Citrus Sinensis ID: 006956

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620----

MEDIEDLLAGSGGGGAPPGFRLPINAVGVNPKYNKNKPRLHDNHLSKTGSLSPKIPGTETIYMKTFGCSHNQSDSEYMAGQLSAFGYALTDNSEEADIWLINTCTVKSPSQSAMDTLIAKCKSAKKPLVVAGCVPQGSRDLKELEGVSIVGVQQIDRVVEVVEETLKGHEVRLLHRKKLPALDLPKVRRNKFVEILPINVGCLGACTYCKTKHARGHLGSYTVESLVGRVRTVIADGVKEVWLSSEDTGAYGRDIGVNLPILLNAIVAELPPDGSTMLRIGMTNPPFILEHLKEIAEVLRHPCVYSFLHVPVQSGSDAVLSAMNREYTLSDFRTVVDTLIELVPGMQIATDIICGFPGETDEDFNQTVNLIKEYKFPQVHISQFYPRPGTPAARMKKVPSAVVKKRSRELTSVFEAFTPYLGMEGRVERIWITEIAADGIHLGYVQVLVPSTGNMLGTSALVKITSVGRWSVFGEVIKILNQVDDKIASNRRISSQVRQDKCSSCSSQNESSACSNEPDPSACGLECCEGKITLEEGQVSWIDRFAEDINSQNVIGWLLRKRKNQLKGVENDVALGSKKKQEWMGGNMGEWGVVDRALLGGMLVSFLIILALLIHVGFRTLSTK

cccHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEccccccccHHHHHHHHHHHcccccccccccccEEEEEcccccccHHHHHHHHHHHHHHccccEEEEcccccccccccccccccEEccccccHHHHHHHHHHcccEEEEcccccccccccccccccccEEEEEcccccccccccEEccccccccccccHHHHHHHHHHHHHcccEEEEEcccccccccccccccHHHHHHHHHHccccccccEEEEcccccHHHHHHHHHHHHHccccccccccccccccccHHHHHHHcccccHHHHHHHHHHHHHHccccEEEccEEEccccccHHHHHHHHHHHHHHcccccEEEcccccccccccccccccHHHHHHHHHHHHHHHHHHcHHHcccccEEEEEEEEEccccEEcccEEEEEcccccccccEEEEEEEEEEccEEEEEEEEEEccccHHHHcHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHccccccccccccccccccEEEcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccc

cccHHHHHccccccccccccccccccccccHHHccccccEEEcccccccHHHHccccccEEEEEEcccccccccHHHHHHHHHHccccccccHHHccEEEEccHHHHHHHHHHHHHHHHHHHHHHHHEEcccccccHHHHHHHcccccEEccccHcHHHHHHHHHHcccEEEEEcccccEEcccccccccccEEEEEEEEcccccEEEEEEEccccccccccHHHHHHHHHHHHHccccEEEEcccccccccccccccHHHHHHHHHHHHccccccEEEEEccccHcccHHHHHHHHHHcccccHcEEccccccccHHHHHHHHccccHHHHHHHHHHHHHHccccEEEccEEEccccccHHHHHHHHHHHHHcccccEEEEEEcccccccccccccccHHHHHHHHHHHHHHHHHHHHHHcccccEEEEEEEcccccccccccEEEEEccccHHccEEEEEEEEEccccccccEEEEEccHcccccccHHHHHHHccccccccccccccccccccccccccccccccccccccccHHHccccccccccccHcHHHHHHHHHcccccccccccccccEEEEEcccccHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc

MEDIEDLlagsggggappgfrlpinavgvnpkynknkprlhdnhlsktgslspkipgtetiymktfgcshnqsdseyMAGQLSAFGyaltdnseeaDIWLINtctvkspsqsaMDTLIAKCksakkplvvagcvpqgsrdlkelegvsivGVQQIDRVVEVVEETLKGHEVRllhrkklpaldlpkvrrnkfveilpinvgclgactycktkharghlgsyTVESLVGRVRTVIADGVKEvwlssedtgaygrdigVNLPILLNAIVaelppdgstmlrigmtnppFILEHLKEIAEVlrhpcvysflhvpvqsgsDAVLSAMNREYTLSDFRTVVDTLIELvpgmqiatdiicgfpgetdedFNQTVNLIkeykfpqvhisqfyprpgtpaarmkkvpsAVVKKRSRELTSVFEAftpylgmegrvERIWITEIAADGIHLGYVQVLvpstgnmlgTSALVKITSVGRWSVFGEVIKILNQVddkiasnrrissqvrqdkcsscssqnessacsnepdpsacgleccegkitleEGQVSWIDRFAEDINSQNVIGWLLRKRKNQLKGVEndvalgskkkqewmggnmgewGVVDRALLGGMLVSFLIILALLIHVgfrtlstk

MEDIEDLlagsggggappgfRLPINAVGVNPKYNknkprlhdnhlsktgslspkipGTETIYMKTFGCSHNQSDSEYMAGQLSAFGYALTDNSEEADIWLINTCTVKSPSQSAMDTLIAKCKSAKKPLVVAGCVpqgsrdlkelegvsivgvqqiDRVVEVVEETLkghevrllhrkklpaldlpkvrrNKFVEILPINVGCLGACTYCKTKHARGHLGSYTVESLVGRVRTVIADGVKEVWLSSEDTGAYGRDIGVNLPILLNAIVAELPPDGSTMLRIGMTNPPFILEHLKEIAEVLRHPCVYSFLHVPVQSGSDAVLSAMNREYTLSDFRTVVDTLIELVPGMQIATDIICGFPGETDEDFNQTVNLIKEYKFPQVHISQFyprpgtpaarmKKVPSavvkkrsreltsvfeaftpylgmegRVERIWITEIAADGIHLGYVQVLVPSTGNMLGTSALVKITSVGRWSVFGEVIKILnqvddkiasnrrissqvrqdkcsscssqNESSACSNEPDPSACGLECCEGKITLEEGQVSWIDRFAEDINSQNVIGWLLRKRknqlkgvendvalgskkkqewmggnMGEWGVVDRALLGGMLVSFLIILALLIHVgfrtlstk

MEDIEDLLagsggggappgFRLPINAVGVNPKYNKNKPRLHDNHLSKTGSLSPKIPGTETIYMKTFGCSHNQSDSEYMAGQLSAFGYALTDNSEEADIWLINTCTVKSPSQSAMDTLIAKCKSAKKPLVVAGCVPQGSRDLKELEGVSIVGVQQIDRVVEVVEETLKGHEVRLLHRKKLPALDLPKVRRNKFVEILPINVGCLGACTYCKTKHARGHLGSYTVESLVGRVRTVIADGVKEVWLSSEDTGAYGRDIGVNLPILLNAIVAELPPDGSTMLRIGMTNPPFILEHLKEIAEVLRHPCVYSFLHVPVQSGSDAVLSAMNREYTLSDFRTVVDTLIELVPGMQIATDIICGFPGETDEDFNQTVNLIKEYKFPQVHISQFYPRPGTPAARMKKVPSAVVKKRSRELTSVFEAFTPYLGMEGRVERIWITEIAADGIHLGYVQVLVPSTGNMLGTSALVKITSVGRWSVFGEVIKILNQVDDKIASNRRISSQVRQDKcsscssqnessacsnePDPSACGLECCEGKITLEEGQVSWIDRFAEDINSQNVIGWLLRKRKNQLKGVENDVALGSKKKQEWMGGNMGEWGVVDRALLGGMLVSFLIILALLIHVGFRTLSTK

***********************I**********************************ETIYMKTFGCSHN****EYMAGQLSAFGYALTDNSEEADIWLINTCTVKSP***AMDTLIAKCKSAKKPLVVAGCVPQGSRDLKELEGVSIVGVQQIDRVVEVVEETLKGHEVRLLHRKKLPALDLPKVRRNKFVEILPINVGCLGACTYCKTKHARGHLGSYTVESLVGRVRTVIADGVKEVWLSSEDTGAYGRDIGVNLPILLNAIVAELPPDGSTMLRIGMTNPPFILEHLKEIAEVLRHPCVYSFLHVPVQSGSDAVLSAMNREYTLSDFRTVVDTLIELVPGMQIATDIICGFPGETDEDFNQTVNLIKEYKFPQVHISQFYP**********************ELTSVFEAFTPYLGMEGRVERIWITEIAADGIHLGYVQVLVPSTGNMLGTSALVKITSVGRWSVFGEVIKILNQVDDKI***********************************CGLECCEGKITLEEGQVSWIDRFAEDINSQNVIGWLLRKRKNQLKGVENDVALGSKKKQEWMGGNMGEWGVVDRALLGGMLVSFLIILALLIHVGFRT****

*EDIEDLLA***************************************************IYMKTFGCSHNQSDSEYMAGQLSAFGYALTDNSEEADIWLINTCTVKSPSQSAMDTLIAKCKSAKKPLVVAGCVPQGSRDLKELEGVSIVGVQQIDRVVEVVEETLKGHEVRLLHRKKLPALDLPKVRRNKFVEILPINVGCLGACTYCKTKHARGHLGSYTVESLVGRVRTVIADGVKEVWLSSEDTGAYGRDIGVNLPILLNAIVAELPPDGSTMLRIGMTNPPFILEHLKEIAEVLRHPCVYSFLHVPVQSGSDAVLSAMNREYTLSDFRTVVDTLIELVPGMQIATDIICGFPGETDEDFNQTVNLIKEYKFPQVHISQFYPRPGTPAARMKKVPSAVVKKRSRELTSVFEAFTPYLGMEGRVERIWITEIAADGIHLGYVQVLVPSTGNMLGTSALVKITSVGRWSVFGEVIKI**************************************************************IDRFAEDINSQNVIG*******************************MGEWGVVDRALLGGMLVSFLIILALLIHVGFRTL***

MEDIEDLLAGSGGGGAPPGFRLPINAVGVNPKYNKNKPRLHDNHLSKTGSLSPKIPGTETIYMKTFGCSHNQSDSEYMAGQLSAFGYALTDNSEEADIWLINTCTVKSPSQSAMDTLIAKCKSAKKPLVVAGCVPQGSRDLKELEGVSIVGVQQIDRVVEVVEETLKGHEVRLLHRKKLPALDLPKVRRNKFVEILPINVGCLGACTYCKTKHARGHLGSYTVESLVGRVRTVIADGVKEVWLSSEDTGAYGRDIGVNLPILLNAIVAELPPDGSTMLRIGMTNPPFILEHLKEIAEVLRHPCVYSFLHVPVQSGSDAVLSAMNREYTLSDFRTVVDTLIELVPGMQIATDIICGFPGETDEDFNQTVNLIKEYKFPQVHISQFYPRPGT****************SRELTSVFEAFTPYLGMEGRVERIWITEIAADGIHLGYVQVLVPSTGNMLGTSALVKITSVGRWSVFGEVIKILNQVDDKIASNR******************************ACGLECCEGKITLEEGQVSWIDRFAEDINSQNVIGWLLRKRKNQLKGVENDVALGSKKKQEWMGGNMGEWGVVDRALLGGMLVSFLIILALLIHVGFRTLSTK

******LLAGSGGGGAPPGFRLPINAVGVNPKYNKNKPRLHDNHLSKTGSLSPKIPGTETIYMKTFGCSHNQSDSEYMAGQLSAFGYALTDNSEEADIWLINTCTVKSPSQSAMDTLIAKCKSAKKPLVVAGCVPQGSRDLKELEGVSIVGVQQIDRVVEVVEETLKGHEVRLLHRKKLPALDLPKVRRNKFVEILPINVGCLGACTYCKTKHARGHLGSYTVESLVGRVRTVIADGVKEVWLSSEDTGAYGRDIGVNLPILLNAIVAELPPDGSTMLRIGMTNPPFILEHLKEIAEVLRHPCVYSFLHVPVQSGSDAVLSAMNREYTLSDFRTVVDTLIELVPGMQIATDIICGFPGETDEDFNQTVNLIKEYKFPQVHISQFYPRPGTPAARMKKVPSAVVKKRSRELTSVFEAFTPYLGMEGRVERIWITEIAADGIHLGYVQVLVPSTGNMLGTSALVKITSVGRWSVFGEVIKILNQVDDKIASNRRISSQV******S***************PSACGLECCEGKITLEEGQVSWIDRFAEDINSQNVIGWLLRKRKNQ*********LGSKKKQEWMGGNMGEWGVVDRALLGGMLVSFLIILALLIHVGFRTLS**

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiii

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no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		624	2.2.26 [Sep-21-2011]
Q6P4Y0		553	Threonylcarbamoyladenosin	yes	no	0.748	0.844	0.518	1e-142
Q6NS26		556	Threonylcarbamoyladenosin	N/A	no	0.748	0.839	0.516	1e-141
Q5VV42		579	Threonylcarbamoyladenosin	yes	no	0.754	0.813	0.505	1e-140
Q7K4W1		552	Threonylcarbamoyladenosin	yes	no	0.689	0.778	0.539	1e-139
Q91WE6		578	Threonylcarbamoyladenosin	yes	no	0.753	0.813	0.503	1e-138
Q6PG34		547	Threonylcarbamoyladenosin	yes	no	0.698	0.797	0.522	1e-136
Q291H5		553	Threonylcarbamoyladenosin	yes	no	0.673	0.759	0.563	1e-135
Q8MXQ7		425	Threonylcarbamoyladenosin	yes	no	0.551	0.809	0.508	1e-96
Q9UXX9		425	Probable threonylcarbamoy	yes	no	0.657	0.964	0.373	3e-77
O59545		425	Probable threonylcarbamoy	yes	no	0.583	0.856	0.392	7e-77

