373
Cdd:TIGR04085   4 GRNSLVVDPDGDVYPCDHFvyPEYKLGNIREDSLEEILNSSKQLEFGRWKSPKLP--EECRSCKYLPLCGGGCPANRYLK 81

                          90
                  ....*....|..
gi 499240617  374 YGDEWA-QDPAC 384
Cdd:TIGR04085  82 TGDINGpKNPLC 93
rSAM_pep_methan TIGR04083
putative peptide-modifying radical SAM enzyme, Mhun_1560 family; Members of this family are ...
 50-193 3.64e-08

putative peptide-modifying radical SAM enzyme, Mhun_1560 family; Members of this family are radical SAM enzymes, homologous to a variety of other peptide-modifying radical SAM, and found primarily in methanogenic archaea.


Pssm-ID: 274966 [Multi-domain]  Cd Length: 376  Bit Score: 54.73  E-value: 3.64e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617   50 CNLKCVHCYAKAvdpEGKDEISTEQAKTIIDDLAQY-GAPVML-FSGGEPLV------RQDLVELAKHATGRGMRAVIST 121
Cdd:TIGR04083  10 CPSKCKYCWSSE---ETSPVMSIDTVKDIVEWLKDFrDDRVTFtFHGGEPLLagadfyRQALPLLSEGLAHLKPEFAMQT 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 499240617  122 NGTLITKEKARELKEVGLSyVGISLDGGEEVHDKFRAvPGSYRRALQGIENCKAEGLKVglRFTINKRNQSE 193
Cdd:TIGR04083  87 NLWLMTPELAEIFAEYNVP-IGSSIDGPEEINDYQRG-EGYYQKTMKGYEIAKEHGLDV--RFICTFTSYSV 154
QueE COG0602
Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]; Organic ...
 50-125 7.38e-08

Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]; Organic radical activating enzyme NrdG/QueE is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440367 [Multi-domain]  Cd Length: 205  Bit Score: 52.45  E-value: 7.38e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499240617  50 CNLKCVHC---YAkaVDPEGKDEISTEQaktIIDDLAQYGAPVMLFSGGEPLVRQDLVELAKHATGRGMRAVISTNGTL 125
Cdd:COG0602   30 CNLRCSWCdtkYA--WDGEGGKRMSAEE---ILEEVAALGARHVVITGGEPLLQDDLAELLEALKDAGYEVALETNGTL 103
rSAM_Cxxx_rpt TIGR04115
radical SAM peptide maturase, CXXX-repeat target family; Members of this radical SAM domain ...
 42-190 9.81e-08

radical SAM peptide maturase, CXXX-repeat target family; Members of this radical SAM domain protein are predicted peptide maturases, similar to PqqE, AlbA, the mycofactocin radical SAM maturase, and many others that share the peptide modification radical SAM protein C-terminal additional 4Fe4S-binding domain (TIGR04085). Members co-occur with a protein of unknown function that may be a chaperone or immunity protein and with a peptide that may have twelve or more cysteines occurring regularly spaced every fourth residue. These Cys residues tend to be flanked by residues with small side chains that provide minimal steric hindrance to crosslink formation by the radical SAM enzyme as in the subtilosin A system.


Pssm-ID: 200366 [Multi-domain]  Cd Length: 359  Bit Score: 53.35  E-value: 9.81e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617   42 VVWNMTRRCNLKCVHCYakAVDPEGKDEISTEQAKTIIDDL----AQYGAPVML--FSGGEPLVRQDLVELAKHATGRGM 115
Cdd:TIGR04115   4 ITFIVTDDCQLACKYCY--QTGKNKNKRMSFETAKKAVDYIlsgnKGFGEPSVIwdFIGGEPLLEIELIDRICDYIKNRM 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  116 -----------RAVISTNGTLITKEKAREL--KEVGLSYVGISLDGGEEVHDKFRAVP---GSYRRALQGIENCKAEGLK 179
Cdd:TIGR04115  82 ielnhpwfnsyRFSFSTNGVCYFEEKVQRFiqKNNQHLSISITIDGTKEKHDSCRVFPdgrGSYDLVVSNAPLWLNQFPY 161

                         170
                  ....*....|.
gi 499240617  180 VGLRFTINKRN 190
Cdd:TIGR04115 162 ASTKVTIAPAD 172
N_Twi_rSAM NF033640
twitch domain-containing radical SAM protein; Members of this family are unusual among radical ...
 50-213 1.64e-07

twitch domain-containing radical SAM protein; Members of this family are unusual among radical SAM proteins in several ways. First, the N-terminal region consists of an iron-sulfur cluster-binding twitch domain (half of a SPASM domain), something usually found C-terminal to the radical SAM domain. Second, the radical SAM domains in many of the members of this family score poorly vs. the Pfam HMM, PF04055 (version 19), used to identify radical SAM. Lastly, the majority of members sequenced to date come from uncultured bacteria from marine or aquifer sources rather than from conventionally cultured bacterial isolates. The function is unknown.