>sp\|Q6P4Y0\|CDKAL_XENTR Threonylcarbamoyladenosine tRNA methylthiotransferase OS=Xenopus tropicalis GN=cdkal1 PE=2 SV=1	Back alignment and function desciption

 Score =  504 bits (1299), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 255/492 (51%), Positives = 344/492 (69%), Gaps = 25/492 (5%)

Query: 1   MEDIEDLLAGSGGGGAPPGFRLPI--NAVGVNPKYNKNKPRLHDNHLSKTGSLSPKIPGT 58
           ++DIED+++ +      P  R     N V    K NKNK +  +     T      IPGT
Sbjct: 9   LDDIEDIVSATD---PKPHDRQNARQNIVPRARKRNKNKIQEEEPPADST------IPGT 59

Query: 59  ETIYMKTFGCSHNQSDSEYMAGQLSAFGYALTDNSEEADIWLINTCTVKSPSQSAMDTLI 118
           + I+++T+GCSHN SD EYMAGQL+A+GY++T+  E+AD+WL+N+CTVKSP++      I
Sbjct: 60  QKIWIRTWGCSHNNSDGEYMAGQLAAYGYSITEQPEQADLWLLNSCTVKSPAEDHFRNSI 119

Query: 119 AKCKSAKKPLVVAGCVPQGSRDLKELEGVSIVGVQQIDRVVEVVEETLKGHEVRLLHRKK 178
            K + A K +V++GCVPQ     + ++G+SI+GVQQIDRVVEVVEET+KGH VRLL +KK
Sbjct: 120 KKAQEANKKVVLSGCVPQAQPRQEYMKGLSIIGVQQIDRVVEVVEETIKGHSVRLLGQKK 179

Query: 179 L-------PALDLPKVRRNKFVEILPINVGCLGACTYCKTKHARGHLGSYTVESLVGRVR 231
                     LDLPK+R+N  +EI+ IN GCL ACTYCKTKHARG L SY VE LV R  
Sbjct: 180 DNGKRLGGARLDLPKIRKNPLIEIISINTGCLNACTYCKTKHARGELASYPVEELVDRAA 239

Query: 232 TVIADGVKEVWLSSEDTGAYGRDIGVNLPILLNAIVAELPPDGSTMLRIGMTNPPFILEH 291
               +GV E+WL+SEDTGAYGRDIG +LP LL  +V E+ P+G+ MLR+GMTNPP+ILEH
Sbjct: 240 QSFQEGVCEIWLTSEDTGAYGRDIGTDLPTLLWKLV-EVIPEGA-MLRLGMTNPPYILEH 297

Query: 292 LKEIAEVLRHPCVYSFLHVPVQSGSDAVLSAMNREYTLSDFRTVVDTLIELVPGMQIATD 351
           L+E+A++L HP VY+FLH+PVQS SD+VL  M REY ++DF+ VVD L E VPG+ IATD
Sbjct: 298 LEEMAKILNHPRVYAFLHIPVQSASDSVLMDMKREYCIADFKRVVDFLKERVPGITIATD 357

Query: 352 IICGFPGETDEDFNQTVNLIKEYKFPQVHISQFYPRPGTPAARMKKVPSAVVKKRSRELT 411
           IICGFPGETDEDF +T+ L++EYKFP + I+QFYPRPGTPAA+M++VP+ V K+R++EL+
Sbjct: 358 IICGFPGETDEDFKETLKLVEEYKFPSLFINQFYPRPGTPAAKMEQVPAHVKKQRTKELS 417

Query: 412 SVFEAFTPYLGMEGRVERIWITEIAADGIHL-----GYVQVLVPSTGNMLGTSALVKITS 466
            +F +++PY    G  + + +TE + D  +       Y QVLVP     +G    VKI  
Sbjct: 418 QLFHSYSPYDHKIGEEQHVLVTEESFDSQYYVSHNRFYEQVLVPKDPAFVGKMVEVKIFE 477

Query: 467 VGRWSVFGEVIK 478
            G+  + G+ ++
Sbjct: 478 AGKHFMKGQPVQ 489

Catalyzes the methylthiolation of N6-threonylcarbamoyladenosine (t(6)A), leading to the formation of 2-methylthio-N6-threonylcarbamoyladenosine (ms(2)t(6)A) at position 37 in tRNAs that read codons beginning with adenine.
Xenopus tropicalis (taxid: 8364)
EC: 2EC: .EC: -EC: .EC: -EC: .EC: -

>sp\|Q6NS26\|CDKAL_XENLA Threonylcarbamoyladenosine tRNA methylthiotransferase OS=Xenopus laevis GN=cdkal1 PE=2 SV=1	Back alignment and function description

>sp\|Q5VV42\|CDKAL_HUMAN Threonylcarbamoyladenosine tRNA methylthiotransferase OS=Homo sapiens GN=CDKAL1 PE=1 SV=1	Back alignment and function description

>sp\|Q7K4W1\|CDKAL_DROME Threonylcarbamoyladenosine tRNA methylthiotransferase OS=Drosophila melanogaster GN=CG6550 PE=2 SV=1	Back alignment and function description

>sp\|Q91WE6\|CDKAL_MOUSE Threonylcarbamoyladenosine tRNA methylthiotransferase OS=Mus musculus GN=Cdkal1 PE=2 SV=1	Back alignment and function description

>sp\|Q6PG34\|CDKAL_DANRE Threonylcarbamoyladenosine tRNA methylthiotransferase OS=Danio rerio GN=cdkal1 PE=2 SV=1	Back alignment and function description

>sp\|Q291H5\|CDKAL_DROPS Threonylcarbamoyladenosine tRNA methylthiotransferase OS=Drosophila pseudoobscura pseudoobscura GN=GA19679 PE=3 SV=1	Back alignment and function description

>sp\|Q8MXQ7\|CDKAL_CAEEL Threonylcarbamoyladenosine tRNA methylthiotransferase OS=Caenorhabditis elegans GN=Y92H12BL.1 PE=3 SV=2	Back alignment and function description

>sp\|Q9UXX9\|AMTAB_PYRAB Probable threonylcarbamoyladenosine tRNA methylthiotransferase OS=Pyrococcus abyssi (strain GE5 / Orsay) GN=PYRAB17290 PE=3 SV=1	Back alignment and function description

>sp\|O59545\|AMTAB_PYRHO Probable threonylcarbamoyladenosine tRNA methylthiotransferase OS=Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) GN=PH1875 PE=3 SV=2	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		624
255561612		630	radical sam protein, putative [Ricinus c	0.995	0.985	0.777	0.0
359493166		622	PREDICTED: CDK5 regulatory subunit-assoc	0.974	0.977	0.750	0.0
224135639		612	predicted protein [Populus trichocarpa]	0.971	0.990	0.761	0.0
449447617		635	PREDICTED: threonylcarbamoyladenosine tR	0.991	0.974	0.729	0.0
449506818		635	PREDICTED: threonylcarbamoyladenosine tR	0.991	0.974	0.725	0.0
356542899		609	PREDICTED: CDKAL1-like protein-like [Gly	0.961	0.985	0.712	0.0
296081133		549	unnamed protein product [Vitis vinifera]	0.857	0.974	0.759	0.0
297839059		602	radical SAM domain-containing protein [A	0.929	0.963	0.687	0.0
18409989		601	Methylthiotransferase [Arabidopsis thali	0.937	0.973	0.691	0.0
357111240		624	PREDICTED: CDK5 regulatory subunit-assoc	0.947	0.947	0.646	0.0

>gi\|255561612\|ref\|XP_002521816.1\| radical sam protein, putative [Ricinus communis] gi\|223539029\|gb\|EEF40626.1\| radical sam protein, putative [Ricinus communis]	Back alignment and taxonomy information

 Score =  960 bits (2482), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 492/633 (77%), Positives = 535/633 (84%), Gaps = 12/633 (1%)

Query: 1   MEDIEDLL-AGSGGGGAPPGFRLPINAVGVNPK--YNKNKPRLHDNHLSKTGSLSPKIPG 57
           MEDIEDLL     GGGAPPGFRLP+N+VGV PK    KNK  L+         LSPKIPG
Sbjct: 1   MEDIEDLLIGSGSGGGAPPGFRLPLNSVGVYPKKIIKKNKGYLNHGISLSQSLLSPKIPG 60

Query: 58  TETIYMKTFGCSHNQSDSEYMAGQLSAFGYALTDNSEEADIWLINTCTVKSPSQSAMDTL 117
           T+TIY+KTFGCSHNQSDSEYMAGQLS+FGYALTD  E+ D+WLINTCTVKSPSQSAMDT+
Sbjct: 61  TQTIYIKTFGCSHNQSDSEYMAGQLSSFGYALTDIPEDGDLWLINTCTVKSPSQSAMDTI 120

Query: 118 IAKCKSAKKPLVVAGCVPQGSRDLKELEGVSIVGVQQIDRVVEVVEETLKGHEVRLLHRK 177
           IAK KSAKKPLVVAGCVPQGSR+LKELEGVSIVGVQQIDRVVEVVEETLKGHEVRLL RK
Sbjct: 121 IAKGKSAKKPLVVAGCVPQGSRNLKELEGVSIVGVQQIDRVVEVVEETLKGHEVRLLTRK 180

Query: 178 KLPALDLPKVRRNKFVEILPINVGCLGACTYCKTKHARGHLGSYTVESLVGRVRTVIADG 237
            LPALDLPKVR+NKFVEILPINVGCLGACTYCKTKHARGHLGSYT++SLVGRVRTV+ DG
Sbjct: 181 TLPALDLPKVRKNKFVEILPINVGCLGACTYCKTKHARGHLGSYTIDSLVGRVRTVVGDG 240

Query: 238 VKEVWLSSEDTGAYGRDIGVNLPILLNAIVAELPPDGSTMLRIGMTNPPFILEHLKEIAE 297
           VKE+WLSSEDTGAYGRDIGVNLP LLNAIV+ELP D STMLRIGMTNPPFILEHLKEIAE
Sbjct: 241 VKEIWLSSEDTGAYGRDIGVNLPRLLNAIVSELPADASTMLRIGMTNPPFILEHLKEIAE 300

Query: 298 VLRHPCVYSFLHVPVQSGSDAVLSAMNREYTLSDFRTVVDTLIELVPGMQIATDIICGFP 357
           VLRHPCVYSFLHVPVQSGSD VL+AMNREYT+S+FRTVVDTL ELVPGMQIATDIICGFP
Sbjct: 301 VLRHPCVYSFLHVPVQSGSDNVLNAMNREYTVSNFRTVVDTLTELVPGMQIATDIICGFP 360

Query: 358 GETDEDFNQTVNLIKEYKFPQVHISQFYPRPGTPAARMKKVPSAVVKKRSRELTSVFEAF 417
           GETD+DF QTV+LI EYK PQVHISQFYPRPGTPAARMKKVPS +VKKRSRELT+VFEAF
Sbjct: 361 GETDDDFAQTVSLINEYKLPQVHISQFYPRPGTPAARMKKVPSNIVKKRSRELTAVFEAF 420

Query: 418 TPYLGMEGRVERIWITEIAADGIHL-----GYVQVLVPSTGNMLGTSALVKITSVGRWSV 472
           TPY GMEGRVERIWITEIA DGIHL     GYVQVLV +   MLGTSA+VKITSVGRWSV
Sbjct: 421 TPYNGMEGRVERIWITEIATDGIHLVGHTKGYVQVLVIAPETMLGTSAIVKITSVGRWSV 480

Query: 473 FGEVIKILNQVDDKIASNRRISSQVRQDKCSSCSSQNESSACSNEPDPSACGLECCEGKI 532
           FGEVI+ LNQ +  +AS  ++ S     K S CS   E+ ACS EP+  ACG E C G+ 
Sbjct: 481 FGEVIQTLNQTNRGVASAEKMPS---GGKYSPCSDPCETCACSKEPESCACGPESCGGQN 537

Query: 533 TLEEGQVSWIDRFAEDINSQNVIGWLLRKRKNQL-KGVENDVALGSKKKQEWMGGNMGEW 591
            LEE  ++  D   ED N +N+IGWLLRKRKNQ  K VEN++AL S KKQEW  G    W
Sbjct: 538 PLEESAIAQNDMLLEDRNRRNLIGWLLRKRKNQTQKIVENNIALESIKKQEWTKGTFSMW 597

Query: 592 GVVDRALLGGMLVSFLIILALLIHVGFRTLSTK 624
           G VDRALLGGMLVS + I+ALL+H+GFRT STK
Sbjct: 598 GAVDRALLGGMLVSLVTIVALLLHLGFRTTSTK 630

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|359493166\|ref\|XP_002268292.2\| PREDICTED: CDK5 regulatory subunit-associated protein 1-like 1-like [Vitis vinifera]	Back alignment and taxonomy information