Pssm-ID: 468123 [Multi-domain]  Cd Length: 396  Bit Score: 52.66  E-value: 1.64e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  50 CNLKCVHCYA-------------KAVDPEGKDEISTEQAKTIIDDLAQYgAP---VMLFSGGEPLVR-------QDLVE- 105
Cdd:NF033640 120 CNLKCRMCGPhsssswakeakklGGPKLGDKKKISWFEDEEFWKWLEEL-LPslkEIYFAGGEPLLIkehykllEKLVEk 198

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617 106 -LAKHatgrgMRAVISTNGTLITK------EKARELKEVGLSyvgISLDGGEEVHDKFRAvPGSYRRALQGIENCKAEGL 178
Cdd:NF033640 199 gRAKN-----IELRYNTNLTVLPDklkdllDLWKKFKSVSIS---ASIDGVGERNEYIRY-GSKWDEIEKNLKKLKEECP 269

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 499240617 179 KVGLRF--TINKRNQSEVPKLFQLLRDLEVPRICFYH 213
Cdd:NF033640 270 NVELRInpTVSALNVLHLPELLDWLLELGLGPIDIYL 306
SPASM_AlbA-like cd21125
Iron-sulfur cluster-binding SPASM domain of antilisterial bacteriocin subtilosin biosynthesis ...
 298-387 3.10e-06

Iron-sulfur cluster-binding SPASM domain of antilisterial bacteriocin subtilosin biosynthesis protein AlbA and similar proteins; Bacillus subtilis antilisterial bacteriocin subtilosin biosynthesis protein AlbA is a radical S-adenosylmethionine (SAM) enzyme that catalyzes the formation of three thioether bonds in the post-translational modification of a linear peptide into the cyclic peptide subtilosin A. The thioether bonds formed are between the sulfur of three cysteine residues and the alpha-carbons of two phenylalanines and one threonine to produce a rigid cyclic peptide. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster. AlbA appears to contain one auxillary Fe-S cluster, similar to the auxillary 4Fe-4S cluster in Bacillus circulans butirosin biosynthetic enzyme BtrN.


Pssm-ID: 410616 [Multi-domain]  Cd Length: 97  Bit Score: 45.17  E-value: 3.10e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617 298 GIGC----ISWDGQV------HADQFwrnhTFGNVLERPFSEIWDDPNIELLHKLKDKKkhvGGRCATCRYLNICGGNFR 367
Cdd:cd21125    4 GAGWksivIDPDGEVypchllHPTEF----KLGNIFEDSLASILKNPVLEIWQTYDPRF---SEHCKKCPFYGICGGGCI 76

                         90       100
                 ....*....|....*....|
gi 499240617 368 ARAEAYYGDEWAQDPACYLT 387
Cdd:cd21125   77 AKSLISYGRFDKPDPYCSLT 96
Tyw1 COG0731
Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily [Translation, ribosomal ...
 45-177 3.97e-06

Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily [Translation, ribosomal structure and biogenesis]; Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440495 [Multi-domain]  Cd Length: 248  Bit Score: 47.88  E-value: 3.97e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  45 NMT--RRCNLKCVHC---YAKAVDPEGKDEISTEQaktIIDDLAQY------GAP---VMLFSG-GEPLVRQDLVELAKH 109
Cdd:COG0731   27 NLIpnKTCNFDCVYCqrgRTTDLTRERREFDDPEE---ILEELIEFlrklpeEARepdHITFSGsGEPTLYPNLGELIEE 103

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 499240617 110 A-TGRGMRAVISTNGTLITKEKARE-LKEVGLSYVgiSLDGG-EEVHDKF-RAVPG-SYRRALQGIENCKAEG 177
Cdd:COG0731  104 IkKLRGIKTALLTNGSLLHRPEVREeLLKADQVYP--SLDAAdEETFRKInRPHPGlSWERIIEGLELFRKLY 174
Fer4_14 pfam13394
4Fe-4S single cluster domain;
49-148 8.39e-06

4Fe-4S single cluster domain;


Pssm-ID: 433171 [Multi-domain]  Cd Length: 115  Bit Score: 44.66  E-value: 8.39e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617   49 RCNLKCVHCYAKAV-DPEGKDEISTEQAKTIIDDLAQ--YGAPVMLFSGGEPLVRQ---DLVELAKHATGRGMRAVIS-- 120
Cdd:pfam13394   5 GCNHSCPGCDNKETwKFNYGEPFTEELEDQIIADLKDsyIKRQGLVLTGGEPLHPWnlpVLLKLLKRVKEEYPSKDIWle 84