>gi\|224135639\|ref\|XP_002327268.1\| predicted protein [Populus trichocarpa] gi\|222835638\|gb\|EEE74073.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|449447617\|ref\|XP_004141564.1\| PREDICTED: threonylcarbamoyladenosine tRNA methylthiotransferase-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449506818\|ref\|XP_004162857.1\| PREDICTED: threonylcarbamoyladenosine tRNA methylthiotransferase-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|356542899\|ref\|XP_003539902.1\| PREDICTED: CDKAL1-like protein-like [Glycine max]	Back alignment and taxonomy information

>gi\|296081133\|emb\|CBI18159.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|297839059\|ref\|XP_002887411.1\| radical SAM domain-containing protein [Arabidopsis lyrata subsp. lyrata] gi\|297333252\|gb\|EFH63670.1\| radical SAM domain-containing protein [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|18409989\|ref\|NP_565035.1\| Methylthiotransferase [Arabidopsis thaliana] gi\|12322201\|gb\|AAG51137.1\|AC069273_8 unknown protein [Arabidopsis thaliana] gi\|14194137\|gb\|AAK56263.1\|AF367274_1 At1g72090/F28P5_4 [Arabidopsis thaliana] gi\|27363418\|gb\|AAO11628.1\| At1g72090/F28P5_4 [Arabidopsis thaliana] gi\|332197151\|gb\|AEE35272.1\| Methylthiotransferase [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|357111240\|ref\|XP_003557422.1\| PREDICTED: CDK5 regulatory subunit-associated protein 1-like 1-like [Brachypodium distachyon]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		624
TAIR\|locus:2030342		601	AT1G72090 [Arabidopsis thalian	0.780	0.810	0.790	1.7e-213
UNIPROTKB\|Q291H5		553	GA19679 "Threonylcarbamoyladen	0.673	0.759	0.565	1.7e-128
UNIPROTKB\|E1BRH0		568	CDKAL1 "Uncharacterized protei	0.674	0.741	0.560	4.6e-128
UNIPROTKB\|Q5VV42		579	CDKAL1 "Threonylcarbamoyladeno	0.754	0.813	0.505	5.3e-127
FB\|FBgn0034214		552	CG6550 [Drosophila melanogaste	0.673	0.760	0.557	1.8e-126
UNIPROTKB\|F1MAW5		578	CDKAL1 "Uncharacterized protei	0.753	0.813	0.505	4.8e-126
UNIPROTKB\|E2RAI1		578	CDKAL1 "CDK5 regulatory subuni	0.714	0.771	0.524	4.8e-126
UNIPROTKB\|F1RUG0		578	CDKAL1 "Uncharacterized protei	0.75	0.809	0.505	6.1e-126
MGI\|MGI:1921765		578	Cdkal1 "CDK5 regulatory subuni	0.753	0.813	0.505	2.1e-125
ZFIN\|ZDB-GENE-040426-1443		547	cdkal1 "CDK5 regulatory subuni	0.701	0.800	0.521	7.2e-123

TAIR\|locus:2030342 AT1G72090 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 2002 (709.8 bits), Expect = 1.7e-213, Sum P(2) = 1.7e-213
 Identities = 396/501 (79%), Positives = 432/501 (86%)

Query:     1 MEDIEDLLXXXXXXXXXXXFRLPINAVGVNPKYNKNKPRLHDNH----LSKTGSLSP--- 53
             MEDIEDLL           FRLP+NAVG+NPK NK+K R+         S   SL+P   
Sbjct:     1 MEDIEDLLAGGVGGAPPG-FRLPLNAVGINPKTNKSK-RISSKPDQITASNRDSLAPPSM 58

Query:    54 KIPGTETIYMKTFGCSHNQSDSEYMAGQLSAFGYALTDNSEEADIWLINTCTVKSPSQSA 113
             KIPGT+TIY+KTFGCSHNQSDSEYMAGQLSAFGYALT+  EEAD+WLINTCTVKSPSQSA
Sbjct:    59 KIPGTQTIYIKTFGCSHNQSDSEYMAGQLSAFGYALTEVPEEADLWLINTCTVKSPSQSA 118

Query:   114 MDTLIAKCKSAKKPLVVAGCVPQGSRDLKELEGVSIVGVQQIDRVVEVVEETLKGHEVRL 173
             M TLI + +S KKPLV+AGCVPQGSRDLKELEGVS+VGVQQIDRVVE+VEETLKGHEVRL
Sbjct:   119 MSTLITRGRSGKKPLVIAGCVPQGSRDLKELEGVSVVGVQQIDRVVEIVEETLKGHEVRL 178

Query:   174 LHRKKLPALDLPKVRRNKFVEILPINVGCLGACTYCKTKHARGHLGSYTVESLVGRVRTV 233
             L RK LPALDLPKVRRN F+EILPINVGCLGACTYCKTKHARGHLGSYTV+SLV RVRTV
Sbjct:   179 LTRKTLPALDLPKVRRNNFIEILPINVGCLGACTYCKTKHARGHLGSYTVDSLVERVRTV 238

Query:   234 IADGVKEVWLSSEDTGAYGRDIGVNLPILLNAIVAELPPDGSTMLRIGMTNPPFILEHLK 293
             I++GVKE+WLSSEDTGAYGRDIGVNLPILLNAIV ELP D STMLRIGMTNPPFILEHLK
Sbjct:   239 ISEGVKEIWLSSEDTGAYGRDIGVNLPILLNAIVKELPSDQSTMLRIGMTNPPFILEHLK 298

Query:   294 EIAEVLRHPCVYSFLHVPVQSGSDAVLSAMNREYTLSDFRTVVDTLIELVPGMQIATDII 353
             EIA VLRHPCVY+FLHVPVQSGSD+VL+AMNREYT S+FRTVVDTL ELVPGMQIATDII
Sbjct:   299 EIAAVLRHPCVYTFLHVPVQSGSDSVLTAMNREYTASEFRTVVDTLTELVPGMQIATDII 358

Query:   354 CGFPGETDEDFNQTVNLIKEYKFPQVHISQFYPRPGTPAARMKKVPSAVVKKRSRELTSV 413
             CGFPGETDEDF+QTV LIK+YKFPQVHISQFYPRPGTPAA+MKKV S +VK+RSRELTSV
Sbjct:   359 CGFPGETDEDFSQTVELIKDYKFPQVHISQFYPRPGTPAAKMKKVQSKIVKQRSRELTSV 418

Query:   414 FEAFTPYLGMEGRVERIWITEIAADGIHL-----GYVQVLVPSTGNMLGTSALVKITSVG 468
             FEAF PY GME R ERIWITE+A DGIHL     GYVQVLV    +MLGTSA+ +ITSVG
Sbjct:   419 FEAFAPYTGMECREERIWITEVATDGIHLVGHTKGYVQVLVTGPESMLGTSAMARITSVG 478

Query:   469 RWSVFGEVIKILNQVDDKIAS 489
             RWSVFGEVI+  +  + +  S
Sbjct:   479 RWSVFGEVIETFSSANRETKS 499

GO:0003824 "catalytic activity" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0009451 "RNA modification" evidence=IEA

GO:0016740 "transferase activity" evidence=IEA

GO:0043412 "macromolecule modification" evidence=IEA

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

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=IDA

GO:0016020 "membrane" evidence=IDA

UNIPROTKB\|Q291H5 GA19679 "Threonylcarbamoyladenosine tRNA methylthiotransferase" [Drosophila pseudoobscura pseudoobscura (taxid:46245)]	Back alignment and assigned GO terms

UNIPROTKB\|E1BRH0 CDKAL1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|Q5VV42 CDKAL1 "Threonylcarbamoyladenosine tRNA methylthiotransferase" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

FB\|FBgn0034214 CG6550 [Drosophila melanogaster (taxid:7227)]	Back alignment and assigned GO terms

UNIPROTKB\|F1MAW5 CDKAL1 "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|E2RAI1 CDKAL1 "CDK5 regulatory subunit-associated protein 1-like 1" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|F1RUG0 CDKAL1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

MGI\|MGI:1921765 Cdkal1 "CDK5 regulatory subunit associated protein 1-like 1" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-040426-1443 cdkal1 "CDK5 regulatory subunit associated protein 1-like 1" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q6P4Y0	CDKAL_XENTR	2, ., -, ., -, ., -	0.5182	0.7483	0.8444	yes	no
Q6PG34	CDKAL_DANRE	2, ., -, ., -, ., -	0.5222	0.6987	0.7970	yes	no
Q291H5	CDKAL_DROPS	2, ., -, ., -, ., -	0.5632	0.6730	0.7594	yes	no
Q91WE6	CDKAL_MOUSE	2, ., -, ., -, ., -	0.5030	0.7532	0.8131	yes	no
Q5VV42	CDKAL_HUMAN	2, ., -, ., -, ., -	0.5051	0.7548	0.8134	yes	no
Q7K4W1	CDKAL_DROME	2, ., -, ., -, ., -	0.5394	0.6891	0.7789	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		624
TIGR01578		420	TIGR01578, MiaB-like-B, MiaB-like tRNA modifying e	1e-146
COG0621		437	COG0621, MiaB, 2-methylthioadenine synthetase [Tra	1e-112
TIGR00089		429	TIGR00089, TIGR00089, radical SAM methylthiotransf	1e-106
TIGR01579		414	TIGR01579, MiaB-like-C, MiaB-like tRNA modifying e	1e-71
PRK14331		437	PRK14331, PRK14331, (dimethylallyl)adenosine tRNA	2e-71
PRK14330		434	PRK14330, PRK14330, (dimethylallyl)adenosine tRNA	8e-67
TIGR01574		438	TIGR01574, miaB-methiolase, tRNA-N(6)-(isopentenyl	3e-66
PRK14328		439	PRK14328, PRK14328, (dimethylallyl)adenosine tRNA	3e-65
PRK14325		444	PRK14325, PRK14325, (dimethylallyl)adenosine tRNA	4e-62
PRK14338		459	PRK14338, PRK14338, (dimethylallyl)adenosine tRNA	8e-60
PRK14327		509	PRK14327, PRK14327, (dimethylallyl)adenosine tRNA	2e-54
PRK14333		448	PRK14333, PRK14333, (dimethylallyl)adenosine tRNA	7e-54
PRK14340		445	PRK14340, PRK14340, (dimethylallyl)adenosine tRNA	1e-51
PRK14339		420	PRK14339, PRK14339, (dimethylallyl)adenosine tRNA	3e-51
PRK14329		467	PRK14329, PRK14329, (dimethylallyl)adenosine tRNA	5e-49
PRK14326		502	PRK14326, PRK14326, (dimethylallyl)adenosine tRNA	7e-49
PRK14337		446	PRK14337, PRK14337, (dimethylallyl)adenosine tRNA	3e-47
TIGR01125		430	TIGR01125, TIGR01125, ribosomal protein S12 methyl	1e-46
PRK14335		455	PRK14335, PRK14335, (dimethylallyl)adenosine tRNA	2e-45
PRK14336		418	PRK14336, PRK14336, (dimethylallyl)adenosine tRNA	4e-44
PRK14334		440	PRK14334, PRK14334, (dimethylallyl)adenosine tRNA	1e-41
smart00729		216	smart00729, Elp3, Elongator protein 3, MiaB family	1e-39
PRK14332		449	PRK14332, PRK14332, (dimethylallyl)adenosine tRNA	2e-35
pfam00919		98	pfam00919, UPF0004, Uncharacterized protein family	2e-26
TIGR04013		382	TIGR04013, B12_SAM_MJ_1487, B12-binding domain/rad	3e-19
COG1032		490	COG1032, COG1032, Fe-S oxidoreductase [Energy prod	4e-19
pfam04055		165	pfam04055, Radical_SAM, Radical SAM superfamily	8e-17
PRK14862		440	PRK14862, rimO, ribosomal protein S12 methylthiotr	9e-17
TIGR04014		434	TIGR04014, B12_SAM_MJ_0865, B12-binding domain/rad	1e-13
COG0635		416	COG0635, HemN, Coproporphyrinogen III oxidase and	9e-08
cd01335		204	cd01335, Radical_SAM, Radical SAM superfamily	1e-05
COG1031		560	COG1031, COG1031, Uncharacterized Fe-S oxidoreduct	5e-05
PRK08207		488	PRK08207, PRK08207, coproporphyrinogen III oxidase	0.004
TIGR01212		302	TIGR01212, TIGR01212, radical SAM protein, TIGR012	0.004

>gnl\|CDD\|233479 TIGR01578, MiaB-like-B, MiaB-like tRNA modifying enzyme, archaeal-type	Back alignment and domain information

 Score =  428 bits (1103), Expect = e-146
 Identities = 194/425 (45%), Positives = 272/425 (64%), Gaps = 14/425 (3%)

Query: 61  IYMKTFGCSHNQSDSEYMAGQLSAFGYALTDNSEEADIWLINTCTVKSPSQSAMDTLIAK 120
           +Y++T+GC+ N  DSE M   L+A+G+ L +N+EEAD+ ++NTCTVK+ ++  M   I  
Sbjct: 2   VYVETYGCTLNNGDSEIMKNSLAAYGHELVNNAEEADLAILNTCTVKNKTEDTMLYRIES 61

Query: 121 CKSAKKPLVVAGCVPQGSRDLKELEGV--SIVGVQQIDRVVEVVEETLKGHEVRLLHRKK 178
                K +VVAGC+PQ  ++     G   S++GVQ IDR+VEVVEETLK        R+ 
Sbjct: 62  LMRNGKHVVVAGCMPQAQKESVYDNGSVASVLGVQAIDRLVEVVEETLKKKVHG--RREA 119

Query: 179 LPALDLPKVRRNKFVEILPINVGCLGACTYCKTKHARGHLGSYTVESLVGRVRTVIADGV 238
              L LPK R+N  +EI+PIN GCLG C+YC TKHARG L SY  E +V + R ++A+G 
Sbjct: 120 GTPLSLPKPRKNPLIEIIPINQGCLGNCSYCITKHARGKLASYPPEKIVEKARQLVAEGC 179

Query: 239 KEVWLSSEDTGAYGRDIGVNLPILLNAIVAELPPDGSTMLRIGMTNPPFILEHLKEIAEV 298
           KE+W++S+DTGAYGRDIG  LP LL  ++ E+P  G   LR+GM NP  +LE L E+A V
Sbjct: 180 KEIWITSQDTGAYGRDIGSRLPELLR-LITEIP--GEFRLRVGMMNPKNVLEILDELANV 236

Query: 299 LRHPCVYSFLHVPVQSGSDAVLSAMNREYTLSDFRTVVDTLIELVPGMQIATDIICGFPG 358
            +H  VY FLH+PVQSGSD+VL  M REYT+SDF  +VD   E  P + ++TDII GFP 
Sbjct: 237 YQHEKVYKFLHLPVQSGSDSVLKEMKREYTVSDFEDIVDKFRERFPDLTLSTDIIVGFPT 296

Query: 359 ETDEDFNQTVNLIKEYKFPQVHISQFYPRPGTPAARMKKVPSAVVKKRSRELTSV----- 413
           ETD+DF +T+ L+++Y+  +++I++F PRPGTPAA+MK++P+ +VKKRS+ LT +     
Sbjct: 297 ETDDDFEETMELLRKYRPEKINITKFSPRPGTPAAKMKRIPTNIVKKRSKRLTKLYEQVL 356

Query: 414 FEAFTPYLGMEGRVERIWITEIA-ADGIHLGYVQVLVPSTGNMLGTSALVKITSVGRWSV 472
            E     +G    V  +       +      Y QV++ S     G  A V+IT      +
Sbjct: 357 LEMRDNLIGTRVHV-LVTKEGKGDSLDDEDAYRQVVIRSRTREPGEFAGVEITGAKTAYL 415

Query: 473 FGEVI 477
            GE+I
Sbjct: 416 IGEII 420

This clade of sequences is closely related to MiaB, a modifier of isopentenylated adenosine-37 of certain eukaryotic and bacterial tRNAs (see TIGR01574). Sequence alignments suggest that this equivalog performs the same chemical transformation as MiaB, perhaps on a different (or differently modified) tRNA base substrate. This clade is a member of a subfamily (TIGR00089) and spans the archaea and eukaryotes. The only archaeal miaB-like genes are in this clade, while eukaryotes have sequences described by This model as well as ones falling within the scope of the MiaB equivalog model [Protein synthesis, tRNA and rRNA base modification]. Length = 420

>gnl\|CDD\|223694 COG0621, MiaB, 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>gnl\|CDD\|232820 TIGR00089, TIGR00089, radical SAM methylthiotransferase, MiaB/RimO family	Back alignment and domain information

>gnl\|CDD\|233480 TIGR01579, MiaB-like-C, MiaB-like tRNA modifying enzyme	Back alignment and domain information

>gnl\|CDD\|184628 PRK14331, PRK14331, (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>gnl\|CDD\|184627 PRK14330, PRK14330, (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>gnl\|CDD\|233476 TIGR01574, miaB-methiolase, tRNA-N(6)-(isopentenyl)adenosine-37 thiotransferase enzyme MiaB	Back alignment and domain information

>gnl\|CDD\|237675 PRK14328, PRK14328, (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>gnl\|CDD\|237673 PRK14325, PRK14325, (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>gnl\|CDD\|184633 PRK14338, PRK14338, (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>gnl\|CDD\|184624 PRK14327, PRK14327, (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>gnl\|CDD\|237677 PRK14333, PRK14333, (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>gnl\|CDD\|237679 PRK14340, PRK14340, (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>gnl\|CDD\|184634 PRK14339, PRK14339, (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>gnl\|CDD\|237676 PRK14329, PRK14329, (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>gnl\|CDD\|237674 PRK14326, PRK14326, (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>gnl\|CDD\|172813 PRK14337, PRK14337, (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>gnl\|CDD\|233279 TIGR01125, TIGR01125, ribosomal protein S12 methylthiotransferase RimO	Back alignment and domain information

>gnl\|CDD\|237678 PRK14335, PRK14335, (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>gnl\|CDD\|184632 PRK14336, PRK14336, (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>gnl\|CDD\|184630 PRK14334, PRK14334, (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>gnl\|CDD\|214792 smart00729, Elp3, Elongator protein 3, MiaB family, Radical SAM	Back alignment and domain information

>gnl\|CDD\|172808 PRK14332, PRK14332, (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional	Back alignment and domain information

>gnl\|CDD\|216191 pfam00919, UPF0004, Uncharacterized protein family UPF0004	Back alignment and domain information

>gnl\|CDD\|234440 TIGR04013, B12_SAM_MJ_1487, B12-binding domain/radical SAM domain protein, MJ_1487 family	Back alignment and domain information

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

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

>gnl\|CDD\|237838 PRK14862, rimO, ribosomal protein S12 methylthiotransferase; Provisional	Back alignment and domain information

>gnl\|CDD\|234441 TIGR04014, B12_SAM_MJ_0865, B12-binding domain/radical SAM domain protein, MJ_0865 family	Back alignment and domain information

>gnl\|CDD\|223708 COG0635, HemN, Coproporphyrinogen III oxidase and related Fe-S oxidoreductases [Coenzyme metabolism]	Back alignment and domain information

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

>gnl\|CDD\|223962 COG1031, COG1031, Uncharacterized Fe-S oxidoreductase [Energy production and conversion]	Back alignment and domain information

>gnl\|CDD\|236187 PRK08207, PRK08207, coproporphyrinogen III oxidase; Provisional	Back alignment and domain information