                          90       100       110
                  ....*....|....*....|....*....|
gi 499240617  121 TNGTLITKEKARELKEV--GLSYVGISLDG 148
Cdd:pfam13394  85 TGYTLAIDFEYPDTEEQlfTLSVIDVLVDG 114
SPASM_Cmo-like cd21121
Iron-sulfur cluster-binding SPASM domain of tungsten-containing aldehyde ferredoxin ...
 294-335 6.82e-04

Iron-sulfur cluster-binding SPASM domain of tungsten-containing aldehyde ferredoxin oxidoreductase cofactor-modifying protein and similar proteins; This group is composed of Pyrococcus furiosus tungsten-containing aldehyde ferredoxin oxidoreductase (AOR; EC 1.2.7.5) cofactor-modifying protein, encoded by the cmo gene, and similar proteins. AOR cofactor-modifying protein is involved in the biosynthesis of a molybdopterin-based tungsten cofactor. Members of this group are radical S-adenosylmethionine (SAM) enzymes with a SPASM domain. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster. This group appears to contain one auxillary Fe-S cluster, similar to the auxillary 4Fe-4S cluster in Bacillus circulans butirosin biosynthetic enzyme BtrN.


Pssm-ID: 410612 [Multi-domain]  Cd Length: 80  Bit Score: 38.05  E-value: 6.82e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 499240617 294 NSGRGIgCISWDGQVHADQF-WRNHT--------------FGNVLERPFSEIWDDPN 335
Cdd:cd21121    6 VEGRSA-FIRVDGEVSPCYFlWHPYRsyingrekevkrviFGNVKEESLLEIWNSPE 61
SPASM pfam13186
Iron-sulfur cluster-binding domain; This domain occurs as an additional C-terminal iron-sulfur ...
 302-334 2.74e-03

Iron-sulfur cluster-binding domain; This domain occurs as an additional C-terminal iron-sulfur cluster binding domain in many radical SAM domain, pfam04055 proteins. The domain occurs in a number of proteins that modify a protein to become an active enzyme, or a peptide to become a ribosomal natural product. The domain is named SPASM because it occurs in the maturases of Subilitosin, PQQ, Anaerobic Sulfatases, and Mycofactocin.


Pssm-ID: 433020 [Multi-domain]  Cd Length: 66  Bit Score: 35.92  E-value: 2.74e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 499240617  302 ISWDGQVH---ADQFWRNHTFGNVLERPFSEIWDDP 334
Cdd:pfam13186  10 ILPDGDVYpcfDDDFVGPIVLGNIREQSLAEIWNSP 45
PFLE_PFLC TIGR02494
glycyl-radical enzyme activating protein; This subset of the radical-SAM family (pfam04055) ...
 31-184 9.64e-03

glycyl-radical enzyme activating protein; This subset of the radical-SAM family (pfam04055) includes a number of probable activating proteins acting on different enzymes all requiring an amino-acid-centered radical. The closest relatives to this family are the pyruvate-formate lyase activating enzyme (PflA, 1.97.1.4, TIGR02493) and the anaerobic ribonucleotide reductase activating enzyme (TIGR02491). Included within this subfamily are activators of hydroxyphenyl acetate decarboxylase (HdpA), benzylsuccinate synthase (BssD), gycerol dehydratase (DhaB2) as well as enzymes annotated in E. coli as activators of different isozymes of pyruvate-formate lyase (PFLC and PFLE) however, these appear to lack characterization and may activate enzymes with distinctive functions. Most of the sequence-level variability between these forms is concentrated within an N-terminal domain which follows a conserved group of three cysteines and contains a variable pattern of 0 to 8 additional cysteines.


Pssm-ID: 274163 [Multi-domain]  Cd Length: 295  Bit Score: 37.70  E-value: 9.64e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617   31 LLQFSKDKKPVVVWNMTRRCNL-KCVH-CYAKAVDPEGKDEISTEQAKTIIDDLAQY---GAPVMlFSGGEPLVRQD-LV 104
Cdd:TIGR02494  66 RLSELADGRNRIIIRREKCTHCgKCTEaCPSGALSIVGEEMTVEEVMRVVLRDSIFYrnsGGGVT-LSGGEPLLQPEfAL 144

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240617  105 ELAKHATGRGMRAVISTNGTLITKEKARELKEVGLSYVGI-SLDggEEVHdkFRAVPGSYRRALQGIENCKAEGLKVGLR 183
Cdd:TIGR02494 145 ALLQACHERGIHTAVETSGFTPWETIEKVLPYVDLFLFDIkHLD--DERH--KEVTGVDNEPILENLEALAAAGKNVVIR 220


                  .
gi 499240617  184 F 184
Cdd:TIGR02494 221 I 221
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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