>gnl\|CDD\|130279 TIGR01212, TIGR01212, radical SAM protein, TIGR01212 family	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		624
KOG4355		547	consensus Predicted Fe-S oxidoreductase [General f	100.0
COG0621		437	MiaB 2-methylthioadenine synthetase [Translation,	100.0
PRK14340		445	(dimethylallyl)adenosine tRNA methylthiotransferas	100.0
PRK14327		509	(dimethylallyl)adenosine tRNA methylthiotransferas	100.0
PRK14332		449	(dimethylallyl)adenosine tRNA methylthiotransferas	100.0
PRK14330		434	(dimethylallyl)adenosine tRNA methylthiotransferas	100.0
PRK14335		455	(dimethylallyl)adenosine tRNA methylthiotransferas	100.0
PRK14329		467	(dimethylallyl)adenosine tRNA methylthiotransferas	100.0
PRK14331		437	(dimethylallyl)adenosine tRNA methylthiotransferas	100.0
TIGR01578		420	MiaB-like-B MiaB-like tRNA modifying enzyme, archa	100.0
PRK14333		448	(dimethylallyl)adenosine tRNA methylthiotransferas	100.0
PRK14336		418	(dimethylallyl)adenosine tRNA methylthiotransferas	100.0
PRK14326		502	(dimethylallyl)adenosine tRNA methylthiotransferas	100.0
PRK14337		446	(dimethylallyl)adenosine tRNA methylthiotransferas	100.0
PRK14325		444	(dimethylallyl)adenosine tRNA methylthiotransferas	100.0
PRK14328		439	(dimethylallyl)adenosine tRNA methylthiotransferas	100.0
TIGR01574		438	miaB-methiolase tRNA-N(6)-(isopentenyl)adenosine-3	100.0
PRK14338		459	(dimethylallyl)adenosine tRNA methylthiotransferas	100.0
PRK14862		440	rimO ribosomal protein S12 methylthiotransferase;	100.0
TIGR00089		429	RNA modification enzyme, MiaB family. This subfami	100.0
PRK14339		420	(dimethylallyl)adenosine tRNA methylthiotransferas	100.0
TIGR01125		430	MiaB-like tRNA modifying enzyme YliG, TIGR01125. T	100.0
PRK14334		440	(dimethylallyl)adenosine tRNA methylthiotransferas	100.0
TIGR01579		414	MiaB-like-C MiaB-like tRNA modifying enzyme. This	100.0
KOG2492		552	consensus CDK5 activator-binding protein [Signal t	100.0
TIGR02026		497	BchE magnesium-protoporphyrin IX monomethyl ester	100.0
PRK00955		620	hypothetical protein; Provisional	100.0
TIGR03471		472	HpnJ hopanoid biosynthesis associated radical SAM	100.0
PRK01254		707	hypothetical protein; Provisional	100.0
PRK05481		289	lipoyl synthase; Provisional	99.97
COG1032		490	Fe-S oxidoreductase [Energy production and convers	99.95
COG1031		560	Uncharacterized Fe-S oxidoreductase [Energy produc	99.94
PRK07094		323	biotin synthase; Provisional	99.93
PRK05904		353	coproporphyrinogen III oxidase; Provisional	99.92
TIGR00510		302	lipA lipoate synthase. The family shows strong seq	99.92
PF00919		98	UPF0004: Uncharacterized protein family UPF0004; I	99.92
PRK12928		290	lipoyl synthase; Provisional	99.92
PRK08599		377	coproporphyrinogen III oxidase; Provisional	99.91
PRK05628		375	coproporphyrinogen III oxidase; Validated	99.91
PRK09058		449	coproporphyrinogen III oxidase; Provisional	99.9
PRK05799		374	coproporphyrinogen III oxidase; Provisional	99.9
PRK08207		488	coproporphyrinogen III oxidase; Provisional	99.89
PRK07379		400	coproporphyrinogen III oxidase; Provisional	99.89
PRK08446		350	coproporphyrinogen III oxidase; Provisional	99.89
TIGR01212		302	radical SAM protein, TIGR01212 family. This unchar	99.89
PRK08898		394	coproporphyrinogen III oxidase; Provisional	99.88
TIGR00539		360	hemN_rel putative oxygen-independent coproporphyri	99.88
PRK08208		430	coproporphyrinogen III oxidase; Validated	99.88
PRK09057		380	coproporphyrinogen III oxidase; Provisional	99.88
PRK06256		336	biotin synthase; Validated	99.87
PRK05660		378	HemN family oxidoreductase; Provisional	99.87
TIGR01210		313	conserved hypothetical protein TIGR01210. This fam	99.86
PRK06582		390	coproporphyrinogen III oxidase; Provisional	99.86
PRK06294		370	coproporphyrinogen III oxidase; Provisional	99.86
smart00729		216	Elp3 Elongator protein 3, MiaB family, Radical SAM	99.85
TIGR00433		296	bioB biotin synthetase. Catalyzes the last step of	99.85
PRK06245		336	cofG FO synthase subunit 1; Reviewed	99.85
PRK08629		433	coproporphyrinogen III oxidase; Provisional	99.85
PLN02428		349	lipoic acid synthase	99.84
TIGR00538		455	hemN oxygen-independent coproporphyrinogen III oxi	99.83
PRK13347		453	coproporphyrinogen III oxidase; Provisional	99.83
PRK09249		453	coproporphyrinogen III oxidase; Provisional	99.83
TIGR00423		309	radical SAM domain protein, CofH subfamily. This p	99.8
COG0635		416	HemN Coproporphyrinogen III oxidase and related Fe	99.8
TIGR03550		322	F420_cofG 7,8-didemethyl-8-hydroxy-5-deazariboflav	99.79
PRK06267		350	hypothetical protein; Provisional	99.79
TIGR01211		522	ELP3 histone acetyltransferase, ELP3 family. The S	99.78
TIGR03551		343	F420_cofH 7,8-didemethyl-8-hydroxy-5-deazariboflav	99.78
COG1242		312	Predicted Fe-S oxidoreductase [General function pr	99.77
cd01335		204	Radical_SAM Radical SAM superfamily. Enzymes of th	99.76
PRK08445		348	hypothetical protein; Provisional	99.75
TIGR03700		351	mena_SCO4494 putative menaquinone biosynthesis pro	99.75
TIGR03699		340	mena_SCO4550 menaquinone biosynthesis protein, SCO	99.75
PF04055		166	Radical_SAM: Radical SAM superfamily; InterPro: IP	99.74
PRK08508		279	biotin synthase; Provisional	99.73
PLN02389		379	biotin synthase	99.71
PRK09240		371	thiH thiamine biosynthesis protein ThiH; Reviewed	99.66
PRK15108		345	biotin synthase; Provisional	99.64
COG1243		515	ELP3 Histone acetyltransferase [Transcription / Ch	99.62
TIGR02351		366	thiH thiazole biosynthesis protein ThiH. Members t	99.6
PRK07360		371	FO synthase subunit 2; Reviewed	99.57
COG0502		335	BioB Biotin synthase and related enzymes [Coenzyme	99.57
PRK00164		331	moaA molybdenum cofactor biosynthesis protein A; R	99.57
PRK08444		353	hypothetical protein; Provisional	99.55
PRK05926		370	hypothetical protein; Provisional	99.53
PRK13361		329	molybdenum cofactor biosynthesis protein A; Provis	99.52
PRK09613		469	thiH thiamine biosynthesis protein ThiH; Reviewed	99.5
TIGR02666		334	moaA molybdenum cofactor biosynthesis protein A, b	99.49
PRK05927		350	hypothetical protein; Provisional	99.48
TIGR02668		302	moaA_archaeal probable molybdenum cofactor biosynt	99.47
TIGR03822		321	AblA_like_2 lysine-2,3-aminomutase-related protein	99.44
PTZ00413		398	lipoate synthase; Provisional	99.42
PLN02951		373	Molybderin biosynthesis protein CNX2	99.42
PRK09234		843	fbiC FO synthase; Reviewed	99.4
PRK09234		843	fbiC FO synthase; Reviewed	99.33
PRK14463		349	ribosomal RNA large subunit methyltransferase N; P	99.32
PRK14455		356	ribosomal RNA large subunit methyltransferase N; P	99.28
TIGR02493		235	PFLA pyruvate formate-lyase 1-activating enzyme. A	99.27
PRK05301		378	pyrroloquinoline quinone biosynthesis protein PqqE	99.25
PRK14466		345	ribosomal RNA large subunit methyltransferase N; P	99.24
TIGR02109		358	PQQ_syn_pqqE coenzyme PQQ biosynthesis protein E.	99.21
PRK14456		368	ribosomal RNA large subunit methyltransferase N; P	99.2
TIGR01290		442	nifB nitrogenase cofactor biosynthesis protein Nif	99.13
TIGR00238		331	KamA family protein. Note that the E. coli homolog	99.13
COG2896		322	MoaA Molybdenum cofactor biosynthesis enzyme [Coen	99.12
COG0320		306	LipA Lipoate synthase [Coenzyme metabolism]	99.12
PRK14457		345	ribosomal RNA large subunit methyltransferase N; P	99.12
TIGR02495		191	NrdG2 anaerobic ribonucleoside-triphosphate reduct	99.11
COG1060		370	ThiH Thiamine biosynthesis enzyme ThiH and related	99.11
PRK14470		336	ribosomal RNA large subunit methyltransferase N; P	99.1
TIGR03470		318	HpnH hopanoid biosynthesis associated radical SAM	99.09
PRK14467		348	ribosomal RNA large subunit methyltransferase N; P	99.09
PRK14460		354	ribosomal RNA large subunit methyltransferase N; P	99.07
PRK14453		347	chloramphenicol/florfenicol resistance protein; Pr	99.07
PRK14468		343	ribosomal RNA large subunit methyltransferase N; P	99.06
PRK14459		373	ribosomal RNA large subunit methyltransferase N; P	99.05
PRK11145		246	pflA pyruvate formate lyase-activating enzyme 1; P	99.05
PRK14461		371	ribosomal RNA large subunit methyltransferase N; P	99.03
PRK11194		372	ribosomal RNA large subunit methyltransferase N; P	99.03
COG2100		414	Predicted Fe-S oxidoreductase [General function pr	99.01
PRK14469		343	ribosomal RNA large subunit methyltransferase N; P	99.01
COG1856		275	Uncharacterized homolog of biotin synthetase [Func	99.0
TIGR00048		355	radical SAM enzyme, Cfr family. A Staphylococcus s	99.0
PRK14464		344	ribosomal RNA large subunit methyltransferase N; P	98.98
PRK14462		356	ribosomal RNA large subunit methyltransferase N; P	98.95
PRK14465		342	ribosomal RNA large subunit methyltransferase N; P	98.92
COG1244		358	Predicted Fe-S oxidoreductase [General function pr	98.9
TIGR03821		321	AblA_like_1 lysine-2,3-aminomutase-related protein	98.9
PRK14454		342	ribosomal RNA large subunit methyltransferase N; P	98.84
TIGR03820		417	lys_2_3_AblA lysine-2,3-aminomutase. This model de	98.79
COG0820		349	Predicted Fe-S-cluster redox enzyme [General funct	98.78
PRK13762		322	tRNA-modifying enzyme; Provisional	98.75
COG0731		296	Fe-S oxidoreductases [Energy production and conver	98.71
KOG2672		360	consensus Lipoate synthase [Coenzyme transport and	98.71
COG2516		339	Biotin synthase-related enzyme [General function p	98.7
TIGR03278		404	methan_mark_10 putative methanogenesis marker prot	98.44
COG0535		347	Predicted Fe-S oxidoreductases [General function p	98.41
KOG2900		380	consensus Biotin synthase [Coenzyme transport and	98.34
PRK13745		412	anaerobic sulfatase-maturase; Provisional	98.33
TIGR02494		295	PFLE_PFLC glycyl-radical enzyme activating protein	98.26
PF01938		61	TRAM: TRAM domain; InterPro: IPR002792 The TRAM (a	98.26
TIGR03365		238	Bsubt_queE 7-cyano-7-deazaguanosine (preQ0) biosyn	98.26
PRK13758		370	anaerobic sulfatase-maturase; Provisional	98.24
COG4277		404	Predicted DNA-binding protein with the Helix-hairp	98.23
COG1533		297	SplB DNA repair photolyase [DNA replication, recom	98.23
COG1180		260	PflA Pyruvate-formate lyase-activating enzyme [Pos	98.05
KOG2535		554	consensus RNA polymerase II elongator complex, sub	98.05
COG0641		378	AslB Arylsulfatase regulator (Fe-S oxidoreductase)	98.02
COG1509		369	KamA Lysine 2,3-aminomutase [Amino acid transport	97.92
cd02068		127	radical_SAM_B12_BD B12 binding domain_like associa	97.76
COG1625		414	Fe-S oxidoreductase, related to NifB/MoaA family [	97.64
PF02310		121	B12-binding: B12 binding domain; InterPro: IPR0061	97.42
TIGR03279		433	cyano_FeS_chp putative FeS-containing Cyanobacteri	97.15
COG1313		335	PflX Uncharacterized Fe-S protein PflX, homolog of	97.1
TIGR00640		132	acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal	97.0
PRK10076		213	pyruvate formate lyase II activase; Provisional	96.98
COG0602		212	NrdG Organic radical activating enzymes [Posttrans	96.75
PF13353		139	Fer4_12: 4Fe-4S single cluster domain; PDB: 3C8F_A	96.5
TIGR02826		147	RNR_activ_nrdG3 anaerobic ribonucleoside-triphosph	96.39
cd02067		119	B12-binding B12 binding domain (B12-BD). This doma	96.36
PF13394		119	Fer4_14: 4Fe-4S single cluster domain; PDB: 1TV8_B	96.2
PRK02261		137	methylaspartate mutase subunit S; Provisional	96.08
cd02065		125	B12-binding_like B12 binding domain (B12-BD). Most	96.0
cd02072		128	Glm_B12_BD B12 binding domain of glutamate mutase	95.56
TIGR01501		134	MthylAspMutase methylaspartate mutase, S subunit.	95.55
cd03174		265	DRE_TIM_metallolyase DRE-TIM metallolyase superfam	95.51
COG2108		353	Uncharacterized conserved protein related to pyruv	95.35
COG5014		228	Predicted Fe-S oxidoreductase [General function pr	95.21
COG2185		143	Sbm Methylmalonyl-CoA mutase, C-terminal domain/su	94.67
TIGR02491		154	NrdG anaerobic ribonucleoside-triphosphate reducta	94.67
cd02071		122	MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 bin	94.38
KOG2876		323	consensus Molybdenum cofactor biosynthesis pathway	93.51
PRK11121		154	nrdG anaerobic ribonucleotide reductase-activating	93.45
PLN02746		347	hydroxymethylglutaryl-CoA lyase	93.33
PRK09426		714	methylmalonyl-CoA mutase; Reviewed	92.68
cd02070		201	corrinoid_protein_B12-BD B12 binding domain of cor	91.67
PRK05692		287	hydroxymethylglutaryl-CoA lyase; Provisional	90.88
cd07938		274	DRE_TIM_HMGL 3-hydroxy-3-methylglutaryl-CoA lyase,	90.51
KOG2492		552	consensus CDK5 activator-binding protein [Signal t	88.9
TIGR02370		197	pyl_corrinoid methyltransferase cognate corrinoid	88.78
cd07948		262	DRE_TIM_HCS Saccharomyces cerevisiae homocitrate s	88.22
cd07939		259	DRE_TIM_NifV Streptomyces rubellomurinus FrbC and	87.84
cd02069		213	methionine_synthase_B12_BD B12 binding domain of m	86.32
PRK11858		378	aksA trans-homoaconitate synthase; Reviewed	85.72
cd07944		266	DRE_TIM_HOA_like 4-hydroxy-2-oxovalerate aldolase-	85.35
PRK14816		182	NADH dehydrogenase subunit B; Provisional	85.32
PRK14818		173	NADH dehydrogenase subunit B; Provisional	84.99
COG3269		73	Predicted RNA-binding protein, contains TRAM domai	84.62
TIGR03217		333	4OH_2_O_val_ald 4-hydroxy-2-oxovalerate aldolase.	83.78
TIGR01957		145	nuoB_fam NADH-quinone oxidoreductase, B subunit. T	83.51
PF00682		237	HMGL-like: HMGL-like of this family is not conserv	81.21
cd07940		268	DRE_TIM_IPMS 2-isopropylmalate synthase (IPMS), N-	80.77
TIGR02660		365	nifV_homocitr homocitrate synthase NifV. This fami	80.51
cd07937		275	DRE_TIM_PC_TC_5S Pyruvate carboxylase and Transcar	80.25

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

Probab=100.00  E-value=8e-97  Score=755.65  Aligned_cols=476  Identities=63%  Similarity=1.037  Sum_probs=449.8

Q ss_pred             CCchhhhhccCCCCCCCCCCCCCCCcceecccccCCCCCc-cCCCCcccCCCCCCCCCCceEEEEecCCccChhHHHHHH
Q 006956            1 MEDIEDLLAGSGGGGAPPGFRLPINAVGVNPKYNKNKPRL-HDNHLSKTGSLSPKIPGTETIYMKTFGCSHNQSDSEYMA   79 (624)
Q Consensus         1 ~~died~~~~~~~~~~~~~~r~~~~~~~v~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~v~i~TlGC~~N~~Dse~~~   79 (624)
                      ||||||++   +++|++|++|++.+.+ |.||.+|+...+ .+.+. +..+.+|.|||+++|||+||||++|++|||||+
T Consensus         1 ~ddiedl~---s~~d~kp~~r~~~~k~-v~pk~~kr~~~k~~q~ee-~~~ps~s~ipgtqki~iktwgcshnnsdseyma   75 (547)
T KOG4355|consen    1 MDDIEDLL---SGGDAKPGFRLPLNKV-VNPKTNKRISSKPDQIEE-SNRPSSSKIPGTQKIYIKTWGCSHNNSDSEYMA   75 (547)
T ss_pred             CccHHHHh---hCCCCCCccccccccc-cccccccccccCchhhhh-cCCCccccCCCccEEEEEeecccCCCchhHHHh
Confidence            79999999   7789999999997665 999987754322 22222 223568999999999999999999999999999


Q ss_pred             HHHHhcCceeeCCCCCCcEEEEeecccccchHHHHHHHHHHHhhCCCCEEEEccccCcChhhhcCCccEEEcCCchhHHH
Q 006956           80 GQLSAFGYALTDNSEEADIWLINTCTVKSPSQSAMDTLIAKCKSAKKPLVVAGCVPQGSRDLKELEGVSIVGVQQIDRVV  159 (624)
Q Consensus        80 ~~L~~~G~~~~~~~~~ADlviINTCtv~~~ae~~~~~~ir~~k~~~~~VVVgGc~aq~~~e~~~~~~d~VvG~~~~~~l~  159 (624)
                      |+|.+.||.++. +++||+|++|||||.++++..+++.|.+.++.++++|++||.||..|++..+.+.+|||.+++++++
T Consensus        76 gqlaaygy~lte-~eeadlwllnsctvknpsed~frn~i~~g~~~~k~~viagcvpqg~p~~dyl~glsvigvqqidrvv  154 (547)
T KOG4355|consen   76 GQLAAYGYALTE-PEEADLWLLNSCTVKNPSEDAFRNLITRGRSGKKPLVIAGCVPQGSPDLDYLEGLSVIGVQQIDRVV  154 (547)
T ss_pred             hhHHhhhhccCC-cccccEEEecccccCCchHHHHHHHHHhhhcCCCceEEEecCCCCCcchhhhcCceEeehhhhhHHH
Confidence            999999999999 9999999999999999999999999999998889999999999999999999999999999999999


Q ss_pred             HHHHHHhcCCeeEeeccccCCCCCCCcccCCceEEEEEeCCCCCCCCCCcccCccCCCcccCCHHHHHHHHHHHHHCCCc
Q 006956          160 EVVEETLKGHEVRLLHRKKLPALDLPKVRRNKFVEILPINVGCLGACTYCKTKHARGHLGSYTVESLVGRVRTVIADGVK  239 (624)
Q Consensus       160 ell~~~~~g~~~~~~~~~~~~~~~lp~~r~~~~~a~I~isrGCp~~CsFC~ip~~rG~~Rsr~~e~Iv~EI~~L~~~Gvk  239 (624)
                      |++++.++|+.++++.+...+++++|+.|+++++..|.|+.||-+.|+||...++||..-++|++++++.++...+.|+.
T Consensus       155 evveetlkghsvrll~rr~~galdlpkvrknplieIi~intgclgaCtyckTkharg~l~sy~~dslvervrt~f~egv~  234 (547)
T KOG4355|consen  155 EVVEETLKGHSVRLLTRRTLGALDLPKVRKNPLIEIISINTGCLGACTYCKTKHARGLLASYPKDSLVERVRTSFEEGVC  234 (547)
T ss_pred             HHHHHHhccceEeeeecccccccCchhhccCCceEEEEeccccccccccccccccccccccCCHHHHHHHHHHHHhcCcE
Confidence            99999999999999988778889999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEeecCCCCCCCCccCCHHHHHHHHHHhCCCCCCceEEEeecCCcchhHHHHHHHHHHhCCCcceeccccCCCCCHHH
Q 006956          240 EVWLSSEDTGAYGRDIGVNLPILLNAIVAELPPDGSTMLRIGMTNPPFILEHLKEIAEVLRHPCVYSFLHVPVQSGSDAV  319 (624)
Q Consensus       240 eI~l~g~d~~~yg~d~~~~l~eLL~~l~~~l~~~~~~~iri~~~~p~~i~~~l~el~~l~~~~~v~~~l~IGlQSgsd~v  319 (624)
                      +||+++.|+++||+|.+.+++.||+++.+.+|  ..+++|+++++|+++.+++++++..+++++++.++|+|+|||||.+
T Consensus       235 eIwltsedTgaygrdig~slp~ll~klv~~iP--e~cmlr~gmTnpP~ilehl~e~a~vlrhp~vYsflhvpvqsgsdsv  312 (547)
T KOG4355|consen  235 EIWLTSEDTGAYGRDIGKSLPKLLWKLVEVIP--ESCMLRAGMTNPPYILEHLEEAAFVLRHPRVYSFLHVPVQSGSDSV  312 (547)
T ss_pred             EEEecccccchhhhhhhhhhHHHHHHHHHhcc--hhhhhhhcCCCCchHHHHHHHHHHHhcCCeEEEEEecccccCchhH
Confidence            99999999999999999999999999999998  7899999999999999999999999999999999999999999999


Q ss_pred             HHhhcCCCCHHHHHHHHHHHHHhCCCCEEEEEEEEcCCCCCHHHHHHHHHHHHHcCCCeEEEEEeeeCCCCccccCCCCC
Q 006956          320 LSAMNREYTLSDFRTVVDTLIELVPGMQIATDIICGFPGETDEDFNQTVNLIKEYKFPQVHISQFYPRPGTPAARMKKVP  399 (624)
Q Consensus       320 Lk~M~R~~t~e~~~e~I~~lr~~~pgi~i~td~IvGfPGETeedf~eTl~fl~el~~~~v~i~~ysP~PGTpa~~~~~vp  399 (624)
                      |..|+|.|...++...++.+++.+|||.|.||||+||||||++||++|++++++++|+.++|++|+|+||||+++|+++|
T Consensus       313 l~emkreyc~~dfk~Vvd~LterVPgi~IATDiIcgFPtETdeDFeeTmeLv~kYKFPslfInQfyPRpGTPAAkmkki~  392 (547)
T KOG4355|consen  313 LTEMKREYCNFDFKIVVDFLTERVPGITIATDIICGFPTETDEDFEETMELVRKYKFPSLFINQFYPRPGTPAAKMKKIP  392 (547)
T ss_pred             HHHHHHHHhhhhHHHHHHHHHhhCCCcEEeeeeeecCCCCchHHHHHHHHHHHHccCchhhhhhcCCCCCChHHhhhccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhCccccCCCcEEEEEEEEEecCCeee-----eeEEEEEcCCCCCCCCEEEEEEEEEecceEEE
Q 006956          400 SAVVKKRSRELTSVFEAFTPYLGMEGRVERIWITEIAADGIHL-----GYVQVLVPSTGNMLGTSALVKITSVGRWSVFG  474 (624)
Q Consensus       400 ~~~~~~R~~~L~~l~~~~~~~~~~vG~~~~VLve~~~~~g~~~-----~y~~V~~~~~~~~~G~~v~V~I~~~~~~~l~g  474 (624)
                      ..++++|.++|.++++++..|...+|+..+|||++.+.|+.++     +|.||+++.+...+|+++.|+||++++|+|.|
T Consensus       393 a~~vkkRTk~ls~lF~sy~pYtd~ige~~rVlVTEva~Dklh~VgHnksYeQVLvp~~~~~mGt~vevrItsvgkfsm~g  472 (547)
T KOG4355|consen  393 AVEVKKRTKALSELFRSYTPYTDEIGELHRVLVTEVAADKLHYVGHNKSYEQVLVPLEYCKMGTWVEVRITSVGKFSMIG  472 (547)
T ss_pred             HHHHHHHHHHHHHHHHhcCCcccccccEEEEEEEEeeccceeeeccccceeEEEeecchhhccceEEEEEEeeeeeeeec
Confidence            9999999999999999999999999999999999999888765     89999999888899999999999999999999


Q ss_pred             EEEecccccc
Q 006956          475 EVIKILNQVD  484 (624)
Q Consensus       475 ~~v~~~~~~~  484 (624)
                      +++...+.+.
T Consensus       473 ep~s~~~d~~  482 (547)
T KOG4355|consen  473 EPASDQEDQT  482 (547)
T ss_pred             cccchhhhcC
Confidence            9998755444

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

>KOG2492 consensus CDK5 activator-binding protein [Signal transduction mechanisms]	Back alignment and domain information

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

>PRK00955 hypothetical protein; Provisional	Back alignment and domain information

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

>PRK01254 hypothetical protein; Provisional	Back alignment and domain information

>PRK05481 lipoyl synthase; Provisional	Back alignment and domain information

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

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

>PRK07094 biotin synthase; Provisional	Back alignment and domain information

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

>TIGR00510 lipA lipoate synthase	Back alignment and domain information

>PF00919 UPF0004: Uncharacterized protein family UPF0004; InterPro: IPR013848 The methylthiotransferase (MTTase) or miaB-like family is named after the (dimethylallyl)adenosine tRNA MTTase miaB protein, which catalyses a C-H to C-S bond conversion in the methylthiolation of tRNA	Back alignment and domain information

>PRK12928 lipoyl synthase; Provisional	Back alignment and domain information

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

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

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

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

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

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

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

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

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

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

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

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

>PRK06256 biotin synthase; Validated	Back alignment and domain information

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

>TIGR01210 conserved hypothetical protein TIGR01210	Back alignment and domain information

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

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

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

>TIGR00433 bioB biotin synthetase	Back alignment and domain information

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

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

>PLN02428 lipoic acid synthase	Back alignment and domain information

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

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

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

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

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

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

>PRK06267 hypothetical protein; Provisional	Back alignment and domain information

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

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

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

>cd01335 Radical_SAM Radical SAM superfamily	Back alignment and domain information

>PRK08445 hypothetical protein; Provisional	Back alignment and domain information

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

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

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

>PRK08508 biotin synthase; Provisional	Back alignment and domain information

>PLN02389 biotin synthase	Back alignment and domain information

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

>PRK15108 biotin synthase; Provisional	Back alignment and domain information

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

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

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

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

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

>PRK08444 hypothetical protein; Provisional	Back alignment and domain information

>PRK05926 hypothetical protein; Provisional	Back alignment and domain information

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

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

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

>PRK05927 hypothetical protein; Provisional	Back alignment and domain information

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

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

>PTZ00413 lipoate synthase; Provisional	Back alignment and domain information

>PLN02951 Molybderin biosynthesis protein CNX2	Back alignment and domain information

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

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

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

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

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

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

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

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

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

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

>TIGR00238 KamA family protein	Back alignment and domain information

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

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

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

>TIGR02495 NrdG2 anaerobic ribonucleoside-triphosphate reductase activating protein	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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

>PF01938 TRAM: TRAM domain; InterPro: IPR002792 The TRAM (after TRM2 and miaB) domain is a 60-70-residue-long module that is found in: Two distinct classes of tRNA-modifying enzymes, namely uridine methylases of the TRM2 family and enzymes of the miaB family that are involved in 2- methylthioadenine formation In several other proteins associated with the translation machinery In a family of small uncharacterised archaeal proteins that are predicted to have a role in the regulation of tRNA modification and/or translation The TRAM domain can be found alone or in association with other domains, such as the catalytic biotin/lipoate synthetase-like domain, the RNA methylase domain, the ribosomal S2 domain and the eIF2-beta domain

Back alignment and domain information

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

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

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

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

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

>KOG2535 consensus RNA polymerase II elongator complex, subunit ELP3/histone acetyltransferase [Chromatin structure and dynamics; Transcription]	Back alignment and domain information

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

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

>cd02068 radical_SAM_B12_BD B12 binding domain_like associated with radical SAM domain	Back alignment and domain information

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

>PF02310 B12-binding: B12 binding domain; InterPro: IPR006158 The cobalamin (vitamin B12) binding domain can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin)	Back alignment and domain information

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

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

>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain	Back alignment and domain information

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

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

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

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

>cd02067 B12-binding B12 binding domain (B12-BD)	Back alignment and domain information

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

>PRK02261 methylaspartate mutase subunit S; Provisional	Back alignment and domain information

>cd02065 B12-binding_like B12 binding domain (B12-BD)	Back alignment and domain information

>cd02072 Glm_B12_BD B12 binding domain of glutamate mutase (Glm)	Back alignment and domain information

>TIGR01501 MthylAspMutase methylaspartate mutase, S subunit	Back alignment and domain information

>cd03174 DRE_TIM_metallolyase DRE-TIM metallolyase superfamily	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

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

>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]	Back alignment and domain information

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

>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain	Back alignment and domain information

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

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

>PLN02746 hydroxymethylglutaryl-CoA lyase	Back alignment and domain information

>PRK09426 methylmalonyl-CoA mutase; Reviewed	Back alignment and domain information

>cd02070 corrinoid_protein_B12-BD B12 binding domain of corrinoid proteins	Back alignment and domain information

>PRK05692 hydroxymethylglutaryl-CoA lyase; Provisional	Back alignment and domain information

>cd07938 DRE_TIM_HMGL 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain	Back alignment and domain information

>KOG2492 consensus CDK5 activator-binding protein [Signal transduction mechanisms]	Back alignment and domain information

>TIGR02370 pyl_corrinoid methyltransferase cognate corrinoid proteins, Methanosarcina family	Back alignment and domain information

>cd07948 DRE_TIM_HCS Saccharomyces cerevisiae homocitrate synthase and related proteins, catalytic TIM barrel domain	Back alignment and domain information

>cd07939 DRE_TIM_NifV Streptomyces rubellomurinus FrbC and related proteins, catalytic TIM barrel domain	Back alignment and domain information

>cd02069 methionine_synthase_B12_BD B12 binding domain of methionine synthase	Back alignment and domain information

>PRK11858 aksA trans-homoaconitate synthase; Reviewed	Back alignment and domain information

>cd07944 DRE_TIM_HOA_like 4-hydroxy-2-oxovalerate aldolase-like, N-terminal catalytic TIM barrel domain	Back alignment and domain information

>PRK14816 NADH dehydrogenase subunit B; Provisional	Back alignment and domain information

>PRK14818 NADH dehydrogenase subunit B; Provisional	Back alignment and domain information

>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]	Back alignment and domain information

>TIGR03217 4OH_2_O_val_ald 4-hydroxy-2-oxovalerate aldolase	Back alignment and domain information

>TIGR01957 nuoB_fam NADH-quinone oxidoreductase, B subunit	Back alignment and domain information

>PF00682 HMGL-like: HMGL-like of this family is not conserved in other members	Back alignment and domain information

>cd07940 DRE_TIM_IPMS 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain	Back alignment and domain information

>TIGR02660 nifV_homocitr homocitrate synthase NifV	Back alignment and domain information

>cd07937 DRE_TIM_PC_TC_5S Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		624
2qgq_A		304	Crystal Structure Of Tm_1862 From Thermotoga Mariti		3e-23
3cix_A		348	X-ray Structure Of The [fefe]-hydrogenase Maturase		3e-06
3ciw_A		348	X-Ray Structure Of The [fefe]-Hydrogenase Maturase		9e-06
3iiz_A		348	X-Ray Structure Of The Fefe-Hydrogenase Maturase Hy		1e-05

>pdb|2QGQ|A Chain A, Crystal Structure Of Tm_1862 From Thermotoga Maritima. Northeast Structural Genomics Consortium Target Vr77 Length = 304

Back alignment and structure

Iteration: 1

Score = 106 bits (265), Expect = 3e-23, Method: Compositional matrix adjust. Identities = 66/218 (30%), Positives = 109/218 (50%), Gaps = 8/218 (3%) Query: 196 LPINVGCLGACTYCKTKHARGHLGSYTVESLVGRVRTVIADGVKEVWLSSEDTGAYGRDI 255 + I+ GC CT+C +G L S ++E + V ++ +G KE+ L ++DT +YG D+ Sbjct: 8 VKISDGCDRGCTFCSIPSFKGSLRSRSIEDITREVEDLLKEGKKEIILVAQDTTSYGIDL 67 Query: 256 GVN--LPILLNAIVAELPPDGSTMLRIGMTNPPFILEHLKEIAEVLRHPCVYSFLHVPVQ 313 LP LL + + +G +R+ +P + E + I+ L V + VPVQ Sbjct: 68 YRKQALPDLLRRLNS---LNGEFWIRVXYLHPDHLTEEI--ISAXLELDKVVKYFDVPVQ 122 Query: 314 SGSDAVLSAMNREYTLSDFRTVVDTLIELVPGMQIATDIICGFPGETDEDFNQTVNLIKE 373 GSD +L R + + + + ++ E P + T II GFPGET+EDF + ++E Sbjct: 123 HGSDKILKLXGRTKSSEELKKXLSSIRERFPDAVLRTSIIVGFPGETEEDFEELKQFVEE 182 Query: 374 YKFPQVHISQFYPRPGTPAARMK-KVPSAVVKKRSREL 410 +F ++ + GT A +K KV K+R EL Sbjct: 183 IQFDKLGAFVYSDEEGTVAFNLKEKVDPEXAKRRQEEL 220

PyMOL of 2qgq

>pdb|3CIX|A Chain A, X-ray Structure Of The [fefe]-hydrogenase Maturase Hyde From Thermotoga Maritima In Complex With Thiocyanate Length = 348

Back alignment and structure

>pdb|3CIW|A Chain A, X-Ray Structure Of The [fefe]-Hydrogenase Maturase Hyde From Thermotoga Maritima Length = 348

Back alignment and structure

>pdb|3IIZ|A Chain A, X-Ray Structure Of The Fefe-Hydrogenase Maturase Hyde From T. Maritima In Complex With S-Adenosyl-L-Methionine Length = 348

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		624
2qgq_A		304	Protein TM_1862; alpha-beta protein, structural ge	6e-43
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-12
1olt_A		457	Oxygen-independent coproporphyrinogen III oxidase;	5e-07
3iix_A		348	Biotin synthetase, putative; adoMet radical, SAM r	1e-05

>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} Length = 304	Back alignment and structure

 Score =  155 bits (394), Expect = 6e-43
 Identities = 81/297 (27%), Positives = 134/297 (45%), Gaps = 33/297 (11%)

Query: 201 GCLGACTYCKTKHARGHLGSYTVESLVGRVRTVIADGVKEVWLSSEDTGAYGRDIG--VN 258
           GC   CT+C     +G L S ++E +   V  ++ +G KE+ L ++DT +YG D+     
Sbjct: 13  GCDRGCTFCSIPSFKGSLRSRSIEDITREVEDLLKEGKKEIILVAQDTTSYGIDLYRKQA 72

Query: 259 LPILLNAIVAELPPDGSTMLRIGMTNP-PFILEHLKEIAEVLRHPCVYSFLHVPVQSGSD 317
           LP LL  + +    +G   +R+   +P     E +  + E      V  +  VPVQ GSD
Sbjct: 73  LPDLLRRLNSL---NGEFWIRVMYLHPDHLTEEIISAMLE---LDKVVKYFDVPVQHGSD 126

Query: 318 AVLSAMNREYTLSDFRTVVDTLIELVPGMQIATDIICGFPGETDEDFNQTVNLIKEYKFP 377
            +L  M R  +  + + ++ ++ E  P   + T II GFPGET+EDF +    ++E +F 
Sbjct: 127 KILKLMGRTKSSEELKKMLSSIRERFPDAVLRTSIIVGFPGETEEDFEELKQFVEEIQFD 186

Query: 378 QVHISQFYPRPGTPAARMK-KVPSAVVKKRSRELTSV-----FEAFTPYLG------MEG 425
           ++    +    GT A  +K KV   + K+R  EL  +           ++G      +EG
Sbjct: 187 KLGAFVYSDEEGTVAFNLKEKVDPEMAKRRQEELLLLQAEISNSRLDRFVGKKLKFLVEG 246

Query: 426 RVERIWI--TEIAA---DGIHLGYVQVLVPSTGNMLGTSALVKITSVGRWSVFGEVI 477
           +  +  +  T   A   DG       V V   G  +G    V I     + ++G VI
Sbjct: 247 KEGKFLVGRTWTEAPEVDG------VVFVRGKGK-IGDFLEVVIKEHDEYDMWGSVI 296

PyMOL of 2qgq

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

>1olt_A Oxygen-independent coproporphyrinogen III oxidase; heme biosynthesis, decarboxylase, radical SAM enzyme, 4Fe- 4 cluster; HET: SAM; 2.07A {Escherichia coli} SCOP: c.1.28.2 Length = 457	Back alignment and structure

>3iix_A Biotin synthetase, putative; adoMet radical, SAM radical, adoMet cleavage, Fe4S4 cluster, HYDE, hydrogenase, maturation, beta barrel; HET: OTY CSO 5AD CPS; 1.25A {Thermotoga maritima} PDB: 3ciw_A* 3iiz_A* 3cix_A* Length = 348	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		624
2qgq_A		304	Protein TM_1862; alpha-beta protein, structural ge	100.0
1olt_A		457	Oxygen-independent coproporphyrinogen III oxidase;	99.91
3t7v_A		350	Methylornithine synthase PYLB; TIM-barrel fold, mu	99.88
3iix_A		348	Biotin synthetase, putative; adoMet radical, SAM r	99.87
1r30_A		369	Biotin synthase; SAM radical protein, TIM barrel,	99.84
1tv8_A		340	MOAA, molybdenum cofactor biosynthesis protein A;	99.7
3c8f_A		245	Pyruvate formate-lyase 1-activating enzyme; adoMet	99.57
2yx0_A		342	Radical SAM enzyme; predicted tRNA modification en	99.55
2z2u_A		311	UPF0026 protein MJ0257; metal binding protein; 2.4	99.34
2a5h_A		416	L-lysine 2,3-aminomutase; radical SAM, four-iron-f	99.25
3rfa_A		404	Ribosomal RNA large subunit methyltransferase N; r	99.14
4fhd_A		368	Spore photoproduct lyase; partial TIM-barrel, DNA	97.51
3can_A		182	Pyruvate-formate lyase-activating enzyme; structur	97.24
2yxb_A		161	Coenzyme B12-dependent mutase; alpha/beta, structu	96.87
1ccw_A		137	Protein (glutamate mutase); coenzyme B12, radical	94.63
1req_A		727	Methylmalonyl-COA mutase; isomerase, intramolecula	93.49
2xij_A		762	Methylmalonyl-COA mutase, mitochondrial; isomerase	93.31
1ydn_A		295	Hydroxymethylglutaryl-COA lyase; TIM-barrel protei	92.14
1y80_A		210	Predicted cobalamin binding protein; corrinoid, fa	91.73
2i2x_B		258	MTAC, methyltransferase 1; TIM barrel and helix bu	91.51
2cw6_A		298	Hydroxymethylglutaryl-COA lyase, mitochondrial; HM	91.21
1xrs_B		262	D-lysine 5,6-aminomutase beta subunit; TIM barrel,	89.92
2ftp_A		302	Hydroxymethylglutaryl-COA lyase; structural genomi	87.94
3kp1_A		763	D-ornithine aminomutase E component; 5 aminomutase	85.71
1req_B		637	Methylmalonyl-COA mutase; isomerase, intramolecula	85.64
1ydo_A		307	HMG-COA lyase; TIM-barrel protein, structural geno	85.53
1nvm_A		345	HOA, 4-hydroxy-2-oxovalerate aldolase; sequestered	81.3
3ezx_A		215	MMCP 1, monomethylamine corrinoid protein 1; N ter	81.18

>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

Probab=100.00  E-value=4.7e-48  Score=404.61  Aligned_cols=280  Identities=28%  Similarity=0.472  Sum_probs=228.2

Q ss_pred             ceEEEEEeCCCCCCCCCCcccCccCCCcccCCHHHHHHHHHHHHHCCCcEEEEeecCCCCCCCCc--cCCHHHHHHHHHH
Q 006956          191 KFVEILPINVGCLGACTYCKTKHARGHLGSYTVESLVGRVRTVIADGVKEVWLSSEDTGAYGRDI--GVNLPILLNAIVA  268 (624)
Q Consensus       191 ~~~a~I~isrGCp~~CsFC~ip~~rG~~Rsr~~e~Iv~EI~~L~~~GvkeI~l~g~d~~~yg~d~--~~~l~eLL~~l~~  268 (624)
                      +..+||++++||+++|+||.+|..+|+.|++++++|++|++.+.+.|+++|+|+|+|++.||.+.  ...+.+|++.+.+
T Consensus         3 ~~~~~v~is~GC~~~C~fC~~~~~~g~~r~r~~e~i~~ei~~l~~~G~~ei~l~g~~~~~yG~~~~~~~~l~~Ll~~l~~   82 (304)
T 2qgq_A            3 RPYAYVKISDGCDRGCTFCSIPSFKGSLRSRSIEDITREVEDLLKEGKKEIILVAQDTTSYGIDLYRKQALPDLLRRLNS   82 (304)
T ss_dssp             CSEEEEESBCCC-------------CCCCBCCHHHHHHHHHHHHHTTCCEEEEECTTGGGTTHHHHSSCCHHHHHHHHHT
T ss_pred             CEEEEEEECCCCCCcCccCCccccCCCceeeCHHHHHHHHHHHHHCCCcEEEEEeEcccccCCCCCcHHHHHHHHHHHHh
Confidence            45789999999999999999999999999999999999999999999999999999999998653  2579999999976


Q ss_pred             hCCCCCCceEEEeecCCcchhHHHHHHHHHHhCCCcceeccccCCCCCHHHHHhhcCCCCHHHHHHHHHHHHHhCCCCEE
Q 006956          269 ELPPDGSTMLRIGMTNPPFILEHLKEIAEVLRHPCVYSFLHVPVQSGSDAVLSAMNREYTLSDFRTVVDTLIELVPGMQI  348 (624)
Q Consensus       269 ~l~~~~~~~iri~~~~p~~i~~~l~el~~l~~~~~v~~~l~IGlQSgsd~vLk~M~R~~t~e~~~e~I~~lr~~~pgi~i  348 (624)
                       .+  +..|+++.+++|..+++++  +..+...+++|+++++|+||+|+++|+.|+|+++.+++.++++.+++.+||+.+
T Consensus        83 -~~--gi~~ir~~~~~p~~l~~e~--l~~l~~~g~~~~~l~i~lqs~s~~vl~~m~r~~t~e~~~~~i~~l~~~~~gi~i  157 (304)
T 2qgq_A           83 -LN--GEFWIRVMYLHPDHLTEEI--ISAMLELDKVVKYFDVPVQHGSDKILKLMGRTKSSEELKKMLSSIRERFPDAVL  157 (304)
T ss_dssp             -SS--SSCEEEECCCCGGGCCHHH--HHHHHHCTTBCCEEECCCBCSCHHHHHHTTCCSCHHHHHHHHHHHHHHCTTCEE
T ss_pred             -cC--CCcEEEEeeeecccCCHHH--HHHHHhCCCCccEEEEecccCCHHHHHHhCCCCCHHHHHHHHHHHHhhCCCCEE
Confidence             44  5679999889999887765  555555666689999999999999999999999999999999999998889999


Q ss_pred             EEEEEEcCCCCCHHHHHHHHHHHHHcCCCeEEEEEeeeCCCCccccCC-CCCHHHHHHHHHHHHHHHHH--hCccccCCC
Q 006956          349 ATDIICGFPGETDEDFNQTVNLIKEYKFPQVHISQFYPRPGTPAARMK-KVPSAVVKKRSRELTSVFEA--FTPYLGMEG  425 (624)
Q Consensus       349 ~td~IvGfPGETeedf~eTl~fl~el~~~~v~i~~ysP~PGTpa~~~~-~vp~~~~~~R~~~L~~l~~~--~~~~~~~vG  425 (624)
                      .+|||+||||||+++|++|++++++++++.+++|+|+|+||||+++++ ++|++++++|.++|+++++.  .+++++++|
T Consensus       158 ~~~~IvG~PgEt~ed~~~t~~~l~~l~~~~v~~~~~~p~pgT~~~~~~~~v~~~~~~~r~~~l~~~~~~~~~~~~~~~~g  237 (304)
T 2qgq_A          158 RTSIIVGFPGETEEDFEELKQFVEEIQFDKLGAFVYSDEEGTVAFNLKEKVDPEMAKRRQEELLLLQAEISNSRLDRFVG  237 (304)
T ss_dssp             EEEEEECCTTCCHHHHHHHHHHHHHHCCSEEEEEECCC-----------CCCHHHHHHHHHHHHHHHHHHHHHHHHTTTT
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHHHHcCCCEEEEEEeeCCCCChhHhCcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence            999999999999999999999999999999999999999999999998 99999999999999999985  467899999


Q ss_pred             cEEEEEEEEEecCCeee----eeEEE-----EEcCCCCCCCCEEEEEEEEEecceEEEEEE
Q 006956          426 RVERIWITEIAADGIHL----GYVQV-----LVPSTGNMLGTSALVKITSVGRWSVFGEVI  477 (624)
Q Consensus       426 ~~~~VLve~~~~~g~~~----~y~~V-----~~~~~~~~~G~~v~V~I~~~~~~~l~g~~v  477 (624)
                      ++++||||+.. ++.+.    +|.+|     +++.+. .+|++++|+|+++..++|.|+++
T Consensus       238 ~~~~vl~e~~~-~~~~~g~~~~~~~~~dg~~~~~~~~-~~g~~~~v~i~~~~~~~l~g~~~  296 (304)
T 2qgq_A          238 KKLKFLVEGKE-GKFLVGRTWTEAPEVDGVVFVRGKG-KIGDFLEVVIKEHDEYDMWGSVI  296 (304)
T ss_dssp             CEEEEEEEEEE-TTEEEEEETTCCTTTSCCEEEESCC-CTTCEEEEEEEEEETTEEEEEEC
T ss_pred             CEEEEEEEecC-CCEEEEECCCCcEeccceEEEcCCC-CCCCEEEEEEEEeeCCeEEEEEE
Confidence            99999999863 33332    56555     776544 78999999999999999999975

PyMOL of 2qgq

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

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

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

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

>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

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

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

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

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

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

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

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

>2yxb_A Coenzyme B12-dependent mutase; alpha/beta, structural genomics, NPPSFA, national project on structural and functional analyses; 1.80A {Aeropyrum pernix}	Back alignment and structure

>1ccw_A Protein (glutamate mutase); coenzyme B12, radical reaction, TIM-barrel rossman-fold, isomerase; HET: CNC TAR; 1.60A {Clostridium cochlearium} SCOP: c.23.6.1 PDB: 1cb7_A* 1b1a_A 1i9c_A* 1be1_A 1fmf_A 1id8_A*	Back alignment and structure

>1req_A Methylmalonyl-COA mutase; isomerase, intramolecular transferase; HET: B12 DCA; 2.00A {Propionibacterium freudenreichii subspshermanii} SCOP: c.1.19.1 c.23.6.1 PDB: 2req_A* 3req_A* 4req_A* 6req_A* 7req_A* 5req_A* 1e1c_A*	Back alignment and structure

>2xij_A Methylmalonyl-COA mutase, mitochondrial; isomerase, organic aciduria, vitamin B12; HET: B12 5AD BTB; 1.95A {Homo sapiens} PDB: 2xiq_A* 3bic_A	Back alignment and structure

>1ydn_A Hydroxymethylglutaryl-COA lyase; TIM-barrel protein, structural genomics, PSI, protein struct initiative; 2.30A {Brucella melitensis}	Back alignment and structure

>1y80_A Predicted cobalamin binding protein; corrinoid, factor IIIM, methyl transferase, structural genomics, PSI, protein structure initiative; HET: B1M; 1.70A {Moorella thermoacetica}	Back alignment and structure

>2i2x_B MTAC, methyltransferase 1; TIM barrel and helix bundle (MTAB), rossman fold and helix B (MTAC); HET: B13; 2.50A {Methanosarcina barkeri}	Back alignment and structure

>2cw6_A Hydroxymethylglutaryl-COA lyase, mitochondrial; HMG-COA lyase, ketogenic enzyme; HET: 3HG; 2.10A {Homo sapiens} PDB: 3mp3_A* 3mp4_A 3mp5_A*	Back alignment and structure

>1xrs_B D-lysine 5,6-aminomutase beta subunit; TIM barrel, rossmann domain, PLP, cobalamin, 5'-deoxyad radical, adenosylcobalamin; HET: B12 PLP 5AD; 2.80A {Clostridium sticklandii} SCOP: c.23.6.1 d.230.4.1	Back alignment and structure

>2ftp_A Hydroxymethylglutaryl-COA lyase; structural genomics, PSI, protein structure initiativ midwest center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa}	Back alignment and structure

>3kp1_A D-ornithine aminomutase E component; 5 aminomutase (OAM), metal binding protein; HET: PLP B12 5AD; 2.01A {Clostridium sticklandii} PDB: 3kow_A* 3koy_A* 3koz_A* 3kp0_A* 3kox_A*	Back alignment and structure

>1req_B Methylmalonyl-COA mutase; isomerase, intramolecular transferase; HET: B12 DCA; 2.00A {Propionibacterium freudenreichii subspshermanii} SCOP: c.1.19.1 c.23.6.1 PDB: 1e1c_B* 2req_B* 3req_B* 4req_B* 5req_B* 6req_B* 7req_B*	Back alignment and structure

>1ydo_A HMG-COA lyase; TIM-barrel protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG,; 2.71A {Bacillus subtilis subsp}	Back alignment and structure

>1nvm_A HOA, 4-hydroxy-2-oxovalerate aldolase; sequestered tunnel, substrate channeling; HET: NAD; 1.70A {Pseudomonas SP} SCOP: a.5.7.1 c.1.10.5	Back alignment and structure

>3ezx_A MMCP 1, monomethylamine corrinoid protein 1; N terminal all helical bundle C terminal rossmann fold, cobalt, metal-binding; HET: HCB; 2.56A {Methanosarcina barkeri}	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		624
d1olta_		441	Oxygen-independent coproporphyrinogen III oxidase	99.86
d1r30a_		312	Biotin synthase {Escherichia coli [TaxId: 562]}	99.79
d1tv8a_		327	Molybdenum cofactor biosynthesis protein A MoaA {S	98.74
d7reqa2		168	Methylmalonyl-CoA mutase alpha subunit, C-terminal	96.81
d7reqb2		163	Methylmalonyl-CoA mutase beta subunit, C-terminal	95.43
d1ccwa_		137	Glutamate mutase, small subunit {Clostridium cochl	93.99
d1xrsb1		160	D-lysine 5,6-aminomutase beta subunit KamE, C-term	93.98
d3bula2		156	Methionine synthase, C-terminal domain {Escherichi	92.15
d1yeza1		68	Hypothetical protein MM1357 {Methanosarcina mazei	91.8
d1yvca1		69	Hypothetical protein MMP0076 {Methanococcus maripa	91.76
d1uwva1		60	rRNA (Uracil-5-)-methyltransferase RumA, N-termina	91.25

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

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Radical SAM enzymes
family: Oxygen-independent coproporphyrinogen III oxidase HemN
domain: Oxygen-independent coproporphyrinogen III oxidase HemN
species: Escherichia coli [TaxId: 562]

Probab=99.86  E-value=3e-21  Score=208.95  Aligned_cols=213  Identities=16%  Similarity=0.233  Sum_probs=161.5

Q ss_pred             ceEEEEEeCCCCCCCCCCcccCccCCC---cccCCHHHHHHHHHHHHH----CCCcEEEEeecCCCCCCCCccCCHHHHH
Q 006956          191 KFVEILPINVGCLGACTYCKTKHARGH---LGSYTVESLVGRVRTVIA----DGVKEVWLSSEDTGAYGRDIGVNLPILL  263 (624)
Q Consensus       191 ~~~a~I~isrGCp~~CsFC~ip~~rG~---~Rsr~~e~Iv~EI~~L~~----~GvkeI~l~g~d~~~yg~d~~~~l~eLL  263 (624)
                      +...||.|-- |++.|+||..+....+   ...+.++.+++||+...+    ..+..|.|.|.+.+....   ..+.+|+
T Consensus        49 plsLYiHiPF-C~~~C~yC~~~~~~~~~~~~~~~Y~~~L~~Ei~~~~~~~~~~~v~~i~~GGGTPt~L~~---~~l~~ll  124 (441)
T d1olta_          49 PLSLYVHIPF-CHKLCYFCGCNKIVTRQQHKADQYLDALEQEIVHRAPLFAGRHVSQLHWGGGTPTYLNK---AQISRLM  124 (441)
T ss_dssp             CEEEEEEECE-ESSCCTTCCSSCEECSCTHHHHHHHHHHHHHHHHHGGGGTTCCEEEEEEEESCGGGSCH---HHHHHHH
T ss_pred             ceEEEEEeCC-CCCCCCCCcCeeecCCCcchHHHHHHHHHHHHHHhhHhcCCCccceeEecCCCcCCCCH---HHHHHHH
Confidence            4556666643 9999999987643322   223347889999987654    246788888876665533   3578888


Q ss_pred             HHHHHhCCCCCCceEEEeecCCcchhHHHHHHHHHHhCCCcceeccccCCCCCHHHHHhhcCCCCHHHHHHHHHHHHHhC
Q 006956          264 NAIVAELPPDGSTMLRIGMTNPPFILEHLKEIAEVLRHPCVYSFLHVPVQSGSDAVLSAMNREYTLSDFRTVVDTLIELV  343 (624)
Q Consensus       264 ~~l~~~l~~~~~~~iri~~~~p~~i~~~l~el~~l~~~~~v~~~l~IGlQSgsd~vLk~M~R~~t~e~~~e~I~~lr~~~  343 (624)
                      +.+.+.+.......+.+. ++|..+++..  +..+.. .+ +++++||+||+|+++|+.|+|.++.+++.++++.+++. 
T Consensus       125 ~~l~~~~~~~~~~e~t~E-~~P~~~~~~~--l~~l~~-~G-~nRiSlGvQs~~~~vl~~i~R~~~~~~~~~~~~~~r~~-  198 (441)
T d1olta_         125 KLLRENFQFNADAEISIE-VDPREIELDV--LDHLRA-EG-FNRLSMGVQDFNKEVQRLVNREQDEEFIFALLNHAREI-  198 (441)
T ss_dssp             HHHHHHSCEEEEEEEEEE-ECSSSCCTHH--HHHHHH-TT-CCEEEEEEECCCHHHHHHHTCCCCHHHHHHHHHHHHHT-
T ss_pred             HHHhhhccccchhccccc-ccccccchHH--HHHHHH-hC-CceEEecchhcchhhhhhhhcCCCHHHHHHHHHHHHhc-
Confidence            888876653233456665 7999888754  444443 33 89999999999999999999999999999999999999 


Q ss_pred             CCCE-EEEEEEEcCCCCCHHHHHHHHHHHHHcCCCeEEEEEeeeCCCCccccCC----CCC-HHHHHHHHHHHHHHH
Q 006956          344 PGMQ-IATDIICGFPGETDEDFNQTVNLIKEYKFPQVHISQFYPRPGTPAARMK----KVP-SAVVKKRSRELTSVF  414 (624)
Q Consensus       344 pgi~-i~td~IvGfPGETeedf~eTl~fl~el~~~~v~i~~ysP~PGTpa~~~~----~vp-~~~~~~R~~~L~~l~  414 (624)
                       |+. +++|+|+|+||||.++|.+|++.+.+++++++.+|.|+..|+|..+...    .+| ++.+.+......+..
T Consensus       199 -g~~~vn~DLI~GlPgqT~~~~~~tl~~~~~l~pd~is~y~~~~~p~~~~~q~~~~~~~lp~~~~~~~~~~~~~~~L  274 (441)
T d1olta_         199 -GFTSTNIDLIYGLPKQTPESFAFTLKRVAELNPDRLSVFNYAHLPTIFAAQRKIKDADLPSPQQKLDILQETIAFL  274 (441)
T ss_dssp             -TCCSCEEEEEESCTTCCHHHHHHHHHHHHHHCCSEEEEEECCCCTTTSGGGGGSCGGGSCCHHHHHHHHHHHHHHH
T ss_pred             -ccceeecccccccCCcchHHHHHHHHHHHhhCCCccccccceeccchhHhhhhccccchhhhHHHHHHHHHHHHHH
Confidence             874 9999999999999999999999999999999999999999999877532    233 444444444443333

PyMOL of d1olta_

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

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

>d7reqa2 c.23.6.1 (A:561-728) Methylmalonyl-CoA mutase alpha subunit, C-terminal domain {Propionibacterium freudenreichii, subsp. shermanii [TaxId: 1744]}	Back information, alignment and structure

>d7reqb2 c.23.6.1 (B:476-638) Methylmalonyl-CoA mutase beta subunit, C-terminal domain {Propionibacterium freudenreichii, subsp. shermanii [TaxId: 1744]}	Back information, alignment and structure

>d1ccwa_ c.23.6.1 (A:) Glutamate mutase, small subunit {Clostridium cochlearium [TaxId: 1494]}	Back information, alignment and structure

>d1xrsb1 c.23.6.1 (B:102-261) D-lysine 5,6-aminomutase beta subunit KamE, C-terminal domain {Clostridium sticklandii [TaxId: 1511]}	Back information, alignment and structure

>d3bula2 c.23.6.1 (A:741-896) Methionine synthase, C-terminal domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1yeza1 b.40.4.12 (A:1-68) Hypothetical protein MM1357 {Methanosarcina mazei [TaxId: 2209]}	Back information, alignment and structure

>d1yvca1 b.40.4.12 (A:1-69) Hypothetical protein MMP0076 {Methanococcus maripaludis [TaxId: 39152]}	Back information, alignment and structure

>d1uwva1 b.40.4.12 (A:15-74) rRNA (Uracil-5-)-methyltransferase RumA, N-terminal domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure